Abstract 3872: Spatial and multi-omics characterization of the tumor microenvironment in colorectal cancer
Authors: Eng Christine L. , Yeong Joe P. , Nguyen Andy , Guo Amanda Y. , Tay Brenda , Chang Mei Mei , Lim Sherlly , Chua Clarinda W. , Srinivasan Harini , Kua Lindsay H. , Lee Fiona Y. , Macalinao Dominique C. , Aung ThinZar , Skanderup Anders J. , Lim Tony K. , Tan Iain B. , Koo Si-Lin 
Published: September 2020

Background: Colorectal cancer is a heterogeneous disease, harboring tremendous differences in genetic mutations, gene expression pathways, and the tumor microenvironment. While there has been recent progress in understanding immune infiltration patterns in colorectal cancer, the majority of patients are thus far largely refractory to immunotherapy, and the underlying mechanism remains poorly understood. Here, we present a large-scale multi-omics analyses on 161 colorectal cancer tumors. More specifically, we aim to characterize the spatial and phenotypic profiles as well as the relationships between the different cell populations in the tumor microenvironment using multiplex immunohistochemistry.

Methods: Tissue microarrays were constructed, comprising the tumor core, close-to-edge, tumor edge, and adjacent normal tissues for each tumor. H&E and multiplex immunohistochemistry were performed by staining 7 markers (cytokeratin [CK], CD3, CD8, FOXP3, CD68, PD-L1 and DAPI). This allows for simultaneous detection of different cell populations, including CK+ epithelial cells, CD68+ macrophages, CD3+ T cells, CD8+ T cells, and FOXP3 regulatory T cells. Further complementing the study were whole genome sequencing to describe genetic mutations and tumor mutation burden, along with whole transcriptome sequencing to investigate differential gene expression and pathway enrichment. MSI status was determined from whole genome sequencing data, and molecular subtypes were called from RNA-sequencing data.

Results: Based upon spatial patterns of immune cell infiltration, we qualitatively and quantitatively describe several immune infiltration subtypes which were further correlated with tumor mutation burden and neoantigen burden, activation of major oncogenic pathways and inflammatory signatures. The density of immune cells varies across the different tumor sites, from the adjacent normal tissue into the tumor core. We have also uncovered interactions between the different cell populations within the tumor microenvironment. Overall, the integration of data from multiple platforms represents a comprehensive interrogation into the complex tumor microenvironment in colorectal cancer.

Conclusion: There exists a substantial variability in the transcriptomic landscape and the immune infiltration patterns across different patients. This demonstrates the complex interplay between the different cell populations in the tumor microenvironment, representing the fine balance between immune activation and suppression.

Citation Format: Christine L. Eng, Joe P. Yeong, Andy Nguyen, Amanda Y. Guo, Brenda Tay, Mei Mei Chang, Sherlly Lim, Clarinda W. Chua, Harini Srinivasan, Lindsay H. Kua, Fiona Y. Lee, Dominique C. Macalinao, ThinZar Aung, Anders J. Skanderup, Tony K. Lim, Iain B. Tan, Si-Lin Koo. Spatial and multi-omics characterization of the tumor microenvironment in colorectal cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3872.