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Date Title Author Journal
2015 Optimizing HER2 assessment in breast cancer: application of automated image analysis.

Oncotopix Clinical, Publicly Sharable

In breast cancer, analysis of HER2 expression is pivotal for treatment decision. This study aimed at comparing digital, automated image analysis with manual reading using the HER2-CONNECT algorithm (Visiopharm) in order to minimize the number of equivocal 2+ scores and the need for reflex fluorescence in situ hybridization (FISH) analysis. Consecutive samples from 462 patients were included. Tissue micro arrays (TMAs) were routinely manufactured including two 2 mm cores from each patient, and each core was assessed in order to ensure the presence of invasive carcinoma. Immunohistochemical staining (IHC) was performed with Roche/Ventanaś HER2 ready-to-use kit. TMAs were scanned in a Zeiss Axio Z1 scanner, and one batch analysis of the HER2-CONNECT algorithm including all core samples was run using Visiopharmś cloud-based software. The automated reading was compared to conventional manual assessment of HER2 protein expression, together with FISH analysis of HER2 gene amplification for borderline (2+) protein expression samples. Compared to FISH analysis, manual assessment of the HER2 protein expression demonstrated a sensitivity of 85.8% and a specificity of 86.0% with 14.0% equivocal samples. With HER2-CONNECT, sensitivity increased to 100 % and specificity to 95.5% with less than 4.5% equivocal. Total agreement when comparing HER2-CONNECT with manual IHC assessment supplemented by FISH for borderline (2+) cases was 93.6%. Application of automated image analysis for HER2 protein expression instead of manual assessment decreases the need for supplementary FISH testing by 68%. In the routine diagnostic setting, this would have significant impact on cost reduction and turn-around time.

Henrik Holten-Rossing, Maj-Lis Møller Talman, Martin Kristensson, Ben Vainer

Henrik Holten-Rossing, Maj-Lis Møller Talman, Martin Kristensson... et al. Breast Cancer Res Treat
2016 Individualized Five-Year Risk Assessment for Oral Pre-malignant Lesion Progression to Cancer

Oncotopix Discovery, Publicly Sharable, paywall

AbstractObjective The standard of care for pre-malignant lesion risk assessment is dysplasia grading by histopathology. With significant overlap between dysplasia grades and high inter- and intra-observer variations, histopathology dysplasia grading alone is not a useful prognostic tool. Our aim is to investigate if a method for quantitatively assessing S100A7, a prognostic biomarker, using image analysis, can better predict clinical outcome in cases with oral dysplasia. Study Design Using Visiopharm image analysis system, we analyzed a cohort of 150 oral biopsy samples to build and test StraticyteTM, a model for an individualized assessment of the 5-year risk of progression of oral pre-cancerous lesions to invasive squamous cell carcinoma. Results Straticyte classified lesions more accurately than histopathological dysplasia grading for risk to progress to cancer over the following five years. The sensitivity of low-risk vs intermediate- and high-risk Straticyte groups was 95% compared to 75% for mild vs moderate and severe dysplasia. Further, the Negative Predictive Value for low-risk vs intermediate- and high-risk Straticyte groups was 78% compared to 59% for mild vs moderate and severe dysplasia. Conclusion By quantitatively assessing S100A7, Straticyte better defines the risk for developing oral squamous cell carcinoma then histopathological dysplasia grading alone.

Jason T K Hwang, Ying R Gu, Mi Shen, Ranju Ralhan, Paul G Walfish, Kenneth P H Pritzker, David Mock

Jason T K Hwang, Ying R Gu, Mi Shen... et al. Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology
2016 The antibody aducanumab reduces Aβ plaques in Alzheimer disease.

Oncotopix Discovery, Publicly Sharable, nice

Alzheimer disease (AD) is characterized by deposition of amyloid-β (Aβ) plaques and neurofibrillary tangles in the brain, accompanied by synaptic dysfunction and neurodegeneration. Antibody-based immunotherapy against A? to trigger its clearance or mitigate its neurotoxicity has so far been unsuccessful. Here we report the generation of aducanumab, a human monoclonal antibody that selectively targets aggregated A?. In a transgenic mouse model of AD, aducanumab is shown to enter the brain, bind parenchymal Aβ, and reduce soluble and insoluble Aβ in a dose-dependent manner. In patients with prodromal or mild AD, one year of monthly intravenous infusions of aducanumab reduces brain Aβ in a dose- and time-dependent manner. This is accompanied by a slowing of clinical decline measured by Clinical Dementia Rating-Sum of Boxes and Mini Mental State Examination scores. The main safety and tolerability findings are amyloid-related imaging abnormalities. These results justify further development of aducanumab for the treatment of AD. Should the slowing of clinical decline be confirmed in ongoing phase 3 clinical trials, it would provide compelling support for the amyloid hypothesis.

Jeff Sevigny, Ping Chiao, Thierry Bussière, Paul H Weinreb, Leslie Williams, Marcel Maier, Robert W Dunstan, Stephen Salloway, Tianle Chen, Yan Ling, John OǴorman, Fang Qian, Mahin F Arastu, Mingwei Li, Sowmya Chollate, Melanie S Brennan, Omar Quintero-Monzon, Robert H Scannevin, H Moore Arnold, Thomas Engber, Kenneth J Rhodes, James Ferrero, Yaming Hang, Alvydas Mikulskis, Jan Grimm, Christoph Hock, Roger M Nitsch, Alfred Sandrock

Jeff Sevigny, Ping Chiao, Thierry Bussière... et al. Nature
2017 Application of automated image analysis reduces the workload of manual screening of sentinel Lymph node biopsies in breast cancer

Oncotopix Clinical, Publicly Sharable

Introduction Breast cancer is one of the most common cancer diseases in women with more than 1.67 million cases diagnosed worldwide each year. In breast cancer, the sentinel lymph node (SLN) pinpoints the first lymph node(s) into which the tumor spreads and it is usually located in the ipsilateral axilla. In patients with no clinical signs of metastatic disease in the axilla, a SLN biopsy (SLNB) is performed. Assessment of metastases in the SLNB is done in a conventional microscope by manually observing a metastasis and measuring its size and/or counting the number of tumor cells. This is done essentially to categorize the type of metastases as macrometastases, micrometastases or isolated tumor cells, which is used to determine which treatment the breast cancer patient will benefit mostly from. The aim of this study was to evaluate whether digital image analysis can be applied as a screening tool for SNLB assessment without compromising the diagnostic accuracy. Materials and methods Consecutive SLNB from 135 patients with localized breast cancer receiving surgery in the period of February to August 2015 were collected and included in this study. Of the 135 patients, 35 were received at Dept. of Pathology, Rigshospitalet, Copenhagen University Hospital, 50 at Dept. of Pathology, Zealand University Hospital, and 50 at Dept. of Pathology, Odense University Hospital. Formalin-fixed and paraffin-embedded tissue sections were analyzed by immunohistochemistry (IHC) using the BenchMark ULTRA Ventana platform. Rigshospitalet used a mixture of cytokeratin CK7 and CK19, Zealand University Hospital used pancytokeratin AE1/AE3 and Odense used pancytokeratin CAM5.2 for detection of epithelial tumor cells. Slides were stained locally. SLNB sections were assessed in a conventional microscope according to national guidelines for SLNB in breast cancer patients. The IHC stained sections were scanned by a Hamamatsu NanoZoomer-XR digital whole slide scanner and the images were analyzed by Visiopharm's software using a custommade algorithm for SLNB in breast cancer. The algorithm was optimized to the cytokeratin antibodies and the local laboratory conditions, based on staining intensity and background staining. Results Conventional microscopy was used as golden standard for assessment of positive tumor cells and compared with digital image analysis (DIA). The algorithm demonstrated a sensitivity of 100% (i.e. no false negative slides were observed), including 67.2%, 19.2% and 56.1% of the slides from the three pathology departments being negative, respectively. This means that on average, the workload could have been decreased by 58.2% by using the digital SLNB algorithm as a screening tool. Discussion and conclusion The SLNB algorithm demonstrated a sensitivity of 100% regardless of the antibody used for IHC and the staining protocol. No false negative slides were observed, which proves that the SLNB algorithm is an ideal screening tool for selecting those slides not necessary for a pathologist to see. Implementation of automated digital image analysis of SLNB in breast cancer would decrease the workload in this context for examining pathologists by almost 60%. This article is protected by copyright. All rights reserved.

Henrik Holten-Rossing, Maj-Lis Møller Talman, Anne Marie Bak Jylling, Anne-Vibeke Laenkholm, Martin Kristensson, Ben Vainer

Henrik Holten-Rossing, Maj-Lis Møller Talman, Anne Marie Bak Jylling... et al. Histopathology
2017 Digital image analysis of her2 immunostained gastric and gastroesophageal junction adenocarcinomas

Oncotopix Discovery, Publicly Sharable

Manual assessment of human epidermal growth factor receptor 2 (HER2) protein expression by immunohistochemistry (IHC) in gastric and gastroesophageal junction (GGEJ) adenocarcinomas is prone to interobserver variability and hampered by tumor heterogeneity and different scoring criteria. Equivocal cases are frequent, requiring additional in situ hybridization analysis. This study aimed to evaluate the accuracy of digital image analysis for the assessment of HER2 protein expression. In total, 110 GGEJ adenocarcinomas were included in tissue microarrays with 3 tissue cores per case. Two immunoassays, PATHWAY and HercepTest, and fluorescent in situ hybridization analysis were performed. The Visiopharm HER2-CONNECT Analysis Protocol Package was applied through the ONCOtopix digital image analysis software platform. HER2 membrane connectivity, calculated by the Analysis Protocol Package, was converted to standard IHC scores applying predetermined cutoff values for breast carcinoma as well as novel cutoff values. Cases with excessive cytoplasmic staining as well as HER2 amplified IHC negative cases were excluded from analysis. Applying HER2-CONNECT with connectivity cutoff values established for breast carcinoma resulted in 72.7% sensitivity and 100% specificity for the identification of HER2 positive gene amplified cases. By application of new cutoff values, the sensitivity increased to 100% without decreased specificity. With the new cutoff values, a 36% to 50% reduction of IHC equivocal cases was obtained. In conclusion, HER2-CONNECT with adjusted cutoff values seem to be an effective tool for standardized assessment of HER2 protein expression in GGEJ adenocarcinomas, decreasing the need for in situ hybridization analyzes.This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal. http://creativecommons.org/licenses/by-nc-nd/4.0/.

Sofie L. Nielsen, Soren Nielsen, Mogens Vyberg

Sofie L. Nielsen, Soren Nielsen, Mogens Vyberg Applied Immunohistochemistry and Molecular Morphology
2018 PD1hi cells associate with clusters of proliferating B-cells in marginal zone lymphoma

Oncotopix Discovery, Publicly Sharable

Background: Abnormally sustained immune reactions drive B-cell proliferation in some cases of marginal zone lymphoma but the CD4+ T-cell subsets, which are likely to contribute to the B-cell responses in the tumour microenvironment, are not well characterised and neither has the spatial distribution of the different subsets in involved lymph nodes been investigated. Methods: Employing a workflow of multiplex semi-automated immunohistochemistry combined with image processing we investigated association between infiltrating T-cells and proliferating lymphoma B-cells. Results: Both total numbers of activating follicular helper (Tfh) cells (defined by high expression of PD1) and suppressive regulatory (Treg) T-cells (defined by FOXP3+ expression) and the Tfh:Treg ratio, assessed over relatively large areas of tissue, varied among cases of marginal zone lymphoma. We determined spatial distribution and demonstrated that PD1hi cells showed significantly more clustering than did FOXP3+. To investigate the association of infiltrating T-cells with lymphoma B-cells we employed Pearson correlation and Morisita-Horn index, statistical measures of interaction. We demonstrated that PD1hi cells were associated with proliferating B-cells and confirmed this by nearest neighbour analysis. Conclusions: The unexpected architectural complexity of T-cell infiltration in marginal zone lymphoma, revealed in this study, further supports a key role for Tfh cells in driving proliferation of lymphoma B-cells. We demonstrate the feasibility of digital analysis of spatial architecture of T-cells within marginal zone lymphoma and future studies will be needed to determine the clinical importance of these observations.

Katherine Wickenden, Nadia Nawaz, Sami Mamand, Deevia Kotecha, Amy L. Wilson, Simon D. Wagner, Matthew J. Ahearne

Katherine Wickenden, Nadia Nawaz, Sami Mamand... et al. Diagnostic Pathology
2018 Clinical significance of CD73 in triple-negative breast cancer: multiplex analysis of a phase III clinical trial

Phenoplex, Publicly Sharable

Background: CD73 is an ecto-enzyme that promotes tumor immune escape through the production of immunosuppressive extracellular adenosine in the tumor microenvironment. Several CD73 inhibitors and adenosine receptor antagonists are being evaluated in phase I clinical trials. Patients and methods: Full-face sections from formalin-fixed paraffin-embedded primary breast tumors from 122 samples of triple-negative breast cancer (TNBC) from the BIG 02-98 adjuvant phase III clinical trial were included in our analysis. Using multiplex immunofluorescence and image analysis, we assessed CD73 protein expression on tumor cells, tumor-infiltrating leukocytes and stromal cells. We investigated the associations between CD73 protein expression with disease-free survival (DFS), overall survival (OS) and the extent of tumor immune infiltration. Results: Our results demonstrated that high levels of CD73 expression on epithelial tumor cells were significantly associated with reduced DFS, OS and negatively correlated with tumor immune infiltration (Spearman's R=-0.50, P < 0.0001). Patients with high levels of CD73 and low levels of tumor-infiltrating leukocytes had the worse clinical outcome. Conclusions: Taken together, our study provides further support that CD73 expression is associated with a poor prognosis and reduced anti-tumor immunity in human TNBC and that targeting CD73 could be a promising strategy to reprogram the tumor microenvironment in this BC subtype.

L. Buisseret, S. Pommey, B. Allard, S. Garaud, M. Bergeron, I. Cousineau, L. Ameye, Y. Bareche, M. Paesmans, J. P.A. Crown, A. Di Leo, S. Loi, M. Piccart-Gebhart, K. Willard-Gallo, C. Sotiriou, John Stagg

L. Buisseret, S. Pommey, B. Allard... et al. Annals of Oncology
2018 Digital image analysis of Ki67 in hot spots is superior to both manual Ki67 and mitotic counts in breast cancer

Oncotopix Clinical, Publicly Sharable

Aims During pathological examination of breast tumours, proliferative activity is routinely evaluated by a count of mitoses. Adding immunohistochemical stains of Ki67 provides extra prognostic and predictive information. However, the currently used methods for these evaluations suffer from imperfect reproducibility. It is still unclear whether analysis of Ki67 should be performed in hot spots, in the tumour periphery, or as an average of the whole tumour section. The aim of this study was to compare the clinical relevance of mitoses, Ki67 and phosphohistone H3 in two cohorts of primary breast cancer specimens (total n = 294). Methods and results Both manual and digital image analysis scores were evaluated for sensitivity and specificity for luminal B versus A subtype as defined by PAM50 gene expression assays, for high versus low transcriptomic grade, for axillary lymph node status, and for prognostic value in terms of prediction of overall and relapse‐free survival. Digital image analysis of Ki67 outperformed the other markers, especially in hot spots. Tumours with high Ki67 expression and high numbers of phosphohistone H3‐positive cells had significantly increased hazard ratios for all‐cause mortality within 10 years from diagnosis. Replacing manual mitotic counts with digital image analysis of Ki67 in hot spots increased the differences in overall survival between the highest and lowest histological grades, and added significant prognostic information. Conclusions Digital image analysis of Ki67 in hot spots is the marker of choice for routine analysis of proliferation in breast cancer.

Gustav Stålhammar, Stephanie Robertson, Lena Wedlund, Michael Lippert, Mattias Rantalainen, Jonas Bergh, Johan Hartman

Gustav Stålhammar, Stephanie Robertson, Lena Wedlund... et al. Histopathology
2019 The immune system in sporadic inclusion body myositis patients is not compromised by blood-flow restricted exercise training

Phenoplex, Publicly Sharable

Background: Sporadic inclusion body myositis (sIBM) is clinically characterised by progressive proximal and distal muscle weakness and impaired physical function while skeletal muscle tissue displays abnormal cellular infiltration of T cells, macrophages, and dendritic cells. Only limited knowledge exists about the effects of low-load blood flow restriction exercise in sIBM patients, and its effect on the immunological responses at the myocellular level remains unknown. The present study is the first to investigate the longitudinal effects of low-load blood flow restriction exercise on innate and adaptive immune markers in skeletal muscle from sIBM patients. Methods: Twenty-two biopsy-validated sIBM patients were randomised into either 12 weeks of low-load blood flow restriction exercise (BFRE) or no exercise (CON). Five patients from the control group completed 12 weeks of BFRE immediately following participation in the 12-week control period leading to an intervention group of 16 patients. Muscle biopsies were obtained from either the m. tibialis anterior or the m. vastus lateralis for evaluation of CD3-, CD8-, CD68-, CD206-, CD244- A nd FOXP3-positive cells by three-colour immunofluorescence microscopy and Visiopharm-based image analysis quantification. A linear mixed model was used for the statistical analysis. Results: Myocellular infiltration of CD3-/CD8+ expressing natural killer cells increased following BFRE (P < 0.05) with no changes in CON. No changes were observed for CD3+/CD8- or CD3+/CD8+ T cells in BFRE or CON. CD3+/CD244+ T cells decreased in CON, while no changes were observed in BFRE. Pronounced infiltration of M1 pro-inflammatory (CD68+/CD206-) and M2 anti-inflammatory (CD68+/CD206+) macrophages were observed at baseline; however, no longitudinal changes in macrophage content were observed for both groups. Conclusions: Low-load blood flow restriction exercise elicited an upregulation in CD3-/CD8+ expressing natural killer cell content, which suggests that 12 weeks of BFRE training evokes an amplified immune response in sIBM muscle. However, the observation of no changes in macrophage or T cell infiltration in the BFRE-trained patients indicates that patients with sIBM may engage in this type of exercise with no risk of intensified inflammatory activity.

Kasper Yde Jensen, Mikkel Jacobsen, Henrik Daa Schrøder, Per Aagaard, Jakob Lindberg Nielsen, Anders Nørkær Jørgensen, Eleanor Boyle, Rune Dueholm Bech, Sofie Rosmark, Louise Pyndt Diederichsen, Ulrik Frandsen

Kasper Yde Jensen, Mikkel Jacobsen, Henrik Daa Schrøder... et al. Arthritis Research and Therapy
2019 Early Treatment with Empagliflozin and GABA Improves β -Cell Mass and Glucose Tolerance in Streptozotocin-Treated Mice

H&E, Oncotopix Discovery, Publicly Sharable

While the autoimmune character of T1D (type 1 diabetes) is being challenged, it is currently recognized that inflammation plays a key role in its development. We hypothesized that glucotoxicity could contribute to β-cell mass destruction through participation in islet inflammation. We evaluated the potential of empagliflozin (EMPA) and GABA (gamma-aminobutyric acid) to protect β-cell mass against glucotoxicity and to increase β-cell mass after diagnosis of T1D. Empagliflozin is a SGLT2 (sodium-dependent glucose cotransporter) inhibitor which thereby blocks glucose recapture by the kidney and promotes glucose excretion in urine. GABA is an inhibitory neurotransmitter, which stimulates α-to-β cell transdifferentiation. In streptozotocin-treated mice, empagliflozin and/or GABA were delivered for a period of five days or three weeks. As compared to untreated T1D mice, EMPA-treated T1D mice had decreased FFA (free fatty acid) levels and improved glucose homeostasis. EMPA-treated T1D mice had higher islet density, with preserved architecture, compared to T1D mice, and EMPA-treated T1D mice also differed from T1D mice by the total absence of immune cell infiltration within islets. Islets from EMPA-treated mice were also less subjected to ER (endoplasmic reticulum) stress and inflammation, as shown by qPCR analysis. Glucose homeostasis parameters and islet area/pancreas area ratio improved, as compared to diabetic controls, when T1D mice were treated for three weeks with GABA and EMPA. T1D EMPA+GABA mice had higher glucagon levels than T1D mice, without modifications of glucagon area/islet area ratios. In conclusion, empagliflozin and GABA, used in monotherapy in streptozotocin-induced diabetic mice, have positive effects on β-cell mass preservation or proliferation through an indirect effect on islet cell inflammation and ER stress. Further research is mandatory to evaluate whether empagliflozin and GABA may be a potential therapeutic target for the protection of β-cell mass after new-onset T1D.

Caroline Daems, Sophie Welsch, Hasnae Boughaleb, Juliette Vanderroost, Annie Robert, Etienne Sokal, Philippe A. Lysy

Caroline Daems, Sophie Welsch, Hasnae Boughaleb... et al. Journal of Diabetes Research
2019 Immune-enrichment of non-small cell lung cancer baseline biopsies for multiplex profiling define prognostic immune checkpoint combinations for patient stratification

Phenoplex, Publicly Sharable, TMA

Background Permanence of front-line management of lung cancer by immunotherapies requires predictive companion diagnostics identifying immune-checkpoints at baseline, challenged by the size and heterogeneity of biopsy specimens. Methods An innovative, tumor heterogeneity reducing, immune-enriched tissue microarray was constructed from baseline biopsies, and multiplex immunofluorescence was used to profile 25 immune-checkpoints and immune-antigens. Results Multiple immune-checkpoints were ranked, correlated with antigen presenting and cytotoxic effector lymphocyte activity, and were reduced with advancing disease. Immune-checkpoint combinations on TILs were associated with a marked survival advantage. Conserved combinations validated on more than 11,000 lung, breast, gastric and ovarian cancer patients demonstrate the feasibility of pan-cancer companion diagnostics. Conclusions In this hypothesis-generating study, deepening our understanding of immune-checkpoint biology, comprehensive protein-protein interaction and pathway mapping revealed that redundant immune-checkpoint interactors associate with positive outcomes, providing new avenues for the deciphering of molecular mechanisms behind effects of immunotherapeutic agents targeting immune-checkpoints analyzed. Derek Bergeron and Amira Ben Amor contributed equally to this work. * Abbreviations: ACT : Adoptive cell transfer ADC : Adenocarcinoma APC : Antigen presenting cells CD3-ICP : ICP expressed on CD3+ TIL CDx : Companion diagnostics CTLA-4 : Cytotoxic T lymphocyte-associated antigen 4 EGA : European Genome-phenome Archive GEO : Gene Expression Omnibus GZMB : Granzyme B HEV : High endothelial venules HLA-DR : Human leukocyte antigen-DR ICP : Immune checkpoint IF : Immunofluorescence IFN-γ : Interferon-gamma IHC : Immunohistochemistry IIC : Infiltrating immune cells IID : Integrated Interaction Database IM : Immunoscore K-M : Kaplan-Meier survival analysis LUAD : Lung adenocarcinoma LUSC : Lung squamous cell carcinoma MFI : Mean fluorescence intensity MP-IF : Multiplex immunofluorescence NAViGaTOR : Network Analysis, Visualization and Graphing, TORonto NK cells : Natural killer cells NSCLC : Non-small cell lung carcinoma OS : Overall survival pathDIP : Pathway Data Integration Portal PD-1 : Programmed death-1 PD-L1 and PD-L2 : Programmed death-1 ligands 1 and 2 PNAd : Peripheral node addressin SCC : Squamous-cell carcinoma TAM : Tumor-associated macrophages TCGA : The Cancer Genome Atlas TCR : T cell receptor TIL : Tumor infiltrating lymphocytes TMA : Tissue microarray TNM : Tumor, node, metastases

Anne Monette, Derek Bergeron, Amira Ben Amor, Liliane Meunier, Christine Caron, Anne Marie Mes-Masson, Nidhameddine Kchir, Kamel Hamzaoui, Igor Jurisica, Réjean Lapointe

Anne Monette, Derek Bergeron, Amira Ben Amor... et al. Journal for ImmunoTherapy of Cancer
2020 Detailed Molecular and Immune Marker Profiling of Archival Prostate Cancer Samples Reveals an Inverse Association between TMPRSS2:ERG Fusion Status and Immune Cell Infiltration

Oncotopix Discovery, Publicly Sharable, TissueAlign

Prostate cancer is a significant global health issue, and limitations to current patient management pathways often result in overtreatment or undertreatment. New ways to stratify patients are urgently needed. We conducted a feasibility study of such novel assessments, looking for associations between genomic changes and lymphocyte infiltration. An innovative workflow using an in-house targeted sequencing panel, immune cell profiling using an image analysis pipeline, RNA sequencing, and exome sequencing in select cases was tested. Gene fusions were profiled by RNA sequencing in 27 of 27 cases, and a significantly higher tumor-infiltrating lymphocyte (TIL) count was noted in tumors without a TMPRSS2:ERG fusion compared with those with the fusion (P = 0.01). Although this finding was not replicated in a larger validation set (n = 436) of The Cancer Genome Atlas images, there was a trend in the same direction. Differential expression analysis of TIL-high and TIL-low tumors revealed the enrichment of both innate and adaptive immune response pathways. Mutations in mismatch repair genes (MLH1 and MSH6 mutations in 1 of 27 cases) were identified. We describe a potential immune escape mechanism in TMPRSS2:ERG fusion-positive tumors. Detailed profiling, as shown herein, can provide novel insights into tumor biology. Likely differences with findings with other cohorts are related to methods used to define region of interest, but this warrants further study in a larger cohort.

Srinivasa R. Rao, Nasullah K. Alham, Elysia Upton, Stacey McIntyre, Richard J. Bryant, Lucia Cerundolo, Emma Bowes, Stephanie Jones, Molly Browne, Ian Mills, Alastair Lamb, Ian Tomlinson, David Wedge, Lisa Browning, Korsuk Sirinukunwattana, Claire Palles, Freddie C. Hamdy, Jens Rittscher, Clare Verrill

Srinivasa R. Rao, Nasullah K. Alham, Elysia Upton... et al. The Journal of Molecular Diagnostics
2020 Digital Image Analysis of Picrosirius Red Staining: A Robust Method for Multi-Organ Fibrosis Quantification and Characterization

Oncotopix Discovery, Publicly Sharable

Current understanding of fibrosis remains incomplete despite the increasing burden of related diseases. Preclinical models are used to dissect the pathogenesis and dynamics of fibrosis, and to evaluate anti-fibrotic therapies. These studies require objective and accurate measurements of fibrosis. Existing histological quantification methods are operator-dependent, organ-specific, and/or need advanced equipment. Therefore, we developed a robust, minimally operator-dependent, and tissue-transposable digital method for fibrosis quantification. The proposed method involves a novel algorithm for more specific and more sensitive detection of collagen fibers stained by picrosirius red (PSR), a computer-assisted segmentation of histological structures, and a new automated morphological classification of fibers according to their compactness. The new algorithm proved more accurate than classical filtering using principal color component (red-green-blue; RGB) for PSR detection. We applied this new method on established mouse models of liver, lung, and kidney fibrosis and demonstrated its validity by evidencing topological collagen accumulation in relevant histological compartments. Our data also showed an overall accumulation of compact fibers concomitant with worsening fibrosis and evidenced topological changes in fiber compactness proper to each model. In conclusion, we describe here a robust digital method for fibrosis analysis allowing accurate quantification, pattern recognition, and multi-organ comparisons useful to understand fibrosis dynamics.

Guillaume E. Courtoy, Isabelle Leclercq, Antoine Froidure, Guglielmo Schiano, Johann Morelle, Olivier Devuyst, François Huaux, Caroline Bouzin

Guillaume E. Courtoy, Isabelle Leclercq, Antoine Froidure... et al. Biomolecules
2020 Validation of an Automated Quantitative Digital Pathology Approach for Scoring TMEM, a Prognostic Biomarker for Metastasis

Oncotopix Discovery, Publicly Sharable

Metastasis causes ~90% of breast cancer mortality. However, standard prognostic tests based mostly on proliferation genes do not measure metastatic potential. Tumor MicroEnvironment of Metastasis (TMEM), an immunohistochemical biomarker for doorways on blood vessels that support tumor cell dissemination is prognostic for metastatic outcome in breast cancer patients. Studies quantifying TMEM doorways have involved manual scoring by pathologists utilizing static digital microscopy: a labor-intensive process unsuitable for use in clinical practice. We report here a validation study evaluating a new quantitative digital pathology (QDP) tool (TMEM-DP) for identification and quantification of TMEM doorways that closely mimics pathologists’ workflow and reduces pathologists’ variability to levels suitable for use in a clinical setting. Blinded to outcome, QDP was applied to a nested case-control study consisting of 259 matched case-control pairs. Sixty subjects of these were manually scored by five pathologists, digitally recorded using whole slide imaging (WSI), and then used for algorithm development and optimization. Validation was performed on the remainder of the cohort. TMEM-DP shows excellent reproducibility and concordance and reduces pathologist time from ~60 min to ~5 min per case. Concordance between manual scoring and TMEM-DP was found to be >0.79. These results show that TMEM-DP is capable of accurately identifying and scoring TMEM doorways (also known as MetaSite score) equivalent to pathologists.

David Entenberg, Maja H. Oktay, Timothy D’alfonso, Paula S. Ginter, Brian D. Robinson, Xiaonan Xue, Thomas E. Rohan, Joseph A. Sparano, Joan G. Jones, John S. Condeelis

David Entenberg, Maja H. Oktay, Timothy D’alfonso... et al. Cancers
2020 PUMA and NOXA Expression in Tumor-Associated Benign Prostatic Epithelial Cells Are Predictive of Prostate Cancer Biochemical Recurrence

Phenoplex, Publicly Sharable, TMA

Background: Given that treatment decisions in prostate cancer (PC) are often based on risk, there remains a need to find clinically relevant prognostic biomarkers to stratify PC patients. We evaluated PUMA and NOXA expression in benign and tumor regions of the prostate using immunofluorescence techniques and determined their prognostic significance in PC. Methods: PUMA and NOXA expression levels were quantified on six tissue microarrays (TMAs) generated from radical prostatectomy samples (n = 285). TMAs were constructed using two cores of benign tissue and two cores of tumor tissue from each patient. Association between biomarker expression and biochemical recurrence (BCR) at 3 years was established using log-rank (LR) and multivariate Cox regression analyses. Results: Kaplan–Meier analysis showed a significant association between BCR and extreme levels (low or high) of PUMA expression in benign epithelial cells (LR = 8.831, p = 0.003). Further analysis revealed a significant association between high NOXA expression in benign epithelial cells and BCR (LR = 14.854, p < 0.001). The combination of extreme PUMA and high NOXA expression identified patients with the highest risk of BCR (LR = 16.778, p < 0.001) in Kaplan–Meier and in a multivariate Cox regression analyses (HR: 2.935 (1.645–5.236), p < 0.001). Conclusions: The combination of PUMA and NOXA protein expression in benign epithelial cells was predictive of recurrence following radical prostatectomy and was independent of PSA at diagnosis, Gleason score and pathologic stage.

Sylvie Clairefond, Benjamin Péant, Véronique Ouellet, Véronique Barrès, Zhe Tian, Dominique Trudel, Pierre I. Karakiewicz, Anne Marie Mes-Masson, Fred Saad

Sylvie Clairefond, Benjamin Péant, Véronique Ouellet... et al. Cancers
2020 A Novel Approach for Quantifying Cancer Cells Showing Hybrid Epithelial/Mesenchymal States in Large Series of Tissue Samples: Towards a New Prognostic Marker

Oncotopix Discovery, Publicly Sharable, Tissuealign

In cancer biology, epithelial-to-mesenchymal transition (EMT) is associated with tumorigenesis, stemness, invasion, metastasis, and resistance to therapy. Evidence of co-expression of epithelial and mesenchymal markers suggests that EMT should be a stepwise process with distinct intermediate states rather than a binary switch. In the present study, we propose a morphological approach that enables the detection and quantification of cancer cells with hybrid E/M states, i.e., which combine partially epithelial (E) and partially mesenchymal (M) states. This approach is based on a sequential immunohistochemistry technique performed on the same tissue section, the digitization of whole slides, and image processing. The aim is to extract quantitative indicators able to quantify the presence of hybrid E/M states in large series of human cancer samples and to analyze their relationship with cancer aggressiveness. As a proof of concept, we applied our methodology to a series of about a hundred urothelial carcinomas and demonstrated that the presence of cancer cells with hybrid E/M phenotypes at the time of diagnosis is strongly associated with a poor prognostic value, independently of standard clinicopathological features. Although validation on a larger case series and other cancer types is required, our data support the hybrid E/M score as a promising prognostic biomarker for carcinoma patients.

Louis Godin, Cédric Balsat, Yves Rémi Van Eycke, Justine Allard, Claire Royer, Myriam Remmelink, Ievgenia Pastushenko, Nicky D’Haene, Cédric Blanpain, Isabelle Salmon, Sandrine Rorive, Christine Decaestecker

Louis Godin, Cédric Balsat, Yves Rémi Van Eycke... et al. Cancers
2020 Prevalence of PD-L1 expression is associated with EMAST, density of peritumoral T-cells and recurrence-free survival in operable non-metastatic colorectal cancer

Oncotopix Discovery, Publicly Sharable

Introduction: Microsatellite instability (MSI) predict response to anti-PD1 immunotherapy in colorectal cancer (CRC). CRCs with MSI have higher infiltration of immune cells related to a better survival. Elevated Microsatellite Alterations at Tetranucleotides (EMAST) is a form of MSI but its association with PD-L1 expression and immune-cell infiltration is not known. Methods: A consecutive, observational cohort of patients undergoing surgery for CRC. EMAST and clinicopathological characteristics were investigated against PD-L1, as well as CD3 and CD8 expression in the invasive margin or tumour centre (Immunoscore). Difference in survival between groups was assessed by log rank test. Results: A total of 149 stage I–III CRCs patients, with a median follow up of 60.1 months. Patients with PD-L1+ tumours (7%) were older (median 79 vs 71 years, p = 0.045) and had EMAST+ cancers (OR 10.7, 95% CI 2.2–51.4, p = 0.001). Recurrence-free survival was longer in cancers with PD-L1+ immune cells (HR 0.35, 95% CI 0.16–0.76, p = 0.008, independent of EMAST) and high Immunoscore (HR 0.10, 95% CI 0.01–0.72, p = 0.022). Patients expressing PD-L1 in immune cells had longer disease-specific survival (HR 0.28, 95% CI 0.10–0.77, p = 0.014). Conclusions: Higher Immunoscore (CD3/CD8 cells) and expression of tumour PD-L1 is found in CRCs with EMAST. Lymphocytic infiltrate and peritumoral PD-L1 expression have prognostic value in CRC.

Martin M. Watson, Dordi Lea, Einar Gudlaugsson, Ivar Skaland, Hanne R. Hagland, Kjetil Søreide

Martin M. Watson, Dordi Lea, Einar Gudlaugsson... et al. Cancer Immunology, Immunotherapy
2020 Dual Targeting of Mesothelin and CD19 with Chimeric Antigen Receptor-Modified T Cells in Patients with Metastatic Pancreatic Cancer

Oncotopix Discovery, Publicly Sharable, Tissuealign

B cells infiltrate pancreatic ductal adenocarcinoma (PDAC) and in preclinical cancer models, can suppress T cell immunosurveillance in cancer. Here, we conducted a pilot study to assess the safety and feasibility of administering lentiviral-transduced chimeric antigen receptor (CAR)-modified autologous T cells redirected against mesothelin to target tumor cells along with CART cells redirected against CD19 to deplete B cells. Both CARs contained 4-1BB and CD3ζ signaling domains. Three patients with chemotherapy-refractory PDAC received 1.5 g/m2 cyclophosphamide prior to separate infusions of lentiviral-transduced T cells engineered to express chimeric anti-mesothelin immunoreceptor SS1 (CART-Meso, 3 × 107/m2) and chimeric anti-CD19 immunoreceptor (CART-19, 3 × 107/m2). Treatment was well tolerated without dose-limiting toxicities. Best response was stable disease (1 of 3 patients). CART-19 (compared to CART-Meso) cells showed the greatest expansion in the blood, although persistence was transient. B cells were successfully depleted in all subjects, became undetectable by 7–10 days post-infusion, and remained undetectable for at least 28 days. Together, concomitant delivery of CART-Meso and CART-19 cells in patients with PDAC is safe. CART-19 cells deplete normal B cells but at the dose tested in these 3 subjects did not improve CART-Meso cell persistence.

Andrew H. Ko, Alexander C. Jordan, Evan Tooker, Simon F. Lacey, Renee B. Chang, Yan Li, Alan P. Venook, Margaret Tempero, Lloyd Damon, Lawrence Fong, Mark H. O'Hara, Bruce L. Levine, J. Joseph Melenhorst, Gabriela Plesa, Carl H. June, Gregory L. Beatty

Andrew H. Ko, Alexander C. Jordan, Evan Tooker... et al. Molecular Therapy
2020 Reduced Protumorigenic Tumor-Associated Macrophages With Statin Use in Premalignant Human Lung Adenocarcinoma

Oncotopix Discovery, Publicly Sharable, TMA

Background: Statins have anticancer properties by acting as competitive inhibitors of the mevalonate pathway. They also have anti-inflammatory activity, but their role in suppressing inflammation in a cancer context has not been investigated to date. Methods: We have analyzed the relationship between statin use and tumor-Associated macrophages (TAMs) in a cohort of 262 surgically resected primary human lung adenocarcinomas. TAMs were evaluated by multiplex immunostaining for the CD68 pan-TAM marker and the CD163 protumorigenic TAM marker followed by digital slide scanning and partially automated quantitation. Links between statin use and tumor stage, virulence, and cancer-specific survival were also investigated in a wider cohort of 958 lung adenocarcinoma cases. All statistical tests were two-sided. Results: We found a statin dose-dependent reduction in protumorigenic TAMs (CD68 CD163 ) in both stromal (P .021) and parenchymal (P .003) compartments within regions of in situ tumor growth, but this association was lost in invasive regions. No statistically significant relationship between statin use and tumor stage was observed, but there was a statin dose-dependent shift towards lower histological grade as assessed by growth pattern (P .028). However, statin use was a predictor of slightly worse cancer-specific survival (P .032), even after accounting for prognostic variables in a multivariable Cox proportional hazards survival model (hazard ratio 1.38, 95% confidence interval 1.04 to 1.84). Conclusions: Statin use is associated with reduced numbers of protumorigenic TAMs within preinvasive lung adenocarcinoma and is related to reduced tumor invasiveness, suggesting a chemo-preventive effect in early tumor development. However, invasive disease is resistant to these effects, and no beneficial relationship between statin use and patient outcome is observed.

Esraa Al Dujaily, Juvenal Baena, Madhumita Das, Marco Sereno, Claire Smith, Tamihiro Kamata, Leah Officer, Catrin Pritchard, John Le Quesne

Esraa Al Dujaily, Juvenal Baena, Madhumita Das... et al. JNCI Cancer Spectrum
2020 Molecular correlates of cisplatin-based chemotherapy response in muscle invasive bladder cancer by integrated multi-omics analysis

Publicly Sharable, TMA, Tissuealign, nice

Overtreatment with cisplatin-based chemotherapy is a major issue in the management of muscle-invasive bladder cancer (MIBC), and currently none of the reported biomarkers for predicting response have been implemented in the clinic. Here we perform a comprehensive multi-omics analysis (genomics, transcriptomics, epigenomics and proteomics) of 300 MIBC patients treated with chemotherapy (neoadjuvant or first-line) to identify molecular changes associated with treatment response. DNA-based associations with response converge on genomic instability driven by a high number of chromosomal alterations, indels, signature 5 mutations and/or BRCA2 mutations. Expression data identifies the basal/squamous gene expression subtype to be associated with poor response. Immune cell infiltration and high PD-1 protein expression are associated with treatment response. Through integration of genomic and transcriptomic data, we demonstrate patient stratification to groups of low and high likelihood of cisplatin-based response. This could pave the way for future patient selection following validation in prospective clinical trials. There are currently only a few biomarkers to predict the response of muscle invasive bladder cancer to therapy. Here, the authors analyse 300 tumors using exome and RNA sequencing and find that tumors with a high degree of genomic instability and a non-basal/squamous gene expression subtype are most likely to respond to treatment.

Ann Taber, Emil Christensen, Philippe Lamy, Iver Nordentoft, Frederik Prip, Sia Viborg Lindskrog, Karin Birkenkamp-Demtröder, Trine Line Hauge Okholm, Michael Knudsen, Jakob Skou Pedersen, Torben Steiniche, Mads Agerbæk, Jørgen Bjerggaard Jensen, Lars Dyrskjøt

Ann Taber, Emil Christensen, Philippe Lamy... et al. Nature Communications
2020 Analysis of spatial relationships between CD8 and FoxP3 cells using digital imaging in head and neck squamous cell carcinoma

Oncotopix Discovery, Publicly Sharable

Purpose/Objective(s): T cell-mediated anti-tumor immune responses are gated in part by the relative abundance of cytotoxic T cells (Teffs) and regulatory (Tregs) in the tumor microenvironment (TME) whereby Treg may impair the efficacy of Teffs. Tregs can affect Teff function by direct cell-to-cell contact or by secretion of soluble mediators, consistent with the hypothesis that proximity of Tregs to Teff within tumor tissues may have prognostic significance. Here we used a novel chromogenic multiplex assay to investigate the spatial relationship of these functionally diverse T cell subsets in HPV positive and HPV negative head and neck squamous cell carcinomas (HNSCCs). Materials/Methods: Twenty head and neck cancer patients with primary tumors of the oropharynx or oral cavity were included in this study of which 10 were HPV positive and 10 HPV negative. Formalin-fixed tissues were stained with antibodies detecting CD8 (Teffs) and FoxP3 (Tregs). At least three different fields at the leading edge of tumor and adjacent stroma were evaluated. Stained tissue sections were digitally scanned at 40x magnification utilizing an iScan HT (Roche, Switzerland) whole-slide imaging scanner. Visiopharm (Visiopharm, Denmark) image analysis software was utilized by a pathologist to analyze the digitized slide images. Result(s): HPV positive tumor tissues contained >3-fold higher numbers of both CD8 and FoxP3 expressing cells when compared to HPV negative tumors whereas the ratios between these cell subsets (CD8/FoxP3) were comparable. The differential density of T-cells in the sampled areas was reflected in a significantly shorter mean distance between CD8+ and FoxP3+ cells in HPV positive (29.92 mum) tumors compared to that of HPV negative (52.56 mum) tumors (p=0.0045, 95% CI: 8.17-37.11). The mean frequency of distances <30mum measured in HPV positive tumors was 98.46 contrasted by 39.44 in HPV negative tumors; this difference was statistically different (p=0.0194). The mean frequency of distances >30mum measured in HPV positive tumors was 37.02 and in HPV negative tumors 36.06. Conclusion(s): Consistent with earlier reports, HPV positive lesions contained more CD8 and FoxP3 expressing T cells than HPV negative lesions. This difference was reflected in statistically significantly closer proximity of Teffs and Tregs in HPV positive lesions, potentially enhancing functional interaction of these T cell subsets in the tumor microenvironment of HPV positive lesions. The implications of these observations for prognosis and response to immunotherapeutic intervention remain to be investigated.Copyright © 2020

M. Stewart, R. Stapp, D. Amin, R. Ganti, U. Nwagu, T. Richa, M. Crippen, R. Zinner, A. Luginbuhl, J. Johnson, V. Bar-Ad, U. Martinez-Outschoorn, C. Solomides, U. Rodeck, J.M. Curry

M. Stewart, R. Stapp, D. Amin... et al. International Journal of Radiation Oncology, Biology, Physics
2020 Visualization, quantification, and mapping of immune cell populations in the tumor microenvironment

Oncotopix Discovery, Phenoplex, Publicly Sharable, Tissuealign, nice

The immune landscape of the tumor microenvironment (TME) is a determining factor in cancer progression and response to therapy. Specifically, the density and the location of immune cells in the TME have important diagnostic and prognostic values. Multiomic profiling of the TME has exponentially increased our understanding of the numerous cellular and molecular networks regulating tumor initiation and progression. However, these techniques do not provide information about the spatial organization of cells or cell-cell interactions. Affordable, accessible, and easy to execute multiplexing techniques that allow spatial resolution of immune cells in tissue sections are needed to complement single cell-based high-throughput technologies. Here, we describe a strategy that integrates serial imaging, sequential labeling, and image alignment to generate virtual multiparameter slides of whole tissue sections. Virtual slides are subsequently analyzed in an automated fashion using user-defined protocols that enable identification, quantification, and mapping of cell populations of interest. The image analysis is done, in this case using the analysis modules Tissuealign, Author, and HISTOmap. We present an example where we applied this strategy successfully to one clinical specimen, maximizing the information that can be obtained from limited tissue samples and providing an unbiased view of the TME in the entire tissue section.

Manuel Flores Molina, Thomas Fabre, Aurélie Cleret-Buhot, Geneviève Soucy, Liliane Meunier, Mohamed N. Abdelnabi, Nicolas Belforte, Simon Turcotte, Naglaa H. Shoukry

Manuel Flores Molina, Thomas Fabre, Aurélie Cleret-Buhot... et al. Journal of Visualized Experiments
2020 Multispectral Imaging Enables Characterization of Intrahepatic Macrophages in Patients With Chronic Liver Disease

Phenoplex, Publicly Sharable

Intrahepatic macrophages influence the composition of the microenvironment, host immune response to liver injury, and development of fibrosis. Compared with stellate cells, the role of macrophages in the development of fibrosis remains unclear. Multispectral imaging allows detection of multiple markers in situ in human formalin-fixed, paraffin-embedded tissue. This cutting-edge technology is ideal for analyzing human liver tissues, as it allows spectral unmixing of fluorophore signals, subtraction of auto-fluorescence, and preservation of hepatic architecture. We analyzed five different antibodies commonly observed on macrophage populations (CD68, MAC387, CD163, CD14, and CD16). After optimization of the monoplex stains and development of a Spectral Library, we combined all of the antibodies into a multiplex protocol and used them to stain biopsies collected from representative patients with chronic liver diseases, including chronic hepatitis C, nonalcoholic steatohepatitis, and autoimmune hepatitis. Various imaging modalities were tested, including cell phenotyping, tissue segmentation, t-distributed stochastic neighbor embedding plots, and phenotype matrices that facilitated comparison and visualization of the identified macrophage and other cellular profiles. We then tested the feasibility of this platform to analyze numerous regions of interest from liver biopsies with multiple patients per group, using batch analysis algorithms. Five populations showed significant differences between patients positive for hepatitis C virus with advanced fibrosis when compared with controls. Three of these were significantly increased in patients with advanced fibrosis when compared to controls, and these included CD163+CD16+, CD68+, and CD68+MAC387+. Conclusion: Spectral imaging microscopy is a powerful tool that enables in situ analysis of macrophages and other cells in human liver biopsies and may lead to more personalized therapeutic approaches in the future. chronic liver diseases HCV, NASH, and AIH

Omar A. Saldarriaga, Benjamin Freiberg, Santhoshi Krishnan, Arvind Rao, Jared Burks, Adam L. Booth, Bradley Dye, Netanya Utay, Monique Ferguson, Abdellah Akil, Minkyung Yi, Laura Beretta, Heather L. Stevenson

Omar A. Saldarriaga, Benjamin Freiberg, Santhoshi Krishnan... et al. Hepatology Communications
2020 A validation study of human epidermal growth factor receptor 2 immunohistochemistry digital imaging analysis and its correlation with human epidermal growth factor receptor 2 fluorescence in situ hybridization results in breast carcinoma

Oncotopix Clinical, Publicly Sharable

Background: The Visiopharm human epidermal growth factor receptor 2 (HER2) digital imaging analysis (DIA) algorithm assesses digitized HER2 immunohistochemistry (IHC) by measuring cell membrane connectivity. We aimed to validate this algorithm for clinical use by comparing with pathologists' scoring and correlating with HER2 fluorescence in situ hybridization (FISH) results. Materials and Methods: The study cohort consisted of 612 consecutive invasive breast carcinoma specimens including 395 biopsies and 217 resections. HER2 IHC slides were scanned using Philips IntelliSite Scanners, and the digital images were analyzed using Visiopharm HER2-CONNECT App to obtain the connectivity values (0-1) and scores (0, 1+, 2+, and 3+). HER2 DIA scores were compared with Pathologists' manual scores, and HER2 connectivity values were correlated with HER2 FISH results. Results: The concordance between HER2 DIA scores and pathologists' scores was 87.3% (534/612). All discordant cases (n = 78) were only one-step discordant (negative to equivocal, equivocal to positive, or vice versa). Five cases (0.8%) showed discordant HER2 IHC DIA and HER2 FISH results, but all these cases had relatively low HER2 copy numbers (between 4 and 6). HER2 IHC connectivity showed significantly better correlation with HER2 copy number than HER2/CEP17 ratio. Conclusions: HER2 IHC DIA demonstrates excellent concordance with pathologists' scores and accurately discriminates between HER2 FISH positive and negative cases. HER2 IHC connectivity has better correlation with HER2 copy number than HER2/CEP17 ratio, suggesting HER2 copy number may be more important in predicting HER2 protein expression, and response to anti-HER2-targeted therapy.

Ramon Hartage, Aidan Li, Scott Hammond, Anil Parwani

Ramon Hartage, Aidan Li, Scott Hammond... et al. Journal of Pathology Informatics
2020 Quantitative digital imaging analysis of HER2 immunohistochemistry predicts the response to anti-HER2 neoadjuvant chemotherapy in HER2-positive breast carcinoma

Oncotopix Clinical, Publicly Sharable

Purpose: Patients with HER2-positive breast cancer commonly receive anti-HER2 neoadjuvant chemotherapy and pathologic complete response (pCR) can be achieved in up to half of the patients. HER2 protein expression detected by immunohistochemistry (IHC) can be quantified using digital imaging analysis (DIA) as a value of membranous connectivity. We aimed to investigate the association HER2 IHC DIA quantitative results with response to anti-HER2 neoadjuvant chemotherapy. Methods: Digitized HER2 IHC whole slide images were analyzed using Visiopharm HER2-CONNECT to obtain quantitative HER2 membranous connectivity from a cohort of 153 HER2+ invasive breast carcinoma cases treated with anti-HER2 neoadjuvant chemotherapy (NAC). HER2 connectivity and other factors including age, histologic grade, ER, PR, and HER2 fluorescence in situ hybridization (FISH) were analyzed for association with the response to anti-HER2 NAC. Results: Eighty-three cases (54.2%) had pCR, while 70 (45.8%) showed residual tumor. Younger age, negative ER/PR, higher HER2 DIA connectivity, higher HER2 FISH ratio and copy number were significantly associated with pCR in univariate analysis. Multivariate analysis demonstrated only age, HER2 DIA connectivity, PR negativity, and HER2 copy number was significantly associated with pCR, whereas HER2 DIA connectivity had the strongest association. Conclusions: HER2 IHC DIA connectivity is the most important factor predicting pCR to anti-HER2 neoadjuvant chemotherapy in patients with HER2-positive breast cancer.

Aidan C. Li, Jing Zhao, Chao Zhao, Zhongliang Ma, Ramon Hartage, Yunxiang Zhang, Xiaoxian Li, Anil V. Parwani

Aidan C. Li, Jing Zhao, Chao Zhao... et al. Breast Cancer Research and Treatment
2020 Automated assessment of Ki-67 in breast cancer: the utility of digital image analysis using virtual triple staining and whole slide imaging

Oncotopix Clinical, Publicly Sharable

Aims: Precise evaluation of proliferative activity is essential for the stratified treatment of luminal-type breast cancer (BC). Immunohistochemical staining of Ki-67 has been widely used to determine proliferative activity and is recognised to be a useful prognostic marker. However, there remains discussion concerning the methodology. We aimed to develop an automated and reliable Ki-67 assessment approach for invasive BC. Materials and results: A retrospective study was designed to include two cohorts consisting of 152 and 261 consecutive patients with luminal-type BC. Representative tissue blocks following surgery were collected, and three serial sections were stained automatically with Ki-67, pan-cytokeratin and p63. The whole slides were scanned digitally and aligned using VirtualTripleStaining – an extension to the VirtualDoubleStaining™ technique provided by Visiopharm software. The aligned files underwent automated invasive cancer detection, hot-spot identification and Ki-67 counting. The automated scores showed a significant positive correlation with the pathologists' scores (r = 0.82, P ' 0.0001). Among selected patients with curative surgery and standard adjuvant therapies (n = 130), the digitally assessed low Ki-67 group ('20%) demonstrated a significantly better prognosis (breast cancer-specific survival, P = 0.030; hazard ratio = 0.038) than the high Ki-67 group. Conclusions: Digital image analysis yielded similar results to the scores determined by experienced pathologists. The prognostic utility was verified in our cohort, and an automated process is expected to have high reproducibility. Although some pitfalls were confirmed and thus need to be monitored by laboratory staff, the application could be utilised for the assessment of BC.

Akira I. Hida, Dzenita Omanovic, Lars Pedersen, Yumi Oshiro, Takashi Ogura, Tsunehisa Nomura, Junichi Kurebayashi, Naoki Kanomata, Takuya Moriya

Akira I. Hida, Dzenita Omanovic, Lars Pedersen... et al. Histopathology
2021 SerpinB13 antibodies promote cell development and resistance to type 1 diabetes

Phenoplex, Publicly Sharable

Pancreatic endocrine cell development is dependent on the rescue of the neurogenin3 (Ngn3) transcription factor from repression by Notch. The signals that prevent Notch signaling, thereby allowing the formation of pancreatic endocrine cells, remain unclear. We show that inhibiting serpinB13, a cathepsin L (CatL) protease inhibitor expressed in the pancreatic epithelium, caused in vitro and in vivo cleavage of the extracellular domain of Notch1. This was followed by a twofold increase in the Ngn3+ progenitor cell population and enhanced conversion of these cells to express insulin. Conversely, both recombinant serpinB13 protein and CatL deficiency down-regulated pancreatic Ngn3+ cell output. Mouse embryonic exposure to inhibitory anti-serpinB13 antibody resulted in increased islet cell mass and improved outcomes in streptozotocin-induced diabetes at 8 weeks of age. Moreover, anti-serpinB13 autoantibodies stimulated Ngn3+ endocrine progenitor formation in the pancreas and were associated with delayed progression to type 1 diabetes (T1D) in children. These data demonstrate long-Term impact of serpinB13 activity on islet biology and suggest that promoting protease activity by blocking this serpin may have prophylactic potential in T1D.

Yury Kryvalap, Matthew L. Jiang, Nadzeya Kryvalap, Cole Hendrickson, Jan Czyzyk

Yury Kryvalap, Matthew L. Jiang, Nadzeya Kryvalap... et al. Science Translational Medicine
2021 Clinical significance of tumor infiltrating lymphocytes in association with hormone receptor expression patterns in epithelial ovarian cancer

Oncotopix Discovery, Publicly Sharable, TMA

Hormone receptor expression patterns often correlate with infiltration of specific lymphocytes in tumors. Specifically, the presence of specific tumor-infiltrating lymphocytes (TILs) with particular hormone receptor expression is reportedly associated with breast cancer, however, this has not been revealed in epithelial ovarian cancer (EOC). Therefore, we investigated the association between hormone receptor expression and TILs in EOC. Here we found that ERα, AR, and GR expression increased in EOC, while PR was significantly reduced and ERβ expression showed a reduced trend compared to normal epithelium. Cluster analysis indicated poor disease-free survival (DFS) in AR+/GR+/PR+ subgroup (triple dominant group); while the Cox proportional-hazards model high-lighted the triple dominant group as an independent prognostic factor for DFS. In addition, significant upregulation of FoxP3+ TILs, PD-1, and PD-L1 was observed in the triple dominant group compared to other groups. NanoString analyses further suggested that tumor necrosis factor (TNF) and/or NF-κB signaling pathways were activated with significant upregulation of RELA, MAP3K5, TNFAIP3, BCL2L1, RIPK1, TRAF2, PARP1, and AKT1 in the triple dominant EOC group. The triple dominant subgroup correlates with poor prognosis in EOC. Moreover, the TNF and/or NF-κB signaling pathways may be responsible for hormone-mediated inhibition of the immune microenvironment.

Gwan Hee Han, Ilseon Hwang, Hanbyoul Cho, Kris Ylaya, Jung A. Choi, Hyunja Kwon, Joon Yong Chung, Stephen M. Hewitt, Jae Hoon Kim

Gwan Hee Han, Ilseon Hwang, Hanbyoul Cho... et al. International Journal of Molecular Sciences
2021 Optimized Culture Conditions for Improved Growth and Functional Differentiation of Mouse and Human Colon Organoids

Oncotopix Discovery, Polaris, Publicly Sharable, RNAScope, Vectra

Background & Aims: Diligent side-by-side comparisons of how different methodologies affect growth efficiency and quality of intestinal colonoids have not been performed leaving a gap in our current knowledge. Here, we summarize our efforts to optimize culture conditions for improved growth and functional differentiation of mouse and human colon organoids. Methods: Mouse and human colon organoids were grown in four different media. Media-dependent long-term growth was measured by quantifying surviving organoids via imaging and a cell viability readout over five passages. The impact of diverse media on differentiation was assessed by quantifying the number of epithelial cell types using markers for enterocytes, stem cells, Goblet cells, and enteroendocrine cells by qPCR and histology upon removal of growth factors. Results: In contrast to Wnt3a-conditioned media, media supplemented with recombinant Wnt3a alone did not support long-term survival of human or mouse colon organoids. Mechanistically, this observation can be attributed to the fact that recombinant Wnt3a did not support stem cell survival or proliferation as demonstrated by decreased LGR5 and Ki67 expression. When monitoring expression of markers for epithelial cell types, the highest level of organoid differentiation was observed after combined removal of Wnt3a, Noggin, and R-spondin from Wnta3a-conditioned media cultures. Conclusion: Our study defined Wnt3a-containing conditioned media as optimal for growth and survival of human and mouse organoids. Furthermore, we established that the combined removal of Wnt3a, Noggin, and R-spondin results in optimal differentiation. This study provides a step forward in optimizing conditions for intestinal organoid growth to improve standardization and reproducibility of this model platform.

Sarah S. Wilson, Martha Mayo, Terry Melim, Heather Knight, Lori Patnaude, Xiaoming Wu, Lucy Phillips, Susan Westmoreland, Robert Dunstan, Edda Fiebiger, Sonia Terrillon

Sarah S. Wilson, Martha Mayo, Terry Melim... et al. Frontiers in Immunology
2021 Increased angiotensin-converting enzyme 2 and loss of alveolar type II cells in COVID-19–related acute respiratory distress syndrome

Phenoplex, Publicly Sharable

Rationale: ACE2 (angiotensin-converting enzyme 2), the entry receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is expressed in type 2 alveolar epithelial cells (AT2) that may play key roles in postinjury repair. An imbalance between ACE2 and ACE has also been hypothesized to contribute to lung injury. Objectives: To characterize the expression and distribution of ACE2 and ACE and to compare AT2 with endothelial cell expression in coronavirus disease (COVID-19)–related or –unrelated acute respiratory distress syndrome (ARDS) and controls. Methods: Lung tissue stainings (using multiplex immunofluorescence) and serum concentrations of ACEs were determined retrospectively in two different cohorts of patients. AT2 and endothelial cells were stained in lung tissue for ProSPC (pro-surfactant protein C) and CD31, respectively. Measurements and Main Results: Pulmonary ACE2 expression was increased in patients with COVID-19–related and –unrelated ARDS (0.06% of tissue area and 0.12% vs. 0.006% for control subjects; P = 0.013 and P, 0.0001, respectively). ACE2 was upregulated in endothelial cells (0.32% and 0.53% vs. 0.01%; P = 0.009 and P, 0.0001) but not in AT2 cells (0.13% and 0.08% vs. 0.03%; P = 0.94 and P = 0.44). Pulmonary expression of ACE was decreased in both COVID-19–related and –unrelated ARDS (P = 0.057 and P = 0.032). Similar increases in ACE2 and decreases in ACE were observed in sera of COVID-19 (P = 0.0054 and P, 0.0001) and non–COVID-19 ARDS (P, 0.0001 and P = 0.016). In addition, AT2 cells were decreased in patients with COVID-19–related ARDS compared with COVID-19–unrelated ARDS (1.395% vs. 2.94%, P = 0.0033). Conclusions: ACE2 is upregulated in lung tissue and serum of both COVID-19–related and –unrelated ARDS, whereas a loss of AT2 cells is selectively observed in COVID-19–related ARDS.

Ludovic Gerard, Marylene Lecocq, Caroline Bouzin, Delphine Hoton, Gregory Schmit, Joao Pinto Pereira, Virginie Montiel, Thomas Plante-Bordeneuve, Pierre François Laterre, Charles Pilette

Ludovic Gerard, Marylene Lecocq, Caroline Bouzin... et al. American Journal of Respiratory and Critical Care Medicine
2021 Signalling of multiple interleukin (IL)-17 family cytokines via IL-17 receptor A drives psoriasis-related inflammatory pathways

Oncotopix Discovery, Publicly Sharable, RNAScope

Background: The interleukin (IL)-23/IL-17 immune axis is of central importance in psoriasis. However, the impact of IL-17 family cytokines other than IL-17A in psoriasis has not been fully established. Objectives: To elucidate the contribution of IL-17 family cytokines in psoriasis. Methods: To address the expression and localization of IL-17 family cytokines, lesional and nonlesional skin samples from patients with psoriasis were analysed by several complementary methods, including quantitative polymerase chain reaction, immunoassays, in situ hybridization and immunohistochemistry. Mechanistic studies assessing the functional activity of IL-17 family cytokines were performed using ex vivo cultured human skin biopsies and primary human keratinocytes. Results: We demonstrated that IL-17A, IL-17F, IL-17A/F and IL-17C are expressed at increased levels in psoriasis lesional skin and induce overlapping gene expression responses in ex vivo cultured human skin that correlate with the transcriptomic signature of psoriasis skin. Furthermore, we showed that brodalumab, in contrast to ixekizumab, normalizes gene expression responses induced by the combination of IL-17A, IL-17F, IL-17A/F and IL-17C in human keratinocytes. Conclusions: Several IL-17 ligands signalling through IL-17RA are overexpressed in psoriasis skin and induce similar psoriasis-related inflammatory pathways demonstrating their relevance in relation to therapeutic intervention in psoriasis.

M. A.X. Tollenaere, J. Hebsgaard, D. A. Ewald, P. Lovato, S. Garcet, X. Li, S. D. Pilger, M. L. Tiirikainen, M. Bertelsen, J. G. Krueger, H. Norsgaard

M. A.X. Tollenaere, J. Hebsgaard, D. A. Ewald... et al. British Journal of Dermatology
2021 Mechanisms and regulation of IL-22-mediated intestinal epithelial homeostasis and repair

Oncotopix Discovery, Publicly Sharable, RNAScope

Aims: Ulcerative colitis and Crohn's disease, collectively known as inflammatory bowel disease (IBD), are chronic inflammatory disorders of the intestine for which key elements in disease initiation and perpetuation are defects in epithelial barrier integrity. Achieving mucosal healing is essential to ameliorate disease outcome and so new therapies leading to epithelial homeostasis and repair are under investigation. This study was designed to determine the mechanisms by which IL-22 regulates intestinal epithelial cell function. Main methods: Human intestinal organoids and resections, as well as mice were used to evaluate the effect of IL-22 on stem cell expansion, proliferation and expression of mucus components. IL-22 effect on barrier function was assessed in polarized T-84 cell monolayers. Butyrate co-treatments and organoid co-cultures with immune cells were performed to monitor the impact of microbial-derived metabolites and inflammatory environments on IL-22 responses. Key findings: IL-22 led to epithelial stem cell expansion, proliferation, barrier dysfunction and anti-microbial peptide production in human and mouse models evaluated. IL-22 also altered the mucus layer by inducing an increase in membrane mucus but a decrease in secreted mucus and goblet cell content. IL-22 had the same effect on anti-microbial peptides and membrane mucus in both healthy and IBD human samples. In contrast, this IL-22-associated epithelial phenotype was different when treatments were performed in presence of butyrate and organoids co-cultured with immune cells. Significance: Our data indicate that IL-22 promotes epithelial regeneration, innate defense and membrane mucus production, strongly supporting the potential clinical utility of IL-22 as a mucosal healing therapy in IBD.

Lori Patnaude, Martha Mayo, Regina Mario, Xiaoming Wu, Heather Knight, Kelly Creamer, Sarah Wilson, Valerie Pivorunas, Jozsef Karman, Lucy Phillips, Robert Dunstan, Rajesh V. Kamath, Bradford McRae, Sonia Terrillon

Lori Patnaude, Martha Mayo, Regina Mario... et al. Life Sciences
2021 A phase Ib/II study of pepinemab in combination with avelumab in advanced non–small cell lung cancer

Oncotopix Discovery, Publicly Sharable, Tissuealign

Purpose: The CLASSICAL-Lung clinical trial tested the combination of pepinemab, an IgG4 humanized mAb targeting semaphorin 4D, with the PD-L1 inhibitor avelumab to assess the effects of coupling increased T-cell infiltration and reversal of immune suppression via pepinemab with sustained T-cell activation via checkpoint inhibition. Patients and Methods: This phase Ib/II, single-arm study was designed to evaluate the safety, tolerability, and efficacy of pepinemab in combination with avelumab in 62 patients with advanced non–small cell lung cancer (NSCLC), including immunotherapy-naïve (ION) patients and patients whose tumors progressed following anti-PD-1/L1 monotherapy (IOF). The main objectives were to evaluate safety/tolerability, establish a recommended phase 2 dose (RP2D), obtain a preliminary evaluation of antitumor activity, and investigate candidate biomarker activity. Results: The combination was well tolerated with no major safety signals identified. Pepinemab, 10 mg/kg with avelumab, 10 mg/kg, every 2 weeks, was selected as the RP2D. Among 21 evaluable ION patients, 5 patients experienced partial responses (PR), 4 patients evidenced clinical benefit ≥1 year, and the disease control rate (DCR) was 81%. Notably, overall response rate with the combination therapy was higher than previously reported for single-agent avelumab in the PD-L1-negative/low population. Among 29 evaluable IOF patients, the combination resulted in a DCR of 59%, including 2 PR and 7 patients with durable clinical benefit of ≥23 weeks. Biomarker analysis of biopsies demonstrated increased CD8 T-cell density correlating with RECIST response criteria. Conclusions: The combination of pepinemab with avelumab was well tolerated in NSCLC and showed signs of antitumor activity in immunotherapy-resistant and PD-L1-negative/low tumors.

Michael R. Shafique, Terrence L. Fisher, Elizabeth E. Evans, John E. Leonard, Desa Rae E. Pastore, Crystal L. Mallow, Ernest Smith, Vikas Mishra, Andreas Schröder, Kevin M. Chin, Joseph T. Beck, Megan A. Baumgart, Ramaswamy Govindan, Nashat Y. Gabrail, Alexander I. Spira, Nagashree Seetharamu, Yanyan Lou, Aaron S. Mansfield, Rachel E. Sanborn, Jonathan W. Goldman, Maurice Zauderer

Michael R. Shafique, Terrence L. Fisher, Elizabeth E. Evans... et al. Clinical Cancer Research
2021 A template to quantify the location and density of CD3 + and CD8 + tumor-infiltrating lymphocytes in colon cancer by digital pathology on whole slides for an objective, standardized immune score assessment

Oncotopix Discovery, Publicly Sharable

Background: In colon cancer, the location and density of tumor-infiltrating lymphocytes (TILs) can classify patients into low and high-risk groups for prognostication. While a commercially available ‘Immunoscore®’ exists, the incurred expenses and copyrights may prevent universal use. The aim of this study was to develop a robust and objective quantification method of TILs in colon cancer. Methods: A consecutive, unselected series of specimens from patients with colon cancer were available for immunohistochemistry and assessment of TILs by automated digital pathology. CD3 + and CD8 + cells at the invasive margin and in tumor center were assessed on consecutive sections using automated digital pathology and image analysis software (Visiopharm®). An algorithm template for whole slide assessment, generated cell counts per square millimeters (cells/mm2), from which the immune score was calculated using distribution volumes. Furthermore, immune score was compared with clinical and histopathological characteristics to confirm its relevance. Results: Based on the quantified TILs numbers by digital image analyses, patients were classified into low (n = 83, 69.7%), intermediate (n = 14, 11.8%) and high (n = 22, 18.5%) immune score groups. High immune score was associated with stage I–II tumors (p = 0.017) and a higher prevalence of microsatellite instable (MSI) tumors (p = 0.030). MSI tumors had a significantly higher numbers of CD3 + TILs in the invasive margin and CD8 + TILs in both tumor center and invasive margin, compared to microsatellite stable (MSS) tumors. Conclusion: A digital template to quantify an easy-to-use immune score corresponds with clinicopathological features and MSI in colon cancer.

Dordi Lea, Martin Watson, Ivar Skaland, Hanne R. Hagland, Melinda Lillesand, Einar Gudlaugsson, Kjetil Søreide

Dordi Lea, Martin Watson, Ivar Skaland... et al. Cancer Immunology, Immunotherapy
2021 Changes in Immune Cell Types with Age in Breast are Consistent with a Decline in Immune Surveillance and Increased Immunosuppression

Oncotopix Discovery, Publicly Sharable

A majority of breast cancers (BC) are age-related and we seek to determine what cellular and molecular changes occur in breast tissue with age that make women more susceptible to cancer initiation. Immune-epithelial cell interactions are important during mammary gland development and the immune system plays an important role in BC progression. The composition of human immune cell populations is known to change in peripheral blood with age and in breast tissue during BC progression. Less is known about changes in immune populations in normal breast tissue and how their interactions with mammary epithelia change with age. We quantified densities of T cells, B cells, and macrophage subsets in pathologically normal breast tissue from 122 different women who ranged in age from 24 to 74 years old. Donor-matched peripheral blood from a subset of 20 donors was analyzed by flow cytometry. Tissue immune cell densities and localizations relative to the epithelium were quantified in situ with machine learning-based image analyses of multiplex immunohistochemistry-stained tissue sections. In situ results were corroborated with flow cytometry analyses of peri-epithelial immune cells from primary breast tissue preparations and transcriptome analyses of public data from bulk tissue reduction mammoplasties. Proportions of immune cell subsets in breast tissue and donor-matched peripheral blood were not correlated. Density (cells/mm2) of T and B lymphocytes in situ decreased with age. T cells and macrophages preferentially localized near or within epithelial bilayers, rather than the intralobular stroma. M2 macrophage density was higher than M1 macrophage density and this difference was due to higher density of M2 in the intralobular stroma. Transcriptional signature analyses suggested age-dependent decline in adaptive immune cell populations and functions and increased innate immune cell activity. T cells and macrophages are so intimately associated with the epithelia that they are embedded within the bilayer, suggesting an important role for immune-epithelial cell interactions. Age-associated decreased T cell density in peri-epithelial regions, and increased M2 macrophage density in intralobular stroma suggests the emergence of a tissue microenvironment that is simultaneously immune-senescent and immunosuppressive with age.

Arrianna Zirbes, Jesuchristopher Joseph, Jennifer C. Lopez, Rosalyn W. Sayaman, Mudaser Basam, Victoria L. Seewaldt, Mark A. LaBarge

Arrianna Zirbes, Jesuchristopher Joseph, Jennifer C. Lopez... et al. Journal of Mammary Gland Biology and Neoplasia
2021 Stabilized epithelial phenotype of cancer cells in primary tumors leads to increased colonization of liver metastasis in pancreatic cancer

Phenoplex, Publicly Sharable, Vectra

Pancreatic ductal adenocarcinoma (PDAC) is therapeutically recalcitrant and metastatic. Partial epithelial to mesenchymal transition (EMT) is associated with metastasis; however, a causal connection needs further unraveling. Here, we use single-cell RNA sequencing and genetic mouse models to identify the functional roles of partial EMT and epithelial stabilization in PDAC growth and metastasis. A global EMT expression signature identifies ∼50 cancer cell clusters spanning the epithelial-mesenchymal continuum in both human and murine PDACs. The combined genetic suppression of Snail and Twist results in PDAC epithelial stabilization and increased liver metastasis. Genetic deletion of Zeb1 in PDAC cells also leads to liver metastasis associated with cancer cell epithelial stabilization. We demonstrate that epithelial stabilization leads to the enhanced collective migration of cancer cells and modulation of the immune microenvironment, which likely contribute to efficient liver colonization. Our study provides insights into the diverse mechanisms of metastasis in pancreatic cancer and potential therapeutic targets.

Julienne L. Carstens, Sujuan Yang, Pedro Correa de Sampaio, Xiaofeng Zheng, Souptik Barua, Kathleen M. McAndrews, Arvind Rao, Jared K. Burks, Andrew D. Rhim, Raghu Kalluri

Julienne L. Carstens, Sujuan Yang, Pedro Correa de Sampaio... et al. Cell Reports
2021 Immunological tumor heterogeneity and diagnostic profiling for advanced and immune therapies

Phenoplex, Publicly Sharable, Ultivue

Immunotherapies have changed the way how we treat cancer at all stages. The understanding of the immune system in individual tumor specimens guides the selection of immune-modulating agents such as immune checkpoint inhibitors alone or in combination with other therapeutic agents that target, modulate or unleash the patient's immune system. Despite the similar histopathological diagnosis, each tumor is unique at its primary site and site of metastasis, also depending on previous treatment regimens or genetic alterations, such as chromosomal instability or acquired mutations. The clinically well-established use of PD-1/PD-L1 inhibitors already requires the assessment of its target molecules in different cells (viable tumor cells alone or in combination with immune cells or immune cells alone) with different thresholds in various indications. Anyhow, checkpoint inhibitors show the best overall response rate when immune effec-tor cells like tumor-infiltrating lymphocytes are in close spatial proximity without being suppressed by other humoral or cellular regulatory mechanisms. Therefore, immune cell-rich tumors ("hot tumors") are usually quite reactive to immune-modulating agents, whereas other immune-depleted or immune-excluded tumor areas are less responsive and require alternative treatment regimens such as modified immune effectors cells or immune-stimulating agents, for example, oncolytic viruses. Here, we summarize the relevance to understand the entire tumor heterogeneity and its environment, the contextual relationship and spatial quantification of all immune and tumor cells along with the genetic background of the individual cancer through the application of multiplex in-situ technologies and the application of machine learning tools. K E Y W O R D S cell therapy, immunotherapy 1 | BACKGROUND Immunology discoveries and advancements come in waves. More than 100 years ago, different immune cells and their separate role in infectious and neoplastic diseases became obvious and some improvement in light microscopy contributed to the development of cancer immunology as a separate subject. With the advancement of analytical methods like immunohistochemistry (IHC), molecular tools, and computational solutions, immunotherapies make a greater impact in our clinical practice. 1 Today, we have advanced diagnostic tools at hand such as digital imaging for the objective and reproducible assessment of multiple markers at a time or on a single tissue slide precisely quantifying the absolute numbers of functionally distinct immune cells as well as their spatial distribution and contextual

Ralf Huss, Christoph Schmid, Mael Manesse, Jeppe Thagaard, Bruno Maerkl

Ralf Huss, Christoph Schmid, Mael Manesse... et al. Advances in Cell and Gene Therapy
2021 Immune microenvironment characterisation and dynamics during anti-HER2-based neoadjuvant treatment in HER2-positive breast cancer

Oncotopix Discovery, Phenoplex, Publicly Sharable, Tissuealign

Despite their recognised role in HER2-positive (HER2+) breast cancer (BC), the composition, localisation and functional orientation of immune cells within tumour microenvironment, as well as its dynamics during anti-HER2 treatment, is largely unknown. We here investigate changes in tumour-immune contexture, as assessed by stromal tumour-infiltrating lymphocytes (sTILs) and by multiplexed spatial cellular phenotyping, during treatment with lapatinib-trastuzumab in HER2+ BC patients (PAMELA trial). Moreover, we evaluate the relationship of tumour-immune contexture with hormone receptor status, intrinsic subtype and immune-related gene expression. sTIL levels increase after 2 weeks of HER2 blockade in HR-negative disease and HER2-enriched subtype. This is linked to a concomitant increase in cell density of all four immune subpopulations (CD3+, CD4+, CD8+, Foxp3+). Moreover, immune contexture analysis showed that immune cells spatially interacting with tumour cells have the strongest association with response to anti-HER2 treatment. Subsequently, sTILs consistently decrease at the surgery in patients achieving pathologic complete response, whereas most residual tumours at surgery remain inflamed, possibly reflecting a progressive loss of function of T cells. Understanding the features of the resulting tumour immunosuppressive microenvironment has crucial implications for the design of new strategies to de-escalate or escalate systemic therapy in early-stage HER2+ BC.

G. Griguolo, G. Serna, T. Pascual, R. Fasani, X. Guardia, N. Chic, L. Paré, S. Pernas, M. Muñoz, M. Oliveira, M. Vidal, A. Llombart-Cussac, J. Cortés, P. Galván, B. Bermejo, N. Martínez, R. López, S. Morales, I. Garau, L. Manso, J. Alarcón, E. Martínez, P. Villagrasa, A. Prat, P. Nuciforo

G. Griguolo, G. Serna, T. Pascual... et al. Precision Oncology
2021 Impaired Dendritic Cell Homing in COVID-19

Phenoplex, Publicly Sharable

The high mortality of COVID-19 is mostly attributed to acute respiratory distress syndrome (ARDS), whose histopathological correlate is diffuse alveolar damage (DAD). Furthermore, severe COVID-19 is often accompanied by a cytokine storm and a disrupted response of the adaptive immune system. Studies aiming to depict this dysregulation have mostly investigated the peripheral cell count as well as the functionality of immune cells. We investigated the impact of SARS-CoV-2 on antigen-presenting cells using multiplexed immunofluorescence. Similar to MERS-CoV and SARS-CoV, SARS-CoV-2 appears to be impairing the maturation of dendritic cells (DCs). DC maturation involves a switch in surface antigen expression, which enables the cells' homing to lymph nodes and the subsequent activation of T-cells. As quantitative descriptions of the local inflammatory infiltrate are still scarce, we compared the cell population of professional antigen-presenting cells (APC) in the lungs of COVID-19 autopsy cases in different stages of DAD. We found an increased count of myeloid dendritic cells (mDCs) in later stages. Interestingly, mDCs also showed no significant upregulation of maturation markers in DAD-specimens with high viral load. Accumulation of immature mDCs, which are unable to home to lymph nodes, ultimately results in an inadequate T-cell response.

Lukas Borcherding, Alime Sema Teksen, Bianca Grosser, Tina Schaller, Klaus Hirschbühl, Rainer Claus, Oliver Spring, Michael Wittmann, Christoph Römmele, Éva Sipos, Bruno Märkl

Lukas Borcherding, Alime Sema Teksen, Bianca Grosser... et al. Frontiers in Medicine
2021 A potent SARS-CoV-2 neutralising nanobody shows therapeutic efficacy in the Syrian golden hamster model of COVID-19

Oncotopix Discovery, Publicly Sharable

Jiandong Huo, Halina Mikolajek, Jordan Clark, Parul Sharma, Anja Kipar, Joshua Dormon, Rosalind Franklin, Institute Chelsea, Norman Rosalind, Franklin Institute, Miriam Weckener, Daniel Clare, Karen Buttigieg, Francisco Salguero, Robert Watson, Daniel Knott

Jiandong Huo, Halina Mikolajek, Jordan Clark... et al. Nat Commun
Cutting-Edge Platforms for Analysis of Immune Cells in the Hepatic Microenvironment—Focus on Tumor-Associated Macrophages in Hepatocellular Carcinoma

Oncotopix Discovery, Publicly Sharable

Simple Summary Hepatocellular carcinoma is the most common primary liver malignancy in the United States. Macrophages are immune cells that play a critical role in the promotion of cancer growth and configuration of the hepatic microenvironment. Studying intrahepatic macrophages is challenging because they are difficult to isolate, they transform their phenotype upon manipulation, and in vivo animal models poorly replicate the liver microenvironment. Understanding the complexity of intrahepatic macrophage populations is crucial because they coordinate antitumoral immunity. Application of novel methods that can detect immune cell phenotypes, along with their spatial co-localization in situ is critical and timely. Abstract The role of tumor-associated macrophages (TAMs) in the pathogenesis of hepatocellular carcinoma (HCC) is poorly understood. Most studies rely on platforms that remove intrahepatic macrophages from the microenvironment prior to evaluation. Cell isolation causes activation and phenotypic changes that may not represent their actual biology and function in situ. State-of-the-art methods provides new strategies to study TAMs without losing the context of tissue architecture and spatial relationship with neighboring cells. These technologies, such as multispectral imaging (e.g., Vectra Polaris), mass cytometry by time-of-flight (e.g., Fluidigm CyTOF), cycling of fluorochromes (e.g., Akoya Biosciences CODEX/PhenoCycler-Fusion, Bruker Canopy, Lunaphore Comet, and CyCIF) and digital spatial profiling or transcriptomics (e.g., GeoMx or Visium, Vizgen Merscope) are being utilized to accurately assess the complex cellular network within the tissue microenvironment. In cancer research, these platforms enable characterization of immune cell phenotypes and expression of potential therapeutic targets, such as PDL-1 and CTLA-4. Newer spatial profiling platforms allow for detection of numerous protein targets, in combination with whole transcriptome analysis, in a single liver biopsy tissue section. Macrophages can also be specifically targeted and analyzed, enabling quantification of both protein and gene expression within specific cell phenotypes, including TAMs. This review describes the workflow of each platform, summarizes recent research using these approaches, and explains the advantages and limitations of each. Keywords: cancer; CyTOF; HCC; liver; macrophages; spectral imaging; hepatic microenvironment; TAMs; TME; spatial genomics; scRNA-seq

DE Millian, OA Saldarriaga, T Wanninger, JK Burks - Cancers, undefined 2022

DE Millian, OA Saldarriaga, T Wanninger... et al. mdpi.com
2021 Automated quantification of sTIL density with H&E-based digital image analysis has prognostic potential in triple-negative breast cancers

Oncotopix Discovery, Publicly Sharable

Around 15% of breast cancer patients are diagnosed as triple-negative (TNBC), which have significantly lower 5-year survival rates (77%) than other types of breast cancer (93%). Our study aimed at developing an image analysis-based biomarker to assess how the immune system interacts with the tumor and investigate the potential added value of stromal tumor-infiltrating lymphocytes (sTIL) for the prognosis of overall survival compared to the manual approach. In a large retrospective cohort of 257 patients, we found that our fully automated hematoxylin and eosin (H&E) image analysis pipeline can quantify sTIL density showing both high concordance with manual scoring and association with the prognosis of patients with TNBC. It also overcomes natural limitations of manual assessment that hinder clinical adoption of the immune biomarker. We conclude that sTIL scoring by automated image analysis has prognostic potential comparable to manual scoring and should be further investigated for future use in a clinical setting. Abstract Triple-negative breast cancer (TNBC) is an aggressive and difficult-to-treat cancer type that represents approximately 15% of all breast cancers. Recently, stromal tumor-infiltrating lymphocytes (sTIL) resurfaced as a strong prognostic biomarker for overall survival (OS) for TNBC patients. Manual assessment has innate limitations that hinder clinical adoption, and the International Immuno-Oncology Biomarker Working Group (TIL-WG) has therefore envisioned that computational assessment of sTIL could overcome these limitations and recommended that any algorithm should follow the manual guidelines where appropriate. However, no existing studies capture all the concepts of the guideline or have shown the same prognostic evidence as manual assessment. In this study, we present a fully automated digital image analysis pipeline and demonstrate that our hematoxylin and eosin (H&E)-based pipeline can provide a quantitative and interpretable score that correlates with the manual pathologist-derived sTIL status, and importantly, can stratify a retrospective cohort into two significant distinct prognostic groups. We found our score to be prognostic for OS (HR: 0.81 CI: 0.72–0.92 p = 0.001) independent of age, tumor size, nodal status, and tumor type in statistical modeling. While prior studies have followed fragments of the TIL-WG guideline, our approach is the first to follow all complex aspects, where appropriate, supporting the TIL-WG vision of computational assessment of sTIL in the future clinical setting. Keywords: deep learning; digital pathology; image analysis; prognostic biomarker; survival analysis; triple-negative breast cancer; tumor microenvironment (TME); tumor-infiltrating lymphocytes

Jeppe Thagaard, Elisabeth Specht Stovgaard, Line Grove Vognsen, Søren Hauberg, Anders Dahl, Thomas Ebstrup, Johan Doré, Rikke Egede Vincentz, Rikke Karlin Jepsen, Anne Roslind, Iben Kümler, Dorte Nielsen, Eva Balslev

Jeppe Thagaard, Elisabeth Specht Stovgaard, Line Grove Vognsen... et al. Cancers
2021 Artificial Intelligence in Toxicologic Pathology: Quantitative Evaluation of Compound-Induced Hepatocellular Hypertrophy in Rats

Oncotopix Discovery, Publicly Sharable

Digital pathology evolved rapidly, enabling more systematic usage of image analysis and development of artificial intelligence (AI) applications. Here, combined AI models were developed to evaluate hepatocellular hypertrophy in rat liver, using commercial AI-based software on hematoxylin and eosin-stained whole slide images. In a first approach, deep learning-based identification of critical tissue zones (centrilobular, midzonal, and periportal) enabled evaluation of region-specific cell size. Mean cytoplasmic area of hepatocytes was calculated via several sequential algorithms including segmentation in microanatomical structures (separation of sinusoids and vessels from hepatocytes), nuclear detection, and area measurements. An increase in mean cytoplasmic area could be shown in groups given phenobarbital, known to induce hepatocellular hypertrophy when compared to control groups, in multiple studies. Quantitative results correlated with the gold standard: observation and grading performed by board-certified veterinary pathologists, liver weights, and gene expression. Furthermore, as a second approach, we introduce for the first time deep learning-based direct detection of hepatocellular hypertrophy with similar results. Cell hypertrophy is challenging to pick up, particularly in milder cases. Additional evaluation of mean cytoplasmic area or direct detection of hypertrophy, combined with histopathological observations and liver weights, is expected to increase accuracy and repeatability of diagnoses and grading by pathologists.

Hannah Pischon, David Mason, Bettina Lawrenz, Olivier Blanck, Anna Lena Frisk, Frederic Schorsch, Valeria Bertani

Hannah Pischon, David Mason, Bettina Lawrenz... et al. Toxicologic Pathology
2021 A Preliminary Study of Deep-Learning Algorithm for Analyzing Multiplex Immunofluorescence Biomarkers in Body Fluid Cytology Specimens

Akoya, Oncotopix Discovery, Phenoplex, Polaris, Publicly Sharable, Tissuealign, Vectra

Introduction: Multiplex biomarker analysis of cytological body fluid specimens is often used to assist cytologists in distiguishing metastatic cancer cells from reactive meso-thelial cells. However, evaluating biomarker expression visually may be challenging, especially when the cells of interest are scant. Deep-learning algorithms (DLAs) may be able to assist cytologists in analyzing multiple biomarker expression at the single cell level in the multiplex fluores-cence imaging (MFI) setting. This preliminary study was performed to test the feasibility of using DLAs to identify immunofluorescence-stained metastatic adenocarcinoma cells in body fluid cytology samples. Methods: A DLA was developed to analyze MFI-stained cells in body fluid cyto-logical samples. A total of 41 pleural fluid samples, comprising of 20 positives and 21 negatives, were retrospectively collected. Multiplex immunofluorescence labeling for MOC31, BerEP4, and calretinin, were performed on cell block sections, and results were analyzed by manual analysis (manual MFI) and DLA analysis (MFI-DLA) independently. Results: All cases with positive original cytological diagnoses showed positive results either by manual MFI or MFI-DLA, but 2 of the 14 (14.3%) original cytologically negative cases had rare cells with positive MOC31 and/or BerEP4 staining in addition to calretinin. Manual MFI analysis and MFI-DLA showed 100% concordance. Conclusion: MFI combined with DLA provides a potential tool to assist in cytological diagnosis of metastatic malignancy in body fluid samples. Larger studies are warranted to test the clinical validity of the approach.

Weibo Yu, Elizabeth Rao, Curtis D Chin, Josephine S Aguilar-Jakthong, Yunfeng Li, Christine Chow, Shu Yu, Grace Wang, Jianyu Rao

Weibo Yu, Elizabeth Rao, Curtis D Chin... et al. Acta Cytologica
2022 Alzheimer disease neuropathology in a patient previously treated with aducanumab

Oncotopix Discovery, Publicly Sharable, nice

Amyloid beta (Aβ) plaque is a defining pathologic feature of Alzheimer disease (AD). Aducanumab, a monoclonal IgG1 that selectively binds aggregated species of Aβ, has been shown by amyloid positron emission tomography (Amyloid PET) to reduce Aβ plaques in patients with prodromal and mild AD. This is the first autopsy report of the AD neuropathology in a patient previously treated with aducanumab. The patient was an 84-year-old woman who was randomized to the placebo arm of the PRIME Phase 1b study (221AD103). The patient progressed to moderate dementia (MMSE = 14/30), beyond the targeted early AD treatment stage, before receiving aducanumab in the long-term extension (LTE). The patient then received 32 monthly doses of aducanumab, titrated up to 6 mg/kg, for a cumulative dose of 186 mg/kg. In the LTE, Amyloid PET scans demonstrated robust Aβ plaque reduction, from a composite standard uptake value ratio (SUVR) of 1.5 at screening to < 1.1 at 56 weeks post-aducanumab dosing. MRI examinations were negative for amyloid-related imaging abnormalities (ARIA). She passed away in hospice care 4 months after her last dose of aducanumab. The postmortem neuropathologic examination confirmed AD neuropathologic changes. Aβ and IBA1 immunohistochemistry assays demonstrated sparse residual Aβ plaque engaged by amoeboid reactive microglia. Phospho-Tau (pTau) immunohistochemistry demonstrated neocortical neurofibrillary degeneration (Braak stage V, NIA/AA Stage B3). However, the density of pTau neuropathology, including neuritic plaque pTau (NP-Tau), appeared lower in the PRIME LTE Patient compared to a reference cohort of untreated Braak stage V–VI, NIA/AA Stage B3 AD cases. Taken together, this case report is the first to provide Amyloid PET and neuropathologic evidence substantiating the impact of aducanumab to reduce Aβ plaque neuropathology in a patient with AD. Furthermore, this report underscores the critical importance of autopsy neuropathology studies to augment our understanding of aducanumab’s mechanism of action and impact on AD biomarkers.

Edward D. Plowey, Thierry Bussiere, Raj Rajagovindan, Jennifer Sebalusky, Stefan Hamann, Christian von Hehn, Carmen Castrillo-Viguera, Alfred Sandrock, Samantha Budd Haeberlein, Christopher H. van Dyck, Anita Huttner

Edward D. Plowey, Thierry Bussiere, Raj Rajagovindan... et al. Acta Neuropathologica
2022 Development of a Fully Automated Method to Obtain Reproducible Lymphocyte Counts in Patients With Colorectal Cancer

Oncotopix Discovery, Publicly Sharable

Colorectal cancer (CRC) is the third most common cancer worldwide. Although clinical outcome varies among patients diagnosed within the same TNM stage it is the cornerstone in treatment decisions as well as follow-up programmes. Tumor-infiltrating lymphocytes have added value when evaluating survival outcomes. The aim of this study was to develop a fully automated method for quantification of subsets of T lymphocytes in the invasive margin and central tumor in patients with CRC based on Deep Learning powered artificial intelligence. The study cohort consisted of 163 consecutive patients with a primary diagnosis of CRC followed by a surgical resection. Double-labeling immunohistochemical staining with cytokeratin in combination with CD3 or CD8, respectively, was performed on 1 representative slide from each patient. Visiopharm Quantitative Digital Pathology software was used to develop Application Protocol Packages for visualization of architectural details (background, normal epithelium, cancer epithelium, surrounding tissue), identification of central tumor and invasive margin as well as subsequent quantitative analysis of immune cells. Fully automated counts for CD3 and CD8 positive T cells were obtained in 93% and 92% of the cases, respectively. In the remaining cases, manual editing was required. In conclusion, the development of a fully automated method for counting CD3+and CD8+lymphocytes in a cohort of patients with CRC provided excellent results eliminating not only observer variability in lymphocyte counts but also in identifying the regions of interest for the quantitative analysis. Validation of the performance of the Application Protocol Packages including clinical correlation is needed.

Anne Marie K. Fiehn, Bjoern Reiss, Mikail Gögenur, Michael Bzorek, Ismail Gögenur

Anne Marie K. Fiehn, Bjoern Reiss, Mikail Gögenur... et al. Applied Immunohistochemistry and Molecular Morphology
2022 Combining TMEM Doorway Score and MenaCalc Score Improves the Prediction of Distant Recurrence Risk in HR+/HER2− Breast Cancer Patients

Publicly Sharable, Tissuealign, nice

Purpose: to develop several digital pathology‐based machine vision algorithms for combining TMEM and MenaCalc scores and determine if a combination of these biomarkers improves the ability to predict development of distant metastasis over and above that of either biomarker alone. Methods: This retrospective study included a subset of 130 patients (65 patients with no recurrence and 65 patients with a recurrence at 5 years) from the Calgary Tamoxifen cohort of breast cancer patients. Patients had confirmed invasive breast cancer and received adjuvant tamoxifen therapy. Of the 130 patients, 86 cases were suitable for analysis in this study. Sequential sections of formalin‐fixed paraffin‐embedded patient samples were stained for TMEM doorways (immunohistochemistry triple staining) and MenaCalc (immunofluorescence staining). Stained sections were imaged, aligned, and then scored for TMEM doorways and MenaCalc. Different ways of combining TMEM doorway and MenaCalc scores were evaluated and compared to identify the best performing combined marker by using the restricted mean survival time (RMST) difference method. Results: the best performing combined marker gave an RMST difference of 5.27 years (95% CI: 1.71–8.37), compared to 3.56 years (95% CI: 0.95–6.1) for the associated standalone TMEM doorway analysis and 2.94 years (95% CI: 0.25–5.87) for the associated standalone MenaCalc analysis. Conclusions: combining TMEM doorway and MenaCalc scores as a new biomarker improves prognostication over that observed with TMEM doorway or MenaCalc Score alone in this cohort of 86 patients.

Xianjun Ye, Maja H. Oktay, Xiaonan Xue, Thomas E. Rohan, Paula S. Ginter, Timothy D’alfonso, Elizabeth N. Kornaga, Don G. Morris, David Entenberg, John S. Condeelis

Xianjun Ye, Maja H. Oktay, Xiaonan Xue... et al. Cancers
2022 Sex-Dependent Hepatoprotective Role of IL-22 Receptor Signaling in Non-Alcoholic Fatty Liver Disease-Related Fibrosis

Phenoplex, Publicly Sharable

Background & Aims: Nonalcoholic fatty liver disease (NAFLD) is a major health problem with complex pathogenesis. Although sex differences in NAFLD pathogenesis have been reported, the mechanisms underlying such differences remain understudied. Interleukin (IL)22 is a pleiotropic cytokine with both protective and/or pathogenic effects during liver injury. IL22 was shown to be hepatoprotective in NAFLD-related liver injury. However, these studies relied primarily on exogenous administration of IL22 and did not examine the sex-dependent effect of IL22. Here, we sought to characterize the role of endogenous IL22-receptor signaling during NAFLD-induced liver injury in males and females. Methods: We used immunofluorescence, flow cytometry, histopathologic assessment, and gene expression analysis to examine IL22 production and characterize the intrahepatic immune landscape in human subjects with NAFLD (n = 20; 11 men and 9 women) and in an in vivo Western high-fat diet–induced NAFLD model in IL22RA knock out mice and their wild-type littermates. Results: Examination of publicly available data sets from 2 cohorts with NAFLD showed increased hepatic IL22 gene expression in females compared with males. Furthermore, our immunofluorescence analysis of liver sections from NAFLD subjects (n = 20) showed increased infiltration of IL22-producing cells in females. Similarly, IL22-producing cells were increased in wild-type female mice with NAFLD and the hepatic IL22/IL22 binding protein messenger RNA ratio correlated with expression of anti-apoptosis genes. The lack of endogenous IL22-receptor signaling (IL22RA knockout) led to exacerbated liver damage, inflammation, apoptosis, and liver fibrosis in female, but not male, mice with NAFLD. Conclusions: Our data suggest a sex-dependent hepatoprotective antiapoptotic effect of IL22-receptor signaling during NAFLD-related liver injury in females.

Mohamed N. Abdelnabi, Manuel Flores Molina, Geneviève Soucy, Vincent Quoc-Huy Trinh, Nathalie Bédard, Sabrina Mazouz, Nathalie Jouvet, Jessica Dion, Sarah Tran, Marc Bilodeau, Jennifer L. Estall, Naglaa H. Shoukry

Mohamed N. Abdelnabi, Manuel Flores Molina, Geneviève Soucy... et al. Cellular and Molecular Gastroenterology and Hepatology
2022 α Cell dysfunction in islets from nondiabetic, glutamic acid decarboxylase autoantibody–positive individuals

Fluidigm, IMC, Phenoplex, Publicly Sharable

BACKGROUND. Multiple islet autoantibodies (AAbs) predict the development of type 1 diabetes (T1D) and hyperglycemia within 10 years. By contrast, T1D develops in only approximately 15% of individuals who are positive for single AAbs (generally against glutamic acid decarboxylase [GADA]); hence, the single GADA+ state may represent an early stage of T1D. METHODS. Here, we functionally, histologically, and molecularly phenotyped human islets from nondiabetic GADA+ and T1D donors. RESULTS. Similar to the few remaining β cells in the T1D islets, GADA+ donor islets demonstrated a preserved insulin secretory response. By contrast, α cell glucagon secretion was dysregulated in both GADA+ and T1D islets, with impaired glucose suppression of glucagon secretion. Single-cell RNA-Seq of GADA+ α cells revealed distinct abnormalities in glycolysis and oxidative phosphorylation pathways and a marked downregulation of cAMP-dependent protein kinase inhibitor β (PKIB), providing a molecular basis for the loss of glucose suppression and the increased effect of 3-isobutyl-1-methylxanthine (IBMX) observed in GADA+ donor islets. CONCLUSION. We found that α cell dysfunction was present during the early stages of islet autoimmunity at a time when β cell mass was still normal, raising important questions about the role of early α cell dysfunction in the progression of T1D.

Nicolai M. Doliba, Andrea V. Rozo, Jeffrey Roman, Wei Qin, Daniel Traum, Long Gao, Jinping Liu, Elisabetta Manduchi, Chengyang Liu, Maria L. Golson, Golnaz Vahedi, Ali Naji, Franz M. Matschinsky, Mark A. Atkinson, Alvin C. Powers, Marcela Brissova, Klaus H. Kaestner, Doris A. Stoffers

Nicolai M. Doliba, Andrea V. Rozo, Jeffrey Roman... et al. The Journal of Clinical Investigation
2022 Neutrophil-mediated fibroblast-tumocell il-6/stat-3 signaling underlies the association between neutrophil-to-lymphocyte ratio dynamics and chemotherapy response in localized pancreatic cancer: A hybrid clinical-preclinical study

Fluidigm, IMC, Phenoplex, Publicly Sharable

Background: Partial/complete pathologic response following neoadjuvant chemotherapy (NAC) in pancreatic cancer (PDAC) patients undergoing pancreatectomy is associated with improved survival. We sought to determine whether neutrophil-to-lymphocyte ratio (NLR) dynamics predict pathologic response following chemotherapy in PDAC, and if manipulating NLR impacts chemosensitivity in preclinical models and uncovers potential mechanistic underpinnings underlying these effects. Methods: Pathologic response in PDAC patients (n=94) undergoing NAC and pancreatectomy (7/2015-12/2019) was dichotomized as partial/complete or poor/absent. Bootstrap-validated multi-variable models assessed associations between pre-chemotherapy NLR (%neutrophils÷%lympho-cytes) or NLR dynamics during chemotherapy (ΔNLR = pre-surgery—pre-chemotherapy NLR) and pathologic response, disease-free survival (DFS), and overall survival (OS). To preclinically model effects of NLR attenuation on chemosensitivity, Ptf1aCre/+; KrasLSL-G12D/+;Tgfbr2flox/flox (PKT) mice and C57BL/6 mice orthotopically injected with KrasLSL-G12D/+;Trp53LSL-R172H/+;Pdx1Cre(KPC) cells were randomized to vehicle, gemcitabine/paclitaxel alone, and NLR-attenuating anti-Ly6G with/without gemcitabine/paclitaxel treatment. Results: In 94 PDAC patients undergoing NAC (median:4 months), pre-chemotherapy NLR (p<0.001) and ΔNLR attenuation during NAC (p=0.002) were independently associated with partial/ complete pathologic response. An NLR score = pre-chemotherapy NLR+ΔNLR correlated with DFS (p=0.006) and OS (p=0.002). Upon preclinical modeling, combining NLR-attenuating anti-Ly6G treatment with gemcitabine/paclitaxel—compared with gemcitabine/paclitaxel or anti-Ly6G alone—not only significantly reduced tumor burden and metastatic outgrowth, but also augmented tumor-infiltrating CD107a+-degranulating CD8+ T-cells (p<0.01) while dampening inflammatory cancer-associated fibroblast (CAF) polarization (p=0.006) and chemoresistant IL-6/STAT-3 signaling in vivo. Neutrophil-derived IL-1β emerged as a novel mediator of stromal inflammation, inducing inflammatory CAF polarization and CAF-tumor cell IL-6/STAT-3 signaling in ex vivo co-cultures. Conclusions: Therapeutic strategies to mitigate neutrophil-CAF-tumor cell IL-1β/IL-6/STAT-3 signaling during NAC may improve pathologic responses and/or survival in PDAC.

Iago de Castro Silva, Anna Bianchi, Nilesh U. Deshpande, Prateek Sharma, Siddharth Mehra, Vanessa Tonin Garrido, Shannon Jacqueline Saigh, Jonathan England, Peter Joel Hosein, Deukwoo Kwon, Nipun B. Merchant, Jashodeep Datta

Iago de Castro Silva, Anna Bianchi, Nilesh U. Deshpande... et al. eLife
2022 Original research: Necroptosis-driving genes RIPK1, RIPK3 and MLKL-p are associated with intratumoral CD3+ and CD8+ T cell density and predict prognosis in hepatocellular carcinoma

Oncotopix Discovery, Publicly Sharable

Background Hepatocellular carcinoma (HCC) is a highly lethal cancer and the second leading cause of cancer-related deaths worldwide. As demonstrated in other solid neoplasms and HCC, infiltrating CD8 + T cells seem to be related to a better prognosis, but the mechanisms affecting the immune landscape in HCC are still mostly unknown. Necroptosis is a programmed, caspase-independent cell death that, unlike apoptosis, evokes immune response by releasing damage-associated molecular factors. However, in HCC, the relationship between the necroptotic machinery and the tumor-infiltrating lymphocytes has not been fully investigated so far. Methods We investigated the association between the main necroptosis-related genes, that is, RIPK1, RIPK3, MLKL-p, and CD3 + /CD8 + tumor-infiltrating T cell by RNA-seq data analysis in 371 patients with primary HCC from The Cancer Genome Atlas and then by immunohistochemistry in two independent cohorts of HCC patients from Italy (82) and Japan (86). Results Our findings highlighted the immunogenetic role of necroptosis and its potential prognostic role in HCC: RIPK1, RIPK3 and MLKL-p were found significantly associated with intratumoral CD3 + and CD8 + T cells. In addition, multivariate survival analysis showed that the expression of RIPK1, RIPK3 and MLKL-p was associated with better overall survival in the two independent cohorts. Conclusions Our results confirmed the immunogenetic properties of necroptosis (NCP) in human HCC, showing that tumor-infiltrating lymphocytes (TILs) and, specifically, CD8+ T cells accumulate in tumors with higher expression of the necroptosis-related genes. These results suggest the importance of further studies to better assess the specific composition, as well as the functional features of the immune environment associated with a necroptotic signature in order to explore new possible diagnostic and immunotherapeutic scenarios.

Lorenzo Nicolè, Tiziana Sanavia, Rocco Cappellesso, Valeria Maffeis, Jun Akiba, Akihiko Kawahara, Yoshiki Naito, Claudia Maria Radu, Paolo Simioni, Davide Serafin, Giuliana Cortese, Maria Guido, Giacomo Zanus, Hirohisa Yano, Ambrogio Fassina

Lorenzo Nicolè, Tiziana Sanavia, Rocco Cappellesso... et al. Journal for Immunotherapy of Cancer
2022 Multi-parametric analysis of human livers reveals variation in intrahepatic inflammation across phases of chronic hepatitis B infection

Phenoplex, Publicly Sharable, Ultivue

Background & Aims: Chronic HBV is clinically categorized into 4 phases by a combination of serum HBV DNA levels, HBeAg status and alanine aminotransferase (ALT): immunotolerant (IT), immune-active (IA), inactive carrier (IC) and HBeAg-negative hepatitis (ENEG). Immune and virological measurements in the blood have proven useful but are insufficient to explain the interrelation between the immune system and the virus since immune dynamics differ in the blood and liver. Furthermore, the inflammatory response in the liver and parenchymal cells cannot be fully captured in blood. Methods: Immunological composition and transcriptional profiles of core needle liver-biopsies in chronic HBV phases were compared to those of healthy controls by multiplex immunofluorescence and RNA-sequencing (n = 37 and 78, respectively) analyses. Results: Irrespective of the phase-specific serological profiles, increased immune-gene expression and frequency was observed in chronic HBV compared to healthy livers. Greater transcriptomic deregulation was seen in IA and ENEG (172 vs. 243 DEGs) than in IT and IC (13 vs. 35 DEGs) livers. Interferon-stimulated genes, immune-activation and exhaustion genes (ICOS, CTLA4, PDCD1) together with chemokine genes (CXCL10, CXCL9) were significantly induced in IA and ENEG livers. Moreover, distinct immune profiles associated with ALT elevation and a more accentuated immune-exhaustion profile (CTLA4, TOX, SLAMF6, FOXP3) were observed in ENEG, which set it apart from the IA phase (LGALS9, PDCD1). Interestingly, all HBV phases showed downregulation of metabolic pathways vs. healthy livers (fatty and bile acid metabolism). Finally, increased leukocyte infiltrate correlated with serum ALT, but not with HBV DNA or viral proteins. Conclusion: Our comprehensive multi-parametric analysis of human livers revealed distinct inflammatory profiles and pronounced differences in intrahepatic gene profiles across all chronic HBV phases in comparison to healthy liver. Lay summary: Immunological studies on chronic HBV remain largely restricted to assessment of peripheral responses due to the limited access to the site of infection, the liver. In this study, we comprehensively analyzed livers from a well-defined cohort of patients with chronic HBV and uninfected controls with state-of-the-art techniques, and evaluated the differences in gene expression profiles and inflammation characteristics across distinct disease phases in patients with chronic HBV.

Noe Rico Montanari, Ricardo Ramírez, Abhishek Aggarwal, Nick van Buuren, Michael Doukas, Christina Moon, Scott Turner, Lauri Diehl, Li Li, Jose D. Debes, Becket Feierbach, Andre Boonstra

Noe Rico Montanari, Ricardo Ramírez, Abhishek Aggarwal... et al. Journal of Hepatology
2022 Immune Contexture and Differentiation Features Predict Outcome in Bladder Cancer

Phenoplex, Publicly Sharable, TMA, Tissuealign

BACKGROUND: An improved risk assessment of patients with bladder cancer (BC) is important to optimize clinical management. OBJECTIVE: To identify whether immune cell subpopulations and cancer cell-intrinsic features are associated with outcome and response to first-line chemotherapy in BC. DESIGN, SETTING, AND PARTICIPANTS: Primary tumor tissue from 785 patients with BC (stage Ta-T4b) were stained using multiplex immunofluorescence (CD3, CD8, FOXP3, CD20, CD68, CD163, and MHC-I) and immunohistochemistry (pancytokeratin, CK5/6, GATA3, programmed death 1 [PD-1], and programmed death ligand 1 [PD-L1]). A digital image analysis quantified staining results within the carcinoma cell and stromal part of the tumor. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Primary endpoints were progression-free survival, recurrence-free survival, and response to first-line chemotherapy. Optimal cutoff values for investigated markers were estimated using maximally selected rank statistics and receiver operating characteristic for each primary endpoint. Time-to-event analyses were performed using Cox regression analyses. RESULTS AND LIMITATIONS: Several immune subpopulations were independently associated with clinical outcomes. Especially, high PD-1 and PD-L1 expression was independently associated with an increased risk of recurrence and progression in non-muscle-invasive tumors, but with a lower risk of recurrence in muscle-invasive tumors. Furthermore, we observed a lower likelihood of response to first-line chemotherapy in patients with basal differentiation features. Finally, a model combining clinical risk factors with our most evident prognosticator improved prediction accuracy compared with clinical risk factors alone for progression in non-muscle-invasive BC and recurrence in muscle-invasive BC. The use of tissue microarrays and a long inclusion period are limitations to this study. CONCLUSIONS: Immune cell subpopulations and cancer cell-intrinsic features are associated with different clinical outcomes in BC. PATIENT SUMMARY: Immune cells play an important role in cancer development and treatment outcomes. Infiltration with specific immune cells and the presence of markers associated with immune evasion in the tumor predict clinical outcomes in bladder cancer.

Ann Taber, Frederik Prip, Philippe Lamy, Mads Agerbæk, Jørgen Bjerggaard Jensen, Torben Steiniche, Lars Dyrskjøt

Ann Taber, Frederik Prip, Philippe Lamy... et al. European Urology Oncology
2022 Immunologic Features in de Novo and Recurrent Glioblastoma Are Associated with Survival Outcomes

Publicly Sharable

Glioblastoma (GBM) is an immunologically "cold"tumor characterized by poor responsiveness to immunotherapy. Standard of care for GBM is surgical resection followed by chemoradiotherapy and maintenance chemotherapy. However, tumor recurrence is the norm, and recurring tumors are found frequently to have acquired molecular changes (e.g., mutations) that may influence their immunobiology. Here, we compared the immune contexture of de novo GBM and recurrent GBM (rGBM) using high-dimensional cytometry and multiplex IHC. Although myeloid and T cells were similarly abundant in de novo and rGBM, their spatial organization within tumors differed and was linked to outcomes. In rGBM, T cells were enriched and activated in perivascular regions and clustered with activated macrophages and fewer regulatory T cells. Moreover, a higher expression of phosphorylated STAT1 by T cells in these regions at recurrence was associated with a favorable prognosis. Together, our data identify differences in the immunobiology of de novo GBM and rGBM and identify perivascular T cells as potential therapeutic targets.

Cécile Alanio, Zev A. Binder, Renee B. Chang, MacLean P. Nasrallah, Devora Delman, Joey H. Li, Oliver Y. Tang, Logan Y. Zhang, Jiasi Vicky Zhang, E. John Wherry, Donald M. O'Rourke, Gregory L. Beatty

Cécile Alanio, Zev A. Binder, Renee B. Chang... et al. Cancer Immunology Research
2022 Identification of Similarities Between Skin Lesions in Patients With Antisynthetase Syndrome and Skin Lesions in Patients With Dermatomyositis by Highly Multiplexed Imaging Mass Cytometry

Fluidigm, IMC, Phenoplex, Publicly Sharable, SBI

Objective: Antisynthetase syndrome (ASyS) and dermatomyositis (DM) are autoimmune disorders that overlap clinically. Given the presence of DM-like skin lesions in ASyS patients, there is debate about whether ASyS is a distinct disease or a subclassification of DM. Recent studies identified differences in type I interferon (IFN) expression between ASyS and DM muscle and finger eruptions. This study was undertaken to elucidate similarities and differences in the pathogenesis of cutaneous disease in ASyS and DM at the single-cell level. Methods: Five ASyS patients and 7 DM patients were recruited from a prospectively collected database of well-characterized DM patients. ASyS patients were clinically confirmed as having ASyS according to the Connors et al criteria and the Solomon et al criteria and the presence of aminoacyl–transfer RNA synthetase antibodies. Immunophenotyping was conducted using immunofluorescence (IF) and imaging mass cytometry (IMC). Results: IF staining for MxA and IFNβ expression revealed up-regulation of type I IFN in ASyS and DM samples compared to healthy control samples (P < 0.05). IMC showed similar numbers of macrophages, T cells, B cells, and dendritic cells in ASyS and DM samples, with no differences in counts (P > 0.05), but an increase in myeloid dendritic cell percentage in DM samples (P < 0.05). Key type I IFN, cytokine, and JAK/STAT pathways were similarly expressed in both ASyS and DM (P > 0.05). At the single-cell level, macrophages positive for phosphorylated stimulator of IFN genes in ASyS samples expressed increased levels of tumor necrosis factor, interluekin-17 (IL-17), and IFNβ (P < 0.001). Conclusion: IMC is a powerful tool that identifies a role for the type I IFN system in DM-like skin lesions in ASyS and DM with some differences at the cellular level, but overall significant overlap, supporting similar therapeutic decision making.

Jay Patel, Adarsh Ravishankar, Spandana Maddukuri, Thomas Vazquez, Madison Grinnell, Victoria P. Werth

Jay Patel, Adarsh Ravishankar, Spandana Maddukuri... et al. Arthritis & Rheumatology
2022 Central nervous system immune interactome is a function of cancer lineage, tumor microenvironment, and STAT3 expression

Akoya, Phenoplex, Polaris, Publicly Sharable, Vectra, nice

BACKGROUND. Immune cell profiling of primary and metastatic CNS tumors has been focused on the tumor, not the tumor microenvironment (TME), or has been analyzed via biopsies. METHODS. En bloc resections of gliomas (n = 10) and lung metastases (n = 10) were analyzed via tissue segmentation and high-dimension Opal 7-color multiplex imaging. Single-cell RNA analyses were used to infer immune cell functionality. RESULTS. Within gliomas, T cells were localized in the infiltrating edge and perivascular space of tumors, while residing mostly in the stroma of metastatic tumors. CD163+ macrophages were evident throughout the TME of metastatic tumors, whereas in gliomas, CD68+, CD11c+CD68+, and CD11c+CD68+CD163+ cell subtypes were commonly observed. In lung metastases, T cells interacted with CD163+ macrophages as dyads and clusters at the brain-tumor interface and within the tumor itself and as clusters within the necrotic core. In contrast, gliomas typically lacked dyad and cluster interactions, except for T cell CD68+ cell dyads within the tumor. Analysis of transcriptomic data in glioblastomas revealed that innate immune cells expressed both proinflammatory and immunosuppressive gene signatures. CONCLUSION. Our results show that immunosuppressive macrophages are abundant within the TME and that the immune cell interactome between cancer lineages is distinct. Further, these data provide information for evaluating the role of different immune cell populations in brain tumor growth and therapeutic responses.

Hinda Najem, Martina Ott, Cynthia Kassab, Arvind Rao, Ganesh Rao, Anantha Marisetty, Adam M. Sonabend, Craig Horbinski, Roel Verhaak, Anand Shankar, Santhoshi N. Krishnan, Frederick S. Varn, Víctor A. Arrieta, Pravesh Gupta, Sherise D. Ferguson, Jason T. Huse, Gregory N. Fuller, James P. Long, Daniel E. Winkowski, Ben A. Freiberg, Charles David James, Leonidas C. Platanias, Maciej S. Lesniak, Jared K. Burks, Amy B. Heimberger

Hinda Najem, Martina Ott, Cynthia Kassab... et al. JCI Insight
2022 Artificial Intelligence in Toxicological Pathology: Quantitative Evaluation of Compound-Induced Follicular Cell Hypertrophy in Rat Thyroid Gland Using Deep Learning Models

Oncotopix Discovery, Publicly Sharable

Digital pathology has recently been more broadly deployed, fueling artificial intelligence (AI) application development and more systematic use of image analysis. Here, two different AI models were developed to evaluate follicular cell hypertrophy in hematoxylin and eosin-stained whole-slide-images of rat thyroid gland, using commercial AI-based-software. In the first, mean cytoplasmic area measuring approach (MCA approach), mean cytoplasmic area was calculated via several sequential deep learning (DL)-based algorithms including segmentation in microanatomical structures (separation of colloid and stroma from thyroid follicular epithelium), nuclear detection, and area measurements. With our additional second, hypertrophy area fraction predicting approach (HAF approach), we present for the first time DL-based direct detection of the histopathological change follicular cell hypertrophy in the thyroid gland with similar results. For multiple studies, increased output parameters (mean cytoplasmic area and hypertrophic area fraction) were shown in groups given different hypertrophy-inducing reference compounds in comparison to control groups. Quantitative results correlated with the gold standard of board-certified veterinary pathologists’ diagnoses and gradings as well as thyroid hormone dependent gene expressions. Accuracy and repeatability of diagnoses and grading by pathologists are expected to be improved by additional evaluation of mean cytoplasmic area or direct detection of hypertrophy, combined with standard histopathological observations.

Valeria Bertani, Olivier Blanck, Davy Guignard, Frederic Schorsch, Hannah Pischon

Valeria Bertani, Olivier Blanck, Davy Guignard... et al. Toxicologic Pathology
2023 Digital image analysis of intraepithelial B-lymphocytes to assess lymphoepithelial lesions in salivary glands of Sjögren’s syndrome patients

Oncotopix Discovery, Publicly Sharable, Tissuealign

Objective: Salivary glands of primary SS (pSS) patients characteristically harbour periductal infiltrates, in which lymphoepithelial lesions (LELs) can develop. LELs are composed of hyperplastic ductal epithelium with infiltrating lymphocytes and may assist in the challenging diagnostic process of pSS. As manual identification of LELs remains difficult, we aimed to identify LELs by using an objective digital image analysis (DIA) algorithm that detects intraepithelial lymphocytes. Methods: A virtual triple-staining technique developed for this study was used to count intraepithelial lymphocytes in consecutive slides stained for CD3 (T-lymphocytes), high-molecular-weight cytokeratin (hmwCK) (striated ducts) and CD20 (B-lymphocytes) in labial and parotid gland biopsies in a diagnostic cohort of 109 sicca patients. Patients were classified as having pSS or non-SS according to the ACR-EULAR classification criteria. Results: T-lymphocytes were detected in almost all analysed ducts of pSS and non-SS sicca patients, whereas intraepithelial B-lymphocytes were present in 59-68% of labial and parotid gland biopsies of pSS patients, against only 2-3% of patients classified as non-SS. Intraepithelial B-lymphocytes were found in almost all striated ducts with hyperplasia (LELs). Remarkably, ∼25% of analysed striated ducts without hyperplasia of pSS patients also contained B-lymphocytes (precursor-LELs). Furthermore, presence of intraepithelial B-lymphocytes was associated with clinical parameters of pSS (i.e. serology). Conclusion: The presence of intraepithelial B-lymphocytes in salivary gland biopsies of sicca patients is a clear indicator of pSS and can be used as an objective alternative to LEL scoring. Therefore, identification of B-lymphocyte-containing ducts should be added to the diagnostic histopathological work-up of patients suspected of pSS.

Martha S. Van Ginkel, Tineke Van Der Sluis, Marian L.C. Bulthuis, Henk J. Buikema, Erlin A. Haacke, Suzanne Arends, Stine Harder, Fred K.L. Spijkervet, Hendrika Bootsma, Arjan Vissink, Frans G.M. Kroese, Bert Van Der Vegt

Martha S. Van Ginkel, Tineke Van Der Sluis, Marian L.C. Bulthuis... et al. Rheumatology (Oxford)
2023 Digitally assessed lymphocyte infiltration in rectal cancer biopsies is associated with pathological response to neoadjuvant therapy

Oncotopix Discovery, Publicly Sharable, nice

A frequently used treatment strategy in locally advanced rectal cancer (RC) is neoadjuvant therapy followed by surgery. Patients treated with neoadjuvant therapy achieve varying pathological response, and currently, predicting the degree of response is challenging. This study examined the association between digitally assessed histopathological features in the diagnostic biopsies and pathological response to neoadjuvant therapy, aiming to find potential predictive biomarkers. 50 patients with RC treated with neoadjuvant chemotherapy and/or radiotherapy followed by surgery were included. Deep learning-based digital algorithms were used to assess the epithelium tumor area percentage (ETP) based on H&E-stained slides, and to quantify the density of CD3+ and CD8+ lymphocytes, as well as the CD8+/CD3+ lymphocyte percentage, based on immunohistochemically stained slides, from the diagnostic tumor biopsies. Pathological response was assessed according to the Mandard method. A good pathological response was defined as tumor regression grade (TRG) 1-2, and a complete pathological response was defined as Mandard TRG 1. Associations between the ETP and lymphocyte densities in the diagnostic biopsies and the pathological response were examined. The density of CD8+ lymphocytes, and the CD8+/CD3+ lymphocyte percentage, were associated with both good and complete response to neoadjuvant therapy, while the density of CD3+ lymphocytes was associated with complete response. The ETP did not correlate with response to neoadjuvant therapy. It is well-known that infiltration of lymphocytes in colorectal cancer is a prognostic biomarker. However, assessment of CD8+ and CD3+ lymphocytes in the diagnostic tumor biopsies of patients with RC may also be useful in predicting response to neoadjuvant therapy.

Dea Natalie Munch Jepsen, Henrik Høeg, Michael Bzorek, Adile Orhan, Jens Ole Eriksen, Ismail Gögenur, Björn Reiss, Anne-Marie Kanstrup Fiehn

Dea Natalie Munch Jepsen, Henrik Høeg, Michael Bzorek... et al. Human pathology
2023 A protein kinase C α and β inhibitor blunts hyperphagia to halt renal function decline and reduces adiposity in a rat model of obesity-driven type 2 diabetes

HE, Oncotopix Discovery, Publicly Sharable

Type 2 diabetes (T2D) and its complications can have debilitating, sometimes fatal consequences for afflicted individuals. The disease can be difficult to control, and therapeutic strategies to prevent T2D-induced tissue and organ damage are needed. Here we describe the results of administering a potent and selective inhibitor of Protein Kinase C (PKC) family members PKCα and PKCβ, Cmpd 1, in the ZSF1 obese rat model of hyperphagia-induced, obesity-driven T2D. Although our initial intent was to evaluate the effect of PKCα/β inhibition on renal damage in this model setting, Cmpd 1 unexpectedly caused a marked reduction in the hyperphagic response of ZSF1 obese animals. This halted renal function decline but did so indirectly and indistinguishably from a pair feeding comparator group. However, above and beyond this food intake effect, Cmpd 1 lowered overall animal body weights, reduced liver vacuolation, and reduced inguinal adipose tissue (iWAT) mass, inflammation, and adipocyte size. Taken together, Cmpd 1 had strong effects on multiple disease parameters in this obesity-driven rodent model of T2D. Further evaluation for potential translation of PKCα/β inhibition to T2D and obesity in humans is warranted.

Ju Wang, Agustin Casimiro-Garcia, Bryce G. Johnson, Jennifer Duffen, Michael Cain, Leigh Savary, Stephen Wang, Prashant Nambiar, Matthew Lech, Shanrong Zhao, Li Xi, Yutian Zhan, Jennifer Olson, James A. Stejskal, Hank Lin, Baohong Zhang, Robert V. Martinez, Katherine Masek-Hammerman, Franklin J. Schlerman, Ken Dower

Ju Wang, Agustin Casimiro-Garcia, Bryce G. Johnson... et al. Scientific Reports
2023 Assessing the role of tumour-associated macrophage subsets in breast cancer subtypes using digital image analysis

Oncotopix Discovery, Publicly Sharable, TMA

Purpose: The number of M1-like and M2-like tumour-associated macrophages (TAMs) and their ratio can play a role in breast cancer development and progression. Early clinical trials using macrophage targeting compounds are currently ongoing. However, the most optimal detection method of M1-like and M2-like macrophage subsets and their clinical relevance in breast cancer is still unclear. We aimed to optimize the assessment of TAM subsets in different breast cancer subtypes, and therefore related TAM subset numbers and ratio to clinicopathological characteristics and clinical outcome. Methods: Tissue microarrays of 347 consecutive primary Luminal-A, Luminal-B, HER2-positive and triple-negative tumours of patients with early-stage breast cancer were serially sectioned and immunohistochemically stained for the pan-macrophage marker CD68 and the M2-like macrophage markers CD163, CSF-1R and CD206. TAM numbers were quantified using a digital image analysis algorithm. M1-like macrophage numbers were calculated by subtracting M2-like TAM numbers from the total TAM number. Results: M2-like markers CD163 and CSF-1R showed a moderate positive association with each other and with CD68 (r ≥ 0.47), but only weakly with CD206 (r ≤ 0.06). CD68 + , CD163 + and CSF-1R + macrophages correlated with tumour grade in Luminal-B tumours (P < 0.001). Total or subset TAM numbers did not correlate with disease outcome in any breast cancer subtype. Conclusion: In conclusion, macrophages and their subsets can be detected by means of a panel of TAM markers and are related to unfavourable clinicopathological characteristics in Luminal-B breast cancer. However, their impact on outcome remains unclear. Preferably, this should be determined in prospective series.

Mieke C. Zwager, Rico Bense, Stijn Waaijer, Si Qi Qiu, Hetty Timmer-Bosscha, Elisabeth G.E. de Vries, Carolien P. Schröder, Bert van der Vegt

Mieke C. Zwager, Rico Bense, Stijn Waaijer... et al. Breast Cancer Research and Treatment
2023 Automated Prognostic Assessment of Endometrial Hyperplasia for Progression Risk Evaluation Using Artificial Intelligence

Oncotopix Discovery, Publicly Sharable

Endometrial hyperplasia is a precursor to endometrial cancer, characterized by excessive proliferation of glands that is distinguishable from normal endometrium. Current classifications define 2 types of EH, each with a different risk of progression to endometrial cancer. However, these schemes are based on visual assessments and, therefore, subjective, possibly leading to overtreatment or undertreatment. In this study, we developed an automated artificial intelligence tool (ENDOAPP) for the measurement of morphologic and cytologic features of endometrial tissue using the software Visiopharm. The ENDOAPP was used to extract features from whole-slide images of PAN-CK+-stained formalin-fixed paraffin-embedded tissue sections from 388 patients diagnosed with endometrial hyperplasia between 1980 and 2007. Follow-up data were available for all patients (mean = 140 months). The most prognostic features were identified by a logistic regression model and used to assign a low-risk or high-risk progression score. Performance of the ENDOAPP was assessed for the following variables: images from 2 different scanners (Hamamatsu XR and S60) and automated placement of a region of interest versus manual placement by an operator. Then, the performance of the application was compared with that of current classification schemes: WHO94, WHO20, and EIN, and the computerized-morphometric risk classification method: D-score. The most significant prognosticators were percentage stroma and the standard deviation of the lesser diameter of epithelial nuclei. The ENDOAPP had an acceptable discriminative power with an area under the curve of 0.765. Furthermore, strong to moderate agreement was observed between manual operators (intraclass correlation coefficient: 0.828) and scanners (intraclass correlation coefficient: 0.791). Comparison of the prognostic capability of each classification scheme revealed that the ENDOAPP had the highest accuracy of 88%-91% alongside the D-score method (91%). The other classification schemes had an accuracy between 83% and 87%. This study demonstrated the use of computer-aided prognosis to classify progression risk in EH for improved patient treatment.

Emma Rewcastle, Einar Gudlaugsson, Melinda Lillesand, Ivar Skaland, Jan P.A. Baak, Emiel A.M. Janssen

Emma Rewcastle, Einar Gudlaugsson, Melinda Lillesand... et al. Modern Pathology
2023 Homogeneity in immune features between colorectal liver metastases better identifies patients with good prognosis compared to pathological response to preoperative chemotherapy

Oncotopix Discovery, Publicly Sharable

In colorectal cancer liver metastases (CRLM), the density of tumor-infiltrating lymphocytes, the expression of class I major histocompatibility complex (MHC-I), and the pathological response to preoperative chemotherapy have been associated with oncological outcomes after complete resection. However, the prognostic significance of the heterogeneity of these features in patients with multiple CRLMs remains under investigation. We used a TMA tissue microarray of 220 mismatch repair-gene proficient CRLMs resected in 97 patients followed prospectively to quantify CD3+ T cells and MHC-I by immunohistochemistry. Histopathological response to preoperative chemotherapy was assessed using standard scoring systems. We tested associations between clinical, immunological, and pathological features with oncologic outcomes. Overall, 29 patients (30.2%) had CRLMs homogeneous for CD3+ T cell infiltration and MHC-I. Patients with immune homogeneous compared to heterogeneous CRLMs had longer median time to recurrence (TTR) (30 vs. 12 months, p = .0018) and disease-specific survival (DSS) (not reached vs. 48 months, p = .0009). At 6 years, 80% of the patients with immune homogeneous CRLMs were still alive. Homogeneity of response to preoperative chemotherapy was seen in 60 (61.9%) and 69 (80.2%) patients according to different grading systems and was not associated with TTR or DSS. CD3 and MHC-I heterogeneity was independent of response to pre-operative chemotherapy and of other clinicopathological variables for their association with oncological outcomes. In patients with multiple CRLMs resected with curative intent, similar adaptive immune features seen across metastases could be more informative than pathological response to pre-operative chemotherapy in predicting oncological outcomes.

David Henault, David Stephen, Pierre Antoine St-Hilaire, Nouredin Messaoudi, Franck Vandenbroucke-Menu, Eve Simoneau, Zhixia Rong, Marylène Plasse, Richard Létourneau, André Roy, Michel Dagenais, Réal Lapointe, Bich Nguyen, Anne Marie Mes-Masson, G. Soucy, Simon Turcotte

David Henault, David Stephen, Pierre Antoine St-Hilaire... et al. OncoImmunology
2023 Liver metastases across cancer types sharing tumor environment immunotolerance can impede immune response therapy and immune monitoring

Oncotopix Discovery, Publicly Sharable

Background Hepatic immune tolerance might contribute to the development of therapeutic resistance to immunotherapy. However, addressing this issue is challenging since the efficacy of immunotherapy in the context of liver metastasis (LM) remains poorly studied. Here, we aimed to establish an LM common immune feature (LMCIF) score to quantify the characteristics of LM immunotolerance across cancer types for assisting clinical disease management. Methods Large-scale clinical data were collected to identify the prognosis of LM. Multi-omics datasets of metastatic cancers with LM special immune-related pathways (LMSIPs) from the Molecular Signatures Database (MSigDB) were used to obtain an LMCIF cluster. Based on differential expression genes (DEGs), a novel LMCIF score for the LMCIF cluster was constructed. In addition, multi-omics, and immunohistochemistry (IHC) data from the public and in-house cohorts were used to explore the features of LM, and LMCIF score. Results Patients with LM had a worse prognosis and significantly lower infiltration of immune cells than patients with metastasis to other organs when analyzed with combined clinical and RNA sequencing data. After extracting the LMCIF cluster from 373 samples by utilizing 29 LMSIPs and validating them in a microarray cohort, an LMCIF score was established to confirm the role of the immunosuppressive environment as a contributor to the poor prognosis of LM across cancer types. Moreover, this LMCIF score could be used to predict the immune response of cancer patients undergoing immunotherapy. Finally, we identified that the majority of the 31 LMCIF genes exhibited a negative correlation with TME cells in LM patients, one of them, KRT19, which possessed the strongest positive correlation with LMCIF score, was confirmed to have an immunosuppressive effect through IHC analysis. Conclusions Our results suggest that LM across cancer types share similar immunological profiles that induce immunotolerance and escape from immune monitoring. The novel LMCIF score represents a common liver metastasis immune cluster for predicting immunotherapy response, the results of which might benefit clinical disease management.

Yuzhen Gao, Shipeng Chen, Hao Wang, Chenghao Wu, Rui An, Guoli Li, Min Yang, Ying Zhou, Yundong Zhou, Xinyou Xie, Hong Yu, Jun Zhang

Yuzhen Gao, Shipeng Chen, Hao Wang... et al. Journal of Advanced Research
2023 Biochemical and morphological responses to post-hepatectomy liver failure in rats

Oncotopix Discovery, Publicly Sharable

The upper limit for partial hepatectomy (PH) in rats is 90%, which is associated with an increased risk of post-hepatectomy liver failure (PHLF), correlating with high mortality. Sixty-eight rats were randomized to 90% PH, sham operation, or no surgery. Further block randomization was performed to determine the time of euthanasia, whether 12, 24, or 48 h after surgery. A general distress score (GDS) was calculated to distinguish between rats with reversible (GDS < 10) and irreversible PHLF (GDS ≥ 10). At euthanasia, the liver remnant and blood were collected. Liver-specific biochemistry and regeneration ratio were measured. Hepatocyte proliferation and volume were estimated using stereological methods. All rats subjected to 90% experienced biochemical PHLF. The biochemical and morphological liver responses did not differ between the groups until 48 h after surgery. At 48 h, liver regeneration and function were significantly improved in survivors. The peak mean regeneration ratio was 15% for rats with irreversible PHLF compared to 26% for rats with reversible PHLF. The 90% PH rat model was associated with PHLF and high mortality. Irreversible PHLF was characterized by impaired liver regeneration capacity and an insufficient ability to metabolize ammonia.

Andrea Lund, Kasper Jarlhelt Andersen, Michelle Meier, Marie Ingemann Pedersen, Anders Riegels Knudsen, Jakob Kirkegård, Frank Viborg Mortensen, Jens Randel Nyengaard

Andrea Lund, Kasper Jarlhelt Andersen, Michelle Meier... et al. Scientific Reports
2023 Spatial Immunoprofiling of Adenoid Cystic Carcinoma Reveals B7-H4 Is a Therapeutic Target for Aggressive Tumors

Fluidigm, IMC, Phenoplex, Publicly Sharable

Purpose: Adenoid cystic carcinoma (ACC) is a heterogeneous malignancy, and no effective systemic therapy exists for metastatic disease. We previously described two prognostic ACC molecular subtypes with distinct therapeutic vulnerabilities, ACC-I and ACC-II. In this study, we explored the ACC tumor microenvironment (TME) using RNA-sequencing and spatial biology to identify potential therapeutic targets. Experimental Design: Tumor samples from 62 ACC patients with available RNA-sequencing data that had been collected as part of previous studies were stained with a panel of 28 validated metal-tagged antibodies. Imaging mass cytometry (IMC) was performed using the Fluidigm Helios CyTOF instrument and analyzed with Visiopharm software. The B7-H4 antibody–drug conjugate AZD8205 was tested in ACC patient-derived xenografts (PDX). Results: RNA deconvolution revealed that most ACCs are immunologically “cold,” with approximately 30% being “hot.” ACC-I tumors with a poor prognosis harbored a higher density of immune cells; however, spatial analysis by IMC revealed that ACC-I immune cells were significantly restricted to the stroma, characterizing an immune-excluded TME. ACC-I tumors overexpressed the immune checkpoint B7-H4, and the degree of immune exclusion was directly correlated with B7-H4 expression levels, an independent predictor of poor survival. Two ACC-I/B7-H4-high PDXs obtained 90% complete responses to a single dose of AZD8205, but none were observed with isotype-conjugated payload or in an ACC-II/B7-H4 low PDX. Conclusions: Spatial analysis revealed that ACC subtypes have distinct TMEs, with enrichment of ACC-I immune cells that are restricted to the stroma. B7-H4 is highly expressed in poor-prognosis ACC-I subtype and is a potential therapeutic target.

Luana Guimaraes Sousa, Daniel J. McGrail, Felippe Lazar Neto, Kaiyi Li, Mario L. Marques-Piubelli, Sammy Ferri-Borgogno, Hui Dai, Yoshitsugu Mitani, Nicole Spardy Burr, Zachary A. Cooper, Krista Kinneer, Maria Angelica Cortez, Shiaw-Yih Lin, Diana Bell, Adel El Naggar, Jared Burks, Renata Ferrarotto

Luana Guimaraes Sousa, Daniel J. McGrail, Felippe Lazar Neto... et al. Clin Cancer Res
2023 MAVS signaling is required for preventing persistent chikungunya heart infection and chronic vascular tissue inflammation

H&E, Oncotopix Discovery, Publicly Sharable

Chikungunya virus (CHIKV) infection has been associated with severe cardiac manifestations, yet, how CHIKV infection leads to heart disease remains unknown. Here, we leveraged both mouse models and human primary cardiac cells to define the mechanisms of CHIKV heart infection. Using an immunocompetent mouse model of CHIKV infection as well as human primary cardiac cells, we demonstrate that CHIKV directly infects and actively replicates in cardiac fibroblasts. In immunocompetent mice, CHIKV is cleared from cardiac tissue without significant damage through the induction of a local type I interferon response from both infected and non-infected cardiac cells. Using mice deficient in major innate immunity signaling components, we found that signaling through the mitochondrial antiviral-signaling protein (MAVS) is required for viral clearance from the heart. In the absence of MAVS signaling, persistent infection leads to focal myocarditis and vasculitis of the large vessels attached to the base of the heart. Large vessel vasculitis was observed for up to 60 days post infection, suggesting CHIKV can lead to vascular inflammation and potential long-lasting cardiovascular complications. This study provides a model of CHIKV cardiac infection and mechanistic insight into CHIKV-induced heart disease, underscoring the importance of monitoring cardiac function in patients with CHIKV infections. Mosquito-borne viruses are serious global public health threats associated with severe atypical cardiovascular manifestations. Here, the authors dissect how chikungunya virus directly infects cardiac tissue leading to heart disease and define key host pathways involved in viral cardiac persistence and tissue damage.

Maria G. Noval, Sophie N. Spector, Eric Bartnicki, Franco Izzo, Navneet Narula, Stephen T. Yeung, Payal Damani-Yokota, M. Zahidunnabi Dewan, Valeria Mezzano, Bruno A. Rodriguez-Rodriguez, Cynthia Loomis, Kamal M. Khanna, Kenneth A. Stapleford

Maria G. Noval, Sophie N. Spector, Eric Bartnicki... et al. Nature Communications
2023 Small Leucine-Rich Proteoglycan PODNL1 Identified as a Potential Tumor Matrix-Mediated Biomarker for Prognosis and Immunotherapy in a Pan-Cancer Setting

Phenoplex, Publicly Sharable

The podocan-like protein 1 (PODNL1), an important member of the small leucine-rich proteoglycans (SLRP) family, is a crucial component of the tumor microenvironment (TME). But its prognostic values and the role in the TME have not been systematically estimated in a pan-cancer setting. Targeting PODNL1, a systematic exploration into the TCGA datasets, reconciling with the analyses of single-cell transcriptomes and immunotherapeutic cohorts in cancers, and validation by tissue microarray-based multiplex immunofluorescence staining was performed. PODNL1 was significantly correlated with the poor prognosis and immunotherapeutic responses in various cancers. In-depth demonstration of molecular mechanisms indicated that PODNL1 expressions were notably positively correlated with cancer-associated fibroblast (CAF) infiltration levels in 33 types of cancers. It also positively correlated with the pan-fibroblast TGF-β response signature score, and the hallmarks including TGF-β, TNF-α, inflammatory response, apical junction, epithelial-mesenchymal transition and hedgehog in pan-cancer. Furthermore, high PODNL1 expressions were positively related with the regulation of tumor-promoting TGF-β signaling through downregulating SMAD2/3:4 heterotrimer regulations transcription and up-regulating the pathway restricted SMAD protein phosphorylation. Single-cell transcriptome analyses and immunofluorescence validations indicated that PODNL1 was predominantly expressed in the cancer cells and CAFs in various cancers. Additionally, the hetero-geneity of cancer genotype-phenotype cross-talking was also observed associated with PODNL1. Our systematic study indicates that PODNL1 plays an important role in the complex regulation network of tumor progression, and lays a foundation for further exploration to develop PODNL1 as a valuable matrix-mediated biomarker for cancer immunotherapy and prognosis in a pan-cancer setting.

Geyang Dai, Yue Sun, Rui Wei, Ling Xi

Geyang Dai, Yue Sun, Rui Wei... et al. Curr. issues mol. biol.
2023 Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of the Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential

Comet, Lunaphore, Phenoplex, Publicly Sharable

Intraductal Papillary Mucinous Neoplasms (IPMNs) of the pancreas are bona fide precursor lesions of pancreatic ductal adenocarcinoma (PDAC). The most common subtype of IPMNs harbor a gastric foveolar-type epithelium, and these low-grade mucinous neoplasms are harbingers of IPMNs with high-grade dysplasia and cancer. The molecular underpinning of gastric differentiation in IPMNs is unknown, although identifying drivers of this indolent phenotype might enable opportunities for intercepting progression to high-grade IPMN and cancer. We conducted spatial transcriptomics on a cohort of IPMNs, followed by orthogonal and cross species validation studies, which established the transcription factor NKX6-2 as a key determinant of gastric cell identity in low-grade IPMNs. Loss of NKX6-2 expression is a consistent feature of IPMN progression, while re-expression of NKX6-2 in murine IPMN lines recapitulates the aforementioned gastric transcriptional program and glandular morphology. Our study identifies NKX6-2 as a previously unknown transcription factor driving indolent gastric differentiation in IPMN pathogenesis.

Marta Sans, Yuki Makino, Jimin Min, Kimal I. Rajapakshe, Michele Yip-Schneider, C. Max Schmidt, Mark W. Hurd, Jared K. Burks, Javier A. Gomez, Fredrik I. Thege, Johannes F. Fahrmann, Robert A. Wolff, Michael P. Kim, Paola A. Guerrero, Anirban Maitra

Marta Sans, Yuki Makino, Jimin Min... et al. Cancer discovery
2023 The Stereotypic Response of the Pulmonary Vasculature to Respiratory Viral Infections: Findings in Mouse Models of SARS-CoV-2, Influenza A and Gammaherpesvirus Infections

Oncotopix Discovery, Publicly Sharable

The respiratory system is the main target of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 19 (COVID-19) where acute respiratory distress syndrome is considered the leading cause of death. Changes in pulmonary blood vessels, among which an endothelialitis/endotheliitis has been particularly emphasized, have been suggested to play a central role in the development of acute lung injury. Similar vascular changes are also observed in animal models of COVID-19. The present study aimed to determine whether the latter are specific for SARS-CoV-2 infection, investigating the vascular response in the lungs of mice infected with SARS-CoV-2 and other respiratory viruses (influenza A and murine gammaherpesvirus) by in situ approaches (histology, immunohistology, morphometry) combined with RNA sequencing and bioinformatic analysis. Non-selective recruitment of monocytes and T and B cells from larger muscular veins and arteries was observed with all viruses, matched by a comparable transcriptional response. There was no evidence of endothelial cell infection in any of the models. Both the morphological investigation and the transcriptomics approach support the interpretation that the lung vasculature in mice mounts a stereotypic response to alveolar and respiratory epithelial damage. This may have implications for the treatment and management of respiratory disease in humans.

Simon De Neck, Rebekah Penrice-Randal, Jordan J. Clark, Parul Sharma, Eleanor G. Bentley, Adam Kirby, Daniele F. Mega, Ximeng Han, Andrew Owen, Julian A. Hiscox, James P. Stewart, Anja Kipar

Simon De Neck, Rebekah Penrice-Randal, Jordan J. Clark... et al. Viruses
2023 Cisplatin exhibits superiority over MMC as a perfusion agent in a peritoneal mesothelioma patient specific organoid HIPEC platform

Phenoplex, Publicly Sharable

Peritoneal mesothelioma (PM) is a rare malignancy with poor prognosis, representing about 10–15% of all mesothelioma cases. Herein we apply PM patient-derived tumor organoids (PTOs) in elucidating personalized HIPEC responses to bypass rarity of disease in generating preclinical data. Specimens were obtained from PM patients undergoing cytoreductive surgery with HIPEC. PTOs were fabricated with tumor cells suspended in ECM-hydrogel and treated with HIPEC regimen parameters. Viability and characterization analyses were performed post-treatment. Treatment efficacy was defined as ≥ 50% viability reduction and p < 0.05 compared to controls. From October 2020 to November 2022, 17 tumors from 7 patients were biofabricated into organoids, with 16/17 (94.1%) sites undergoing comparative 37° and 42° treatments with cisplatin and mitomycin C (MMC). Hyperthermic cisplatin and MMC enhanced cytotoxicity which reduced treatment viability by 25% and 22%, respectively, compared to normothermia. Heated cisplatin displayed the greatest cytotoxicity, with efficacy in 12/16 (75%) tumors and an average viability of 38% (5–68%). Heated MMC demonstrated efficacy in 7/16 (43.8%) tumors with an average treatment viability of 51% (17–92.3%). PTOs fabricated from distinct anatomic sites exhibited site-specific variability in treatment responses. PM PTOs exhibit patient and anatomic location treatment responses suggestive of underlying disease clonality. In PM organoids cisplatin is superior to MMC in HIPEC.

Steven D. Forsythe, Richard A. Erali, Nicholas Edenhoffer, William Meeker, Nadeem Wajih, Cecilia R. Schaaf, Preston Laney, Cristian D. Vanezuela, Wencheng Li, Edward A. Levine, Shay Soker, Konstantinos I. Votanopoulos

Steven D. Forsythe, Richard A. Erali, Nicholas Edenhoffer... et al. Scientific Reports
2023 Radiomics using computed tomography to predict CD73 expression and prognosis of colorectal cancer liver metastases

Phenoplex, Publicly Sharable, TMA

Finding a noninvasive radiomic surrogate of tumor immune features could help identify patients more likely to respond to novel immune checkpoint inhibitors. Particularly, CD73 is an ectonucleotidase that catalyzes the breakdown of extracellular AMP into immunosuppressive adenosine, which can be blocked by therapeutic antibodies. High CD73 expression in colorectal cancer liver metastasis (CRLM) resected with curative intent is associated with early recurrence and shorter patient survival. The aim of this study was hence to evaluate whether machine learning analysis of preoperative liver CT-scan could estimate high vs low CD73 expression in CRLM and whether such radiomic score would have a prognostic significance. We trained an Attentive Interpretable Tabular Learning (TabNet) model to predict, from preoperative CT images, stratified expression levels of CD73 (CD73High vs. CD73Low) assessed by immunofluorescence (IF) on tissue microarrays. Radiomic features were extracted from 160 segmented CRLM of 122 patients with matched IF data, preprocessed and used to train the predictive model. We applied a five-fold cross-validation and validated the performance on a hold-out test set. TabNet provided areas under the receiver operating characteristic curve of 0.95 (95% CI 0.87 to 1.0) and 0.79 (0.65 to 0.92) on the training and hold-out test sets respectively, and outperformed other machine learning models. The TabNet-derived score, termed rad-CD73, was positively correlated with CD73 histological expression in matched CRLM (Spearman’s ρ = 0.6004; P < 0.0001). The median time to recurrence (TTR) and disease-specific survival (DSS) after CRLM resection in rad-CD73High vs rad-CD73Low patients was 13.0 vs 23.6 months (P = 0.0098) and 53.4 vs 126.0 months (P = 0.0222), respectively. The prognostic value of rad-CD73 was independent of the standard clinical risk score, for both TTR (HR = 2.11, 95% CI 1.30 to 3.45, P < 0.005) and DSS (HR = 1.88, 95% CI 1.11 to 3.18, P = 0.020). Our findings reveal promising results for non-invasive CT-scan-based prediction of CD73 expression in CRLM and warrant further validation as to whether rad-CD73 could assist oncologists as a biomarker of prognosis and response to immunotherapies targeting the adenosine pathway.

Ralph Saber, David Henault, Nouredin Messaoudi, Rolando Rebolledo, Emmanuel Montagnon, Geneviève Soucy, John Stagg, An Tang, Simon Turcotte, Samuel Kadoury

Ralph Saber, David Henault, Nouredin Messaoudi... et al. Journal of Translational Medicine
2023 Inhibition of microsomal prostaglandin E2 synthase reduces collagen deposition in melanoma tumors and may improve immunotherapy efficacy by reducing T cell exhaustion

Akoya, Oncotopix Discovery, Publicly Sharable, Vectra Polaris

The arachidonic acid pathway participates in immunosuppression in various types of cancer. Our previous observation detailed that microsomal prostaglandin E2 synthase 1 (mPGES-1), an enzyme downstream of cyclooxygenase 2 (COX-2), limited antitumor immunity in melanoma; in addition, genetic depletion of mPGES-1 specifically enhanced immune checkpoint blockade therapy. The present study set out to distinguish the roles of mPGES-1 from those of COX-2 in tumor immunity and determine the potential of mPGES-1 inhibitors for reinforcing immunotherapy in melanoma. Genetic deletion of mPGES-1 showed different profiles of prostaglandin metabolites from that of COX-2 deletion. In our syngeneic mouse model, mPGES-1–deficient cells exhibited similar tumorigenicity to that of COX-2–deficient cells, despite a lower ability to suppress PGE2 synthesis by mPGES-1 depletion, indicating the presence of factors other than PGE2 that are likely to regulate tumor immunity. RNA sequencing analysis revealed that mPGES-1 depletion reduced the expressions of collagen-related genes, which have been found to be associated with immunosuppressive signatures. In our mouse model, collagen was reduced in mPGES-1–deficient tumors, and phenotypic analysis of tumor-infiltrating lymphocytes indicated that mPGES-1-deficient tumors had fewer TIM3+ exhausted CD8+ T cells compared with COX-2–deficient tumors. CAY10678, an mPGES-1 inhibitor, was equivalent to celecoxib, a selective COX-2 inhibitor, in reinforcing anti–PD-1 treatment. Our study indicates that mPGES-1 inhibitors represent a promising adjuvant for immunotherapies in melanoma by reducing collagen deposition and T cell exhaustion.

Yasunari Fukuda, Sun-Hee Kim, Matias A. Bustos, Sung-Nam Cho, Jason Roszik, Jared K. Burks, Hong Kim, Dave S.B. Hoon, Elizabeth A. Grimm, Suhendan Ekmekcioglu

Yasunari Fukuda, Sun-Hee Kim, Matias A. Bustos... et al. Cancer Research Communications
2023 Assessing Oral Epithelial Dysplasia Risk for Transformation to Cancer: Comparison Between Histologic Grading Systems Versus S100A7 Immunohistochemical Signature-based Grading

Oncotopix Discovery, Publicly Sharable, Straticyte

While a 3-tier oral epithelial dysplasia grading system has been utilized for decades, it is widely recognized as a sub-optimal risk indicator for transformation to cancer. A 2-tier grading system has been proposed, although not yet validated. In this study, the 3-tier and 2-tier dysplasia grading systems, and an S100A7 immunohistochemical signature-based grading system were compared to assess prediction of risk of transformation to oral cancer. Formalin-fixed, paraffin-embedded biopsy specimens with known clinical outcomes were obtained retrospectively from a cohort of 48 patients. Hematoxylin and eosin-stained slides were used for the 2-and 3-tier dysplasia grading, while S100A7 for biomarker signature-based assessment was based on immunohistochemistry. Inter-observer variability was determined using Cohen's kappa (K) statistic with Cox regression disease free survival analysis used to determine if any of the methods were a predictor of transformation to oral squamous cell carcinoma. Both the 2-and 3-tier dysplasia grading systems ranged from slight to substantial inter-observer agreement (Kw between 0.093 to 0.624), with neither system a good predictor of transformation to cancer (at least P = 0.231; (P > > > 0.05). In contrast, the S100A7 immunohistochemical signature-based grading system showed almost perfect inter-observer agreement (Kw = 0.892) and was a good indicator of transformation to cancer (P = 0.047 and 0.030). The inherent grading challenges with oral epithelial dysplasia grading systems and the lack of meaningful prediction of transformation to carcinoma highlights the significant need for a more objective, quantitative, and reproducible risk assessment tool such as the S100A7 immunohistochemical signature-based system.

Mark Roger Darling, Jason T K Hwang, Benjamin J Dickson, Jean-Claude Cutz, Samih Salama, Christina Mccord, Kenneth P H Pritzker, David Mock, Lester D R Thompson

Mark Roger Darling, Jason T K Hwang, Benjamin J Dickson... et al. Applied Immunohistochemistry & Molecular Morphology
2023 Estimating tissue-specific TNF mRNA levels prior to anti-TNFα treatment may support therapeutic optimisation in IBD patients

ISH, Oncotopix Discovery, Publicly Sharable, RNAScope

Background and aims: Tumour necrosis factor-α (TNF) antagonists have improved the management of inflammatory bowel disease (IBD), however, their usage and administration persist to be suboptimal. Here, we examined the relationship between tissue-specific TNF mRNA expression in mucosal biopsies from IBD patients and anti-TNF treatment response. Methods: Archived tissue samples from patients with luminal IBD that had all been or were in treatment with anti-TNF were included (18 adults and 24 paediatric patients). Patients were stratified into three groups according to anti-TNF response: responders, primary non-responders (PNR) and secondary loss of response (SLOR). TNF mRNA was detected using RNAscope in situ hybridisation (ISH) and the expression was quantified using image analysis. Results: The ISH analysis showed varying occurrence of TNF mRNA positive cells located in lamina propria and often with increased density in lymphoid follicles (LF). Consequently, expression estimates were obtained in whole tissue areas with and without LF. Significantly higher TNF mRNA expression levels were measured in adults compared to paediatric patients in both the analyses with and without LF (p = .015 and p = .016, respectively). Considering the relation to response, the adult and paediatric patients were evaluated separately. In adults, the TNF expression estimates were higher in PNRs compared to responders with and without LF (p = .017 and p = .024, respectively). Conclusion: Our data indicate that adult PNR have significantly higher TNF mRNA levels than responders. This suggests that higher anti-TNF dose may be considered for IBD patients with high TNF mRNA expression estimates from the start of treatment. Keywords: Image analysis; Paediatric IBD; Tumour necrosis factor; inflammation; lymphoid follicle; mucosal TNF mRNA; quantitative in situ hybridisation; treatment non-response.

Jaslin P James, Schnack Nielsen, Ebbe Langholz, Mikkel Malham, Estrid Høgdall, & Lene, Buhl Riis, Boye Schnack Nielsen, Lene Buhl Riis

Jaslin P James, Schnack Nielsen, Ebbe Langholz... et al. Scand J Gastroenterol
2023 Artificial Intelligence-Aided Diagnosis of Breast Cancer Lymph Node Metastasis on Histologic Slides in a Digital Workflow

Oncotopix Clinical, Publicly Sharable

Abstract

Identifying lymph node (LN) metastasis in invasive breast carcinoma (IBC) can be tedious and time consuming. We investigated an artificial intelligence (AI) algorithm to detect LN metastasis by screening H&E slides in a clinical digital workflow. The study included two sentinel LN (SLN) cohorts (validation cohort with 234 SLNs and consensus cohort with 102 SLNs) and one non-sentinel LN (NSLN) cohort (258 LNs enriched with lobular carcinoma and post-neoadjuvant therapy cases). All H&E slides were scanned into whole slide images (WSI) in clinical digital workflow and WSIs were automatically batch analyzed using Visiopharm (VIS) metastasis AI algorithm. For SLN validation cohort, VIS metastasis AI algorithm detected all 46 metastases including 19 macrometastases, 26 micrometastases, 1 with isolated tumor cells (ITC) with a sensitivity of 100%, specificity of 41.5%, positive predictive value (PPV) of 29.5% and negative predictive value (NPV) of 100%. The false positivity was caused by histiocytes (52.7%), crushed lymphocytes (18.2%), and others, which were readily recognized during pathologists' reviews. For SLN consensus cohort, three pathologists examined all VIS AI annotated H&E slides and cytokeratin IHC slides with similar average concordance rates (99% for both modalities). However, the average time consumed by pathologists using VIS AI annotated slides was significantly less than the time using IHC slides (0.6 vs 1.0 minute, p=0.0377). For NSLN cohort, AI algorithm detected all 81 metastases, including 23 from lobular carcinoma and 31 from post-neoadjuvant chemotherapy cases with sensitivity of 100%, specificity of 78.5%, PPV of 68.1%, and NPV of 100%. VIS AI algorithm showed perfect sensitivity and NPV in detecting LN metastasis and less time consumed, suggesting its potential utility as a screening modality in routine clinical digital pathology workflow to improve efficiency.

Bindu Challa, Maryam Tahir, Yan Hu, David Kellough, Giovani Lujan, Shaoli Sun, Anil V. Parwani, Zaibo Li

Bindu Challa, Maryam Tahir, Yan Hu... et al. Modern Pathology
2023 The Prognostic Role of the Immune Microenvironment in Sinonasal Intestinal-Type Adenocarcinoma: A Computer-Assisted Image Analysis of CD3+ and CD8+ Tumor-Infiltrating Lymphocytes

Oncotopix Discovery, Publicly Sharable

The prognostic value of conventional histopathological parameters in the sinonasal intestinal-type adenocarcinoma (ITAC) has been debated and novel variables should be investigated. Increasing evidence demonstrated that the evolution of cancer is strongly dependent upon the complex interactions within tumor microenvironment. The aim of this retrospective study was to assess the features of immune microenvironment in terms of CD3+ and CD8+ cells in a series of ITAC and explore their prognostic role, as well as their relations with clinicopathological variables. A computer-assisted image analysis of CD3+ and CD8+ tumor-infiltrating lymphocytes (TIL) density was conducted on surgical specimens of 51 patients with ITAC that underwent a curative treatment including surgery. ITAC displays variable TIL density, which is associated with OS. In a univariate model, the density of CD3+ TIL was significantly related to OS (p = 0.012), whereas the association with CD8+ TIL density resulted in being non-significant (p = 0.056). Patients with intermediate CD3+ TIL density were associated with the best outcome, whereas 5-year OS was the lowest for intermediate CD8+ TIL density. CD3+ TIL density maintained a significant association with OS in the multivariable analysis. TIL density was not significantly related to demographic and clinicopathological variables. CD3+ TIL density was independently associated with OS in a non-linear fashion and patients with intermediate CD3+ TIL density had the best outcome. Though based on a preliminary analysis on a relatively small series of patients, this finding makes TIL density a potential independent prognostic factor of ITAC.

Marco Ferrari, Lara Alessandrini, Enrico Savietto, Diego Cazzador, Gloria Schiavo, Stefano Taboni, Andrea L. C. Carobbio, Leonardo Calvanese, Giacomo Contro, Piergiorgio Gaudioso, Enzo Emanuelli, Marta Sbaraglia, Elisabetta Zanoletti, Gino Marioni, Angelo P. Dei Tos, Piero Nicolai

Marco Ferrari, Lara Alessandrini, Enrico Savietto... et al. Journal of Personalized Medicine
2023 The alarmin interleukin-33 promotes the expansion and preserves the stemness of Tcf-1+ CD8+ T cells in chronic viral infection

Oncotopix Discovery, Publicly Sharable

T cell factor 1 (Tcf-1) expressing CD8+ T cells exhibit stem-like self-renewing capacity, rendering them key for immune defense against chronic viral infection and cancer. Yet, the signals that promote the formation and maintenance of these stem-like CD8+ T cells (CD8+SL) remain poorly defined. Studying CD8+ T cell differentiation in mice with chronic viral infection, we identified the alarmin interleukin-33 (IL-33) as pivotal for the expansion and stem-like functioning of CD8+SL as well as for virus control. IL-33 receptor (ST2)-deficient CD8+ T cells exhibited biased end differentiation and premature loss of Tcf-1. ST2-deficient CD8+SL responses were restored by blockade of type I interferon signaling, suggesting that IL-33 balances IFN-I effects to control CD8+SL formation in chronic infection. IL-33 signals broadly augmented chromatin accessibility in CD8+SL and determined these cells' re-expansion potential. Our study identifies the IL-33-ST2 axis as an important CD8+SL-promoting pathway in the context of chronic viral infection.

Anna-Friederike Marx, Sandra M. Kallert, Tobias M. Brunner, José A. Villegas, Florian Geier, Jonas Fixemer, Tiago Abreu-Mota, Peter Reuther, Weldy V. Bonilla, Jelizaveta Fadejeva, Mario Kreutzfeldt, Ingrid Wagner, Patricia Aparicio-Domingo, Leo Scarpellino, Mélanie Charmoy, Daniel T. Utzschneider, Claudia Hagedorn, Min Lu, Karen Cornille, Karsten Stauffer, Florian Kreppel, Doron Merkler, Dietmar Zehn, Werner Held, Sanjiv A. Luther, Max Löhning, Daniel D. Pinschewer

Anna-Friederike Marx, Sandra M. Kallert, Tobias M. Brunner... et al. Immunity
2023 High ATP6V1B1 expression is associated with poor prognosis and platinum‑based chemotherapy resistance in epithelial ovarian cancer

Oncotopix Discovery, Publicly Sharable, TMA

Gwan Han, Hee Yun, Joon-Yong Chung, Jae-Hoon Kim, Hanbyoul Cho

Gwan Han, Hee Yun, Joon-Yong Chung... et al. Oncology reports
2023 Effects of needle puncturing on re-vascularization and follicle survival in xenotransplanted human ovarian tissue

Oncotopix Discovery, Publicly Sharable

Ovarian tissue transplantation can restore fertility in young cancer survivors, however the detrimental loss of follicles following transplantation of cryopreserved ovarian tissue is hampering the efficiency of the procedure. This study investigates whether needle puncturing prior to transplantation can enhance revascularization and improve follicle survival in xenotransplanted human ovarian cortex. Cryopreserved human ovarian cortex pieces (N = 36) from 20 women aged 24–36 years were included. During the thawing process, each piece of tissue was cut in halves; one half serving as the untreated control and the other half was punctured approximately 150–200 times with a 29-gauge needle. The cortex pieces were transplanted subcutaneously to immunodeficient mice for 3, 6 and 10 days (N = 8 patients) and for 4 weeks (N = 12 patients). After 3, 6 and 10 days, revascularization of the ovarian xenografts were assessed using immunohistochemical detection of CD31 and gene expression of angiogenic factors (Vegfα, Angptl4, Ang1, and Ang2), and apoptotic factors (BCL2 and BAX) were performed by qPCR. Follicle density and morphology were evaluated in ovarian xenografts after 4 weeks. A significant increase in the CD31 positive area in human ovarian xenografts was evident from day 3 to 10, but no significant differences were observed between the needle and control group. The gene expression of Vegfα was consistently higher in the needle group compared to control at all three time points, but not statistically significant. The expression of Ang1 and Ang2 increased significantly from day 3 to day 10 in the control group (p < 0.001, p = 0.0023), however, in the needle group this increase was not observed from day 6 to 10 (Ang2 p = 0.027). The BAX/BCL2 ratio was similar in the needle and control groups. After 4-weeks xenografting, follicle density (follicles/mm3, mean ± SEM) was higher in the needle group (5.18 ± 2.24) compared to control (2.36 ± 0.67) (p = 0.208), and a significant lower percentage of necrotic follicles was found in the needle group (19%) compared to control (36%) (p = 0.045). Needle puncturing of human ovarian cortex prior to transplantation had no effect on revascularization of ovarian grafts after 3, 6 and 10 days xenotransplantation. However, needle puncturing did affect angiogenic genes and improved follicle morphology.

Hanna Ørnes Olesen, Susanne Elisabeth Pors, Cristina Subiran Adrados, Mette Christa Zeuthen, Linn Salto Mamsen, Anette Tønnes Pedersen, Stine Gry Kristensen

Hanna Ørnes Olesen, Susanne Elisabeth Pors, Cristina Subiran Adrados... et al. Reproductive Biology and Endocrinology
2023 Patients with fibrosis from non-alcoholic steatohepatitis have heterogeneous intrahepatic macrophages and therapeutic targets

Phenoplex, Publicly Sharable

Background and Aims In clinical trials for reducing fibrosis in NASH patients, therapeutics that target macrophages have had variable results. We evaluated intrahepatic macrophages in patients with non-alcoholic steatohepatitis to determine if fibrosis influenced phenotypes and expression of CCR2 and Galectin-3. Approach & Results We used nCounter to analyze liver biopsies from well-matched patients with minimal (n=12) or advanced (n=12) fibrosis to determine which macrophage-related genes would be significantly different. Known therapy targets (e.g., CCR2 and Galectin-3) were significantly increased in patients with cirrhosis. However, several genes (e.g., CD68, CD16, and CD14) did not show significant differences, and CD163, a marker of pro-fibrotic macrophages was significantly decreased with cirrhosis. Next, we analyzed patients with minimal (n=6) or advanced fibrosis (n=5) using approaches that preserved hepatic architecture by multiplex-staining with anti-CD68, Mac387, CD163, CD14, and CD16. Spectral data were analyzed using deep learning/artificial intelligence to determine percentages and spatial relationships. This approach showed patients with advanced fibrosis had increased CD68+, CD16+, Mac387+, CD163+, and CD16+CD163+ populations. Interaction of CD68+ and Mac387+ populations was significantly increased in patients with cirrhosis and enrichment of these same phenotypes in individuals with minimal fibrosis correlated with poor outcomes. Evaluation of a final set of patients (n=4) also showed heterogenous expression of CD163, CCR2, Galectin-3, and Mac387, and significant differences were not dependent on fibrosis stage or NAFLD activity. Conclusions Approaches that leave hepatic architecture intact, like multispectral imaging, may be paramount to developing effective treatments for NASH. In addition, understanding individual differences in patients may be required for optimal responses to macrophage-targeting therapies. * AIH NAFLD NAS NASH

Omar A Saldarriaga, Santhoshi Krishnan, Timothy G Wanninger, Morgan Oneka, Arvind Rao, Daniel Bao, Esteban Arroyave, Joseph Gosnell, Michael Kueht, Akshata Moghe, Daniel Millian, Jingjing Jiao, Jessica I Sanchez, Heidi Spratt, Laura Beretta, Heather L Stevenson, Associate Professor

Omar A Saldarriaga, Santhoshi Krishnan, Timothy G Wanninger... et al. medRxiv
2023 Expansion of Phenotypically Altered Dendritic Cell Populations in the Small Airways and Alveolar Parenchyma in Patients with Chronic Obstructive Pulmonary Disease

Oncotopix Discovery, Publicly Sharable

Contrasting the antigen-presenting dendritic cells (DCs) in the conducting airways, the alveolar DC populations in human lungs have remained poorly investigated. Consequently , little is known about how alveolar DCs are altered in diseases such as chronic obstructive pulmonary disease (COPD). This study maps multiple tissue DC categories in the distal lung across COPD severities. Specifically, single-multiplex immunohistochemistry was applied to quantify langerin/ CD207 + , CD1a + , BDCA2 + , and CD11c + subsets in distal lung compartments from patients with COPD (GOLD stage I-IV) and never-smoking and smoking controls. In the alveolar pa-renchyma, increased numbers of CD1a + langerin − (p < 0.05) and BDCA-2 + DCs (p < 0.001) were observed in advanced COPD compared with controls. Alveolar CD11c + DCs also increased in advanced COPD (p < 0.01). In small airways, lan-gerin + and BDCA-2 + DCs were also significantly increased. Contrasting the small airway DCs, most alveolar DC subsets frequently extended luminal protrusions. Importantly, alve-olar and small airway langerin + DCs in COPD lungs displayed site-specific marker profiles. Further, multiplex immunohis-tochemistry with single-cell quantification was used to specifically profile langerin DCs and reveal site-specific expression patterns of the maturation and activation markers S100, fascin, MHC2, and B7. Taken together, our results show that clinically advanced COPD is associated with increased levels of multiple alveolar DC populations exhibiting features of both adaptive and innate immunity phenotypes. This expansion is likely to contribute to the distal lung immunopathol-ogy in COPD patients.

Michiko Mori, Carl-Magnus Clausson, Caroline Sanden, Jimmie Jönsson, Cecilia K Andersson, Premkumar Siddhuraj, Medya Shikhagaie, Karolina Åkesson, Anders Bergqvist, Claes-Göran Löfdahl, Jonas S Erjefält

Michiko Mori, Carl-Magnus Clausson, Caroline Sanden... et al. Research Article J Innate Immun
2024 Addition of tumor microenvironment immune cell composition to improve the performance of a predictive model for oral squamous cell carcinoma

Oncotopix Discovery, Publicly Sharable, TMA, Tissuealign

Background Conventional clinicopathological characteristics insufficiently predict prognosis in oral squamous cell carcinoma (OSCC). We aimed to assess the added predictive value of tumor microenvironment immune cell composition (TMICC) in addition to conventional clinicopathological characteristics. Methods Primary tumor samples of 290 OSCC patients were immunohistochemically stained for CD4, CD8, CD20, CD68, CD163, CD57, FoxP3 and Programmed cell Death Ligand 1. Additionally, clinicopathological characteristics were obtained from patients’ medical files. Predictive models were trained and validated by conducting Least Absolute Shrinkage and Selection Operator (LASSO) regression analyses with cross-validation. To quantify the added predictive power of TMICC within models, receiver operating characteristic (ROC) analyses were used. Results Recurrence occurred in 74 patients (25.5%). Conventional clinicopathological characteristics (tumor localization, pathological T-stage, pathological N-stage, extracapsular spread, resection margin, differentiation grade, perineural invasion, lymphovascular invasion) and treatment modality, were used to build a LASSO logistic regression-based predictive model. Addition of TMICC to the model resulted in a comparable AUC of respectively 0.79 (±0.01) and 0.76 (±0.1) in the training and test sets. The model indicated that high numbers of CD4+ T cells protected against recurrence. Lymph node metastasis, extracapsular spread, perineural invasion, positive surgical margins and reception of adjuvant treatment were associated with increased risk for recurrence. Conclusions The TMICC, specifically the number of CD4+ T cells, is an independent predictor , however, addition to conventional clinicopathological characteristics does not improve the performance of a predictive model for recurrence in OSCC.

Sangeeta K. Bisheshar, Martine F. van der Kamp, Julius de Vries, Lorian Slagter-Menkema, Ed M.D. Schuuring, Gerton A. Lunter, Gyorgy B. Halmos, Bert van der Vegt

Sangeeta K. Bisheshar, Martine F. van der Kamp, Julius de Vries... et al. Oral Oncology
2024 In vivo bioluminescence imaging of the intracerebral fibroin-controlled AAV-α-synuclein diffusion for monitoring the central nervous system and peripheral expression

Oncotopix Discovery, Publicly Sharable

Among the several animal models of α-synucleinopathies, the well-known viral vector-mediated delivery of wild-type or mutated (A53T) α-synuclein requires new tools to increase the lesion in mice and follow up in vivo expression. To this end, we developed a bioluminescent expression reporter of the human A53T-α-synuclein gene using the NanoLuc system into an AAV2/9, embedded or not in a fibroin solution to stabilise its expression in space and time. We first verified the expression of the fused protein in vitro on transfected cells by bioluminescence and Western blotting. Next, two groups of C57Bl6Jr mice were unilaterally injected with the AAV-NanoLuc-human-A53T-α-synuclein above the substantia nigra combined (or not) with fibroin. We first show that the in vivo cerebral bioluminescence signal was more intense in the presence of fibroin. Using immunohistochemistry, we find that the human-A53T-α-synuclein protein is more restricted to the ipsilateral side with an overall greater magnitude of the lesion when fibroin was added. However, we also detected a bioluminescence signal in peripheral organs in both conditions, confirmed by the presence of viral DNA corresponding to the injected AAV in the liver using qPCR.

Claire Mazzocco, Coralie Genevois, Qin Li, Evelyne Doudnikoff, Nathalie Dutheil, Thierry Leste-Lasserre, Marie-Laure Arotcarena, Erwan Bezard

Claire Mazzocco, Coralie Genevois, Qin Li... et al. Scientific Reports
2024 Spatial profiling of ovarian carcinoma and tumor microenvironment evolution under neoadjuvant chemotherapy

Phenoplex, Publicly Sharable, TMA

Purpose: Immune tumor microenvironment (iTME) determines ovarian cancer development. This study investigates changes in HLA-I expression, CD8+/Foxp3 ratio, CD8+ cells and coregulators density at diagnosis and upon neoadjuvant chemotherapy (NACT), correlating changes with clinical outcomes. Experimental design: Multiplexed immune profiling and cell clustering analysis was performed on paired matched OC samples to characterize the iTME at diagnosis and under NACT from patients enrolled in the CHIVA trial (NCT01583322). Results: Several immune cells (IC) subsets and immune coregulators were quantified pre-/post-NACT. At diagnosis, patients with higher CD8+ T cells and HLA-1+ enriched tumors were associated with ­better outcome. The CD8+/Foxp3+ ratio increased significantly post-NACT in favor of increased immune surveillance and the influx of CD8+ T cells predicted better outcomes. Clustering analysis stratified pre-NACT tumors into 4 subsets: high Binf, enriched in B clusters; high Tinf, low Tinf, according to their CD8+ density; and desert clusters. At baseline, these clusters were not correlated with patient outcomes. Under NACT, tumors segregated into 3 clusters: high BinfTinf, low Tinf and desert. The high BinfTinf, more diverse in IC composition encompassing T, B and NK cell, correlated with improved survival. PD-L1 was rarely expressed, while TIM-3, LAG- and IDO-1 were more prevalent. Conclusions: Several iTMEs exist during tumor evolution and NACT impact on iTME is heterogeneous. Clustering analysis of patients, unravels several IC subsets within OC and can guide future personalized approaches. Targeting different checkpoints such as TIM-3, LAG-3 and IDO-1, more prevalent than PD-L1, could more effectively harness anti-tumor immunity in this anti-PD-L1 resistant malignancy.

Elisa Yaniz-Galende, Qinghe Zeng, Juan Francisco Grau-Bejar, Christophe Klein, Félix Blanc-Durand, Audrey Le Formal, Eric Pujade-Lauraine, Laure Chardin, Elodie Edmond, Virginie Marty, Isabelle Ray-Coquard, Florence Joly, Gwenaël Ferron, Patricia Pautier, Dominique Berton-Rigaud, Alain Lortholary, Nadine Dohollou, Christophe Desauw, Michel Fabbro, Emmanuelle Malaurie, Nathalie Bonichon-Lamichhane, Diana Bello Roufai, Justine Gantzer, Etienne Rouleau, Catherine Genestie, Alexandra Leary

Elisa Yaniz-Galende, Qinghe Zeng, Juan Francisco Grau-Bejar... et al. Clinical cancer research
2024 Exploring the prognostic value of circular RNAs in pancreatic ductal adenocarcinoma using genome-wide expression profiling

Oncotopix Discovery, Publicly Sharable, RNAScope

Background/Objectives Median survival of pancreatic ductal adenocarcinoma (PDAC) is around eight months and new prognostic tools are needed. Circular RNAs (circRNAs) have gained interest in different types of cancer. However, only a few studies have evaluated their potential in PDAC. We aimed to identify the most differentially expressed circRNAs in PDAC compared to controls and to explore their potential as prognostic markers. Methods Using frozen specimens with PDAC and controls, we performed RNA sequencing and identified 20,440 unique circRNAs. A custom code set of capture- and reporter probes for NanoString nCounter analysis was designed to target 152 circRNAs, based on abundancy, differential expression and literature study. Expression of these 152 circRNAs was examined in 108 formalin-fixed and paraffin-embedded surgical PDAC specimens and controls. The spatial expression of one of the most promising candidates, ciRS-7 (hsa_circ_0001946), was evaluated by chromogenic in situ hybridization (CISH) of multi-punch tissue microarrays (TMAs) and digital imaging analysis. Results Based on circRNA expression profiles, we identified different PDAC subclusters. The 30 most differentially expressed circRNAs showed log2 fold changes from -3.43 to 0.94, where circNRIP1 (hsa_circ_0004771), circMBOAT2 (hsa_circ_0007334) and circRUNX1 (hsa_circ_0002360) held significant prognostic value in multivariable analysis. CiRS-7 was absent in PDAC cells but highly expressed in tumor microenvironment. Conclusions We identified several new circRNAs with biomarker potential, three of which showed an independent prognostic value in surgically treated PDAC. We also found that ciRS-7 is absent in cancer cells but abundant in tumor microenvironment and may have potential as marker of activated stroma. Keywords circRNA pancreatic ductal adenocarcinoma RNA sequencing prognosis survival

Siri Vreim Ørbeck, Theresa Jakobsen, Juan Luis García-Rodríguez, Mark Burton, Lukas Gammelgaard Rasmussen, Jesper Dupont Ewald, Claus Wilki Fristrup, Per Pfeiffer, Michael Bau Mortensen, Lasse Sommer Kristensen, Sönke Detlefsen

Siri Vreim Ørbeck, Theresa Jakobsen, Juan Luis García-Rodríguez... et al. Pancreatology
2024 Concordance between ER, PR, Ki67, and HER2-low expression in breast cancer by MammaTyper RT-qPCR and immunohistochemistry: implications for the practising pathologist

Oncotopix Discovery, Publicly Sharable

Background: There are limited data on the role of multigene tests and their correlation with immuno-histochemistry (IHC), especially on core biopsy. MammaTyper is a quantitative conformite Eur-opeeanne (CE) marked, National Institute for Health and Care excellence (NICE) approved, in in vitro diagnostic quantitative real-time polymerase chain reaction (RT-qPCR) test for assessment of mRNA expression of four biomarkers (ESR1, PGR, ERBB2, MKI67). Methods: We evaluated the concordance of Mamma-Typer with oestrogen receptor (ER), progesterone receptor (PR), HER2, and Ki67 by IHC on 133 core needle biopsies of breast cancer. HER2 was positive if IHC 3+ or 2+ and fluorescence in situ hybridization (FISH)-amplified. Global and hotspot Ki67 expression was analysed using a cutoff of ≥20% assessed manually and by digital image analysis. Agreements were expressed as overall percent agreement (OPA), positive percent agreement (PPA), negative percent agreement (NPA), and Cohen's kappa. Results: RT-qPCR results of ESR1 were highly con-cordant with IHC with OPA of 94.7% using 1% cutoff and 91.7% when the low ER-positive category was included. The PPA and NPA between RT-qPCR and IHC for PR was 91.5% and 88.0%, respectively, when using the 1% cutoff. For ERBB2/HER2, the OPA was 95% and the PPA was 84.6%. 40 of 72 HER2 IHC score 0 tumours were classified as ERBB2 low. Best concordance between MKI67 by MammaTyper and Ki67 IHC was achieved using hotspot digital image analysis (OPA: 87.2%, PPA: 90.6%, NPA: 80%). Conclusion: RT-qPCR-based assessment of the mRNA expression of ESR1, PGR, ERBB2, and MKI67 showed high concordance with IHC, suggesting that the Mam-maTyper test on core needle biopsies represents a reliable, efficient, and reproducible alternative for breast cancer classification and refining HER2 low categorisation. aJoint senior authors. Abbreviations: CI, confidence interval; CISH, chromogenic in situ hybridisation; ER, oestrogen receptor alpha protein; ERBB2, ERB-B2 tyrosine kinase 2/human epidermal growth factor receptor 2 gene; ESR1, oestrogen receptor 1 gene; FFPE, formalin-fixed paraffin-embedded; FISH, fluorescent in situ hybridisation; HER2, ERB-B2 tyrosine kinase 2/human epidermal growth factor receptor 2 protein; IHC, immunohistochemistry; Ki67, marker of proliferation Ki67 protein; MKI67, marker of proliferation Ki67 gene; MT, MammaTyper; PA, percent agreement; PGR, progesterone receptor gene; PR, progesterone receptor protein.

Nahla M Badr, Mohamed Zaakouk, Qi Zhang, Daniel Kearns, Anthony Kong, Abeer M Shaaban, Badr N M, Shaaban A M

Nahla M Badr, Mohamed Zaakouk, Qi Zhang... et al. Histopathology
2024 Targeting sinonasal undifferentiated carcinoma with a combinatory immunotherapy approach

Phenoplex, Publicly Sharable

Purpose: Sinonasal undifferentiated carcinoma (SNUC) is a rare, aggressive malignancy of the sinonasal cavity with poor prognosis and limited treatment options. To investigate the potential for SNUC sensitivity to combinatory immunotherapy, we performed in vitro studies with SNUC cell lines and used multi-spectral immunofluorescence to characterize the in vivo patient SNUC tumor immune microenvironment (TIME). Experimental design: Human-derived SNUC cell lines were used for in vitro studies of tumor cell susceptibility to natural killer (NK) cell-based immunotherapeutic strategies. Tumor samples from 14 treatment naïve SNUC patients were examined via multi-spectral immunofluorescence and clinical correlations assessed. Results: Anti-PD-L1 blockade enhanced NK cell lysis of SNUC cell lines ∼5.4 fold (P ≤ 0.0001). This effect was blocked by a CD16 neutralizing antibody demonstrating activity through an antibody-dependent cellular cytotoxicity (ADCC) mediated pathway. ADCC-dependent lysis of SNUC cells was further enhanced by upregulation of PD-L1 on tumor cells by exogenous interferon-gamma (IFN-γ) administration or interleukin-15 (IL-15) stimulated IFN-γ release from NK cells. Combination treatment with anti-PD-L1 blockade and IL-15 superagonism enhanced NK-cell killing of SNUC cells 9.6-fold (P ≤ 0.0001). Untreated SNUC patient tumor samples were found to have an NK cell infiltrate and PD-L1+ tumor cells at a median of 5.4 cells per mm2. A striking 55.7-fold increase in CKlow tumor cell/NK cell interactions was observed in patients without disease recurrence after treatment (P = 0.022). Patients with higher CD3+CD8+ in the stroma had a significantly improved 5-year overall survival (P = 0.0029) and a significant increase in CKlow tumor cell/CD8+ cytotoxic T cell interactions was noted in long-term survivors (P = 0.0225). Conclusion: These data provide the pre-clinical rationale for ongoing investigation into combinatory immunotherapy approaches for SNUC.

Austin T.K. Hoke, Yoko Takahashi, Michelle R. Padget, Javier Gomez, Moran Amit, Jared Burks, Diana Bell, Tongxin Xie, Patrick Soon-Shiong, James W. Hodge, Ehab Y. Hanna, Nyall R. London

Austin T.K. Hoke, Yoko Takahashi, Michelle R. Padget... et al. Translational Oncology
2024 Effects of sporadic inclusion body myositis on skeletal muscle fibre type specific morphology and markers of regeneration and inflammation

Phenoplex, Publicly Sharable

Sporadic inclusion body myositis (sIBM) is a subgroup of idiopathic inflammatory myopathies characterised by progressive muscle weakness and skeletal muscle inflammation. Quantitative data on the myofibre morphology in sIBM remains scarce. Further, no previous study has examined fibre type association of satellite cells (SC), myonuclei number, macrophages, capillaries, and myonuclear domain (MD) in sIBM patients. Muscle biopsies from sIBM patients (n = 18) obtained previously (NCT02317094) were included in the analysis for fibre type-specific myofibre cross-sectional area (mCSA), SCs, myonuclei and macrophages, myonuclear domain, and capillarisation. mCSA (p < 0.001), peripheral myonuclei (p < 0.001) and MD (p = 0.005) were higher in association with type 1 (slow-twitch) than type 2 (fast-twitch) fibres. Conversely, quiescent SCs (p < 0.001), centrally placed myonuclei (p = 0.03), M1 macrophages (p < 0.002), M2 macrophages (p = 0.013) and capillaries (p < 0.001) were higher at type 2 fibres compared to type 1 fibres. In contrast, proliferating (Pax7+/Ki67+) SCs (p = 0.68) were similarly associated with each fibre type. Type 2 myofibres of late-phase sIBM patients showed marked signs of muscle atrophy (i.e. reduced mCSA) accompanied by higher numbers of associated quiescent SCs, centrally placed myonuclei, macrophages and capillaries compared to type 1 fibres. In contrast, type 1 fibres were suffering from pathological enlargement with larger MDs as well as fewer nuclei and capillaries per area when compared with type 2 fibres. More research is needed to examine to which extent different therapeutic interventions including targeted exercise might alleviate these fibre type-specific characteristics and countermeasure their consequences in impaired functional performance.

Kasper Yde Jensen, Jakob Lindberg Nielsen, Per Aagaard, Mikkel Jacobsen, Anders Nørkaer Jørgensen, Rune Dueholm Bech, Ulrik Frandsen, Louise Pyndt Diederichsen, Henrik Daa Schrøder

Kasper Yde Jensen, Jakob Lindberg Nielsen, Per Aagaard... et al. Rheumatology International
2024 Exploring alveolar recruitability using positive end-expiratory pressure in mice overexpressing TGF-β1: a structure–function analysis

Oncotopix Discovery, Publicly Sharable, Stereology

Pre-injured lungs are prone to injury progression in response to mechanical ventilation. Heterogeneous ventilation due to (micro)atelectases imparts injurious strains on open alveoli (known as volutrauma). Hence, recruitment of (micro)atelectases by positive end-expiratory pressure (PEEP) is necessary to interrupt this vicious circle of injury but needs to be balanced against acinar overdistension. In this study, the lung-protective potential of alveolar recruitment was investigated and balanced against overdistension in pre-injured lungs. Mice, treated with empty vector (AdCl) or adenoviral active TGF-β1 (AdTGF-β1) were subjected to lung mechanical measurements during descending PEEP ventilation from 12 to 0 cmH2O. At each PEEP level, recruitability tests consisting of two recruitment maneuvers followed by repetitive forced oscillation perturbations to determine tissue elastance (H) and damping (G) were performed. Finally, lungs were fixed by vascular perfusion at end-expiratory airway opening pressures (Pao) of 20, 10, 5 and 2 cmH2O after a recruitment maneuver, and processed for design-based stereology to quantify derecruitment and distension. H and G were significantly elevated in AdTGF-β1 compared to AdCl across PEEP levels. H was minimized at PEEP = 5–8 cmH2O and increased at lower and higher PEEP in both groups. These findings correlated with increasing septal wall folding (= derecruitment) and reduced density of alveolar number and surface area (= distension), respectively. In AdTGF-β1 exposed mice, 27% of alveoli remained derecruited at Pao = 20 cmH2O. A further decrease in Pao down to 2 cmH2O showed derecruitment of an additional 1.1 million alveoli (48%), which was linked with an increase in alveolar size heterogeneity at Pao = 2–5 cmH2O. In AdCl, decreased Pao resulted in septal folding with virtually no alveolar collapse. In essence, in healthy mice alveoli do not derecruit at low PEEP ventilation. The potential of alveolar recruitability in AdTGF-β1 exposed mice is high. H is optimized at PEEP 5–8 cmH2O. Lower PEEP folds and larger PEEP stretches septa which results in higher H and is more pronounced in AdTGF-β1 than in AdCl. The increased alveolar size heterogeneity at Pao = 5 cmH2O argues for the use of PEEP = 8 cmH2O for lung protective mechanical ventilation in this animal model.

Franziska Roeder, Tina Röpke, Lara-Kristin Steinmetz, Martin Kolb, Ulrich A. Maus, Bradford J. Smith, Lars Knudsen

Franziska Roeder, Tina Röpke, Lara-Kristin Steinmetz... et al. Scientific Reports
2024 Spatial omics reveals molecular changes in focal cortical dysplasia type II

Oncotopix Discovery, Phenoplex, Publicly Sharable

Focal cortical dysplasia (FCD) represents a group of diverse localized cortical lesions that are highly epileptogenic and occur due to abnormal brain development caused by genetic mutations, involving the mammalian target of rapamycin (mTOR). These somatic mutations lead to mosaicism in the affected brain, posing challenges to unravel the direct and indirect functional consequences of these mutations. To comprehensively characterize the impact of mTOR mutations on the brain, we employed here a multimodal approach in a preclinical mouse model of FCD type II (Rheb), focusing on spatial omics techniques to define the proteomic and lipidomic changes. Mass Spectrometry Imaging (MSI) combined with fluorescence imaging and label free proteomics, revealed insight into the brain's lipidome and proteome within the FCD type II affected region in the mouse model. MSI visualized disrupted neuronal migration and differential lipid distribution including a reduction in sulfatides in the FCD type II-affected region, which play a role in brain myelination. MSI-guided laser capture microdissection was conducted on FCD type II and control regions, followed by label free proteomics, revealing changes in myelination pathways by oligodendrocytes. Surgical resections of FCD type IIb and postmortem human cortex were analyzed by bulk transcriptomics to unravel the interplay between genetic mutations and molecular changes in FCD type II. Our comparative analysis of protein pathways and enriched Gene Ontology pathways related to myelination in the FCD type II-affected mouse model and human FCD type IIb transcriptomics highlights the animal model's translational value. This dual approach, including mouse model proteomics and human transcriptomics strengthens our understanding of the functional consequences arising from somatic mutations in FCD type II, as well as the identification of pathways that may be used as therapeutic strategies in the future. Focal cortical dysplasia Mass spectrometry imaging Proteomics Transcriptomics Lipidomics Spatial omics

Isabeau Vermeulen, Natalia Rodriguez-Alvarez, Liesbeth François, Delphine Viot, Fariba Poosti, Eleonora Aronica, Stefanie Dedeurwaerdere, Patrick Barton, Berta Cillero-Pastor, Ron M.A. Heeren

Isabeau Vermeulen, Natalia Rodriguez-Alvarez, Liesbeth François... et al. Neurobiology of Disease
2024 Targeting IL-13 with tralokinumab normalizes type 2 inflammation in atopic dermatitis both early and at 2 years

Oncotopix Discovery, Publicly Sharable

Background Tralokinumab is a monoclonal antibody that specifically neutralizes interleukin (IL)-13, a key driver of skin inflammation and barrier abnormalities in atopic dermatitis (AD). This study evaluated early and 2-year impacts of IL-13 neutralization on skin and serum biomarkers following tralokinumab treatment in adults with moderate-to-severe AD. Methods Skin biopsies and blood samples were evaluated from a subset of patients enrolled in the Phase 3 ECZTRA 1 (NCT03131648) and the long-term extension ECZTEND (NCT03587805) trials. Gene expression was assessed by RNA sequencing; protein expression was assessed by immunohistochemistry and immunoassay. Results Tralokinumab improved the transcriptomic profile of lesional skin by Week 4. Mean improvements in the expression of genes dysregulated in AD were 39% at Week 16 and 85% at 2 years with tralokinumab, with 15% worsening at Week 16 with placebo. At Week 16, tralokinumab significantly decreased type 2 serum biomarkers (CCL17/TARC, periostin, and IgE), reduced epidermal thickness versus placebo, and increased loricrin coverage versus baseline. Two years of tralokinumab treatment significantly reduced expression of genes in the Th2 (IL4R, IL31, CCL17, and CCL26), Th1 (IFNG), and Th17/Th22 (IL22, S100A7, S100A8, and S100A9) pathways as well as increased expression of epidermal differentiation and barrier genes (CLDN1 and LOR). Tralokinumab also shifted atherosclerosis signaling pathway genes (SELE, IL-37, and S100A8) toward non-lesional expression. Conclusion Tralokinumab treatment improved epidermal pathology, reduced systemic markers of type 2 inflammation, and shifted expression of key AD biomarkers in skin towards non-lesional levels, further highlighting the key role of IL-13 in the pathogenesis of AD.

Emma Guttman-Yassky, Kenji Kabashima, Delphine Staumont-Salle, | Walter, K Nahm, Sylvia Pauser, Joel Correa, Da Rosa, | Britta, Cathrina Martel, | Daniel, Elenius Madsen, Mads Røpke, Petra Arlert, Louise Steffensen, Andrew Blauvelt, Kristian Reich

Emma Guttman-Yassky, Kenji Kabashima, Delphine Staumont-Salle... et al. Allergy
2024 Unconventional human CD61 pairing with CD103 promotes TCR signaling and antigen-specific T cell cytotoxicity

Oncotopix Discovery, Publicly Sharable, Tissuealign

Cancer remains one of the leading causes of mortality worldwide, leading to increased interest in utilizing immunotherapy strategies for better cancer treatments. In the past decade, CD103+ T cells have been associated with better clinical prognosis in patients with cancer. However, the specific immune mechanisms contributing toward CD103-mediated protective immunity remain unclear. Here, we show an unexpected and transient CD61 expression, which is paired with CD103 at the synaptic microclusters of T cells. CD61 colocalization with the T cell antigen receptor further modulates downstream T cell antigen receptor signaling, improving antitumor cytotoxicity and promoting physiological control of tumor growth. Clinically, the presence of CD61+ tumor-infiltrating T lymphocytes is associated with improved clinical outcomes, mediated through enhanced effector functions and phenotype with limited evidence of cellular exhaustion. In conclusion, this study identified an unconventional and transient CD61 expression and pairing with CD103 on human immune cells, which potentiates a new target for immune-based cellular therapies. CD103+ T cells are associated with control over tumors but how this is mediated is unclear. Here the authors show that CD61 colocalizes and functionally combines with CD103 in the T cell synaptic response to promote antitumor T cell responses.

Megat H. B. A. Hamid, Pablo F. Cespedes, Chen Jin, Ji-Li Chen, Uzi Gileadi, Elie Antoun, Zhu Liang, Fei Gao, Renuka Teague, Nikita Manoharan, David Maldonado-Perez, Nasullah Khalid-Alham, Lucia Cerundolo, Raul Ciaoca, Svenja S. Hester, Adán Pinto-Fernández, Simeon D. Draganov, Iolanda Vendrell, Guihai Liu, Xuan Yao, Audun Kvalvaag, Delaney C. C. Dominey-Foy, Charunya Nanayakkara, Nikolaos Kanellakis, Yi-Ling Chen, Craig Waugh, Sally-Ann Clark, Kevin Clark, Paul Sopp, Najib M. Rahman, Clare Verrill, Benedikt M. Kessler, Graham Ogg, Ricardo A. Fernandes, Roman Fisher, Yanchun Peng, Michael L. Dustin, Tao Dong

Megat H. B. A. Hamid, Pablo F. Cespedes, Chen Jin... et al. Nature Immunology
2024 Histopathological comparison of Sjögren-related features between paired labial and parotid salivary gland biopsies of sicca patients

Oncotopix Discovery, Publicly Sharable

Objectives To compare focus score (FS) and other histopathological features between paired labial and parotid salivary gland biopsies in a diagnostic cohort of suspected Sjögren’s disease (SjD) patients. Methods Labial and parotid salivary gland biopsies were simultaneously obtained from patients with sicca complaints, suspected of having SjD. Biopsies were formalin fixed and paraffin embedded. Sections were stained with haematoxylin & eosin (H&E) and for CD3, CD20, CD45, cytokeratin, CD21, Bcl6, activation induced deaminase (AID), and IgA/IgG. FS and other histopathological features characteristic for SjD were analysed. Results Based on the expert opinion of three experienced rheumatologists, 36 patients were diagnosed as SjD and 63 as non-SjD sicca patients. When taking all patients together, absolute agreement of various histopathological features between labial and parotid biopsies was high and varied between 80% (FS) and 93% ((pre-)lymphoepithelial lesions (LELs)). More labial gland biopsies had a FS ≥ 1 compared with their parotid counterpart. Accordingly, the area of infiltrate was larger in labial gland biopsies. When considering only SjD patients, labial glands contained significantly less B-lymphocytes, GCs/mm2 and less severe LELs compared with parotid glands. Conclusion Labial and parotid glands from SjD patients contain similar histopathological key features, and thus both glands can be used for diagnosis and classification of SjD. However, parotid salivary glands reveal more evident B-lymphocyte related features, while labial glands exhibit more inflammation, which may be partially unrelated to SjD. Sjögren’s disease, histopathology, gland biopsy, sicca, labial gland, parotid salivary gland Topic: biopsy sjogren's syndrome lip parotid gland salivary glands histopathology tests salivary gland biopsy

Uzma Nakshbandi, Martha S Van Ginkel, Gwenny M P J Verstappen, Fred K L Spijkervet, Suzanne Arends, Erlin A Haacke, Silvia C Liefers, Arjan Vissink, Hendrika Bootsma, Frans G M Kroese, Bert Van Der Vegt, U Nakshbandi

Uzma Nakshbandi, Martha S Van Ginkel, Gwenny M P J Verstappen... et al. Rheumatology
2024 Artificial intelligence algorithm accurately assesses oestrogen receptor immunohistochemistry in metastatic breast cancer cytology specimens: A pilot study

Oncotopix Discovery, Publicly Sharable

Objective The Visiopharm artificial intelligence (AI) algorithm for oestrogen receptor (ER) immunohistochemistry (IHC) in whole slide images (WSIs) has been successfully validated in surgical pathology. This study aimed to assess its efficacy in cytology specimens. Methods The study cohort comprised 105 consecutive cytology specimens with metastatic breast carcinoma. ER IHC WSIs were seamlessly integrated into the Visiopharm platform from the Image Management System (IMS) during our routine digital workflow, and an AI algorithm was employed for analysis. ER AI scores were compared with pathologists' manual consensus scores. Optimization steps were implemented and evaluated to reduce discordance. Results The overall concordance between pathologists' scores and AI scores was excellent (99/105, 94.3%). Six cases exhibited discordant results, including two false-negative (FN) cases due to abundant histiocytes incorrectly counted as negatively stained tumour cells by AI, two FN cases owing to weak staining, and two false-positive (FP) cases where pigmented macrophages were erroneously counted as positively stained tumour cells by AI. The Pearson correlation coefficient of ER-positive percentages between pathologists' and AI scores was 0.8483. Optimization steps, such as lowering the cut-off threshold and additional training using higher input magnification, significantly improved accuracy. Conclusions The automated ER AI algorithm demonstrated excellent concordance with pathologists' assessments and accurately differentiated ER-positive from ER-negative metastatic breast carcinoma cytology cases. However, precision in identifying tumour cells in cytology specimens requires further enhancement.

Brenna C. Li, Scott Hammond, Anil V. Parwani, Rulong Shen

Brenna C. Li, Scott Hammond, Anil V. Parwani... et al. Cytopathology
2024 Number of intraepithelial lymphocytes and presence of a subepithelial band in normal colonic mucosa differs according to stainings and evaluation method

Oncotopix Discovery, Publicly Sharable

Chronic watery diarrhea is a frequent symptom. In approximately 10% of the patients, a diagnosis of microscopic colitis (MC) is established. The diagnosis relies on specific, but sometimes subtle, histopathological findings. As the histology of normal intestinal mucosa vary, discriminating subtle features of MC from normal tissue can be challenging and therefore auxiliary stainings are increasingly used. The aim of this study was to determine the variance in number of intraepithelial lymphocytes (IELs) and presence of a subepithelial band in normal ileum and colonic mucosa, according to different stains and digital assessment. Sixty-one patients without diarrhea referred to screening colonoscopy due to a positive feacal blood test and presenting with endoscopically normal mucosa were included. Basic histological features, number of IELs, and thickness of a subepithelial band was manually evaluated and a deep learning-based algorithm was developed to digitally determine the number of IELs in each of the two compartments; surface epithelium and cryptal epithelium, and the density of lymphocytes in the lamina propria compartment. The number of IELs was significantly higher on CD3-stained slides compared with slides stained with Hematoxylin-and-Eosin (HE) (p<0.001), and even higher numbers were reached using digital analysis. No significant difference between right and left colon in IELs or density of CD3-positive lymphocytes in lamina propria was found. No subepithelial band was present in HE-stained slides while a thin band was visualized on special stains. Conclusively, in this cohort of prospectively collected ileum and colonic biopsies from asymptomatic patients, the range of IELs and detection of a subepithelial collagenous band varied depending on the stain and method used for assessment. As assessment of biopsies from patients with diarrhea constitute a considerable workload in the pathology departments digital image analysis is highly desired. Knowledge provided by the present study highlight important differences that should be considered before introducing this method in the clinic.

Anne-Marie Kanstrup Fiehn, Peter Johan Heiberg Engel, Ulla Engel, Dea Natalie Munch Jepsen, Thomas Blixt, Julie Rasmussen, Signe Wildt, Wojciech Cebula, Andreea-Raluca Diac, Lars Kristian Munck

Anne-Marie Kanstrup Fiehn, Peter Johan Heiberg Engel, Ulla Engel... et al. Journal of Pathology Informatics
2024 Relative contributions of osteal macrophages and osteoclasts to postnatal bone development in CSF1R-deficient rats and phenotype rescue following wild-type bone marrow cell transfer 2 Short running title: Myeloid cell contributions to rat bone development Statements and Declarations

Oncotopix Discovery, Publicly Sharable

1 Macrophage and osteoclast proliferation, differentiation and survival are regulated by colony-2 stimulating factor-1 receptor (CSF1R) signaling. Osteopetrosis associated with Csf1 and Csf1r 3 mutations has been attributed to the loss of osteoclasts and deficiency in bone resorption. Here we 4 demonstrate that homozygous Csf1r mutation in rat leads to delayed postnatal skeletal ossification 5 associated with substantial loss of osteal macrophages (osteomacs) in addition to osteoclasts. 6 Osteosclerosis and site-specific skeletal abnormalities were reversed by intraperitoneal transfer of 7 wild-type bone marrow cells (BMT) at weaning. Following BMT, IBA1 + macrophages were 8 detected before TRAP + osteoclasts at sites of ossification restoration. These observations extend 9 evidence that osteomacs independently contribute to bone anabolism and are required for normal 10 postnatal bone growth and morphogenesis. 11 12

Lena Batoon, Sahar Keshvari, Katharine M Irvine, Eileen Ho, Melanie Caruso, Anuj Sehgal, Susan M Millard, David A Hume, Allison R Pettit

Lena Batoon, Sahar Keshvari, Katharine M Irvine... et al. Journal of Leukocyte Biology
2024 The Chemistry in Immunohistochemistry: A Reply From UK NEQAS

Publicly Sharable, Qualitopix

Andrew Dodson, Suzanne Parry

Andrew Dodson, Suzanne Parry Archives of Pathology & Laboratory Medicine
2024 VEGF expression disparities in brainstem motor neurons of the SOD1G93A ALS model: Correlations with neuronal vulnerability

Publicly Sharable, Stereology

Amyotrophic lateral sclerosis (ALS) is a rare neuromuscular disease characterized by severe muscle weakness mainly due to degeneration and death of motor neurons. A peculiarity of the neurodegenerative processes is the variable susceptibility among distinct neuronal populations, exemplified by the contrasting resilience of motor neurons innervating the ocular motor system and the more vulnerable facial and hypoglossal motor neurons. The crucial role of vascular endothelial growth factor (VEGF) as a neuroprotective factor in the nervous system is well-established since a deficit of VEGF has been related to motoneuronal degeneration. In this study, we investigated the survival of ocular, facial, and hypoglossal motor neurons utilizing the murine SOD1G93A ALS model at various stages of the disease. Our primary objective was to determine whether the survival of the different brainstem motor neurons was linked to disparate VEGF expression levels in resilient and susceptible motor neurons throughout neurodegeneration. Our findings revealed a selective loss of motor neurons exclusively within the vulnerable nuclei. Furthermore, a significantly higher level of VEGF was detected in the more resistant motor neurons, the extraocular ones. We also examined whether TDP-43 dynamics in the brainstem motor neuron of SOD mice was altered. Our data suggests that the increased VEGF levels observed in extraocular motor neurons may potentially underlie their resistance during the neurodegenerative processes in ALS in a TDP-43-independent manner. Our work might help to better understand the underlying mechanisms of selective vulnerability of motor neurons in ALS.

Silvia Silva-Hucha, M. Estrella Fernández de Sevilla, Kirsty M. Humphreys, Fiona E. Benson, Jaime M. Franco, David Pozo, Angel M. Pastor, Sara Morcuende

Silvia Silva-Hucha, M. Estrella Fernández de Sevilla, Kirsty M. Humphreys... et al. Neurotherapeutics
2024 In brief Interrogation of endothelial and mural cells in brain metastasis reveals key immune-regulatory mechanisms

Oncotopix Discovery, Publicly Sharable

Article Interrogation of endothelial and mural cells in brain metastasis reveals key immune-regulatory mechanisms Graphical abstract Highlights d We performed single-cell and bulk RNA-seq of human BrM and healthy brain vascular cells d BrMs are defined by pathological endothelial and mural cell subtypes d We created a preclinical platform by integrating human data with mouse BrM models d This interspecies analysis revealed CD276 as a potential therapeutic target for BrM The brain tumor-associated vasculature is a key component of the tumor microenvironment in brain metastasis, protecting cancer cells from immune attack and interfering with the delivery of therapeutic agents into the brain. In this study, Bejarano et al. unravel the vascular heterogeneity in human BrM and further construct a preclinical platform to design novel vascular-targeted therapeutic strategies for the treatment of these aggressive tumors. SUMMARY Brain metastasis (BrM) is a common malignancy, predominantly originating from lung, melanoma, and breast cancers. The vasculature is a key component of the BrM tumor microenvironment with critical roles in regulating metastatic seeding and progression. However, the heterogeneity of the major BrM vascular components, namely endothelial and mural cells, is still poorly understood. We perform single-cell and bulk RNA-sequencing of sorted vascular cell types and detect multiple subtypes enriched specifically in BrM compared to non-tumor brain, including previously unrecognized immune regulatory subtypes. We integrate the human data with mouse models, creating a platform to interrogate vascular targets for the treatment of BrM. We find that the CD276 immune checkpoint molecule is significantly upregulated in the BrM vasculature, and anti-CD276 blocking antibodies prolonged survival in preclinical trials. This study provides important insights into the complex interactions between the vasculature, immune cells, and cancer cells, with translational relevance for designing therapeutic interventions.

Leire Bejarano, Annamaria Kauzlaric, Eleni Lamprou, Roy T Daniel, Monika E Hegi, Johanna A Joyce Correspondence, Joao Lourenco, Nadine Fournier, Michelle Ballabio, Roberto Colotti, Roeltje Maas, Sabine Galland, Matteo Massara, Klara Soukup, Johanna Lilja, Jean-Philippe Brouland, Andreas F Hottinger, Johanna A Joyce

Leire Bejarano, Annamaria Kauzlaric, Eleni Lamprou... et al. Cancer Cell
2024 Immune mapping of human tuberculosis and sarcoidosis lung granulomas

Phenoplex, Publicly Sharable

Tuberculosis (TB) and sarcoidosis are both granulomatous diseases. Here, we compared the immunological microenvironments of granulomas from TB and sarcoidosis patients using in situ sequencing (ISS) transcriptomic analysis and multiplexed immunolabeling of tissue sections. TB lesions consisted of large necrotic and cellular granulomas, whereas “multifocal” granulomas with macrophages or epitheloid cell core and a T-cell rim were observed in sarcoidosis samples. The necrotic core in TB lesions was surrounded by macrophages and encircled by a dense T-cell layer. Within the T-cell layer, compact B-cell aggregates were observed in most TB samples. These B-cell clusters were vascularized and could contain defined B-/T-cell and macrophage-rich areas. The ISS of 40–60 immune transcripts revealed the enriched expression of transcripts involved in homing or migration to lymph nodes, which formed networks at single-cell distances in lymphoid areas of the TB lesions. Instead, myeloid-annotated regions were enriched in CD68 , CD14 , ITGAM , ITGAX , and CD4 mRNA. CXCL8 and IL1B mRNA were observed in granulocytic areas in which M. tuberculosis was also detected. In line with ISS data indicating tertiary lymphoid structures, immune labeling of TB sections expressed markers of high endothelial venules, follicular dendritic cells, follicular helper T cells, and lymph-node homing receptors on T cells. Neither ISS nor immunolabeling showed evidence of tertiary lymphoid aggregates in sarcoidosis samples. Together, our finding suggests that despite their heterogeneity, the formation of tertiary immune structures is a common feature in granulomas from TB patients.

B Carow, V Muliadi, K Skålén, C Yokota, G Kathamuthu, T Setiabudiawan, C Lange, K Scheu, K Gaede, T Goldmann, A Pandita, K Masood, S Pervez, J Grunewald, Z Hasan, M Levin, M Rottenberg

B Carow, V Muliadi, K Skålén... et al. Frontiers in Immunology
2024 Global, neuronal or β cell-specific deletion of inceptor improves glucose homeostasis in male mice with diet-induced obesity

Phenoplex, Publicly Sharable

Insulin resistance is an early complication of diet-induced obesity (DIO)1, potentially leading to hyperglycaemia and hyperinsulinaemia, accompanied by adaptive β cell hypertrophy and development of type 2 diabetes2. Insulin not only signals via the insulin receptor (INSR), but also promotes β cell survival, growth and function via the insulin-like growth factor 1 receptor (IGF1R)3–6. We recently identified the insulin inhibitory receptor (inceptor) as the key mediator of IGF1R and INSR desensitization7. But, although β cell-specific loss of inceptor improves β cell function in lean mice7, it warrants clarification whether inceptor signal inhibition also improves glycaemia under conditions of obesity. We assessed the glucometabolic effects of targeted inceptor deletion in either the brain or the pancreatic β cells under conditions of DIO in male mice. In the present study, we show that global and neuronal deletion of inceptor, as well as its adult-onset deletion in the β cells, improves glucose homeostasis by enhancing β cell health and function. Moreover, we demonstrate that inceptor-mediated improvement in glucose control does not depend on inceptor function in agouti-related protein-expressing or pro-opiomelanocortin neurons. Our data demonstrate that inceptor inhibition improves glucose homeostasis in mice with DIO, hence corroborating that inceptor is a crucial regulator of INSR and IGF1R signalling. In male mice with diet-induced obesity, deletion of insulin inhibitory receptor (inceptor) in the whole body, in the brain and in pancreatic β cells improves glucose homeostasis, underlining a role of inceptor in regulating glucose homeostasis in the brain and pancreas.

Gerald Grandl, Gustav Collden, Jin Feng, Sreya Bhattacharya, Felix Klingelhuber, Leopold Schomann, Sara Bilekova, Ansarullah, Weiwei Xu, Fataneh Fathi Far, Monica Tost, Tim Gruber, Aimée Bastidas-Ponce, Qian Zhang, Aaron Novikoff, Arkadiusz Liskiewicz, Daniela Liskiewicz, Cristina Garcia-Caceres, Annette Feuchtinger, Matthias H. Tschöp, Natalie Krahmer, Heiko Lickert, Timo D. Müller

Gerald Grandl, Gustav Collden, Jin Feng... et al. Nature Metabolism
2024 XIAP overexpressing inflammatory breast cancer patients have high infiltration of immunosuppressive subsets and increased TNFR1 signaling targetable with Birinapant

Oncotopix Discovery, Publicly Sharable

Objective To assess the expression pattern of X-linked inhibitor of apoptosis protein (XIAP), a cellular stress sensor, and delineate the associated changes in the tumor immune microenvironment (TiME) for prognostic value and new therapeutic targets in inflammatory breast cancer (IBC). Methods Immunohistochemistry was conducted to assess the spatial localization of immune subsets, XIAP, and PDL1 expression in IBC and non-inflammatory breast cancer (nIBC) pretreatment tumors (n = 142). Validation and further exploration were performed by gene expression analysis of patient tumors along with signaling studies in a co-culture model. Results High XIAP in 37/81 IBC patients correlated significantly with high PD-L1, increased infiltration of FOXP3+ Tregs, CD163+ tumor-associated macrophages (TAMs), low CD8/CD163 ratio in both tumor stroma (TS) and invasive margins (IM), and higher CD8+ T cells and CD79α+ B cells in the IM. Gene set enrichment analysis identified cellular stress response- and inflammation-related genes along with tumor necrosis factor receptor 1 (TNFR1) expression in high-XIAP IBC tumors. Induction of TNFR1 and XIAP was observed when patient-derived SUM149 IBC cells were co-cultured with human macrophage-conditioned media simulating TAMs, further demonstrating that the TNF-α signaling pathway is a likely candidate governing TAM-induced XIAP overexpression in IBC cells. Finally, addition of Birinapant, a pan IAP antagonist, induced cell death in the pro-survival cytokine-enriched conditions. Conclusion Using immunophenotyping and gene expression analysis in patient biospecimens along with in silico modeling and a preclinical model with a pan-IAP antagonist, this study revealed an interplay between increased TAMs, TNF-α signaling, and XIAP activation during (immune) stress in IBC. These data demonstrate the potential of IAP antagonists as immunomodulators for improving IBC therapeutic regimens.

Christophe Van Berckelaer, Steven Van Laere, Seayoung Lee, Michael A Morse, Joseph Geradts, Luc Dirix, Mark Kockx, François Bertucci, Peter Van Dam, Gayathri R Devi

Christophe Van Berckelaer, Steven Van Laere, Seayoung Lee... et al. Translational Oncology
2024 Artificial intelligence’s impact on breast cancer pathology: a literature review

Oncotopix Clinical, Publicly Sharable

his review discusses the profound impact of artificial intelligence (AI) on breast cancer (BC) diagnosis and management within the field of pathology. It examines the various applications of AI across diverse aspects of BC pathology, highlighting key findings from multiple studies. Integrating AI into routine pathology practice stands to improve diagnostic accuracy, thereby contributing to reducing avoidable errors. Additionally, AI has excelled in identifying invasive breast tumors and lymph node metastasis through its capacity to process large whole-slide images adeptly. Adaptive sampling techniques and powerful convolutional neural networks mark these achievements. The evaluation of hormonal status, which is imperative for BC treatment choices, has also been enhanced by AI quantitative analysis, aiding interobserver concordance and reliability. Breast cancer grading and mitotic count evaluation also benefit from AI intervention. AI-based frameworks effectively classify breast carcinomas, even for moderately graded cases that traditional methods struggle with. Moreover, AI-assisted mitotic figures quantification surpasses manual counting in precision and sensitivity, fostering improved prognosis. The assessment of tumor-infiltrating lymphocytes in triple-negative breast cancer using AI yields insights into patient survival prognosis. Furthermore, AI-powered predictions of neoadjuvant chemotherapy response demonstrate potential for streamlining treatment strategies. Addressing limitations, such as preanalytical variables, annotation demands, and differentiation challenges, is pivotal for realizing AI’s full potential in BC pathology. Despite the existing hurdles, AI’s multifaceted contributions to BC pathology hold great promise, providing enhanced accuracy, efficiency, and standardization. Continued research and innovation are crucial for overcoming obstacles and fully harnessing AI’s transformative capabilities in breast cancer diagnosis and assessment. Graphical Abstract: (Figure presented.) HER2 ER lymph node metastasis

Amr Soliman, Zaibo Li, Anil V. Parwani

Amr Soliman, Zaibo Li, Anil V. Parwani Diagnostic Pathology
2024 Integrin-αvβ6 targeted peptide-toxin therapy in a novel αvβ6-expressing immunocompetent model of pancreatic cancer

Oncotopix Discovery, Publicly Sharable

Previously we reported that a novel αvβ6-specific peptide-drug conjugate (SG3299) could eliminate established human pancreatic ductal adenocarcinoma (PDAC) xenografts. However the development of effective therapies for PDAC, which is an essential need, must show efficacy in relevant immunocompetent animals. Previously we reported that the KPC mouse transgenic PDAC model that closely recapitulates most stages of development of human PDAC, unlike in humans, failed to express αvβ6 on their tumours or metastases. In this study we have taken the KPC-derived PDAC line TB32043 and engineered a variant line (TB32043mb6S2) that expresses mouse integrin αvβ6. We report that orthotopic implantation of the αvβ6 over-expressing TB32043mb6S2 cells promotes shorter overall survival and increase in metastases. Moreover, systemic treatment of mice with established TB32043mb6S2 tumours in the pancreas with SG2399 lived significantly longer (p < 0.001; mean OS 48d) compared with PBS or control SG3511 (mean OS 25.5d and 26d, respectively). Thus SG3299 is confirmed as a promising candidate therapeutic for the therapy of PDAC.

Nicholas F. Brown, Elizabeth R. Murray, Lauren C. Cutmore, Philip Howard, Luke Masterson, Francesca Zammarchi, John A. Hartley, Patrick H. van Berkel, John F. Marshall

Nicholas F. Brown, Elizabeth R. Murray, Lauren C. Cutmore... et al. Pancreatology
2024 C3d-Targeted factor H inhibits tissue complement in disease models and reduces glomerular injury without affecting circulating complement

Phenoplex, Publicly Sharable

Complement-mediated diseases can be treated using systemic inhibitors. However, complement components are abundant in circulation, affecting systemic inhibitors’ exposure and efficacy. Furthermore, because of complement's essential role in immunity, systemic treatments raise infection risk in patients. To address these challenges, we developed antibody fusion proteins combining the alternative-pathway complement inhibitor factor H (fH1–5) with an anti-C3d monoclonal antibody (C3d-mAb-2fH). Because C3d is deposited at sites of complement activity, this molecule localizes to tissue complement while minimizing circulating complement engagement. These fusion proteins bind to deposited complement in diseased human skin sections and localize to activated complement in a primate skin injury model. We further explored the pharmacology of C3d-mAb-2fH proteins in rodent models with robust tissue complement activation. Doses of C3d-mAb-2fH >1 mg/kg achieved >75% tissue complement inhibition in mouse and rat injury models while avoiding circulating complement blockade. Glomerular-specific complement inhibition reduced proteinuria and preserved podocyte foot-process architecture in rat membranous nephropathy, indicating disease-modifying efficacy. These data indicate that targeting local tissue complement results in durable and efficacious complement blockade in skin and kidney while avoiding systemic inhibition, suggesting broad applicability of this approach in treating a range of complement-mediated diseases.

Fei Liu, Sarah T. Ryan, Kelly C. Fahnoe, Jennifer G. Morgan, Anne E. Cheung, Michael J. Storek, Alejandro Best, Hui A. Chen, Monica Locatelli, Shuyun Xu, Enno Schmidt, Leon F. Schmidt-Jiménez, Katja Bieber, Joel M. Henderson, Christine G. Lian, Admar Verschoor, Ralf J. Ludwig, Ariela Benigni, Giuseppe Remuzzi, David J. Salant, Susan L. Kalled, Joshua M. Thurman, V. Michael Holers, Shelia M. Violette, Stefan Wawersik

Fei Liu, Sarah T. Ryan, Kelly C. Fahnoe... et al. Molecular Therapy
2024 B cells orchestrate tolerance to the neuromyelitis optica autoantigen AQP4

Phenoplex, Publicly Sharable

Neuromyelitis optica is a paradigmatic autoimmune disease of the central nervous system, in which the water-channel protein AQP4 is the target antigen1. The immunopathology in neuromyelitis optica is largely driven by autoantibodies to AQP42. However, the T cell response that is required for the generation of these anti-AQP4 antibodies is not well understood. Here we show that B cells endogenously express AQP4 in response to activation with anti-CD40 and IL-21 and are able to present their endogenous AQP4 to T cells with an AQP4-specific T cell receptor (TCR). A population of thymic B cells emulates a CD40-stimulated B cell transcriptome, including AQP4 (in mice and humans), and efficiently purges the thymic TCR repertoire of AQP4-reactive clones. Genetic ablation of Aqp4 in B cells rescues AQP4-specific TCRs despite sufficient expression of AQP4 in medullary thymic epithelial cells, and B-cell-conditional AQP4-deficient mice are fully competent to raise AQP4-specific antibodies in productive germinal-centre responses. Thus, the negative selection of AQP4-specific thymocytes is dependent on the expression and presentation of AQP4 by thymic B cells. As AQP4 is expressed in B cells in a CD40-dependent (but not AIRE-dependent) manner, we propose that thymic B cells might tolerize against a group of germinal-centre-associated antigens, including disease-relevant autoantigens such as AQP4. The immune system is tolerized against the neuromyelitis optica autoantigen AQP4 by thymic B cells, which present their endogenous AQP4 to AQP4-reactive thymocytes.

A Afzali, L Nirschl, C Sie, M Pfaller, O Ulianov, T Hassler, C Federle, E Petrozziello, S Kalluri, Hsin Hsiang Chen, Sofia Tyystjärvi, Andreas Muschaweckh, Katja Lammens, Claire Delbridge, Andreas Büttner, Katja Steiger, Gönül Seyhan, Ole Petter Ottersen, Rupert Öllinger, Roland Rad, Sebastian Jarosch, Adrian Straub, Anton Mühlbauer, Simon Grassmann, Bernhard Hemmer, Jan P. Böttcher, Ingrid Wagner, Mario Kreutzfeldt, Doron Merkler, Irene Bonafonte Pardàs, Marc Schmidt Supprian, Veit R. Buchholz, Sylvia Heink, Dirk H. Busch, Ludger Klein, Thomas Korn

A Afzali, L Nirschl, C Sie... et al. Nature
2024 Molecular, Metabolic, and Subcellular Mapping of the Tumor Immune Microenvironment via 3D Targeted and Non-Targeted Multiplex Multi-Omics Analyses

COMET, Lunaphore, Phenoplex, Publicly Sharable, Tissuealign

Simple Summary A tumor tissue is composed of not only cancer cells but also other cell types and microorganisms that communicate among themselves in a three-dimensional (3D) space to support cancer cell growth. Using two different gynecologic tumor tissue samples, we integrated multiple new techniques using a suite of newly developed analytical methods to simultaneously identify expression of genes, metabolites, and proteins in single tissue ‘voxels’. These tissue voxels contain cells, genes from those cells and microorganisms, and the stromal context of proteins (collagen), glycans, metabolites, and peptides, all identified in the 3D space within a tumor tissue. We have successfully demonstrated different arrays of analytes expressed by cancer cells and their neighboring cells in different regions of the tumor tissue. Understanding how cancer cells communicate with other cell types in the 3D space of the tumor tissue will allow for the identification of new therapeutic targets for the treatment of these diseases. Abstract Most platforms used for the molecular reconstruction of the tumor–immune microenvironment (TIME) of a solid tumor fail to explore the spatial context of the three-dimensional (3D) space of the tumor at a single-cell resolution, and thus lack information about cell–cell or cell–extracellular matrix (ECM) interactions. To address this issue, a pipeline which integrated multiplex spatially resolved multi-omics platforms was developed to identify crosstalk signaling networks among various cell types and the ECM in the 3D TIME of two FFPE (formalin-fixed paraffin embedded) gynecologic tumor samples. These platforms include non-targeted mass spectrometry imaging (glycans, metabolites, and peptides) and Stereo-seq (spatial transcriptomics) and targeted seqIF (IHC proteomics). The spatially resolved imaging data in a two- and three-dimensional space demonstrated various cellular neighborhoods in both samples. The collection of spatially resolved analytes in a voxel (3D pixel) across serial sections of the tissue was also demonstrated. Data collected from this analytical pipeline were used to construct spatial 3D maps with single-cell resolution, which revealed cell identity, activation, and energized status. These maps will provide not only insights into the molecular basis of spatial cell heterogeneity in the TIME, but also novel predictive biomarkers and therapeutic targets, which can improve patient survival rates.

Sammy Ferri-Borgogno, Jared K. Burks, Erin H. Seeley, Trevor D. McKee, Danielle L. Stolley, Akshay V. Basi, Javier A. Gomez, Basant T. Gamal, Shamini Ayyadhury, Barrett C. Lawson, Melinda S. Yates, Michael J. Birrer, Karen H. Lu, Samuel C. Mok

Sammy Ferri-Borgogno, Jared K. Burks, Erin H. Seeley... et al. Cancers
2024 Adipocyte p53 coordinates the response to intermittent fasting by regulating adipose tissue immune cell landscape

Oncotopix Discovery, Publicly Sharable

In obesity, sustained adipose tissue (AT) inflammation constitutes a cellular memory that limits the effectiveness of weight loss interventions. Yet, the impact of fasting regimens on the regulation of AT immune infiltration is still elusive. Here we show that intermittent fasting (IF) exacerbates the lipid-associated macrophage (LAM) inflammatory phenotype of visceral AT in obese mice. Importantly, this increase in LAM abundance is strongly p53 dependent and partly mediated by p53-driven adipocyte apoptosis. Adipocyte-specific deletion of p53 prevents LAM accumulation during IF, increases the catabolic state of adipocytes, and enhances systemic metabolic flexibility and insulin sensitivity. Finally, in cohorts of obese/diabetic patients, we describe a p53 polymorphism that links to efficacy of a fasting-mimicking diet and that the expression of p53 and TREM2 in AT negatively correlates with maintaining weight loss after bariatric surgery. Overall, our results demonstrate that p53 signalling in adipocytes dictates LAM accumulation in AT under IF and modulates fasting effectiveness in mice and humans. Adipose tissue (AT) inflammation is strongly associated with obesity and constitutes an obesogenic memory upon weight loss. Here, the authors show that intermittent fasting leads to an adipocyte p53-signaling dependent emergence of lipid-associated macrophages in visceral AT of obese mice which limits the systemic fasting response.

Isabel Reinisch, Helene Michenthaler, Alba Sulaj, Elisabeth Moyschewitz, Jelena Krstic, Markus Galhuber, Ruonan Xu, Zina Riahi, Tongtong Wang, Nemanja Vujic, Melina Amor, Riccardo Zenezini Chiozzi, Martin Wabitsch, Dagmar Kolb, Anastasia Georgiadi, Lisa Glawitsch, Ellen Heitzer, Tim J. Schulz, Michael Schupp, Wenfei Sun, Hua Dong, Adhideb Ghosh, Anne Hoffmann, Dagmar Kratky, Laura C. Hinte, Ferdinand von Meyenn, Albert J. R. Heck, Matthias Blüher, Stephan Herzig, Christian Wolfrum, Andreas Prokesch

Isabel Reinisch, Helene Michenthaler, Alba Sulaj... et al. Nature Communications
2024 Cone photoreceptor phosphodiesterase PDE6H inhibition regulates cancer cell growth and metabolism, replicating the dark retina response

Oncotopix Discovery, Publicly Sharable

PDE6H encodes PDE6γ′, the inhibitory subunit of the cGMP-specific phosphodiesterase 6 in cone photoreceptors. Inhibition of PDE6, which has been widely studied for its role in light transduction, increases cGMP levels. The purpose of this study is to characterise the role of PDE6H in cancer cell growth. From an siRNA screen for 487 genes involved in metabolism, PDE6H was identified as a controller of cell cycle progression in HCT116 cells. Role of PDE6H in cancer cell growth and metabolism was studied through the effects of its depletion on levels of cell cycle controllers, mTOR effectors, metabolite levels, and metabolic energy assays. Effect of PDE6H deletion on tumour growth was also studied in a xenograft model. PDE6H knockout resulted in an increase of intracellular cGMP levels, as well as changes to the levels of nucleotides and key energy metabolism intermediates. PDE6H knockdown induced G1 cell cycle arrest and cell death and reduced mTORC1 signalling in cancer cell lines. Both knockdown and knockout of PDE6H resulted in the suppression of mitochondrial function. HCT116 xenografts revealed that PDE6H deletion, as well as treatment with the PDE5/6 inhibitor sildenafil, slowed down tumour growth and improved survival, while sildenafil treatment did not have an additive effect on slowing the growth of PDE6γ′-deficient tumours. Our results indicate that the changes in cGMP and purine pools, as well as mitochondrial function which is observed upon PDE6γ′ depletion, are independent of the PKG pathway. We show that in HCT116, PDE6H deletion replicates many effects of the dark retina response and identify PDE6H as a new target in preventing cancer cell proliferation and tumour growth.

Ceren Yalaz, Esther Bridges, Nasullah K. Alham, Christos E. Zois, Jianzhou Chen, Karim Bensaad, Ana Miar, Elisabete Pires, Ruth J. Muschel, James S. O. McCullagh, Adrian L. Harris

Ceren Yalaz, Esther Bridges, Nasullah K. Alham... et al. Cancer & Metabolism
2024 Correlation between Histopathological Prognostic Tumor Characteristics and [18F]FDG Uptake in Corresponding Metastases in Newly Diagnosed Metastatic Breast Cancer

Oncotopix Discovery, Publicly Sharable

Background: In metastatic breast cancer (MBC), [18F]fluorodeoxyglucose positron emission tomography/computed tomography ([18F]FDG-PET/CT) can be used for staging. We evaluated the correlation between BC histopathological characteristics and [18F]FDG uptake in corresponding metastases. Patients and Methods: Patients with non-rapidly progressive MBC of all subtypes prospectively underwent a baseline histological metastasis biopsy and [18F]FDG-PET. Biopsies were assessed for estrogen, progesterone, and human epidermal growth factor receptor 2 (ER, PR, HER2); Ki-67; and histological subtype. [18F]FDG uptake was expressed as maximum standardized uptake value (SUVmax) and results were expressed as geometric means. Results: Of 200 patients, 188 had evaluable metastasis biopsies, and 182 of these contained tumor. HER2 positivity and Ki-67 ≥ 20% were correlated with higher [18F]FDG uptake (estimated geometric mean SUVmax 10.0 and 8.8, respectively; p = 0.0064 and p = 0.014). [18F]FDG uptake was lowest in ER-positive/HER2-negative BC and highest in HER2-positive BC (geometric mean SUVmax 6.8 and 10.0, respectively; p = 0.0058). Although [18F]FDG uptake was lower in invasive lobular carcinoma (n = 31) than invasive carcinoma NST (n = 146) (estimated geometric mean SUVmax 5.8 versus 7.8; p = 0.014), the metastasis detection rate was similar. Conclusions: [18F]FDG-PET is a powerful tool to detect metastases, including invasive lobular carcinoma. Although BC histopathological characteristics are related to [18F]FDG uptake, [18F]FDG-PET and biopsy remain complementary in MBC staging (NCT01957332).

Jorianne Boers, Bertha Eisses, Mieke C. Zwager, Jasper J. L. van Geel, Frederike Bensch, Erik F. J. de Vries, Geke A. P. Hospers, Andor W. J. M. Glaudemans, Adrienne H. Brouwers, Martijn A. M. den Dekker, Sjoerd G. Elias, Evelien J. M. Kuip, Carla M. L. van Herpen, Agnes Jager, Astrid A. M. van der Veldt, Daniela E. Oprea-Lager, Elisabeth G. E. de Vries, Bert van der Vegt, Willemien C. Menke-van der Houven van Oordt, Carolina P. Schröder

Jorianne Boers, Bertha Eisses, Mieke C. Zwager... et al. Diagnostics
2024 Automated imaging analysis of Ki-67 immunohistochemistry on whole slide images of cell blocks from pancreatic neuroendocrine neoplasms

Oncotopix Discovery, Publicly Sharable

Introduction Accurate grading of pancreatic neuroendocrine tumors (PanNETs) relies on the assessment of Ki-67 immunohistochemistry (IHC). While digital imaging analysis (DIA) has been employed for Ki-67 IHC assessment in surgical specimens, its applicability to cytologic specimens remains underexplored. This study aimed to evaluate an automated DIA for assessing Ki-67 IHC on PanNET cell blocks. Materials and methods The study included 61 consecutive PanNETs and 5 pancreatic neuroendocrine carcinomas. Ki-67 IHC slides from cell blocks were digitally scanned into whole slide images using Philips IntelliSite Scanners and analyzed in batches using the Visiopharm Ki-67 App in a digital workflow. Ki-67 scores obtained through DIA were compared to pathologists' manual scores. Results The Pearson correlation coefficient of the percentage of Ki-67-stained nuclei between DIA reads and the originally reported reads was 0.9681. Concordance between DIA Ki-67 grades and pathologists’ Ki-67 grades was observed in 92.4% (61/66) of cases with the calculated Cohen's Kappa coefficient of 0.862 (almost perfect agreement). Discordance between DIA and pathologists’ consensus reads occurred in 5 PanNET cases which were upgraded from G1 to G2 by DIA due to contaminated Ki-67-stained inflammatory cells. Conclusions DIA demonstrated excellent concordance with pathologists’ assessments, with only minor grading discrepancies. However, the essential role of pathologists in confirming results is emphasized to enhance overall accuracy.

Nada Shaker, Rulong Shen, Abberly Lott Limbach, Swati Satturwar, Peter Kobalka, Saman Ahmadian, Shaoli Sun, Wei Chen, Giovanni Lujan, Ashwini Esnakula, Anil Parwani, Zaibo Li

Nada Shaker, Rulong Shen, Abberly Lott Limbach... et al. Journal of the American Society of Cytopathology
2024 Disease-Associated Neurotoxic Astrocyte Markers in Alzheimer Disease Based on Integrative Single-Nucleus RNA Sequencing

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Alzheimer disease (AD) is an irreversible neurodegenerative disease, and astrocytes play a key role in its onset and progression. The aim of this study is to analyze the characteristics of neurotoxic astrocytes and identify novel molecular targets for slowing down the progression of AD. Single-nucleus RNA sequencing (snRNA-seq) data were analyzed from various AD cohorts comprising about 210,654 cells from 53 brain tissue. By integrating snRNA-seq data with bulk RNA-seq data, crucial astrocyte types and genes associated with the prognosis of patients with AD were identified. The expression of neurotoxic astrocyte markers was validated using 5 × FAD and wild-type (WT) mouse models, combined with experiments such as western blot, quantitative real-time PCR (qRT-PCR), and immunofluorescence. A group of neurotoxic astrocytes closely related to AD pathology was identified, which were involved in inflammatory responses and pathways related to neuron survival. Combining snRNA and bulk tissue data, ZEP36L, AEBP1, WWTR1, PHYHD1, DST and RASL12 were identified as toxic astrocyte markers closely related to disease severity, significantly elevated in brain tissues of 5 × FAD mice and primary astrocytes treated with Aβ. Among them, WWTR1 was significantly increased in astrocytes of 5 × FAD mice, driving astrocyte inflammatory responses, and has been identified as an important marker of neurotoxic astrocytes. snRNA-seq analysis reveals the biological functions of neurotoxic astrocytes. Six genes related to AD pathology were identified and validated, among which WWTR1 may be a novel marker of neurotoxic astrocytes.

Wuhan Yu, Yin Li, Fuxin Zhong, Zhangjing Deng, Jiani Wu, Weihua Yu, Yang Lü

Wuhan Yu, Yin Li, Fuxin Zhong... et al. Cellular and Molecular Neurobiology
2024 UPP1 promotes lung adenocarcinoma progression through the induction of an immunosuppressive microenvironment

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The complexity of the tumor microenvironment (TME) is a crucial factor in lung adenocarcinoma (LUAD) progression. To gain deeper insights into molecular mechanisms of LUAD, we perform an integrative single-cell RNA sequencing (scRNA-seq) data analysis of 377,574 cells from 117 LUAD patient samples. By linking scRNA-seq data with bulk gene expression data, we identify a cluster of prognostic-related UPP1high tumor cells. These cells, primarily situated at the invasive front of tumors, display a stronger association with the immunosuppressive components in the TME. Our cytokine array analysis reveals that the upregulation of UPP1 in tumor cells leads to the increased release of various immunosuppressive cytokines, with TGF-β1 being particularly prominent. Furthermore, this UPP1 upregulation also elevates the expression of PD-L1 through the PI3K/AKT/mTOR pathway, which contributes to the suppression of CD8 + T cells. Cytometry by time-of-flight (CyTOF) analysis provides additional evidence of the role of UPP1 in shaping the immunosuppressive nature of the TME. Using patient-derived organoids (PDOs), we discover that UPP1high tumors exhibit relatively increased sensitivity to Bosutinib and Dasatinib. Collectively, our study highlights the immunosuppressive role of UPP1 in LUAD, and these findings may provide insights into the molecular features of LUAD and facilitate the development of personalized treatment strategies. Characterising the tumour microenvironment features of lung adenocarcinoma (LUAD) remains crucial. Here, the authors perform single cell RNA sequencing data analysis of 117 LUAD samples and functional assays and highlight the immunosuppressive role of UPP1high tumour cells.

Yin Li, Manling Jiang, Ling Aye, Li Luo, Yong Zhang, Fengkai Xu, Yongqi Wei, Dan Peng, Xiang He, Jie Gu, Xiaofang Yu, Guoping Li, Di Ge, Chunlai Lu

Yin Li, Manling Jiang, Ling Aye... et al. Nature Communications
2024 Multiomics profiling of Urothelial Carcinoma in Situ reveals CIS specific gene signature and immune characteristics

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Urothelial carcinoma in situ (CIS) is an aggressive phenotype of non-muscle-invasive bladder cancer. Molecular features unique to CIS compared to high-grade papillary tumors are underexplored. RNA sequencing of CIS, papillary tumors, and normal urothelium showed lower immune marker expression in CIS compared to papillary tumors. We identified a 46-gene expression signature in CIS samples including selectively upregulated known druggable targets MTOR, TYK2, AXIN1, CPT1B, GAK, and PIEZO1 and selectively downregulated BRD2 and NDUFB2. High expression of selected genes was significantly associated with CIS in an independent dataset. Mutation analysis of matched CIS and papillary tumors revealed shared mutations between samples across time points and mutational heterogeneity. CCDC138 was the most frequently mutated gene in CIS. The immunological landscape showed higher levels of PD-1-positive cells in CIS lesions compared to papillary tumors. We identified CIS lesions to have distinct characteristics compared to papillary tumors potentially contributing to the aggressive phenotype.

Meenakshi Anurag, Trine Strandgaard, Sung Han Kim, Yongchao Dou, Eva Comperat, Hikmat Al-Ahmadie, Brant A. Inman, Ann Taber, Iver Nordentoft, Jørgen Bjerggaard Jensen, Lars Dyrskjøt, Seth P. Lerner

Meenakshi Anurag, Trine Strandgaard, Sung Han Kim... et al. iScience
2024 Dietary intervention reverses molecular markers of hepatocellular senescence in the GAN diet-induced obese and biopsy-confirmed mouse model of NASH

Oncotopix Discovery, Publicly Sharable

Background: Hepatocellular senescence may be a causal factor in the development and progression of non-alcoholic steatohepatitis (NASH). The most effective currently available treatment for NASH is lifestyle intervention, including dietary modification. This study aimed to evaluate the effects of dietary intervention on hallmarks of NASH and molecular signatures of hepatocellular senescence in the Gubra-Amylin NASH (GAN) diet-induced obese (DIO) and biopsy-confirmed mouse model of NASH. Methods: GAN DIO-NASH mice with liver biopsy-confirmed NASH and fibrosis received dietary intervention by switching to chow feeding (chow reversal) for 8, 16 or 24 weeks. Untreated GAN DIO-NASH mice and chow-fed C57BL/6J mice served as controls. Pre-to-post liver biopsy histology was performed for within-subject evaluation of NAFLD Activity Score and fibrosis stage. Terminal endpoints included blood/liver biochemistry, quantitative liver histology, mitochondrial respiration and RNA sequencing. Results: Chow-reversal promoted substantial benefits on metabolic outcomes and liver histology, as demonstrated by robust weight loss, complete resolution of hepatomegaly, hypercholesterolemia, elevated transaminase levels and hepatic steatosis in addition to attenuation of inflammatory markers. Notably, all DIO-NASH mice demonstrated ≥ 2 point significant improvement in NAFLD Activity Score following dietary intervention. While not improving fibrosis stage, chow-reversal reduced quantitative fibrosis markers (PSR, collagen 1a1, α-SMA), concurrent with improved liver mitochondrial respiration, complete reversal of p21 overexpression, lowered γ-H2AX levels and widespread suppression of gene expression markers of hepatocellular senescence. Conclusions: Dietary intervention (chow reversal) substantially improves metabolic, biochemical and histological hallmarks of NASH and fibrosis in GAN DIO-NASH mice. These benefits were reflected by progressive clearance of senescent hepatocellular cells, making the model suitable for profiling potential senotherapeutics in preclinical drug discovery for NASH.

Mathias Flensted-Jensen, Denise Oró, Emma A. Rørbeck, Chen Zhang, Martin Rønn Madsen, Andreas Nygaard Madsen, Jenny Norlin, Michael Feigh, Steen Larsen, Henrik H. Hansen

Mathias Flensted-Jensen, Denise Oró, Emma A. Rørbeck... et al. BMC Gastroenterology
2024 Investigation of Gastrointestinal Toxicities Associated with Concurrent Abdominal Radiation Therapy and the Tyrosine Kinase Inhibitor Sunitinib in a Mouse Model

Oncotopix Discovery, Publicly Sharable

Tyrosine kinase inhibitors (TKIs) may be combined with radiation therapy (RT) to enhance tumor control; however, increased incidences of gastrointestinal (GI) toxicity have been reported with this combination. We hypothesize that toxicity is due to compromised intestinal healing caused by inhibition of vascular repair and proliferation pathways. This study explores underlying tissue toxicity associated with abdominal RT and concurrent sunitinib in a mouse model. Four groups of CD-1 mice were treated with 12 Gy abdominal RT, oral sunitinib, abdominal RT + sunitinib, or sham treatment. Mice received oral sunitinib or the vehicle via gavage for 14 days. On day 7, mice were irradiated with 12 Gy abdominal RT or sham treated. Mice were euthanized on day 14 and intestinal tract was harvested for semiquantitative histopathologic evaluation and immunohistochemical quantification of proliferation (Ki67 Ki-67) and vascular density (CD31). Non-irradiated groups had stable weights while abdominal irradiation resulted in weight loss, with mice receiving RT + SUN having greater weight loss than mice receiving RT alone. Semiquantitative analysis showed significant increases in inflammation in irradiated groups. The difference in the density of CD31+ cells was significantly increased in RT alone compared to SUN alone. Ki67+ density was not significant. In summary, we identify a lack of angiogenic response in irradiated GI tissues when abdominal RT is combined with a TKI, which may correlate with clinical toxicities seen in canine and human patients receiving combined treatment.

Melpo Christofidou-Solomidou, Amber R Prebble, Bailey Latka, Braden Burdekin, Del Leary, Mac Harris, Daniel Regan, Mary-Keara Boss

Melpo Christofidou-Solomidou, Amber R Prebble, Bailey Latka... et al. International Journal of Molecular Sciences
2024 Long-term impact of maternal obesity on the gliovascular unit and ephrin signaling in the hippocampus of adult offspring

Oncotopix Discovery, Publicly Sharable, Stereology

Children born to obese mothers are at increased risk of developing mood disorders and cognitive impairment. Experimental studies have reported structural changes in the brain such as the gliovascular unit as well as activation of neuroinflammatory cells as a part of neuroinflammation processing in aged offspring of obese mothers. However, the molecular mechanisms linking maternal obesity to poor neurodevelopmental outcomes are not well established. The ephrin system plays a major role in a variety of cellular processes including cell–cell interaction, synaptic plasticity, and long-term potentiation. Therefore, in this study we determined the impact of maternal obesity in pregnancy on cortical, hippocampal development, vasculature and ephrin-A3/EphA4-signaling, in the adult offspring in mice. Maternal obesity was induced in mice by a high fat/high sugar Western type of diet (HF/HS). We collected brain tissue (prefrontal cortex and hippocampus) from 6-month-old offspring of obese and lean (control) dams. Hippocampal volume, cortical thickness, myelination of white matter, density of astrocytes and microglia in relation to their activity were analyzed using 3-D stereological quantification. mRNA expression of ephrin-A3, EphA4 and synaptic markers were measured by qPCR in the brain tissue. Moreover, expression of gap junction protein connexin-43, lipocalin-2, and vascular CD31/Aquaporin 4 were determined in the hippocampus by immunohistochemistry. Volume of hippocampus and cortical thickness were significantly smaller, and myelination impaired, while mRNA levels of hippocampal EphA4 and post-synaptic density (PSD) 95 were significantly lower in the hippocampus in the offspring of obese dams as compared to offspring of controls. Further analysis of the hippocampal gliovascular unit indicated higher coverage of capillaries by astrocytic end-feet, expression of connexin-43 and lipocalin-2 in endothelial cells in the offspring of obese dams. In addition, offspring of obese dams demonstrated activation of microglia together with higher density of cells, while astrocyte cell density was lower. Maternal obesity affects brain size, impairs myelination, disrupts the hippocampal gliovascular unit and decreases the mRNA expression of EphA4 and PSD-95 in the hippocampus of adult offspring. These results indicate that the vasculature–glia cross-talk may be an important mediator of altered synaptic plasticity, which could be a link between maternal obesity and neurodevelopmental/neuropsychiatric disorders in the offspring.

Seyedeh Marziyeh, Jabbari Shiadeh, Fanny Goretta, Pernilla Svedin, Thomas Jansson, Carina Mallard, Maryam Ardalan

Seyedeh Marziyeh, Jabbari Shiadeh, Fanny Goretta... et al. Journal of Neuroinflammation
2024 Immunohistochemical double nuclear staining for cell-specific automated quantification of the proliferation index – A promising diagnostic aid for melanocytic lesions

Oncotopix Discovery, Publicly Sharable

Aims Pathologists often use immunohistochemical staining of the proliferation marker Ki67 in their diagnostic assessment of melanocytic lesions. However, the interpretation of Ki67 can be challenging. We propose a new workflow to improve the diagnostic utility of the Ki67-index. In this workflow, Ki67 is combined with the melanocytic tumour-cell marker SOX10 in a Ki67/SOX10 double nuclear stain. The Ki67-index is then quantified automatically using digital image analysis (DIA). The aim of this study was to optimise and test three different multiplexing methods for Ki67/SOX10 double nuclear staining. Methods Multiplex immunofluorescence (mIF), multiplex immunohistochemistry (mIHC), and multiplexed immunohistochemical consecutive staining on single slide (MICSSS) were optimised for Ki67/SOX10 double nuclear staining. DIA applications were designed for automated quantification of the Ki67-index. The methods were tested on a pilot case-control cohort of benign and malignant melanocytic lesions (n = 23). Results Using the Ki67/SOX10 double nuclear stain, malignant melanocytic lesions could be completely distinguished from benign lesions by the Ki67-index. The Ki67-index cut-offs were 1.8% (mIF) and 1.5% (mIHC and MICSSS). The AUC of the automatically quantified Ki67-index based on double nuclear staining was 1.0 (95% CI: 1.0;1.0), whereas the AUC of conventional Ki67 single-stains was 0.87 (95% CI: 0.71;1.00). Conclusions The novel Ki67/SOX10 double nuclear stain highly improved the diagnostic precision of Ki67 interpretation. Both mIHC and mIF were useful methods for Ki67/SOX10 double nuclear staining, whereas the MICSSS method had challenges in the current setting. The Ki67/SOX10 double nuclear stain shows potential as a valuable diagnostic aid for melanocytic lesions. Previous article in issue

Mette Bak Brogård, Patricia Switten Nielsen, Kristina Bang Christensen, Jeanette Bæhr Georgsen, Anne Wandler, Johanne Lade-Keller, Torben Steiniche

Mette Bak Brogård, Patricia Switten Nielsen, Kristina Bang Christensen... et al. Pathology - Research and Practice
2024 Neuroimmune Activation and Microglia Reactivity in Female Rats Following Alcohol Dependence

Oncotopix Discovery, Publicly Sharable

The rates of alcohol use disorder among women are growing, yet little is known about how the female brain is affected by alcohol. The neuroimmune system, and specifically microglia, have been implicated in mediating alcohol neurotoxicity, but most preclinical studies have focused on males. Further, few studies have considered changes to the microglial phenotype when examining the effects of ethanol on brain structure and function. Therefore, we quantified microglial reactivity in female rats using a binge model of alcohol dependence, assessed through morphological and phenotypic marker expression, coupled with regional cytokine levels. In a time- and region-dependent manner, alcohol altered the microglial number and morphology, including the soma and process area, and the overall complexity within the corticolimbic regions examined, but no significant increases in the proinflammatory markers MHCII or CD68 were observed. The majority of cytokine and growth factor levels examined were similarly unchanged. However, the expression of the proinflammatory cytokine TNFα was increased, and the anti-inflammatory IL-10, decreased. Thus, female rats showed subtle differences in neuroimmune reactivity compared to past work in males, consistent with reports of enhanced neuroimmune responses in females across the literature. These data suggest that specific neuroimmune reactions in females may impact their susceptibility to alcohol neurotoxicity and other neurodegenerative events with microglial contributions.

Jennifer K. Melbourne, Jessica I. Wooden, Erika R. Carlson, Chinchusha Anasooya Shaji, Kimberly Nixon

Jennifer K. Melbourne, Jessica I. Wooden, Erika R. Carlson... et al. International Journal of Molecular Sciences
2024 Evaluation of long acting GLP1R/GCGR agonist in a DIO and biopsy-confirmed mouse model of NASH suggest a beneficial role of GLP-1/glucagon agonism in NASH patients

NASH, Oncotopix Discovery, Publicly Sharable

Objective: The metabolic benefits of GLP-1 receptor (GLP-1R) agonists on glycemic and weight control are well established as therapy for type 2 diabetes and obesity. Glucagon's ability to increase energy expenditure is well described, and the combination of these mechanisms-of-actions has the potential to further lower hepatic steatosis in metabolic disorders and could therefore be attractive for the treatment for non-alcoholic steatohepatitis (NASH). Here, we have investigated the effects of a dual GLP-1/glucagon receptor agonist NN1177 on hepatic steatosis, fibrosis, and inflammation in a preclinical mouse model of NASH. Having observed strong effects on body weight loss in a pilot study with NN1177, we hypothesized that direct engagement of the hepatic glucagon receptor (GCGR) would result in a superior effect on steatosis and other liver related parameters as compared to the GLP-1R agonist semaglutide at equal body weight. Methods: Male C57Bl/6 mice were fed a diet high in trans-fat, fructose, and cholesterol (Diet-Induced Obese (DIO)-NASH) for 36 weeks. Following randomization based on the degree of fibrosis at baseline, mice were treated once daily with subcutaneous administration of a vehicle or three different doses of NN1177 or semaglutide for 8 weeks. Hepatic steatosis, inflammation and fibrosis were assessed by immunohistochemistry and morphometric analyses. Plasma levels of lipids and liver enzymes were determined, and hepatic gene expression was analyzed by RNA sequencing. Results: NN1177 dose-dependently reduced body weight up to 22% compared to vehicle treatment. Plasma levels of ALT, a measure of liver injury, were reduced in all treatment groups with body weight loss. The dual agonist reduced hepatic steatosis to a greater extent than semaglutide at equal body weight loss, as demonstrated by three independent methods. Both the co-agonist and semaglutide significantly decreased histological markers of inflammation such as CD11b and Galectin-3, in addition to markers of hepatic stellate activation (αSMA) and fibrosis (Collagen I). Interestingly, the maximal beneficial effects on above mentioned clinically relevant endpoints of NN1177 treatment on hepatic health appear to be achieved with the middle dose tested. Administering the highest dose resulted in a further reduction of liver fat and accompanied by a massive induction in genes involved in oxidative phosphorylation and resulted in exaggerated body weight loss and a downregulation of a module of co-expressed genes involved in steroid hormone biology, bile secretion, and retinol and linoleic acid metabolism that are also downregulated due to NASH itself. Conclusions: These results indicate that, in a setting of overnutrition, the liver health benefits of activating the fasting-related metabolic pathways controlled by the glucagon receptor displays a bell-shaped curve. This observation is of interest to the scientific community, due to the high number of ongoing clinical trials attempting to leverage the positive effects of glucagon biology to improve metabolic health.

Thomas Monfeuga, Jenny Norlin, Anne Bugge, Elisabeth D. Gaalsgaard, Cesar A. Prada-Medina, Markus Latta, Sanne S. Veidal, Pia S. Petersen, Michael Feigh, Dorte Holst

Thomas Monfeuga, Jenny Norlin, Anne Bugge... et al. Molecular metabolism
2024 cGAS-STING pathway expression correlates with genomic instability and immune cell infiltration in breast cancer

Oncotopix Discovery, Publicly Sharable, TMA

Genomic instability, as caused by oncogene-induced replication stress, can lead to the activation of inflammatory signaling, involving the cGAS-STING and JAK-STAT pathways. Inflammatory signaling has been associated with pro-tumorigenic features, but also with favorable response to treatment, including to immune checkpoint inhibition. In this study, we aim to explore relations between inflammatory signaling, markers of replication stress, and immune cell infiltration in breast cancer. Expression levels of cGAS-STING signaling components (STING, phospho-TBK1, and phospho-STAT1), replication stress markers (γH2AX and pRPA), replication stress-related proto-oncogenes (Cyclin E1 and c-Myc) and immune cell markers (CD20, CD4, and CD57) are determined immunohistochemically on primary breast cancer samples (n = 380). RNA-sequencing data from TCGA (n = 1082) and METABRIC (n = 1904) are used to calculate cGAS-STING scores. pTBK1, pSTAT1 expression and cGAS-STING pathway scores are all increased in triple-negative breast cancers compared to other subtypes. Expression of γH2AX, pRPA, Cyclin E1, c-Myc, and immune cell infiltration positively correlate with p-STAT1 expression ( P 0.001). Additionally, we observe significant positive associations between expression of pTBK1 and γH2AX, pRPA, c-Myc, and number of CD4+ cells and CD20+ cells. Also, cGAS-STING scores are correlated with genomic instability metrics, such as homologous recombination deficiency ( P  < 0.001) and tumor mutational burden ( P  < 0.01). Moreover, data from the I-SPY2 clinical trial (n = 71) confirms that higher cGAS-STING scores are observed in breast cancer patients who responded to immunotherapy combined with chemotherapy. In conclusion, the cGAS-STING pathway is highly expressed in TNBCs and is correlated with genomic instability and immune cell infiltration.

Mengting Chen, Shibo Yu, Tineke van der Sluis, Mieke C. Zwager, Carolien P. Schröder, Bert van der Vegt, Marcel A. T. M. van Vugt

Mengting Chen, Shibo Yu, Tineke van der Sluis... et al. NPJ Breast Cancer
2024 Proliferation and immunohistochemistry for p53, CD25 and CK20 in predicting prognosis of non-muscle invasive papillary urothelial carcinomas

Oncotopix Discovery, Publicly Sharable

Non-muscle invasive papillary urothelial carcinoma is a prevalent disease with a high recurrence tendency. Good prognostic and reproducible biomarkers for tumor recurrence and disease progression are lacking. Currently, WHO grade and tumor stage are essential in risk stratification and treatment decision-making. Here we present the prognostic value of proliferation markers (Ki67, mitotic activity index (MAI) and PPH3) together with p53, CD25 and CK20 immunohistochemistry (IHC). In this population-based retrospective study, 349 primary non-muscle invasive bladder cancers (NMIBC) were available. MAI and PPH3 were calculated manually according to highly standardized previously described methods, Ki-67 by the semi-automated QPRODIT quantification system, p53 and CD25 by the fully automated digital image analysis program Visipharm® and CK20 with the help of the semi-quantitative immunoreactive score (IRS). Survival analyses with log rank test, as well as univariate and multivariate Cox regression analyses were performed for all investigated variables. Age and multifocality were the only significant variables for tumor recurrence. All investigated variables, except gender, were significantly associated with stage progression. In multivariate analysis, MAI was the only prognostic variable for stage progression (p<0.001).

Vebjørn Kvikstad, Melinda Lillesand, Einar Gudlaugsson, Ok Målfrid Mangrud, Emma Rewcastle, Ivar Skaland, Jan P. A. Baak, Emiel A. M. Janssen

Vebjørn Kvikstad, Melinda Lillesand, Einar Gudlaugsson... et al. PLOS ONE
2024 Dose-dependent reduction of somatic expansions but not Htt aggregates by di-valent siRNA-mediated silencing of MSH3 in HdhQ111 mice

Phenoplex, Publicly Sharable

Huntington's disease (HD) is a progressive neurodegenerative disorder caused by CAG trinucleotide repeat expansions in exon 1 of the HTT gene. In addition to germline CAG expansions, somatic repeat expansions in neurons also contribute to HD pathogenesis. The DNA mismatch repair gene, MSH3, identified as a genetic modifier of HD onset and progression, promotes somatic CAG expansions, and thus presents a potential therapeutic target. However, what extent of MSH3 protein reduction is needed to attenuate somatic CAG expansions and elicit therapeutic benefits in HD disease models is less clear. In our study, we employed potent di-siRNAs to silence mouse Msh3 mRNA expression in a dose-dependent manner in HdhQ111/+ mice and correlated somatic Htt CAG instability with MSH3 protein levels from simultaneously isolated DNA and protein after siRNA treatment. Our results reveal a linear correlation with a proportionality constant of ~ 1 between the prevention of somatic Htt CAG expansions and MSH3 protein expression in vivo, supporting MSH3 as a rate-limiting step in somatic expansions. Intriguingly, despite a 75% reduction in MSH3 protein levels, striatal nuclear HTT aggregates remained unchanged. We also note that evidence for nuclear Msh3 mRNA that is inaccessible to RNA interference was found, and that MSH6 protein in the striatum was upregulated following MSH3 knockdown in HdhQ111/+ mice. These results provide important clues to address critical questions for the development of therapeutic molecules targeting MSH3 as a potential therapeutic target for HD.

Rachelle Driscoll, Lucas Hampton, Neeta A. Abraham, J. Douglas Larigan, Nadine F. Joseph, Juan C. Hernandez-Vega, Sarah Geisler, Fu-Chia Yang, Matthew Deninger, David T. Tran, Natasha Khatri, Bruno M. D. C. Godinho, Garth A. Kinberger, Daniel R. Montagna, Warren D. Hirst, Catherine L. Guardado, Kelly E. Glajch, H. Moore Arnold, Corrie L. Gallant-Behm, Andreas Weihofen

Rachelle Driscoll, Lucas Hampton, Neeta A. Abraham... et al. Scientific Reports
2024 Targeting the NAT10/NPM1 axis abrogates PD-L1 expression and improves the response to immune checkpoint blockade therapy

Oncotopix Discovery, Publicly Sharable

PD-1/PD-L1 play a crucial role as immune checkpoint inhibitors in various types of cancer. Although our previous study revealed that NPM1 was a novel transcriptional regulator of PD-L1 and stimulated the transcription of PD-L1, the underlying regulatory mechanism remains incompletely characterized. Various human cancer cell lines were used to validate the role of NPM1 in regulating the transcription of PD-L1. The acetyltransferase NAT10 was identified as a facilitator of NPM1 acetylation by coimmunoprecipitation and mass spectrometry. The potential application of combined NAT10 inhibitor and anti-CTLA4 treatment was evaluated by an animal model. We demonstrated that NPM1 enhanced the transcription of PD-L1 in various types of cancer, and the acetylation of NPM1 played a vital role in this process. In particular, NAT10 facilitated the acetylation of NPM1, leading to enhanced transcription and increased expression of PD-L1. Moreover, our findings demonstrated that Remodelin, a compound that inhibits NAT10, effectively reduced NPM1 acetylation, leading to a subsequent decrease in PD-L1 expression. In vivo experiments indicated that Remodelin combined with anti-CTLA-4 therapy had a superior therapeutic effect compared with either treatment alone. Ultimately, we verified that the expression of NAT10 exhibited a positive correlation with the expression of PD-L1 in various types of tumors, serving as an indicator of unfavorable prognosis. This study suggests that the NAT10/NPM1 axis is a promising therapeutic target in malignant tumors.

Ge Qin, Fan Bai, Huabin Hu, Jianwei Zhang, Weixiang Zhan, Zehua Wu, Jianxia Li, Yang Fu, Yanhong Deng

Ge Qin, Fan Bai, Huabin Hu... et al. Molecular Medicine
2024 Integrative Analyses of Pyrimidine Salvage Pathway-Related Genes Revealing the Associations Between UPP1 and Tumor Microenvironment

Phenoplex, Publicly Sharable

Background: The pyrimidine salvage pathway plays a critical role in tumor progression and patient outcomes. The roles of pyrimidine salvage pathway-related genes (PSPGs) in cancer, however, are not fully understood. This study aims to depict the characteristics of PSPGs across various cancers. Methods: An integrative pan-cancer analysis of six PSPGs (CDA, UCK1, UCK2, UCKL1, UPP1, and UPP2) was conducted using TCGA data, single-cell RNA sequencing datasets, and patient samples. Single-cell transcriptome analysis and RT-qPCR were used to validate the relation between UPP1 and cytokines. Flow cytometry was performed to validate the role of UPP1 in immune checkpoint regulation. The correlation between UPP1 and tumor associated neutrophils (TAN) were investigated and validated by single-cell transcriptome analysis and tissue microarrays (TMAs). Results: PSPGs showed low mutation rates but significant copy number variations, particularly amplifications in UCKL1, UPP1, and UCK2 across various cancers. DNA methylation patterns varied, with notable negative correlations between methylation and gene expression in UPP1. PSPGs were broadly up-regulated in multiple cancers, with correlations to clinical staging and prognosis. Proteomic data further confirmed these findings. Functional analysis revealed PSPGs’ associations with tumor proliferation, metastasis, and various signaling pathways. UPP1 showed strong correlations with the tumor microenvironment (TME), particularly with cytokines, immune checkpoints, and various immune cells. Single-cell transcriptome analysis confirmed these associations, highlighting UPP1’s influence on cytokine expression and immune checkpoint regulation. In esophageal squamous cell carcinoma (ESCC), UPP1-high tumor cells were significantly associated with immunosuppressive cells in the TME. Spatial analysis using TMAs revealed that UPP1+ tumor cells were predominantly located at the invasive margin and closely associated with neutrophils, correlating with poorer patient prognosis. Conclusion: Our study depicted the multi-dimensional view of PSPGs in cancer, with a particular focus on UPP1’s role in the TME. Targeting UPP1 holds promise as a potential strategy for cancer therapy.

Yin Li, Manling Jiang, Yongqi Wei, Xiang He, Guoping Li, Chunlai Lu, Di Ge

Yin Li, Manling Jiang, Yongqi Wei... et al. Journal of Inflammation Research
2024 Effects of gene replacement therapy with resamirigene bilparvovec (AT132) on skeletal muscle pathology in X-linked myotubular myopathy: results from a substudy of the ASPIRO open-label clinical trial

Oncotopix Discovery, Publicly Sharable

Summary

Background

X-linked myotubular myopathy (XLMTM) is a rare, life-threatening congenital muscle disease caused by mutations in the MTM1 gene that result in profound muscle weakness, significant respiratory insufficiency, and high infant mortality. There is no approved disease-modifying therapy for XLMTM. Resamirigene bilparvovec (AT132; rAAV8-Des-hMTM1) is an investigational adeno-associated virus (AAV8)-mediated gene replacement therapy designed to deliver MTM1 to skeletal muscle cells and achieve long-term correction of XLMTM-related muscle pathology. The clinical trial ASPIRO (NCT03199469) investigating resamirigene bilparvovec in XLMTM is currently paused while the risk:benefit balance associated with this gene therapy is further investigated.

Methods

Muscle biopsies were taken before treatment and 24 and 48 weeks after treatment from ten boys with XLMTM in a clinical trial of resamirigene bilparvovec (ASPIRO; NCT03199469). Comprehensive histopathological analysis was performed.

Findings

Baseline biopsies uniformly showed findings characteristic of XLMTM, including small myofibres, increased internal or central nucleation, and central aggregates of organelles. Biopsies taken at 24 weeks post-treatment showed marked improvement of organelle localisation, without apparent increases in myofibre size in most participants. Biopsies taken at 48 weeks, however, did show statistically significant increases in myofibre size in all nine biopsies evaluated at this timepoint. Histopathological endpoints that did not demonstrate statistically significant changes with treatment included the degree of internal/central nucleation, numbers of triad structures, fibre type distributions, and numbers of satellite cells. Limited (predominantly mild) treatment-associated inflammatory changes were seen in biopsy specimens from five participants.

Interpretation

Muscle biopsies from individuals with XLMTM treated with resamirigene bilparvovec display statistically significant improvement in organelle localisation and myofibre size during a period of substantial improvements in muscle strength and respiratory function. This study identifies valuable histological endpoints for tracking treatment-related gains with resamirigene bilparvovec, as well as endpoints that did not show strong correlation with clinical improvement in this human study.

Funding

Astellas Gene Therapies (formerly Audentes Therapeutics, Inc.).

Michael W. Lawlor, Benedikt Schoser, Marta Margeta, Caroline A. Sewry, Karra A. Jones, Perry B. Shieh, Nancy L. Kuntz, Barbara K. Smith, James J. Dowling, Wolfgang Müller-Felber, Carsten G. Bönnemann, Andreea M. Seferian, Astrid Blaschek, Sarah Neuhaus, A. Reghan Foley, Dimah N. Saade, Etsuko Tsuchiya, Ummulwara R. Qasim, Margaret Beatka, Mariah J. Prom, Emily Ott, Susan Danielson, Paul Krakau, Suresh N. Kumar, Hui Meng, Mark Vanden Avond, Clive Wells, Heather Gordish-Dressman, Alan H. Beggs, Sarah Christensen, Edward Conner, Emma S. James, Jun Lee, Chanchal Sadhu, Weston Miller, Bryan Sepulveda, Fatbardha Varfaj, Suyash Prasad, Salvador Rico

Michael W. Lawlor, Benedikt Schoser, Marta Margeta... et al. eBioMedicine
2024 Heterogeneity in intrahepatic macrophage populations and druggable target expression in patients with steatotic liver disease-related fibrosis

Akoya, MASH, NASH, Phenoimager, Phenoplex, Publicly Sharable, nice

Clinical trials for reducing fibrosis in steatotic liver disease (SLD) have targeted macrophages with variable results. We evaluated intrahepatic macrophages in patients with SLD to determine if activity scores or fibrosis stages influenced phenotypes and expression of druggable targets, such as CCR2 and galectin-3. Liver biopsies from controls or patients with minimal or advanced fibrosis were subject to gene expression analysis using nCounter to determine differences in macrophage-related genes (n = 30). To investigate variability among individual patients, we compared additional biopsies by staining them with multiplex antibody panels (CD68/CD14/CD16/CD163/Mac387 or CD163/CCR2/galectin-3/Mac387) followed by spectral imaging and spatial analysis. Algorithms that utilize deep learning/artificial intelligence were applied to create cell cluster plots, phenotype profile maps, and to determine levels of protein expression (n = 34). Several genes known to be pro-fibrotic (e.g. CD206, TREM2, CD163, and ARG1) showed either no significant differences or significantly decreased with advanced fibrosis. Although marked variability in gene expression was observed in individual patients with cirrhosis, several druggable targets and their ligands (e.g. CCR2, CCR5, CCL2, CCL5, and LGALS3) were significantly increased when compared to patients with minimal fibrosis. Antibody panels identified populations that were significantly increased (e.g. Mac387+), decreased (e.g. CD14+), or enriched (e.g. interactions of Mac387) in patients that had progression of disease or advanced fibrosis. Despite heterogeneity in patients with SLD, several macrophage phenotypes and druggable targets showed a positive correlation with increasing NAFLD activity scores and fibrosis stages.Patients with SLD have markedly varied macrophage- and druggable target-related gene and protein expression in their livers. Several patients had relatively high expression, while others were like controls. Overall, patients with more advanced disease had significantly higher expression of CCR2 and galectin-3 at both the gene and protein levels. Appreciating individual differences within the hepatic microenvironment of patients with SLD may be paramount to developing effective treatments. These results may explain why such a small percentage of patients have responded to macrophage-targeting therapies and provide additional support for precision medicine-guided treatment of chronic liver diseases. Keywords: Cardiometabolic risk factors, Chemokines, Infiltrating monocytes, Inflammation, NanoString nCounter, Multispectral imaging, MASLD, Visiopharm

Omar A. Saldarriaga, Timothy G. Wanninger, Esteban Arroyave, Joseph Gosnell, Santhoshi Krishnan, Morgan Oneka, Daniel Bao, Daniel E. Millian, Michael L. Kueht, Akshata Moghe, Jingjing Jiao, Jessica I. Sanchez, Heidi Spratt, Laura Beretta, Arvind Rao, Jared K. Burks, Heather L. Stevenson

Omar A. Saldarriaga, Timothy G. Wanninger, Esteban Arroyave... et al. JHEP Reports
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