{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T07:22:54Z","timestamp":1790752974838,"version":"4.1.0"},"reference-count":40,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2020,12,19]],"date-time":"2020-12-19T00:00:00Z","timestamp":1608336000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["307773"],"award-info":[{"award-number":["307773"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006306","name":"Sigrid Jus\u00e9liuksen S\u00e4\u00e4ti\u00f6","doi-asserted-by":"publisher","award":["-"],"award-info":[{"award-number":["-"]}],"id":[{"id":"10.13039\/501100006306","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010711","name":"Sy\u00f6p\u00e4s\u00e4\u00e4ti\u00f6","doi-asserted-by":"publisher","award":["-"],"award-info":[{"award-number":["-"]}],"id":[{"id":"10.13039\/501100010711","id-type":"DOI","asserted-by":"publisher"}]},{"name":"iCAN Digital Precision Cancer Medicine Flagship","award":["-"],"award-info":[{"award-number":["-"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cancers"],"abstract":"<jats:p>Uterine leiomyomas are benign smooth muscle tumors occurring in 70% of women of reproductive age. The majority of leiomyomas harbor one of three well-established genetic changes: a hotspot mutation in MED12, overexpression of HMGA2, or biallelic loss of FH. The majority of studies have classified leiomyomas by complex and costly methods, such as whole-genome sequencing, or by combining multiple traditional methods, such as immunohistochemistry and Sanger sequencing. The type of specimens and the amount of resources available often determine the choice. A more universal, cost-effective, and scalable method for classifying leiomyomas is needed. The aim of this study was to evaluate whether RNA sequencing can accurately classify formalin-fixed paraffin-embedded (FFPE) leiomyomas. We performed 3\u2032RNA sequencing with 44 leiomyoma and 5 myometrium FFPE samples, revealing that the samples clustered according to the mutation status of MED12, HMGA2, and FH. Furthermore, we confirmed each subtype in a publicly available fresh frozen dataset. These results indicate that a targeted 3\u2032RNA sequencing panel could serve as a cost-effective and robust tool for stratifying both fresh frozen and FFPE leiomyomas. This study also highlights 3\u2032RNA sequencing as a promising method for studying the abundance of unexploited tissue material that is routinely stored in hospital archives.<\/jats:p>","DOI":"10.3390\/cancers12123839","type":"journal-article","created":{"date-parts":[[2020,12,21]],"date-time":"2020-12-21T04:12:01Z","timestamp":1608523921000},"page":"3839","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["3\u2032RNA Sequencing Accurately Classifies Formalin-Fixed Paraffin-Embedded Uterine Leiomyomas"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0443-0625","authenticated-orcid":false,"given":"Miika","family":"Mehine","sequence":"first","affiliation":[{"name":"Applied Tumor Genomics Research Program, University of Helsinki, 00014 Helsinki, Finland"},{"name":"Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Khamaiseh","sequence":"additional","affiliation":[{"name":"Applied Tumor Genomics Research Program, University of Helsinki, 00014 Helsinki, Finland"},{"name":"Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland"},{"name":"iCAN Digital Precision Cancer Medicine Flagship, 00014 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Terhi","family":"Ahvenainen","sequence":"additional","affiliation":[{"name":"Applied Tumor Genomics Research Program, University of Helsinki, 00014 Helsinki, Finland"},{"name":"Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland"},{"name":"iCAN Digital Precision Cancer Medicine Flagship, 00014 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tuomas","family":"Heikkinen","sequence":"additional","affiliation":[{"name":"Applied Tumor Genomics Research Program, University of Helsinki, 00014 Helsinki, Finland"},{"name":"Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"\u00c4yr\u00e4v\u00e4inen","sequence":"additional","affiliation":[{"name":"Applied Tumor Genomics Research Program, University of Helsinki, 00014 Helsinki, Finland"},{"name":"Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland"},{"name":"Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1275-7356","authenticated-orcid":false,"given":"P\u00e4ivi","family":"Pakarinen","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P\u00e4ivi","family":"H\u00e4rkki","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0079-9807","authenticated-orcid":false,"given":"Annukka","family":"Pasanen","sequence":"additional","affiliation":[{"name":"Applied Tumor Genomics Research Program, University of Helsinki, 00014 Helsinki, Finland"},{"name":"Department of Pathology, University of Helsinki and HUSLAB, Helsinki University Hospital, 00029 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ralf","family":"B\u00fctzow","sequence":"additional","affiliation":[{"name":"Applied Tumor Genomics Research Program, University of Helsinki, 00014 Helsinki, Finland"},{"name":"Department of Pathology, University of Helsinki and HUSLAB, Helsinki University Hospital, 00029 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4615-3825","authenticated-orcid":false,"given":"Pia","family":"Vahteristo","sequence":"additional","affiliation":[{"name":"Applied Tumor Genomics Research Program, University of Helsinki, 00014 Helsinki, Finland"},{"name":"Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland"},{"name":"iCAN Digital Precision Cancer Medicine Flagship, 00014 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,12,19]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1111\/1471-0528.14640","article-title":"Epidemiology of uterine fibroids: A systematic review","volume":"124","author":"Stewart","year":"2017","journal-title":"BJOG Int. J. Obs. Gynaecol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1177\/1933719111432867","article-title":"Medical treatment of uterine leiomyoma","volume":"19","author":"Sabry","year":"2012","journal-title":"Reprod. Sci."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1646","DOI":"10.1056\/NEJMcp1411029","article-title":"Uterine fibroids","volume":"372","author":"Stewart","year":"2015","journal-title":"N. Engl. J. Med."},{"key":"ref_4","unstructured":"Kurman, R.J., Carcangiu, M.L., Herrington, S., and Young, R.H. (2014). WHO Classification of Tumours of Female Reproductive Organs, IARC Publications. [4th ed.]."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1016\/j.fertnstert.2014.06.050","article-title":"Genomics of uterine leiomyomas: Insights from high-throughput sequencing","volume":"102","author":"Mehine","year":"2014","journal-title":"Fertil. Steril."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1007\/s10689-011-9428-z","article-title":"Hereditary leiomyomatosis and renal cell cancer: Update on clinical and molecular characteristics","volume":"10","author":"Lehtonen","year":"2011","journal-title":"Fam. Cancer"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1315","DOI":"10.1073\/pnas.1518752113","article-title":"Integrated data analysis reveals uterine leiomyoma subtypes with distinct driver pathways and biomarkers","volume":"113","author":"Mehine","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"48769","DOI":"10.18632\/oncotarget.17953","article-title":"Genetic heterogeneity in leiomyomas of deep soft tissue","volume":"8","author":"Panagopoulos","year":"2017","journal-title":"Oncotarget"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1528","DOI":"10.1002\/ijc.27424","article-title":"MED12 mutations in uterine fibroids\u2013Their relationship to cytogenetic subgroups","volume":"131","author":"Markowski","year":"2012","journal-title":"Int. J. Cancer"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1016\/j.fertnstert.2020.05.036","article-title":"HMGA2-mediated tumorigenesis through angiogenesis in leiomyoma","volume":"114","author":"Li","year":"2020","journal-title":"Fertil. Steril."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1038\/s41598-017-01199-0","article-title":"Multiple clinical characteristics separate MED12-mutation-positive and-negative uterine leiomyomas","volume":"7","author":"Heinonen","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.cancergencyto.2004.08.025","article-title":"Updates on the cytogenetics and molecular genetics of bone and soft tissue tumors: Leiomyoma","volume":"158","author":"Sandberg","year":"2005","journal-title":"Cancer Genet. Cytogenet."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1186\/s12943-017-0672-1","article-title":"Characterization of MED12, HMGA2, and FH alterations reveals molecular variability in uterine smooth muscle tumors","volume":"16","author":"Frizzell","year":"2017","journal-title":"Mol. Cancer"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"4069","DOI":"10.1016\/j.celrep.2019.11.077","article-title":"Integrated epigenome, exome, and transcriptome analyses reveal molecular subtypes and homeotic transformation in uterine fibroids","volume":"29","author":"George","year":"2019","journal-title":"Cell Rep."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1002\/path.2932","article-title":"Aberrant succination of proteins in fumarate hydratase-deficient mice and HLRCC patients is a robust biomarker of mutation status","volume":"225","author":"Bardella","year":"2011","journal-title":"J. Pathol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1089\/bio.2012.0052","article-title":"Archived formalin-fixed paraffin-embedded (FFPE) blocks: A valuable underexploited resource for extraction of DNA, RNA, and protein","volume":"11","author":"Kokkat","year":"2013","journal-title":"Biopreserv. Biobank."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Von Ahlfen, S., Missel, A., Bendrat, K., and Schlumpberger, M. (2007). Determinants of RNA quality from FFPE samples. PLoS ONE, 2.","DOI":"10.1371\/journal.pone.0001261"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1016\/j.semcancer.2019.07.010","article-title":"RNA sequencing for research and diagnostics in clinical oncology","volume":"60","author":"Buzdin","year":"2020","journal-title":"Semin. Cancer Biol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1038\/s41576-019-0150-2","article-title":"RNA sequencing: The teenage years","volume":"20","author":"Stark","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"i","DOI":"10.1038\/nmeth.f.376","article-title":"QuantSeq 3\u2019 mRNA sequencing for RNA quantification","volume":"11","author":"Moll","year":"2014","journal-title":"Nat. Methods"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1315","DOI":"10.1111\/1755-0998.12529","article-title":"Evaluation of TagSeq, a reliable low-cost alternative for RNAseq","volume":"16","author":"Lohman","year":"2016","journal-title":"Mol. Ecol. Resour."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Turnbull, A.K., Selli, C., Martinez-Perez, C., Fernando, A., Renshaw, L., Keys, J., Figueroa, J.D., He, X., Tanioka, M., and Munro, A.F. (2020). Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches. BMC Bioinform., 21.","DOI":"10.1186\/s12859-020-3365-5"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"D886","DOI":"10.1093\/nar\/gky1016","article-title":"CADD: Predicting the deleteriousness of variants throughout the human genome","volume":"47","author":"Rentzsch","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/j.cell.2018.12.015","article-title":"Predicting splicing from primary sequence with deep learning","volume":"176","author":"Jaganathan","year":"2019","journal-title":"Cell"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Klemke, M., Muller, M.H., Wosniok, W., Markowski, D.N., Nimzyk, R., Helmke, B.M., and Bullerdiek, J. (2014). Correlated expression of HMGA2 and PLAG1 in thyroid tumors, uterine leiomyomas and experimental models. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0088126"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1300","DOI":"10.1038\/ejhg.2013.33","article-title":"MED12 exon 2 mutations in histopathological uterine leiomyoma variants","volume":"21","author":"Vahteristo","year":"2013","journal-title":"Eur. J. Hum. Genet."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1405","DOI":"10.1038\/bjc.2016.130","article-title":"MED12 mutations and FH inactivation are mutually exclusive in uterine leiomyomas","volume":"114","author":"Mehine","year":"2016","journal-title":"Br. J. Cancer"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"4650","DOI":"10.1002\/cncr.31754","article-title":"Loss of ATRX\/DAXX expression and alternative lengthening of telomeres in uterine leiomyomas","volume":"124","author":"Ahvenainen","year":"2018","journal-title":"Cancer"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2237","DOI":"10.1093\/humrep\/deaa187","article-title":"Systematic molecular and clinical analysis of uterine leiomyomas from fertile-aged women undergoing myomectomy","volume":"35","author":"Pasanen","year":"2020","journal-title":"Hum. Reprod."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: Ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2013A Python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Kallio, M.A., Tuimala, J.T., Hupponen, T., Klemel\u00c3\u00a4, P., Gentile, M., Scheinin, I., Koski, M., K\u00c3\u00a4ki, J., and Korpelainen, E.I. (2011). Chipster: User-friendly analysis software for microarray and other high-throughput data. BMC Genom., 12.","DOI":"10.1186\/1471-2164-12-507"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_36","first-page":"11.10.1","article-title":"From FastQ data to high confidence variant calls: The genome analysis toolkit best practices pipeline","volume":"43","author":"Carneiro","year":"2013","journal-title":"Curr. Protoc. Bioinform."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/nbt.2514","article-title":"Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples","volume":"31","author":"Cibulskis","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"2580","DOI":"10.1038\/s41596-018-0052-3","article-title":"Discovery of potential causative mutations in human coding and noncoding genome with the interactive software BasePlayer","volume":"13","author":"Katainen","year":"2018","journal-title":"Nat. Protoc."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Talevich, E., Shain, A.H., Botton, T., and Bastian, B.C. (2016). CNVkit: Genome-Wide copy number detection and visualization from targeted DNA sequencing. PLoS Comput. Biol., 12.","DOI":"10.1371\/journal.pcbi.1004873"}],"container-title":["Cancers"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2072-6694\/12\/12\/3839\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T10:47:22Z","timestamp":1760179642000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2072-6694\/12\/12\/3839"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,12,19]]},"references-count":40,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2020,12]]}},"alternative-id":["cancers12123839"],"URL":"https:\/\/doi.org\/10.3390\/cancers12123839","relation":{},"ISSN":["2072-6694"],"issn-type":[{"value":"2072-6694","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,12,19]]}}}