Whole‐exome sequencing analyses of colorectal cancer with Fusobacterium nucleatum
Authors: Nishihara Reiko , Chan Andrew T , Mu Jasmine , Giannakis Marios , Mima Kosume , Qian Zhi Rong , Bullman Susan , Kostic Aleksandar , Huttenhower Curtis , Garrett Wendy , Giovannucci Edward , Meyerson Matthew , Garraway Levi , Fuchus Charles , Ogino Shuji 
Published: November 2023

IntroductionGut microbiota plays an important role in intestinal cancer pathogenesis. An accumulating body of evidence demonstrates the association between Fusobacterium nucleatum (F. nucleatum) and colorectal cancer. However, the underlying mechanistic basis of tumorigenesis remains to be investigated.MethodWithin 600 colorectal cancer patients from the Nurses' Health Study and the Health Professionals Follow‐up Study, F. nucleatum DNA was measured in formalin‐fixed paraffin‐embedded specimens using a quantitative PCR assay. We performed whole‐exome sequencing analyses to identify characteristics of somatic mutations in tumors with F. nucleatum compared with tumors without. The hypermutated phenotype was defined as cancer with the mutation rate of more than 12 per mega base. Significantly mutated genes were identified based on the MutSigCV computational tool that accounted for regional heterogeneity in mutation rates across the genome. Mutations in MHC class I genes were identified using the POLYSOLVER algorithm.ResultsF. nucleatum was present in 86 colorectal cancer tumors, of which 43 (50%) were tumors with a hypermutated phenotype (hypermutators). Colorectal cancer with F. nucleatum was more likely to be a hypermutator compared to cancer without F. nucleatum (chi‐square test, P<0.001). The colorectal cancer‐specific mortality rate was highest in patients with non‐hypermutated phenotype with F. nucleatum, when compared to the rest of patients (i.e., those with hypermutated phenotype with or without F. nucleatum, or non‐hypermutated phenotype with F. nucleatum). Among hypermutated tumors, the HLA‐B mutation was found in 26 cases, and the mutation rate was higher in cancer with F. nucleatum (58%) compared to cancer without F. nucleatum (42%) (Fisher's exact test, P=0.009). Among hypermutated tumors, the MHC class I genes (including HLA‐A, HLA‐B, and HLA‐C) tended to be mutated in cancer with F. nucleatum, but the result was not statistically significant (Fisher's exact test, P=0.24).DiscussionThe whole‐exome sequencing analyses suggest that colorectal cancer with F. nucleatum tended to exhibit the hypermutated phenotype. Mutations in immune‐related genes might be involved in the link between F. nucleatum and colorectal carcinogenesis. The somatic mutational landscape provides a new insight into carcinogenic mechanisms of F. nucleatum in colorectal cancer.Support or Funding InformationThis work was conducted with the support of a KL2/Catalyst Medical Research Investigator Training award from Harvard Catalyst/The Harvard Clinical and Translational Science Center (National Center for Research Resources and the National Center for Advancing Translational Sciences, NIH, Award KL2 TR001100; M.G.). This work was also supported by the Dana‐Farber Cancer Institute Leadership Council (M.G.), the 2014 Colon Cancer Alliance‐AACR Fellowship for Biomarker Research Grant Number 14‐40‐40‐GIAN (M.G.), the Perry S. Levy Endowed Fellowship (M.G.), the Project P Fund (C.S.F.), and the Friends of the Dana‐Farber Cancer Institute (S.O.), as well as NIH grants K07CA190673 (R.N.), K24 DK098311 (A.T.C.), R01 CA137178 (A.T.C.), P01 CA87969, UM1 CA186107,P01 CA55075, UM1 CA167552, R01 CA151993 (S.O.), R35 CA197735 (S.O.), R01 CA118553 (C.S.F.), R01 CA168141 (C.S.F.), and P50 CA127003 (M.G., L.A.G., C.S.F.).