{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T16:45:05Z","timestamp":1769013905406,"version":"3.49.0"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,31]],"date-time":"2022-12-31T00:00:00Z","timestamp":1672444800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100007479","name":"Fondazione Cariparo","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007479","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009950","name":"Ministry of Education","doi-asserted-by":"publisher","award":["PRIN 2017 2017PPS2X4_003"],"award-info":[{"award-number":["PRIN 2017 2017PPS2X4_003"]}],"id":[{"id":"10.13039\/100009950","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fondazione AIRC per la Ricerca sul Cancro, Milan, Italy","award":["2017 20052"],"award-info":[{"award-number":["2017 20052"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Chromosomal translocations in cancer genomes, key players in many types of cancers, generate chimeric proteins that drive oncogenesis. Genomes with chromosomal rearrangements can also produce fusion circular RNAs (f-circRNAs) by backsplicing of chimeric transcripts, as first shown in leukemias with PML::RAR\u03b1 and KMT2A::MLLT3 translocations and later in solid cancers. F-circRNAs contribute to the oncogenic processes and reinforce the oncogenic activity of chimeric proteins. In leukemia with KMT2A::AFF1 (MLL::AF4) fusions, we previously reported specific alterations of circRNA expression, but nothing was known about f-circRNAs. Due to the presence of two chimeric sequences, fusion and backsplice junctions, the identification of f-circRNAs with available tools is challenging, possibly resulting in the underestimation of this RNA species, especially when the breakpoint is not known. We developed CircFusion, a new software tool to detect linear fusion transcripts and f-circRNAs from RNA-seq data, both in samples for which the breakpoints are known and when the information about the joined exons is missing. CircFusion can detect linear and circular chimeric transcripts deriving from the main and reciprocal translocations also in the presence of multiple breakpoints, which are common in malignant cells. Benchmarking tests on simulated and real datasets of cancer samples with previously experimentally determined f-circRNAs showed that CircFusion provides reliable predictions and outperforms available methods for f-circRNA detection. We discovered and validated novel f-circRNAs in acute leukemia harboring KMT2A::AFF1 rearrangements, leading the way to future functional studies aimed to unveil their role in this malignancy.<\/jats:p>","DOI":"10.1093\/bib\/bbac589","type":"journal-article","created":{"date-parts":[[2022,12,31]],"date-time":"2022-12-31T06:22:19Z","timestamp":1672467739000},"source":"Crossref","is-referenced-by-count":10,"title":["Discovery of fusion circular RNAs in leukemia with <i>KMT2A::AFF1<\/i> rearrangements by the new software CircFusion"],"prefix":"10.1093","volume":"24","author":[{"given":"Anna","family":"Dal Molin","sequence":"first","affiliation":[{"name":"University of Padova Department of Molecular Medicine, , Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caterina","family":"Tretti Parenzan","sequence":"additional","affiliation":[{"name":"IRP-Istituto di Ricerca Pediatrica Onco-Hematology, Stem Cell Transplant and Gene Therapy Laboratory, , Padova, 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Biology, , Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lueder H","family":"Meyer","sequence":"additional","affiliation":[{"name":"Ulm University Medical Center Department of Pediatrics and Adolescent Medicine, , Ulm, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Geertruij","family":"te Kronnie","sequence":"additional","affiliation":[{"name":"University of Padova Department of Molecular Medicine, , Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Silvia","family":"Bresolin","sequence":"additional","affiliation":[{"name":"Ulm University Medical Center Department of Pediatrics and Adolescent Medicine, , Ulm, Germany"},{"name":"University of Padova Department of Maternal and Child Health, , Padova, 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