Fusion transcripts landscape in hepatocellular carcinoma and potential impact on the expression of fusion partners

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dc.contributor.authorIslakoglu, Yasemin Oztemur
dc.contributor.authorKorhan, Peyda
dc.contributor.authorBinokay, Leman
dc.contributor.authorKeles, Baris
dc.contributor.authorBagirsakci, Ezgi
dc.contributor.authorTascioglu, Meryem Uludag
dc.contributor.authorSamdanci, Emine
dc.date.accessioned2026-04-04T13:33:32Z
dc.date.available2026-04-04T13:33:32Z
dc.date.issued2025
dc.departmentİnönü Üniversitesi
dc.description.abstractFusion transcripts (FTs) are RNA molecules, also known as chimeric transcripts, formed through chromosomal rearrangements or transcriptional processes, contributing to tumorigenesis. This study systematically examined tumour-specific FTs in hepatocellular carcinoma (HCC) using high-throughput RNA sequencing data from independent datasets and The Cancer Genome Atlas (TCGA). Our meta cohort analysis included 328 HCC samples. Using STAR-Fusion, we identified 15 novel tumour-specific FTs, with SERPINA1-H19 as the most recurrent fusion event. Comparative expression analysis of fusion partner genes revealed significant downregulation in HCC tumours relative to normal adjacent liver tissues (NAT). We validated the expression levels of the key partner genes with 436 TCGA samples serving as an in silico validation cohort and in wet lab validation cohorts with 42 samples. ALB, APOA2, IGF2, MT2A, SERPINA1, and H19, which are key liver-associated genes, were frequently involved in tumour-specific fusion events suggesting either a loss of tumour suppressor property or gaining a novel function playing a role in hepatocarcinogenesis. Detailed characterization of SERPINA1-H19 identified 16 transcript variants with distinct structural modifications that may impact its functional output. Furthermore, low expression of SERPINA1 and H19 was associated with more aggressive HCC phenotypes. Overall, this study established a comprehensive repository of FTs for the first time, offering valuable insights into their role in HCC and their potential to serve as diagnostic and prognostic biomarkers for HCC.
dc.description.sponsorshipScientific and Technological Research Council of Turkey (TUEBITAK) [120C216]; COST Action-Translational Control in Cancer European Network (TRANSLACORE) [CA21154]
dc.description.sponsorshipThis work was supported by The Scientific and Technological Research Council of Turkey (TUEBITAK) [Project No. 120C216], and by the COST Action CA21154-Translational Control in Cancer European Network (TRANSLACORE).
dc.identifier.doi10.1080/15476286.2025.2529036
dc.identifier.endpage16
dc.identifier.issn1547-6286
dc.identifier.issn1555-8584
dc.identifier.issue1
dc.identifier.orcid0000-0003-4966-2980
dc.identifier.orcid0009-0006-6293-5778
dc.identifier.orcid0000-0001-6706-1375
dc.identifier.pmid40613496
dc.identifier.scopus2-s2.0-105010285964
dc.identifier.scopusqualityQ1
dc.identifier.startpage1
dc.identifier.urihttps://doi.org/10.1080/15476286.2025.2529036
dc.identifier.urihttps://hdl.handle.net/11616/109225
dc.identifier.volume22
dc.identifier.wosWOS:001530480900001
dc.identifier.wosqualityQ2
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.language.isoen
dc.publisherTaylor & Francis Inc
dc.relation.ispartofRna Biology
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.snmzKA_WOS_20250329
dc.subjectFusion transcript
dc.subjecthepatocellular carcinoma
dc.subjectRNA-seq
dc.subjectbiomarker
dc.subjectSERPINA1
dc.subjectH19
dc.titleFusion transcripts landscape in hepatocellular carcinoma and potential impact on the expression of fusion partners
dc.typeArticle

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