{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T22:36:58Z","timestamp":1787870218077,"version":"build-2784847793"},"reference-count":69,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2024,12,10]],"date-time":"2024-12-10T00:00:00Z","timestamp":1733788800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000289","name":"Cancer Research UK","doi-asserted-by":"publisher","award":["RG96894"],"award-info":[{"award-number":["RG96894"]}],"id":[{"id":"10.13039\/501100000289","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["WT203144"],"award-info":[{"award-number":["WT203144"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["RGPIN-2018- 05865"],"award-info":[{"award-number":["RGPIN-2018- 05865"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100015668","name":"Ontario Ministry of Research and Innovation","doi-asserted-by":"publisher","award":["ER17-13-102"],"award-info":[{"award-number":["ER17-13-102"]}],"id":[{"id":"10.13039\/501100015668","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001805","name":"Canada Foundation for Innovation","doi-asserted-by":"publisher","award":["37659"],"award-info":[{"award-number":["37659"]}],"id":[{"id":"10.13039\/501100001805","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>RNA-modifying enzymes have recently garnered considerable attention due to their relevance in cancer biology, identifying them as potential targets for novel therapeutic intervention. THUMPD3 was recently identified as an RNA methyltransferase catalysing N<jats:sup>2<\/jats:sup>-methylguanosine (m<jats:sup>2<\/jats:sup>G) within certain tRNAs. In this study, we unveil a novel role for THUMPD3 in lung cancer cells. Depletion of the enzyme from lung cancer cells significantly impairs their fitness, negatively impacting key cellular processes such as proliferation and migration. Notably, exogenous expression of THUMPD3 in normal lung fibroblasts stimulates their proliferation rate. Additionally, transcriptome-wide analyses reveal that depletion of THUMPD3 from lung cancer cells induces substantial changes in the expression of cell surface proteins, including those comprising the extracellular matrix (ECM). We further demonstrate that THUMPD3 maintains expression of an extra-domain B (EDB) containing pro-tumour isoform of <jats:italic>Fibronectin-1<\/jats:italic> mRNA, encoding FN1, an important ECM protein. Crucially, depletion of THUMPD3 promotes an alternative splicing event that removes the EDB-encoding exon from <jats:italic>Fibronectin-1<\/jats:italic>. This is consistent with THUMPD3 depletion reducing cellular proliferation and migration. Moreover, depletion of THUMPD3 selectively and preferentially affects the alternative splicing of ECM and cell adhesion molecule encoding transcripts, as well as those encoding neurodevelopmental proteins. Overall, these findings highlight THUMPD3 as an important player in regulating cancer-relevant alternative splicing and they provide a rationale for further investigations into THUMPD3 as a candidate target in anti-cancer therapy.<\/jats:p>","DOI":"10.1371\/journal.pone.0314655","type":"journal-article","created":{"date-parts":[[2024,12,10]],"date-time":"2024-12-10T18:28:54Z","timestamp":1733855334000},"page":"e0314655","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["THUMPD3 regulates alternative splicing of ECM transcripts in human lung cancer cells and promotes proliferation and migration"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0106-6998","authenticated-orcid":true,"given":"Marie","family":"Klimontova","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francisco","family":"Campos-Laborie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalie","family":"Webster","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Byron","family":"Andrews","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6435-1764","authenticated-orcid":true,"given":"Kimberley Chung","family":"Kim Chung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8933-970X","authenticated-orcid":true,"given":"Ryan","family":"Hili","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tony","family":"Kouzarides","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6312-4436","authenticated-orcid":true,"given":"Andrew J.","family":"Bannister","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,12,10]]},"reference":[{"key":"pone.0314655.ref001","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/S0140-6736(16)30958-8","article-title":"Lung cancer: current therapies and new targeted treatments","volume":"389","author":"FR Hirsch","year":"2017","journal-title":"Lancet"},{"issue":"13","key":"pone.0314655.ref002","doi-asserted-by":"crossref","first-page":"2785","DOI":"10.1002\/cncr.31551","article-title":"Annual Report to the Nation on the Status of Cancer, part I: National cancer statistics","volume":"124","author":"KA Cronin","year":"2018","journal-title":"Cancer"},{"issue":"1","key":"pone.0314655.ref003","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.lungcan.2014.07.020","article-title":"Metastatic sites and survival in lung cancer","volume":"86","author":"M Riihim\u00e4ki","year":"2014","journal-title":"Lung Cancer"},{"key":"pone.0314655.ref004","doi-asserted-by":"crossref","first-page":"267","DOI":"10.3389\/fonc.2018.00267","article-title":"Drug Resistance in Non-Small Cell Lung Cancer: A Potential for NOTCH Targeting?","volume":"8","author":"V Sosa Iglesias","year":"2018","journal-title":"Front Oncol"},{"issue":"4","key":"pone.0314655.ref005","doi-asserted-by":"crossref","first-page":"M111.014647","DOI":"10.1074\/mcp.M111.014647","article-title":"The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices","volume":"11","author":"A Naba","year":"2012","journal-title":"Mol Cell Proteomics"},{"key":"pone.0314655.ref006","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/j.biomaterials.2017.03.008","article-title":"Comprehensive proteomic characterization of stem cell-derived extracellular matrices","volume":"128","author":"H Ragelle","year":"2017","journal-title":"Biomaterials"},{"issue":"4","key":"pone.0314655.ref007","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1038\/s41568-020-00329-7","article-title":"The matrix in cancer","volume":"21","author":"TR Cox","year":"2021","journal-title":"Nat Rev Cancer"},{"key":"pone.0314655.ref008","doi-asserted-by":"crossref","first-page":"1766","DOI":"10.3389\/fonc.2020.01766","article-title":"The Role of the ECM in Lung Cancer Dormancy and Outgrowth","volume":"10","author":"AL Parker","year":"2020","journal-title":"Front Oncol"},{"issue":"1","key":"pone.0314655.ref009","doi-asserted-by":"crossref","first-page":"1734","DOI":"10.1038\/s41467-017-01430-6","article-title":"An extracellular matrix-related prognostic and predictive indicator for early-stage non-small cell lung cancer","volume":"8","author":"SB Lim","year":"2017","journal-title":"Nat Commun"},{"issue":"19","key":"pone.0314655.ref010","doi-asserted-by":"crossref","first-page":"7025","DOI":"10.3390\/ijms21197025","article-title":"Prognostic Significance of Stromal Periostin Expression in Non-Small Cell Lung Cancer","volume":"21","author":"K Ratajczak-Wielgomas","year":"2020","journal-title":"Int J Mol Sci"},{"issue":"28","key":"pone.0314655.ref011","doi-asserted-by":"crossref","first-page":"E5625","DOI":"10.1073\/pnas.1707054114","article-title":"Quantitative proteomics identify Tenascin-C as a promoter of lung cancer progression and contributor to a signature prognostic of patient survival","volume":"114","author":"V Gocheva","year":"2017","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pone.0314655.ref012","doi-asserted-by":"crossref","first-page":"1601","DOI":"10.1038\/s12276-022-00821-0","article-title":"Detection technologies for RNA modifications","volume":"54","author":"Y Zhang","year":"2022","journal-title":"Exp Mol Med"},{"issue":"Database issue","key":"pone.0314655.ref013","doi-asserted-by":"crossref","first-page":"D195","DOI":"10.1093\/nar\/gkq1028","article-title":"The RNA Modification Database, RNAMDB: 2011 update","volume":"39","author":"WA Cantara","year":"2011","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"pone.0314655.ref014","doi-asserted-by":"crossref","first-page":"D231","DOI":"10.1093\/nar\/gkab1083","article-title":"MODOMICS: a database of RNA modification pathways. 2021 update","volume":"50","author":"P Boccaletto","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"pone.0314655.ref015","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/j.canlet.2020.01.021","article-title":"Writers, readers and erasers of RNA modifications in cancer","volume":"474","author":"R Esteve-Puig","year":"2020","journal-title":"Cancer Lett"},{"issue":"6","key":"pone.0314655.ref016","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1038\/s41568-020-0253-2","article-title":"Role of RNA modifications in cancer","volume":"20","author":"I Barbieri","year":"2020","journal-title":"Nat Rev Cancer"},{"key":"pone.0314655.ref017","doi-asserted-by":"crossref","first-page":"e201302015","DOI":"10.5936\/csbj.201302015","article-title":"MD simulation studies to investigate iso-energetic conformational behaviour of modified nucleosides m(2)G and m(2) 2G present in tRNA","volume":"5","author":"RS Bavi","year":"2013","journal-title":"Comput Struct Biotechnol J"},{"issue":"7","key":"pone.0314655.ref018","doi-asserted-by":"crossref","first-page":"2295","DOI":"10.1093\/nar\/gkm104","article-title":"Ribosomal RNA guanine-(N2)-methyltransferases and their targets","volume":"35","author":"PV Sergiev","year":"2007","journal-title":"Nucleic Acids Research"},{"issue":"20","key":"pone.0314655.ref019","doi-asserted-by":"crossref","first-page":"11900","DOI":"10.1093\/nar\/gkab927","article-title":"THUMPD3-TRMT112 is a m2G methyltransferase working on a broad range of tRNA substrates","volume":"49","author":"WQ Yang","year":"2021","journal-title":"Nucleic Acids Res"},{"issue":"14","key":"pone.0314655.ref020","doi-asserted-by":"crossref","first-page":"7496","DOI":"10.1093\/nar\/gkad487","article-title":"N2-methylguanosine modifications on human tRNAs and snRNA U6 are important for cell proliferation, protein translation and pre-mRNA splicing","volume":"51","author":"C Wang","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"pone.0314655.ref021","first-page":"gkad1243","article-title":"THUMPD2 catalyzes the N2-methylation of U6 snRNA of the spliceosome catalytic center and regulates pre-mRNA splicing and retinal degeneration","author":"WQ Yang","year":"2024","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"pone.0314655.ref022","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1016\/j.cell.2011.02.013","article-title":"Hallmarks of cancer: the next generation","volume":"144","author":"D Hanahan","year":"2011","journal-title":"Cell"},{"key":"pone.0314655.ref023","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/1478-811X-8-31","article-title":"PARP-1 cleavage fragments: signatures of cell-death proteases in neurodegeneration","volume":"8","author":"GV Chaitanya","year":"2010","journal-title":"Cell Commun Signal"},{"issue":"1","key":"pone.0314655.ref024","doi-asserted-by":"crossref","first-page":"238","DOI":"10.3390\/cancers14010238","article-title":"The Functional Role of Extracellular Matrix Proteins in Cancer","volume":"14","author":"NV Popova","year":"2022","journal-title":"Cancers (Basel)"},{"issue":"7","key":"pone.0314655.ref025","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1080\/01902140591007236","article-title":"ED-B fibronectin in non-small cell lung carcinoma","volume":"31","author":"ZA Khan","year":"2005","journal-title":"Exp Lung Res"},{"issue":"1","key":"pone.0314655.ref026","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1007\/s00432-013-1538-6","article-title":"Abundant in vitro expression of the oncofetal ED-B-containing fibronectin translates into selective pharmacodelivery of (131)I-L19SIP in a prostate cancer patient","volume":"140","author":"R Locher","year":"2014","journal-title":"J Cancer Res Clin Oncol"},{"issue":"1","key":"pone.0314655.ref027","doi-asserted-by":"crossref","first-page":"27","DOI":"10.3390\/cells9010027","article-title":"Fibronectin in Cancer: Friend or Foe","volume":"9","author":"TC Lin","year":"2019","journal-title":"Cells"},{"issue":"1","key":"pone.0314655.ref028","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1002\/ajmg.b.10796","article-title":"Association study between the fibronectin gene and schizophrenia","volume":"116B","author":"K Nakata","year":"2003","journal-title":"Am J Med Genet B Neuropsychiatr Genet"},{"key":"pone.0314655.ref029","doi-asserted-by":"crossref","first-page":"512","DOI":"10.3389\/fimmu.2020.00512","article-title":"Versican-A Critical Extracellular Matrix Regulator of Immunity and Inflammation","volume":"11","author":"TN Wight","year":"2020","journal-title":"Front Immunol"},{"issue":"14","key":"pone.0314655.ref030","doi-asserted-by":"crossref","first-page":"R626","DOI":"10.1016\/j.cub.2013.06.019","article-title":"Three functions of cadherins in cell adhesion","volume":"23","author":"JL Ma\u00eetre","year":"2013","journal-title":"Curr Biol"},{"issue":"3","key":"pone.0314655.ref031","doi-asserted-by":"crossref","first-page":"202","DOI":"10.4161\/19336918.2014.994919","article-title":"Cadherins and catenins in dendrite and synapse morphogenesis","volume":"9","author":"E Seong","year":"2015","journal-title":"Cell Adh Migr"},{"issue":"13","key":"pone.0314655.ref032","doi-asserted-by":"crossref","first-page":"3466","DOI":"10.3390\/cancers15133466","article-title":"Regulation and Functions of \u03b16-Integrin (CD49f) in Cancer Biology","volume":"15","author":"R Khademi","year":"2023","journal-title":"Cancers (Basel)"},{"issue":"1","key":"pone.0314655.ref033","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1038\/labinvest.2015.133","article-title":"Afadin is localized at cell-cell contact sites in mesangial cells and regulates migratory polarity","volume":"96","author":"H Tsurumi","year":"2016","journal-title":"Lab Invest"},{"issue":"5","key":"pone.0314655.ref034","first-page":"1527","article-title":"LINC00265 Promotes IL-1\u03b2-Induced Chondrocyte Inflammation and Extracellular Matrix Degradation by Activating the MAPK\/NF-\u03baB Pathway","volume":"36","author":"P Zhao","year":"2022","journal-title":"J Biol Regul Homeost Agents"},{"issue":"8","key":"pone.0314655.ref035","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1080\/15384047.2019.1598766","article-title":"The LncRNA LINC00963 facilitates osteosarcoma proliferation and invasion by suppressing miR-204-3p\/FN1 axis","volume":"20","author":"Y Zhou","year":"2019","journal-title":"Cancer Biol Ther"},{"key":"pone.0314655.ref036","doi-asserted-by":"crossref","first-page":"36768","DOI":"10.1038\/srep36768","article-title":"Identification of novel MYO18A interaction partners required for myoblast adhesion and muscle integrity","volume":"6","author":"JM Cao","year":"2016","journal-title":"Sci Rep"},{"issue":"1","key":"pone.0314655.ref037","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1101\/gad.179283.111","article-title":"Phactr4 regulates directional migration of enteric neural crest through PP1, integrin signaling, and cofilin activity","volume":"26","author":"Y Zhang","year":"2012","journal-title":"Genes Dev"},{"issue":"8","key":"pone.0314655.ref038","doi-asserted-by":"crossref","first-page":"e12107","DOI":"10.14814\/phy2.12107","article-title":"Folliculin regulates cell-cell adhesion, AMPK, and mTORC1 in a cell-type-specific manner in lung-derived cells","volume":"2","author":"D Khabibullin","year":"2014","journal-title":"Physiol Rep"},{"issue":"8","key":"pone.0314655.ref039","doi-asserted-by":"crossref","first-page":"1214","DOI":"10.4161\/auto.24870","article-title":"I\u03baB kinase complex (IKK) triggers detachment-induced autophagy in mammary epithelial cells independently of the PI3K-AKT-MTORC1 pathway","volume":"9","author":"N Chen","year":"2013","journal-title":"Autophagy"},{"issue":"3","key":"pone.0314655.ref040","first-page":"245","article-title":"Ependymal Cells Require Anks1a for Their Proper Development","volume":"42","author":"S Park","year":"2019","journal-title":"Mol Cells"},{"issue":"5","key":"pone.0314655.ref041","doi-asserted-by":"crossref","first-page":"1044","DOI":"10.1111\/liv.14831","article-title":"Exome sequencing in patient-parent trios suggests new candidate genes for early-onset primary sclerosing cholangitis","volume":"41","author":"SM Haisma","year":"2021","journal-title":"Liver Int"},{"issue":"2","key":"pone.0314655.ref042","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1016\/j.ajhg.2016.07.004","article-title":"Biallelic Mutations in Citron Kinase Link Mitotic Cytokinesis to Human Primary Microcephaly","volume":"99","author":"H Li","year":"2016","journal-title":"Am J Hum Genet"},{"issue":"Pt 21","key":"pone.0314655.ref043","doi-asserted-by":"crossref","first-page":"5095","DOI":"10.1113\/jphysiol.2009.178236","article-title":"Neurobeachin, a protein implicated in membrane protein traffic and autism, is required for the formation and functioning of central synapses","volume":"587","author":"L Medrihan","year":"2009","journal-title":"J Physiol"},{"issue":"8","key":"pone.0314655.ref044","doi-asserted-by":"crossref","first-page":"943","DOI":"10.1242\/dmm.030148","article-title":"Therapeutic strategies for spinal muscular atrophy: SMN and beyond","volume":"10","author":"M Bowerman","year":"2017","journal-title":"Dis Model Mech"},{"issue":"5","key":"pone.0314655.ref045","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1016\/j.ajhg.2014.10.007","article-title":"Mutations in SNX14 cause a distinctive autosomal-recessive cerebellar ataxia and intellectual disability syndrome","volume":"95","author":"AC Thomas","year":"2014","journal-title":"Am J Hum Genet"},{"issue":"5","key":"pone.0314655.ref046","doi-asserted-by":"crossref","first-page":"898","DOI":"10.1002\/jimd.12149","article-title":"TANGO2 deficiency as a cause of neurodevelopmental delay with indirect effects on mitochondrial energy metabolism","volume":"42","author":"E Jennions","year":"2019","journal-title":"J Inherit Metab Dis"},{"issue":"5","key":"pone.0314655.ref047","doi-asserted-by":"crossref","first-page":"1158","DOI":"10.1016\/j.ajhg.2008.03.018","article-title":"A defect in the TUSC3 gene is associated with autosomal recessive mental retardation","volume":"82","author":"M Garshasbi","year":"2008","journal-title":"Am J Hum Genet"},{"issue":"9","key":"pone.0314655.ref048","doi-asserted-by":"crossref","first-page":"3739","DOI":"10.1038\/s41380-022-01577-9","article-title":"Deficiency of the ywhaz gene, involved in neurodevelopmental disorders, alters brain activity and behaviour in zebrafish","volume":"27","author":"E Ant\u00f3n-Galindo","year":"2022","journal-title":"Mol Psychiatry"},{"issue":"1","key":"pone.0314655.ref049","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/s12943-016-0579-2","article-title":"EMT and stemness: flexible processes tuned by alternative splicing in development and cancer progression","volume":"16","author":"D Pradella","year":"2017","journal-title":"Mol Cancer"},{"key":"pone.0314655.ref050","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.matbio.2022.05.003","article-title":"The alternative matrisome: Alternative splicing of ECM proteins in development, homeostasis and tumor progression","volume":"111","author":"Z Rekad","year":"2022","journal-title":"Matrix Biol"},{"issue":"8","key":"pone.0314655.ref051","doi-asserted-by":"crossref","first-page":"1826","DOI":"10.3390\/cells9081826","article-title":"Overexpression of Extradomain-B Fibronectin is Associated with Invasion of Breast Cancer Cells","volume":"9","author":"A Vaidya","year":"2020","journal-title":"Cells"},{"issue":"1","key":"pone.0314655.ref052","doi-asserted-by":"crossref","first-page":"5120","DOI":"10.1038\/s41467-020-18794-x","article-title":"Concepts of extracellular matrix remodelling in tumour progression and metastasis","volume":"11","author":"J Winkler","year":"2020","journal-title":"Nat Commun"},{"issue":"6","key":"pone.0314655.ref053","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1038\/ejhg.2014.165","article-title":"Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome","volume":"23","author":"A Kuechler","year":"2015","journal-title":"Eur J Hum Genet"},{"issue":"2","key":"pone.0314655.ref054","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1038\/nrm3742","article-title":"A day in the life of the spliceosome","volume":"15","author":"AG Matera","year":"2014","journal-title":"Nat Rev Mol Cell Biol"},{"key":"pone.0314655.ref055","doi-asserted-by":"crossref","first-page":"9849","DOI":"10.2147\/OTT.S227995","article-title":"Thumpd3-as1 is correlated with non-small cell lung cancer and regulates self-renewal through mir-543 and onecut2","volume":"12","author":"J Hu","year":"2019","journal-title":"OncoTargets Ther"},{"issue":"1","key":"pone.0314655.ref056","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1186\/s13045-020-00951-w","article-title":"Roles of METTL3 in cancer: mechanisms and therapeutic targeting","volume":"13","author":"C Zeng","year":"2020","journal-title":"J Hematol Oncol"},{"issue":"3","key":"pone.0314655.ref057","doi-asserted-by":"crossref","first-page":"498","DOI":"10.4161\/cc.8.3.7701","article-title":"Single-vector inducible lentiviral RNAi system for oncology target validation","volume":"8","author":"D Wiederschain","year":"2009","journal-title":"Cell Cycle"},{"issue":"35","key":"pone.0314655.ref058","doi-asserted-by":"crossref","first-page":"13057","DOI":"10.1073\/pnas.0802655105","article-title":"PTEN-deficient cancers depend on PIK3CB","volume":"105","author":"S Wee","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"4","key":"pone.0314655.ref059","doi-asserted-by":"crossref","first-page":"25","DOI":"10.15171\/ijb.1350","article-title":"Development of a Stable Cell Line, Overexpressing Human T-cell Immunoglobulin Mucin 1","volume":"13","author":"M Ebrahimi","year":"2015","journal-title":"Iran J Biotechnol"},{"issue":"7","key":"pone.0314655.ref060","doi-asserted-by":"crossref","first-page":"e0232565","DOI":"10.1371\/journal.pone.0232565","article-title":"An ImageJ plugin for the high throughput image analysis of in vitro scratch wound healing assays","volume":"15","author":"A Suarez-Arnedo","year":"2020","journal-title":"PLoS One"},{"issue":"11","key":"pone.0314655.ref061","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1002\/cbic.201700093","article-title":"The Profile and Dynamics of RNA Modifications in Animals","volume":"18","author":"P Van Delft","year":"2017","journal-title":"Chembiochem"},{"issue":"1","key":"pone.0314655.ref062","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"A Dobin","year":"2013","journal-title":"Bioinformatics"},{"issue":"12","key":"pone.0314655.ref063","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":"MI Love","year":"2014","journal-title":"Genome Biol"},{"key":"pone.0314655.ref064","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing","volume":"57","author":"Y. Benjamini","year":"1995","journal-title":"Journal of the Royal Statistical Society: Series B (Methodological)"},{"issue":"2","key":"pone.0314655.ref065","first-page":"275","article-title":"False discovery rates: a new deal","volume":"18","author":"M Stephens","year":"2017","journal-title":"Biostatistics"},{"issue":"12","key":"pone.0314655.ref066","doi-asserted-by":"crossref","first-page":"2084","DOI":"10.1093\/bioinformatics\/bty895","article-title":"Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences","volume":"35","author":"A Zhu","year":"2019","journal-title":"Bioinformatics"},{"issue":"5","key":"pone.0314655.ref067","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"G Yu","year":"2012","journal-title":"OMICS"},{"key":"pone.0314655.ref068","doi-asserted-by":"crossref","first-page":"e11752","DOI":"10.7554\/eLife.11752","article-title":"A new view of transcriptome complexity and regulation through the lens of local splicing variations","volume":"5","author":"J Vaquero-Garcia","year":"2016","journal-title":"Elife"},{"issue":"1","key":"pone.0314655.ref069","doi-asserted-by":"crossref","first-page":"1230","DOI":"10.1038\/s41467-023-36585-y","article-title":"RNA splicing analysis using heterogeneous and large RNA-seq datasets","volume":"14","author":"J Vaquero-Garcia","year":"2023","journal-title":"Nat Commun"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0314655","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,12,10]],"date-time":"2024-12-10T18:29:21Z","timestamp":1733855361000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0314655"}},"subtitle":[],"editor":[{"given":"Xianmin","family":"Zhu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,12,10]]},"references-count":69,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2024,12,10]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0314655","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,12,10]]}}}