{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,25]],"date-time":"2026-10-25T01:23:54Z","timestamp":1792891434218,"version":"4.5.0"},"reference-count":51,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T00:00:00Z","timestamp":1766966400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020","award":["899417-CIRCULAR VISION"],"award-info":[{"award-number":["899417-CIRCULAR VISION"]}]},{"name":"Italian Ministry of Health with \u201cCurrent Research funds"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,2,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background and Aims<\/jats:title>\n                    <jats:p>Inflammatory bowel disease (IBD) is a gastrointestinal, auto-inflammatory disease with a chronic relapsing and remitting course, whose diagnosis is based on several examinations assessing intestinal inflammation and clinical assessment. Furthermore, only 40%-60% of patients respond to therapy, making identification of reliable markers of disease or predictors of disease course and therapy response of great interest to the medical community. The existence of extrachromosomal circular DNA (eccDNA) is well established, and has become a promising biomarker for different types of cancer. Here, we investigate eccDNA in patients affected by IBD.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Intestinal biopsies were collected from patients and from healthy controls. Circular DNA was enriched, sequenced, identified with Circle Finder, and annotated with bedtools. Patients were then stratified based on disease type and activity.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Intestinal tissue from IBD patients contained significantly higher levels of eccDNAs than tissue from healthy controls. eccDNA production also was significantly increased in patients with active ulcerative colitis compared to patients in remission. In Crohn\u2019s disease, eccDNAs were more abundant than in healthy controls, though the difference between active and inactive Crohn\u2019s disease was less defined. Furthermore, eccDNAs containing fragments from specific genes were consistently found in a large proportion of patients with IBD, while healthy controls presented with a more stochastic eccDNA pattern.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Here, we uncover an IBD-specific pattern of eccDNA production from intestinal biopsies. Furthermore, we have identified genic hotspots that characterize active disease. We propose that eccDNA containing specific gene fragments (eg, NRG1 and ZPMF2) could represent a promising new biomarker tool for patients with IBD.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/ecco-jcc\/jjaf237","type":"journal-article","created":{"date-parts":[[2025,12,26]],"date-time":"2025-12-26T12:36:16Z","timestamp":1766752576000},"source":"Crossref","is-referenced-by-count":3,"title":["Inflammatory bowel disease (IBD) is associated with increased intestinal extrachromosomal circular DNA: an emerging biomarker for IBD type and activity"],"prefix":"10.1093","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4396-1613","authenticated-orcid":false,"given":"Valentina","family":"Petito","sequence":"first","affiliation":[{"name":"CeMAD Translational Research Laboratories, Digestive Disease Center (CeMAD), Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario \u201cA. Gemelli\u201d IRCCS , Rome 00168,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniela","family":"Gerovska","sequence":"additional","affiliation":[{"name":"Computational Biology and Systems Biomedicine, Biogipuzkoa Health Research Institute , San Sebastian 20014,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7591-6473","authenticated-orcid":false,"given":"Antonia","family":"Piazzesi","sequence":"additional","affiliation":[{"name":"Management and Diagnostic Innovations & Clinical Pathways Research Area, Unit of Microbiome, Bambino Ges\u00f9 Children\u2019s Hospital, IRCCS , Rome 00146,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5347-7641","authenticated-orcid":false,"given":"Federica","family":"di Vincenzo","sequence":"additional","affiliation":[{"name":"CeMAD Translational Research Laboratories, Digestive Disease Center (CeMAD), Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario \u201cA. 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Gemelli\u201d IRCCS, Universit\u00e0 Cattolica del Sacro Cuore , Rome 00168,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Letizia","family":"Masi","sequence":"additional","affiliation":[{"name":"CeMAD Translational Research Laboratories, Digestive Disease Center (CeMAD), Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario \u201cA. Gemelli\u201d IRCCS , Rome 00168,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valeria","family":"Emoli","sequence":"additional","affiliation":[{"name":"CeMAD Translational Research Laboratories, Digestive Disease Center (CeMAD), Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario \u201cA. 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Gemelli\u201d IRCCS, Universit\u00e0 Cattolica del Sacro Cuore , Rome 00168,","place":["Italy"]},{"name":"Department of Life Science, Health, and Health Professions, Link Campus University , Rome 00165,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lorenza","family":"Putignani","sequence":"additional","affiliation":[{"name":"Department of Life Science, Health, and Health Professions, Link Campus University , Rome 00165,","place":["Italy"]},{"name":"Unit of Microbiomics and Unit of Research of Microbiome, Bambino Ges\u00f9 Children\u2019s Hospital, IRCCS , Rome 00146,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio","family":"Gasbarrini","sequence":"additional","affiliation":[{"name":"CeMAD Translational Research Laboratories, Digestive Disease Center (CeMAD), Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario \u201cA. 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