It has been well established that the tumor microenvironment (TME), which comprises cancer cells, stromal cells, and surrounding extracellular matrix, plays a critical role in cancer development, progression, and control. The immunological components within tumors, known as the tumor immune microenvironment (TiME), have also been implicated in tumor development, recurrence, and metastasis. Effective strategies for cancer immunotherapies will require a deep understanding of the factors that shape both the TME and TiME. Here, we describe a spatial multiomics approach that utilizes RNAscope™ ISH technology paired with high-plex whole-slide spatial phenotyping with the PhenoCycler™-Fusion platform. This two-step approach is compatible with human FFPE tissues and enables researchers to characterize the spatial biology of the TiME more accurately by detecting RNA and protein markers on serial sections. The resulting multiomic data more accurately reveal the interplay between TME and TiME by giving insight into cell lineages, surrounding structures, as well as secreted chemokines and cytokines that exist within the TME ecosystem.

Niyati Jhaveri¹, HaYeun Ji¹, Anushka Dikshit², Jessica Yuan¹, Emerald Doolittle², Steve Zhou², Maithreyan Srinivasan², Bassem B. Cheikh¹, Fabian Schneider³, James Mansfield³, Julia Kennedy-Darling¹, Oliver Braubach¹

1. Akoya Biosciences, Menlo Park, CA
2. Advanced Cell Diagnostics, a Bio-Techne Brand, Newark, CA
3. Visiopharm A/S, Horsholm, Denmark