Nanopore sequencing of the microbiome in fecal immunochemical test samples for colorectal cancer screening | LC26

Abstract
Early detection of precursor lesions (PL) or early-stage colorectal cancer (CRC) could hamper cancer development or improve survival rates, and there is a critical need for non-invasive biomarkers. Growing evidence implicates intestinal microbiota in CRC development and progression. The aim of this study was to evaluate intestinal microbiome from residual Fecal Immunochemical Test (FIT) samples as a biomarker for CRC screening. Residual stool samples from Brazilian FIT-positive individuals (n=133) were classified based on colonoscopy as no lesions (N) (n=30), non-advanced adenoma (NAA) (n=46), advanced adenoma (AA) (n=13), or colorectal cancer (CA) (n=44). We assessed the impact of two FIT tubes and a specific collection device for microbiome analysis (n=3). Bacterial DNA from FIT samples underwent 16S rRNA sequencing using Oxford Nanopore MinION (R10.4.1). Reads were processed with Dorado, aligned using Emu to a curated full-length 16S database, and analyzed in QIIME 2. Alpha diversity, beta diversity, and differential abundance were evaluated using Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC). Alpha diversity was significantly higher in CA compared with N and NAA (p <0.01). Beta diversity showed clear compositional separation among CA, AA, NAA, and N (p = 0.001). Differential abundance revealed progressively increasing dysbiosis along the adenoma–carcinoma pathway, with Fusobacterium nucleatum enriched in CA samples. No differences in species composition were observed among the tested collection tubes. In conclusion, profiling the microbiome from routinely residual FIT samples is feasible and reveals shifts in diversity along the adenoma–carcinoma pathway, highlighting the promise of FIT-based microbiome signatures as non-invasive biomarkers for early CRC detection in Brazilian screening population.

Biography
Mariana Bisarro dos Reis is a biologist with a Master’s and PhD in Genetics and over two decades of experience in molecular and translational cancer research. Her postdoctoral work at Barretos Cancer Hospital advanced non-invasive colorectal cancer biomarkers using circulating DNA, stool DNA, and microbiome profiling through nanopore sequencing. She is currently a research intern in the University of North Carolina (UNC) Department of Pathology, analyzing the long-read sequencing data to identify microbiome signatures of precursor lesions and CRC for screening in resource-limited settings globally.