A. L. Butash1, T. Kawaguchi2, L. Yan3, Q. Qi3, X. Peng3, M. Asaoka1, G. Mann1, E. Otsuji2, K. Takabe1 1Roswell Park Cancer Institute,Department Of Surgery,Buffalo, NY, USA 2Kyoto Prefectural University of Medicine,Department of Surgery,Kyoto, KYOTO, Japan 3Roswell Park Cancer Institute,Department Of Bioinformatics And Biostatistics,Buffalo, NY, USA
Introduction:
Tumor heterogeneity arises from differences among cancer cells that are inherited during cell division. It implies the coexistence of sub-populations of cancer cells that differ in their genetic, phenotypic, or behavioral characteristics. Several studies have documented a role for intra-tumor heterogeneity (ITH) in driving tumor progression and treatment resistance in colon cancer. However, ITH, especially related to intra-tumor immune microenvironment, is not well examined in colon cancers. In this study, we aim to examine the association of ITH and immune gene signatures and its clinical relevance in colon cancers.
Methods:
Integrated genomic and clinical data was collected from colon cancer patients in The Cancer Genome Atlas (TCGA). ITH was estimated by calculating Mutant Allele Tumor Heterogeneity (MATH) using computational analyses. Intra-tumor immune signatures and tumor infiltrating immune cell composition were calculated using integrated transcriptomics and CIBERSORT or TIMER, respectively. Clinical relevance was assessed by Kaplan-Meier survival curve.
Results:
Colorectal tumors with high ITH were found to have fewer activated CD4 T-cells (p<0.0074) and CD8 T-cells (p<0.0084) when compared to tumors with low ITH. A similar trend was seen with decreased expression of immune checkpoint molecules; such as PD-1, PDL-1, CTLA4, and LAG3 (p<0.01, p<0.0067, p<0.023, p<0.005 respectively) in tumors with high ITH, reflecting the overall decreased presence of immune cells. Expression of cytolytic molecules; PRF1 (p<0.0046) and GZMA (p<0.00059), as well as the immune cytolytic activity (p<0.0023) were also lower in tumors with high ITH. We also retrieved a genomic classifier created of >200,000 microsatellite loci to identify microsatellite instability (MSI), and found that MSI-high tumors showed lower ITH, suggesting that genomic instability could be associated with intra-tumor heterogeneity. MSI-high tumors were associated with low ITH (p<0.0001). Gene Set Enrichment Analysis (GSEA) demonstrated that enrichment of immune-response gene sets was observed in the lower ITH tumors. Low MATH was associated with improved overall survival (OS) while high MATH demonstrated worse survival (p<0.029), as well as disease-free survival (p<0.0093). In right sided colorectal tumors, low ITH was associated with improved survival (p<0.0023), but this trend was not observed with left sided colorectal tumors in this patient population.
Conclusion:
We found that low ITH was associated with enhanced intra-tumor immunogenicity or immune response and is prognostic of improved survival in colon cancer. Our study is in agreement with the notion that ITH is determined by tumor immune microenvironment including anti-tumor immunity, which is expected to have future implications for clinical application.