{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,15]],"date-time":"2025-10-15T22:42:24Z","timestamp":1760568144060,"version":"build-2065373602"},"reference-count":23,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,10,16]],"date-time":"2025-10-16T00:00:00Z","timestamp":1760572800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>X-linked deafness 2 (DFNX2) is a rare hereditary hearing loss characterized by progressive conductive and sensorineural hearing loss and a pathognomonic temporal bone deformity. DFNX2 is caused by mutations in the coding sequence or deletions upstream of <jats:italic>POU3F4<\/jats:italic>. Only 12 upstream deletions of <jats:italic>POU3F4<\/jats:italic> associated with DFNX2 have been reported, and the precise mechanisms underlying its pathogenesis remain fully elucidated.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Whole-genome Sequencing (WGS) and linkage analysis were performed to identify potential genetic etiologies. Gap-PCR and Sanger sequencing were used to validate candidate pathogenic variants and elucidate the breakpoints. Quantitative Polymerase Chain Reaction (qPCR) was conducted to evaluate the altered expression of both POU3F4 and its downstream target genes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Here, we identified a novel deletion approximately 795.5\u00a0kb in length, located about 140\u00a0kb upstream of POU3F4 in a large Chinese family. All patients are hemizygous for this deletion, and the breakpoints have been confirmed to be located at GRCh37(chrX): g.81840743_82636209. Additionally, qPCR analysis demonstrated a significant reduction in the expression levels of both POU3F4 and its downstream target genes in the affected patients, which had not been reported in previous studies. We expand the spectrum of pathogenic deletions upstream of POU3F4 associated with DFNX2.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>This study provides new molecular evidence that deletions upstream of <jats:italic>POU3F4<\/jats:italic> can disrupt the expression of POU3F4 and its downstream target genes in humans. Our results also enhance the understanding of the pathogenic mechanisms underlying DFNX2 associated with these deletions, as well as the downstream gene networks of POU3F4.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fgene.2025.1641999","type":"journal-article","created":{"date-parts":[[2025,10,15]],"date-time":"2025-10-15T22:10:14Z","timestamp":1760566214000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["A novel deletion upstream of POU3F4 in a Chinese family with X-linked deafness 2 and a literature review"],"prefix":"10.3389","volume":"16","author":[{"given":"Yanting","family":"Yang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shengwen","family":"Huang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yao","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dan","family":"Mu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ting","family":"Bai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaosha","family":"Jing","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lingling","family":"Xing","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongqian","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2025,10,16]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1367","DOI":"10.1387\/ijdb.072428ma","article-title":"Understanding the regulatory genome","volume":"53","author":"Alonso","year":"2009","journal-title":"Int. J. Dev. Biol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"1065","DOI":"10.1001\/archotol.126.9.1065","article-title":"Sensorineural hearing loss and Mondini dysplasia caused by a deletion at locus DFN3","volume":"126","author":"Arellano","year":"2000","journal-title":"Arch. Otolaryngol. Head. Neck Surg."},{"key":"B3","doi-asserted-by":"publisher","first-page":"1695","DOI":"10.3390\/biomedicines11061695","article-title":"Clinical and molecular aspects associated with defects in the transcription factor POU3F4: a review","volume":"11","author":"Bernardinelli","year":"2023","journal-title":"Biomedicines"},{"key":"B4","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1186\/s13023-022-02235-7","article-title":"Genetic findings of sanger and nanopore single-molecule sequencing in patients with X-linked hearing loss and incomplete partition type III","volume":"17","author":"Chen","year":"2022","journal-title":"Orphanet J. Rare Dis."},{"key":"B5","doi-asserted-by":"publisher","first-page":"3057","DOI":"10.1007\/s00405-013-2386-3","article-title":"Audiological and surgical evidence for the presence of a third window effect for the conductive hearing loss in DFNX2 deafness irrespective of types of mutations","volume":"270","author":"Choi","year":"2013","journal-title":"Eur. Arch. Otorhinolaryngol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1038\/s41587-021-01025-z","article-title":"Precise genomic deletions using paired prime editing","volume":"40","author":"Choi","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"B7","doi-asserted-by":"publisher","first-page":"327","DOI":"10.2174\/1389202919666171218163046","article-title":"X-linked sensorineural hearing loss: a literature review","volume":"19","author":"Corvino","year":"2018","journal-title":"Curr. Genomics"},{"key":"B8","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1126\/science.7839145","article-title":"Association between X-linked mixed deafness and mutations in the POU domain gene POU3F4","volume":"267","author":"de Kok","year":"1995","journal-title":"Science"},{"key":"B9","doi-asserted-by":"publisher","first-page":"1229","DOI":"10.1093\/hmg\/5.9.1229","article-title":"Identification of a hot spot for microdeletions in patients with X-linked deafness type 3 (DFN3) 900 kb proximal to the DFN3 gene POU3F4","volume":"5","author":"de Kok","year":"1996","journal-title":"Hum. Mol. Genet."},{"key":"B10","doi-asserted-by":"publisher","first-page":"24377","DOI":"10.1074\/jbc.M116.752329","article-title":"Different DNA end configurations dictate which NHEJ components are most important for joining efficiency","volume":"291","author":"Hhy","year":"2016","journal-title":"J. Biol. Chem."},{"key":"B11","doi-asserted-by":"publisher","first-page":"1235","DOI":"10.1016\/j.cell.2007.11.037","article-title":"A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders","volume":"131","author":"Ja","year":"2007","journal-title":"Cell"},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1042\/BSR20203740","article-title":"Study of complex structural variations of X-linked deafness-2 based on single-molecule sequencing","volume":"41","author":"Jiang","year":"2021","journal-title":"Biosci. Rep."},{"key":"B13","doi-asserted-by":"publisher","first-page":"e108216","DOI":"10.1371\/journal.pone.0108216","article-title":"Deficiency of transcription factor Brn4 disrupts cochlear gap junction plaques in a model of DFN3 non-syndromic deafness","volume":"9","author":"Kidokoro","year":"2014","journal-title":"PLOS One"},{"key":"B14","doi-asserted-by":"publisher","first-page":"2196","DOI":"10.1111\/pbi.14122","article-title":"Targeted large fragment deletion in plants using paired crRNAs with type I CRISPR system","volume":"21","author":"Li","year":"2023","journal-title":"Plant Biotechnol. J."},{"key":"B15","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative PCR and the 2(-delta delta C(T)) method","volume":"25","author":"Livak","year":"2001","journal-title":"Methods San. Diego Calif."},{"key":"B16","doi-asserted-by":"publisher","first-page":"2551","DOI":"10.1002\/j.1460-2075.1992.tb05320.x","article-title":"Brain 4: a novel mammalian POU domain transcription factor exhibiting restricted brain-specific expression","volume":"11","author":"Mathis","year":"1992","journal-title":"EMBO J."},{"key":"B17","first-page":"64","article-title":"X-linked mixed deafness with congenital fixation of the stapedial footplate and perilymphatic gusher","volume":"7","author":"Nance","year":"1971","journal-title":"Birth Defects Orig. Artic. Ser."},{"key":"B18","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1111\/j.1399-0004.2007.00913.x","article-title":"Sex-linked deafness","volume":"73","author":"Petersen","year":"2008","journal-title":"Clin. Genet."},{"key":"B19","doi-asserted-by":"publisher","first-page":"e109043","DOI":"10.1371\/journal.pone.0109043","article-title":"Pou3f4-mediated regulation of ephrin-b2 controls temporal bone development in the mouse","volume":"9","author":"Raft","year":"2014","journal-title":"PLOS One"},{"key":"B20","doi-asserted-by":"publisher","first-page":"1110","DOI":"10.1016\/j.molcel.2019.05.032","article-title":"Regulatory landscaping: how enhancer-promoter communication is sculpted in 3D","volume":"74","author":"Robson","year":"2019","journal-title":"Mol. Cell"},{"key":"B21","doi-asserted-by":"publisher","first-page":"2230","DOI":"10.1097\/00005537-200212000-00019","article-title":"A new classification for cochleovestibular malformations","volume":"112","author":"Sennaroglu","year":"2002","journal-title":"Laryngoscope"},{"key":"B22","doi-asserted-by":"publisher","first-page":"R85","DOI":"10.1186\/gb-2011-12-9-r85","article-title":"Reducing the exome search space for mendelian diseases using genetic linkage analysis of exome genotypes","volume":"12","author":"Smith","year":"2011","journal-title":"Genome Biol."},{"key":"B23","doi-asserted-by":"publisher","first-page":"e14174","DOI":"10.7717\/peerj.14174","article-title":"Gene expression profiles for in vitro human stem cell differentiation into osteoblasts and osteoclasts: a systematic review","volume":"10","author":"Zainal Ariffin","year":"2022","journal-title":"PeerJ"}],"container-title":["Frontiers in Genetics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2025.1641999\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,15]],"date-time":"2025-10-15T22:10:14Z","timestamp":1760566214000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2025.1641999\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,16]]},"references-count":23,"alternative-id":["10.3389\/fgene.2025.1641999"],"URL":"https:\/\/doi.org\/10.3389\/fgene.2025.1641999","relation":{},"ISSN":["1664-8021"],"issn-type":[{"value":"1664-8021","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,16]]},"article-number":"1641999"}}