{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,11]],"date-time":"2026-05-11T14:50:23Z","timestamp":1778511023350,"version":"3.51.4"},"reference-count":50,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2021,7,22]],"date-time":"2021-07-22T00:00:00Z","timestamp":1626912000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Choroideremia (CHM) is a X-linked recessive chorioretinal dystrophy due to deficiency of the CHM gene product, i.e., Rab escort protein isoform 1 (REP1). To date, gene therapy for CHM has shown variable effectiveness, likely because the underlying pathogenic mechanisms as well as genotype-phenotype correlation are not yet fully known. Small nucleotide variants leading to premature termination codons (PTCs) are a major cause of CHM, but about 20% of patients has CHM gene deletions. To improve understanding of the disease mechanisms, we analyzed molecular features of seven deletions involving the CHM gene sequence. We mapped the deletion breakpoints by using polymerase chain reaction, sequencing and array comparative genomic hybridization; to identify rearrangement-promoting DNA sequences, we analyzed genomic architecture surrounding the breakpoint regions. Moreover, in some CHM patients with different mutation types, we measured transcript level of CHM and of CHML, encoding the REP2 isoform. Scattered along the whole CHM gene and in close proximity to the deletion breakpoints we found numerous repeat elements that generate a locus-specific rearrangement hot spot. Unexpectedly, patients with non-PTC variants had increased expression of the aberrant CHM mRNA; CHML expression was higher than normal in a patient lacking CHM and its putative regulatory sequences. This latest evidence suggests that mechanisms regulating CHM and CHML gene expression are worthy of further study, because their full knowledge could be also useful for developing effective therapies for this hitherto untreatable inherited retinal degeneration.<\/jats:p>","DOI":"10.3390\/genes12081111","type":"journal-article","created":{"date-parts":[[2021,7,22]],"date-time":"2021-07-22T22:35:31Z","timestamp":1626993331000},"page":"1111","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Molecular Characterization of Choroideremia-Associated Deletions Reveals an Unexpected Regulation of CHM Gene Transcription"],"prefix":"10.3390","volume":"12","author":[{"given":"Tiziana","family":"Fioretti","sequence":"first","affiliation":[{"name":"CEINGE-Biotecnologie Avanzate s.c. a r.l., Via G. Salvatore 486, 80145 Naples, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8179-5970","authenticated-orcid":false,"given":"Valentina","family":"Di Iorio","sequence":"additional","affiliation":[{"name":"Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Via S. Pansini 5, 80131 Naples, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3884-1043","authenticated-orcid":false,"given":"Barbara","family":"Lombardo","sequence":"additional","affiliation":[{"name":"CEINGE-Biotecnologie Avanzate s.c. a r.l., Via G. Salvatore 486, 80145 Naples, Italy"},{"name":"Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesca","family":"De Falco","sequence":"additional","affiliation":[{"name":"CEINGE-Biotecnologie Avanzate s.c. a r.l., Via G. Salvatore 486, 80145 Naples, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1858-2833","authenticated-orcid":false,"given":"Armando","family":"Cevenini","sequence":"additional","affiliation":[{"name":"CEINGE-Biotecnologie Avanzate s.c. a r.l., Via G. Salvatore 486, 80145 Naples, Italy"},{"name":"Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5833-8333","authenticated-orcid":false,"given":"Fabio","family":"Cattaneo","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesco","family":"Testa","sequence":"additional","affiliation":[{"name":"Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Via S. Pansini 5, 80131 Naples, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6894-9317","authenticated-orcid":false,"given":"Lucio","family":"Pastore","sequence":"additional","affiliation":[{"name":"CEINGE-Biotecnologie Avanzate s.c. a r.l., Via G. Salvatore 486, 80145 Naples, Italy"},{"name":"Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesca","family":"Simonelli","sequence":"additional","affiliation":[{"name":"Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Via S. Pansini 5, 80131 Naples, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4255-7312","authenticated-orcid":false,"given":"Gabriella","family":"Esposito","sequence":"additional","affiliation":[{"name":"CEINGE-Biotecnologie Avanzate s.c. a r.l., Via G. Salvatore 486, 80145 Naples, Italy"},{"name":"Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2021,7,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"57","DOI":"10.3109\/13816810.2011.620056","article-title":"Choroideremia, a review of general findings and pathogenesis","volume":"33","author":"Coussa","year":"2012","journal-title":"Ophthalmic Genet."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1016\/j.ophtha.2009.01.016","article-title":"Fundus autofluorescence in carriers of choroideremia and correlation with electrophysiologic and psychophysical data","volume":"116","author":"Preising","year":"2009","journal-title":"Ophthalmology"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.ajo.2019.06.002","article-title":"Spectrum of disease severity and phenotype in choroideremia carriers","volume":"207","author":"Jauregui","year":"2019","journal-title":"Am. J. Ophthalmol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1093\/hmg\/3.7.1047","article-title":"Mutation spectrum in the CHM gene of Danish and Swedish choroideremia patients","volume":"3","author":"Schwartz","year":"1994","journal-title":"Hum. Mol. Genet."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1016\/0092-8674(93)90639-8","article-title":"cDNA cloning of component A of Rab geranylgeranyl transferase and demonstration of its role as a Rab escort protein","volume":"73","author":"Andres","year":"1993","journal-title":"Cell"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"2111","DOI":"10.1016\/S0021-9258(17)42142-9","article-title":"REP-2, a Rab escort protein encoded by the choroideremia-like gene","volume":"269","author":"Cremers","year":"1994","journal-title":"J. Biol. Chem."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"652","DOI":"10.1042\/BST0330652","article-title":"Targeting of Rab GTPases to cellular membranes","volume":"33","author":"Ali","year":"2005","journal-title":"Biochem. Soc. Trans."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1882","DOI":"10.1091\/mbc.e02-10-0639","article-title":"Membrane targeting of Rab GTPases is influenced by the prenylation motif","volume":"14","author":"Gomes","year":"2003","journal-title":"Mol. Biol Cell"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Strunnikova, N.V., Barb, J., Sergeev, Y.V., Thiagarajasubramanian, A., Silvin, C., Munson, P.J., and Macdonald, I.M. (2009). Loss-of-function mutations in Rab escort protein 1 [REP-1] affect intracellular transport in fibroblasts and monocytes of choroideremia patients. PLoS ONE, 4.","DOI":"10.1371\/journal.pone.0008402"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"8158","DOI":"10.1167\/iovs.14-15751","article-title":"Choroideremia is a systemic disease with lymphocyte crystals and plasma lipid and RBC membrane abnormalities","volume":"56","author":"Zhang","year":"2015","journal-title":"Investig. Ophthalmol. Vis. Sci."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1460","DOI":"10.1002\/humu.21591","article-title":"Comprehensive mutation analysis [20 families] of the choroideremia gene reveals a missense variant that prevents the binding of REP1 with Rab geranylgeranyl transferase","volume":"32","author":"Esposito","year":"2011","journal-title":"Hum. Mutat."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2239","DOI":"10.1515\/cclm-2013-0209","article-title":"Prenatal molecular diagnosis of inherited neuromuscular diseases: Duchenne\/Becker muscular dystrophy, myotonic dystrophy type 1 and spinal muscular atrophy","volume":"51","author":"Esposito","year":"2013","journal-title":"Clin. Chem. Lab. Med."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1167\/tvst.9.3.17","article-title":"Perspectives on Gene Therapy: Choroideremia Represents a Challenging Model for the Treatment of Other Inherited Retinal Degenerations","volume":"9","author":"MacDonald","year":"2020","journal-title":"Transl Vis. Sci. Technol."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Abbouda, A., Avogaro, F., Moosajee, M., and Vingolo, E.M. (2021). Update on Gene Therapy Clinical Trials for Choroideremia and Potential Experimental Therapies. Medicina, 57.","DOI":"10.3390\/medicina57010064"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1399","DOI":"10.1097\/IAE.0000000000002151","article-title":"Association between genotype and disease progression in Italian Stargardt patients: A retrospective natural history study","volume":"39","author":"Orrico","year":"2019","journal-title":"Retina"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"e1490","DOI":"10.1002\/mgg3.1490","article-title":"A putative frameshift variant in the CHM gene is associated with an unexpected splicing alteration in a choroideremia patient","volume":"8","author":"Fioretti","year":"2020","journal-title":"Mol. Genet. Genom. Med."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1002\/(SICI)1098-1004(1997)9:2<110::AID-HUMU2>3.0.CO;2-D","article-title":"Molecular basis of choroideremia [CHM] mutations involving the Rab escort protein-1 [REP-1] gene","volume":"9","author":"Schwartz","year":"1997","journal-title":"Hum. Mutat"},{"key":"ref_18","first-page":"535","article-title":"Molecular genetic diagnostic techniques in choroideremia","volume":"20","author":"Furgoch","year":"2014","journal-title":"Mol. Vis."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1002\/humu.24174","article-title":"CHM mutation spectrum and disease: An update at the time of human therapeutic trials","volume":"42","author":"Zeitz","year":"2021","journal-title":"Hum. Mutat."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1002\/mgg3.208","article-title":"Analysis of a large choroideremia dataset does not suggest a preference for inclusion of certain genotypes in future trials of gene therapy","volume":"4","author":"Freund","year":"2016","journal-title":"Mol. Genet. Genom. Med."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/0888-7543(89)90312-1","article-title":"Physical fine mapping of the choroideremia locus using Xq21 deletions associated with complex syndromes","volume":"4","author":"Cremers","year":"1989","journal-title":"Genomics"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"2564","DOI":"10.1002\/ajmg.a.31995","article-title":"Molecular characterization of a novel X-linked syndrome involving developmental delay and deafness","volume":"143","author":"Hildebrand","year":"2007","journal-title":"Am. J. Med. Genet. A"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"4096","DOI":"10.1167\/iovs.08-2044","article-title":"Syndromic choroideremia, sublocalization of phenotypes associated with Martin-Probst deafness mental retardation syndrome","volume":"49","author":"Poloschek","year":"2008","journal-title":"Investig. Ophthalmol. Vis. Sci"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.spen.2010.02.008","article-title":"Identification of an X-linked deletion syndrome through comparative genomic hybridization microarray","volume":"17","author":"Rush","year":"2010","journal-title":"Semin. Pediatr. Neurol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1093\/hmg\/ddh073","article-title":"Implications of human genome architecture for rearrangement-based disorders, the genomic basis of disease","volume":"13","author":"Shaw","year":"2004","journal-title":"Hum. Mol. Genet."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1167\/iovs.18-25501","article-title":"CHM\/REP1 transcript expression and loss of visual function in patients affected by choroideremia","volume":"60","author":"Esposito","year":"2019","journal-title":"Investig. Ophthalmol. Vis. Sci."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"66","DOI":"10.3109\/13816810.2011.623261","article-title":"Choroideremia, effect of age on visual acuity in patients and female carriers","volume":"33","author":"Coussa","year":"2012","journal-title":"Ophthalmic Genet."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1294","DOI":"10.1002\/humu.21359","article-title":"Hereditary fructose intolerance, functional study of two novel ALDOB natural variants and characterization of a partial gene deletion","volume":"31","author":"Esposito","year":"2010","journal-title":"Hum. Mutat"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1057","DOI":"10.1038\/jhg.2017.84","article-title":"Precise mapping of 17 deletion breakpoints within the central hotspot deletion region [introns 50 and 51] of the DMD gene","volume":"62","author":"Esposito","year":"2017","journal-title":"J. Hum. Genet."},{"key":"ref_30","first-page":"547","article-title":"A 15-year molecular analysis of DMD\/BMD, genetic features in a large cohort","volume":"2","author":"Carsana","year":"2010","journal-title":"Front. Biosci."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"2609847","DOI":"10.1155\/2018\/2609847","article-title":"Formyl Peptide Receptor 1 Modulates Endothelial Cell Functions by NADPH Oxidase-Dependent VEGFR2 Transactivation","volume":"2018","author":"Cattaneo","year":"2018","journal-title":"Oxid. Med. Cell Longev."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.cca.2017.11.016","article-title":"Unraveling unusual X-chromosome patterns during fragile-X syndrome genetic testing","volume":"476","author":"Esposito","year":"2018","journal-title":"Clin. Chim. Acta"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/s13039-015-0120-0","article-title":"Phenotypic and genetic characterization of a family carrying two Xq21.1-21.3 interstitial deletions associated with syndromic hearing loss","volume":"8","author":"Iossa","year":"2015","journal-title":"Mol. Cytogenet."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1016\/j.gene.2013.10.074","article-title":"Identification of a deletion in the NDUFS4 gene using array-comparative genomic hybridization in a patient with suspected mitochondrial respiratory disease","volume":"535","author":"Lombardo","year":"2014","journal-title":"Gene"},{"key":"ref_35","first-page":"2134","article-title":"CHM gene molecular analysis and X-chromosome inactivation pattern determination in two families with choroideremia","volume":"149","author":"Zenteno","year":"2009","journal-title":"Am. J. Med. Genet. A"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1002\/humu.23212","article-title":"Single-base substitutions in the CHM promoter as a cause of choroideremia","volume":"38","author":"Radziwon","year":"2017","journal-title":"Hum. Mutat."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"229","DOI":"10.3109\/13816810.2012.752016","article-title":"Copy number variant analysis in CHM to detect duplications underlying choroideremia","volume":"34","author":"Chi","year":"2013","journal-title":"Ophthalmic Genet."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"6033","DOI":"10.1167\/iovs.16-20230","article-title":"The spectrum of CHM gene mutations in choroideremia and their relationship to clinical phenotype","volume":"57","author":"Simunovic","year":"2016","journal-title":"Investig. Ophthalmol. Vis. Sci."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.molcel.2010.03.002","article-title":"A functional link between the histone demethylase PHF8 and the transcription factor ZNF711 in X-linked mental retardation","volume":"38","author":"Christensen","year":"2010","journal-title":"Mol. Cell"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1038\/ng.367","article-title":"A systematic large-scale resequencing screen of X-chromosome coding exons in mental retardation","volume":"41","author":"Tarpey","year":"2009","journal-title":"Nat. Genet."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"2759","DOI":"10.1093\/humrep\/deh502","article-title":"Mutation analysis of two candidate genes for premature ovarian failure; DACH2 and POF1B","volume":"19","author":"Bione","year":"2004","journal-title":"Hum. Reprod."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Zhang, Y., Liu, Y., Li, Y., Duan, Y., Zhang, K., Wang, J., and Dai, Y. (2014). Exome sequencing identifies mutations in ABCD1 and DACH2 in two brothers with a distinct phenotype. BMC Med. Genet., 15.","DOI":"10.1186\/s12881-014-0105-6"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1887","DOI":"10.1167\/iovs.14-16302","article-title":"Large gene deletion and changes in corneal endothelial cells in a family with choroideremia","volume":"56","author":"Lee","year":"2015","journal-title":"Investig. Ophthalmol. Vis. Sci."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1315","DOI":"10.1167\/iovs.07-1169","article-title":"New type of mutations in three Spanish families with choroideremia","volume":"49","author":"Villaverde","year":"2008","journal-title":"Investig. Ophthalmol. Vis. Sci."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1865","DOI":"10.1093\/hmg\/ddz028","article-title":"Nonsense-mediated mRNA decay efficiency varies in choroideremia providing a target to boost small molecule therapeutics","volume":"28","author":"Sarkar","year":"2019","journal-title":"Hum. Mol. Genet."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1002\/humu.1380020108","article-title":"Identification of mutations in Danish choroideremia families","volume":"2","author":"Schwartz","year":"1993","journal-title":"Hum. Mutat"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1126","DOI":"10.1016\/j.ajhg.2013.10.028","article-title":"Disruption of autoregulatory feedback by a mutation in a remote, ultraconserved PAX6 enhancer causes aniridia","volume":"93","author":"Bhatia","year":"2013","journal-title":"Am. J. Hum. Genet."},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"K\u00f6hnke, M., Delon, C., Hastie, M.L., Nguyen, U.T., Wu, Y.W., Waldmann, H., Goody, R.S., Gorman, J.J., and Alexandrov, K. (2013). Rab GTPase prenylation hierarchy and its potential role in choroideremia disease. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0081758"},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Cehajic Kapetanovic, J., Barnard, A.R., and MacLaren, R.E. (2019). Molecular therapies for choroideremia. Genes, 10.","DOI":"10.3390\/genes10100738"},{"key":"ref_50","first-page":"7490","article-title":"Choroideremia: From genetic and clinical phenotyping to gene therapy and future treatments","volume":"10","author":"Mitsios","year":"2018","journal-title":"Adv. Ophthalmol."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/12\/8\/1111\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T06:33:18Z","timestamp":1760164398000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/12\/8\/1111"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,7,22]]},"references-count":50,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2021,8]]}},"alternative-id":["genes12081111"],"URL":"https:\/\/doi.org\/10.3390\/genes12081111","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,7,22]]}}}