2020 AACR: Quantification of tumor-infiltrating immune cell populations with an augmented transcriptome

Comprehensive characterization of the tumor and tumor microenvironment (TME) can improve our understanding of tumor progression and treatment outcomes. In particular, quantification of the immune infiltrate has the potential to inform mechanisms of immune escape and predict response to therapy. Standard experimental approaches exist to enumerate tumor-infiltrating immune cells, but they can have practical limitations of throughput, number of markers, or sample requirements. RNA sequencing can be used as a scalable solution to comprehensively profile the immune cell composition of the TME. By identifying marker genes that are expressed by specific immune cell types, we can create a computational method to quantify the abundance of these cell types in a mixed sample. However, care must be taken to verify that such computational analysis accurately reflects the underlying immune cell composition. Here, we utilize our transcriptome platform, ImmunoID NeXT, to develop and evaluate a methodology for immune cell quantification. We compare our transcriptome-based quantification to orthogonal measurements of immune cell abundance to ensure accuracy, and highlight the utility of the methodology by comparing results across samples from diverse tumor types.

To address the challenge of providing characterization of both the tumor and TME, we have developed the ImmunoID NeXT Platform®, an augmented, immuno-oncology-optimized exome/transcriptome platform designed to provide comprehensive information from a single FFPE tumor sample.