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Nogueira C, Pereira C, Silva L, Laranjeira M, Lopes A, Neiva R, Rodrigues E, Campos T, Martins E, Bandeira A, Coelho M, Magalhães M, Damásio J, Gaspar A, Janeiro P, Gomes AL, Ferreira AC, Jacinto S, Vieira JP, Diogo L, Santos H, Mendonça C, Vilarinho L. The genetic landscape of mitochondrial diseases in the next-generation sequencing era: a Portuguese cohort study. Front Cell Dev Biol 2024; 12:1331351. [PMID: 38465286 PMCID: PMC10920333 DOI: 10.3389/fcell.2024.1331351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/30/2024] [Indexed: 03/12/2024] Open
Abstract
Introduction: Rare disorders that are genetically and clinically heterogeneous, such as mitochondrial diseases (MDs), have a challenging diagnosis. Nuclear genes codify most proteins involved in mitochondrial biogenesis, despite all mitochondria having their own DNA. The development of next-generation sequencing (NGS) technologies has revolutionized the understanding of many genes involved in the pathogenesis of MDs. In this new genetic era, using the NGS approach, we aimed to identify the genetic etiology for a suspected MD in a cohort of 450 Portuguese patients. Methods: We examined 450 patients using a combined NGS strategy, starting with the analysis of a targeted mitochondrial panel of 213 nuclear genes, and then proceeding to analyze the whole mitochondrial DNA. Results and Discussion: In this study, we identified disease-related variants in 134 (30%) analyzed patients, 88 with nuclear DNA (nDNA) and 46 with mitochondrial DNA (mtDNA) variants, most of them being pediatric patients (66%), of which 77% were identified in nDNA and 23% in mtDNA. The molecular analysis of this cohort revealed 72 already described pathogenic and 20 novel, probably pathogenic, variants, as well as 62 variants of unknown significance. For this cohort of patients with suspected MDs, the use of a customized gene panel provided a molecular diagnosis in a timely and cost-effective manner. Patients who cannot be diagnosed after this initial approach will be further selected for whole-exome sequencing. Conclusion: As a national laboratory for the study and research of MDs, we demonstrated the power of NGS to achieve a molecular etiology, expanding the mutational spectrum and proposing accurate genetic counseling in this group of heterogeneous diseases without therapeutic options.
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Affiliation(s)
- C. Nogueira
- Research & Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - C. Pereira
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - L. Silva
- Research & Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - Mateus Laranjeira
- Research & Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - A. Lopes
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - R. Neiva
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - E. Rodrigues
- Inherited Metabolic Diseases Reference Centre, São João Hospital University Centre, Porto, Portugal
| | - T. Campos
- Inherited Metabolic Diseases Reference Centre, São João Hospital University Centre, Porto, Portugal
| | - E. Martins
- Inherited Metabolic Diseases Reference Centre, Santo António Hospital University Centre, Porto, Portugal
| | - A. Bandeira
- Inherited Metabolic Diseases Reference Centre, Santo António Hospital University Centre, Porto, Portugal
| | - M. Coelho
- Inherited Metabolic Diseases Reference Centre, Santo António Hospital University Centre, Porto, Portugal
| | - M. Magalhães
- Neurology Department, Santo António Hospital University Centre, Porto, Portugal
| | - J. Damásio
- Neurology Department, Santo António Hospital University Centre, Porto, Portugal
| | - A. Gaspar
- Inherited Metabolic Diseases Reference Centre, Lisboa Norte Hospital University Centre, Lisboa, Portugal
| | - P Janeiro
- Inherited Metabolic Diseases Reference Centre, Lisboa Norte Hospital University Centre, Lisboa, Portugal
| | - A. Levy Gomes
- Neurology Department, Lisboa Norte Hospital University Centre, Lisboa, Portugal
| | - A. C. Ferreira
- Inherited Metabolic Diseases Reference Centre, Lisboa Central Hospital Centre, Lisboa, Portugal
| | - S. Jacinto
- Inherited Metabolic Diseases Reference Centre, Lisboa Central Hospital Centre, Lisboa, Portugal
| | - J. P. Vieira
- Inherited Metabolic Diseases Reference Centre, Lisboa Central Hospital Centre, Lisboa, Portugal
| | - L. Diogo
- Inherited Metabolic Diseases Reference Centre, Coimbra Hospital and University Centre, Coimbra, Portugal
| | - H. Santos
- Inherited Metabolic Diseases Reference Centre, Vila Nova de Gaia Hospital Centre, Vila Nova de Gaia, Portugal
| | - C. Mendonça
- Pediatric Department, Faro Hospital and University Centre, Faro, Portugal
| | - L. Vilarinho
- Research & Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
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Joo SY, Jang SH, Kim JA, Kim SJ, Kim B, Kim HY, Choi JY, Gee HY, Jung J. Prevalence and Clinical Characteristics of Mitochondrial DNA Mutations in Korean Patients With Sensorineural Hearing Loss. J Korean Med Sci 2023; 38:e355. [PMID: 38084023 PMCID: PMC10713439 DOI: 10.3346/jkms.2023.38.e355] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/12/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Mutations in mitochondrial DNA (mtDNA) are associated with several genetic disorders, including sensorineural hearing loss. However, the prevalence of mtDNA mutations in a large cohort of Korean patients with hearing loss has not yet been investigated. Thus, this study aimed to investigate the frequency of mtDNA mutations in a cohort of with pre- or post-lingual hearing loss of varying severity. METHODS A total of 711 Korean families involving 1,099 individuals were evaluated. Six mitochondrial variants associated with deafness (MTRNR1 m.1555A>G, MTTL1 m.3243A>G, MTCO1 m.7444G>A and m.7445A>G, and MTTS1 m.7471dupC and m.7511T>C) were screened using restriction fragment length polymorphism. The prevalence of the six variants was also analyzed in a large control dataset using whole-genome sequencing data from 4,534 Korean individuals with unknown hearing phenotype. RESULTS Overall, 12 of the 711 (1.7%) patients with hearing loss had mtDNA variants, with 10 patients from independent families positive for the MTRNR1 m.1555A>G mutation and 2 patients positive for the MTCO1 m.7444G>A mutation. The clinical characteristics of patients with the mtDNA variants were characterized by post-lingual progressive hearing loss due to the m.1555A>G variant (9 of 472; 1.9%). In addition, 18/4,534 (0.4%) of the Korean population have mitochondrial variants associated with hearing loss, predominantly the m.1555A>G variant. CONCLUSION A significant proportion of Korean patients with hearing loss is affected by the mtDNA variants, with the m.1555A>G variant being the most prevalent. These results clarify the genetic basis of hearing loss in the Korean population and emphasize the need for genetic testing for mtDNA variants.
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Affiliation(s)
- Sun Young Joo
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
- Won-Sang Lee Institute for Hearing Loss, Seoul, Korea
| | - Seung Hyun Jang
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
- Won-Sang Lee Institute for Hearing Loss, Seoul, Korea
| | - Jung Ah Kim
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
- Won-Sang Lee Institute for Hearing Loss, Seoul, Korea
| | - Se Jin Kim
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
- Won-Sang Lee Institute for Hearing Loss, Seoul, Korea
| | - Bonggi Kim
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
| | - Hye-Youn Kim
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
- Won-Sang Lee Institute for Hearing Loss, Seoul, Korea
| | - Jae Young Choi
- Won-Sang Lee Institute for Hearing Loss, Seoul, Korea
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
| | - Heon Yung Gee
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
- Won-Sang Lee Institute for Hearing Loss, Seoul, Korea.
| | - Jinsei Jung
- Won-Sang Lee Institute for Hearing Loss, Seoul, Korea
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea.
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Wong TS, Belaramani KM, Chan CK, Chan WK, Chan WLL, Chang SK, Cheung SN, Cheung KY, Cheung YF, Chong SCJ, Chow CKJ, Chung HYB, Fan SYF, Fok WMJ, Fong KW, Fung THS, Hui KF, Hui TH, Hui J, Ko CH, Kwan MC, Kwok MKA, Kwok SSJ, Lai MS, Lam YO, Lam CW, Lau MC, Law CYE, Lee WC, Lee HCH, Lee CN, Leung KH, Leung KY, Li SH, Ling TKJ, Liu KTT, Lo FM, Lui HT, Luk CO, Luk HM, Ma CK, Ma K, Ma KH, Mew YN, Mo A, Ng SF, Poon WKG, Rodenburg R, Sheng B, Smeitink J, Szeto CLC, Tai SM, Tse CTA, Tsung LYL, Wong HMJ, Wong WYW, Wong KK, Wong SNS, Wong CNV, Wong WSS, Wong CKF, Wu SP, Wu HFJ, Yau MM, Yau KCE, Yeung WL, Yeung HMJ, Yip KKE, Young PHT, Yuan G, Yuen YPL, Yuen CL, Fung CW. Mitochondrial diseases in Hong Kong: prevalence, clinical characteristics and genetic landscape. Orphanet J Rare Dis 2023; 18:43. [PMID: 36859275 PMCID: PMC9979401 DOI: 10.1186/s13023-023-02632-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/06/2023] [Indexed: 03/03/2023] Open
Abstract
OBJECTIVE To determine the prevalence of mitochondrial diseases (MD) in Hong Kong (HK) and to evaluate the clinical characteristics and genetic landscape of MD patients in the region. METHODS This study retrospectively reviewed the phenotypic and molecular characteristics of MD patients from participating public hospitals in HK between January 1985 to October 2020. Molecularly and/or enzymatically confirmed MD cases of any age were recruited via the Clinical Analysis and Reporting System (CDARS) using relevant keywords and/or International Classification of Disease (ICD) codes under the HK Hospital Authority or through the personal recollection of treating clinicians among the investigators. RESULTS A total of 119 MD patients were recruited and analyzed in the study. The point prevalence of MD in HK was 1.02 in 100,000 people (95% confidence interval 0.81-1.28 in 100,000). 110 patients had molecularly proven MD and the other nine were diagnosed by OXPHOS enzymology analysis or mitochondrial DNA depletion analysis with unknown molecular basis. Pathogenic variants in the mitochondrial genome (72 patients) were more prevalent than those in the nuclear genome (38 patients) in our cohort. The most commonly involved organ system at disease onset was the neurological system, in which developmental delay, seizures or epilepsy, and stroke-like episodes were the most frequently reported presentations. The mortality rate in our cohort was 37%. CONCLUSION This study is a territory-wide overview of the clinical and genetic characteristics of MD patients in a Chinese population, providing the first available prevalence rate of MD in Hong Kong. The findings of this study aim to facilitate future in-depth evaluation of MD and lay the foundation to establish a local MD registry.
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Affiliation(s)
- Tsz-Sum Wong
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, SAR, People's Republic of China
| | - Kiran M Belaramani
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong, SAR, People's Republic of China
| | - Chun-Kong Chan
- Department of Medicine and Geriatrics, United Christian Hospital, Hong Kong, SAR, People's Republic of China
| | - Wing-Ki Chan
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, SAR, People's Republic of China
| | - Wai-Lun Larry Chan
- Department of Medicine, Alice Ho Miu Ling Nethersole Hospital, Hong Kong, SAR, People's Republic of China
| | - Shek-Kwan Chang
- Department of Medicine, Queen Mary Hospital, Hong Kong, SAR, People's Republic of China
| | - Sing-Ngai Cheung
- Department of Medicine and Geriatrics, Kwong Wah Hospital, Hong Kong, SAR, People's Republic of China
| | - Ka-Yin Cheung
- Department of Medicine and Geriatrics, United Christian Hospital, Hong Kong, SAR, People's Republic of China
| | - Yuk-Fai Cheung
- Department of Medicine, Queen Elizabeth Hospital, Hong Kong, SAR, People's Republic of China
| | - Shuk-Ching Josephine Chong
- Department of Paediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, SAR, People's Republic of China
| | - Chi-Kwan Jasmine Chow
- Department of Paediatrics and Adolescent Medicine, Queen Elizabeth Hospital, Hong Kong, SAR, People's Republic of China
| | - Hon-Yin Brian Chung
- Department of Paediatrics & Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, People's Republic of China
- Hong Kong Genome Institute, Hong Kong, SAR, People's Republic of China
| | - Sin-Ying Florence Fan
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong, SAR, People's Republic of China
| | - Wai-Ming Joshua Fok
- Department of Medicine, Yan Chai Hospital, Hong Kong, SAR, People's Republic of China
| | - Ka-Wing Fong
- Department of Medicine, Queen Elizabeth Hospital, Hong Kong, SAR, People's Republic of China
| | - Tsui-Hang Sharon Fung
- Department of Paediatrics and Adolescent Medicine, Kwong Wah Hospital, Hong Kong, SAR, People's Republic of China
| | - Kwok-Fai Hui
- Department of Medicine and Geriatrics, United Christian Hospital, Hong Kong, SAR, People's Republic of China
| | - Ting-Hin Hui
- Department of Medicine and Geriatrics, United Christian Hospital, Hong Kong, SAR, People's Republic of China
| | - Joannie Hui
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong, SAR, People's Republic of China
| | - Chun-Hung Ko
- Department of Paediatrics and Adolescent Medicine, Caritas Medical Centre, Hong Kong, SAR, People's Republic of China
| | - Min-Chung Kwan
- Department of Medicine and Geriatrics, Kwong Wah Hospital, Hong Kong, SAR, People's Republic of China
| | - Mei-Kwan Anne Kwok
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong, SAR, People's Republic of China
| | - Sung-Shing Jeffrey Kwok
- Department of Chemical Pathology, Prince of Wales Hospital, Hong Kong, SAR, People's Republic of China
| | - Moon-Sing Lai
- Department of Medicine, North District Hospital, Hong Kong, SAR, People's Republic of China
| | - Yau-On Lam
- Department of Medicine and Geriatrics, United Christian Hospital, Hong Kong, SAR, People's Republic of China
| | - Ching-Wan Lam
- Department of Pathology, The University of Hong Kong, Hong Kong, SAR, People's Republic of China
| | - Ming-Chung Lau
- Department of Paediatrics and Adolescent Medicine, United Christian Hospital, Hong Kong, SAR, People's Republic of China
| | - Chun-Yiu Eric Law
- Department of Chemical Pathology, Queen Mary Hospital, Hong Kong, SAR, People's Republic of China
| | - Wing-Cheong Lee
- Department of Paediatrics and Adolescent Medicine, Pamela Youde Nethersole Eastern Hospital, Hong Kong, SAR, People's Republic of China
| | - Han-Chih Hencher Lee
- Department of Chemical Pathology, Princess Margaret Hospital, Hong Kong, SAR, People's Republic of China
| | - Chin-Nam Lee
- Department of Medicine, Pamela Youde Nethersole Eastern Hospital, Hong Kong, SAR, People's Republic of China
| | - Kin-Hang Leung
- Department of Medicine, Queen Elizabeth Hospital, Hong Kong, SAR, People's Republic of China
| | - Kit-Yan Leung
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, SAR, People's Republic of China
| | - Siu-Hung Li
- Department of Medicine, North District Hospital, Hong Kong, SAR, People's Republic of China
| | - Tsz-Ki Jacky Ling
- Department of Chemical Pathology, Queen Mary Hospital, Hong Kong, SAR, People's Republic of China
| | - Kam-Tim Timothy Liu
- Department of Paediatrics and Adolescent Medicine, Pamela Youde Nethersole Eastern Hospital, Hong Kong, SAR, People's Republic of China
| | - Fai-Man Lo
- Department of Health, Clinical Genetic Service, Hong Kong, SAR, People's Republic of China
| | - Hiu-Tung Lui
- Department of Medicine, Tseung Kwan O Hospital, Hong Kong, SAR, People's Republic of China
| | - Ching-On Luk
- Department of Medicine, Queen Elizabeth Hospital, Hong Kong, SAR, People's Republic of China
| | - Ho-Ming Luk
- Clinical Genetics Service Unit, Hong Kong Children's Hospital, Hong Kong, SAR, People's Republic of China
| | - Che-Kwan Ma
- Department of Paediatrics and Adolescent Medicine, United Christian Hospital, Hong Kong, SAR, People's Republic of China
| | - Karen Ma
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong, SAR, People's Republic of China
| | - Kam-Hung Ma
- Department of Paediatrics and Adolescent Medicine, Alice Ho Miu Ling Nethersole hospital, Hong Kong, SAR, People's Republic of China
| | - Yuen-Ni Mew
- Department of Medicine and Geriatrics, United Christian Hospital, Hong Kong, SAR, People's Republic of China
| | - Alex Mo
- Department of Paediatrics and Adolescent Medicine, Kwong Wah Hospital, Hong Kong, SAR, People's Republic of China
| | - Sui-Fun Ng
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, SAR, People's Republic of China
| | - Wing-Kit Grace Poon
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, Hong Kong, SAR, People's Republic of China
| | - Richard Rodenburg
- Department of Paediatrics, Radboud Centre for Mitochondrial Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen Medicine Centre, Nijmegen, The Netherlands
| | - Bun Sheng
- Department of Medicine and Geriatrics, Princess Margaret Hospital, Hong Kong, SAR, People's Republic of China
| | - Jan Smeitink
- Department of Paediatrics, Radboud Centre for Mitochondrial Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen Medicine Centre, Nijmegen, The Netherlands
| | - Cheuk-Ling Charing Szeto
- Department of Medicine and Geriatrics, United Christian Hospital, Hong Kong, SAR, People's Republic of China
| | - Shuk-Mui Tai
- Department of Paediatrics and Adolescent Medicine, Pamela Youde Nethersole Eastern Hospital, Hong Kong, SAR, People's Republic of China
| | - Choi-Ting Alan Tse
- Department of Medicine, Yan Chai Hospital, Hong Kong, SAR, People's Republic of China
| | - Li-Yan Lilian Tsung
- Department of Paediatrics and Adolescent Medicine, Pamela Youde Nethersole Eastern Hospital, Hong Kong, SAR, People's Republic of China
| | - Ho-Ming June Wong
- Department of Medicine and Geriatrics, Caritas Medical Centre, Hong Kong, SAR, People's Republic of China
| | - Wing-Yin Winnie Wong
- Department of Medicine and Geriatrics, Caritas Medical Centre, Hong Kong, SAR, People's Republic of China
| | - Kwok-Kui Wong
- Department of Medicine, Yan Chai Hospital, Hong Kong, SAR, People's Republic of China
| | - Suet-Na Sheila Wong
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong, SAR, People's Republic of China
| | - Chun-Nei Virginia Wong
- Department of Paediatrics & Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, People's Republic of China
| | - Wai-Shan Sammy Wong
- Department of Pathology, Queen Elizabeth Hospital, Hong Kong, SAR, People's Republic of China
| | - Chi-Kin Felix Wong
- Department of Chemical Pathology, Queen Mary Hospital, Hong Kong, SAR, People's Republic of China
| | - Shun-Ping Wu
- Department of Paediatrics and Adolescent Medicine, Queen Elizabeth Hospital, Hong Kong, SAR, People's Republic of China
| | - Hiu-Fung Jerome Wu
- Department of Medicine and Geriatrics, Princess Margaret Hospital, Hong Kong, SAR, People's Republic of China
| | - Man-Mut Yau
- Department of Paediatrics and Adolescent Medicine, Tseung Kwan O Hospital, Hong Kong, SAR, People's Republic of China
| | - Kin-Cheong Eric Yau
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, SAR, People's Republic of China
| | - Wai-Lan Yeung
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong, SAR, People's Republic of China
| | - Hon-Ming Jonas Yeung
- Department of Medicine, Alice Ho Miu Ling Nethersole Hospital, Hong Kong, SAR, People's Republic of China
| | - Kin-Keung Edwin Yip
- Department of Medicine and Geriatrics, Ruttonjee and Tang Shiu Kin Hospitals, Hong Kong, SAR, People's Republic of China
| | - Pui-Hong Terence Young
- Department of Medicine and Geriatrics, Ruttonjee and Tang Shiu Kin Hospitals, Hong Kong, SAR, People's Republic of China
| | - Gao Yuan
- Department of Medicine, Queen Mary Hospital, Hong Kong, SAR, People's Republic of China
| | - Yuet-Ping Liz Yuen
- Department of Chemical Pathology, Hong Kong Children's Hospital, Hong Kong, SAR, People's Republic of China
| | - Chi-Lap Yuen
- Department of Medicine and Geriatrics, Tuen Mun Hospital, Hong Kong, SAR, People's Republic of China
| | - Cheuk-Wing Fung
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong, SAR, People's Republic of China.
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Mitochondrial tRNAGln 4394C>T Mutation May Contribute to the Clinical Expression of 1555A>G-Induced Deafness. Genes (Basel) 2022; 13:genes13101794. [PMID: 36292680 PMCID: PMC9602358 DOI: 10.3390/genes13101794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
The mitochondrial 1555A>G mutation plays a critical role in aminoglycoside-induced and non-syndromic hearing loss (AINSHL). Previous studies have suggested that mitochondrial secondary variants may modulate the clinical expression of m.1555A>G-induced deafness, but the molecular mechanism has remained largely undetermined. In this study, we investigated the contribution of a deafness-associated tRNAGln 4394C>T mutation to the clinical expression of the m.1555A>G mutation. Interestingly, a three-generation family with both the m.1555A>G and m.4394C>T mutations exhibited a higher penetrance of hearing loss than another family harboring only the m.1555A>G mutation. At the molecular level, the m.4394C>T mutation resides within a very conserved nucleotide of tRNAGln, which forms a new base-pairing (7T-66A) and may affect tRNA structure and function. Using trans-mitochondrial cybrid cells derived from three subjects with both the m.1555A>G and m.4394C>T mutations, three patients with only the m.1555A>G mutation and three control subjects without these primary mutations, we observed that cells with both the m.1555A>G and m.4394C>T mutations exhibited more severely impaired mitochondrial functions than those with only the m.1555A>G mutation. Furthermore, a marked decrease in mitochondrial RNA transcripts and respiratory chain enzymes was observed in cells harboring both the m.1555A>G and m.4394C>T mutations. Thus, our data suggest that the m.4394C>T mutation may play a synergistic role in the m.1555A>G mutation, enhancing mitochondrial dysfunctions and contributing to a high penetrance of hearing loss in families with both mtDNA pathogenic mutations.
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Ray M, Sarkar S, Sable MN. Genetics Landscape of Nonsyndromic Hearing Loss in Indian Populations. J Pediatr Genet 2021; 11:5-14. [PMID: 35186384 PMCID: PMC8847051 DOI: 10.1055/s-0041-1740532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/12/2021] [Indexed: 12/16/2022]
Abstract
Congenital nonsyndromic hearing loss (NSHL) has been considered as one of the most prevalent chronic disorder in children. It affects the physical and mental conditions of a large children population worldwide. Because of the genetic heterogeneity, the identification of target gene is very challenging. However, gap junction β-2 ( GJB2 ) is taken as the key gene for hearing loss, as its involvement has been reported frequently in NSHL cases. This study aimed to identify the association of GJB2 mutants in different Indian populations based on published studies in Indian population. This will provide clear genetic fundamental of NSHL in Indian biogeography, which would be helpful in the diagnosis process.
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Affiliation(s)
- Manisha Ray
- Department of Pathology and Lab Medicine, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India
| | - Saurav Sarkar
- Department of Otolaryngology, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India
| | - Mukund Namdev Sable
- Department of Pathology and Lab Medicine, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India,Address for correspondence Mukund Namdev Sable, MD Department of Pathology and Lab Medicine, All India Institute of Medical SciencesBhubaneswar 751019, OdishaIndia
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Murtaza M, Zargar MH, Ali O, Khan IS, Ali MN. Spectrum and frequency of connexin 26 & connexin 30 gene mutations in patients with congenital hearing loss from Ladakh India. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Vanniya S P, Chandru J, Jeffrey JM, Rabinowitz T, Brownstein Z, Krishnamoorthy M, Avraham KB, Cheng L, Shomron N, Srisailapathy CRS. PNPT1, MYO15A, PTPRQ, and SLC12A2-associated genetic and phenotypic heterogeneity among hearing impaired assortative mating families in Southern India. Ann Hum Genet 2021; 86:1-13. [PMID: 34374074 DOI: 10.1111/ahg.12442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 12/24/2022]
Abstract
The study was conducted between 2018 and 2020. From a cohort of 113 hearing impaired (HI), five non-DFNB12 probands identified with heterozygous CDH23 variants were subjected to exome analysis. This resolved the etiology of hearing loss (HL) in four South Indian assortative mating families. Six variants, including three novel ones, were identified in four genes: PNPT1 p.(Ala46Gly) and p.(Asn540Ser), MYO15A p.(Leu1485Pro) and p.(Tyr1891Ter), PTPRQ p.(Gln1336Ter), and SLC12A2 p.(Pro988Ser). Compound heterozygous PNPT1 variants were associated with DFNB70 causing prelingual profound sensorineural hearing loss (SNHL), vestibular dysfunction, and unilateral progressive vision loss in one family. In the second family, MYO15A variants in the myosin motor domain, including a novel variant, causing DFNB3, were found to be associated with prelingual profound SNHL. A novel PTPRQ variant was associated with postlingual progressive sensorineural/mixed HL and vestibular dysfunction in the third family with DFNB84A. In the fourth family, the SLC12A2 novel variant was found to segregate with severe-to-profound HL causing DFNA78, across three generations. Our results suggest a high level of allelic, genotypic, and phenotypic heterogeneity of HL in these families. This study is the first to report the association of PNPT1, PTPRQ, and SLC12A2 variants with HL in the Indian population.
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Affiliation(s)
- Paridhy Vanniya S
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, India
| | - Jayasankaran Chandru
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, India.,LifeBytes India Pvt. Ltd., Bengaluru, India
| | - Justin Margret Jeffrey
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, India
| | - Tom Rabinowitz
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zippora Brownstein
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Mathuravalli Krishnamoorthy
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, India
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Le Cheng
- BGI Genomics, Shenzhen, P. R. China
| | - Noam Shomron
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - C R Srikumari Srisailapathy
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, India
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8
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Amritkumar P, Jeffrey JM, Chandru J, Vanniya S P, Kalaimathi M, Ramakrishnan R, Karthikeyen NP, Srikumari Srisailapathy CR. Role of DFNB1 mutations in hereditary hearing loss among assortative mating hearing impaired families from South India. BMC MEDICAL GENETICS 2018; 19:105. [PMID: 29921236 PMCID: PMC6008914 DOI: 10.1186/s12881-018-0609-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/18/2018] [Indexed: 08/14/2023]
Abstract
Background DFNB1, the first locus to have been associated with deafness, has two major genes GJB2 & GJB6, whose mutations have played vital role in hearing impairment across many ethnicities in the world. In our present study we have focused on the role of these mutations in assortative mating hearing impaired families from south India. Methods One hundred and six assortatively mating hearing impaired (HI) families of south Indian origin comprising of two subsets: 60 deaf marrying deaf (DXD) families and 46 deaf marrying normal hearing (DXN) families were recruited for this study. In the 60 DXD families, 335 members comprising of 118 HI mates, 63 other HI members and 154 normal hearing members and in the 46 DXN families, 281 members comprising of 46 HI and their 43 normal hearing partners, 50 other HI members and 142 normal hearing family members, participated in the molecular study. One hundred and sixty five (165) healthy normal hearing volunteers were recruited as controls for this study. All the participating members were screened for variants in GJB2 and GJB6 genes and the outcome of gene mutations were compared in the subsequent generation in begetting deaf offspring. Results The DFNB1 allele frequencies for DXD mates and their offspring were 36.98 and 38.67%, respectively and for the DXN mates and their offspring were 22.84 and 24.38%, respectively. There was a 4.6% increase in the subsequent generation in the DXD families, while a 6.75% increase in the DXN families, which demonstrates the role of assortative mating along with consanguinity in the increase of DFNB1 mutations in consecutive generations. Four novel variants, p.E42D (in GJB2 gene), p.Q57R, p.E101Q, p.R104H (in GJB6 gene) were also identified in this study. Conclusion This is the first study from an Indian subcontinent reporting novel variants in the coding region of GJB6 gene. This is perhaps the first study in the world to test real-time, the hypothesis proposed by Nance et al. in 2000 (intense phenotypic assortative mating mechanism can double the frequency of the commonest forms of recessive deafness [DFNB1]) in assortative mating HI parental generation and their offspring.
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Affiliation(s)
- Pavithra Amritkumar
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, India.,Current affiliation: PG and Research Department of Biotechnology, Women's Christian College, Chennai, India
| | - Justin Margret Jeffrey
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, India
| | - Jayasankaran Chandru
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, India
| | - Paridhy Vanniya S
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, India
| | - M Kalaimathi
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, India
| | - Rajagopalan Ramakrishnan
- Department of ENT, SRM Medical College Hospital and Research Centre, SRM Institute of Science and Technology, Kattankulathur, India
| | - N P Karthikeyen
- DOAST Hearing Care Center, Anna Nagar, Chennai, 600040, India
| | - C R Srikumari Srisailapathy
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, India.
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9
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Meng F, He Z, Tang X, Zheng J, Jin X, Zhu Y, Ren X, Zhou M, Wang M, Gong S, Mo JQ, Shu Q, Guan MX. Contribution of the tRNA Ile 4317A→G mutation to the phenotypic manifestation of the deafness-associated mitochondrial 12S rRNA 1555A→G mutation. J Biol Chem 2018; 293:3321-3334. [PMID: 29348176 DOI: 10.1074/jbc.ra117.000530] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/14/2018] [Indexed: 12/28/2022] Open
Abstract
The 1555A→G mutation in mitochondrial 12S rRNA has been associated with aminoglycoside-induced and non-syndromic deafness in many individuals worldwide. Mitochondrial genetic modifiers are proposed to influence the phenotypic expression of m.1555A→G mutation. Here, we report that a deafness-susceptibility allele (m.4317A→G) in the tRNAIle gene modulates the phenotype expression of m.1555A→G mutation. Strikingly, a large Han Chinese pedigree carrying both m.4317A→G and m.1555A→G mutations exhibited much higher penetrance of deafness than those carrying only the m.1555A→G mutation. The m.4317A→G mutation affected a highly conserved adenine at position 59 in the T-loop of tRNAIle We therefore hypothesized that the m.4317A→G mutation alters both structure and function of tRNAIle Using lymphoblastoid cell lines derived from members of Chinese families (three carrying both m.1555A→G and m.4317A→G mutations, three harboring only m.1555A→G mutation, and three controls lacking these mutations), we found that the cell lines bearing both m.4317A→G and m.1555A→G mutations exhibited more severe mitochondrial dysfunctions than those carrying only the m.1555A→G mutation. We also found that the m.4317A→G mutation perturbed the conformation, stability, and aminoacylation efficiency of tRNAIle These m.4317A→G mutation-induced alterations in tRNAIle structure and function aggravated the defective mitochondrial translation and respiratory phenotypes associated with the m.1555A→G mutation. Furthermore, mutant cell lines bearing both m.4317A→G and m.1555A→G mutations exhibited greater reductions in the mitochondrial ATP levels and membrane potentials and increasing production of reactive oxygen species than those carrying only the m.1555A→G mutation. Our findings provide new insights into the pathophysiology of maternally inherited deafness arising from the synergy between mitochondrial 12S rRNA and tRNA mutations.
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Affiliation(s)
- Feilong Meng
- From the Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China.,the Institute of Genetics
| | - Zheyun He
- the Attardi Institute of Mitochondrial Biomedicine, School of Life Sciences, and.,the Institute of Liver Diseases, Ningbo Secondary Hospital, Ningbo, Zhejiang 315010, China
| | - Xiaowen Tang
- the Attardi Institute of Mitochondrial Biomedicine, School of Life Sciences, and
| | - Jing Zheng
- From the Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China.,the Institute of Genetics
| | | | - Yi Zhu
- Department of Otolaryngology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Xiaoyan Ren
- the Attardi Institute of Mitochondrial Biomedicine, School of Life Sciences, and
| | - Mi Zhou
- From the Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China.,the Institute of Genetics
| | - Meng Wang
- From the Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China.,the Institute of Genetics
| | - Shasha Gong
- the Institute of Genetics.,the School of Medicine, Taizhou College, Taizhou, Zhejiang 318000, China, and
| | - Jun Qin Mo
- the Department of Pathology, Rady Children's Hospital, University of California at San Diego, San Diego, California 92123
| | - Qiang Shu
- From the Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China,
| | - Min-Xin Guan
- From the Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China, .,the Institute of Genetics.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, and.,Joint Institute of Genetics and Genome Medicine between Zhejiang University and University of Toronto, Zhejiang University, Hangzhou, Zhejiang 310058, China
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