{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"medRxiv"}],"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:18:30Z","timestamp":1792790310549,"version":"4.5.0"},"posted":{"date-parts":[[2026,9,15]]},"group-title":"Gastroenterology","reference-count":18,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T00:00:00Z","timestamp":1789430400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"name":"Wake Forest University School of Medicine Department of Pathology","id":[{"id":"https:\/\/ror.org\/0207ad724","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Background and Aims<\/jats:title>\n                  <jats:p>Fibrostenotic stricture is a severe complication of Crohn\u2019s disease (CD) that affect up to 50% of patients over their lifetime, causing irreversible narrowing of the intestinal lumen and bowel obstruction, but the molecular programs that distinguish stenotic from non-stenotic inflammation and the relative contributions of fibrosis and smooth-muscle remodeling remain incompletely characterized. We aimed to dissect bowel-wall compartment-specific and histology-defined remodeling programs in fibrostenotic CD.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>Matched full-thickness terminal ileal tissues from 4 patients with fibrostenotic CD were sampled from stenotic stricture (SS), non-stenotic inflamed bowel (NS), and non-inflamed bowel (NI). Histomorphology-guided NanoString GeoMx whole-transcriptome profiling was performed across mucosa, muscularis mucosae, submucosa, and muscularis propria. GeoMx data were processed by standard software provided by GeoMx platform. DESeq2 models included patient identity as a blocking factor, and the analysis was performed in 74 histologically valid regions of interest (ROIs) representing full spectrum of CD histopathologies. DEGs were defined as adjusted P &lt; .05 and |log2FC| &gt;= 1.0.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Out of 18,677 genes analyzed in each of the ROIs, direct SS-versus-NS comparison identified 0 significant DEGs in mucosa, 18 in muscularis mucosae, 43 in submucosa, and 0 in muscularis propria. NS-versus-NI submucosa showed 132 DEGs (131 increased, 1 decreased), dominated by humoral\/plasma-cell genes with a modest stromal-remodeling component. SS-versus-NI submucosa showed 144 DEGs (138 increased, 6 decreased) with coordinated contractile, extracellular-matrix\/remodeling and cell-matrix adhesion programs. Muscularized versus fibrotic SS submucosa showed 219 DEGs, with marked enrichment of contractile and remodeling genes in muscularized regions. Excluding 5 follicle-containing submucosal ROIs markedly altered the NS comparison but not the core SS fibromuscular program. Exploratory follicular-niche analyses showed that lymphoid follicle-rich (LFR) submucosa was lymphoid\/B-cell enriched relative to lymphoid follicle-null (LFN) areas; SS-LFR nevertheless acquired a stronger fibroblast\/ECM program relative to NS-LFR, while CCL19 was the only significant LFR-versus-LFN DEG within SS.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>Fibrostenotic CD is characterized by spatially concentrated submucosal fibromuscular remodeled inflammatory program. Non-stenotic submucosa is heterogeneous and may already show regional stromal remodeling, whereas established stenosis displays a broader and more robust ECM-contractile-adhesion phenotype with molecularly distinct fibrotic and muscularized niches.<\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2026.09.14.26363080","type":"posted-content","created":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T01:00:22Z","timestamp":1789520422000},"source":"Crossref","is-referenced-by-count":0,"title":["Layer-Resolved Spatial Transcriptomic Profiling Reveals Distinct Fibrotic and Muscularizing Submucosal Niches in Fibrostenotic Crohn\u2019s Disease"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8833-1098","authenticated-orcid":false,"given":"Xianyong","family":"Gui","sequence":"first","affiliation":[{"name":"Department of Pathology, Atrium Health Wake Forest Baptist Medical Center, Wake Forest University School of Medicine, Winston-Salem, NC"},{"name":"Comprehensive Cancer Center, Atrium Health Wake Forest Baptist Medical Center, Wake Forest University School of Medicine, Winston-Salem, NC"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9451-4886","authenticated-orcid":false,"given":"Guangxu","family":"Jin","sequence":"additional","affiliation":[{"name":"Comprehensive Cancer Center, Atrium Health Wake Forest Baptist Medical Center, Wake Forest University School of Medicine, Winston-Salem, NC"},{"name":"Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC"},{"name":"Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC"},{"name":"JINAI L.L.C., Winston-Salem, NC"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0530-2150","authenticated-orcid":false,"given":"David L.","family":"Caudell","sequence":"additional","affiliation":[{"name":"Department of Pathology, Atrium Health Wake Forest Baptist Medical Center, Wake Forest University School of Medicine, Winston-Salem, NC"},{"name":"Comprehensive Cancer Center, Atrium Health Wake Forest Baptist Medical Center, Wake Forest University School of Medicine, Winston-Salem, NC"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026091805051021000_2026.09.14.26363080v1.1","doi-asserted-by":"publisher","DOI":"10.1097\/MIB.0000000000000043"},{"key":"2026091805051021000_2026.09.14.26363080v1.2","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1159\/000528312","article-title":"Molecular basis of intestinal fibrosis in inflammatory bowel disease","volume":"7","year":"2022","journal-title":"Inflamm Intest Dis"},{"key":"2026091805051021000_2026.09.14.26363080v1.3","doi-asserted-by":"crossref","first-page":"4060","DOI":"10.3390\/jcm14124060","article-title":"Intestinal fibrosis in Crohn\u2019s disease: pathophysiology, diagnosis, and new therapeutic targets","volume":"14","year":"2025","journal-title":"J Clin Med"},{"key":"2026091805051021000_2026.09.14.26363080v1.4","doi-asserted-by":"crossref","first-page":"1331","DOI":"10.5858\/2001-125-1331-OMOTSB","article-title":"Obliterative muscularization of the small bowel submucosa in Crohn disease: a possible mechanism of small bowel obstruction","volume":"125","year":"2001","journal-title":"Arch Pathol Lab Med"},{"key":"2026091805051021000_2026.09.14.26363080v1.5","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/j.humpath.2018.03.004","article-title":"Luminally polarized mural and vascular remodeling in ileal strictures of Crohn\u2019s disease","volume":"79","year":"2018","journal-title":"Human 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Colitis"},{"key":"2026091805051021000_2026.09.14.26363080v1.12","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1186\/s12876-025-04312-0","article-title":"Elucidating the role of IgA plasma cells and PECAM1-CD38 interaction in intestinal fibrosis: a single-cell RNA sequencing analysis in Crohn\u2019s disease","volume":"25","year":"2025","journal-title":"BMJ Gastroenterol"},{"key":"2026091805051021000_2026.09.14.26363080v1.13","doi-asserted-by":"crossref","first-page":"1502","DOI":"10.1093\/ibd\/izaf021","article-title":"Novel transcriptomic signatures in fibrostenotic Crohn\u2019s disease: dysregulated pathways, promising biomarkers, and putative therapeutic targets","volume":"31","year":"2025","journal-title":"Inflamm Bowel Dis"},{"key":"2026091805051021000_2026.09.14.26363080v1.14","doi-asserted-by":"crossref","first-page":"101701","DOI":"10.1016\/j.jcmgh.2025.101701","article-title":"Elucidating a myofibroblast-dominated fibrotic niche in Crohn\u2019s disease-associated fibrostenosis through high-resolution spatial transcriptomics","volume":"20","year":"2026","journal-title":"Cell Mol Gastroenterol Hepatol"},{"key":"2026091805051021000_2026.09.14.26363080v1.15","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1093\/ibd\/izae292","article-title":"New insights into the pathogenesis of intestinal fibrosis in inflammatory bowel diseases: focusing on intestinal smooth muscle cells","volume":"31","year":"2025","journal-title":"Inflamm Bowel Dis"},{"key":"2026091805051021000_2026.09.14.26363080v1.16","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.202461"},{"key":"2026091805051021000_2026.09.14.26363080v1.17","doi-asserted-by":"publisher","DOI":"10.1172\/JCI173835"},{"key":"2026091805051021000_2026.09.14.26363080v1.18","doi-asserted-by":"crossref","first-page":"e179472","DOI":"10.1172\/JCI179472","article-title":"TWIST1+FAP+ fibroblasts in the pathogenesis of intestinal fibrosis in Crohn\u2019s disease","volume":"134","year":"2024","journal-title":"J Clin Invest"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.09.14.26363080","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T12:05:18Z","timestamp":1789733118000},"score":1,"resource":{"primary":{"URL":"http:\/\/medrxiv.org\/lookup\/doi\/10.64898\/2026.09.14.26363080"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,15]]},"references-count":18,"URL":"https:\/\/doi.org\/10.64898\/2026.09.14.26363080","relation":{},"subject":[],"published":{"date-parts":[[2026,9,15]]},"subtype":"preprint"}}