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Chang L, Ji R, Sa R, Huge J, An C. Whole-exome sequencing of pathogenic genes in a family with congenital heart disease: A case report. Medicine (Baltimore) 2024; 103:e36977. [PMID: 38306576 PMCID: PMC10843419 DOI: 10.1097/md.0000000000036977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/22/2023] [Indexed: 02/04/2024] Open
Abstract
RATIONALE Congenital heart disease (CHD) is the most common birth defect and an important cause of noninfectious deaths in infants and children. It has high prevalence globally, placing an enormous burden on society and families. Studies of individuals with hereditary or sporadic CHD have provided strong evidence for its genetic basis. The aim of this study was to identify causative gene variants in a Chinese family with congenital heart disease. PATIENT CONCERNS AND DIAGNOSES Three generations of a CHD family were recruited. Proband III.9 was diagnosed with congenital heart disease at age 11 months, and the echocardiogram showed arterial ductus arteriosus, with a left-to-right shunt at the level of the arteries. Precedent III.10 was a twin of Proband III.9 who was diagnosed with congenital heart disease at age 11 months, in whom the echocardiogram revealed an arterial ductus arteriosus, an unenclosed patent ductus arteriosus, and a left to right shunt at the level of the arteries (second figure). III.8 was diagnosed with congenital heart disease at age 15, but echocardiography in this study showed no abnormalities. No cardiac abnormalities were detected in any of his parents, grandparents, or maternal grandparents. We performed whole-exome sequencing on CHD sufferers and their unexpressing family members to investigate the genetic causes of CHD in this family line. Exome sequencing identified 4 mutation sites in this family line. The variant c.3245A>G (p.His1082Arg) of the AMER1 gene was consistent with concomitant X-chromosome recessive inheritance, the variant c.238G>C (p.Val80Leu) of the KCNE1 gene was consistent with autosomal accessory inheritance, and the other 2 variants did not conform to the law of the mode of inheritance of the disease. OUTCOMES The first identified variant, c.3245A>G (p.His1082Arg) of the AMER1 gene, with X-chromosome recessive inheritance, and the variant c.238G>C (p.Val80Leu) of the KCNE1 gene, which has been reported as autosomal dominant, may be the causative agent of CHD in this family line. These findings broaden the genetic scope of congenital heart disease and could help in the development of targeted drugs for the treatment of congenital heart disease.
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Affiliation(s)
- Li Chang
- Department of Pathophysiology, Basic Medicine College of Inner Mongolia Medical University, Hohhot, China
- Rehabilitation Department, Ordos Central Hospital, Ordos, China
| | - Renhui Ji
- Department of Pathophysiology, Basic Medicine College of Inner Mongolia Medical University, Hohhot, China
- Rehabilitation Department, Ordos Central Hospital, Ordos, China
| | - Rina Sa
- Rehabilitation Department, Ordos Central Hospital, Ordos, China
- Department of Pediatrics, Ordos Central Hospital, Ordos, China
| | - Jiletu Huge
- Department of Pediatrics, Ordos Central Hospital, Ordos, China
| | - Caiyan An
- Department of Pathophysiology, Basic Medicine College of Inner Mongolia Medical University, Hohhot, China
- Rehabilitation Department, Ordos Central Hospital, Ordos, China
- Foundational and Translational Medical Research Center, Department of Allergy and General Surgery, Hohhot First Hospital, Hohhot, China
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Chen J, Zhang P, Peng M, Liu B, Wang X, Du S, Lu Y, Mu X, Lu Y, Wang S, Wu Y. An additional whole-exome sequencing study in 102 panel-undiagnosed patients: A retrospective study in a Chinese craniosynostosis cohort. Front Genet 2022; 13:967688. [PMID: 36118902 PMCID: PMC9481236 DOI: 10.3389/fgene.2022.967688] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Craniosynostosis (CRS) is a disease with prematurely fused cranial sutures. In the last decade, the whole-exome sequencing (WES) was widely used in Caucasian populations. The WES largely contributed in genetic diagnosis and exploration on new genetic mechanisms of CRS. In this study, we enrolled 264 CRS patients in China. After a 17-gene-panel sequencing designed in the previous study, 139 patients were identified with pathogenic/likely pathogenic (P/LP) variants according to the ACMG guideline as positive genetic diagnosis. WES was then performed on 102 patients with negative genetic diagnosis by panel. Ten P/LP variants were additionally identified in ten patients, increasing the genetic diagnostic yield by 3.8% (10/264). The novel variants in ANKH, H1-4, EIF5A, SOX6, and ARID1B expanded the mutation spectra of CRS. Then we designed a compatible research pipeline (RP) for further exploration. The RP could detect all seven P/LP SNVs and InDels identified above, in addition to 15 candidate variants found in 13 patients with worthy of further study. In sum, the 17-gene panel and WES identified positive genetic diagnosis for 56.4% patients (149/264) in 16 genes. At last, in our estimation, the genetic testing strategy of “Panel-first” saves 24.3% of the cost compared with “WES only”, suggesting the “Panel-first” is an economical strategy.
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Affiliation(s)
- Jieyi Chen
- Department of Plastic Surgery, Huashan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ping Zhang
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Meifang Peng
- The Core Laboratory in Medical Center of Clinical Research, Department of Molecular Diagnostics & Endocrinology, Shanghai Ninth People’s Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bo Liu
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Xiao Wang
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Siyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yao Lu
- School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xiongzheng Mu
- Department of Plastic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
- *Correspondence: Yingzhi Wu, ; Sijia Wang, ; Yulan Lu,
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Yingzhi Wu, ; Sijia Wang, ; Yulan Lu,
| | - Yingzhi Wu
- Department of Plastic Surgery, Huashan Hospital, Fudan University, Shanghai, China
- *Correspondence: Yingzhi Wu, ; Sijia Wang, ; Yulan Lu,
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Chen J, Cuevas P, Dworan J, Dawid I, Turkkahraman H, Tran K, Delgado-Calle J, Bellido T, Gorski J, Liu B, Brunski J, Helms J. Wnt/β-catenin Signaling Controls Maxillofacial Hyperostosis. J Dent Res 2022; 101:793-801. [PMID: 35114849 PMCID: PMC10850863 DOI: 10.1177/00220345211067705] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The roles of Wnt/β-catenin signaling in regulating the morphology and microstructure of craniomaxillofacial (CMF) bones was explored using mice carrying a constitutively active form of β-catenin in activating Dmp1-expressing cells (e.g., daβcatOt mice). By postnatal day 24, daβcatOt mice exhibited midfacial truncations coupled with maxillary and mandibular hyperostosis that progressively worsened with age. Mechanistic insights into the basis for the hyperostotic facial phenotype were gained through molecular and cellular analyses, which revealed that constitutively activated β-catenin in Dmp1-expressing cells resulted in an increase in osteoblast number and an increased rate of mineral apposition. An increase in osteoblasts was accompanied by an increase in osteocytes, but they failed to mature. The resulting CMF bone matrix also had an abundance of osteoid, and in locations where compact lamellar bone typically forms, it was replaced by porous, woven bone. The hyperostotic facial phenotype was progressive. These findings identify for the first time a ligand-independent positive feedback loop whereby unrestrained Wnt/β-catenin signaling results in a CMF phenotype of progressive hyperostosis combined with architecturally abnormal, poorly mineralized matrix that is reminiscent of craniotubular disorders in humans.
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Affiliation(s)
- J. Chen
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - P.L. Cuevas
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
| | - J.S. Dworan
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
- Medical University of Vienna, Department of Anatomy, Center for Anatomy and Cell Biology, Vienna, Austria
| | - I. Dawid
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
| | - H. Turkkahraman
- Indiana University School of Dentistry, Department of Orthodontics & Oral Facial Genetics, Indianapolis, IN, USA
| | - K. Tran
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
| | - J. Delgado-Calle
- Department of Physiology & Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - T. Bellido
- Department of Physiology & Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - J.P. Gorski
- Department of Oral and Craniofacial Sciences, School of Dentistry, and Center of Excellence in Mineralized Tissue Research, University of Missouri–Kansas City, Kansas City, MO, USA
| | - B. Liu
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
| | - J.B. Brunski
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
| | - J.A. Helms
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
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Mi J, Parthasarathy P, Halliday BJ, Morgan T, Dean J, Nowaczyk MJM, Markie D, Robertson SP, Wade EM. Deletion of Exon 1 in AMER1 in Osteopathia Striata with Cranial Sclerosis. Genes (Basel) 2020; 11:genes11121439. [PMID: 33265914 PMCID: PMC7760256 DOI: 10.3390/genes11121439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/26/2020] [Accepted: 11/26/2020] [Indexed: 12/29/2022] Open
Abstract
Osteopathia striata with cranial sclerosis (OSCS) is an X-linked dominant condition characterised by metaphyseal striations, macrocephaly, cleft palate, and developmental delay in affected females. Males have a more severe phenotype with multi-organ malformations, and rarely survive. To date, only frameshift and nonsense variants in exon 2, the single coding exon of AMER1, or whole gene deletions have been reported to cause OSCS. In this study, we describe two families with phenotypic features typical of OSCS. Exome sequencing and multiplex ligation-dependent probe amplification (MLPA) did not identify pathogenic variants in AMER1. Therefore, genome sequencing was employed which identified two deletions containing the non-coding exon 1 of AMER1 in the families. These families highlight the importance of considering variants or deletions of upstream non-coding exons in conditions such as OSCS, noting that often such exons are not captured on probe or enrichment-based platforms because of their high G/C content.
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Affiliation(s)
- Jingyi Mi
- Department of Women’s and Children’s Health, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (J.M.); (P.P.); (B.J.H.); (T.M.); (E.M.W.)
| | - Padmini Parthasarathy
- Department of Women’s and Children’s Health, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (J.M.); (P.P.); (B.J.H.); (T.M.); (E.M.W.)
| | - Benjamin J. Halliday
- Department of Women’s and Children’s Health, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (J.M.); (P.P.); (B.J.H.); (T.M.); (E.M.W.)
| | - Tim Morgan
- Department of Women’s and Children’s Health, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (J.M.); (P.P.); (B.J.H.); (T.M.); (E.M.W.)
| | - John Dean
- North of Scotland Regional Genetics Service, NHS Grampian, Ashgrove House, Foresterhill, Aberdeen AB25 2ZA, UK;
| | - Malgorzata J. M. Nowaczyk
- Department of Pathology and Molecular Medicine, Health Sciences Centre, McMaster University, Hamilton, ON L8S 4K1, Canada;
| | - David Markie
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand;
| | - Stephen P. Robertson
- Department of Women’s and Children’s Health, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (J.M.); (P.P.); (B.J.H.); (T.M.); (E.M.W.)
- Correspondence: ; Tel.: +64-(0)3-479-7469
| | - Emma M. Wade
- Department of Women’s and Children’s Health, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (J.M.); (P.P.); (B.J.H.); (T.M.); (E.M.W.)
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García-Aznar JM, Ramírez N, De Uña D, Santiago E, Monserrat L. Whole Exome Sequencing Provides the Correct Diagnosis in a Case of Osteopathia Striata with Cranial Sclerosis: Case Report of a Novel Frameshift Mutation in AMER1. J Pediatr Genet 2020; 10:139-146. [PMID: 33996185 DOI: 10.1055/s-0040-1710058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/17/2020] [Indexed: 10/24/2022]
Abstract
The diagnosis of rare diseases with multisystem manifestations can constitute a difficult process that delays the determination of the underlying cause. Whole exome sequencing (WES) provides a suitable option to examine multiple target genes associated with several disorders that display common features. In this study, we report the case of a female patient suspected of having Sotos syndrome. Screening for the initially selected genes, considering Sotos syndrome and Sotos-like disorders, did not identify any pathogenic variants that could explain the phenotype. The extended analysis, which considered all genes in the exome associated with features consistent with those shown by the studied patient, revealed a novel frameshift variant in the AMER1 gene, responsible for osteopathia striata with cranial sclerosis. WES analysis and an updated revision of previously reported disease-causing mutations, proved useful to reach an accurate diagnosis and guide further examination to identify critical abnormalities.
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Affiliation(s)
| | - Noelia Ramírez
- Pediatric Division, Hospital Virgen de Altagracia, Manzanares, Spain
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Große A, Perner B, Naumann U, Englert C. Zebrafish Wtx is a negative regulator of Wnt signaling but is dispensable for embryonic development and organ homeostasis. Dev Dyn 2019; 248:866-881. [PMID: 31290212 DOI: 10.1002/dvdy.84] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 06/20/2019] [Accepted: 06/28/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The X-chromosomally linked gene WTX is a human disease gene and a member of the AMER family. Mutations in WTX are found in Wilms tumor, a form of pediatric kidney cancer and in patients suffering from OSCS (Osteopathia striata with cranial sclerosis), a sclerosing bone disorder. Functional data suggest WTX to be an inhibitor of the Wnt/β-catenin signaling pathway. Deletion of Wtx in mouse leads to perinatal death, impeding the analysis of its physiological role. RESULTS To gain insights into the function of Wtx in development and homeostasis we have used zebrafish as a model and performed both knockdown and knockout studies using morpholinos and transcription activator-like effector nucleases (TALENs), respectively. Wtx knockdown led to increased Wnt activity and embryonic dorsalization. Also, wtx mutants showed a transient upregulation of Wnt target genes in the context of caudal fin regeneration. Surprisingly, however, wtx as well as wtx/amer2/amer3 triple mutants developed normally, were fertile and did not show any anomalies in organ maintenance. CONCLUSIONS Our data show that members of the zebrafish wtx/amer gene family, while sharing a partially overlapping expression pattern do not compensate for each other. This observation demonstrates a remarkable robustness during development and regeneration in zebrafish.
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Affiliation(s)
- Andreas Große
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Birgit Perner
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Uta Naumann
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Christoph Englert
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany.,Institute of Biochemistry and Biophysics, Friedrich-Schiller-University Jena, Jena, Germany
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Brommage R, Ohlsson C. High Fidelity of Mouse Models Mimicking Human Genetic Skeletal Disorders. Front Endocrinol (Lausanne) 2019; 10:934. [PMID: 32117046 PMCID: PMC7010808 DOI: 10.3389/fendo.2019.00934] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 12/23/2019] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED The 2019 International Skeletal Dysplasia Society nosology update lists 441 genes for which mutations result in rare human skeletal disorders. These genes code for enzymes (33%), scaffolding proteins (18%), signal transduction proteins (16%), transcription factors (14%), cilia proteins (8%), extracellular matrix proteins (5%), and membrane transporters (4%). Skeletal disorders include aggrecanopathies, channelopathies, ciliopathies, cohesinopathies, laminopathies, linkeropathies, lysosomal storage diseases, protein-folding and RNA splicing defects, and ribosomopathies. With the goal of evaluating the ability of mouse models to mimic these human genetic skeletal disorders, a PubMed literature search identified 260 genes for which mutant mice were examined for skeletal phenotypes. These mouse models included spontaneous and ENU-induced mutants, global and conditional gene knockouts, and transgenic mice with gene over-expression or specific base-pair substitutions. The human X-linked gene ARSE and small nuclear RNA U4ATAC, a component of the minor spliceosome, do not have mouse homologs. Mouse skeletal phenotypes mimicking human skeletal disorders were observed in 249 of the 260 genes (96%) for which comparisons are possible. A supplemental table in spreadsheet format provides PubMed weblinks to representative publications of mutant mouse skeletal phenotypes. Mutations in 11 mouse genes (Ccn6, Cyp2r1, Flna, Galns, Gna13, Lemd3, Manba, Mnx1, Nsd1, Plod1, Smarcal1) do not result in similar skeletal phenotypes observed with mutations of the homologous human genes. These discrepancies can result from failure of mouse models to mimic the exact human gene mutations. There are no obvious commonalities among these 11 genes. Body BMD and/or radiologic dysmorphology phenotypes were successfully identified for 28 genes by the International Mouse Phenotyping Consortium (IMPC). Forward genetics using ENU mouse mutagenesis successfully identified 37 nosology gene phenotypes. Since many human genetic disorders involve hypomorphic, gain-of-function, dominant-negative and intronic mutations, future studies will undoubtedly utilize CRISPR/Cas9 technology to examine transgenic mice having genes modified to exactly mimic variant human sequences. Mutant mice will increasingly be employed for drug development studies designed to treat human genetic skeletal disorders. SIGNIFICANCE Great progress is being made identifying mutant genes responsible for human rare genetic skeletal disorders and mouse models for genes affecting bone mass, architecture, mineralization and strength. This review organizes data for 441 human genetic bone disorders with regard to heredity, gene function, molecular pathways, and fidelity of relevant mouse models to mimic the human skeletal disorders. PubMed weblinks to citations of 249 successful mouse models are provided.
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Affiliation(s)
- Robert Brommage
- Department of Internal Medicine and Clinical Nutrition, Centre for Bone and Arthritis Research, Institute of Medicine, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- *Correspondence: Robert Brommage
| | - Claes Ohlsson
- Department of Internal Medicine and Clinical Nutrition, Centre for Bone and Arthritis Research, Institute of Medicine, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Department of Drug Treatment, Sahlgrenska University Hospital, Gothenburg, Sweden
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