Microgeographic Proteomic Networks of the Human Colonic Mucosa and Their Association With Inflammatory Bowel Disease

Xiaoxiao Li, James LeBlanc, David Elashoff, Ian Howard Mchardy, Maomeng Tong, Bennett Roth, Andrew Ippoliti, Gildardo Barron, Dermot McGovern, Keely McDonald, Rodney Newberry, Thomas Graeber, Steve Horvath, Lee Goodglick, Jonathan Braun

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Background & Aims Interactions between mucosal cell types, environmental stressors, and intestinal microbiota contribute to pathogenesis in inflammatory bowel disease (IBD). Here, we applied metaproteomics of the mucosal–luminal interface to study the disease-related biology of the human colonic mucosa. Methods We recruited a discovery cohort of 51 IBD and non-IBD subjects endoscopically sampled by mucosal lavage at 6 colonic regions, and a validation cohort of 38 no-IBD subjects. Metaproteome data sets were produced for each sample and analyzed for association with colonic site and disease state using a suite of bioinformatic approaches. Localization of select proteins was determined by immunoblot analysis and immunohistochemistry of human endoscopic biopsy samples. Results Co-occurrence analysis of the discovery cohort metaproteome showed that proteins at the mucosal surface clustered into modules with evidence of differential functional specialization (eg, iron regulation, microbial defense) and cellular origin (eg, epithelial or hemopoietic). These modules, validated in an independent cohort, were differentially associated spatially along the gastrointestinal tract, and 7 modules were associated selectively with non-IBD, ulcerative colitis, and/or Crohn's disease states. In addition, the detailed composition of certain modules was altered in disease vs healthy states. We confirmed the predicted spatial and disease-associated localization of 28 proteins representing 4 different disease-related modules by immunoblot and immunohistochemistry visualization, with evidence for their distribution as millimeter-scale microgeographic mosaic. Conclusions These findings suggest that the mucosal surface is a microgeographic mosaic of functional networks reflecting the local mucosal ecology, whose compositional differences in disease and healthy samples may provide a unique readout of physiologic and pathologic mucosal states.

Original languageEnglish (US)
Pages (from-to)567-583
Number of pages17
JournalCMGH
Volume2
Issue number5
DOIs
StatePublished - 2016

Fingerprint

Inflammatory Bowel Diseases
Proteomics
Mucous Membrane
Immunohistochemistry
Colonic Diseases
Proteins
Therapeutic Irrigation
Ecology
Computational Biology
Ulcerative Colitis
Crohn Disease
Gastrointestinal Tract
Cohort Studies
Iron
Biopsy

Keywords

  • Ecology
  • Inflammatory Bowel Disease
  • Metaproteomics
  • Mucosal
  • Networks

ASJC Scopus subject areas

  • Hepatology
  • Gastroenterology

Cite this

Microgeographic Proteomic Networks of the Human Colonic Mucosa and Their Association With Inflammatory Bowel Disease. / Li, Xiaoxiao; LeBlanc, James; Elashoff, David; Mchardy, Ian Howard; Tong, Maomeng; Roth, Bennett; Ippoliti, Andrew; Barron, Gildardo; McGovern, Dermot; McDonald, Keely; Newberry, Rodney; Graeber, Thomas; Horvath, Steve; Goodglick, Lee; Braun, Jonathan.

In: CMGH, Vol. 2, No. 5, 2016, p. 567-583.

Research output: Contribution to journalArticle

Li, X, LeBlanc, J, Elashoff, D, Mchardy, IH, Tong, M, Roth, B, Ippoliti, A, Barron, G, McGovern, D, McDonald, K, Newberry, R, Graeber, T, Horvath, S, Goodglick, L & Braun, J 2016, 'Microgeographic Proteomic Networks of the Human Colonic Mucosa and Their Association With Inflammatory Bowel Disease', CMGH, vol. 2, no. 5, pp. 567-583. https://doi.org/10.1016/j.jcmgh.2016.05.003
Li, Xiaoxiao ; LeBlanc, James ; Elashoff, David ; Mchardy, Ian Howard ; Tong, Maomeng ; Roth, Bennett ; Ippoliti, Andrew ; Barron, Gildardo ; McGovern, Dermot ; McDonald, Keely ; Newberry, Rodney ; Graeber, Thomas ; Horvath, Steve ; Goodglick, Lee ; Braun, Jonathan. / Microgeographic Proteomic Networks of the Human Colonic Mucosa and Their Association With Inflammatory Bowel Disease. In: CMGH. 2016 ; Vol. 2, No. 5. pp. 567-583.
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AU - Li, Xiaoxiao

AU - LeBlanc, James

AU - Elashoff, David

AU - Mchardy, Ian Howard

AU - Tong, Maomeng

AU - Roth, Bennett

AU - Ippoliti, Andrew

AU - Barron, Gildardo

AU - McGovern, Dermot

AU - McDonald, Keely

AU - Newberry, Rodney

AU - Graeber, Thomas

AU - Horvath, Steve

AU - Goodglick, Lee

AU - Braun, Jonathan

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N2 - Background & Aims Interactions between mucosal cell types, environmental stressors, and intestinal microbiota contribute to pathogenesis in inflammatory bowel disease (IBD). Here, we applied metaproteomics of the mucosal–luminal interface to study the disease-related biology of the human colonic mucosa. Methods We recruited a discovery cohort of 51 IBD and non-IBD subjects endoscopically sampled by mucosal lavage at 6 colonic regions, and a validation cohort of 38 no-IBD subjects. Metaproteome data sets were produced for each sample and analyzed for association with colonic site and disease state using a suite of bioinformatic approaches. Localization of select proteins was determined by immunoblot analysis and immunohistochemistry of human endoscopic biopsy samples. Results Co-occurrence analysis of the discovery cohort metaproteome showed that proteins at the mucosal surface clustered into modules with evidence of differential functional specialization (eg, iron regulation, microbial defense) and cellular origin (eg, epithelial or hemopoietic). These modules, validated in an independent cohort, were differentially associated spatially along the gastrointestinal tract, and 7 modules were associated selectively with non-IBD, ulcerative colitis, and/or Crohn's disease states. In addition, the detailed composition of certain modules was altered in disease vs healthy states. We confirmed the predicted spatial and disease-associated localization of 28 proteins representing 4 different disease-related modules by immunoblot and immunohistochemistry visualization, with evidence for their distribution as millimeter-scale microgeographic mosaic. Conclusions These findings suggest that the mucosal surface is a microgeographic mosaic of functional networks reflecting the local mucosal ecology, whose compositional differences in disease and healthy samples may provide a unique readout of physiologic and pathologic mucosal states.

AB - Background & Aims Interactions between mucosal cell types, environmental stressors, and intestinal microbiota contribute to pathogenesis in inflammatory bowel disease (IBD). Here, we applied metaproteomics of the mucosal–luminal interface to study the disease-related biology of the human colonic mucosa. Methods We recruited a discovery cohort of 51 IBD and non-IBD subjects endoscopically sampled by mucosal lavage at 6 colonic regions, and a validation cohort of 38 no-IBD subjects. Metaproteome data sets were produced for each sample and analyzed for association with colonic site and disease state using a suite of bioinformatic approaches. Localization of select proteins was determined by immunoblot analysis and immunohistochemistry of human endoscopic biopsy samples. Results Co-occurrence analysis of the discovery cohort metaproteome showed that proteins at the mucosal surface clustered into modules with evidence of differential functional specialization (eg, iron regulation, microbial defense) and cellular origin (eg, epithelial or hemopoietic). These modules, validated in an independent cohort, were differentially associated spatially along the gastrointestinal tract, and 7 modules were associated selectively with non-IBD, ulcerative colitis, and/or Crohn's disease states. In addition, the detailed composition of certain modules was altered in disease vs healthy states. We confirmed the predicted spatial and disease-associated localization of 28 proteins representing 4 different disease-related modules by immunoblot and immunohistochemistry visualization, with evidence for their distribution as millimeter-scale microgeographic mosaic. Conclusions These findings suggest that the mucosal surface is a microgeographic mosaic of functional networks reflecting the local mucosal ecology, whose compositional differences in disease and healthy samples may provide a unique readout of physiologic and pathologic mucosal states.

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