Microgeographic Proteomic Networks of the Human Colonic Mucosa and Their Association With Inflammatory Bowel Disease.
OBJECTIVE
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.
Department of Molecular and Medical Pharmacology, University of California Los Angeles David Geffen School of Medicine, Los Angeles, California; Department of Pathology and Laboratory Medicine, University of California Los Angeles David Geffen School of Medicine, Los Angeles, California; Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California.
Xiaoxiao
X
Li
Department of Pathology and Laboratory Medicine, University of California Los Angeles David Geffen School of Medicine, Los Angeles, California.
James
J
LeBlanc
Department of Medicine, University of California Los Angeles David Geffen School of Medicine, Los Angeles, California.
David
D
Elashoff
Department of Pathology and Laboratory Medicine, University of California Los Angeles David Geffen School of Medicine, Los Angeles, California.
Ian
I
McHardy
Department of Molecular and Medical Pharmacology, University of California Los Angeles David Geffen School of Medicine, Los Angeles, California.
Maomeng
M
Tong
Department of Medicine, University of California Los Angeles David Geffen School of Medicine, Los Angeles, California.
Bennett
B
Roth
Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California.
Andrew
A
Ippoliti
Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California.
Gildardo
G
Barron
Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California.
Dermot
D
McGovern
Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri.
Keely
K
McDonald
Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri.
Rodney
R
Newberry
Department of Molecular and Medical Pharmacology, University of California Los Angeles David Geffen School of Medicine, Los Angeles, California.
Thomas
T
Graeber
Department of Human Genetics and Biostatistics, University of California Los Angeles David Geffen School of Medicine, Los Angeles, California.
Steve
S
Horvath
Department of Pathology and Laboratory Medicine, University of California Los Angeles David Geffen School of Medicine, Los Angeles, California.
Lee
L
Goodglick
Department of Molecular and Medical Pharmacology, University of California Los Angeles David Geffen School of Medicine, Los Angeles, California; Department of Pathology and Laboratory Medicine, University of California Los Angeles David Geffen School of Medicine, Los Angeles, California.
Jonathan
J
Braun
ANOVA, analysis of variance; CD, Crohn’s disease; Ecology; HBD, human β-defensin; HD5, human alpha defensin 5; HNP, human neutrophil peptide; HPLC, high-performance liquid chromatography; IBD, inflammatory bowel disease; IHC, immunohistochemistry; Inflammatory Bowel Disease; MALDI, matrix-assisted laser desorption/ionization; MFN, mucosal functional network; MLI, mucosal–luminal interface; MS/MS, tandem mass spectrometry; Metaproteomics; Mucosal; NLME, nonlinear mixed-effect model; Networks; PVCA, principal variance component analysis; TOF, time of flight; UC, ulcerative colitis; WGCNA, weighted correlation network analysis