1
|
Sharma N, Kumari D, Panigrahi I, Khetarpal P. A systematic review of the monogenic causes of Non-Syndromic Hearing Loss (NSHL) and discussion of Current Diagnosis and Treatment options. Clin Genet 2023; 103:16-34. [PMID: 36089522 DOI: 10.1111/cge.14228] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 12/13/2022]
Abstract
Hearing impairment is one of the most widespread inheritable sensory disorder affecting at least 1 in every 1000 born. About two-third of hereditary hearing loss (HHL) disorders are non-syndromic. To provide comprehensive update of monogenic causes of non-syndromic hearing loss (NSHL), literature search has been carried out with appropriate keywords in the following databases-PubMed, Google Scholar, Cochrane library, and Science Direct. Out of 2214 papers, 271 papers were shortlisted after applying inclusion and exclusion criterion. Data extracted from selected papers include information about gene name, identified pathogenic variants, ethnicity of the patient, age of onset, gender, title, authors' name, and year of publication. Overall, pathogenic variants in 98 different genes have been associated with NSHL. These genes have important role to play during early embryonic development in ear structure formation and hearing development. Here, we also review briefly the recent information about diagnosis and treatment approaches. Understanding pathogenic genetic variants are helpful in the management of affected and may offer targeted therapies in future.
Collapse
Affiliation(s)
- Nandita Sharma
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Divya Kumari
- Department of Pediatrics Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Inusha Panigrahi
- Department of Pediatrics Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Preeti Khetarpal
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| |
Collapse
|
3
|
Ignatieva EV, Matrosova EA. Disease-associated genetic variants in the regulatory regions of human genes: mechanisms of action on transcription and genomic resources for dissecting these mechanisms. Vavilovskii Zhurnal Genet Selektsii 2021; 25:18-29. [PMID: 34541447 PMCID: PMC8408020 DOI: 10.18699/vj21.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 11/21/2022] Open
Abstract
Whole genome and whole exome sequencing technologies play a very important role in the studies of the genetic aspects of the pathogenesis of various diseases. The ample use of genome-wide and exome-wide association study
methodology (GWAS and EWAS) made it possible to identify a large number of genetic variants associated with diseases.
This information is accumulated in the databases like GWAS central, GWAS catalog, OMIM, ClinVar, etc. Most of the variants identified by the GWAS technique are located in the noncoding regions of the human genome. According to the
ENCODE project, the fraction of regions in the human genome potentially involved in transcriptional control is many times
greater than the fraction of coding regions. Thus, genetic variation in noncoding regions of the genome can increase the
susceptibility to diseases by disrupting various regulatory elements (promoters, enhancers, silencers, insulator regions,
etc.). However, identification of the mechanisms of influence of pathogenic genetic variants on the diseases risk is difficult
due to a wide variety of regulatory elements. The present review focuses on the molecular genetic mechanisms by which
pathogenic genetic variants affect gene expression. At the same time, attention is concentrated on the transcriptional level
of regulation as an initial step in the expression of any gene. A triggering event mediating the effect of a pathogenic genetic
variant on the level of gene expression can be, for example, a change in the functional activity of transcription factor binding sites (TFBSs) or DNA methylation change, which, in turn, affects the functional activity of promoters or enhancers. Dissecting the regulatory roles of polymorphic loci have been impossible without close integration of modern experimental
approaches with computer analysis of a growing wealth of genetic and biological data obtained using omics technologies.
The review provides a brief description of a number of the most well-known public genomic information resources containing data obtained using omics technologies, including (1) resources that accumulate data on the chromatin states and the
regions of transcription factor binding derived from ChIP-seq experiments; (2) resources containing data on genomic loci,
for which allele-specific transcription factor binding was revealed based on ChIP-seq technology; (3) resources containing
in silico predicted data on the potential impact of genetic variants on the transcription factor binding sites
Collapse
Affiliation(s)
- E V Ignatieva
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - E A Matrosova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| |
Collapse
|
4
|
Fang X, Zhang Y, Cai J, Lu T, Hu J, Yuan F, Chen P. Identification of novel candidate pathogenic genes in pituitary stalk interruption syndrome by whole-exome sequencing. J Cell Mol Med 2020; 24:11703-11717. [PMID: 32864857 PMCID: PMC7579688 DOI: 10.1111/jcmm.15781] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 06/25/2020] [Accepted: 07/30/2020] [Indexed: 12/19/2022] Open
Abstract
Pituitary stalk interruption syndrome (PSIS) is a type of congenital malformation of the anterior pituitary, which leads to isolated growth hormone deficiency or multiple hypothalamic-pituitary deficiencies. Many genetic factors have been explored, but they only account for a minority of the genetic aetiology. To identify novel PSIS pathogenic genes, we conducted whole-exome sequencing with 59 sporadic PSIS patients, followed by filtering gene panels involved in pituitary development, holoprosencephaly and midline abnormality. A total of 81 heterozygous variants, distributed among 59 genes, were identified in 50 patients, with 31 patients carrying polygenic variants. Fourteen of the 59 pathogenic genes clustered to the Hedgehog pathway. Of them, PTCH1 and PTCH2, inhibitors of Hedgehog signalling, showed the most frequent heterozygous mutations (22%, seven missense and one frameshift mutations were identified in 13 patients). Moreover, five novel heterozygous null variants in genes including PTCH2 (p.S391fs, combined with p.L104P), Hedgehog acyltransferase (p.R280X, de novo), MAPK3 (p.H50fs), EGR4 (p.G22fs, combined with LHX4 p.S263N) and SPG11 (p.Q1624X), which lead to truncated proteins, were identified. In conclusion, genetic mutations in the Hedgehog signalling pathway might underlie the complex polygenic background of PSIS, and the findings of our study could extend the understanding of PSIS pathogenic genes.
Collapse
Affiliation(s)
- Xuqian Fang
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuwen Zhang
- Department of Endocrinology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jialin Cai
- Clinical Research Center, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tingwei Lu
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junjie Hu
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fei Yuan
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peizhan Chen
- Clinical Research Center, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
5
|
De la Casa-Fages B, Fernández-Eulate G, Gamez J, Barahona-Hernando R, Morís G, García-Barcina M, Infante J, Zulaica M, Fernández-Pelayo U, Muñoz-Oreja M, Urtasun M, Olaskoaga A, Zelaya V, Jericó I, Saez-Villaverde R, Catalina I, Sola E, Martínez-Sáez E, Pujol A, Ruiz M, Schlüter A, Spinazzola A, Muñoz-Blanco JL, Grandas F, Holt I, Álvarez V, López de Munaín A. Parkinsonism and spastic paraplegia type 7: Expanding the spectrum of mitochondrial Parkinsonism. Mov Disord 2019; 34:1547-1561. [PMID: 31433872 DOI: 10.1002/mds.27812] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 07/02/2019] [Accepted: 07/14/2019] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Pathogenic variants in the spastic paraplegia type 7 gene cause a complicated hereditary spastic paraplegia phenotype associated with classical features of mitochondrial diseases, including ataxia, progressive external ophthalmoplegia, and deletions of mitochondrial DNA. OBJECTIVES To better characterize spastic paraplegia type 7 disease with a clinical, genetic, and functional analysis of a Spanish cohort of spastic paraplegia type 7 patients. METHODS Genetic analysis was performed in patients suspecting hereditary spastic paraplegia and in 1 patient with parkinsonism and Pisa syndrome, through next-generation sequencing, whole-exome sequencing, targeted Sanger sequencing, and multiplex ligation-dependent probe analysis, and blood mitochondrial DNA levels determined by quantitative polymerase chain reaction. RESULTS Thirty-five patients were found to carry homozygous or compound heterozygous pathogenic variants in the spastic paraplegia type 7 gene. Mean age at onset was 40 years (range, 12-63); 63% of spastic paraplegia type 7 patients were male, and three-quarters of all patients had at least one allele with the c.1529C>T (p.Ala510Val) mutation. Eighty percent of the cohort showed a complicated phenotype, combining ataxia and progressive external ophthalmoplegia (65% and 26%, respectively). Parkinsonism was observed in 21% of cases. Analysis of blood mitochondrial DNA indicated that both patients and carriers of spastic paraplegia type 7 pathogenic variants had markedly lower levels of mitochondrial DNA than control subjects (228 per haploid nuclear DNA vs. 176 vs. 573, respectively; P < 0.001). CONCLUSIONS Parkinsonism is a frequent finding in spastic paraplegia type 7 patients. Spastic paraplegia type 7 pathogenic variants impair mitochondrial DNA homeostasis irrespective of the number of mutant alleles, type of variant, and patient or carrier status. Thus, spastic paraplegia type 7 supports mitochondrial DNA maintenance, and variants in the gene may cause parkinsonism owing to mitochondrial DNA abnormalities. Moreover, mitochondrial DNA blood analysis could be a useful biomarker to detect at risk families. © 2019 International Parkinson and Movement Disorder Society.
Collapse
Affiliation(s)
- Beatriz De la Casa-Fages
- Department of Neurology, Hospital General Universitario Gregorio Marañon, Madrid, Spain.,Movement Disorders Unit, National Referral Center for rare diseases with Movement Disorders (CSUR), Hospital General Universitario Gregorio Marañon, Madrid, Spain.,Neurosciences Area, Instituto Investigacion Sanitaria Gregorio Marañon, Madrid, Spain
| | - Gorka Fernández-Eulate
- Department of Neurology, Hospital Universitario Donostia, San Sebastian, Spain.,Department of Neurosciences, Instituto Biodonostia, San Sebastian, Spain
| | - Josep Gamez
- Department of Neurology, Hospital General Universitari Vall d'Hebron-UAB-VHIR, Barcelona, Spain.,European Reference Network on Rare Neurological Diseases (ERN-RND), Hospital General Universitari Vall d'Hebron-UAB, Barcelona, Spain
| | - Raúl Barahona-Hernando
- Department of Neurology, Hospital General Universitario Gregorio Marañon, Madrid, Spain.,ALS-Neuromuscular Unit, Hospital General Universitario Gregorio Marañon, Madrid, Spain.,Department of Neurology, Hospital Ruber Juan Bravo, Grupo Quironsalud, Madrid, Spain
| | - Germán Morís
- Instituto de Investigación Biosanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Department of Neurology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | | | - Jon Infante
- Department of Neurology, Hospital Universitario Marques de Valdecilla-IDIVAL, University of Cantabria, Santander, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Institute Carlos III, Spain
| | - Miren Zulaica
- Department of Neurosciences, Instituto Biodonostia, San Sebastian, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Institute Carlos III, Spain
| | | | - Mikel Muñoz-Oreja
- Department of Neurosciences, Instituto Biodonostia, San Sebastian, Spain
| | - Miguel Urtasun
- Department of Neurology, Hospital Universitario Donostia, San Sebastian, Spain
| | | | - Victoria Zelaya
- Department of Pathology, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - Ivonne Jericó
- Department of Neurology, Complejo Hospitalario de Navarra, Pamplona, Spain
| | | | - Irene Catalina
- Department of Neurology, Hospital General Universitario Gregorio Marañon, Madrid, Spain.,ALS-Neuromuscular Unit, Hospital General Universitario Gregorio Marañon, Madrid, Spain
| | - Emma Sola
- Department of Pathology, Hospital General Universitario Gregorio Marañon, Madrid, Spain
| | - Elena Martínez-Sáez
- Department of Pathology, Hospital General Universitari Vall d'Hebron-UAB-VHIR, Barcelona, Spain.,Department of Medicine, UAB, Barcelona, Spain
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,Center for Biomedical Research on Rare Diseases (CIBERER), Institute Carlos III, Madrid, Spain
| | - Montserrat Ruiz
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,Center for Biomedical Research on Rare Diseases (CIBERER), Institute Carlos III, Madrid, Spain
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,Center for Biomedical Research on Rare Diseases (CIBERER), Institute Carlos III, Madrid, Spain
| | - Antonella Spinazzola
- Department of Clinical Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London, United Kingdom.,MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology and National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Jose Luis Muñoz-Blanco
- Department of Neurology, Hospital General Universitario Gregorio Marañon, Madrid, Spain.,Neurosciences Area, Instituto Investigacion Sanitaria Gregorio Marañon, Madrid, Spain.,ALS-Neuromuscular Unit, Hospital General Universitario Gregorio Marañon, Madrid, Spain
| | - Francisco Grandas
- Department of Neurology, Hospital General Universitario Gregorio Marañon, Madrid, Spain.,Movement Disorders Unit, National Referral Center for rare diseases with Movement Disorders (CSUR), Hospital General Universitario Gregorio Marañon, Madrid, Spain.,Neurosciences Area, Instituto Investigacion Sanitaria Gregorio Marañon, Madrid, Spain
| | - Ian Holt
- Department of Neurosciences, Instituto Biodonostia, San Sebastian, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Victoria Álvarez
- Instituto de Investigación Biosanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Genetics Laboratory, AGC Medicine Laboratory, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Adolfo López de Munaín
- Department of Neurology, Hospital Universitario Donostia, San Sebastian, Spain.,Department of Neurosciences, Instituto Biodonostia, San Sebastian, Spain.,Department of Neurosciences UPV/EHU, San Sebastian, Spain.,Ciberned, Ministry of Science, Innovation and Universities, Madrid, Spain
| |
Collapse
|