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Zafeer MF, Ramzan M, Duman D, Mutlu A, Seyhan S, Kalcioglu T, Fitoz S, DeRosa BA, Guo S, Dykxhoorn DM, Tekin M. Human Organoids for Rapid Validation of Gene Variants Linked to Cochlear Malformations. RESEARCH SQUARE 2024:rs.3.rs-4474071. [PMID: 38947059 PMCID: PMC11213182 DOI: 10.21203/rs.3.rs-4474071/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Developmental anomalies of the hearing organ, the cochlea, are diagnosed in approximately one-fourth of individuals with congenital deafness. Most patients with cochlear malformations remain etiologically undiagnosed due to insufficient knowledge about underlying genes or the inability to make conclusive interpretations of identified genetic variants. We used exome sequencing for genetic evaluation of hearing loss associated with cochlear malformations in three probands from unrelated families. We subsequently generated monoclonal induced pluripotent stem cell (iPSC) lines, bearing patient-specific knockins and knockouts using CRISPR/Cas9 to assess pathogenicity of candidate variants. We detected FGF3 (p.Arg165Gly) and GREB1L (p.Cys186Arg), variants of uncertain significance in two recognized genes for deafness, and PBXIP1 (p.Trp574*) in a candidate gene. Upon differentiation of iPSCs towards inner ear organoids, we observed significant developmental aberrations in knockout lines compared to their isogenic controls. Patient-specific single nucleotide variants (SNVs) showed similar abnormalities as the knockout lines, functionally supporting their causality in the observed phenotype. Therefore, we present human inner ear organoids as a tool to rapidly validate the pathogenicity of DNA variants associated with cochlear malformations.
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2
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Zhao E, Bomback M, Khan A, Murthy SK, Solowiejczyk D, Vora NL, Gilmore KL, Giordano JL, Wapner RJ, Sanna-Cherchi S, Lyford A, Jelin AC, Gharavi AG, Hays T. The expanded spectrum of human disease associated with GREB1L likely includes complex congenital heart disease. Prenat Diagn 2024; 44:343-351. [PMID: 38285371 PMCID: PMC11040453 DOI: 10.1002/pd.6527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
OBJECTIVE GREB1L has been linked prenatally to Potter's sequence, as well as less severe anomalies of the kidney, uterus, inner ear, and heart. The full phenotypic spectrum is unknown. The purpose of this study was to characterize known and novel pre- and postnatal phenotypes associated with GREB1L. METHODS We solicited cases from the Fetal Sequencing Consortium, screened a population-based genomic database, and conducted a comprehensive literature search to identify disease cases associated with GREB1L. We present a detailed phenotypic spectrum and molecular changes. RESULTS One hundred twenty-seven individuals with 51 unique pathogenic or likely pathogenic GREB1L variants were identified. 24 (47%) variants were associated with isolated kidney anomalies, 19 (37%) with anomalies of multiple systems, including one case of hypoplastic left heart syndrome, five (10%) with isolated sensorineural hearing loss, two (4%) with isolated uterine agenesis; and one (2%) with isolated tetralogy of Fallot. CONCLUSION GREB1L may cause complex congenital heart disease (CHD) in humans. Clinicians should consider GREB1L testing in the setting of CHD, and cardiac screening in the setting of GREB1L variants.
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Affiliation(s)
- Emily Zhao
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Miles Bomback
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Atlas Khan
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Sarath Krishna Murthy
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - David Solowiejczyk
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Neeta L. Vora
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, North Carolina, USA
| | - Kelly L. Gilmore
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, North Carolina, USA
| | - Jessica L. Giordano
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
| | - Ronald J. Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
| | - Simone Sanna-Cherchi
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Alex Lyford
- Department of Mathematics and Statistics, Middlebury College, Middlebury, Vermont, USA
| | - Angie C. Jelin
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ali G. Gharavi
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Thomas Hays
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
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3
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Fan L, Shen G, Liu M, Liang Y, Yao J, Ding Z, Li Z, Feng X, Zhang J, Shen X. Renal Hypodysplasia/Aplasia 3 Caused by a Rare Variant of GREB1L With Incomplete Penetrance in a Chinese Family. Urology 2024; 185:49-53. [PMID: 38309594 DOI: 10.1016/j.urology.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/15/2023] [Accepted: 01/10/2024] [Indexed: 02/05/2024]
Abstract
Renal agenesis represents the most severe form of congenital anomalies of the kidney and urinary tract. Bilateral renal agenesis is almost invariably fatal at birth and has high genetic heterogeneity. Here we report on a Chinese family with two pregnancies affected by a prenatal form of bilateral renal agenesis. Trio-WES was conducted to explore the underlying genetic cause and identified a novel nonsense variant (c .2621G>A: p. Trp874Ter) in the GREB1L gene. Based on previous research, pathogenic mutations in GREB1L can cause renal hypodysplasia/aplasia-3 (RHDA3) with autosomal dominant inheritance. Sanger sequencing performed on the family members revealed that the variant was vertically transmitted from the maternal grandfather through the unaffected mother to the two affected fetuses, fully demonstrating the incomplete dominance of the disease. Our study extends the mutational spectrum associated with RHDA3 and contributes to a more general understanding for the complex genetic inheritance of GREB1L.
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Affiliation(s)
- Lihong Fan
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Guosong Shen
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Mingsong Liu
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Yufei Liang
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Juan Yao
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Zhongying Ding
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Zhi Li
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Xiangping Feng
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Jinghui Zhang
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Xueping Shen
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China.
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4
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Maksiutenko EM, Barbitoff YA, Nasykhova YA, Pachuliia OV, Lazareva TE, Bespalova ON, Glotov AS. The Landscape of Point Mutations in Human Protein Coding Genes Leading to Pregnancy Loss. Int J Mol Sci 2023; 24:17572. [PMID: 38139401 PMCID: PMC10743817 DOI: 10.3390/ijms242417572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Pregnancy loss is the most frequent complication of a pregnancy which is devastating for affected families and poses a significant challenge for the health care system. Genetic factors are known to play an important role in the etiology of pregnancy loss; however, despite advances in diagnostics, the causes remain unexplained in more than 30% of cases. In this review, we aggregated the results of the decade-long studies into the genetic risk factors of pregnancy loss (including miscarriage, termination for fetal abnormality, and recurrent pregnancy loss) in euploid pregnancies, focusing on the spectrum of point mutations associated with these conditions. We reviewed the evolution of molecular genetics methods used for the genetic research into causes of pregnancy loss, and collected information about 270 individual genetic variants in 196 unique genes reported as genetic cause of pregnancy loss. Among these, variants in 18 genes have been reported by multiple studies, and two or more variants were reported as causing pregnancy loss for 57 genes. Further analysis of the properties of all known pregnancy loss genes showed that they correspond to broadly expressed, highly evolutionary conserved genes involved in crucial cell differentiation and developmental processes and related signaling pathways. Given the features of known genes, we made an effort to construct a list of candidate genes, variants in which may be expected to contribute to pregnancy loss. We believe that our results may be useful for prediction of pregnancy loss risk in couples, as well as for further investigation and revealing genetic etiology of pregnancy loss.
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Affiliation(s)
| | - Yury A. Barbitoff
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (E.M.M.); (Y.A.N.); (O.V.P.); (T.E.L.); (O.N.B.)
| | | | | | | | | | - Andrey S. Glotov
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (E.M.M.); (Y.A.N.); (O.V.P.); (T.E.L.); (O.N.B.)
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5
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Bernheim S, Borgel A, Le Garrec JF, Perthame E, Desgrange A, Michel C, Guillemot L, Sart S, Baroud CN, Krezel W, Raimondi F, Bonnet D, Zaffran S, Houyel L, Meilhac SM. Identification of Greb1l as a genetic determinant of crisscross heart in mice showing torsion of the heart tube by shortage of progenitor cells. Dev Cell 2023; 58:2217-2234.e8. [PMID: 37852253 DOI: 10.1016/j.devcel.2023.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/28/2023] [Accepted: 09/20/2023] [Indexed: 10/20/2023]
Abstract
Despite their burden, most congenital defects remain poorly understood, due to lack of knowledge of embryological mechanisms. Here, we identify Greb1l mutants as a mouse model of crisscross heart. Based on 3D quantifications of shape changes, we demonstrate that torsion of the atrioventricular canal occurs together with supero-inferior ventricles at E10.5, after heart looping. Mutants phenocopy partial deficiency in retinoic acid signaling, which reflect overlapping pathways in cardiac precursors. Spatiotemporal gene mapping and cross-correlated transcriptomic analyses further reveal the role of Greb1l in maintaining a pool of dorsal pericardial wall precursor cells during heart tube elongation, likely by controlling ribosome biogenesis and cell differentiation. Consequently, we observe growth arrest and malposition of the outflow tract, which are predictive of abnormal tube remodeling in mutants. Our work on a rare cardiac malformation opens novel perspectives on the origin of a broader spectrum of congenital defects associated with GREB1L in humans.
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Affiliation(s)
- Ségolène Bernheim
- Université Paris Cité, Imagine-Institut Pasteur, Unit of Heart Morphogenesis, INSERM UMR1163, 75015 Paris, France
| | - Adrien Borgel
- Université Paris Cité, Imagine-Institut Pasteur, Unit of Heart Morphogenesis, INSERM UMR1163, 75015 Paris, France
| | - Jean-François Le Garrec
- Université Paris Cité, Imagine-Institut Pasteur, Unit of Heart Morphogenesis, INSERM UMR1163, 75015 Paris, France
| | - Emeline Perthame
- Université Paris Cité, Imagine-Institut Pasteur, Unit of Heart Morphogenesis, INSERM UMR1163, 75015 Paris, France; Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015 Paris, France
| | - Audrey Desgrange
- Université Paris Cité, Imagine-Institut Pasteur, Unit of Heart Morphogenesis, INSERM UMR1163, 75015 Paris, France
| | - Cindy Michel
- Université Paris Cité, Imagine-Institut Pasteur, Unit of Heart Morphogenesis, INSERM UMR1163, 75015 Paris, France
| | - Laurent Guillemot
- Université Paris Cité, Imagine-Institut Pasteur, Unit of Heart Morphogenesis, INSERM UMR1163, 75015 Paris, France
| | - Sébastien Sart
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bio-Engineering, Department of Genomes and Genetics, 75015 Paris, France
| | - Charles N Baroud
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bio-Engineering, Department of Genomes and Genetics, 75015 Paris, France; Laboratoire d'Hydrodynamique, CNRS, École polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Wojciech Krezel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Institut de la Santé et de la Recherche Médicale (U1258), Centre National de la Recherche Scientifique (UMR7104), Université de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg, 67404 Illkirch, France
| | - Francesca Raimondi
- Pediatric Radiology Unit, Hôpital universitaire Necker-Enfants Malades, APHP, Université Paris Cité, 149 Rue de Sèvres, 75015 Paris, France; M3C-Necker, Hôpital universitaire Necker-Enfants Malades, APHP, Université Paris Cité, 149 Rue de Sèvres, 75015 Paris, France
| | - Damien Bonnet
- M3C-Necker, Hôpital universitaire Necker-Enfants Malades, APHP, Université Paris Cité, 149 Rue de Sèvres, 75015 Paris, France
| | | | - Lucile Houyel
- M3C-Necker, Hôpital universitaire Necker-Enfants Malades, APHP, Université Paris Cité, 149 Rue de Sèvres, 75015 Paris, France
| | - Sigolène M Meilhac
- Université Paris Cité, Imagine-Institut Pasteur, Unit of Heart Morphogenesis, INSERM UMR1163, 75015 Paris, France.
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6
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Jolly A, Du H, Borel C, Chen N, Zhao S, Grochowski CM, Duan R, Fatih JM, Dawood M, Salvi S, Jhangiani SN, Muzny DM, Koch A, Rouskas K, Glentis S, Deligeoroglou E, Bacopoulou F, Wise CA, Dietrich JE, Van den Veyver IB, Dimas AS, Brucker S, Sutton VR, Gibbs RA, Antonarakis SE, Wu N, Coban-Akdemir ZH, Zhu L, Posey JE, Lupski JR. Rare variant enrichment analysis supports GREB1L as a contributory driver gene in the etiology of Mayer-Rokitansky-Küster-Hauser syndrome. HGG ADVANCES 2023; 4:100188. [PMID: 37124138 PMCID: PMC10130500 DOI: 10.1016/j.xhgg.2023.100188] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/24/2023] [Indexed: 05/02/2023] Open
Abstract
Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is characterized by aplasia of the female reproductive tract; the syndrome can include renal anomalies, absence or dysgenesis, and skeletal anomalies. While functional models have elucidated several candidate genes, only WNT4 (MIM: 603490) variants have been definitively associated with a subtype of MRKH with hyperandrogenism (MIM: 158330). DNA from 148 clinically diagnosed MRKH probands across 144 unrelated families and available family members from North America, Europe, and South America were exome sequenced (ES) and by family-based genomics analyzed for rare likely deleterious variants. A replication cohort consisting of 442 Han Chinese individuals with MRKH was used to further reproduce GREB1L findings in diverse genetic backgrounds. Proband and OMIM phenotypes annotated using the Human Phenotype Ontology were analyzed to quantitatively delineate the phenotypic spectrum associated with GREB1L variant alleles found in our MRKH cohort and those previously published. This study reports 18 novel GREB1L variant alleles, 16 within a multiethnic MRKH cohort and two within a congenital scoliosis cohort. Cohort-wide analyses for a burden of rare variants within a single gene identified likely damaging variants in GREB1L (MIM: 617782), a known disease gene for renal hypoplasia and uterine abnormalities (MIM: 617805), in 16 of 590 MRKH probands. GREB1L variant alleles, including a CNV null allele, were found in 8 MRKH type 1 probands and 8 MRKH type II probands. This study used quantitative phenotypic analyses in a worldwide multiethnic cohort to identify and strengthen the association of GREB1L to isolated uterine agenesis (MRKH type I) and syndromic MRKH type II.
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Affiliation(s)
- Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | | | - Na Chen
- Department of Obstetrics and Gynaecology, Beijing 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases and Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Chinese Academy of Medical Sciences, Beijing 100730, China
| | | | - Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Sejal Salvi
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Shalini N. Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
| | - André Koch
- University of Tübingen, Department of Obstetrics and Gynecology, Tübingen, Germany
| | - Konstantinos Rouskas
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Athens 16672, Greece
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Stavros Glentis
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Athens 16672, Greece
| | - Efthymios Deligeoroglou
- Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, First Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, Aghia Sophia Children’s Hospital, Athens 11527, Greece
| | - Flora Bacopoulou
- Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, First Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, Aghia Sophia Children’s Hospital, Athens 11527, Greece
| | - Carol A. Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
- McDermott Center for Human Growth and Development, Department of Pediatrics and Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Jennifer E. Dietrich
- Department of Obstetrics and Gynecology, Houston, TX, USA
- Department of Pediatrics, BCM, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Ignatia B. Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Department of Obstetrics and Gynecology, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Antigone S. Dimas
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Athens 16672, Greece
| | - Sara Brucker
- University of Tübingen, Department of Obstetrics and Gynecology, Tübingen, Germany
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Stylianos E. Antonarakis
- University of Geneva Medical School, 1211 Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva, University of Geneva, 1205 Geneva, Switzerland
- Medigenome, the Swiss Institute of Genomic Medicine, 1207 Geneva, Switzerland
| | - Nan Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases and Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zeynep H. Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Lan Zhu
- Department of Obstetrics and Gynaecology, Beijing 100730, China
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
- Department of Pediatrics, BCM, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
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7
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Aldè M, Cantarella G, Zanetti D, Pignataro L, La Mantia I, Maiolino L, Ferlito S, Di Mauro P, Cocuzza S, Lechien JR, Iannella G, Simon F, Maniaci A. Autosomal Dominant Non-Syndromic Hearing Loss (DFNA): A Comprehensive Narrative Review. Biomedicines 2023; 11:1616. [PMID: 37371710 DOI: 10.3390/biomedicines11061616] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Autosomal dominant non-syndromic hearing loss (HL) typically occurs when only one dominant allele within the disease gene is sufficient to express the phenotype. Therefore, most patients diagnosed with autosomal dominant non-syndromic HL have a hearing-impaired parent, although de novo mutations should be considered in all cases of negative family history. To date, more than 50 genes and 80 loci have been identified for autosomal dominant non-syndromic HL. DFNA22 (MYO6 gene), DFNA8/12 (TECTA gene), DFNA20/26 (ACTG1 gene), DFNA6/14/38 (WFS1 gene), DFNA15 (POU4F3 gene), DFNA2A (KCNQ4 gene), and DFNA10 (EYA4 gene) are some of the most common forms of autosomal dominant non-syndromic HL. The characteristics of autosomal dominant non-syndromic HL are heterogenous. However, in most cases, HL tends to be bilateral, post-lingual in onset (childhood to early adulthood), high-frequency (sloping audiometric configuration), progressive, and variable in severity (mild to profound degree). DFNA1 (DIAPH1 gene) and DFNA6/14/38 (WFS1 gene) are the most common forms of autosomal dominant non-syndromic HL affecting low frequencies, while DFNA16 (unknown gene) is characterized by fluctuating HL. A long audiological follow-up is of paramount importance to identify hearing threshold deteriorations early and ensure prompt treatment with hearing aids or cochlear implants.
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Affiliation(s)
- Mirko Aldè
- Department of Clinical Sciences and Community Health, University of Milan, 20090 Milan, Italy
- Department of Specialist Surgical Sciences, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy
- Otology Study Group of the Young-Otolaryngologists of the International Federations of Oto-Rhino-Laryngological Societies (YO-IFOS), 75000 Paris, France
| | - Giovanna Cantarella
- Department of Clinical Sciences and Community Health, University of Milan, 20090 Milan, Italy
- Department of Specialist Surgical Sciences, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy
| | - Diego Zanetti
- Department of Clinical Sciences and Community Health, University of Milan, 20090 Milan, Italy
- Department of Specialist Surgical Sciences, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy
| | - Lorenzo Pignataro
- Department of Clinical Sciences and Community Health, University of Milan, 20090 Milan, Italy
- Department of Specialist Surgical Sciences, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy
| | - Ignazio La Mantia
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
| | - Luigi Maiolino
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
| | - Salvatore Ferlito
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
| | - Paola Di Mauro
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
| | - Salvatore Cocuzza
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
| | - Jérôme René Lechien
- Otology Study Group of the Young-Otolaryngologists of the International Federations of Oto-Rhino-Laryngological Societies (YO-IFOS), 75000 Paris, France
| | - Giannicola Iannella
- Otology Study Group of the Young-Otolaryngologists of the International Federations of Oto-Rhino-Laryngological Societies (YO-IFOS), 75000 Paris, France
| | - Francois Simon
- Otology Study Group of the Young-Otolaryngologists of the International Federations of Oto-Rhino-Laryngological Societies (YO-IFOS), 75000 Paris, France
| | - Antonino Maniaci
- Otology Study Group of the Young-Otolaryngologists of the International Federations of Oto-Rhino-Laryngological Societies (YO-IFOS), 75000 Paris, France
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
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8
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Wu S, Wang X, Dai S, Zhang G, Zhou J, Shen Y. A novel missense mutation in GREB1L identified in a three-generation family with renal hypodysplasia/aplasia-3. Orphanet J Rare Dis 2022; 17:413. [PMID: 36371238 PMCID: PMC9652819 DOI: 10.1186/s13023-022-02553-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/11/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Renal hypodysplasia/aplasia-3 (RHDA3), as the most severe end of the spectrum of congenital anomalies of the kidney and urinary tract, is mainly caused by mutations in GREB1L. However, the mutations in GREB1L identified to date only explain a limited proportion of RHDA3 cases, and the mechanism of GREB1L mutations causing RHDA3 is unclear. RESULTS According to whole-exome sequencing, a three-generation family suffering from RHDA3 was investigated with a novel missense mutation in GREB1L, c.4507C>T. All three-generation patients suffered from unilateral absent kidney. This missense mutation resulted in sharp downregulation of mRNA and protein expression, which might lead to RHDA3. Mechanistically, through RNA-sequencing, it was found that the mRNA levels of PAX2 and PTH1R, which are key molecules involved in the development of the kidney, were significantly downregulated by knocking out GREB1L in vitro. CONCLUSIONS This novel missense mutation in GREB1L can be helpful in the genetic diagnosis of RHDA3, and the discovery of the potential mechanism that GREB1L mutations involved in RHDA3 pathogenesis can promote the adoption of optimal treatment measures and the development of personalized medicine directly targeting these effects.
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Affiliation(s)
- Sixian Wu
- grid.13291.380000 0001 0807 1581Joint Laboratory of Reproductive Medicine, Gynaecology and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Xiang Wang
- grid.13291.380000 0001 0807 1581Joint Laboratory of Reproductive Medicine, Gynaecology and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Siyu Dai
- grid.13291.380000 0001 0807 1581Joint Laboratory of Reproductive Medicine, Gynaecology and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Guohui Zhang
- grid.13291.380000 0001 0807 1581Joint Laboratory of Reproductive Medicine, Gynaecology and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Jiaojiao Zhou
- grid.412901.f0000 0004 1770 1022Division of Ultrasound, West China Hospital of Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Ying Shen
- grid.13291.380000 0001 0807 1581Joint Laboratory of Reproductive Medicine, Gynaecology and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
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9
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Adadey SM, Aboagye ET, Esoh K, Acharya A, Bharadwaj T, Lin NS, Amenga-Etego L, Awandare GA, Schrauwen I, Leal SM, Wonkam A. A novel autosomal dominant GREB1L variant associated with non-syndromic hearing impairment in Ghana. BMC Med Genomics 2022; 15:237. [PMID: 36357908 PMCID: PMC9648021 DOI: 10.1186/s12920-022-01391-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/08/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Childhood hearing impairment (HI) is genetically heterogeneous with many implicated genes, however, only a few of these genes are reported in African populations. METHODS This study used exome and Sanger sequencing to resolve the possible genetic cause of non-syndromic HI in a Ghanaian family. RESULTS We identified a novel variant c.3041G > A: p.(Gly1014Glu) in GREB1L (DFNA80) in the index case. The GREB1L: p.(Gly1014Glu) variant had a CADD score of 26.5 and was absent from human genomic databases such as TopMed and gnomAD. In silico homology protein modeling approaches displayed major structural differences between the wildtype and mutant proteins. Additionally, the variant was predicted to probably affect the secondary protein structure that may impact its function. Publicly available expression data shows a higher expression of Greb1L in the inner ear of mice during development and a reduced expression in adulthood, underscoring its importance in the development of the inner ear structures. CONCLUSION This report on an African individual supports the association of GREB1L variant with non-syndromic HI and extended the evidence of the implication of GREB1L variants in HI in diverse populations.
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Affiliation(s)
- Samuel Mawuli Adadey
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, LG 54, Accra, Ghana
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Elvis Twumasi Aboagye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, LG 54, Accra, Ghana
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Kevin Esoh
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Anushree Acharya
- Department of Neurology, Center for Statistical Genetics, Sergievsky Center, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Thashi Bharadwaj
- Department of Neurology, Center for Statistical Genetics, Sergievsky Center, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Nicole S Lin
- Department of Neurology, Center for Statistical Genetics, Sergievsky Center, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, LG 54, Accra, Ghana
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, LG 54, Accra, Ghana
| | - Isabelle Schrauwen
- Department of Neurology, Center for Statistical Genetics, Sergievsky Center, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Suzanne M Leal
- Department of Neurology, Center for Statistical Genetics, Sergievsky Center, Columbia University Medical Centre, New York, NY, 10032, USA
- Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa.
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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10
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Buchert R, Schenk E, Hentrich T, Weber N, Rall K, Sturm M, Kohlbacher O, Koch A, Riess O, Brucker SY, Schulze-Hentrich JM. Genome Sequencing and Transcriptome Profiling in Twins Discordant for Mayer-Rokitansky-Küster-Hauser Syndrome. J Clin Med 2022; 11:jcm11195598. [PMID: 36233463 PMCID: PMC9573672 DOI: 10.3390/jcm11195598] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/23/2022] Open
Abstract
To identify potential genetic causes for Mayer-Rokitansky-Küster-Hauser syndrome (MRKH), we analyzed blood and rudimentary uterine tissue of 5 MRKH discordant monozygotic twin pairs. Assuming that a variant solely identified in the affected twin or affected tissue could cause the phenotype, we identified a mosaic variant in ACTR3B with high allele frequency in the affected tissue, low allele frequency in the blood of the affected twin, and almost absent in blood of the unaffected twin. Focusing on MRKH candidate genes, we detected a pathogenic variant in GREB1L in one twin pair and their unaffected mother showing a reduced phenotypic penetrance. Furthermore, two variants of unknown clinical significance in PAX8 and WNT9B were identified. In addition, we conducted transcriptome analysis of affected tissue and observed perturbations largely similar to those in sporadic cases. These shared transcriptional changes were enriched for terms associated with estrogen and its receptors pointing at a role of estrogen in MRKH pathology. Our genome sequencing approach of blood and uterine tissue of discordant twins is the most extensive study performed on twins discordant for MRKH so far. As no clear pathogenic differences were detected, research to evaluate other regulatory layers are required to better understand the complex etiology of MRKH.
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Affiliation(s)
- Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Elisabeth Schenk
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Thomas Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Nico Weber
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
| | - Katharina Rall
- Department of Women’s Health, University of Tübingen, 72076 Tübingen, Germany
- Rare Disease Center Tübingen, University of Tübingen, 72076 Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Germany
- Institute for Translational Bioinformatics, University Hospital Tübingen, 72076 Tübingen, Germany
| | - André Koch
- Research Institute for Women’s Health, University of Tübingen, 72076 Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- Rare Disease Center Tübingen, University of Tübingen, 72076 Tübingen, Germany
| | - Sara Y. Brucker
- Department of Women’s Health, University of Tübingen, 72076 Tübingen, Germany
- Rare Disease Center Tübingen, University of Tübingen, 72076 Tübingen, Germany
| | - Julia M. Schulze-Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Germany
- Correspondence: ; Tel.: +49-7071-29-72276
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11
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Kremer H, del Castillo I. Genetics of Hearing Impairment. Genes (Basel) 2022; 13:genes13050852. [PMID: 35627237 PMCID: PMC9140334 DOI: 10.3390/genes13050852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 12/04/2022] Open
Affiliation(s)
- Hannie Kremer
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Ignacio del Castillo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
- Correspondence:
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12
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Bharadwaj T, Schrauwen I, Acharya A, Nouel‐Saied LM, Väisänen M, Kraatari M, Rahikkala E, Jarvela I, Kotimäki J, Leal SM. Autosomal recessive nonsyndromic hearing impairment in two Finnish families due to the population enriched CABP2 c.637+1G>T variant. Mol Genet Genomic Med 2022; 10:e1866. [PMID: 35150090 PMCID: PMC8922966 DOI: 10.1002/mgg3.1866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/10/2021] [Accepted: 12/14/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The genetic architecture of hearing impairment in Finland is largely unknown. Here, we investigated two Finnish families with autosomal recessive nonsyndromic symmetrical moderate-to-severe hearing impairment. METHODS Exome and custom capture next-generation sequencing were used to detect the underlying cause of hearing impairment. RESULTS In both Finnish families, we identified a homozygous pathogenic splice site variant c.637+1G>T in CAPB2 that is known to cause autosomal recessive nonsyndromic hearing impairment. Four CABP2 variants have been reported to underlie autosomal recessive nonsyndromic hearing impairment in eight families from Iran, Turkey, Pakistan, Italy, and Denmark. Of these variants, the pathogenic splice site variant c.637+1G>T is the most prevalent. The c.637+1G>T variant is enriched in the Finnish population, which has undergone multiple bottlenecks that can lead to the higher frequency of certain variants including those involved in disease. CONCLUSION We report two Finnish families with hearing impairment due to the CABP2 splice site variant c.637+1G>T.
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Affiliation(s)
- Thashi Bharadwaj
- Center for Statistical GeneticsGertrude H. Sergievsky Center, and the Department of NeurologyColumbia University Medical CenterNew YorkNYUSA
| | - Isabelle Schrauwen
- Center for Statistical GeneticsGertrude H. Sergievsky Center, and the Department of NeurologyColumbia University Medical CenterNew YorkNYUSA
| | - Anushree Acharya
- Center for Statistical GeneticsGertrude H. Sergievsky Center, and the Department of NeurologyColumbia University Medical CenterNew YorkNYUSA
| | - Liz M. Nouel‐Saied
- Center for Statistical GeneticsGertrude H. Sergievsky Center, and the Department of NeurologyColumbia University Medical CenterNew YorkNYUSA
| | - Marja‐Leena Väisänen
- Northern Finland Laboratory Centre NordLab and Medical Research CentreOulu University Hospital and University of OuluOuluFinland
| | - Minna Kraatari
- Department of Clinical GeneticsPEDEGO Research Unit and Medical Research Center OuluOulu University Hospital and University of OuluOuluFinland
| | - Elisa Rahikkala
- Department of Clinical GeneticsPEDEGO Research Unit and Medical Research Center OuluOulu University Hospital and University of OuluOuluFinland
- Institute of BiomedicineUniversity of TurkuTurkuFinland
| | - Irma Jarvela
- Department of Medical GeneticsUniversity of HelsinkiHelsinkiFinland
| | - Jouko Kotimäki
- Department of OtorhinolaryngologyKainuu Central HospitalKajaaniFinland
| | - Suzanne M. Leal
- Center for Statistical GeneticsGertrude H. Sergievsky Center, and the Department of NeurologyColumbia University Medical CenterNew YorkNYUSA
- Taub Institute for Alzheimer’s Disease and the Aging BrainColumbia University Medical CenterNew YorkNYUSA
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13
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Kim BJ, Jeon H, Lee SY, Yi N, Han JH, Seo GH, Oh SH, Choi BY. Major Contribution of GREB1L Alterations to Severe Inner Ear Malformation Largely in a Non-mendelian Fashion. Clin Exp Otorhinolaryngol 2022; 15:115-118. [PMID: 35012281 PMCID: PMC8901951 DOI: 10.21053/ceo.2021.01935] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/20/2021] [Indexed: 11/22/2022] Open
Affiliation(s)
- Bong Jik Kim
- Department of Otolaryngology-Head and Neck Surgery, Chungnam National University Sejong Hospital, Chungnam National University College of Medicine, Sejong, Korea
| | - Hyoungwon Jeon
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Sang-Yeon Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Nayoung Yi
- Department of Otolaryngology-Head and Neck Surgery, Chungnam National University Sejong Hospital, Chungnam National University College of Medicine, Sejong, Korea
| | - Jin Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | | | - Seung-Ha Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, 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
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14
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Machado DA, Ontiveros AE, Behringer RR. Mammalian uterine morphogenesis and variations. Curr Top Dev Biol 2022; 148:51-77. [DOI: 10.1016/bs.ctdb.2021.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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15
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Adeyemo A, Faridi R, Chattaraj P, Yousaf R, Tona R, Okorie S, Bharadwaj T, Nouel-Saied LM, Acharya A, Schrauwen I, Morell RJ, Leal SM, Friedman TB, Griffith AJ, Roux I. Genomic analysis of childhood hearing loss in the Yoruba population of Nigeria. Eur J Hum Genet 2021; 30:42-52. [PMID: 34837038 PMCID: PMC8738750 DOI: 10.1038/s41431-021-00984-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/02/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Although variant alleles of hundreds of genes are associated with sensorineural deafness in children, the genes and alleles involved remain largely unknown in the Sub-Saharan regions of Africa. We ascertained 56 small families mainly of Yoruba ethno-lingual ancestry in or near Ibadan, Nigeria, that had at least one individual with nonsyndromic, severe-to-profound, prelingual-onset, bilateral hearing loss not attributed to nongenetic factors. We performed a combination of exome and Sanger sequencing analyses to evaluate both nuclear and mitochondrial genomes. No biallelic pathogenic variants were identified in GJB2, a common cause of deafness in many populations. Potential causative variants were identified in genes associated with nonsyndromic hearing loss (CIB2, COL11A1, ILDR1, MYO15A, TMPRSS3, and WFS1), nonsyndromic hearing loss or Usher syndrome (CDH23, MYO7A, PCDH15, and USH2A), and other syndromic forms of hearing loss (CHD7, OPA1, and SPTLC1). Several rare mitochondrial variants, including m.1555A>G, were detected in the gene MT-RNR1 but not in control Yoruba samples. Overall, 20 (33%) of 60 independent cases of hearing loss in this cohort of families were associated with likely causal variants in genes reported to underlie deafness in other populations. None of these likely causal variants were present in more than one family, most were detected as compound heterozygotes, and 77% had not been previously associated with hearing loss. These results indicate an unusually high level of genetic heterogeneity of hearing loss in Ibadan, Nigeria and point to challenges for molecular genetic screening, counseling, and early intervention in this population.
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Affiliation(s)
- Adebolajo Adeyemo
- Institute of Child Health, College of Medicine, University of Ibadan, Ibadan, Nigeria.
| | - Rabia Faridi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Parna Chattaraj
- Otolaryngology Branch, NIDCD, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Rizwan Yousaf
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Risa Tona
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Samuel Okorie
- Institute of Child Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Thashi Bharadwaj
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA
| | - Liz M Nouel-Saied
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA
| | - Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA
| | - Robert J Morell
- Genomics and Computational Biology Core, NIDCD, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA.,Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Andrew J Griffith
- Otolaryngology Branch, NIDCD, National Institutes of Health, Bethesda, MD, 20892, USA.,Department of Otolaryngology, College of Medicine, University of Tennessee Health Science Center, 910 Madison Avenue, Memphis, TN, 38163, USA
| | - Isabelle Roux
- Otolaryngology Branch, NIDCD, National Institutes of Health, Bethesda, MD, 20892, USA.
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16
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Naz S. Molecular genetic landscape of hereditary hearing loss in Pakistan. Hum Genet 2021; 141:633-648. [PMID: 34308486 DOI: 10.1007/s00439-021-02320-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/17/2021] [Indexed: 01/13/2023]
Abstract
Approximately 14.5 million Pakistani individuals have a hearing loss and half of these cases may be due to genetic causes. Though significant progress has been made in uncovering genetic variants for recessively inherited nonsyndromic deafness, Pendred syndrome, and Usher syndromes, the same is not true for dominantly inherited hearing loss, most syndromic cases and deafness with complex inheritance patterns. Variants of 57 genes have been reported to cause nonsyndromic recessive deafness in Pakistan, though most are rare. Variants of just five genes GJB2, HGF, MYO7A, SLC26A4, and TMC1 together explain 57% of profound deafness while those of GJB2, MYO15A, OTOF, SLC26A4, TMC1, and TMPRSS3 account for 47% of moderate to severe hearing loss. In contrast, although variants of at least 39 genes have been implicated in different deafness syndromes, their prevalence in the population and the spectrum of mutations have not been explored. Furthermore, research on genetics of deafness has mostly focused on individuals from the Punjab province and needs to be extended to other regions of Pakistan. Identifying the genes and their variants causing deafness in all ethnic groups is important as it will pinpoint rare as well as recurrent mutations. This information may ultimately help in offering genetic counseling and future treatments.
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Affiliation(s)
- Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan.
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17
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Identification of Novel Candidate Genes and Variants for Hearing Loss and Temporal Bone Anomalies. Genes (Basel) 2021; 12:genes12040566. [PMID: 33924653 PMCID: PMC8069784 DOI: 10.3390/genes12040566] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/01/2021] [Accepted: 04/08/2021] [Indexed: 01/09/2023] Open
Abstract
Background: Hearing loss remains an important global health problem that is potentially addressed through early identification of a genetic etiology, which helps to predict outcomes of hearing rehabilitation such as cochlear implantation and also to mitigate the long-term effects of comorbidities. The identification of variants for hearing loss and detailed descriptions of clinical phenotypes in patients from various populations are needed to improve the utility of clinical genetic screening for hearing loss. Methods: Clinical and exome data from 15 children with hearing loss were reviewed. Standard tools for annotating variants were used and rare, putatively deleterious variants were selected from the exome data. Results: In 15 children, 21 rare damaging variants in 17 genes were identified, including: 14 known hearing loss or neurodevelopmental genes, 11 of which had novel variants; and three candidate genes IST1, CBLN3 and GDPD5, two of which were identified in children with both hearing loss and enlarged vestibular aqueducts. Patients with variants within IST1 and MYO18B had poorer outcomes after cochlear implantation. Conclusion: Our findings highlight the importance of identifying novel variants and genes in ethnic groups that are understudied for hearing loss.
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18
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Wonkam-Tingang E, Schrauwen I, Esoh KK, Bharadwaj T, Nouel-Saied LM, Acharya A, Nasir A, Leal SM, Wonkam A. A novel variant in DMXL2 gene is associated with autosomal dominant non-syndromic hearing impairment (DFNA71) in a Cameroonian family. Exp Biol Med (Maywood) 2021; 246:1524-1532. [PMID: 33715530 DOI: 10.1177/1535370221999746] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Approximately half of congenital hearing impairment cases are inherited, with non-syndromic hearing impairment (NSHI) being the most frequent clinical entity of genetic hearing impairment cases. A family from Cameroon with NSHI was investigated by performing exome sequencing using DNA samples obtained from three family members, followed by direct Sanger sequencing in additional family members and controls participants. We identified an autosomal dominantly inherited novel missense variant [NM_001174116.2:c.918G>T; p.(Q306H)] in DMXL2 gene (MIM:612186) that co-segregates with mild to profound non-syndromic sensorineural hearing impairment . The p.(Q306H) variant which substitutes a highly conserved glutamine residue is predicted deleterious by various bioinformatics tools and is absent from several genome databases. This variant was also neither found in 121 apparently healthy controls without a family history of hearing impairment , nor 112 sporadic NSHI cases from Cameroon. There is one previous report of a large Han Chinese NSHI family that segregates a missense variant in DMXL2. The present study provides additional evidence that DMXL2 is involved in hearing impairment etiology, and we suggest DMXL2 should be considered in diagnostic hearing impairment panels.
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Affiliation(s)
- Edmond Wonkam-Tingang
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA
| | - Kevin K Esoh
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Thashi Bharadwaj
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA
| | - Liz M Nouel-Saied
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA
| | - Anushree Acharya
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA
| | - Abdul Nasir
- Synthetic Protein Engineering Lab (SPEL), Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea
| | - Suzanne M Leal
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
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Kyei Barffour I, Kyei Baah Kwarkoh R. GREB1L as a candidate gene of Mayer-Rokitansky-Küster-Hauser Syndrome. Eur J Med Genet 2021; 64:104158. [PMID: 33548512 DOI: 10.1016/j.ejmg.2021.104158] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/10/2020] [Accepted: 01/30/2021] [Indexed: 01/14/2023]
Abstract
Mayer-Rokitansky-Küster-Hauser (MRKH) Syndrome is a sex development disorder that affects 1 in every 4500 46, XX live births. At least a subset of MRKH syndrome is genetically related to which various candidate genes have been identified. The growth regulation by estrogen in breast cancer 1-like gene (GREB1L) is an androgen-regulated gene reported to be a co-activator of the retinoic acid receptor gene (RAR). Thus expression levels of GREB1L have implications on renal system cellular differentiation, morphogenesis, and homeostasis in vertebrates. Variants of GREB1L have been reported in familial and sporadic MRKH Syndrome and more importantly, in a three-generation family ofMRKH syndrome propositae. Much the same way, Mutants of GREB1L have also been identified in isolated bilateral renal agenesis and deafness both of which are extra-genital tract anomalies in MRKH type 2. Again, renal agenesis transgenic mice have been produced from an E13.5 CRISPR/cas9 GREB1L mutagenesis. Though no GREB1L mutation has been reported in cardiac malformation, there is evidence that GREB1L is involved in ventricular development. Here, we intorigate evidence that projects GREB1L as a candidate gene of Mayer-Rokitansky-Küster-Hauser Syndrome and propose that functional validation analysis to that effect is imparative.
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Affiliation(s)
- Isaac Kyei Barffour
- Department of Biomedical Sciences, School of Allied Health Sciences, College of Health and Allied Sciences, University of Cape Coast, Ghana.
| | - Roselind Kyei Baah Kwarkoh
- Department of Physician Assistant Studies, School of Allied Health Sciences, College of Health and Allied Sciences, University of Cape Coast, Ghana
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Wonkam-Tingang E, Schrauwen I, Esoh KK, Bharadwaj T, Nouel-Saied LM, Acharya A, Nasir A, Adadey SM, Mowla S, Leal SM, Wonkam A. Bi-Allelic Novel Variants in CLIC5 Identified in a Cameroonian Multiplex Family with Non-Syndromic Hearing Impairment. Genes (Basel) 2020; 11:genes11111249. [PMID: 33114113 PMCID: PMC7690789 DOI: 10.3390/genes11111249] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/20/2020] [Accepted: 10/20/2020] [Indexed: 11/16/2022] Open
Abstract
DNA samples from five members of a multiplex non-consanguineous Cameroonian family, segregating prelingual and progressive autosomal recessive non-syndromic sensorineural hearing impairment, underwent whole exome sequencing. We identified novel bi-allelic compound heterozygous pathogenic variants in CLIC5. The variants identified, i.e., the missense [NM_016929.5:c.224T>C; p.(L75P)] and the splicing (NM_016929.5:c.63+1G>A), were validated using Sanger sequencing in all seven available family members and co-segregated with hearing impairment (HI) in the three hearing impaired family members. The three affected individuals were compound heterozygous for both variants, and all unaffected individuals were heterozygous for one of the two variants. Both variants were absent from the genome aggregation database (gnomAD), the Single Nucleotide Polymorphism Database (dbSNP), and the UK10K and Greater Middle East (GME) databases, as well as from 122 apparently healthy controls from Cameroon. We also did not identify these pathogenic variants in 118 unrelated sporadic cases of non-syndromic hearing impairment (NSHI) from Cameroon. In silico analysis showed that the missense variant CLIC5-p.(L75P) substitutes a highly conserved amino acid residue (leucine), and is expected to alter the stability, the structure, and the function of the CLIC5 protein, while the splicing variant CLIC5-(c.63+1G>A) is predicted to disrupt a consensus donor splice site and alter the splicing of the pre-mRNA. This study is the second report, worldwide, to describe CLIC5 involvement in human hearing impairment, and thus confirms CLIC5 as a novel non-syndromic hearing impairment gene that should be included in targeted diagnostic gene panels.
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Affiliation(s)
- Edmond Wonkam-Tingang
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (E.W.-T.); (K.K.E.); (S.M.A.)
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer’s Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA; (I.S.); (T.B.); (L.M.N.-S.); (A.A.); (S.M.L.)
| | - Kevin K. Esoh
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (E.W.-T.); (K.K.E.); (S.M.A.)
| | - Thashi Bharadwaj
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer’s Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA; (I.S.); (T.B.); (L.M.N.-S.); (A.A.); (S.M.L.)
| | - Liz M. Nouel-Saied
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer’s Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA; (I.S.); (T.B.); (L.M.N.-S.); (A.A.); (S.M.L.)
| | - Anushree Acharya
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer’s Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA; (I.S.); (T.B.); (L.M.N.-S.); (A.A.); (S.M.L.)
| | - Abdul Nasir
- Synthetic Protein Engineering Lab (SPEL), Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea;
| | - Samuel M. Adadey
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (E.W.-T.); (K.K.E.); (S.M.A.)
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG 54, Ghana
| | - Shaheen Mowla
- Division of Haematology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa;
| | - Suzanne M. Leal
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer’s Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA; (I.S.); (T.B.); (L.M.N.-S.); (A.A.); (S.M.L.)
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (E.W.-T.); (K.K.E.); (S.M.A.)
- Correspondence: ; Tel.: +27-21-4066-307
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