Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer

Objective To evaluate the potential for diagnosing colorectal cancer (CRC) from faecal metagenomes. Design We performed metagenome-wide association studies on faecal samples from 74 patients with CRC and 54 controls from China, and validated the results in 16 patients and 24 controls from Denmark. We further validated the biomarkers in two published cohorts from France and Austria. Finally, we employed targeted quantitative PCR (qPCR) assays to evaluate diagnostic potential of selected biomarkers in an independent Chinese cohort of 47 patients and 109 controls. Results Besides confirming known associations of Fusobacterium nucleatum and Peptostreptococcus stomatis with CRC, we found significant associations with several species, including Parvimonas micra and Solobacterium moorei. We identified 20 microbial gene markers that differentiated CRC and control microbiomes, and validated 4 markers in the Danish cohort. In the French and Austrian cohorts, these four genes distinguished CRC metagenomes from controls with areas under the receiver-operating curve (AUC) of 0.72 and 0.77, respectively. qPCR measurements of two of these genes accurately classified patients with CRC in the independent Chinese cohort with AUC=0.84 and OR of 23. These genes were enriched in early-stage (I–II) patient microbiomes, highlighting the potential for using faecal metagenomic biomarkers for early diagnosis of CRC. Conclusions We present the first metagenomic profiling study of CRC faecal microbiomes to discover and validate microbial biomarkers in ethnically different cohorts, and to independently validate selected biomarkers using an affordable clinically relevant technology. Our study thus takes a step further towards affordable non-invasive early diagnostic biomarkers for CRC from faecal samples.

[1]  G Sundqvist,et al.  Taxonomy, ecology, and pathogenicity of the root canal flora. , 1994, Oral surgery, oral medicine, and oral pathology.

[2]  A. Moser,et al.  Intestinal neoplasia in the ApcMin mouse: independence from the microbial and natural killer (beige locus) status. , 1997, Cancer research.

[3]  R. Moletta,et al.  Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis , 1997, Applied and environmental microbiology.

[4]  J. Kaprio,et al.  Environmental and heritable factors in the causation of cancer--analyses of cohorts of twins from Sweden, Denmark, and Finland. , 2000, The New England journal of medicine.

[5]  B. Kremer,et al.  Peptostreptococcus micros coaggregates with Fusobacterium nucleatum and non-encapsulated Porphyromonas gingivalis. , 2000, FEMS microbiology letters.

[6]  Fuhui Long,et al.  Feature selection based on mutual information criteria of max-dependency, max-relevance, and min-redundancy , 2003, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[7]  D. Grenier,et al.  Binding of Actinobacillus actinomycetemcomitans lipopolysaccharides to Peptostreptococcus micros stimulates tumor necrosis factor alpha production by macrophage-like cells. , 2005, Oral microbiology and immunology.

[8]  B. Gulluoglu,et al.  A possible role of Bacteroides fragilis enterotoxin in the aetiology of colorectal cancer. , 2006, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[9]  B. Snel,et al.  Toward Automatic Reconstruction of a Highly Resolved Tree of Life , 2006, Science.

[10]  V. Baracos,et al.  Investigations of branched-chain amino acids and their metabolites in animal models of cancer. , 2006, The Journal of nutrition.

[11]  E. Holmes,et al.  Culture-independent analysis of the gut microbiota in colorectal cancer and polyposis. , 2008, Environmental microbiology.

[12]  W. Foulkes,et al.  Inherited susceptibility to common cancers. , 2008, The New England journal of medicine.

[13]  H. Herfarth,et al.  Modulation of the Intestinal Microbiota Alters Colitis-Associated Colorectal Cancer Susceptibility , 2009, PloS one.

[14]  C. Seder,et al.  From the Midwestern Vascular Surgical Society Clostridium septicum aortitis : Report of two cases and review of the literature , 2022 .

[15]  H. Tjalsma,et al.  Association between Streptococcus bovis and Colon Cancer , 2009, Journal of Clinical Microbiology.

[16]  Cynthia L Sears,et al.  A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses , 2009, Nature Medicine.

[17]  Gabriel Cuevas-Ramos,et al.  Escherichia coli induces DNA damage in vivo and triggers genomic instability in mammalian cells , 2010, Proceedings of the National Academy of Sciences.

[18]  John P A Ioannidis,et al.  Beyond genome-wide association studies: genetic heterogeneity and individual predisposition to cancer. , 2010, Trends in genetics : TIG.

[19]  C. Compton,et al.  The American Joint Committee on Cancer: the 7th Edition of the AJCC Cancer Staging Manual and the Future of TNM , 2010, Annals of Surgical Oncology.

[20]  C. Mathers,et al.  Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008 , 2010, International journal of cancer.

[21]  P. Bork,et al.  A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.

[22]  H. Holt,et al.  Solobacterium moorei Bacteremia: Identification, Antimicrobial Susceptibility, and Clinical Characteristics , 2011, Journal of Clinical Microbiology.

[23]  R. Knight,et al.  Supervised classification of human microbiota. , 2011, FEMS microbiology reviews.

[24]  F. Clavel-Chapelon,et al.  Blood lipid and lipoprotein concentrations and colorectal cancer risk in the European Prospective Investigation into Cancer and Nutrition , 2011, Gut.

[25]  J. Tap,et al.  Microbial Dysbiosis in Colorectal Cancer (CRC) Patients , 2011, PloS one.

[26]  Peter Williams,et al.  IMG: the integrated microbial genomes database and comparative analysis system , 2011, Nucleic Acids Res..

[27]  C. Xiang,et al.  Human Intestinal Lumen and Mucosa-Associated Microbiota in Patients with Colorectal Cancer , 2012, PloS one.

[28]  C. Quince,et al.  Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics , 2012, PloS one.

[29]  Susumu Goto,et al.  KEGG for integration and interpretation of large-scale molecular data sets , 2011, Nucleic Acids Res..

[30]  C. Datz,et al.  Adenoma-linked barrier defects and microbial products drive IL-23/IL-17-mediated tumour growth , 2012, Nature.

[31]  B. Birren,et al.  Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. , 2012, Genome research.

[32]  Mimi Y. Kim,et al.  A longitudinal study of serum insulin and glucose levels in relation to colorectal cancer risk among postmenopausal women , 2011, British Journal of Cancer.

[33]  Richard A. Moore,et al.  Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. , 2012, Genome research.

[34]  Qiang Feng,et al.  A metagenome-wide association study of gut microbiota in type 2 diabetes , 2012, Nature.

[35]  Belgin Dogan,et al.  Intestinal Inflammation Targets Cancer-Inducing Activity of the Microbiota , 2012, Science.

[36]  J. Goedert,et al.  Human gut microbiome and risk for colorectal cancer. , 2013, Journal of the National Cancer Institute.

[37]  Alexandros Stamatakis,et al.  Metagenomic species profiling using universal phylogenetic marker genes , 2013, Nature Methods.

[38]  M. R. Rubinstein,et al.  Fusobacterium nucleatum promotes colorectal carcinogenesis by modulating E-cadherin/β-catenin signaling via its FadA adhesin. , 2013, Cell host & microbe.

[39]  M. Gomes-Marcondes,et al.  Leucine modulates the effect of Walker factor, a proteolysis-inducing factor-like protein from Walker tumours, on gene expression and cellular activity in C2C12 myotubes. , 2013, Cytokine.

[40]  C. Mathers,et al.  GLOBOCAN 2012 v1.0, Cancer Incidence and Mortality Worldwide: IARC CancerBase No. 11 [Internet]. Lyon, France: International Agency for Research on Cancer , 2013 .

[41]  M. Meyerson,et al.  Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. , 2013, Cell host & microbe.

[42]  P. Schloss,et al.  The Human Gut Microbiome as a Screening Tool for Colorectal Cancer , 2014, Cancer Prevention Research.

[43]  Jens Roat Kultima,et al.  An integrated catalog of reference genes in the human gut microbiome , 2014, Nature Biotechnology.

[44]  P. Schloss,et al.  Dynamics and associations of microbial community types across the human body , 2014, Nature.

[45]  Jens Roat Kultima,et al.  Potential of fecal microbiota for early‐stage detection of colorectal cancer , 2014 .

[46]  Herbert Tilg,et al.  Gut microbiome development along the colorectal adenoma-carcinoma sequence , 2015 .