biostudies-literatureChen YVetenskapsrådetThe Swedish Childhood Cancer FundKarolinska InstitutetSwedish Cancer SocietySwedish Research CouncilWellcome TrustCancerfondenRegion Stockholme2404510https://www.ebi.ac.uk/biostudies/studies/S-EPMC11892499biostudies-literatureUnknown11(41)Synovial Sarcomas (SS) are characterized by the presence of the SS18::SSX fusion gene, which protein product induce chromatin changes through remodeling of the BAF complex. To elucidate the genomic events that drive phenotypic diversity in SS, we performed RNA and targeted DNA sequencing on 91 tumors from 55 patients. Our results were verified by proteomic analysis, public gene expression cohorts and single-cell RNA sequencing. Transcriptome profiling identified three distinct SS subtypes resembling the known histological subtypes: SS subtype I and was characterized by hyperproliferation, evasion of immune detection and a poor prognosis. SS subtype II and was dominated by a vascular-stromal component and had a significantly better outcome. SS Subtype III was characterized by biphasic diffeAdvanced science (Weinheim, Baden-Wurttemberg, Germany)Molecular Profiling Defines Three Subtypes of Synovial Sarcoma.PMC118924992018-059732018–05973211122190029JCIAOB2019-0008;OB2017-0013;KF2016-0003Leo IRLarsson OZhao BEhnman MSiavelis ILin YLehtio JLiu XJohansson HLi XHesla ACHaglund CCao XHuang WKZhang YTsagkozis PZeng JChen YSu Yde Flon FHPapakonstantinou AfalseMolecular Profiling Defines Three Subtypes of Synovial Sarcoma.Synovial Sarcomas (SS) are characterized by the presence of the SS18::SSX fusion gene, which protein product induce chromatin changes through remodeling of the BAF complex. To elucidate the genomic events that drive phenotypic diversity in SS, we performed RNA and targeted DNA sequencing on 91 tumors from 55 patients. Our results were verified by proteomic analysis, public gene expression cohorts and single-cell RNA sequencing. Transcriptome profiling identified three distinct SS subtypes resembling the known histological subtypes: SS subtype I and was characterized by hyperproliferation, evasion of immune detection and a poor prognosis. SS subtype II and was dominated by a vascular-stromal component and had a significantly better outcome. SS Subtype III was characterized by biphasic diffe2024-01-01T00:00:00Z2024 Nov2025-04-22T20:51:46.883Z2025-04-06T03:20:36.264ZS-EPMC118924993925702910.1002/advs.202404510