Tumor Microbial Biodiversity and Microsatellite Instability in Colorectal Cancer

Background: There is growing interest in characterizing how the gut microbiome is related to colorectal cancer (CRC) progression and etiology after several species have been found to be strongly enriched in certain molecular subtypes of CRC tumors. DNA mismatch repair deficiency in CRC is associated with a favorable prognosis and positive response to immunotherapy, and it can be characterized by the presence of tumor microsatellite instability (MSI). Here, we explore the relationship between MSI status and tumor microbial biodiversity. Methods: The Seattle site of the Colon Cancer Family Registry (SCCFR) recruited patients diagnosed with incident CRC from 1998 – 2007. Tumor tissue samples were assessed for MSI status and targeted sequencing of the V3-V4 hypervariable region of the prokaryotic 16S rRNA gene was performed. We used an adaptive test of alpha diversity (aMiAD) that incorporates a set of abundance-based and phylogenetic alpha diversity metrics to estimate the association of microbial biodiversity with MSI status. Differential abundance analysis was performed using ANCOM-BC to identify specific enriched genera in tumor tissue based on MSI status. The alpha diversity analyses and differential abundance analyses were both adjusted for age, sex, smoking history, and tumor location in the subset of the SCCFR patients with complete profiling of all measures (N = 632). Results: The adaptive aMiAD effect estimate was -1.08 (p = 0.29), indicating a non-statistically significant negative association of alpha diversity on MSI status, with MSI-high tumors having lower estimated alpha diversity. We identified 20 differentially abundant genera in MSI tumors, with 8 enriched genera and 12 depleted genera in MSI-high tumors. The genera that were most strongly enriched in MSI-high tumors were Gemella and Lawsonella, while the most strongly depleted genera in MSI-high tumors were Sporolactobacillaceae and Cloacibacterium. Conclusions: We failed to detect an association between any of the individual alpha diversity measures or the adaptive alpha diversity measure with MSI status, though all measures concordantly estimated a depletion of alpha diversity in the MSI-high tumors. We find evidence of differential abundance of certain genera dependent on MSI status, including several genera that have not been previously identified as associated with MSI status.