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Wang T, Ren W, Fu F, Wang H, Li Y, Duan J. Digenic CHD7 and SMCHD1 inheritance Unveils phenotypic variability in a family mainly presenting with hypogonadotropic hypogonadism. Heliyon 2024; 10:e23272. [PMID: 38148819 PMCID: PMC10750161 DOI: 10.1016/j.heliyon.2023.e23272] [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: 09/20/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023] Open
Abstract
Objectives CHARGE syndrome is a congenital hereditary condition involving multiple systems. Patients are easily misdiagnosed with idiopathic hypogonadotropic hypogonadism (IHH) due to the overlap of clinical manifestations. An accurate clinical diagnosis remains challenging when the predominant clinical manifestation resembles hypogonadotropic hypogonadism. Methods This original research is conducted based on the genetic finding and analysis of clinical cases. Whole-exome sequencing (WES) and in-silico analyse were performed on two sisters to investigate the pathogenesis in this family. Homology modelling was conducted to evaluate structural changes in the variants. Results WES and Sanger sequencing revealed two siblings carrying a nonsense mutation (NM_017780.4: c.115C > T) in exon 2 of CHD7 inherited from a mildly affected mother and a missense mutation (NM_015295.3: c.2582T > C) in exon 20 of SMCHD1 inherited from an asymptomatic father. The nonsense mutation in CHD7 was predicted to generate nonsense-mediated decay, whereas the missense mutation in SMCHD1 decreased protein stability. Conclusions We identified digenic CHD7 and SMCHD1 mutations in IHH-associated diseases for the first time and verified the synergistic role of oligogenic inheritance. It was also determined that WES is an effective tool for distinguishing diseases with overlapping features and establishing a molecular diagnosis for cases with digenic or oligogenic hereditary disorders, which is beneficial for timely treatment, and family genetic counseling.
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Affiliation(s)
- Tian Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wu Ren
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Fangfang Fu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hairong Wang
- Wuhan KDWS Biological Technology Co.,Ltd, Wuhan, 430000, China
| | - Yan Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jie Duan
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
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Cariboni A, Balasubramanian R. Kallmann syndrome and idiopathic hypogonadotropic hypogonadism: The role of semaphorin signaling on GnRH neurons. Handb Clin Neurol 2021; 182:307-315. [PMID: 34266601 DOI: 10.1016/b978-0-12-819973-2.00022-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Idiopathic hypogonadotropic hypogonadism and Kallmann syndrome are rare genetic disorders characterized by isolated gonadotropin-releasing hormone (GnRH) deficiency (IGD) and delayed or absent puberty. Defective GnRH neuron migration during development or secretion of mature GnRH neurons secondary to molecular defects in several key developmental and neuroendocrine pathways are thought to be the primary causes of these disorders. Recent studies have highlighted the importance of semaphorins and their receptors in this system, by showing that these molecules play distinct roles during the development and plasticity of these neurons. Accordingly, mutations in the semaphoring-signaling pathway genes have been found in patients affected by IGD, underlying the importance of semaphorin-mediated signaling pathways in the neuroendocrine axis that control reproduction.
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Affiliation(s)
- Anna Cariboni
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy.
| | - Ravikumar Balasubramanian
- Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital & Harvard Medical School, Boston, MA, United States
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Ross JP, Leblond CS, Laurent SB, Spiegelman D, Dionne-Laporte A, Camu W, Dupré N, Dion PA, Rouleau GA. Oligogenicity, C9orf72 expansion, and variant severity in ALS. Neurogenetics 2020; 21:227-242. [PMID: 32385536 DOI: 10.1007/s10048-020-00612-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/04/2020] [Indexed: 12/14/2022]
Abstract
"Oligogenic inheritance" is used to describe cases where more than one rare pathogenic variant is observed in the same individual. While multiple variants can alter disease presentation, the necessity of multiple variants to instigate pathogenesis has not been addressed in amyotrophic lateral sclerosis (ALS). We sequenced ALS-associated genes in C9orf72-expansion-positive and negative ALS patients, alongside unaffected controls, to test the importance of oligogenicity and variant deleteriousness in ALS. We found that all groups had similar numbers of rare variants, but that variant severity was significantly higher in C9orf72-negative ALS cases, suggesting sufficiency of C9orf72 expansion to cause ALS alone.
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Affiliation(s)
- Jay P Ross
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Claire S Leblond
- Human Genetics and Cognitive functions, Institut Pasteur, UMR 3571 CNRS, Sorbonne Paris Cité, University Paris Diderot, Paris, France
| | - Sandra B Laurent
- Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, H3A 2B4, Canada
| | - Dan Spiegelman
- Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, H3A 2B4, Canada
| | - Alexandre Dionne-Laporte
- Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, H3A 2B4, Canada
| | - William Camu
- Clinique du Motoneurone, Explorations neurologiques, CHU Gui de Chauliac, Université de Montpellier, Montpellier, France
| | - Nicolas Dupré
- Division of Neurosciences, CHU de Québec, Université Laval, Québec City, QC, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Québec City, QC, Canada
| | - Patrick A Dion
- Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, H3A 2B4, Canada
| | - Guy A Rouleau
- Department of Human Genetics, McGill University, Montréal, QC, Canada.
- Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada.
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, H3A 2B4, Canada.
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Lattante S, Doronzio PN, Marangi G, Conte A, Bisogni G, Bernardo D, Russo T, Lamberti D, Patrizi S, Apollo FP, Lunetta C, Scarlino S, Pozzi L, Zollino M, Riva N, Sabatelli M. Coexistence of variants in TBK1 and in other ALS-related genes elucidates an oligogenic model of pathogenesis in sporadic ALS. Neurobiol Aging 2019; 84:239.e9-239.e14. [PMID: 31000212 DOI: 10.1016/j.neurobiolaging.2019.03.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 03/04/2019] [Accepted: 03/19/2019] [Indexed: 11/19/2022]
Abstract
Variants in tank-binding kinase 1 (TBK1) are responsible for a significant proportion of amyotrophic lateral sclerosis (ALS) cases. In the present study, we analyzed variants in TBK1 extracted by targeted sequencing of 32 genes in a group of 406 Italian patients with ALS. We identified 7 different TBK1 variants in 7 sporadic cases, resulting in a frequency of 1.7%. Three patients had missense variants (p.R357Q, p.R358H, and p.R724C), one patient had a small deletion (p.E618del), and 3 had truncating variants (p.Y482*, p.R229*, and p.N681*). Notably, we found that 4 patients had an additional variant in ALS-related genes: 2 in OPTN and 2 in the 3'UTR region of FUS. By studying an independent group of 7 TBK1-mutated patients previously reported, we found another variant in the 3'UTR region of FUS in one patient. The presence of a second variant in TBK1 variant carriers is an interesting finding that needs to be investigated in larger cohorts of patients. These findings suggest that TBK1 belongs to the category of genes conferring a significantly increased risk but not sufficient to cause disease.
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Affiliation(s)
- Serena Lattante
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Unità Operativa Complessa di Genetica Medica, Roma, Italy; Università Cattolica del Sacro Cuore, Istituto di Medicina Genomica, Roma, Italy
| | - Paolo Niccolò Doronzio
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Unità Operativa Complessa di Genetica Medica, Roma, Italy; Università Cattolica del Sacro Cuore, Istituto di Medicina Genomica, Roma, Italy
| | - Giuseppe Marangi
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Unità Operativa Complessa di Genetica Medica, Roma, Italy; Università Cattolica del Sacro Cuore, Istituto di Medicina Genomica, Roma, Italy
| | | | | | | | - Tommaso Russo
- Dipartimento Scienze dell'invecchiamento, Neurologiche, Ortopediche e della testa-collo, Fondazione Policlinico Universitario A. Gemelli IRCCS, UOC Neurologia, Roma, Italy; Università Cattolica del Sacro Cuore, Istituto di Neurologia, Roma, Italy
| | - Dante Lamberti
- Unità di Oncogenomica ed Epigenetica, IRCCS Istituto Nazionale Tumori Regina Elena, Roma, Italy
| | - Sara Patrizi
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Unità Operativa Complessa di Genetica Medica, Roma, Italy; Università Cattolica del Sacro Cuore, Istituto di Medicina Genomica, Roma, Italy
| | - Francesco Paolo Apollo
- Divisione di Neurologia, Ospedale Casa Sollievo della Sofferenza IRCCS, San Giovanni Rotondo, Italy
| | | | - Stefania Scarlino
- Divisione di Neuroscienze, Dipartimento di Neurologia, Istituto di Neurologia Sperimentale (INSPE), Istituto Scientifico San Raffaele, Milano, Italy
| | - Laura Pozzi
- Divisione di Neuroscienze, Dipartimento di Neurologia, Istituto di Neurologia Sperimentale (INSPE), Istituto Scientifico San Raffaele, Milano, Italy
| | - Marcella Zollino
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Unità Operativa Complessa di Genetica Medica, Roma, Italy; Università Cattolica del Sacro Cuore, Istituto di Medicina Genomica, Roma, Italy
| | - Nilo Riva
- Divisione di Neuroscienze, Dipartimento di Neurologia, Istituto di Neurologia Sperimentale (INSPE), Istituto Scientifico San Raffaele, Milano, Italy
| | - Mario Sabatelli
- Centro Clinico NEMO, Roma, Italy; Dipartimento Scienze dell'invecchiamento, Neurologiche, Ortopediche e della testa-collo, Fondazione Policlinico Universitario A. Gemelli IRCCS, UOC Neurologia, Roma, Italy; Università Cattolica del Sacro Cuore, Istituto di Neurologia, Roma, Italy.
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Crawford BD, Gillies CE, Robertson CC, Kretzler M, Otto EA, Vega-Warner V, Sampson MG. Evaluating Mendelian nephrotic syndrome genes for evidence for risk alleles or oligogenicity that explain heritability. Pediatr Nephrol 2017; 32:467-76. [PMID: 27766458 DOI: 10.1007/s00467-016-3513-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/25/2016] [Accepted: 08/29/2016] [Indexed: 01/08/2023]
Abstract
BACKGROUND More than 30 genes can harbor rare exonic variants sufficient to cause nephrotic syndrome (NS), and the number of genes implicated in monogenic NS continues to grow. However, outside the first year of life, the majority of affected patients, particularly in ancestrally mixed populations, do not have a known monogenic form of NS. Even in those children classified with a monogenic form of NS, there is phenotypic heterogeneity. Thus, we have only discovered a fraction of the heritability of NS-the underlying genetic factors contributing to phenotypic variation. Part of the "missing heritability" for NS has been posited to be explained by patients harboring coding variants across one or more previously implicated NS genes, insufficient to cause NS in a classical Mendelian manner, but that nonetheless have a sufficient impact on protein function to cause disease. However, systematic evaluation in patients with NS for rare or low-frequency risk alleles within single genes, or in combination across genes ("oligogenicity"), has not been reported. To determine whether, compared with a reference population, patients with NS have either a significantly increased burden of protein-altering variants ("risk-alleles"), or a unique combination of them ("oligogenicity"), in a set of 21 genes implicated in Mendelian forms of NS. METHODS In 303 patients with NS enrolled in the Nephrotic Syndrome Study Network (NEPTUNE), we performed targeted amplification paired with next-generation sequencing of 21 genes implicated in monogenic NS. We created a high-quality variant call set and compared it with a variant call set of the same genes in a reference population composed of 2,535 individuals from phase 3 of the 1000 Genomes Project. We created both a "stringent" and a "relaxed" pathogenicity-filtering pipeline, applied them to both cohorts, and computed the burden of variants in the entire gene set per cohort, the burden of variants in the entire gene set per individual, the burden of variants within a single gene per cohort, and unique combinations of variants across two or more genes per cohort. RESULTS With few exceptions when using the relaxed filter, and which are likely the result of confounding by population stratification, NS patients did not have a significantly increased burden of variants in Mendelian NS genes in comparison to a reference cohort, nor was there any evidence for oligogenicity. This was true when using both the relaxed and the stringent variant pathogenicity filter. CONCLUSION In our study, there were no significant differences in the burden or particular combinations of low-frequency or rare protein-altering variants in a previously implicated Mendelian NS genes cohort between North American patients with NS and a reference population. Studies in larger independent cohorts or meta-analyses are needed to assess the generalizability of our discoveries and also address whether there is in fact small but significant enrichment of risk alleles or oligogenicity in NS cases that was undetectable with this current sample size. It is still possible that rare protein-altering variants in these genes, insufficient to cause Mendelian disease, still contribute to NS as risk alleles and/or via oligogenicity. However, we suggest that more accurate bioinformatic analyses and the incorporation of functional assays would be necessary to identify bona fide instances of this form of genetic architecture as a contributor to the heritability of NS.
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