Abstract A08: Tumor microbiome in subtypes of mismatch repair-deficient colorectal cancer
Authors: Joo Jihoon E. , Clendenning Mark , Mahmood Khalid , Rosty Christophe , Winship Ingrid M. , Jenkins Mark A. , Buchanan Daniel D. 
Published: December 2020

Abstract
Background: Colorectal cancer (CRC) comprises different molecular subtypes, including those tumors that develop defective DNA mismatch repair (MMR) evidenced by microsatellite instability (MSI) and/or loss of MMR protein expression (MMR-deficiency). Tumor MMR-deficiency can result from inherited causes, namely germline mutations in the MMR genes (Lynch syndrome) or from somatic inactivation resulting from hypermethylation of the MLH1 gene promoter or from biallelic somatic mutations. Little is known about the etiologies of these cancers or the avenues for risk amelioration. We hypothesized that dysbiosis of the gut microbiome is a risk factor for the development of MMR-deficient subtypes of CRC and that the microbiome composition differs between inherited and somatic MMR-deficient CRC.
Materials and Methods: The microbiome composition was determined by 16S rRNA sequencing of the V3-V4 regions in DNA extracted from 94 FFPE-derived tumor specimens comprised of 14 MMR-proficient CRCs and 80 MMR-deficient CRCs from the Australasian Colorectal Cancer Family Registry. The MMR-deficient CRCs comprised three subtypes: 35 people with germline MMR gene mutations (Lynch syndrome), 13 people with sporadic MLH1 hypermethylated CRCs, and 32 people with suspected Lynch syndrome (no germline or MLH1 methylation). LEfse analyses were used to identify differential abundance in taxa between groups.
Results: In all tumor samples, Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Fusobacteria were most abundant. Of these, the Firmicute population was significantly higher in the MMR-proficient than MMR-deficient CRCs (0.33 v 0.19, P &lt; 0.05). When compared with the Lynch syndrome-related CRCs, we found 22 bacterial species, including Corynebacteriaceae, that were significantly more abundant in MLH1 hypermethylated tumors (P &lt; 0.05), whereas we found 4 species significantly more abundant, including Enterobacter, in suspected Lynch syndrome group. Although the microbial diversity was notably smaller compared with the sporadic groups, several species of the family Comamanadaceae including Acidovorax were abundant in Lynch syndrome tumors (P &lt; 0.05). Fusobacterium nucleatum was detected in 11/35 (31.4%) Lynch syndrome-related CRCs, 5/13 (38.5%) MLH1 hypermethylated CRCs, 13/32 (40.6%) suspected Lynch syndrome CRCs, and 4/14 (28.6%) sporadic MMR-proficient CRCs.
Conclusions: Inherited and somatic subtypes of MMR-deficient CRC show significant differences in their tumor microbiome composition where Lynch syndrome-related MMR-deficient CRC showed a reduced microbiome diversity compared with somatic MMR-deficient CRC. Further validation of these findings will improve our understanding of MMR-deficient CRC tumorigenesis and aid in CRC prevention through the identification of modifiable microbial risk factors.
Citation Format: Jihoon E. Joo, Mark Clendenning, Khalid Mahmood, Christophe Rosty, Ingrid M. Winship, Mark A. Jenkins, Daniel D. Buchanan. Tumor microbiome in subtypes of mismatch repair-deficient colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr A08.