Contributed by Philippe J. Sansonetti, September 27, 2019 (sent for review July 17, 2019; reviewed by Guido Grandi and Sven Pettersson)
This study advances our appreciation and understanding of the role of colon dysbiosis in the pathogenesis of colorectal cancer. In a human pilot study of 266 individuals, greater epigenomic (methylation) DNA alterations correlated with CRC and microbiota composition. Beyond this correlative evidence, when germ-free mice received fresh feces from CRC patients and their healthy controls, the former animals developed colon epithelial renewal, more precancerous lesions, and increased tissue and blood DNA methylation in intestinal tissues. Confirmation was obtained in a larger cohort of 1,000 patients, indicating that CRC-associated dysbiosis may promote colon carcinogenesis via epigenome dysregulation. Gene methylation can therefore serve as a marker for CRC and likely for predicting efficacy of prebiotic supplementation in average-risk individuals.
Sporadic colorectal cancer (CRC) is a result of complex interactions between the host and its environment. Environmental stressors act by causing host cell DNA alterations implicated in the onset of cancer. Here we investigate the stressor ability of CRC-associated gut dysbiosis as causal agent of host DNA alterations. The epigenetic nature of these alterations was investigated in humans and in mice. Germ-free mice receiving fecal samples from subjects with normal colonoscopy or from CRC patients were monitored for 7 or 14 wk. Aberrant crypt foci, luminal microbiota, and DNA alterations (colonic exome sequencing and methylation patterns) were monitored following human feces transfer. CRC-associated microbiota induced higher numbers of hypermethylated genes in murine colonic mucosa (vs. healthy controls’ microbiota recipients). Several gene promoters including SFRP1,2,3, PENK, NPY, ALX4, SEPT9, and WIF1 promoters were found hypermethylated in CRC but not in normal tissues or effluents from fecal donors. In a pilot study (n = 266), the blood methylation levels of 3 genes (Wif1, PENK, and NPY) were shown closely associated with CRC dysbiosis. In a validation study (n = 1,000), the cumulative methylation index (CMI) of these genes was significantly higher in CRCs than in controls. Further, CMI appeared as an independent risk factor for CRC diagnosis as shown by multivariate analysis that included fecal immunochemical blood test. Consequently, fecal bacterial species in individuals with higher CMI in blood were identified by whole metagenomic analysis. Thus, CRC-related dysbiosis induces methylation of host genes, and corresponding CMIs together with associated bacteria are potential biomarkers for CRC.
↵2K.K. and P.J.S. contributed equally to this work.
Author contributions: I.S. designed research; I.S., E.B., S.C., A.A., B.N., C.B., N.d.A., S.R., F.C.-P., T.P., and P.J.S. performed research; I.S., E.B., A.A., N.d.A., F.C.-P., D.M., K.K., and P.J.S. analyzed data; and I.S., T.P., K.K., and P.J.S. wrote the paper.
Reviewers: G.G., University of Trento; and S.P., Lee Kong Chian School of Medicine.
Competing interest statement: I.S. shares rights in 3 patents: EP B31120, EP2635705, and EP 2955232 A1 20151216 based on methods for diagnosing adenomas and/or colorectal cancer.
Data deposition: Data related to this paper are available from the European Nucleotide Archive (ENA) database (http://www.ebi.ac.uk/ena) under the accession nos. ERX3622297–ERX3622402, ERR3628499–ERR3628604, ERS3936180–ERS3936285, and PRJEB35144.
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1912129116/-/DCSupplemental.
Published under the PNAS license.
