Abstract 2124: Hotspots of sequence variability in gut microbial metagenomic datasets and their association with colorectal cancer

Abstract

Abstract The gut microbiome has been found to impact host predisposition to disease. Previous research shows that certain species of microbes, encoding pro-inflammatory factors, increase the probability of developing dysplasia and colorectal cancer (CRC). Recently, through the oligotyping approach, we found genetic variants for an amplified region of usp, a genotoxic protein made by E. coli in the gut. These different variants were present in healthy, adenoma and CRC clinical stool samples. To our surprise, the same positions of genetic variability found experimentally were confirmed by BLAST analyses of shotgun metagenomic data from a case-control study conducted in France and Washington D.C. In this work, using the same metagenomics data, we searched for hotspots of genetic variability in the sequences for five genes with known pro-inflammatory and toxicity profiles: usp, tcpC, gelE, clbB, and clbN. More importantly, we extended our analyses to cover the entire length of these genes using a command line approach to BLAST+. The sequence reads for both clbB and clbN lacked coverage, rendering their analysis unquantifiable. The output data for both tcpC and gelE showed high levels of homology between the sequences of the healthy and CRC patients. However, we found twenty-nine hotspots in the usp gene, thirteen of which cause a modification in the primary structure of the protein. Among these thirteen positions, nine were different in cases and controls suggesting that these hotspots of variation are associated with CRC. All these results provide insight into both the link between variability and pathogenicity, and the viability of shotgun sequencing for such types of analyses. Citation Format: Rachell M. Martinez-Ramirez, Miguel M. Girod-Hoffman, Abiel Roche-Lima, Kelvin Carrasquillo-Carrión, Josué Pérez-Santiago, Abel Baerga-Ortiz. Hotspots of sequence variability in gut microbial metagenomic datasets and their association with 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 2124.