Abstract 611: Colibactin mutation signatures are associated with a distinct colorectal cancer clinicopathologic phenotype
Authors: Lumish Melissa A. , Luthra Anisha , Asawa Simran , Cambuli Francesco , Donoghue Mark , Woo Hyung Jun , Cercek Andrea , Yaeger Rona , Shia Jinru , Sanchez-Vega Francisco , Ganesh Karuna 
Published: July 2021

PURPOSE: Alterations in the gut microbiome contribute to colorectal cancer (CRC) pathogenesis. The genotoxin colibactin, produced by pks+ E. coli, directly binds to DNA, leaving genetic scars at A-T rich motifs that can be identified by whole genome/exome sequencing (WGS/WES) as hexanucleotide mutation signatures SBS28 and SBS41. Here, we investigated whether MSK-IMPACT, a clinical targeted exon capture assay with lower genomic coverage (341-468 cancer associated exons), could be used to identify colibactin mutation signatures (CMS) and provide insight into associated clinicopathologic phenotypes.

METHODS: From an institutional pan-cancer cohort of 36,158 tumors assayed using MSK-IMPACT, we identified 11,864 samples (1,386 CRC) with at least 20 mutations and applied TempoSig, an algorithm which uses maximum likelihood-based extraction of mutational signature proportions. Tumors with at least 10% of all mutations attributed to SBS28/41 were deemed CMS+. Due to the association of POLE mutations and microsatellite instability with distinct phenotypes, we excluded these cases from our analysis.

RESULTS: Consistent with prior reports based on WGS/WES, our MSK-IMPACT TempoSig pipeline identified CMS positivity in multiple cancers, notably gastrointestinal (GI) and head and neck cancers. Ampullary tumors (25%) and GI neuroendocrine tumors (8%) had the highest SBS28 and SBS41 positivity respectively. Among microsatellite stable CRCs, we identified 52 patients with at least one sample positive for SBS28 (N=25) or SBS41 (N=27). Compared with CMS negative tumors, SBS28+ but not SBS41+ tumors had higher chromosomal instability as quantified by fraction of the genome altered by copy number alterations (SBS28+: 33.4% vs. SBS28-: 22.3%, P&lt;.01), lower tumor mutation burden (SBS28+: 7.9/Mb vs. SBS28-: 8.8/Mb, P=.011), and a trend toward younger median age at sampling (57 (IQR 46-66) vs. 61 (IQR 51-70), P=.095). SBS28+ tumors harbored more frequent mutations in DNA damage repair (DDR) genes ATR (7.1 vs. 0.5%, P=.02) and ATM (14.3 vs. 4.1%, P=.03). Overall survival from diagnosis was decreased in patients with SBS28+ compared with SBS41+ tumors (22.0 vs. 43.7 months, P&lt;.07), regardless of initial stage (P&lt;.01). Histopathology revealed increased TILs in 13% of evaluable SBS28+ and 7% of SBS41+ tumors, while RNA FISH using a probe targeting the clbP gene required for colibactin synthesis was negative in all CMS+ samples, suggesting that colibactin mutagenesis is an early event not requiring persistent pks+ E. coli colonization.

CONCLUSIONS: TempoSig enables rigorous identification of colibactin mutation signatures in clinically utilized MSK-IMPACT targeted exon datasets. SBS28+ CRCs are clinically distinct and associated with early onset, poor prognosis and DDR pathway alterations. In ongoing studies, we are investigating the therapeutic implications of these findings.

Citation Format: Melissa A. Lumish, Anisha Luthra, Simran Asawa, Francesco Cambuli, Mark Donoghue, Hyung Jun Woo, Andrea Cercek, Rona Yaeger, Jinru Shia, Francisco Sanchez-Vega, Karuna Ganesh. Colibactin mutation signatures are associated with a distinct colorectal cancer clinicopathologic phenotype [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 611.