Colorectal Cancer Subtyping With Microbiome—A Game Changer for Personalized Medicine?

See “Oncomicrobial community profiling identifies clinicomolecular and prognostic subtypes of colorectal cancer,” by Mouradov D, Greenfield P, Li S, et al, on page 104. See “Oncomicrobial community profiling identifies clinicomolecular and prognostic subtypes of colorectal cancer,” by Mouradov D, Greenfield P, Li S, et al, on page 104. Colorectal cancer (CRC) was one of earliest solid tumors to be molecularly characterized, and the cascade of genetic events involved in the initiation and progression of CRC are well established.1Vogelstein B. Fearon E.R. Hamilton S.R. et al.Genetic alterations during colorectal-tumor development.N Engl J Med. 1988; 319: 525-532Crossref PubMed Scopus (5955) Google Scholar Advances in “omics” platforms encompassing genomic, epigenetic, transcriptomic, and immunologic data have led to an international effort to consolidate consensus molecular subtypes (CMS) of CRC in 2015,2Guinney J. Dienstmann R. Wang X. et al.The consensus molecular subtypes of colorectal cancer.Nat Med. 2015; 21: 1350-1356Crossref PubMed Scopus (2876) Google Scholar including micro-satellite instability (MSI)–immune (CMS1), canonical (CMS2), metabolic (CMS3), and mesenchymal (CMS4). Although CMS has proven to be a robust classification in capturing the tumor biology of CRC, conflicting results have been reported for CMS as predictor of therapy response.3Fontana E. Eason K. Cervantes A. et al.Context matters—consensus molecular subtypes of colorectal cancer as biomarkers for clinical trials.Ann Oncol. 2019; 30: 520-527Abstract Full Text Full Text PDF PubMed Scopus (65) Google Scholar This implies that CMS only partially reflects tumoral features that affect drug response, and alternative elements, such as tumor heterogeneity and micro-environment, are potential complicating factors for CRC prognostication. Research over the past decade has established the gut microbiome as an indispensable component of tumor micro-environment that co-evolves with CRC development.4Nakatsu G. Li X. Zhou H. et al.Gut mucosal microbiome across stages of colorectal carcinogenesis.Nat Commun. 2015; 6: 8727Crossref PubMed Scopus (421) Google Scholar CRC-associated dysbiosis is causative in tumorigenesis5Wong S.H. Zhao L. Zhang X. et al.Gavage of fecal samples from patients with colorectal cancer promotes intestinal carcinogenesis in germ-free and conventional Mice.Gastroenterology. 2017; 153: 1621-1633.e6Abstract Full Text Full Text PDF PubMed Scopus (362) Google Scholar and can predict patient survival.6Lin Y. Lau H.C. Liu Y. et al.Altered mycobiota signatures and enriched pathogenic Aspergillus rambellii are associated with colorectal cancer based on multicohort fecal metagenomic analyses.Gastroenterology. 2022; 163: 908-921Abstract Full Text Full Text PDF PubMed Scopus (21) Google Scholar,7Nakatsu G. Zhou H. Wu W.K.K. et al.Alterations in enteric virome are associated with colorectal cancer and survival outcomes.Gastroenterology. 2018; 155: 529-541.e5Abstract Full Text Full Text PDF PubMed Scopus (199) Google Scholar Emerging preclinical evidence has also suggested gut microbiota as potential modifiers of drug response,8Zhao R. Coker O.O. Wu J. et al.Aspirin reduces colorectal tumor development in mice and gut microbes reduce its bioavailability and chemopreventive effects.Gastroenterology. 2020; 159: 969-983.e4Abstract Full Text Full Text PDF PubMed Scopus (62) Google Scholar,9Yu T. Guo F. Yu Y. et al.Fusobacterium nucleatum promotes chemoresistance to colorectal cancer by modulating autophagy.Cell. 2017; 170: 548-563.e16Abstract Full Text Full Text PDF PubMed Scopus (1078) Google Scholar highlighting gut microbes as confounding factors that might limit the utility of molecular-based signatures such as CMS. In this issue of Gastroenterology, Mouradov et al10Mouradov D. Greenfield P. Li S. et al.Oncomicrobial community profiling identifies clinicomolecular and prognostic subtypes of colorectal cancer.Gastroenterology. 2023; 165: 104-120Abstract Full Text Full Text PDF Scopus (5) Google Scholar seek to establish a novel microbiota-based stratification strategy for CRC, its correlation with molecular features of CRC, and its prognostic implications. In this study, Mouradov et al enrolled 2 independent cohorts with a total of 716 CRC patients and performed bacterial 16S rRNA gene sequencing of tumors and normal colon mucosa in 2 independent cohorts. In parallel, molecular characterization of CRC tumors, such as MSI, DNA methylation (CpG island methylator phenotype [CIMP]), mutation signature, chromosome instability (CIN), and CMS, was conducted to integrate genomic, epi-genetic, and meta-genomic features in these patients. Previous studies that attempted to subgroup CRC patients either lack detailed clinico-molecular information4Nakatsu G. Li X. Zhou H. et al.Gut mucosal microbiome across stages of colorectal carcinogenesis.Nat Commun. 2015; 6: 8727Crossref PubMed Scopus (421) Google Scholar or have limited cohort size.11Hale V.L. Jeraldo P. Chen J. et al.Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers.Genome Med. 2018; 10: 78Crossref PubMed Scopus (74) Google Scholar As expected, Mouradov et al identified the enrichment of pathogenic microbes together with depletion of protective commensal bacteria. Taking the top 30 bacteria enriched in CRC and an equal number of depleted species, tumor microbiomes are clustered into major onco-microbial community subtypes (OCS). OCS1 is enriched in oral pathogens, most notably Fusobacterium nucleatum, a diagnostic biomarker for CRC.12Liang Q.Y. Chiu J. Chen Y.X. et al.Fecal bacteria act as novel biomarkers for noninvasive diagnosis of colorectal cancer.Clin Cancer Res. 2017; 23: 2061-2070Crossref PubMed Scopus (211) Google Scholar OCS3 is dominated by tumor-associated Proteobacteria species. In contrast, OCS2 maintains tumor-depleted protective bacteria from Firmicutes and Bacteroidetes species. Such segregation of CRC patients into OCS groups is neatly replicated in an independent validation cohort. However, because both cohorts are from the same country, and race and ethnicity are not reported, the broader implication of OCS in the context of ethnic and geographic disparities remains to be determined. For example, African-Americans have increased sulfidogenic pathogens B wadsworthia13Yazici C. Wolf P.G. Kim H. et al.Race-dependent association of sulfidogenic bacteria with colorectal cancer.Gut. 2017; 66: 1983-1994Crossref PubMed Scopus (119) Google Scholar and F nucleatum14Farhana L. Antaki F. Murshed F. et al.Gut microbiome profiling and colorectal cancer in African Americans and Caucasian Americans.World J Gastrointest Pathophysiol. 2018; 9: 47-58Crossref PubMed Google Scholar compared with white Americans, and in this study sulfate-producing bacteria are detected in OCS2, a signature associated with protective bacteria. Next, the inter-relationship between OCS and molecular characteristics of CRC patients was explored. The most distinguishing feature is the association of OCS1 with CMS1 and its related features, including right-sidedness, high-grade, micro-satellite instability–high (MSI-H), CIMP positivity, and BRAFV600E and FBXW7 mutations. This confirms the observations of enriched oral microbes, eg, F nucleatum, in MSI-H CRC.11Hale V.L. Jeraldo P. Chen J. et al.Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers.Genome Med. 2018; 10: 78Crossref PubMed Scopus (74) Google Scholar Although studies have reported that F nucleatum and other oral pathogens are causative in CRC, none have specifically studied their roles in MSI-H CRC. Future work should address their mechanistic inter-play and implications in CRC diagnosis and treatment. Meanwhile, OCS2 and OCS3 were left-sided, harboring CIN, non-CMS1, and enriched for DNA damage signature by reactive oxygen species (ROS). However, there are no distinct distribution patterns with respect to CMS2–4 or key driver mutations. Whether this translates to a lesser function of gut microbiome in CMS2–4 cancers is unclear, although ROS induction might exacerbate genomic instability, which is frequent in CMS2 CRC subtype.2Guinney J. Dienstmann R. Wang X. et al.The consensus molecular subtypes of colorectal cancer.Nat Med. 2015; 21: 1350-1356Crossref PubMed Scopus (2876) Google Scholar It would be interesting to sub-classify CRC cases based on combined CMS and OCS signatures, but the limited sample size with both microbial and clinico-molecular features in this study precludes deeper evaluation. Based on in silico prediction of gene content, OCS groups showed differential metabolic preference for carbohydrates, amino acids, and fatty acids that might account for the pathogenic effect of gut microbes, but such analyses are speculative at best and would require experimental validation. From the clinical perspective, an interesting observation by Mouradov et al is that the protective bacteria-enriched OCS2 had better survival than OCS1 and OCS3 for micro-satellite–stable tumors, inferring the role of protective bacteria in modulating drug response. Emerging preclinical evidence has indeed implied function of probiotic bacteria in suppressing CRC15Li Q. Hu W. Liu W.X. et al.Streptococcus thermophilus inhibits colorectal tumorigenesis through secreting beta-galactosidase.Gastroenterology. 2021; 160: 1179-1193.e14Abstract Full Text Full Text PDF PubMed Scopus (70) Google Scholar and potentiating the efficacy of chemotherapy.16Donohoe D.R. Holley D. Collins L.B. et al.A gnotobiotic mouse model demonstrates that dietary fiber protects against colorectal tumorigenesis in a microbiota- and butyrate-dependent manner.Cancer Discov. 2014; 4: 1387-1397Crossref PubMed Scopus (304) Google Scholar Besides, protective bacteria promote immune checkpoint blockade (ICB) therapy responsiveness in preclinical and clinical studies.17Bender M.J. McPherson A.C. Phelps C.M. et al.Dietary tryptophan metabolite released by intratumoral Lactobacillus reuteri facilitates immune checkpoint inhibitor treatment.Cell. 2023; 186: 1846-1862.e26Abstract Full Text Full Text PDF PubMed Scopus (9) Google Scholar Although ICB has revolutionized cancer management, its use in CRC is restricted to MSI-H CRC, and no biomarkers are available to predict ICB response in micro-satellite–stable CRC. Immune signature is not analyzed in this paper; future studies should elucidate the interplay between OCS subtypes and tumor immunology to reveal potential biomarkers for patient stratification or probiotic interventions for boosting ICB therapy. Conversely, pathogenic bacteria can be targeted to overcome microbial-associated drug resistance. Nevertheless, the selective targeting of gut microbiome remains challenging and could have discordant effects in a context-dependent manner. Fusobacterium nucleatum, for example, promotes chemo-resistance in CRC via activating autophagy9Yu T. Guo F. Yu Y. et al.Fusobacterium nucleatum promotes chemoresistance to colorectal cancer by modulating autophagy.Cell. 2017; 170: 548-563.e16Abstract Full Text Full Text PDF PubMed Scopus (1078) Google Scholar but paradoxically augments the efficacy of anti–PD-L1 response by inducing interferon-γ–expressing intra-tumoral CD8+ T cells.18Gao Y. Bi D. Xie R. et al.Fusobacterium nucleatum enhances the efficacy of PD-L1 blockade in colorectal cancer.Signal Transduct Target Ther. 2021; 6: 398Crossref PubMed Scopus (52) Google Scholar Targeting this bacterium in OCS1 should be tailored toward micro-satellite–stable CRC treated with combination chemotherapy (FOLFOX/FOLFIRI). In summary, Mouradov et al demonstrate that gut microbiome signatures can identify CRC subtypes that are associated with established clinical and molecular features and could be useful for patient prognostication. Multi-dimensional profiling of molecular, microbiome. and immunologic landscapes in large multi-center cohorts will confirm the additive value of OCS or other microbial-based biomarkers in improving the predictive power of molecular biomarkers, such as CMS, in personalized medicine. This will also generate biologically relevant hypotheses for further development of microbial-based therapies for selected groups of CRC patients. Finally, these classification efforts must be optimized to a manageable number of markers to enable cost-effective implementation in the clinic. Oncomicrobial Community Profiling Identifies Clinicomolecular and Prognostic Subtypes of Colorectal CancerGastroenterologyVol. 165Issue 1PreviewThis study describes a gut bacteria-based classification system for bowel cancer that delineates 3 distinct subtypes that differ in tumor features and patient outcomes. Full-Text PDF Molecular Profile of MSH6-Associated Colorectal Carcinomas Shows Distinct Features From Other Lynch Syndrome–Associated Colorectal CarcinomasGastroenterologyVol. 165Issue 1PreviewLynch syndrome (LS) is the most common hereditary colorectal cancer (CRC) syndrome and is caused by pathogenic constitutional variants in 1 of the mismatch repair (MMR) genes, including MLH1, MSH2 (EPCAM), MSH6, and PMS2. Although generally referred to as 1 entity, LS exhibits a highly heterogeneous phenotype, exemplified by major differences in cancer penetrance between MMR gene variant carriers.1 These differences imply that the quality of colonoscopy, optimal surveillance intervals, treatment, preventive strategies, and other aspects of care likely differ between LS subgroups. Full-Text PDF Open Access