{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,6]],"date-time":"2026-11-06T06:35:18Z","timestamp":1793946918741,"version":"4.8.0"},"reference-count":56,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2024,5,3]],"date-time":"2024-05-03T00:00:00Z","timestamp":1714694400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"name":"Portuguese Group for the Study of IBD"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background and Aims<\/jats:title>\n                  <jats:p>Stricturing [B2] and penetrating [B3] ileal Crohn\u2019s disease have been reported to present similar levels of histopathological transmural fibrosis. This study aimed to compare the fibrosis-related transcriptomic profiles of penetrating and stricturing ileal Crohn\u2019s disease.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>Using Nanostring technology and comparative bioinformatics, we analysed the expression of 787 fibrosis-related genes in 36 ileal surgical specimens, 12 B2 and 24 B3, the latter including 12 cases with associated stricture[s] [B3s] and 12 without [B3o]. Quality control of extracted RNA was performed according to Nanostring parameters and principal component analysis for the distribution analysis. For the selection of the differentially expressed genes, a p-adjusted &amp;lt;0.05 and fold change \u2264-1.5 or \u22651.5 were adopted. Quantitative polymerase chain reaction (qPCR) and immunohistochemistry analyses were used to validate selected differentially expressed genes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We included 34 patients with B2 and B3 phenotypes, balanced for age at diagnosis, age at surgery, gender, Crohn\u2019s disease localisation, perianal disease, and therapy. Inflammation and fibrosis histopathological scoring were similar in all cases. B2 and B3 groups showed a very good clustering regarding 30 significantly differentially expressed genes, all being remarkably upregulated in B3. More than half of these genes were involved in Crohn\u2019s disease fibrogenesis, and eight differentially expressed genes were so in other organs. The most significantly active biological processes and pathways in penetrating disease were response to TGF\u03b2 and matrix organisation and degradation, as validated by immunohistochemistry.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>Despite the histopathological similarities in fibrosis between stricturing and penetrating ileal Crohn\u2019s disease, their fibrosis-related transcriptomic profiles are distinct. Penetrating disease exhibits a distinctive transcriptomic landscape related to enhanced matrix remodelling.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/ecco-jcc\/jjae064","type":"journal-article","created":{"date-parts":[[2024,5,3]],"date-time":"2024-05-03T14:27:16Z","timestamp":1714746436000},"page":"1741-1752","source":"Crossref","is-referenced-by-count":2,"title":["Fibrosis-related Transcriptome Unveils a Distinctive Remodelling Matrix Pattern in Penetrating Ileal Crohn\u2019s Disease"],"prefix":"10.1093","volume":"18","author":[{"given":"Helena","family":"Tavares de Sousa","sequence":"first","affiliation":[{"name":"Gastroenterology Department, Algarve University Hospital Center [CHUA] , Portim\u00e3o ,","place":["Portugal"]},{"name":"ABC\u2014Algarve Biomedical Center, University of Algarve , Faro ,","place":["Portugal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marta","family":"Ferreira","sequence":"additional","affiliation":[{"name":"Computer Science Department, Faculty of Sciences, University of Porto , Porto ,","place":["Portugal"]},{"name":"Institute of Molecular Pathology and Immunology, University of Porto [IPATIMUP] , Porto ,","place":["Portugal"]},{"name":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade [i3S], University of Porto , Porto ,","place":["Portugal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3377-0530","authenticated-orcid":false,"given":"Irene","family":"Gullo","sequence":"additional","affiliation":[{"name":"Institute of Molecular Pathology and Immunology, University of Porto [IPATIMUP] , Porto ,","place":["Portugal"]},{"name":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade [i3S], University of Porto , Porto ,","place":["Portugal"]},{"name":"Department of Pathology, Centro Hospitalar de S\u00e3o Jo\u00e3o , Porto ,","place":["Portugal"]},{"name":"Department of Pathology, Faculty of Medicine of the University of Porto [FMUP] , Porto ,","place":["Portugal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana Mafalda","family":"Rocha","sequence":"additional","affiliation":[{"name":"Institute of Molecular Pathology and Immunology, University of Porto [IPATIMUP] , Porto ,","place":["Portugal"]},{"name":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade [i3S], University of Porto , Porto ,","place":["Portugal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Pedro","sequence":"additional","affiliation":[{"name":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade [i3S], University of Porto , Porto ,","place":["Portugal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dina","family":"Leit\u00e3o","sequence":"additional","affiliation":[{"name":"Department of Pathology, Faculty of Medicine of the University of Porto [FMUP] , Porto ,","place":["Portugal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carla","family":"Oliveira","sequence":"additional","affiliation":[{"name":"Institute of Molecular Pathology and Immunology, University of Porto [IPATIMUP] , Porto ,","place":["Portugal"]},{"name":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade [i3S], University of Porto , Porto ,","place":["Portugal"]},{"name":"Department of Pathology, Centro Hospitalar de S\u00e3o Jo\u00e3o , Porto ,","place":["Portugal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"F\u00e1tima","family":"Carneiro","sequence":"additional","affiliation":[{"name":"Institute of Molecular Pathology and Immunology, University of Porto [IPATIMUP] , Porto ,","place":["Portugal"]},{"name":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade [i3S], University of Porto , Porto ,","place":["Portugal"]},{"name":"Department of Pathology, Centro Hospitalar de S\u00e3o Jo\u00e3o , Porto ,","place":["Portugal"]},{"name":"Department of Pathology, Faculty of Medicine of the University of Porto [FMUP] , Porto ,","place":["Portugal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2634-9668","authenticated-orcid":false,"given":"Fernando","family":"Magro","sequence":"additional","affiliation":[{"name":"Unit of Pharmacology and Therapeutics, Department of Biomedicine, Faculty of Medicine of the University of Porto [FMUP] ,","place":["Portugal"]},{"name":"Department of Gastroenterology, S\u00e3o Jo\u00e3o University Hospital Center , Porto ,","place":["Portugal"]},{"name":"CINTESIS@RISE, Faculty of Medicine, University of Porto , Porto 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