{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T21:20:01Z","timestamp":1790630401504,"version":"4.1.0"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2022,10,7]],"date-time":"2022-10-07T00:00:00Z","timestamp":1665100800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100007028","name":"Leona M. and Harry B. Helmsley Charitable Trust","doi-asserted-by":"publisher","award":["G-2007-04028"],"award-info":[{"award-number":["G-2007-04028"]}],"id":[{"id":"10.13039\/100007028","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007028","name":"Leona M. and Harry B. Helmsley Charitable Trust","doi-asserted-by":"publisher","award":["G-2204-05197"],"award-info":[{"award-number":["G-2204-05197"]}],"id":[{"id":"10.13039\/100007028","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["CCF2007029"],"award-info":[{"award-number":["CCF2007029"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Crohn\u2019s disease is a lifelong disease characterized by chronic inflammation of the gastrointestinal tract. Defining the cellular and transcriptional composition of the mucosa at different stages of disease progression is needed for personalized therapy in Crohn\u2019s.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Ileal biopsies were obtained from (1) control subjects (n\u2005=\u20056), (2) treatment-na\u00efve patients (n\u2005=\u20057), and (3) established (n\u2005=\u200514) Crohn\u2019s patients along with remission (n\u2005=\u20053) and refractory (n\u2005=\u200511) treatment groups. The biopsies processed using 10x Genomics single cell 5' yielded 139\u2005906 cells. Gene expression count matrices of all samples were analyzed by reciprocal principal component integration, followed by clustering analysis. Manual annotations of the clusters were performed using canonical gene markers. Cell type proportions, differential expression analysis, and gene ontology enrichment were carried out for each cell type.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We identified 3 cellular compartments with 9 epithelial, 1 stromal, and 5 immune cell subtypes. We observed differences in the cellular composition between control, treatment-na\u00efve, and established groups, with the significant changes in the epithelial subtypes of the treatment-na\u00efve patients, including microfold, tuft, goblet, enterocyte,s and BEST4+ cells. Surprisingly, fewer changes in the composition of the immune compartment were observed; however, gene expression in the epithelial and immune compartment was different between Crohn\u2019s phenotypes, indicating changes in cellular activity.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Our study identified cellular and transcriptional signatures associated with treatment-na\u00efve Crohn\u2019s disease that collectively point to dysfunction of the intestinal barrier with an increase in inflammatory cellular activity. Our analysis also highlights the heterogeneity among patients within the same disease phenotype, shining a new light on personalized treatment responses and strategies.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/ibd\/izac201","type":"journal-article","created":{"date-parts":[[2022,10,7]],"date-time":"2022-10-07T13:13:55Z","timestamp":1665148435000},"page":"274-285","source":"Crossref","is-referenced-by-count":32,"title":["Assessing Cellular and Transcriptional Diversity of Ileal Mucosa Among Treatment-Na\u00efve and Treated Crohn\u2019s Disease"],"prefix":"10.1093","volume":"29","author":[{"given":"Sushma Chowdary","family":"Maddipatla","sequence":"first","affiliation":[{"name":"Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children\u2019s Healthcare of Atlanta, Emory University School of Medicine , Atlanta, GA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vasantha 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