Comparative analysis of the tumor immune microenvironment (TIME) in primary and metastatic sites of microsatellite stable (MSS) and microsatellite instability-high (MSI) colorectal cancer

Authors Marwan G. Fakih, Jian Ye, jiye@coh.org, ChongKai Wang, Colt Egelston, Minxuan Huang, Jacob Mercer, Michael A. Thompson, Jun Gong


We have previously reported significant differences between the tumor immune microenvironment (TIME) of primary colorectal cancer (CRC-P) and different metastatic sites. Increased immune cell infiltration, B-cells, and CD8 cells and decreased macrophages were noted in CRC-P and lung metastatic (LuM) lesions compared to liver (LM) and peritoneum (PM) metastases. We expanded our work to MSI CRC and compared their TIME to respective MSS tumor sites.


De-identified cases of MSS and MSI metastatic CRC that underwent next-generation sequencing with the Tempus xT assay were selected from the Tempus Database. Gene expression patterns of immune cells, including B, T (CD4+, CD8+), NK cells, and macrophages, were used to predict relative intra-tumor abundance. MSI and MSS cohorts included CRC-P, LM, and PM. LuM was analyzed only in MSS tumors due to the limited number of MSI LuM. Tumor mutational burden (TMB), neoantigen burden, and proportion of immune cells in CRC-P, LM, and PM were compared across MSI and MSS patients. Chi-squared/Fischer’s exact tests or Kruskal-Wallis tests were used to assess statistical significance.


A total of 208 MSI and 6,732 MSS tumors were subject of analysis. No differences were noted in TMB, neoantigen load, or PD-L1 expression between MSI CRC-P, LM, or PM. Across the 3 tissue groups, the median TMB and neoantigen tumor burden were significantly higher in MSI cohorts when compared to MSS cohorts (p<0.001). Compared to MSS LM, MSI LM exhibited a higher percentage of CD8 cells (p=0.002) and NK cells (p<0.001), with a trend towards a lower percentage of macrophages (p=0.14). Similar differences were noted for MSI PM compared to MSS PM (CD8 cells p=0.018, NK cells p=0.044 and macrophages p=0.023). The TIME of MSS LuM lesions shared more similarities with that of MSI LM/PM than MSS LM/PM.


MSI LM and PM have a more favorable TIME than respective MSS metastases, explaining the discordance in response to checkpoint inhibitors (CPI) and reported CPI benefits in MSI cases across all metastatic sites. MSS LuM have a comparable TIME to MSI metastatic sites, explaining the recently reported benefits from CPI therapy in this group.