Colorectal cancer-associated microbiota contributes to oncogenic epigenetic signatures

Iradj Sobhani; Emma Bergsten; Séverine Couffin; Aurélien Amiot; Biba Nebbad; Caroline Barau; Nicola de’Angelis; Sylvie Rabot; Florence Canoui-Poitrine; Denis Mestivier; Thierry Pédron; Khashayarsha Khazaie; Philippe J. Sansonetti

doi:10.1073/pnas.1912129116

Colorectal cancer-associated microbiota contributes to oncogenic epigenetic signatures

Iradj Sobhani, Emma Bergsten, Séverine Couffin, Aurélien Amiot, Biba Nebbad, Caroline Barau, Nicola de’Angelis, Sylvie Rabot, Florence Canoui-Poitrine, Denis Mestivier, Thierry Pédron, Khashayarsha Khazaie, Philippe J. Sansonetti

Allergy, Asthma and Clinical Immunology

Research output: Contribution to journal › Article › peer-review

35 Scopus citations

Abstract

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.

Original language	English (US)
Pages (from-to)	24285-24295
Number of pages	11
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	116
Issue number	48
DOIs	https://doi.org/10.1073/pnas.1912129116
State	Published - Nov 26 2019

Keywords

Biomarker
Cancer
Colon
Gene methylation
Microbiota

ASJC Scopus subject areas

General

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10.1073/pnas.1912129116

Cite this

Sobhani, I., Bergsten, E., Couffin, S., Amiot, A., Nebbad, B., Barau, C., de’Angelis, N., Rabot, S., Canoui-Poitrine, F., Mestivier, D., Pédron, T., Khazaie, K., & Sansonetti, P. J. (2019). Colorectal cancer-associated microbiota contributes to oncogenic epigenetic signatures. Proceedings of the National Academy of Sciences of the United States of America, 116(48), 24285-24295. https://doi.org/10.1073/pnas.1912129116

Sobhani, I, Bergsten, E, Couffin, S, Amiot, A, Nebbad, B, Barau, C, de’Angelis, N, Rabot, S, Canoui-Poitrine, F, Mestivier, D, Pédron, T, Khazaie, K & Sansonetti, PJ 2019, 'Colorectal cancer-associated microbiota contributes to oncogenic epigenetic signatures', Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 48, pp. 24285-24295. https://doi.org/10.1073/pnas.1912129116

@article{85c0e3c57577422ea536baf5d1ae4d25,

title = "Colorectal cancer-associated microbiota contributes to oncogenic epigenetic signatures",

abstract = "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{\textquoteright} 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.",

keywords = "Biomarker, Cancer, Colon, Gene methylation, Microbiota",

author = "Iradj Sobhani and Emma Bergsten and S{\'e}verine Couffin and Aur{\'e}lien Amiot and Biba Nebbad and Caroline Barau and Nicola de{\textquoteright}Angelis and Sylvie Rabot and Florence Canoui-Poitrine and Denis Mestivier and Thierry P{\'e}dron and Khashayarsha Khazaie and Sansonetti, {Philippe J.}",

note = "Funding Information: We thank all patients for their participation and physicians who invited them to participate; they are the following gastroenterologists: Drs. E. Zrihen, O. Pecriaux, J. Samama, M. Petit, Ph. Cattan, M. Cavicchi, Ch. Locher, G. Gattineau, M. Parieto, M. Mozer, A. Rosenbaum, Ph. Capelle, D. Levoir, F. Maille, Ph. Lebourgeois, Ph. De Land, E. Chanteloup, M. Simon, F. Mal, and F. Iglicki. We thank also Drs. J. Tran VanHieu and M. L. Auriault for pathology analyses in human and animals; Prof. S. Loric for biochemistry analysis in mice; Prof. T. Simon, A. Touati, J. Tap, V. Jarrousse, A. Bado, and J. P. Fouret for animal experiments and help managing; A. Wolfe for revising the English; S. Peyvandi for assisting with the animal and molecular experiments; E. Guery and L. Segaux for their statistical contributions; C. Vialette for data managing; A. Caidia (Bioinformatics Core Laboratory) for 16S rRNA analysis; and Catherine Philippe for SCFA analyses in mice. We thank all technicians and scientific consultants from Facult{\'e} de M{\'e}decine site Piti{\'e} Salp{\^e}tri{\`e}re (Assistance Publique-H{\^o}pitaux de Paris [APHP]), Unit{\'e} Mixte de Service (UMS) 29 Omic Platform p3s for technical help on EPIC methylation array study in mice, and all members of clinical monitoring group from the Unit{\'e} de Recherche Clinique de l{\textquoteright}Est Parisien (URC-Est) H{\^o}pital Saint-Antoine, APHP. We thank all the technicians from the Anaxem germ-free animal facility of the Micalis Institute for breeding the germ-free mice and carrying out FMT and gnotobiotic mice care and monitoring. We thank Dr. Abdulmohammad Pezeshki and Ms. Shatha Awaad for assistance with the analysis of inflammation in mouse colons and Katja Brunner for editing the manuscript. Funding was provided by French Institut of Cancer and Ministry of Health (grant PHRC 2011-VatnimadAOM09268) and French Society of Gastroenterology (grant for fecal test screening), Ligue Nationale Contre le Cancer for fecal test screening and the Institut National du CAncer (INCA, Canc{\'e}rop{\^o}le Ile de France, Grant for Microbiota and CRC), and National Institute of Health and Medical Research (INSERM) partially financed under the Institut Th{\'e}matique Multi-Organisme program (ITMO). This work was sponsored by APHP, INSERM. ClinicalTrials.gov registration number is NCT 01270360. Funding Information: ACKNOWLEDGMENTS. We thank all patients for their participation and physicians who invited them to participate; they are the following gastroenterologists: Drs. E. Zrihen, O. Pecriaux, J. Samama, M. Petit, Ph. Cattan, M. Cavicchi, Ch. Locher, G. Gattineau, M. Parieto, M. Mozer, A. Rosenbaum, Ph. Capelle, D. Levoir, F. Maille, Ph. Lebourgeois, Ph. De Land, E. Chanteloup, M. Simon, F. Mal, and F. Iglicki. We thank also Drs. J. Tran VanHieu and M. L. Auriault for pathology analyses in human and animals; Prof. S. Loric for biochemistry analysis in mice; Prof. T. Simon, A. Touati, J. Tap, V. Jarrousse, A. Bado, and J. P. Fouret for animal experiments and help managing; A. Wolfe for revising the English; S. Peyvandi for assisting with the animal and molecular experiments; E. Guery and L. Segaux for their statistical contributions; C. Vialette for data managing; A. Caidia (Bioinformatics Core Laboratory) for 16S rRNA analysis; and Catherine Philippe for SCFA analyses in mice. We thank all technicians and scientific consultants from Facult{\'e} de M{\'e}decine site Piti{\'e} Salp{\^e}tri{\`e}re (Assistance Publique-H{\^o}pitaux de Paris [APHP]), Unit{\'e} Mixte de Service (UMS) 29 Omic Platform p3s for technical help on EPIC methylation array study in mice, and all members of clinical monitoring group from the Unit{\'e} de Recherche Clinique de l{\textquoteright}Est Parisien (URC-Est) H{\^o}pital Saint-Antoine, APHP. We thank all the technicians from the Anaxem germ-free animal facility of the Micalis Institute for breeding the germ-free mice and carrying out FMT and gnotobiotic mice care and monitoring. We thank Dr. Abdulmohammad Pezeshki and Ms. Shatha Awaad for assistance with the analysis of inflammation in mouse colons and Katja Brunner for editing the manuscript. Funding was provided by French Institut of Cancer and Ministry of Health (grant PHRC 2011-VatnimadAOM09268) and French Society of Gastroenterology (grant for fecal test screening), Ligue Nationale Contre le Cancer for fecal test screening and the Institut National du CAncer (INCA, Canc{\'e}rop{\^o}le Ile de France, Grant for Microbiota and CRC), and National Institute of Health and Medical Research (INSERM) partially financed under the Institut Th{\'e}matique Multi-Organisme program (ITMO). This work was sponsored by APHP, INSERM. ClinicalTrials.gov registration number is NCT 01270360. Publisher Copyright: {\textcopyright} 2019 National Academy of Sciences. All rights reserved.",

year = "2019",

month = nov,

day = "26",

doi = "10.1073/pnas.1912129116",

language = "English (US)",

volume = "116",

pages = "24285--24295",

journal = "Proceedings of the National Academy of Sciences of the United States of America",

issn = "0027-8424",

publisher = "National Academy of Sciences",

number = "48",

}

TY - JOUR

T1 - Colorectal cancer-associated microbiota contributes to oncogenic epigenetic signatures

AU - Sobhani, Iradj

AU - Bergsten, Emma

AU - Couffin, Séverine

AU - Amiot, Aurélien

AU - Nebbad, Biba

AU - Barau, Caroline

AU - de’Angelis, Nicola

AU - Rabot, Sylvie

AU - Canoui-Poitrine, Florence

AU - Mestivier, Denis

AU - Pédron, Thierry

AU - Khazaie, Khashayarsha

AU - Sansonetti, Philippe J.

N1 - Funding Information: We thank all patients for their participation and physicians who invited them to participate; they are the following gastroenterologists: Drs. E. Zrihen, O. Pecriaux, J. Samama, M. Petit, Ph. Cattan, M. Cavicchi, Ch. Locher, G. Gattineau, M. Parieto, M. Mozer, A. Rosenbaum, Ph. Capelle, D. Levoir, F. Maille, Ph. Lebourgeois, Ph. De Land, E. Chanteloup, M. Simon, F. Mal, and F. Iglicki. We thank also Drs. J. Tran VanHieu and M. L. Auriault for pathology analyses in human and animals; Prof. S. Loric for biochemistry analysis in mice; Prof. T. Simon, A. Touati, J. Tap, V. Jarrousse, A. Bado, and J. P. Fouret for animal experiments and help managing; A. Wolfe for revising the English; S. Peyvandi for assisting with the animal and molecular experiments; E. Guery and L. Segaux for their statistical contributions; C. Vialette for data managing; A. Caidia (Bioinformatics Core Laboratory) for 16S rRNA analysis; and Catherine Philippe for SCFA analyses in mice. We thank all technicians and scientific consultants from Faculté de Médecine site Pitié Salpêtrière (Assistance Publique-Hôpitaux de Paris [APHP]), Unité Mixte de Service (UMS) 29 Omic Platform p3s for technical help on EPIC methylation array study in mice, and all members of clinical monitoring group from the Unité de Recherche Clinique de l’Est Parisien (URC-Est) Hôpital Saint-Antoine, APHP. We thank all the technicians from the Anaxem germ-free animal facility of the Micalis Institute for breeding the germ-free mice and carrying out FMT and gnotobiotic mice care and monitoring. We thank Dr. Abdulmohammad Pezeshki and Ms. Shatha Awaad for assistance with the analysis of inflammation in mouse colons and Katja Brunner for editing the manuscript. Funding was provided by French Institut of Cancer and Ministry of Health (grant PHRC 2011-VatnimadAOM09268) and French Society of Gastroenterology (grant for fecal test screening), Ligue Nationale Contre le Cancer for fecal test screening and the Institut National du CAncer (INCA, Cancéropôle Ile de France, Grant for Microbiota and CRC), and National Institute of Health and Medical Research (INSERM) partially financed under the Institut Thématique Multi-Organisme program (ITMO). This work was sponsored by APHP, INSERM. ClinicalTrials.gov registration number is NCT 01270360. Funding Information: ACKNOWLEDGMENTS. We thank all patients for their participation and physicians who invited them to participate; they are the following gastroenterologists: Drs. E. Zrihen, O. Pecriaux, J. Samama, M. Petit, Ph. Cattan, M. Cavicchi, Ch. Locher, G. Gattineau, M. Parieto, M. Mozer, A. Rosenbaum, Ph. Capelle, D. Levoir, F. Maille, Ph. Lebourgeois, Ph. De Land, E. Chanteloup, M. Simon, F. Mal, and F. Iglicki. We thank also Drs. J. Tran VanHieu and M. L. Auriault for pathology analyses in human and animals; Prof. S. Loric for biochemistry analysis in mice; Prof. T. Simon, A. Touati, J. Tap, V. Jarrousse, A. Bado, and J. P. Fouret for animal experiments and help managing; A. Wolfe for revising the English; S. Peyvandi for assisting with the animal and molecular experiments; E. Guery and L. Segaux for their statistical contributions; C. Vialette for data managing; A. Caidia (Bioinformatics Core Laboratory) for 16S rRNA analysis; and Catherine Philippe for SCFA analyses in mice. We thank all technicians and scientific consultants from Faculté de Médecine site Pitié Salpêtrière (Assistance Publique-Hôpitaux de Paris [APHP]), Unité Mixte de Service (UMS) 29 Omic Platform p3s for technical help on EPIC methylation array study in mice, and all members of clinical monitoring group from the Unité de Recherche Clinique de l’Est Parisien (URC-Est) Hôpital Saint-Antoine, APHP. We thank all the technicians from the Anaxem germ-free animal facility of the Micalis Institute for breeding the germ-free mice and carrying out FMT and gnotobiotic mice care and monitoring. We thank Dr. Abdulmohammad Pezeshki and Ms. Shatha Awaad for assistance with the analysis of inflammation in mouse colons and Katja Brunner for editing the manuscript. Funding was provided by French Institut of Cancer and Ministry of Health (grant PHRC 2011-VatnimadAOM09268) and French Society of Gastroenterology (grant for fecal test screening), Ligue Nationale Contre le Cancer for fecal test screening and the Institut National du CAncer (INCA, Cancéropôle Ile de France, Grant for Microbiota and CRC), and National Institute of Health and Medical Research (INSERM) partially financed under the Institut Thématique Multi-Organisme program (ITMO). This work was sponsored by APHP, INSERM. ClinicalTrials.gov registration number is NCT 01270360. Publisher Copyright: © 2019 National Academy of Sciences. All rights reserved.

PY - 2019/11/26

Y1 - 2019/11/26

N2 - 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.

AB - 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.

KW - Biomarker

KW - Cancer

KW - Colon

KW - Gene methylation

KW - Microbiota

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UR - http://www.scopus.com/inward/citedby.url?scp=85075517115&partnerID=8YFLogxK

U2 - 10.1073/pnas.1912129116

DO - 10.1073/pnas.1912129116

M3 - Article

C2 - 31712445

AN - SCOPUS:85075517115

SN - 0027-8424

VL - 116

SP - 24285

EP - 24295

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

IS - 48

ER -

Colorectal cancer-associated microbiota contributes to oncogenic epigenetic signatures

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