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Tissue-layer-resolved proteome landscape of Crohn’s disease strictures highlights potential drivers of fibrosis progression
Johannes Alfredsson, Carina Sihlbom Wallem, Maja Östling, Hanna de la Croix, Elinor Bexe-Lindskog, Mary Jo Wick
Johannes Alfredsson, Carina Sihlbom Wallem, Maja Östling, Hanna de la Croix, Elinor Bexe-Lindskog, Mary Jo Wick
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Research Article Cell biology Gastroenterology

Tissue-layer-resolved proteome landscape of Crohn’s disease strictures highlights potential drivers of fibrosis progression

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Abstract

The chronic inflammation of Crohn’s disease frequently leads to fibrosis and muscular hypertrophy of the intestinal wall. This often culminates in strictures, a serious condition lacking directed therapy. Severe pathological changes occur in the submucosa and muscularis propria intestinal wall layers of strictures, yet stricture-associated proteome changes in these layers is unexplored. We perform unbiased proteomics on submucosa and muscularis propria microdissected from transmural sections of strictured and nonstrictured ileum. Proteome changes in strictured submucosa reflected a transition from homeostasis to tissue remodeling, inflammation, and smooth muscle changes. Top submucosal features included reduced vascular components and lipid metabolism proteins accompanied by increased proteins with immune-, ECM-, or stress-related functions, including CTHRC1, TNC, IL-16, MZB1, and TXNDC5. In parallel, predominant changes in strictured muscularis propria included increased ECM (POSTN) and immune (mast cell CPA3) proteins alongside decreased proteins with lipid metabolic, mitochondrial, or key muscle functions. Finally, trends of differentially expressed proteins along nonstrictured submucosa suggest progressive profibrotic tissue remodeling and muscle expansion as proximity to strictures increases. The comprehensive proteome map presented here offers tissue-layer-resolved insight into the stricture microenvironment and potential drivers of fibrotic disease, providing a valuable resource to fuel biomarker and therapeutic target research.

Authors

Johannes Alfredsson, Carina Sihlbom Wallem, Maja Östling, Hanna de la Croix, Elinor Bexe-Lindskog, Mary Jo Wick

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Figure 3

Changes in markers for SMCs, immune cells, and ECM components characterize the MP of STR tissue.

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Changes in markers for SMCs, immune cells, and ECM components characteri...
(A) PCA plot (PC1 vs. PC3) with axis PC score box-and-whisker plots (top and right) for batch-corrected MP TMT data with complete observations. The percentage in the axis titles indicates the proportion of variance explained by each PC. Samples are color coded by tissue type, and STR and NSTR samples from the same individual are connected by lines. Axis box-and-whisker plots show the median (center line), IQR (box), whiskers extending to the smallest and largest values within 1.5 times the IQR, and outliers plotted as individual points. (B) Plot visualizing Pearson’s correlation coefficients between markers and PC1/PC3. Markers are color coded by assigned categories indicated below the plot with differentially expressed (DE) proteins indicated by triangles. Marker clusters and representative proteins discussed in the text are highlighted with ellipses and labels, respectively. (C and D) DE analysis results for markers from STRvCTRL and STRvNSTR comparisons within the MP layer. DE was tested using linear mixed-effects models with model-based contrasts of estimated marginal means (EMM), with degrees of freedom estimated using the Kenward-Roger method; P values were adjusted for multiple testing using the Benjamini-Hochberg method to control the false discovery rate (FDR). The coloring and labeling of individual proteins in C and D is consistent with B. (C) Bar plots showing DE results for the cell markers labeled in B, arranged by cell type annotation and colors according to the bottom of B. (D) Volcano plots of core matrisome proteins.

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ISSN 2379-3708

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