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Bitarafan F, Seyedena SY, Mahmoudi M, Garshasbi M. Identification of novel variants in Iranian consanguineous pedigrees with nonsyndromic hearing loss by next-generation sequencing. J Clin Lab Anal 2020; 34:e23544. [PMID: 32864763 PMCID: PMC7755797 DOI: 10.1002/jcla.23544] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 07/24/2020] [Accepted: 07/29/2020] [Indexed: 12/17/2022] Open
Abstract
Background The extremely high genetic heterogeneity of hearing loss due to diverse group of genes encoding proteins required for development, function, and maintenance of the complex auditory system makes the genetic diagnosis of this disease challenging. Up to now, 121 different genes have been identified for nonsyndromic hearing loss (NSHL), of which 76 genes are responsible for the most common forms of NSHL, autosomal recessive nonsyndromic hearing loss (ARNSHL). Methods After excluding mutations in the most common ARNSHL gene, GJB2, by Sanger sequencing, genetic screening for a panel of genes responsible for hereditary hearing impairment performed in 9 individuals with ARNSHL from unrelated Iranian consanguineous pedigrees. Results One compound heterozygote and eight homozygote variants, of which five are novel, were identified: CDH23:p.(Glu1970Lys), and p.(Ala1072Asp), GIPC3:p.(Asn82Ser), and (p.Thr41Lys), MYO7A:p.[Phe456Phe]; p.[Met708Val], and p.(Gly163Arg), TECTA:p.(Leu17Leufs*19), OTOF:c.1392+1G>A, and TRIOBP:p.(Arg1068*). Sanger sequencing confirmed the segregation of the variants with the disease in each family. Conclusion Finding more variants and expanding the spectrum of hearing impairment mutations can increase the diagnostic value of molecular testing in the screening of patients and can improve counseling to minimize the risk of having affected children for at risk couples.
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Affiliation(s)
- Fatemeh Bitarafan
- Department of Biology, Faculty of Biological Sciences, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Seyed Yousef Seyedena
- Department of Biology, Faculty of Biological Sciences, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Mahdi Mahmoudi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Teheran, Iran
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Campos C, Fragoso S, Luís R, Pinto F, Brito C, Esteves S, Pataco M, Santos S, Machado P, Vicente JB, Costa Rosa J, Cavaco BM, Moura C, Pojo M. High-Throughput Sequencing Identifies 3 Novel Susceptibility Genes for Hereditary Melanoma. Genes (Basel) 2020; 11:genes11040403. [PMID: 32276436 PMCID: PMC7230562 DOI: 10.3390/genes11040403] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 12/19/2022] Open
Abstract
Cutaneous melanoma is one of the most aggressive human cancers due to its high invasiveness. Germline mutations in high-risk melanoma susceptibility genes have been associated with development hereditary melanoma; however, most genetic culprits remain elusive. To unravel novel susceptibility genes for hereditary melanoma, we performed whole exome sequencing (WES) on eight patients with multiple primary melanomas, high number of nevi, and negative for high and intermediate-risk germline mutations. Thirteen new potentially pathogenic variants were identified after bioinformatics analysis and validation. CDH23, ARHGEF40, and BRD9 were identified as the most promising susceptibility genes in hereditary melanoma. In silico analysis of CDH23 and ARHGEF40 variants provided clues for altered protein structure and function associated with the identified mutations. Then, we also evaluated the clinical value of CDH23, ARHGEF40, and BRD9 expression in sporadic melanoma by using the TCGA dataset (n = 461). No differences were observed in BRD9 expression between melanoma and normal skin samples, nor with melanoma stage, whereas ARHGEF40 was found overexpressed, and CDH23 was downregulated and its loss was associated with worse survival. Altogether, these results reveal three novel genes with clinical relevance in hereditary and sporadic melanoma.
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Affiliation(s)
- Catarina Campos
- Unidade de Investigação em Patobiologia Molecular (UIPM) do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
| | - Sofia Fragoso
- Unidade de Investigação em Patobiologia Molecular (UIPM) do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
| | - Rafael Luís
- Unidade de Investigação em Patobiologia Molecular (UIPM) do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
| | - Filipe Pinto
- i3S-Institute for Research and Innovation in Health, University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
| | - Cheila Brito
- Unidade de Investigação em Patobiologia Molecular (UIPM) do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
| | - Susana Esteves
- Unidade de Investigação Clínica (UIC) do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
| | - Margarida Pataco
- Unidade de Investigação em Patobiologia Molecular (UIPM) do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
| | - Sidónia Santos
- Unidade de Investigação em Patobiologia Molecular (UIPM) do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
| | - Patrícia Machado
- Unidade de Investigação em Patobiologia Molecular (UIPM) do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
| | - João B. Vicente
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República (EAN), 2780-157 Oeiras, Portugal
| | - Joaninha Costa Rosa
- Serviço de Anatomia Patológica do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
- NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal
| | - Branca M. Cavaco
- Unidade de Investigação em Patobiologia Molecular (UIPM) do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
| | - Cecília Moura
- Clínica de Risco Familiar do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
- Serviço de Dermatologia do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
| | - Marta Pojo
- Unidade de Investigação em Patobiologia Molecular (UIPM) do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
- Correspondence: ; Tel.: +351-21-722-9800 (ext. 1794)
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Al-Kindi MN, Al-Khabouri MJ, Al-Lamki KA, Palombo F, Pippucci T, Romeo G, Al-Wardy NM. In silico analysis of a novel causative mutation in Cadherin23 gene identified in an Omani family with hearing loss. J Genet Eng Biotechnol 2020; 18:8. [PMID: 32115674 PMCID: PMC7049540 DOI: 10.1186/s43141-020-0021-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/19/2020] [Indexed: 12/28/2022]
Abstract
Background Hereditary hearing loss is a heterogeneous group of complex disorders with an overall incidence of one in every 500 newborns presented as syndromic and non-syndromic forms. Cadherin-related 23 (CDH23) is one of the listed deafness causative genes. It is found to be expressed in the stereocilia of hair cells and in the retina photoreceptor cells. Defective CDH23 have been associated mostly with prelingual severe-to-profound sensorineural hearing loss (SNHL) in either syndromic (USH1D) or non-syndromic SNHL (DFNB12) deafness. The purpose of this study was to identify causative mutations in an Omani family diagnosed with severe-profound sensorineural hearing loss by whole exome sequencing technique and analyzing the detected variant in silico for pathogenicity using several in silico mutation prediction software. Results A novel homozygous missense variant, c.A7436C (p. D2479A), in exon 53 of CDH23 was detected in the family while the control samples were all negative for the detected variant. In silico mutation prediction analysis showed the novel substituted D2479A to be deleterious and protein destabilizing mutation at a conserved site on CDH23 protein. Conclusion In silico mutation prediction analysis might be used as a useful molecular diagnostic tool benefiting both genetic counseling and mutation verification. The aspartic acid 2479 alanine missense substitution might be the main disease-causing mutation that damages CDH23 function and could be used as a genetic hearing loss marker for this particular Omani family.
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Affiliation(s)
- Mohammed Nasser Al-Kindi
- Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, P.O. Box 35, Al-Khoud, 123, Muscat, Oman
| | - Mazin Jawad Al-Khabouri
- Department of Otolaryngology and Head and Neck Surgery, Al Nahda Hospital, Ministry of Health, Muscat, Oman
| | - Khalsa Ahmad Al-Lamki
- Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, P.O. Box 35, Al-Khoud, 123, Muscat, Oman
| | - Flavia Palombo
- Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Tommaso Pippucci
- Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Giovanni Romeo
- Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Nadia Mohammed Al-Wardy
- Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, P.O. Box 35, Al-Khoud, 123, Muscat, Oman.
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Xu T, Zhu W, Wang P, Li H, Yu S. Identification of novel cadherin 23 variants in a Chinese family with hearing loss. Mol Med Rep 2019; 20:2609-2616. [PMID: 31322239 PMCID: PMC6691240 DOI: 10.3892/mmr.2019.10503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 05/09/2019] [Indexed: 11/09/2022] Open
Abstract
The aim of the present study was to elucidate the role of the non-syndromic autosomal recessive deafness 12 allelic variant of cadherin 23 (CDH23) in Chinese patients with non-syndromic hearing loss. The present study focused on a Chinese family with hearing loss in which there were two siblings with autosomal, recessive deafness, ranging from severe to profound hearing loss over all frequencies. DNA sequencing was used to assess the genetic factors in the disease etiology. The data revealed a compound heterozygous mutation of CDH23 in both patients. Genetic CDH23 variants are known to be responsible for non-syndromic hearing loss, and CDH23 variants frequently occur in various populations, including Japanese and Republic of Korean. Results from the present study, indicated a significant contribution of CDH23 variants to the non-syndromic hearing loss in Chinese patients.
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Affiliation(s)
- Tianni Xu
- Department of Otolaryngology‑Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Wei Zhu
- Department of Otolaryngology‑Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Ping Wang
- Department of Otolaryngology‑Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Haonan Li
- Department of Otolaryngology‑Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Shuyuan Yu
- Department of Otolaryngology‑Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
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Deterioration in Distortion Product Otoacoustic Emissions in Auditory Neuropathy Patients With Distinct Clinical and Genetic Backgrounds. Ear Hear 2019; 40:184-191. [PMID: 29688962 DOI: 10.1097/aud.0000000000000586] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
OBJECTIVES Auditory neuropathy (AN) is a clinical disorder characterized by the absence of auditory brainstem response and presence of otoacoustic emissions. A gradual loss of otoacoustic emissions has been reported for some cases of AN. Such cases could be diagnosed as cochlear hearing loss and lead to misunderstanding of the pathology when patients first visit clinics after the loss of otoacoustic emissions. The purpose of this study was to investigate the time course of changes in distortion product otoacoustic emissions (DPOAEs) in association with patients' genetic and clinical backgrounds, including the use of hearing aids. DESIGN DPOAE measurements from 31 patients with AN were assessed. Genetic analyses for GJB2, OTOF, and mitochondrial m.1555A> G and m.3243A> G mutations were conducted for all cases, and the analyses for CDH23 and OPA1 were conducted for the selected cases. Patients who were younger than 10 years of age at the time of AN diagnosis were designated as the pediatric AN group (22 cases), and those who were 18 years of age or older were designated as the adult AN group (9 cases). DPOAE was measured at least twice in all patients. The response rate for DPOAEs was defined and analyzed. RESULTS The pediatric AN group comprised 10 patients with OTOF mutations, 1 with GJB2 mutations, 1 with OPA1 mutation, and 10 with indefinite causes. Twelve ears (27%) showed no change in DPOAE, 20 ears (46%) showed a decrease in DPOAE, and 12 ears (27%) lost DPOAE. Loss of DPOAE occurred in one ear (2%) at 0 years of age and four ears (9%) at 1 year of age. The time courses of DPOAEs in patients with OTOF mutations were divided into those with early loss and those with no change, indicating that the mechanism for deterioration of DPOAEs includes not only the OTOF mutations but also other common modifier factors. Most, but not all, AN patients who used hearing aids showed deterioration of DPOAEs after the start of using hearing aids. A few AN patients also showed deterioration of DPOAEs before using hearing aids. The adult AN group comprised 2 patients with OPA1 mutations, 2 with OTOF mutations, and 5 with indefinite causes. Four ears (22%) showed no change in DPOAE, 13 ears (72%) showed a decrease, and one ear (6%) showed a loss of DPOAE. Although the ratio of DPOAE decrease was higher in the adult AN group than in the pediatric AN group, the ratio of DPOAE loss was lower in the adult AN group. DPOAE was not lost in all four ears with OPA1 mutations and in all four ears with OTOF mutations in the adult group. CONCLUSIONS DPOAE was decreased or lost in approximately 70% of pediatric and about 80% of adult AN patients. Eleven percent of pediatric AN patients lost DPOAEs by 1 year of age. Genetic factors were thought to have influenced the time course of DPOAEs in the pediatric AN group. In most adult AN patients, DPOAE was rarely lost regardless of the genetic cause.
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Alimardani M, Hosseini SM, Khaniani MS, Haghi MR, Eslahi A, Farjami M, Chezgi J, Derakhshan SM, Mojarrad M. Targeted Mutation Analysis of the SLC26A4, MYO6, PJVK and CDH23 Genes in Iranian Patients with AR Nonsyndromic Hearing Loss. Fetal Pediatr Pathol 2019; 38:93-102. [PMID: 30582396 DOI: 10.1080/15513815.2018.1547336] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
BACKGROUND Hearing loss (HL) is the most prevalent sensory disorder. The over 100 genes implicated in autosomal recessive nonsyndromic hearing loss (ARNSHL) makes it difficult to analyze and determine the accurate genetic causes of hearing loss. We sought to de?ne the frequency of seven hearing loss-Causing causing genetic Variants in four genes in an Iranian population with hearing loss. MATERIALS AND METHODS One hundred ARNSHL patients with normal GJB2/GJB6 genes were included, and targeted mutations in SLC26A4, MYO6, PJVK and CDH23 genes were analyzed by ARMS-PCR. The negative and positive results were confirmed by the Sanger sequencing. RESULTS We found only two mutations, one in MYO6 (c.554-1 G > A) gene and another in PJVK (c.547C > T). CONCLUSION c.554-1G > A and c.547C > T mutations are responsible for 1% each of the Iranian ARNSHL patients. These genes are not a frequent cause of ARNSHL in an Iranian population.
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Affiliation(s)
- Maliheh Alimardani
- a Neurosciences Research Center , Tabriz University of Medical Science , Tabriz , Iran.,b Department of Medical Genetics , Tabriz University of Medical Sciences , Tabriz , Iran.,c Student Research Committee, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran
| | - Seyed Mojtaba Hosseini
- c Student Research Committee, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran.,d Department of Medical Genetics , Mashhad University of Medical Sciences , Mashhad , Iran
| | - Mahmoud Shekari Khaniani
- b Department of Medical Genetics , Tabriz University of Medical Sciences , Tabriz , Iran.,e Ebne Sina Medical Genetic Diagnostic Laboratory , Tabriz University of Medical Sciences , Tabriz , Iran
| | - Mohsen Rajati Haghi
- f Department of Head and Neck Surgery, ENT Research Center , Mashhad University of Medical Sciences , Mashhad , Iran
| | - Atieh Eslahi
- c Student Research Committee, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran.,d Department of Medical Genetics , Mashhad University of Medical Sciences , Mashhad , Iran
| | - Mashsa Farjami
- c Student Research Committee, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran.,d Department of Medical Genetics , Mashhad University of Medical Sciences , Mashhad , Iran
| | - Javad Chezgi
- c Student Research Committee, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran.,d Department of Medical Genetics , Mashhad University of Medical Sciences , Mashhad , Iran
| | - Sima Mansoori Derakhshan
- a Neurosciences Research Center , Tabriz University of Medical Science , Tabriz , Iran.,b Department of Medical Genetics , Tabriz University of Medical Sciences , Tabriz , Iran.,e Ebne Sina Medical Genetic Diagnostic Laboratory , Tabriz University of Medical Sciences , Tabriz , Iran
| | - Majid Mojarrad
- d Department of Medical Genetics , Mashhad University of Medical Sciences , Mashhad , Iran.,g Medical Genetics Research Center, School of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran
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Sabiha B, Ali J, Yousafzai YM, Haider SA. Novel deleterious mutation in MYO7A, TH and EVC2 in two Pakistani brothers with familial deafness. Pak J Med Sci 2018; 35:17-22. [PMID: 30881389 PMCID: PMC6408642 DOI: 10.12669/pjms.35.1.98] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Objective In Pakistan, 74% of consanguineous marriages are among the first cousins. Continuity of consanguineous marriages over generations increases the risk of recessive diseases such as deafness. The objective of this study was to investigate genetic origin of Pakistani deaf brothers with parents of consanguineous marriage. Methods DNA was extracted from the blood through Qiagen kit. Paired-end sequencing library was prepared according to protocol of Illumina's TruSight Rapid Capture kit and TruSight Inherited Disease Panel. Library was normalized and used for Next Generation Sequencing through MiSeq. NGS data were analyzed using various bioinformatics tools. Results Both brothers were found to have novel deleterious mutation in MYO7A (c.2476G>A) while the younger brother had additional novel deleterious mutation in TH (c.43C>T) and EVC2 (c.2614C>T) genes. Conclusion It is concluded that in addition to novel mutations in MYO7A, TH and EVC2, the CDH23 and GJB2 can also be responsible for deafness in the family with consanguineous marriages.
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Affiliation(s)
- Bibi Sabiha
- Bibi Sabiha, Center for Genomic Sciences, Rehman Medical College, Phase-V, Hayatabad, Peshawar, KP, Pakistan
| | - Johar Ali
- Johar Ali, Center for Genomic Sciences, Rehman Medical College, Phase-V, Hayatabad, Peshawar, KP, Pakistan
| | - Yasar Mehmood Yousafzai
- Yasar Mehmood Yousafzai, Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Syed Adnan Haider
- Syed Adnan Haider, Center for Genomic Sciences, Rehman Medical College, Phase-V, Hayatabad, Peshawar, KP, Pakistan
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Xu T, Zhu W, Wang P. The p.P240L variant of CDH23 and the risk of nonsyndromic hearing loss: a meta-analysis. Eur Arch Otorhinolaryngol 2018; 276:11-16. [DOI: 10.1007/s00405-018-5160-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 10/04/2018] [Indexed: 01/11/2023]
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Jaiganesh A, Narui Y, Araya-Secchi R, Sotomayor M. Beyond Cell-Cell Adhesion: Sensational Cadherins for Hearing and Balance. Cold Spring Harb Perspect Biol 2018; 10:a029280. [PMID: 28847902 PMCID: PMC6008173 DOI: 10.1101/cshperspect.a029280] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cadherins form a large family of proteins often involved in calcium-dependent cellular adhesion. Although classical members of the family can provide a physical bond between cells, a subset of special cadherins use their extracellular domains to interlink apical specializations of single epithelial sensory cells. Two of these cadherins, cadherin-23 (CDH23) and protocadherin-15 (PCDH15), form extracellular "tip link" filaments that connect apical bundles of stereocilia on hair cells essential for inner-ear mechanotransduction. As these bundles deflect in response to mechanical stimuli from sound or head movements, tip links gate hair-cell mechanosensitive channels to initiate sensory perception. Here, we review the unusual and diverse structural properties of these tip-link cadherins and the functional significance of their deafness-related missense mutations. Based on the structural features of CDH23 and PCDH15, we discuss the elasticity of tip links and models that bridge the gap between the nanomechanics of cadherins and the micromechanics of hair-cell bundles during inner-ear mechanotransduction.
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Affiliation(s)
- Avinash Jaiganesh
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Yoshie Narui
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Raul Araya-Secchi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
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Frey S, Eichler A, Stonawski V, Kriebel J, Wahl S, Gallati S, Goecke TW, Fasching PA, Beckmann MW, Kratz O, Moll GH, Heinrich H, Kornhuber J, Golub Y. Prenatal Alcohol Exposure Is Associated With Adverse Cognitive Effects and Distinct Whole-Genome DNA Methylation Patterns in Primary School Children. Front Behav Neurosci 2018; 12:125. [PMID: 29997484 PMCID: PMC6028559 DOI: 10.3389/fnbeh.2018.00125] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 06/06/2018] [Indexed: 12/22/2022] Open
Abstract
Prenatal alcohol exposure (PAE) is known to elicit a broad range of systemic effects, including neurophysiological alterations that result in adverse behavioral and cognitive outcomes. However, molecular pathways underlying these long-term intrauterine effects remain to be investigated. Here, we tested a hypothesis that PAE may lead to epigenetic alterations to the DNA resulting in attentional and cognitive alterations of the children. We report the results of the study that included 156 primary school children of the Franconian Cognition and Emotion Studies (FRANCES) cohort which were tested for an objective marker of PAE, ethyl glucuronide (EtG) in meconium at birth. Thirty-two newborns were found to be exposed to alcohol with EtG values above 30 ng/g (EtG+). Previously we described PAE being associated with lower IQ and smaller amplitude of the event-related potential component P3 in go trials (Go-P3), which indicates a reduced capacity of attentional resources. Whole-genome methylation analysis of the buccal cell DNA revealed 193 differentially methylated genes in children with positive meconium EtG, that were clustered into groups involved in epigenetic modifications, neurodegeneration, neurodevelopment, axon guidance and neuronal excitability. Furthermore, we detected mediation effects of the methylation changes in DPP10 and SLC16A9 genes on the EtG related cognitive and attention-related deficits. Our results suggest that system-wide epigenetic changes are involved in long-term effects of PAE. In particular, we show an epigenetic mediation of PAE effects on cognition and attention-related processes.
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Affiliation(s)
- Stefan Frey
- Department of Child and Adolescent Mental Health, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Anna Eichler
- Department of Child and Adolescent Mental Health, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Valeska Stonawski
- Department of Child and Adolescent Mental Health, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, German Research Center for Environmental Health - Institute of Epidemiology II, Helmholtz Zentrum München, Munich, Germany
| | - Simone Wahl
- Research Unit of Molecular Epidemiology, German Research Center for Environmental Health - Institute of Epidemiology II, Helmholtz Zentrum München, Munich, Germany
| | - Sabina Gallati
- Division of Human Genetics, Department of Paediatrics, Inselspital University of Bern, Bern, Switzerland
| | - Tamme W Goecke
- Department of Obstetrics and Gynecology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.,Department of Obstetrics and Gynecology, RWTH Aachen University, Aachen, Germany
| | - Peter A Fasching
- Department of Obstetrics and Gynecology, RWTH Aachen University, Aachen, Germany
| | - Matthias W Beckmann
- Department of Obstetrics and Gynecology, RWTH Aachen University, Aachen, Germany
| | - Oliver Kratz
- Department of Child and Adolescent Mental Health, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Gunther H Moll
- Department of Child and Adolescent Mental Health, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Hartmut Heinrich
- Department of Child and Adolescent Mental Health, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.,kbo-Heckscher-Klinikum, Munich, Germany
| | - Johannes Kornhuber
- Department of Psychiatry and Psychotherapy, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Yulia Golub
- Department of Child and Adolescent Mental Health, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.,Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Dresden, Germany
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11
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Kim BJ, Kim AR, Han JH, Lee C, Oh DY, Choi BY. Discovery of MYH14 as an important and unique deafness gene causing prelingually severe autosomal dominant nonsyndromic hearing loss. J Gene Med 2017; 19. [PMID: 28221712 DOI: 10.1002/jgm.2950] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/04/2017] [Accepted: 02/17/2017] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Pathogenic variants of MYH14 are known to be associated (in either a syndromic or nonsyndromic manner) with hearing loss. Interestingly, all reported cases to date of MYH14-related nonsyndromic hearing loss with detailed phenotypes have demonstrated mild-to-moderate progressive hearing loss with postlingual onset. METHODS In the present study, targeted resequencing (TRS) of known deafness genes was performed to identify the causative variant in two multiplex families segregating autosomal dominant (AD) inherited hearing loss. RESULTS TRS uncovered two novel variants of MYH14 (c.A572G: p.Asp191Gly in the myosin head domain and c.C73T:p.Gln25* in exon 2) from two multiplex deafness Korean families. Notably, both probands showed phenotypes of congenital or prelingual severe hearing loss. It is remarkably uncommon to encounter such a severe-to-profound, prelingual, AD hearing loss. Given that the first variant, p. Asp191Gly, was the first documented missense allele discovered in the myosin head domain of this gene related to either congenital or prelingual severe nonsyndromic hearing loss, and also that the second variant, p. Gln25*, lead to a null allele, more severe phenotypes from our probands may have been the result of either genotype-phenotype correlation or genetic backgrounds, or both. CONCLUSIONS In the present study, we report that MYH14 can manifest as nonsyndromic prelingual severe sensorineural hearing loss in an AD fashion in Koreans. The results of the present study suggest that further genetic studies of similar patients should consider MYH14 as a causative gene, and cochlear implantation during infant or early childhood should be indicated for those patients with certain MYH14 pathogenic variants.
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Affiliation(s)
- Bong Jik Kim
- Wide River Institute of Immunology, Seoul National University College of Medicine, Seoul, South Korea.,Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, South Korea
| | - Ah Reum Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, South Korea
| | - Jin Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Chung Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Doo Yi Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
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12
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Alkowari MK, Vozzi D, Bhagat S, Krishnamoorthy N, Morgan A, Hayder Y, Logendra B, Najjar N, Gandin I, Gasparini P, Badii R, Girotto G, Abdulhadi K. Targeted sequencing identifies novel variants involved in autosomal recessive hereditary hearing loss in Qatari families. Mutat Res 2017; 800-802:29-36. [PMID: 28501645 DOI: 10.1016/j.mrfmmm.2017.05.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/11/2017] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
Hereditary hearing loss is characterized by a very high genetic heterogeneity. In the Qatari population the role of GJB2, the worldwide HHL major player, seems to be quite limited compared to Caucasian populations. In this study we analysed 18 Qatari families affected by non-syndromic hearing loss using a targeted sequencing approach that allowed us to analyse 81 genes simultaneously. Thanks to this approach, 50% of these families (9 out of 18) resulted positive for the presence of likely causative alleles in 6 different genes: CDH23, MYO6, GJB6, OTOF, TMC1 and OTOA. In particular, 4 novel alleles were detected while the remaining ones were already described to be associated to HHL in other ethnic groups. Molecular modelling has been used to further investigate the role of novel alleles identified in CDH23 and TMC1 genes demonstrating their crucial role in Ca2+ binding and therefore possible functional role in proteins. Present study showed that an accurate molecular diagnosis based on next generation sequencing technologies might largely improve molecular diagnostics outcome leading to benefits for both genetic counseling and definition of recurrence risk.
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Affiliation(s)
- Moza K Alkowari
- Division of Experimental Genetics, Sidra Medical and Research Centre, Doha, Qatar
| | - Diego Vozzi
- Medical Genetics, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | | | - Navaneethakrishnan Krishnamoorthy
- Division of Experimental Genetics, Sidra Medical and Research Centre, Doha, Qatar; Heart Science Centre, National Heart and Lung Institute, Imperial College London, United Kingdom
| | - Anna Morgan
- Medical Genetics, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy; Medical Sciences, Chirurgical and Health Department, University of Trieste, Trieste, Italy
| | | | | | | | - Ilaria Gandin
- Medical Genetics, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Paolo Gasparini
- Medical Genetics, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy; Medical Sciences, Chirurgical and Health Department, University of Trieste, Trieste, Italy
| | - Ramin Badii
- Molecular Genetics Laboratory, HMC, Doha, Qatar
| | - Giorgia Girotto
- Medical Genetics, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy; Medical Sciences, Chirurgical and Health Department, University of Trieste, Trieste, Italy.
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13
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Kim BJ, Kim AR, Lee C, Kim SY, Kim NKD, Chang MY, Rhee J, Park MH, Koo SK, Kim MY, Han JH, Oh SH, Park WY, Choi BY. Discovery of CDH23 as a Significant Contributor to Progressive Postlingual Sensorineural Hearing Loss in Koreans. PLoS One 2016; 11:e0165680. [PMID: 27792758 PMCID: PMC5085094 DOI: 10.1371/journal.pone.0165680] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 10/14/2016] [Indexed: 11/19/2022] Open
Abstract
CDH23 mutations have mostly been associated with prelingual severe-to-profound sensorineural hearing loss (SNHL) in either syndromic or nonsyndromic SNHL (DFNB12). Herein, we demonstrate the contribution of CDH23 mutations to postlingual nonsyndromic SNHL (NS-SNHL). We screened 32 Korean adult probands with postlingual NS-SNHL sporadically or in autosomal recessive fashion using targeted panel or whole exome sequencing. We identified four (12.5%, 4/32) potential postlingual DFNB12 families that segregated the recessive CDH23 variants, qualifying for our criteria along with rapidly progressive SNHL. Three of the four families carried one definite pathogenic CDH23 variant previously known as the prelingual DFNB12 variant in a trans configuration with rare CDH23 variants. To determine the contribution of rare CDH23 variants to the postlingual NS-SNHL, we checked the minor allele frequency (MAF) of CDH23 variants detected from our postlingual NS-SNHL cohort and prelingual NS-SNHL cohort, among the 2040 normal control chromosomes. The allele frequency of these CDH23 variants in our postlingual cohort was 12.5%, which was significantly higher than that of the 2040 control chromosomes (5.53%), confirming the contribution of these rare CDH23 variants to postlingual NS-SNHL. Furthermore, MAF of rare CDH23 variants from the postlingual NS-SNHL group was significantly higher than that from the prelingual NS-SNHL group. This study demonstrates an important contribution of CDH23 mutations to poslingual NS-SNHL and shows that the phenotypic spectrum of DFNB12 can be broadened even into the presbycusis, depending on the pathogenic potential of variants. We also propose that pathogenic potential of CDH23 variants and the clinical fate of DFNB12 may be predicted by MAF.
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Affiliation(s)
- Bong Jik Kim
- Department of Otorhinolaryngology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Ah Reum Kim
- Department of Otorhinolaryngology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Chung Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Suwon, Korea
| | - So Young Kim
- Department of Otorhinolaryngology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | | | - Mun Young Chang
- Department of Otorhinolaryngology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jihye Rhee
- Department of Otorhinolaryngology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Mi-Hyun Park
- Division of Intractable Diseases, Center for Biomedical Sciences, National Institute of Health, Chungcheongbuk-do, Korea
| | - Soo Kyung Koo
- Division of Intractable Diseases, Center for Biomedical Sciences, National Institute of Health, Chungcheongbuk-do, Korea
| | - Min Young Kim
- Department of Otorhinolaryngology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Jin Hee Han
- Department of Otorhinolaryngology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Seung-ha Oh
- Department of Otorhinolaryngology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
- Department of Molecular Cell Biology, School of Medicine, Sungkyunkwan University, Suwon, Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology, Seoul National University Bundang Hospital, Seongnam, Korea
- * E-mail:
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14
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Han KH, Kim AR, Kim MY, Ahn S, Oh SH, Song JH, Choi BY. Establishment of a Flexible Real-Time Polymerase Chain Reaction-Based Platform for Detecting Prevalent Deafness Mutations Associated with Variable Degree of Sensorineural Hearing Loss in Koreans. PLoS One 2016; 11:e0161756. [PMID: 27583405 PMCID: PMC5008798 DOI: 10.1371/journal.pone.0161756] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/11/2016] [Indexed: 11/19/2022] Open
Abstract
Many cutting-edge technologies based on next-generation sequencing (NGS) have been employed to identify candidate variants responsible for sensorineural hearing loss (SNHL). However, these methods have limitations preventing their wide clinical use for primary screening, in that they remain costly and it is not always suitable to analyze massive amounts of data. Several different DNA chips have been developed for screening prevalent mutations at a lower cost. However, most of these platforms do not offer the flexibility to add or remove target mutations, thereby limiting their wider use in a field that requires frequent updates. Therefore, we aimed to establish a simpler and more flexible molecular diagnostic platform based on ethnicity-specific mutation spectrums of SNHL, which would enable bypassing unnecessary filtering steps in a substantial portion of cases. In addition, we expanded the screening platform to cover varying degrees of SNHL. With this aim, we selected 11 variants of 5 genes (GJB2, SLC26A4, MTRNR1, TMPRSS3, and CDH23) showing high prevalence with varying degrees in Koreans and developed the U-TOP™ HL Genotyping Kit, a real-time PCR-based method using the MeltingArray technique and peptide nucleic acid probes. The results of 271 DNA samples with wild type sequences or mutations in homo- or heterozygote form were compared between the U-TOP™ HL Genotyping Kit and Sanger sequencing. The positive and negative predictive values were 100%, and this method showed perfect agreement with Sanger sequencing, with a Kappa value of 1.00. The U-TOP™ HL Genotyping Kit showed excellent performance in detecting varying degrees and phenotypes of SNHL mutations in both homozygote and heterozygote forms, which are highly prevalent in the Korean population. This platform will serve as a useful and cost-effective first-line screening tool for varying degrees of genetic SNHL and facilitate genome-based personalized hearing rehabilitation for the Korean population.
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Affiliation(s)
- Kyu-Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, National Medical Center, Seoul, Korea
| | - Ah Reum Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Min Young Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Soyeon Ahn
- Medical Research Collaborating Center, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Seung-Ha Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Ju Hun Song
- Department of Otorhinolaryngology-Head and Neck Surgery, National Medical Center, Seoul, Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
- Wide River Institute of Immunology, Seoul National University College of Medicine, Hongcheon, Korea
- * E-mail:
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15
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Shen C, Gao J, Sheng Y, Dou J, Zhou F, Zheng X, Ko R, Tang X, Zhu C, Yin X, Sun L, Cui Y, Zhang X. Genetic Susceptibility to Vitiligo: GWAS Approaches for Identifying Vitiligo Susceptibility Genes and Loci. Front Genet 2016; 7:3. [PMID: 26870082 PMCID: PMC4740779 DOI: 10.3389/fgene.2016.00003] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/11/2016] [Indexed: 01/15/2023] Open
Abstract
Vitiligo is an autoimmune disease with a strong genetic component, characterized by areas of depigmented skin resulting from loss of epidermal melanocytes. Genetic factors are known to play key roles in vitiligo through discoveries in association studies and family studies. Previously, vitiligo susceptibility genes were mainly revealed through linkage analysis and candidate gene studies. Recently, our understanding of the genetic basis of vitiligo has been rapidly advancing through genome-wide association study (GWAS). More than 40 robust susceptible loci have been identified and confirmed to be associated with vitiligo by using GWAS. Most of these associated genes participate in important pathways involved in the pathogenesis of vitiligo. Many susceptible loci with unknown functions in the pathogenesis of vitiligo have also been identified, indicating that additional molecular mechanisms may contribute to the risk of developing vitiligo. In this review, we summarize the key loci that are of genome-wide significance, which have been shown to influence vitiligo risk. These genetic loci may help build the foundation for genetic diagnosis and personalize treatment for patients with vitiligo in the future. However, substantial additional studies, including gene-targeted and functional studies, are required to confirm the causality of the genetic variants and their biological relevance in the development of vitiligo.
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Affiliation(s)
- Changbing Shen
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University Hefei, China
| | - Jing Gao
- Department of Dermatology, The Second Affiliated Hospital, Anhui Medical University Hefei, China
| | - Yujun Sheng
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University Hefei, China
| | - Jinfa Dou
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University Hefei, China
| | - Fusheng Zhou
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University Hefei, China
| | - Xiaodong Zheng
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University Hefei, China
| | - Randy Ko
- Department of Biochemistry, University of New Mexico Albuquerque, NM, USA
| | - Xianfa Tang
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University Hefei, China
| | - Caihong Zhu
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University Hefei, China
| | - Xianyong Yin
- Department of Genetics and Renaissance Computing Institute, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Liangdan Sun
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University Hefei, China
| | - Yong Cui
- Department of Dermatology, China-Japan Friendship Hospital Beijing, China
| | - Xuejun Zhang
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical UniversityHefei, China; Department of Dermatology, The Second Affiliated Hospital, Anhui Medical UniversityHefei, China
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16
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Cracking the Code of Human Diseases Using Next-Generation Sequencing: Applications, Challenges, and Perspectives. BIOMED RESEARCH INTERNATIONAL 2015; 2015:161648. [PMID: 26665001 PMCID: PMC4668301 DOI: 10.1155/2015/161648] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 09/30/2015] [Accepted: 10/18/2015] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) technologies have greatly impacted on every field of molecular research mainly because they reduce costs and increase throughput of DNA sequencing. These features, together with the technology's flexibility, have opened the way to a variety of applications including the study of the molecular basis of human diseases. Several analytical approaches have been developed to selectively enrich regions of interest from the whole genome in order to identify germinal and/or somatic sequence variants and to study DNA methylation. These approaches are now widely used in research, and they are already being used in routine molecular diagnostics. However, some issues are still controversial, namely, standardization of methods, data analysis and storage, and ethical aspects. Besides providing an overview of the NGS-based approaches most frequently used to study the molecular basis of human diseases at DNA level, we discuss the principal challenges and applications of NGS in the field of human genomics.
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17
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Kim SY, Kim AR, Kim NKD, Kim MY, Jeon EH, Kim BJ, Han YE, Chang MY, Park WY, Choi BY. Strong founder effect of p.P240L in CDH23 in Koreans and its significant contribution to severe-to-profound nonsyndromic hearing loss in a Korean pediatric population. J Transl Med 2015; 13:263. [PMID: 26264712 PMCID: PMC4534105 DOI: 10.1186/s12967-015-0624-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 07/30/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite the prevalence of CDH23 mutations in East Asians, its large size hinders investigation. The pathologic mutation p.P240L in CDH23 is common in East Asians. However, whether this mutation represents a common founder or a mutational hot spot is unclear. The prevalence of CDH23 mutations with prelingual severe-to-profound sporadic or autosomal recessive sensorineural hearing loss (arSNHL) is unknown in Koreans. METHODS From September 2010 to October 2014, children with severe-to-profound sporadic or arSNHL without phenotypic markers, and their families, were tested for mutations in connexins GJB2, GJB6 and GJB3. Sanger sequencing of CDH23 p.P240L was performed on connexin-negative samples without enlarged vestibular aqueducts (EVA), followed by targeted resequencing of 129 deafness genes, including CDH23, unless p.P240L homozygotes were detected in the first screening. Four p.P240L-allele-linked STR markers were genotyped in 40 normal-hearing control subjects, and the p.P240L carriers in the hearing-impaired cohort, to identify the haplotypes. RESULTS Four (3.1 %) of 128 children carried two CDH23 mutant alleles, and SLC26A4 and GJB2 accounted for 18.0 and 17.2 %, respectively. All four children showed profound nonsyndromic SNHL with minimal residual hearing. Interestingly, all had at least one p.P240L mutant allele. Analysis of p.P240L-linked STR markers in these children and other postlingual hearing-impaired adults carrying p.P240L revealed that p.P240L was mainly carried on a single haplotype. CONCLUSIONS p.P240L contributed significantly to Korean pediatric severe arSNHL with a strong founder effect, with implications for future phylogenetic studies. Screening for p.P240L as a first step in GJB2-negative arSNHL Koreans without EVA is recommended.
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Affiliation(s)
- So Young Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.
| | - Ah Reum Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.
| | - Nayoung K D Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.
| | - Min Young Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 300 Gumi-dong, Bundang-gu, Seongnam, 463-707, Korea.
| | - Eun-Hee Jeon
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 300 Gumi-dong, Bundang-gu, Seongnam, 463-707, Korea.
| | - Bong Jik Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Dankook University Hospital, Cheonan, Korea.
| | - Young Eun Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.
| | - Mun Young Chang
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea. .,Department of Molecular Cell Biology, School of Medicine, Sungkyunkwan University, Seoul, Korea.
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 300 Gumi-dong, Bundang-gu, Seongnam, 463-707, Korea. .,Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, Korea.
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Rui X, Li Y, Jin F, Li F. TMPRSS3 is a novel poor prognostic factor for breast cancer. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:5435-5442. [PMID: 26191247 PMCID: PMC4503118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 04/21/2015] [Indexed: 06/04/2023]
Abstract
It has recently been reported that transmembrane protease, serine 3 (TMPRSS3) is overexpressed in cancer. However, TMPRSS3 expression and its biological roles in breast cancer (BC) have not been reported. This study aims to investigate the TMPRSS3 expression in BC and its relation with the outcome of the BC. This study involves a total of 149 BC tissues and adjacent non-cancerous tissues that were diagnosed between 2004 and 2007. Immunohistochemistry is used to compare the pattern of TMPRSS3 expression in BC and in adjacent non-cancerous tissues. Kaplan-Meier and Cox regression analyses were used to assess the prognostic significance of TMPRSS3 expression among BC patients. The results are as follow: TMPRSS3 expression is significantly in BC compared to adjacent non-cancerous tissues. High TMPRSS3 expression was related to TNM stage, lymph node metastasis, and Ki-67 expression. Furthermore, the overall survival (OS) and disease-free survival (DFS) in BC patients with high TMPRSS3 expression were lower than those in patients with low TMPRSS3 expression. Based on multivariate analysis, lymph node metastasis, TNM stage and TMPRSS3 expression are independent prognostic factors for OS in BC, while lymph node metastasis and TMPRSS3 expression are independent prognostic factors for DFS in BC. This study proves that TMPRSS3 expression is an independent prognostic factor for BC patients. Bioinformatic analysis of potential TMPRSS3 binding proteins revealed that TMPRSS3 could be a key regulator of cancer pathways. This study helps us better understand the function of TMPRSS3 in cancer.
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Affiliation(s)
- Xue Rui
- Department of Breast Surgery, General Surgery, First Hospital of China Medical UniversityShenyang 110001, China
| | - Yanshu Li
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical UniversityShenyang 110001, China
| | - Feng Jin
- Department of Breast Surgery, General Surgery, First Hospital of China Medical UniversityShenyang 110001, China
| | - Feng Li
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical UniversityShenyang 110001, China
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Vona B, Nanda I, Hofrichter MAH, Shehata-Dieler W, Haaf T. Non-syndromic hearing loss gene identification: A brief history and glimpse into the future. Mol Cell Probes 2015; 29:260-70. [PMID: 25845345 DOI: 10.1016/j.mcp.2015.03.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/19/2015] [Accepted: 03/23/2015] [Indexed: 11/27/2022]
Abstract
From the first identified non-syndromic hearing loss gene in 1995, to those discovered in present day, the field of human genetics has witnessed an unparalleled revolution that includes the completion of the Human Genome Project in 2003 to the $1000 genome in 2014. This review highlights the classical and cutting-edge strategies for non-syndromic hearing loss gene identification that have been used throughout the twenty year history with a special emphasis on how the innovative breakthroughs in next generation sequencing technology have forever changed candidate gene approaches. The simplified approach afforded by next generation sequencing technology provides a second chance for the many linked loci in large and well characterized families that have been identified by linkage analysis but have presently failed to identify a causative gene. It also discusses some complexities that may restrict eventual candidate gene discovery and calls for novel approaches to answer some of the questions that make this simple Mendelian disorder so intriguing.
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Affiliation(s)
- Barbara Vona
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany.
| | - Indrajit Nanda
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | | | - Wafaa Shehata-Dieler
- Comprehensive Hearing Center, Department of Otorhinolaryngology, Plastic, Aesthetic and Reconstructive Surgery, University Hospital, Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
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Gao X, Dai P. Impact of next-generation sequencing on molecular diagnosis of inherited non-syndromic hearing loss. J Otol 2014. [DOI: 10.1016/j.joto.2014.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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