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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 5

DE proteins associated with vascular structures and lipid metabolism show a marked decrease in the STR SM.

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DE proteins associated with vascular structures and lipid metabolism sho...
The analysis followed a funnel-like approach starting with all DE proteins (A) (Supplemental Figure 8B), and then identifying themes among DE proteins with the highest fold changes (B) and finally identifying top-ranked proteins (C and D). (A) Scatter plots visualizing weighted estimate (WE, log2 scale) in the STRvCTRL versus STRvNSTR comparisons. The 2 inner horizontal and vertical dotted lines mark the percentiles (“p”) for each respective comparison’s WE, used for thresholding and color coding. The diagonal line (y = x) represents equal WEs in both comparisons. (B) STRING protein-protein interaction network of the top 25% of DE proteins with the highest deviation (WE) from STRvCTRL or STRvNSTR. Edges represent interaction scores of ≥0.4. Functional themes/keywords have been annotated to summarize the primary characteristics of these highly DE proteins. Nodes are colored according to A. In A and B, the top 30 proteins are labeled; those discussed more specifically are in bold. Proteins outside the top 30 but discussed in the text are in italics. (C and D) In parallel, a ranking score was calculated and used to identify top-ranked proteins. (C) Ranking score dot plots for DE proteins in each comparison, with the top 30 ranked proteins in larger dot size and the top 5 labeled. Note that the scoring incorporates directionality; proteins with stronger negative changes receive more negative scores. (D) The top 30 negative DE proteins in ranked order, with the top 5 shown in larger font, providing details about DE comparisons (symbol size, shape) and relation to thresholds in A (color).

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