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Kim AH, Sakin I, Viviano S, Tuncel G, Aguilera SM, Goles G, Jeffries L, Ji W, Lakhani SA, Kose CC, Silan F, Oner SS, Kaplan OI, Ergoren MC, Mishra-Gorur K, Gunel M, Sag SO, Temel SG, Deniz E. CC2D1A causes ciliopathy, intellectual disability, heterotaxy, renal dysplasia, and abnormal CSF flow. Life Sci Alliance 2024; 7:e202402708. [PMID: 39168639 PMCID: PMC11339347 DOI: 10.26508/lsa.202402708] [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: 03/11/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 08/23/2024] Open
Abstract
Intellectual and developmental disabilities result from abnormal nervous system development. Over a 1,000 genes have been associated with intellectual and developmental disabilities, driving continued efforts toward dissecting variant functionality to enhance our understanding of the disease mechanism. This report identified two novel variants in CC2D1A in a cohort of four patients from two unrelated families. We used multiple model systems for functional analysis, including Xenopus, Drosophila, and patient-derived fibroblasts. Our experiments revealed that cc2d1a is expressed explicitly in a spectrum of ciliated tissues, including the left-right organizer, epidermis, pronephric duct, nephrostomes, and ventricular zone of the brain. In line with this expression pattern, loss of cc2d1a led to cardiac heterotaxy, cystic kidneys, and abnormal CSF circulation via defective ciliogenesis. Interestingly, when we analyzed brain development, mutant tadpoles showed abnormal CSF circulation only in the midbrain region, suggesting abnormal local CSF flow. Furthermore, our analysis of the patient-derived fibroblasts confirmed defective ciliogenesis, further supporting our observations. In summary, we revealed novel insight into the role of CC2D1A by establishing its new critical role in ciliogenesis and CSF circulation.
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Affiliation(s)
- Angelina Haesoo Kim
- https://ror.org/03pnmqc26 Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Irmak Sakin
- Department of ENT, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Acibadem University School of Medicine, Istanbul, Turkey
| | - Stephen Viviano
- https://ror.org/03pnmqc26 Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Gulten Tuncel
- https://ror.org/02x8svs93 DESAM Research Institute, Near East University, Nicosia, Cyprus
| | | | - Gizem Goles
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Lauren Jeffries
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Weizhen Ji
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Saquib A Lakhani
- https://ror.org/03pnmqc26 Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Canan Ceylan Kose
- Canakkale 18 March University, Faculty of Medicine, Department of Medical Genetics, Canakkale, Turkey
| | - Fatma Silan
- Canakkale 18 March University, Faculty of Medicine, Department of Medical Genetics, Canakkale, Turkey
| | - Sukru Sadik Oner
- Department of Pharmacology, Goztepe Prof. Dr. Suleyman Yalcin City Hospital, Istanbul, Turkey
- Istanbul Medeniyet University, Science and Advanced Technologies Research Center (BILTAM), Istanbul, Turkey
| | - Oktay I Kaplan
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| | - Mahmut Cerkez Ergoren
- https://ror.org/02x8svs93 Department of Medical Genetics, Faculty of Medicine, Near East University, Nicosia, Cyprus
| | - Ketu Mishra-Gorur
- https://ror.org/03pnmqc26 Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Murat Gunel
- https://ror.org/03pnmqc26 Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Yale Program in Brain Tumor Research, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Sebnem Ozemri Sag
- Department of Medical Genetics, Faculty of Medicine, Uludag University, Bursa, Turkey
| | - Sehime G Temel
- Department of Medical Genetics, Faculty of Medicine, Uludag University, Bursa, Turkey
- Department of Histology and Embryology and Health Sciences Institute, Department of Translational Medicine, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Engin Deniz
- https://ror.org/03pnmqc26 Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
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2
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Yang X, Zhao Z, Wang C, Wang W, Zhang L. Four mutations identified in Chinese families with autosomal dominant congenital cataracts by next-generation sequencing. Genes Genomics 2024; 46:917-925. [PMID: 38869770 DOI: 10.1007/s13258-024-01525-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 05/17/2024] [Indexed: 06/14/2024]
Abstract
BACKGROUND Congenital cataracts, which can arise due to a combination of factors like environmental influences and genetic predisposition, significantly impact children's visual health globally. The occurrence rate of congenital cataracts varies from 0. 63 to 9.74 per 10,000 births. There are 7.4 instances per 10,000 children, with the highest occurrence seen in Asia. Symptoms of the disease include clouding of the lens and visual impairment. Timely identification of the condition plays a crucial role in the management and outlook of pediatric patients. OBJECTIVE This investigation aimed to discover causative mutations in four separate Chinese family lineages. METHODS The detailed clinical data and family history of four Chinese families with autosomal dominant congenital cataracts were carefully documented. Examination of the Whole Exome Sequencing was utilized to identify the genetic anomalies present in the familial cases. Subsequent validation of the identified mutations was carried out using PCR and Sanger sequencing. Following this, various computational predictive programs were utilized to evaluate how the mutations impact the structure and function of the protein. RESULTS The sequencing results reveal four potential disease-causing mutations: c.436G > A (p.V146M) of CRYBB2 Family 1, c.26G > T (p.R9I) of GJA3 in family 2, c.227G > A (p.R76H) of GJA8 in family 3, c.-168G > T of FTL in family 4. Among them, the causative mutation in Family GJA3 is novel, and Family FTL is a rare cataract syndrome. These familial mutations showed complete co-segregation with the affected individuals, with no presence in unaffected family members or the 100 controls. Several bioinformatic prediction tools also support the likely pathogenicity of these mutations. CONCLUSION Our findings expand the mutational and phenotypic spectrum of genes associated with congenital cataracts and provide clues to the pathogenesis of congenital cataracts. These data also demonstrate the importance of NGS technology for the molecular diagnosis of congenital cataract patients.
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Affiliation(s)
- Xinyi Yang
- Eye Hospital, The First Affiliated Hospital of Harbin Medical University, Harbin, 150000, China
| | - Zitong Zhao
- Eye Hospital, The First Affiliated Hospital of Harbin Medical University, Harbin, 150000, China
| | - Chun Wang
- Eye Hospital, The First Affiliated Hospital of Harbin Medical University, Harbin, 150000, China
| | - Wenxuan Wang
- Eye Hospital, The First Affiliated Hospital of Harbin Medical University, Harbin, 150000, China
| | - Lu Zhang
- Eye Hospital, The First Affiliated Hospital of Harbin Medical University, Harbin, 150000, China.
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3
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Ghaffar A, Akhter T, Strømme P, Misceo D, Khan A, Frengen E, Umair M, Isidor B, Cogné B, Khan AA, Bruel AL, Sorlin A, Kuentz P, Chiaverini C, Innes AM, Zech M, Baláž M, Havrankova P, Jech R, Ahmed ZM, Riazuddin S, Riazuddin S. Variants of NAV3, a neuronal morphogenesis protein, cause intellectual disability, developmental delay, and microcephaly. Commun Biol 2024; 7:831. [PMID: 38977784 PMCID: PMC11231287 DOI: 10.1038/s42003-024-06466-1] [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: 01/04/2024] [Accepted: 06/18/2024] [Indexed: 07/10/2024] Open
Abstract
Microtubule associated proteins (MAPs) are widely expressed in the central nervous system, and have established roles in cell proliferation, myelination, neurite formation, axon specification, outgrowth, dendrite, and synapse formation. We report eleven individuals from seven families harboring predicted pathogenic biallelic, de novo, and heterozygous variants in the NAV3 gene, which encodes the microtubule positive tip protein neuron navigator 3 (NAV3). All affected individuals have intellectual disability (ID), microcephaly, skeletal deformities, ocular anomalies, and behavioral issues. In mouse brain, Nav3 is expressed throughout the nervous system, with more prominent signatures in postmitotic, excitatory, inhibiting, and sensory neurons. When overexpressed in HEK293T and COS7 cells, pathogenic variants impaired NAV3 ability to stabilize microtubules. Further, knocking-down nav3 in zebrafish led to severe morphological defects, microcephaly, impaired neuronal growth, and behavioral impairment, which were rescued with co-injection of WT NAV3 mRNA and not by transcripts encoding the pathogenic variants. Our findings establish the role of NAV3 in neurodevelopmental disorders, and reveal its involvement in neuronal morphogenesis, and neuromuscular responses.
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Affiliation(s)
- Amama Ghaffar
- Department of Otorhinolaryngology-Head & Neck Surgery, School of Medicine University of Maryland, Baltimore, MD, USA
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Tehmeena Akhter
- Department of Otorhinolaryngology-Head & Neck Surgery, School of Medicine University of Maryland, Baltimore, MD, USA
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Petter Strømme
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Doriana Misceo
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Amjad Khan
- Faculty of Biological Sciences, Department of Zoology, University of Lakki Marwat, 28420, Khyber, Pakhtunkhwa, Pakistan
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübinge, 72076, Germany
- Alexander von Humboldt Fellowship Foundation, Berlin, 10117, Germany
| | - Eirik Frengen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Muhammad Umair
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Bertrand Isidor
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000, Nantes, France
| | - Benjamin Cogné
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000, Nantes, France
| | - Asma A Khan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ange-Line Bruel
- INSERM UMR1231 GAD "Génétique des Anomalies du Développement", FHU-TRANSLAD, Université de Bourgogne Franche-Comté, Dijon, France
| | - Arthur Sorlin
- INSERM UMR1231 GAD "Génétique des Anomalies du Développement", FHU-TRANSLAD, Université de Bourgogne Franche-Comté, Dijon, France
- National Center of Genetics (NCG), Laboratoire national de santé (LNS), 1, rue Louis Rech, L-3555, Dudelange, Luxembourg
| | - Paul Kuentz
- INSERM UMR1231 GAD "Génétique des Anomalies du Développement", FHU-TRANSLAD, Université de Bourgogne Franche-Comté, Dijon, France
| | | | - A Micheil Innes
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Munich, Neuherberg, Germany
- Institute of Human Genetics, Technical University of Munich, School of Medicine, Munich, Germany
- Institute for Advanced Study, Technical University of Munich, Lichtenbergstrasse 2 a, D-85748, Garching, Germany
| | - Marek Baláž
- First Department of Neurology, Faculty of Medicine, St. Anne's University Hospital, and CEITEC, Masaryk University, Brno, Czech Republic
| | - Petra Havrankova
- Department of Neurology, Charles University, First Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Robert Jech
- Department of Neurology, Charles University, First Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Zubair M Ahmed
- Department of Otorhinolaryngology-Head & Neck Surgery, School of Medicine University of Maryland, Baltimore, MD, USA
| | - Sheikh Riazuddin
- Jinnah Burn and Reconstructive Surgery Centre, Allama Iqbal Medical Research, University of Health Sciences, Lahore, Pakistan
| | - Saima Riazuddin
- Department of Otorhinolaryngology-Head & Neck Surgery, School of Medicine University of Maryland, Baltimore, MD, USA.
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Shi S, Tang X, Long S, Yang J, Wang T, Wang H, Hu T, Shi J, Huang G, Qiao S, Lin T. A novel homozygous LRRC6 mutation causes male infertility with asthenozoospermia and primary ciliary dyskinesia in humans. Andrology 2024. [PMID: 38934611 DOI: 10.1111/andr.13685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/28/2024] [Accepted: 06/02/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Dysfunction of motile cilia, including respiratory cilia and sperm flagella, typically leads to primary ciliary dyskinesia and male infertility or low fertility in humans. Genetic defects of LRRC6 have been associated with primary ciliary dyskinesia and asthenozoospermia due to abnormal ultrastructure of ciliated axonemes. OBJECTIVES To identify novel mutations of the LRRC6 gene related to multiple morphological abnormalities of the sperm flagella and male infertility and investigate the underlying molecular mechanisms involved. MATERIALS AND METHODS The LRRC6 mutations were identified by whole exome sequencing and confirmed with Sanger sequencing. Papanicolaou staining, scanning, and transmission electron microscopy were performed to investigate the morphological and ultrastructural characteristics of spermatozoa. Further tandem mass tagging proteomics analyses were performed to explore the effect of mutations and confirmed by immunostaining and western blotting. Intracytoplasmic sperm injection was applied for the assisted reproductive therapy of males harboring biallelic LRRC6 mutations. RESULTS In this study, we identified a novel homozygous LRRC6 mutation in a consanguineous family, characterized by asthenozoospermia and primary ciliary dyskinesia. Further Semen parameter and morphology analysis demonstrate that the novel LRRC6 mutation leads to a significant reduction in sperm flagella length, a decrease in sperm progressive motility parameters, and abnormalities of sperm ultrastructure. Specifically, the absence of outer dynein arms and inner dynein arms, and incomplete mitochondrial sheath in the flagellar mid-piece were observed by transmission electron microscopy. In addition, tandem mass tagging proteomics analysis revealed that spermatozoa obtained from patients harboring the LRRC6 mutation exhibited a significant decrease in the expression levels of proteins related to the assembly and function of dynein axonemal arms. Functional analysis revealed that this novel LRRC6 mutation disrupted the function of the leucine-rich repeat containing 6 protein, which in turn affects the expression of the dynein arm proteins and leucine-rich repeat containing 6-interacting proteins CCDC40, SPAG1, and ZMYND10. Finally, we reported a successful pregnancy through assisted reproductive technology with intracytoplasmic sperm injection in the female partner of the proband. DISCUSSION AND CONCLUSION This study highlights the identification of a novel homozygous LRRC6 mutation in a consanguineous family and its impact on sperm progressive motility, morphology, and sperm kinetics parameters, which could facilitate the genetic diagnosis of asthenozoospermia and offer valuable perspectives for future genetic counseling endeavors.
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Affiliation(s)
- Shengjia Shi
- Reproductive center, Northwest Women's and Children's Hospital, Xi'an, China
| | - Xiangrong Tang
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Shunhua Long
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Yang
- Reproductive center, Northwest Women's and Children's Hospital, Xi'an, China
| | - Tianwei Wang
- Reproductive center, Northwest Women's and Children's Hospital, Xi'an, China
| | - Hongmei Wang
- Basic Medical College, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Tingwenyi Hu
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Juanzi Shi
- Reproductive center, Northwest Women's and Children's Hospital, Xi'an, China
| | - Guoning Huang
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Sen Qiao
- Reproductive center, Northwest Women's and Children's Hospital, Xi'an, China
| | - Tingting Lin
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
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5
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Xu Z, Sadleir L, Goel H, Jiao X, Niu Y, Zhou Z, de Valles-Ibáñez G, Poke G, Hildebrand M, Lieffering N, Qin J, Yang Z. Genotype and phenotype correlation of PHACTR1-related neurological disorders. J Med Genet 2024; 61:536-542. [PMID: 38272663 DOI: 10.1136/jmg-2023-109638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024]
Abstract
BACKGROUND PHACTR1 (phosphatase and actin regulators) plays a key role in cortical migration and synaptic activity by binding and regulating G-actin and PPP1CA. This study aimed to expand the genotype and phenotype of patients with de novo variants in PHACTR1 and analyse the impact of variants on protein-protein interaction. METHODS We identified seven patients with PHACTR1 variants by trio-based whole-exome sequencing. Additional two subjects were ascertained from two centres through GeneMatcher. The genotype-phenotype correlation was determined, and AlphaFold-Multimer was used to predict protein-protein interactions and interfaces. RESULTS Eight individuals carried missense variants and one had CNV in the PHACTR1. Infantile epileptic spasms syndrome (IESS) was the unifying phenotype in eight patients with missense variants of PHACTR1. They could present with other types of seizures and often exhibit drug-resistant epilepsy with a poor prognosis. One patient with CNV displayed a developmental encephalopathy phenotype. Using AlphaFold-Multimer, our findings indicate that PHACTR1 and G-actin-binding sequences overlap with PPP1CA at the RPEL3 domain, which suggests possible competition between PPP1CA and G-actin for binding to PHACTR1 through a similar polymerisation interface. In addition, patients carrying missense variants located at the PHACTR1-PPP1CA or PHACTR1-G-actin interfaces consistently exhibit the IESS phenotype. These missense variants are mostly concentrated in the overlapping sequence (RPEL3 domain). CONCLUSIONS Patients with variants in PHACTR1 can have a phenotype of developmental encephalopathy in addition to IESS. Moreover, our study confirmed that the variants affect the binding of PHACTR1 to G-actin or PPP1CA, resulting in neurological disorders in patients.
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Affiliation(s)
- Zhao Xu
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Lynette Sadleir
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington, New Zealand
| | - Himanshu Goel
- Hunter Genetics, Waratah, New South Wales, Australia
| | - Xianru Jiao
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Yue Niu
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Zongpu Zhou
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Guillem de Valles-Ibáñez
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington, New Zealand
| | - Gemma Poke
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington, New Zealand
| | - Michael Hildebrand
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Heidelberg, Victoria, Australia
- Neuroscience Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, South Brisbane, Queensland, Australia
| | - Nico Lieffering
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington, New Zealand
| | - Jiong Qin
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Zhixian Yang
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
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6
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Afridi TUK, Fatima A, Satti HS, Akram Z, Yousafzai IK, Naeem WB, Fatima N, Ali A, Iqbal Z, Khan A, Shahzad M, Liu C, Toft M, Zhang F, Tariq M, Davis EE, Khan TN. Exome sequencing in four families with neurodevelopmental disorders: genotype-phenotype correlation and identification of novel disease-causing variants in VPS13B and RELN. Mol Genet Genomics 2024; 299:55. [PMID: 38771357 DOI: 10.1007/s00438-024-02149-y] [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: 11/19/2023] [Accepted: 04/30/2024] [Indexed: 05/22/2024]
Abstract
Neurodevelopmental disorders (NDDs) are a clinically and genetically heterogeneous group of early-onset pediatric disorders that affect the structure and/or function of the central or peripheral nervous system. Achieving a precise molecular diagnosis for NDDs may be challenging due to the diverse genetic underpinnings and clinical variability. In the current study, we investigated the underlying genetic cause(s) of NDDs in four unrelated Pakistani families. Using exome sequencing (ES) as a diagnostic approach, we identified disease-causing variants in established NDD-associated genes in all families, including one hitherto unreported variant in RELN and three recurrent variants in VPS13B, DEGS1, and SPG11. Overall, our study highlights the potential of ES as a tool for clinical diagnosis.
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Affiliation(s)
- Tehseen Ullah Khan Afridi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Ambrin Fatima
- Department of Biological and Biomedical Sciences, The Aga Khan University, Karachi, 74800, Pakistan
| | - Humayoon Shafique Satti
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Zaineb Akram
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Imran Khan Yousafzai
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Wajahat Bin Naeem
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Nasreen Fatima
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Asmat Ali
- Department of Biological and Biomedical Sciences, The Aga Khan University, Karachi, 74800, Pakistan
| | - Zafar Iqbal
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Ayaz Khan
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Muhammad Shahzad
- Department of Neurosurgery, District Headquarter Hospital, Kohat, Pakistan
| | - Chunyu Liu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Mathias Toft
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Feng Zhang
- Institute of Medical Genetics and Genomics, Fudan University, Shanghai, 200438, China
| | - Muhammad Tariq
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Erica E Davis
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA.
- Department of Pediatrics and Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Tahir N Khan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan.
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA.
- Department of Pediatrics and Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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7
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Usmani MA, Ghaffar A, Shahzad M, Akram J, Majeed AI, Malik K, Fatima K, Khan AA, Ahmed ZM, Riazuddin S, Riazuddin S. A Missense Variant in HACE1 Is Associated with Intellectual Disability, Epilepsy, Spasticity, and Psychomotor Impairment in a Pakistani Kindred. Genes (Basel) 2024; 15:580. [PMID: 38790209 PMCID: PMC11121239 DOI: 10.3390/genes15050580] [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: 04/01/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Intellectual disability (ID), which affects around 2% to 3% of the population, accounts for 0.63% of the overall prevalence of neurodevelopmental disorders (NDD). ID is characterized by limitations in a person's intellectual and adaptive functioning, and is caused by pathogenic variants in more than 1000 genes. Here, we report a rare missense variant (c.350T>C; p.(Leu117Ser)) in HACE1 segregating with NDD syndrome with clinical features including ID, epilepsy, spasticity, global developmental delay, and psychomotor impairment in two siblings of a consanguineous Pakistani kindred. HACE1 encodes a HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1 (HACE1), which is involved in protein ubiquitination, localization, and cell division. HACE1 is also predicted to interact with several proteins that have been previously implicated in the ID phenotype in humans. The p.(Leu117Ser) variant replaces an evolutionarily conserved residue of HACE1 and is predicted to be deleterious by various in silico algorithms. Previously, eleven protein truncating variants of HACE1 have been reported in individuals with NDD. However, to our knowledge, p.(Leu117Ser) is the second missense variant in HACE1 found in an individual with NDD.
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Affiliation(s)
- Muhammad A. Usmani
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (M.A.U.); (A.G.)
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan; (M.S.); (J.A.); (S.R.)
- Jinnah Burn and Reconstructive Surgery Center, Allama Iqbal Medical College, University of Health Sciences, Lahore 54550, Pakistan
| | - Amama Ghaffar
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (M.A.U.); (A.G.)
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore 54500, Pakistan
| | - Mohsin Shahzad
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan; (M.S.); (J.A.); (S.R.)
| | - Javed Akram
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan; (M.S.); (J.A.); (S.R.)
| | - Aisha I. Majeed
- Department of Radiology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan;
| | - Kausar Malik
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore 54500, Pakistan
| | - Khushbakht Fatima
- Department of Applied Health Sciences, University of Management and Technology, Lahore 54500, Pakistan;
| | - Asma A. Khan
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore 54500, Pakistan
| | - Zubair M. Ahmed
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (M.A.U.); (A.G.)
- Department of Molecular Biology and Biochemistry, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Sheikh Riazuddin
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan; (M.S.); (J.A.); (S.R.)
- Jinnah Burn and Reconstructive Surgery Center, Allama Iqbal Medical College, University of Health Sciences, Lahore 54550, Pakistan
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (M.A.U.); (A.G.)
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore 54500, Pakistan
- Department of Molecular Biology and Biochemistry, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
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8
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Bamaga A, Muthaffar O, Alyazidi A, Bahowarth S, Shawli M, Alotibi F, Alsehemi M, Almohammal M, Alawwadh A, Alghamdi N. MED23 pathogenic variant: genomic-phenotypic analysis. J Med Life 2024; 17:500-507. [PMID: 39144687 PMCID: PMC11320618 DOI: 10.25122/jml-2024-0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/02/2024] [Indexed: 08/16/2024] Open
Abstract
The mediator complex subunit 23 (MED23) gene encodes a protein that acts as a tail module mediator complex, a multi-subunit co-activator involved in several cellular activities. MED23 has been shown to have substantial roles in myogenesis and other molecular mechanisms. The functions of MED23 in the neurological system remain unclear and the clinical phenotype is not thoroughly described. Whole exome sequencing was used to identify a novel mutation in the MED23 gene. DNA capture probes using next-generation sequencing-based copy number variation analysis with Illumina array were performed. The clinical, demographic, neuroimaging, and electrophysiological data of the patients were collected, and similarly, the data of all reported cases in the literature were extracted to compare findings. Screening a total of 9,662 articles, we identified 22 main regulatory processes for the MED23 gene, including suppressive activity for carcinogenic processes. MED23 is also involved in the brain's neurogenesis and functions. The identified cases mainly presented with intellectual disability (87.5%) and developmental delay (50%). Seizures were present in only 18.75% of the patients. Slow backgrounds and spike and sharp-wave complexes were reported on the electroencephalogram (EEG) of a few patients and delayed myelination, thin corpus callosum, and pontine hypoplasia on magnetic resonance imaging (MRI). The MED23 gene regulates several processes in which its understanding promotes considerable therapeutic potential for patients. It is crucial to consider genetic and laboratory testing, particularly when encountering potential carriers. Intellectual disability and developmental delay are the most notable clinical signs with heterogeneous features on EEG and MRI.
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Affiliation(s)
- Ahmed Bamaga
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Neuromuscular Medicine Unit, Department of Pediatrics, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Osama Muthaffar
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anas Alyazidi
- Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sarah Bahowarth
- Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed Shawli
- Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fahad Alotibi
- Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Matar Alsehemi
- Pediatric Neurology Unit, Department of Pediatrics, King Fahad Hospital, Albaha, Saudi Arabia
| | | | - Adel Alawwadh
- Department of Pediatrics, Khamis Mushait Maternity and Children Hospital, Abha, Saudi Arabia
| | - Njood Alghamdi
- Faculty of Medicine, Albaha University, Albaha, Saudi Arabia
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9
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Khan H, Harripaul R, Mikhailov A, Herzi S, Bowers S, Ayub M, Shabbir MI, Vincent JB. Biallelic variants identified in 36 Pakistani families and trios with autism spectrum disorder. Sci Rep 2024; 14:9230. [PMID: 38649688 PMCID: PMC11035605 DOI: 10.1038/s41598-024-57942-x] [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: 08/30/2023] [Accepted: 03/22/2024] [Indexed: 04/25/2024] Open
Abstract
With its high rate of consanguineous marriages and diverse ethnic population, little is currently understood about the genetic architecture of autism spectrum disorder (ASD) in Pakistan. Pakistan has a highly ethnically diverse population, yet with a high proportion of endogamous marriages, and is therefore anticipated to be enriched for biallelic disease-relate variants. Here, we attempt to determine the underlying genetic abnormalities causing ASD in thirty-six small simplex or multiplex families from Pakistan. Microarray genotyping followed by homozygosity mapping, copy number variation analysis, and whole exome sequencing were used to identify candidate. Given the high levels of consanguineous marriages among these families, autosomal recessively inherited variants were prioritized, however de novo/dominant and X-linked variants were also identified. The selected variants were validated using Sanger sequencing. Here we report the identification of sixteen rare or novel coding variants in fifteen genes (ARAP1, CDKL5, CSMD2, EFCAB12, EIF3H, GML, NEDD4, PDZD4, POLR3G, SLC35A2, TMEM214, TMEM232, TRANK1, TTC19, and ZNF292) in affected members in eight of the families, including ten homozygous variants in four families (nine missense, one loss of function). Three heterozygous de novo mutations were also identified (in ARAP1, CSMD2, and NEDD4), and variants in known X-linked neurodevelopmental disorder genes CDKL5 and SLC35A2. The current study offers information on the genetic variability associated with ASD in Pakistan, and demonstrates a marked enrichment for biallelic variants over that reported in outbreeding populations. This information will be useful for improving approaches for studying ASD in populations where endogamy is commonly practiced.
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Affiliation(s)
- Hamid Khan
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Centre for Addiction and Mental Health, 250 College St, Toronto, ON, M5T 1R8, Canada
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, Pakistan
| | - Ricardo Harripaul
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Centre for Addiction and Mental Health, 250 College St, Toronto, ON, M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Anna Mikhailov
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Centre for Addiction and Mental Health, 250 College St, Toronto, ON, M5T 1R8, Canada
| | - Sumayah Herzi
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Centre for Addiction and Mental Health, 250 College St, Toronto, ON, M5T 1R8, Canada
| | - Sonya Bowers
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Centre for Addiction and Mental Health, 250 College St, Toronto, ON, M5T 1R8, Canada
| | | | - Muhammad Imran Shabbir
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, Pakistan
| | - John B Vincent
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Centre for Addiction and Mental Health, 250 College St, Toronto, ON, M5T 1R8, Canada.
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
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10
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Pan X, Tao AM, Lu S, Ma M, Hannan SB, Slaugh R, Drewes Williams S, O'Grady L, Kanca O, Person R, Carter MT, Platzer K, Schnabel F, Abou Jamra R, Roberts AE, Newburger JW, Revah-Politi A, Granadillo JL, Stegmann APA, Sinnema M, Accogli A, Salpietro V, Capra V, Ghaloul-Gonzalez L, Brueckner M, Simon MEH, Sweetser DA, Glinton KE, Kirk SE, Wangler MF, Yamamoto S, Chung WK, Bellen HJ. De novo variants in FRYL are associated with developmental delay, intellectual disability, and dysmorphic features. Am J Hum Genet 2024; 111:742-760. [PMID: 38479391 PMCID: PMC11023917 DOI: 10.1016/j.ajhg.2024.02.007] [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: 08/23/2023] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 04/07/2024] Open
Abstract
FRY-like transcription coactivator (FRYL) belongs to a Furry protein family that is evolutionarily conserved from yeast to humans. The functions of FRYL in mammals are largely unknown, and variants in FRYL have not previously been associated with a Mendelian disease. Here, we report fourteen individuals with heterozygous variants in FRYL who present with developmental delay, intellectual disability, dysmorphic features, and other congenital anomalies in multiple systems. The variants are confirmed de novo in all individuals except one. Human genetic data suggest that FRYL is intolerant to loss of function (LoF). We find that the fly FRYL ortholog, furry (fry), is expressed in multiple tissues, including the central nervous system where it is present in neurons but not in glia. Homozygous fry LoF mutation is lethal at various developmental stages, and loss of fry in mutant clones causes defects in wings and compound eyes. We next modeled four out of the five missense variants found in affected individuals using fry knockin alleles. One variant behaves as a severe LoF variant, whereas two others behave as partial LoF variants. One variant does not cause any observable defect in flies, and the corresponding human variant is not confirmed to be de novo, suggesting that this is a variant of uncertain significance. In summary, our findings support that fry is required for proper development in flies and that the LoF variants in FRYL cause a dominant disorder with developmental and neurological symptoms due to haploinsufficiency.
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Affiliation(s)
- Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Alice M Tao
- Vagelos School of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Shabab B Hannan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Rachel Slaugh
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Sarah Drewes Williams
- Division of Genetic and Genomic Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Lauren O'Grady
- Division of Medical Genetics & Metabolism, Massachusetts General for Children, Boston, MA, USA; MGH Institute of Health Professions, Charlestown, MA, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | | | - Melissa T Carter
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Franziska Schnabel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Amy E Roberts
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Medicine, Division of Genetics, Boston Children's Hospital, Boston, MA, USA
| | - Jane W Newburger
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Anya Revah-Politi
- Institute for Genomic Medicine and Precision Genomics Laboratory, Columbia University Irving Medical Center, New York, NY, USA
| | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Margje Sinnema
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Andrea Accogli
- Division of Medical Genetics, Department of Medicine, McGill University Health Center, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, University College London Institute of Neurology, Queen Square, London, UK
| | - Valeria Capra
- Unit of Medical Genetics and Genomics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Lina Ghaloul-Gonzalez
- Division of Genetic and Genomic Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Martina Brueckner
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Marleen E H Simon
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - David A Sweetser
- Division of Medical Genetics & Metabolism, Massachusetts General for Children, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kevin E Glinton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Genetics, Texas Children's Hospital, Houston, TX, USA
| | - Susan E Kirk
- Section of Hematology/Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Cancer and Hematology Center, Houston, TX, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan & Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Wendy K Chung
- Departments of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
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11
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Shen B, Shen Q, Zeng Q, Zhang L, Li X. Silenced-C5ar1 improved multiple organ injury in sepsis rats via inhibiting neutrophil extracellular trap. J Mol Histol 2024; 55:69-81. [PMID: 38165570 PMCID: PMC10830609 DOI: 10.1007/s10735-023-10172-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 10/21/2023] [Indexed: 01/04/2024]
Abstract
Sepsis has a systemic inflammatory response syndrome caused by infection. While neutrophils play contradictory roles in different stages of sepsis. Neutrophils have been proven to play an antibacterial role by producing neutrophil extracellular traps (NETs). Although the NET is beneficial to bacteria resistance, abnormal NET increases tissue damage. The complement C5a receptor 1 (C5ar1) is a gene related to strong inflammatory reactions and is found to be associated with inflammatory factors. This study found that there were 45 down-regulated genes and 704 up-regulated genes in sepsis rats by transcriptome sequencing. And those genes were significantly related to inflammation and immunity by GO and KEGG enrichment analysis involving the chemokine signaling pathway, the Toll-like receptor (TLR) signaling pathway, and the Fc gamma R-mediated phagocytosis. Additionally, the C5ar1 gene was significantly upregulated with interesting potential in sepsis and used for further study. This study used cecum ligation and puncture (CLP) rats that were respectively injected intravenously with PBS or the lentivirus vector to explore the effect of C5ar1 on CLP rats. It demonstrated that silenced- C5ar1 inhibited the ALT, AST, BUN, and CREA levels, improved the lung and spleen injury, and reduced the TNF-α, IL-6, IL-1β, IL-10, cf-DNA, and cfDNA/MPO levels. Additionally, silenced C5ar1 inhibited the TLR2, TLR4, and peptidylarginine deiminase 4 expression levels, which suggested the improvement of silenced C5ar1 on sepsis via inhibiting NETs and the TLR signaling pathway. This study provides a basis and new direction for the study of treatment on sepsis.
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Affiliation(s)
- Bin Shen
- Department of Infectious Diseases, Huzhou Central Hospital, Huzhou, 313000, China
| | - Qikai Shen
- Department of Intensive Care Units, Huzhou Central Hospital, Huzhou, 313000, China
| | - Qingqiu Zeng
- Department of Infectious Diseases, Huzhou Central Hospital, Huzhou, 313000, China
| | - Lingyan Zhang
- Department of Infectious Diseases, Huzhou Central Hospital, Huzhou, 313000, China
| | - Xiaofeng Li
- Department of Infectious Diseases, Huzhou Central Hospital, Huzhou, 313000, China.
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12
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Schaffrath R, Brinkmann U. Diphthamide - a conserved modification of eEF2 with clinical relevance. Trends Mol Med 2024; 30:164-177. [PMID: 38097404 DOI: 10.1016/j.molmed.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 02/17/2024]
Abstract
Diphthamide, a complex modification on eukaryotic translation elongation factor 2 (eEF2), assures reading-frame fidelity during translation. Diphthamide and enzymes for its synthesis are conserved in eukaryotes and archaea. Originally identified as target for diphtheria toxin (DT) in humans, its clinical relevance now proves to be broader than the link to pathogenic bacteria. Diphthamide synthesis enzymes (DPH1 and DPH3) are associated with cancer, and DPH gene mutations can cause diphthamide deficiency syndrome (DDS). Finally, new analyses provide evidence that diphthamide may restrict propagation of viruses including SARS-CoV-2 and HIV-1, and that DPH enzymes are targeted by viruses for degradation to overcome this restriction. This review describes how diphthamide is synthesized and functions in translation, and covers its clinical relevance in human development, cancer, and infectious diseases.
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Affiliation(s)
- Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany.
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany.
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13
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Hussain SI, Muhammad N, Shah SUD, Fardous F, Khan SA, Khan N, Rehman AU, Siddique M, Wasan SA, Niaz R, Ullah H, Khan N, Muhammad N, Mirza MU, Wasif N, Khan S. Structural and functional implications of SLC13A3 and SLC9A6 mutations: an in silico approach to understanding intellectual disability. BMC Neurol 2023; 23:353. [PMID: 37794328 PMCID: PMC10548666 DOI: 10.1186/s12883-023-03397-y] [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: 05/24/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Intellectual disability (ID) is a condition that varies widely in both its clinical presentation and its genetic underpinnings. It significantly impacts patients' learning capacities and lowers their IQ below 70. The solute carrier (SLC) family is the most abundant class of transmembrane transporters and is responsible for the translocation of various substances across cell membranes, including nutrients, ions, metabolites, and medicines. The SLC13A3 gene encodes a plasma membrane-localized Na+/dicarboxylate cotransporter 3 (NaDC3) primarily expressed in the kidney, astrocytes, and the choroid plexus. In addition to three Na + ions, it brings four to six carbon dicarboxylates into the cytosol. Recently, it was discovered that patients with acute reversible leukoencephalopathy and a-ketoglutarate accumulation (ARLIAK) carry pathogenic mutations in the SLC13A3 gene, and the X-linked neurodevelopmental condition Christianson Syndrome is caused by mutations in the SLC9A6 gene, which encodes the recycling endosomal alkali cation/proton exchanger NHE6, also called sodium-hydrogen exchanger-6. As a result, there are severe impairments in the patient's mental capacity, physical skills, and adaptive behavior. METHODS AND RESULTS Two Pakistani families (A and B) with autosomal recessive and X-linked intellectual disorders were clinically evaluated, and two novel disease-causing variants in the SLC13A3 gene (NM 022829.5) and the SLC9A6 gene (NM 001042537.2) were identified using whole exome sequencing. Family-A segregated a novel homozygous missense variant (c.1478 C > T; p. Pro493Leu) in the exon-11 of the SLC13A3 gene. At the same time, family-B segregated a novel missense variant (c.1342G > A; p.Gly448Arg) in the exon-10 of the SLC9A6 gene. By integrating computational approaches, our findings provided insights into the molecular mechanisms underlying the development of ID in individuals with SLC13A3 and SLC9A6 mutations. CONCLUSION We have utilized in-silico tools in the current study to examine the deleterious effects of the identified variants, which carry the potential to understand the genotype-phenotype relationships in neurodevelopmental disorders.
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Affiliation(s)
- Syeda Iqra Hussain
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Nazif Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Salah Ud Din Shah
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Fardous Fardous
- Department of Medical Lab Technology, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Sher Alam Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Niamatullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Adil U Rehman
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Mehwish Siddique
- Department of Zoology, Government Post Graduate College for Women, Satellite Town, Gujranwala, Pakistan
| | - Shoukat Ali Wasan
- Department of Botany, Faculty of Natural Sciences, Shah Abdul Latif University, Khairpur, Sindh, Pakistan
| | - Rooh Niaz
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Hafiz Ullah
- Gomal Center of Biochemistry and Biotechnology (GCBB), Gomal University D. I. Khan, D. I. Khan, Pakistan
| | - Niamat Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Noor Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, N9B 1C4, Canada
| | - Naveed Wasif
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany.
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan.
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14
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Breger K, Kunkler CN, O'Leary NJ, Hulewicz JP, Brown JA. Ghost authors revealed: The structure and function of human N 6 -methyladenosine RNA methyltransferases. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1810. [PMID: 37674370 PMCID: PMC10915109 DOI: 10.1002/wrna.1810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 09/08/2023]
Abstract
Despite the discovery of modified nucleic acids nearly 75 years ago, their biological functions are still being elucidated. N6 -methyladenosine (m6 A) is the most abundant modification in eukaryotic messenger RNA (mRNA) and has also been detected in non-coding RNAs, including long non-coding RNA, ribosomal RNA, and small nuclear RNA. In general, m6 A marks can alter RNA secondary structure and initiate unique RNA-protein interactions that can alter splicing, mRNA turnover, and translation, just to name a few. Although m6 A marks in human RNAs have been known to exist since 1974, the structures and functions of methyltransferases responsible for writing m6 A marks have been established only recently. Thus far, there are four confirmed human methyltransferases that catalyze the transfer of a methyl group from S-adenosylmethionine (SAM) to the N6 position of adenosine, producing m6 A: methyltransferase-like protein (METTL) 3/METTL14 complex, METTL16, METTL5, and zinc-finger CCHC-domain-containing protein 4. Though the methyltransferases have unique RNA targets, all human m6 A RNA methyltransferases contain a Rossmann fold with a conserved SAM-binding pocket, suggesting that they utilize a similar catalytic mechanism for methyl transfer. For each of the human m6 A RNA methyltransferases, we present the biological functions and links to human disease, RNA targets, catalytic and kinetic mechanisms, and macromolecular structures. We also discuss m6 A marks in human viruses and parasites, assigning m6 A marks in the transcriptome to specific methyltransferases, small molecules targeting m6 A methyltransferases, and the enzymes responsible for hypermodified m6 A marks and their biological functions in humans. Understanding m6 A methyltransferases is a critical steppingstone toward establishing the m6 A epitranscriptome and more broadly the RNome. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Kurtis Breger
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Charlotte N Kunkler
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Nathan J O'Leary
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jacob P Hulewicz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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15
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Naqvi SF, Yıldız-Bölükbaşı E, Afzal M, Nalbant G, Mumtaz S, Tolun A, Malik S. Homozygous Mutations in Thyroid Peroxidase (TPO) in Hypothyroidism with Intellectual Disability, Developmental Delay, and Hearing and Ocular Anomalies in Two Families: Severe Manifestation of Untreated TPO-deficiency Poses a Diagnostic Dilemma. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2023; 96:347-365. [PMID: 37780999 PMCID: PMC10524819 DOI: 10.59249/ssrg6507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Intellectual disability (ID) involves compromised intellectual, learning and cognitive skills, and behavioral capabilities with reduced psychomotor skills. One of the preventable causes of ID is congenital hypothyroidism (CH), which may be due to biallelic mutations in thyroid peroxidase (TPO). In low- and middle-income countries with no newborn screening programs, CH poses a great risk of ID and long-term morbidity. We report two large Pakistani families with a total of 16 patients afflicted with CH. Detailed clinical and behavioral assessments, SNP-based homozygosity mapping, linkage analysis, and exome sequencing were performed. Initially, affected individuals were referred as suffering ID (in 11 of 16 patients) and developmental delay (in 14). Secondary/associated features were verbal apraxia (in 13), goiter (in 12), short stature (in 11), limb hypotonia (in 14), no pubertal onset (five of 10 of age ≥14 years), high myopia (in eight), muscle cramps (in six), and in some, variable microcephaly and enuresis/encopresis, fits, chronic fatigue, and other behavioral symptoms, which are not characteristics of CH. Molecular genetic analyses led to the discovery of homozygous variants in TPO: novel missense variant c.719A>G (p.Asp240Gly) in family 1 and rare c.2315A>G (p.Tyr772Cys) in family 2. In low-resource countries where neonatal screening programs do not include a CH test, the burden of neurodevelopmental disorders is likely to be increased due to untreated CH. Secondly, in the background of the high prevalence of recessive disorders due to high parental consanguinity, the severe manifestation of TPO-deficiency mimics a wide range of neurological and other presentations posing a diagnostic dilemma.
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Affiliation(s)
- Syeda Farwa Naqvi
- Human Genetics Program, Department of Zoology, Faculty
of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Esra Yıldız-Bölükbaşı
- Department of Molecular Biology and Genetics, Boğaziçi
University, Istanbul, Türkiye
| | - Muhammad Afzal
- Human Genetics Program, Department of Zoology, Faculty
of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Gökhan Nalbant
- Department of Biostatistics and Bioinformatics,
Institute of Health Sciences, Acibadem Mehmet Ali Aydınlar University, Istanbul,
Türkiye
| | - Sara Mumtaz
- Department of Biological Sciences, National University
of Medical Sciences, Rawalpindi, Pakistan
| | - Aslıhan Tolun
- Department of Molecular Biology and Genetics, Istanbul
Technical University, Istanbul, Türkiye
| | - Sajid Malik
- Human Genetics Program, Department of Zoology, Faculty
of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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16
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Ütkür K, Mayer K, Khan M, Manivannan T, Schaffrath R, Brinkmann U. DPH1 and DPH2 variants that confer susceptibility to diphthamide deficiency syndrome in human cells and yeast models. Dis Model Mech 2023; 16:dmm050207. [PMID: 37675463 PMCID: PMC10538292 DOI: 10.1242/dmm.050207] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/21/2023] [Indexed: 09/08/2023] Open
Abstract
The autosomal-recessive diphthamide deficiency syndrome presents as intellectual disability with developmental abnormalities, seizures, craniofacial and additional morphological phenotypes. It is caused by reduced activity of proteins that synthesize diphthamide on human translation elongation factor 2. Diphthamide synthesis requires seven proteins (DPH1-DPH7), with clinical deficiency described for DPH1, DPH2 and DPH5. A limited set of variant alleles from syndromic patients has been functionally analyzed, but databases (gnomAD) list additional so far uncharacterized variants in human DPH1 and DPH2. Because DPH enzymes are conserved among eukaryotes, their functionality can be assessed in yeast and mammalian cells. Our experimental assessment of known and uncharacterized DPH1 and DPH2 missense alleles showed that six variants are tolerated despite inter-species conservation. Ten additional human DPH1 (G113R, A114T, H132P, H132R, S136R, C137F, L138P, Y152C, S221P, H240R) and two DPH2 (H105P, C341Y) variants showed reduced functionality and hence are deficiency-susceptibility alleles. Some variants locate close to the active enzyme center and may affect catalysis, while others may impact on enzyme activation. In sum, our study has identified functionally compromised alleles of DPH1 and DPH2 genes that likely cause diphthamide deficiency syndrome.
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Affiliation(s)
- Koray Ütkür
- Institut für Biologie,Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany
| | - Klaus Mayer
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany
| | - Maliha Khan
- Institut für Biologie,Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany
| | - Thirishika Manivannan
- Institut für Biologie,Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany
| | - Raffael Schaffrath
- Institut für Biologie,Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany
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17
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Lai ZH, Liu XY, Song YY, Zhou HY, Zeng LL. Case report: Hereditary spastic paraplegia with a novel homozygous mutation in ZFYVE26. Front Neurol 2023; 14:1160110. [PMID: 37681008 PMCID: PMC10482258 DOI: 10.3389/fneur.2023.1160110] [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: 02/06/2023] [Accepted: 06/16/2023] [Indexed: 09/09/2023] Open
Abstract
Hereditary spastic paraplegia (HSP) is a group of neurodegenerative diseases with genetic and clinical heterogeneity characterized by spasticity and weakness of the lower limbs. It includes four genetic inheritance forms: autosomal dominant inheritance (AD), autosomal recessive inheritance (AR), X-linked inheritance, and mitochondrial inheritance. To date, more than 82 gene loci have been found to cause HSP, and SPG15 (ZFYVE26) is one of the most common autosomal recessive hereditary spastic paraplegias (ARHSPs) with a thin corpus callosum (TCC), presents with early cognitive impairment and slowly progressive leg weakness. Here, we reported a homozygous pathogenic variant in ZFYVE26. A 19-year-old Chinese girl was admitted to our hospital presenting with a 2-year progressive bilateral leg spasticity and weakness; early cognitive impairment; corpus callosum dysplasia; chronic neurogenic injury of the medulla oblongata supplied muscles; and bilateral upper and lower limbs on electromyogram (EMG). Based on these clinical and electrophysiological features, HSP was suspected. Exome sequencing of the family was performed by high-throughput sequencing, and an analysis of the patient showed a ZFYVE26 NM_015346: c.7111dupA p.(M2371Nfs*51) homozygous mutation. This case reported a new ZFYVE26 pathogenic variant, which was different from the SPG15 gene mutation reported earlier.
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Affiliation(s)
- Ze-hua Lai
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Neurology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiao-ying Liu
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuan-yue Song
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hai-yan Zhou
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li-li Zeng
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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18
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Previtali R, Leidi A, Basso M, Izzo G, Stignani C, Spaccini L, Iascone M, Veggiotti P, Bova SM. Case report: Early-onset parkinsonism among the neurological features in children with PHACTR1 variants. Front Neurol 2023; 14:1181015. [PMID: 37483454 PMCID: PMC10359812 DOI: 10.3389/fneur.2023.1181015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/19/2023] [Indexed: 07/25/2023] Open
Abstract
PACHTR1 is expressed in cardiovascular and neurological tissues. In the brain, it has a role in pre- and post-natal maturation. Previously reported PHACTR1-mutated patients showed early-onset epilepsy and intellectual disability. We describe two unreported cases with de novo pathogenic variants in PHACTR1 and their clinical pictures, compared with those of cases already reported in the literature. In line with previous reports, the two patients presented early-onset developmental and epileptic encephalopathy. In addition, one patient developed a speech disorder and a progressive movement disorder characterized by hypertonus, hypo-bradykinesia, hypomimia, ataxic gait, and retropulsion. She was treated with levodopa without any clinical improvement. Pathogenic variants in PHACTR1 may result in a cardiological or neurological phenotype. Severe developmental delay, intellectual disability, and early-onset developmental and epileptic encephalopathy are the main features of PHACTR1-mutated patients with neurological involvement. Movement and speech disorders have never previously been described and could be new features of the neurological phenotype.
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Affiliation(s)
| | | | | | - Giana Izzo
- Department of Pediatric Radiology and Neuroradiology, V. Buzzi Children's Hospital, Milan, Italy
| | - Cecilia Stignani
- Department of Pediatric Orthopedics, V. Buzzi Children's Hospital, Milan, Italy
| | - Luigina Spaccini
- Clinical Genetics Unit, Department of Obstetrics and Gynecology, V. Buzzi Children's Hospital, University of Milan, Milan, Italy
| | - Maria Iascone
- Molecular Genetics Section, Medical Genetics Laboratory, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Pierangelo Veggiotti
- Department of Biomedical and Clinical Sciences, L. Sacco, University of Milan, Milan, Italy
- Pediatric Neurology Unit, Vittore Buzzi Children's Hospital, Milan, Italy
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19
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Ishaq R, Ilyas M, Habiba U, Amin MNU, Saeed S, Raja GK, Shaiq PA, Ahmed ZM. Whole Exome Sequencing Reveals Clustering of Variants of Known Vitiligo Genes in Multiplex Consanguineous Pakistani Families. Genes (Basel) 2023; 14:genes14051118. [PMID: 37239478 DOI: 10.3390/genes14051118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/12/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Vitiligo is an autoimmune complex pigmentation disease characterized by non-pigmented patches on the surface of the skin that affect approximately 0.5-2% population worldwide. The exact etiology is still unknown; however, vitiligo is hypothesized to be a multifactorial and genetically heterogeneous condition. Therefore, the current study is designed to investigate the anthropometric presentation and genetic spectrum of vitiligo in fifteen consanguineous Pakistani families. The clinical evaluation of participating individuals revealed varying degrees of disease severity, with 23 years as the average age of disease onset. The majority of the affected individuals had non-segmental vitiligo (NSV). Whole exome sequencing analysis revealed clustering of rare variants of known vitiligo-associated genes. For instance, in the affected individuals of family VF-12, we identified three novel rare variants of PTPN22 (c.1108C>A), NRROS (c.197C>T) and HERC2 (c.10969G>A) genes. All three variants replaced evolutionarily conserved amino acid residues in encoded proteins, which are predicted to impact the ionic interactions in the secondary structure. Although various in silico algorithms predicted low effect sizes for these variants individually, the clustering of them in affected individuals increases the polygenic burden of risk alleles. To our knowledge, this is the first study that highlights the complex etiology of vitiligo and genetic heterogeneity in multiplex consanguineous Pakistani families.
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Affiliation(s)
- Rafaqat Ishaq
- University Institute of Biochemistry and Biotechnology, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi 46300, Pakistan
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 20742, USA
| | - Muhammad Ilyas
- University Institute of Biochemistry and Biotechnology, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi 46300, Pakistan
- Department of Medical Laboratory Technology, Riphah International University, Malakand Campus, Malakand 23010, Pakistan
| | - Umme Habiba
- University Institute of Biochemistry and Biotechnology, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Muhammad Noor Ul Amin
- University Institute of Biochemistry and Biotechnology, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Sadia Saeed
- University Institute of Biochemistry and Biotechnology, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi 46300, Pakistan
- Department of Clinical Molecular Biology, EpiGen, Institute of Clinical Medicine, University of Oslo, 0313 Oslo, Norway
| | - Ghazala Kaukab Raja
- University Institute of Biochemistry and Biotechnology, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Pakeeza Arzoo Shaiq
- University Institute of Biochemistry and Biotechnology, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Zubair M Ahmed
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 20742, USA
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 20742, USA
- Department of Ophthalmology and Visual Sciences, School of Medicine, University of Maryland, Baltimore, MD 20742, USA
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20
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Lei K, Xu R, Wang Q, Xiong Q, Zhou X, Li Q, Seriwatanachai D, Lin S, Zhou C, Yuan Q. METTL5 regulates cranial suture fusion via Wnt signaling. FUNDAMENTAL RESEARCH 2023; 3:369-376. [PMID: 38933773 PMCID: PMC11197682 DOI: 10.1016/j.fmre.2022.04.005] [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: 02/10/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 11/20/2022] Open
Abstract
METTL5 is a methyltransferase that mediates eukaryotic 18S ribosomal RNA m6A modification, and its mutations lead to intellectual disability, microcephaly, and facial dysmorphism in patients. However, the role of METTL5 in craniofacial development remains poorly understood. This study demonstrates that Mettl5 knockout mice exhibit poor ossification, widened cranial sutures, and a cleidocranial dysplasia-like phenotype. Deletion of Mettl5 leads to increased proliferation and decreased osteogenic differentiation of suture mesenchymal stem cells. Mechanistically, we find that Wnt signaling is significantly downregulated after Mettl5 knockout. Overall, we reveal an essential role of METTL5 in craniofacial development and osteogenic differentiation of suture mesenchymal stem cells, making METTL5 a potential diagnostic and therapeutic target for craniofacial developmental diseases.
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Affiliation(s)
- Kexin Lei
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Ruoshi Xu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Qian Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Qiuchan Xiong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Xinyi Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Qiwen Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Dutmanee Seriwatanachai
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok 73170, Thailand
| | - Shuibin Lin
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Chenchen Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Quan Yuan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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21
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Yahia A, Hamed AAA, Mohamed IN, Elseed MA, Salih MA, El-Sadig SM, Siddig HE, Nasreldien AEM, Abdullah MA, Elzubair M, Omer FY, Bakhiet AM, Abubaker R, Abozar F, Adil R, Emad S, Musallam MA, Eltazi IZM, Omer Z, Malik H, Mohamed MOE, Elhassan AA, Mohamed EOE, Ahmed AKMA, Ahmed EAA, Eltaraifee E, Hussein BK, Abd Allah ASI, Salah L, Nimir M, Tag Elseed OM, Elhassan TEA, Elbashier A, Alfadul ESA, Fadul M, Ali KF, Taha SOMA, Bushara EE, Amin M, Koko M, Ibrahim ME, Ahmed AE, Elsayed LEO, Stevanin G. Clinical phenotyping and genetic diagnosis of a large cohort of Sudanese families with hereditary spinocerebellar degenerations. Eur J Hum Genet 2023:10.1038/s41431-023-01344-6. [PMID: 37012327 DOI: 10.1038/s41431-023-01344-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 02/12/2023] [Accepted: 03/13/2023] [Indexed: 04/05/2023] Open
Abstract
Hereditary spinocerebellar degenerations (SCDs) is an umbrella term that covers a group of monogenic conditions that share common pathogenic mechanisms and include hereditary spastic paraplegia (HSP), cerebellar ataxia, and spinocerebellar ataxia. They are often complicated with axonal neuropathy and/or intellectual impairment and overlap with many neurological conditions, including neurodevelopmental disorders. More than 200 genes and loci inherited through all modes of Mendelian inheritance are known. Autosomal recessive inheritance predominates in consanguineous communities; however, autosomal dominant and X-linked inheritance can also occur. Sudan is inhabited by genetically diverse populations, yet it has high consanguinity rates. We used next-generation sequencing, genotyping, bioinformatics analysis, and candidate gene approaches to study 90 affected patients from 38 unrelated Sudanese families segregating multiple forms of SCDs. The age-at-onset in our cohort ranged from birth to 35 years; however, most patients manifested childhood-onset diseases (the mean and median ages at onset were 7.5 and 3 years, respectively). We reached the genetic diagnosis in 63% and possibly up to 73% of the studied families when considering variants of unknown significance. Combining the present data with our previous analysis of 25 Sudanese HSP families, the success rate reached 52-59% (31-35/59 families). In this article we report candidate variants in genes previously known to be associated with SCDs or other phenotypically related monogenic disorders. We also highlight the genetic and clinical heterogeneity of SCDs in Sudan, as we did not identify a major causative gene in our cohort, and the potential for discovering novel SCD genes in this population.
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Affiliation(s)
- Ashraf Yahia
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan.
- Paris Brain Institute - ICM, CNRS UMR7225, INSERM 1127, Sorbonne University, F-75000, Paris, France.
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet and Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden.
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Solna, Sweden.
| | - Ahlam A A Hamed
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Inaam N Mohamed
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Maha A Elseed
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Mustafa A Salih
- Division of Pediatric Neurology, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
- College of Medicine, AlMughtaribeen University, Khartoum, Sudan
| | | | | | - Ali Elsir Musa Nasreldien
- Pediatric Neurology Department, Red Cross Memorial Children Hospital (RCWMCH), University of Cape Town (UCT), Cape Town, South Africa
| | | | - Maha Elzubair
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | | | | | - Rayan Abubaker
- Sudanese Neurogenetics Research group, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
- National University Biomedical Research Institute, National University, Khartoum, Sudan
| | - Fatima Abozar
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Rawaa Adil
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Sara Emad
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | | | - Isra Z M Eltazi
- Neurology Department, Hamad Medical Corporation, Doha, Qatar
| | - Zulfa Omer
- Department of Hematology and Medical Oncology, University of Cincinnati Medical Center, Ohio, USA
| | - Hiba Malik
- Department of Neurology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Mayada O E Mohamed
- Division of Emergency Medicine, Sudan Medical Specialization Board, Khartoum, Sudan
| | - Ali A Elhassan
- Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan
| | | | - Ahmed K M A Ahmed
- Department of Molecular Neuroscience, Graduate school of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
- WPI Immunology Frontier Research Center, Osaka University, 3-1, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | | | | | - Bidour K Hussein
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | | | - Lina Salah
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Mohamed Nimir
- Department of Pathology, University Hospitals Coventry and Warwickshire NHS Trust, Coventry, UK
- Warwick Medical School, University of Warwick, Coventry, UK
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | | | | | | | | | - Moneeb Fadul
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Khalil F Ali
- Department of Cardiology, Royal Derby Hospital, Derby, UK
| | | | | | - Mutaz Amin
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Al-Neelain University, Khartoum, Sudan
| | - Mahmoud Koko
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | | | - Ammar E Ahmed
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Liena E O Elsayed
- Department of Basic Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, P.O.Box 84428, Riyadh, 11671, Saudi Arabia
| | - Giovanni Stevanin
- Paris Brain Institute - ICM, CNRS UMR7225, INSERM 1127, Sorbonne University, F-75000, Paris, France.
- Univ. Bordeaux, CNRS, INCIA, UMR 5287, F-33000, Bordeaux, France.
- EPHE, PSL Research university, CNRS, INCIA, UMR 5287, F-75000, Paris, France.
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22
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Zare Ashrafi F, Akhtarkhavari T, Fattahi Z, Asadnezhad M, Beheshtian M, Arzhangi S, Najmabadi H, Kahrizi K. Emerging Epidemiological Data on Rare Intellectual Disability Syndromes from Analyzing the Data of a Large Iranian Cohort. ARCHIVES OF IRANIAN MEDICINE 2023; 26:186-197. [PMID: 38301078 PMCID: PMC10685746 DOI: 10.34172/aim.2023.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 02/25/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND Intellectual disability (ID) is a genetically heterogeneous condition, and so far, 1679 human genes have been identified for this phenotype. Countries with a high rate of parental consanguinity, such as Iran, provide an excellent opportunity to identify the remaining novel ID genes, especially those with an autosomal recessive (AR) mode of inheritance. This study aimed to investigate the most prevalent ID genes identified via next-generation sequencing (NGS) in a large ID cohort at the Genetics Research Center (GRC) of the University of Social Welfare and Rehabilitation Sciences. METHODS First, we surveyed the epidemiological data of 619 of 1295 families in our ID cohort, who referred to the Genetics Research Center from all over the country between 2004 and 2021 for genetic investigation via the NGS pipeline. We then compared our data with those of several prominent studies conducted in consanguineous countries. Data analysis, including cohort data extraction, categorization, and comparison, was performed using the R program version 4.1.2. RESULTS We categorized the most common ID genes that were mutated in more than two families into 17 categories. The most common syndromic ID in our cohort was AP4 deficiency syndrome, and the most common non-syndromic autosomal recessive intellectual disability (ARID) gene was ASPM. We identified two unrelated families for the 36 ID genes. We found 14 genes in common between our cohort and the Arab and Pakistani groups, of which three genes (AP4M1, AP4S1, and ADGRG1) were repeated more than once. CONCLUSION To date, there has been no comprehensive targeted NGS platform for the detection of ID genes in our country. Due to the large sample size of our study, our data may provide the initial step toward designing an indigenously targeted NGS platform for the diagnosis of ID, especially common ARID in our population.
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Affiliation(s)
- Farzane Zare Ashrafi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Tara Akhtarkhavari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Asadnezhad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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23
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A Biallelic Truncating Variant in the TPR Domain of GEMIN5 Associated with Intellectual Disability and Cerebral Atrophy. Genes (Basel) 2023; 14:genes14030707. [PMID: 36980979 PMCID: PMC10048441 DOI: 10.3390/genes14030707] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/17/2023] Open
Abstract
GEMIN5 is a multifunctional RNA-binding protein required for the assembly of survival motor neurons. Several bi-allelic truncating and missense variants in this gene are reported to cause a neurodevelopmental disorder characterized by cerebellar atrophy, intellectual disability (ID), and motor dysfunction. Whole exome sequencing of a Pakistani consanguineous family with three brothers affected by ID, cerebral atrophy, mobility, and speech impairment revealed a novel homozygous 3bp-deletion NM_015465.5:c.3162_3164del that leads to the loss of NM_015465.5 (NP_056280.2):p. (Asp1054_Ala1055delinsGlu) amino acid in one of the α-helixes of the tetratricopeptide repeats of GEMIN5. In silico 3D representations of the GEMIN5 dimerization domain show that this variant likely affects the orientation of the downstream sidechains out of the helix axis, which would affect the packing with neighboring helices. The phenotype of all affected siblings overlaps well with previously reported patients, suggesting that NM_015465.5: c.3162_3164del (NP_056280.2):p. (Asp1054_Ala1055delinsGlu) is a novel GEMIN5 pathogenic variant. Overall, our data expands the molecular and clinical phenotype of the recently described neurodevelopmental disorder with cerebellar atrophy and motor dysfunction (NEDCAM) syndrome.
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Abstract
Although differential transcription drives the development of multicellular organisms, the ultimate readout of a protein-coding gene is ribosome-dependent mRNA translation. Ribosomes were once thought of as uniform molecular machines, but emerging evidence indicates that the complexity and diversity of ribosome biogenesis and function should be given a fresh look in the context of development. This Review begins with a discussion of different developmental disorders that have been linked with perturbations in ribosome production and function. We then highlight recent studies that reveal how different cells and tissues exhibit variable levels of ribosome production and protein synthesis, and how changes in protein synthesis capacity can influence specific cell fate decisions. We finish by touching upon ribosome heterogeneity in stress responses and development. These discussions highlight the importance of considering both ribosome levels and functional specialization in the context of development and disease.
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Affiliation(s)
- Chunyang Ni
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Michael Buszczak
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
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Salzano E, Niceta M, Pizzi S, Radio FC, Busè M, Mercadante F, Barresi S, Ferrara A, Mancini C, Tartaglia M, Piccione M. Case report: Novel compound heterozygosity for pathogenic variants in MED23 in a syndromic patient with postnatal microcephaly. Front Neurol 2023; 14:1090082. [PMID: 36824420 PMCID: PMC9941528 DOI: 10.3389/fneur.2023.1090082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/11/2023] [Indexed: 02/10/2023] Open
Abstract
Biallelic loss-of-function variants in MED23 cause a recessive syndromic intellectual disability condition with or without epilepsy (MRT18). Due to the small number of reported individuals, the clinical phenotype of the disorder has not been fully delineated yet, and the spectrum and frequency of neurologic features have not been fully characterized. Here, we report a 5-year-old girl with compound heterozygous for two additional MED23 variants. Besides global developmental delay, axial hypotonia and peripheral increased muscular tone, absent speech, and generalized tonic seizures, which fit well MRT18, the occurrence of postnatal progressive microcephaly has been here documented. A retrospective assessment of the previously reported clinical data for these subjects confirms the occurrence of postnatal progressive microcephaly as a previously unappreciated feature of the phenotype of MED23-related disorder.
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Affiliation(s)
- Emanuela Salzano
- Medical Genetics Unit, AOOR Villa Sofia-Cervello Hospitals, Palermo, Italy,*Correspondence: Emanuela Salzano ✉
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | - Martina Busè
- Medical Genetics Unit, AOOR Villa Sofia-Cervello Hospitals, Palermo, Italy
| | | | - Sabina Barresi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Arturo Ferrara
- Medical Genetics Unit, AOOR Villa Sofia-Cervello Hospitals, Palermo, Italy
| | - Cecilia Mancini
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Maria Piccione
- Medical Genetics Unit, AOOR Villa Sofia-Cervello Hospitals, Palermo, Italy,Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
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Li Y, Li Y, Wang Y, Meng L, Tan C, Du J, Tan YQ, Nie H, Zhang Q, Lu G, Lin G, Li H, Zhang H, Tu C. Identification of novel biallelic LRRC6 variants in male Chinese patients with primary ciliary dyskinesia and infertility. J Assist Reprod Genet 2023; 40:41-51. [PMID: 36515799 PMCID: PMC9840726 DOI: 10.1007/s10815-022-02681-z] [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: 10/06/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
PURPOSE The aim of this study is to identify the genetic cause of primary ciliary dyskinesia (PCD) and male infertility in two unrelated Han Chinese families. METHODS We performed whole-exome sequencing in two unrelated male Han Chinese patients suffering from infertility and PCD to identify the pathogenic variants. Ultrastructural and immunostaining analyses of patient's spermatozoa were performed to characterize the effect of the variants. The pathogenicity of the variants was validated using patient's spermatozoa by western blotting and immunostaining analysis. Intracytoplasmic sperm injection (ICSI) was conducted in the affected families. RESULTS Three variants in leucine-rich repeat containing 6 (LRRC6) [patient 1(compound heterozygote): NM_012472: c.538C > T, (p.R180*) and c.64dupT, (p.S22Ffs*19); patient 2 (homozygote): c.863C > A, (p.P288H)] were identified in two unrelated patients with PCD and male infertility. These variants were predicated deleterious and were absent or rare in human population genome data. LRRC6-mutant spermatozoa showed a highly aberrant morphology and ultrastructure with lacked inner and outer dynein arms. The LRRC6 protein was present along the normal sperm flagella, and was significantly decreased in the mutated spermatozoa. Interestingly, both patients were able to conceive through ICSI and birthed a healthy baby. CONCLUSION Our results extend the LRRC6 variant spectrum and provide reproductive guidance to families suffering from PCD-linked infertility caused by LRRC6 variants.
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Affiliation(s)
- Yunhao Li
- Hunan Guangxiu Hospital, Hunan Normal University, Changsha, 410081, China
| | - Yong Li
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, China
| | - Ying Wang
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, China
| | - Lanlan Meng
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
| | - Chen Tan
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, China
| | - Juan Du
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
| | - Yue-Qiu Tan
- Hunan Guangxiu Hospital, Hunan Normal University, Changsha, 410081, China
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
| | - Hongchuan Nie
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
| | - Qianjun Zhang
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
| | - Guangxiu Lu
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
| | - Huanzhu Li
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China.
- College of Life Sciences, Hunan Normal University, Changsha, China.
| | - Huan Zhang
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, China.
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China.
| | - Chaofeng Tu
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, China.
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China.
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Bilches Medinas D, Malik S, Yıldız‐Bölükbaşı E, Borgonovo J, Saaranen MJ, Urra H, Pulgar E, Afzal M, Contreras D, Wright MT, Bodaleo F, Quiroz G, Rozas P, Mumtaz S, Díaz R, Rozas C, Cabral‐Miranda F, Piña R, Valenzuela V, Uyan O, Reardon C, Woehlbier U, Brown RH, Sena‐Esteves M, Gonzalez‐Billault C, Morales B, Plate L, Ruddock LW, Concha ML, Hetz C, Tolun A. Mutation in protein disulfide isomerase A3 causes neurodevelopmental defects by disturbing endoplasmic reticulum proteostasis. EMBO J 2022; 41:e105531. [PMID: 34904718 PMCID: PMC8762563 DOI: 10.15252/embj.2020105531] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/23/2021] [Accepted: 10/14/2021] [Indexed: 01/19/2023] Open
Abstract
Recessive gene mutations underlie many developmental disorders and often lead to disabling neurological problems. Here, we report identification of a homozygous c.170G>A (p.Cys57Tyr or C57Y) mutation in the gene coding for protein disulfide isomerase A3 (PDIA3, also known as ERp57), an enzyme that catalyzes formation of disulfide bonds in the endoplasmic reticulum, to be associated with syndromic intellectual disability. Experiments in zebrafish embryos show that PDIA3C57Y expression is pathogenic and causes developmental defects such as axonal disorganization as well as skeletal abnormalities. Expression of PDIA3C57Y in the mouse hippocampus results in impaired synaptic plasticity and memory consolidation. Proteomic and functional analyses reveal that PDIA3C57Y expression leads to dysregulation of cell adhesion and actin cytoskeleton dynamics, associated with altered integrin biogenesis and reduced neuritogenesis. Biochemical studies show that PDIA3C57Y has decreased catalytic activity and forms disulfide-crosslinked aggregates that abnormally interact with chaperones in the endoplasmic reticulum. Thus, rare disease gene variant can provide insight into how perturbations of neuronal proteostasis can affect the function of the nervous system.
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The emerging importance of METTL5-mediated ribosomal RNA methylation. Exp Mol Med 2022; 54:1617-1625. [PMID: 36266443 PMCID: PMC9636144 DOI: 10.1038/s12276-022-00869-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 07/21/2022] [Accepted: 08/11/2022] [Indexed: 01/19/2023] Open
Abstract
The study of the epitranscriptome has thus far focused largely on mRNA methylation. Recent human genetics studies suggest that methylation of ribosomal RNA also contributes to brain development and cognition. In particular, the m6A modification at the A-1832 position of the 18S rRNA is installed by METTL5. Mutations or deletions of Mettl5 in humans and mice, respectively, cause abnormal translation and gene expression that in turn mediates stem cell behaviors such as differentiation. In this review, we provide an overview of the current knowledge of the methyltransferase METTL5, as well as the molecular biology surrounding m6A on rRNA and how it regulates cell behavior.
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Next-generation whole exome sequencing to delineate the genetic basis of primary congenital glaucoma. Sci Rep 2022; 12:17218. [PMID: 36241656 PMCID: PMC9568502 DOI: 10.1038/s41598-022-20939-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 09/21/2022] [Indexed: 01/06/2023] Open
Abstract
To delineate the genetic bases of primary congenital glaucoma (PCG), we ascertained a large cohort consisting of 48 consanguineous families. Of these, we previously reported 26 families with mutations in CYP1B1 and six families with LTBP2, whereas the genetic bases responsible for PCG in 16 families remained elusive. We employed next-generation whole exome sequencing to delineate the genetic basis of PCG in four of these 16 familial cases. Exclusion of linkage to reported PCG loci was established followed by next-generation whole exome sequencing, which was performed on 10 affected individuals manifesting cardinal systems of PCG belonging to four unresolved families along with four control samples consisting of genomic DNAs of individuals harboring mutations in CYP1B1 and LTBP2. The analyses of sequencing datasets failed to identify potential causal alleles in the 10 exomes whereas c.1169G > A (p. Arg390His) in CYP1B1 and c.3427delC (p.Gln1143Argfs*35) in LTBP2 were identified in the control samples. Taken together, next-generation whole exome sequencing failed to delineate the genetic basis of PCG in familial cases excluded from mutations in CYP1B1 and LTBP2. These data strengthen the notion that compound heterozygous coding variants or non-coding variants might contribute to PCG.
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Khan A, Tian S, Tariq M, Khan S, Safeer M, Ullah N, Akbar N, Javed I, Asif M, Ahmad I, Ullah S, Satti HS, Khan R, Naeem M, Ali M, Rendu J, Fauré J, Dieterich K, Latypova X, Baig SM, Malik NA, Zhang F, Khan TN, Liu C. NGS-driven molecular diagnosis of heterogeneous hereditary neurological disorders reveals novel and known variants in disease-causing genes. Mol Genet Genomics 2022; 297:1601-1613. [PMID: 36002593 DOI: 10.1007/s00438-022-01945-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/11/2022] [Indexed: 11/28/2022]
Abstract
Hereditary neurological disorders (HNDs) are a clinically and genetically heterogeneous group of disorders. These disorders arise from the impaired function of the central or peripheral nervous system due to aberrant electrical impulses. More than 600 various neurological disorders, exhibiting a wide spectrum of overlapping clinical presentations depending on the organ(s) involved, have been documented. Owing to this clinical heterogeneity, diagnosing these disorders has been a challenge for both clinicians and geneticists and a large number of patients are either misdiagnosed or remain entirely undiagnosed. Contribution of genetics to neurological disorders has been recognized since long; however, the complete picture of the underlying molecular bases are under-explored. The aim of this study was to accurately diagnose 11 unrelated Pakistani families with various HNDs deploying NGS as a first step approach. Using exome sequencing and gene panel sequencing, we successfully identified disease-causing genomic variants these families. We report four novel variants, one each in, ECEL1, NALCN, TBR1 and PIGP in four of the pedigrees. In the rest of the seven families, we found five previously reported pathogenic variants in POGZ, FA2H, PLA2G6 and CYP27A1. Of these, three families segregate a homozygous 18 bp in-frame deletion of FA2H, indicating a likely founder mutation segregating in Pakistani population. Genotyping for this mutation can help low-cost population wide screening in the corresponding regions of the country. Our findings not only expand the existing repertoire of mutational spectrum underlying neurological disorders but will also help in genetic testing of individuals with HNDs in other populations.
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Affiliation(s)
- Ayaz Khan
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Shixiong Tian
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, 200438, China
| | - Muhammad Tariq
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Sheraz Khan
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Muhammad Safeer
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Naimat Ullah
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Nazia Akbar
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Iram Javed
- Department of Paediatric Neurology, Children Hospital and Institute of Child Health, Faisalabad, Pakistan
| | - Mahnoor Asif
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Ilyas Ahmad
- Institute for Cardiogenetics, University of Lübeck, DZHK (German Research Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, University Heart Center Lübeck, Lübeck, Germany
| | - Shahid Ullah
- Department of General Surgery, Hayatabad Medical Complex, Peshawar, 2500, Pakistan
| | - Humayoon Shafique Satti
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Raees Khan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan.,NUMS Institute of Advance Studies and Research, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Muhammad Naeem
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Mahwish Ali
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan.,NUMS Institute of Advance Studies and Research, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - John Rendu
- Inserm, U1216, CHU Grenoble Alpes, Grenoble Institute of Neurosciences, University of Grenoble Alpes, 38000, Grenoble, France
| | - Julien Fauré
- Inserm, U1216, CHU Grenoble Alpes, Grenoble Institute of Neurosciences, University of Grenoble Alpes, 38000, Grenoble, France
| | - Klaus Dieterich
- Inserm, U1209, CHU Grenoble Alpes, Institute of Advanced Biosciences, University of Grenoble Alpes, 38000, Grenoble, France
| | - Xenia Latypova
- Inserm, U1216, CHU Grenoble Alpes, Grenoble Institute of Neurosciences, University of Grenoble Alpes, 38000, Grenoble, France
| | - Shahid Mahmood Baig
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan.,Pakistan Science Foundation, Constitution Avenue, Islamabad, Pakistan
| | - Naveed Altaf Malik
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Institute of Reproduction and Development, Fudan University, Shanghai, 200438, China
| | - Tahir Naeem Khan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan. .,NUMS Institute of Advance Studies and Research, National University of Medical Sciences, Rawalpindi, 46000, Pakistan. .,Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Lurie Children's Hospital, Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, United States.
| | - Chunyu Liu
- Obstetrics and Gynecology Hospital, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Institute of Reproduction and Development, Fudan University, Shanghai, 200438, China.
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De Novo ZMYND8 variants result in an autosomal dominant neurodevelopmental disorder with cardiac malformations. Genet Med 2022; 24:1952-1966. [PMID: 35916866 DOI: 10.1016/j.gim.2022.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 12/25/2022] Open
Abstract
PURPOSE ZMYND8 encodes a multidomain protein that serves as a central interactive hub for coordinating critical roles in transcription regulation, chromatin remodeling, regulation of super-enhancers, DNA damage response and tumor suppression. We delineate a novel neurocognitive disorder caused by variants in the ZMYND8 gene. METHODS An international collaboration, exome sequencing, molecular modeling, yeast two-hybrid assays, analysis of available transcriptomic data and a knockdown Drosophila model were used to characterize the ZMYND8 variants. RESULTS ZMYND8 variants were identified in 11 unrelated individuals; 10 occurred de novo and one suspected de novo; 2 were truncating, 9 were missense, of which one was recurrent. The disorder is characterized by intellectual disability with variable cardiovascular, ophthalmologic and minor skeletal anomalies. Missense variants in the PWWP domain of ZMYND8 abolish the interaction with Drebrin and missense variants in the MYND domain disrupt the interaction with GATAD2A. ZMYND8 is broadly expressed across cell types in all brain regions and shows highest expression in the early stages of brain development. Neuronal knockdown of the DrosophilaZMYND8 ortholog results in decreased habituation learning, consistent with a role in cognitive function. CONCLUSION We present genomic and functional evidence for disruption of ZMYND8 as a novel etiology of syndromic intellectual disability.
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Sánchez-Luquez KY, Carpena MX, Karam SM, Tovo-Rodrigues L. The contribution of whole-exome sequencing to intellectual disability diagnosis and knowledge of underlying molecular mechanisms: A systematic review and meta-analysis. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108428. [PMID: 35905832 DOI: 10.1016/j.mrrev.2022.108428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 01/01/2023]
Abstract
Whole-exome sequencing (WES) is useful for molecular diagnosis, family genetic counseling, and prognosis of intellectual disability (ID). However, ID molecular diagnosis ascertainment based on WES is highly dependent on de novo mutations (DNMs) and variants of uncertain significance (VUS). The quantification of DNM frequency in ID molecular diagnosis ascertainment and the biological mechanisms common to genes with VUS may provide objective information about WES use in ID diagnosis and etiology. We aimed to investigate and estimate the rate of ID molecular diagnostic assessment by WES, quantify the contribution of DNMs to this rate, and biologically and functionally characterize the genes whose mutations were identified through WES. A PubMed/Medline, Web of Science, Scopus, Science Direct, BIREME, and PsycINFO systematic review and meta-analysis was performed, including studies published between 2010 and 2022. Thirty-seven articles with data on ID molecular diagnostic yield using the WES approach were included in the review. WES testing accounted for an overall diagnostic rate of 42% (Confidence interval (CI): 35-50%), while the estimate restricted to DNMs was 11% (CI: 6-18%). Genetic information on mutations and genes was extracted and split into two groups: (1) genes whose mutation was used for positive molecular diagnosis, and (2) genes whose mutation led to uncertain molecular diagnosis. After functional enrichment analysis, in addition to their expected roles in neurodevelopment, genes from the first group were enriched in epigenetic regulatory mechanisms, immune system regulation, and circadian rhythm control. Genes from uncertain diagnosis cases were enriched in the renin angiotensin pathway. Taken together, our results support WES as an important approach to the molecular diagnosis of ID. The results also indicated relevant pathways that may underlie the pathogenesis of ID with the renin-angiotensin pathway being suggested to be a potential pathway underlying the pathogenesis of ID.
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Affiliation(s)
| | - Marina Xavier Carpena
- Postgraduate Program in Epidemiology, Universidade Federal de Pelotas, Pelotas, Brazil.
| | - Simone M Karam
- Postgraduate Program in Public Health, Universidade Federal do Rio Grande, Rio Grande, Brazil.
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Masih S, Moirangthem A, Shambhavi A, Rai A, Mandal K, Saxena D, Nilay M, Agrawal N, Srivastava S, Sait H, Phadke SR. Deciphering the molecular landscape of microcephaly in 87 Indian families by exome sequencing. Eur J Med Genet 2022; 65:104520. [PMID: 35568357 DOI: 10.1016/j.ejmg.2022.104520] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/21/2022] [Accepted: 05/08/2022] [Indexed: 11/25/2022]
Abstract
Microcephaly is a frequent feature of neurodevelopmental disorders (NDDs). Our study presents the heterogeneous spectrum of genetic disorders in patients with microcephaly either in isolated form or in association with other neurological and extra-neural abnormalities. We present data of 91 patients from 87 unrelated families referred to our clinic during 2016-2020 and provide a comprehensive clinical and genetic landscape in the studied cohort. Molecular diagnosis using exome sequencing was made in 45 families giving a yield of 51.7%. In 9 additional families probable causative variants were detected. We identified disease causing variations in 49 genes that are involved in different functional pathways Among these, 36 had an autosomal recessive pattern, 8 had an autosomal dominant pattern (all inherited de novo), and 5 had an X-linked pattern. In 41 probands where sequence variations in autosomal recessive genes were identified 31 were homozygotes (including 16 from non-consanguineous families). The study added 28 novel pathogenic/likely pathogenic variations. The study also calls attention to phenotypic variability and expansion in spectrum as well as uncovers genes where microcephaly is not reported previously or is a rare finding. We here report phenotypes associated with the genes for ultra-rare NDDs with microcephaly namely ATRIP, MINPP1, PNPLA8, AIMP2, ANKLE2, NCAPD2 and TRIT1.
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Affiliation(s)
- Suzena Masih
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Amita Moirangthem
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Arya Shambhavi
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Archana Rai
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Kausik Mandal
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Deepti Saxena
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Mayank Nilay
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Neha Agrawal
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Somya Srivastava
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Haseena Sait
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India.
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Bauer G, Buchert R, Haack TB, Harting I, Gutschalk A. CCDC82 frameshift mutation associated with intellectual disability, spastic paraparesis, and dysmorphic features. Clin Genet 2022; 102:80-81. [PMID: 35373332 DOI: 10.1111/cge.14135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Gregor Bauer
- Department of Neurology, University of Heidelberg, Heidelberg, Germany
| | - Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Inga Harting
- Department of Neuroradiology, University of Heidelberg, Heidelberg, Germany
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Delineating the Molecular and Phenotypic Spectrum of the CNGA3-Related Cone Photoreceptor Disorder in Pakistani Families. Genes (Basel) 2022; 13:genes13040617. [PMID: 35456423 PMCID: PMC9031457 DOI: 10.3390/genes13040617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/10/2022] [Accepted: 03/21/2022] [Indexed: 11/17/2022] Open
Abstract
Cone photoreceptor dysfunction represents a clinically heterogenous group of disorders characterized by nystagmus, photophobia, reduced central or color vision, and macular dystrophy. Here, we described the molecular findings and clinical manifestations of achromatopsia, a partial or total absence of color vision, co-segregating with three known missense variants of CNGA3 in three large consanguineous Pakistani families. Fundus examination and optical coherence tomography (OCT) imaging revealed myopia, thin retina, retinal pigment epithelial cells loss at fovea/perifovea, and macular atrophy. Combination of Sanger and whole exome sequencing revealed three known homozygous missense variants (c.827A>G, p.(Asn276Ser); c.847C>T, p.(Arg283Trp); c.1279C>T, p.(Arg427Cys)) in CNGA3, the α-subunit of the cyclic nucleotide-gated cation channel in cone photoreceptor cells. All three variants are predicted to replace evolutionary conserved amino acids, and to be pathogenic by specific in silico programs, consistent with the observed altered membrane targeting of CNGA3 in heterologous cells. Insights from our study will facilitate counseling regarding the molecular and phenotypic landscape of CNGA3-related cone dystrophies.
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Yahia A, Ayed IB, Hamed AA, Mohammed IN, Elseed MA, Bakhiet AM, Guillot-Noel L, Abozar F, Adil R, Emad S, Abubaker R, Musallam MA, Eltazi IZM, Omer Z, Maaroof OM, Soussi A, Bouzid A, Kmiha S, Kamoun H, Salih MA, Ahmed AE, Elsayed L, Masmoudi S, Stevanin G. Genetic diagnosis in Sudanese and Tunisian families with syndromic intellectual disability through exome sequencing. Ann Hum Genet 2022; 86:181-194. [PMID: 35118659 DOI: 10.1111/ahg.12460] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/24/2021] [Accepted: 01/17/2022] [Indexed: 12/20/2022]
Abstract
BACKGROUND Intellectual disability is a form of neurodevelopmental disorders that begin in childhood and is characterized by substantial intellectual difficulties as well as difficulties in conceptual, social, and practical areas of living. Several genetic and nongenetic factors contribute to its development; however, its most severe forms are generally attributed to single-gene defects. High-throughput technologies and data sharing contributed to the diagnosis of hundreds of single-gene intellectual disability subtypes. METHOD We applied exome sequencing to identify potential variants causing syndromic intellectual disability in six Sudanese patients from four unrelated families. Data sharing through the Varsome portal corroborated the diagnosis of one of these patients and a Tunisian patient investigated through exome sequencing. Sanger sequencing validated the identified variants and their segregation with the phenotypes in the five studied families. RESULT We identified three pathogenic/likely pathogenic variants in CCDC82, ADAT3, and HUWE1 and variants of uncertain significance in HERC2 and ATP2B3. The patients with the CCDC82 variants had microcephaly and spasticity, two signs absent in the two previously reported families with CCDC82-related intellectual disability. CONCLUSION In conclusion, we report new patients with pathogenic mutations in the genes CCDC82, ADAT3, and HUWE1. We also highlight the possibility of extending the CCDC82-linked phenotype to include spastic paraplegia and microcephaly.
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Affiliation(s)
- Ashraf Yahia
- Department of Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan.,Department of Biochemistry, Faculty of Medicine, National University, Khartoum, Sudan.,Institut du Cerveau - Paris Brain Institute, ICM, Sorbonne Université, INSERM, CNRS, APHP, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
| | - Ikhlas Ben Ayed
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), LR15CBS07, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia.,Medical Genetic Department, Hedi Chaker Hospital, Sfax, Tunisia
| | - Ahlam A Hamed
- Department of Pediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Inaam N Mohammed
- Department of Pediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Maha A Elseed
- Department of Pediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Aisha M Bakhiet
- Department of Psychiatry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Lena Guillot-Noel
- Institut du Cerveau - Paris Brain Institute, ICM, Sorbonne Université, INSERM, CNRS, APHP, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
| | - Fatima Abozar
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Rawaa Adil
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Sara Emad
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Rayan Abubaker
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan.,National University Biomedical Research Institute (NUBRI), National University, Khartoum, Sudan
| | | | - Isra Z M Eltazi
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Zulfa Omer
- Department of Hematology and Medical Oncology, University of Cincinnati Medical Center, Cincinnati, Ohio, USA
| | - Omer M Maaroof
- Council of Diagnostic Radiology, Sudan Medical Specialization Board, Khartoum, Sudan
| | - Amal Soussi
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), LR15CBS07, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Amal Bouzid
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), LR15CBS07, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Sana Kmiha
- Laboratory of Human Molecular Genetics, LR33ES99, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia.,Department of pediatrics, Hedi Chaker Hospital, Sfax, Tunisia
| | - Hassen Kamoun
- Medical Genetic Department, Hedi Chaker Hospital, Sfax, Tunisia.,Laboratory of Human Molecular Genetics, LR33ES99, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Mustafa A Salih
- Division of Pediatric Neurology, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Pediatrics, College of Medicine, AlMughtaribeen University, Khartoum, Sudan
| | - Ammar E Ahmed
- Department of Physiology, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Liena Elsayed
- Department of Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan.,Department of Basic Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, 11671, Saudi Arabia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), LR15CBS07, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Giovanni Stevanin
- Institut du Cerveau - Paris Brain Institute, ICM, Sorbonne Université, INSERM, CNRS, APHP, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
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Biallelic in-frame deletion of SOX4 is associated with developmental delay, hypotonia and intellectual disability. Eur J Hum Genet 2022; 30:243-247. [PMID: 34750527 PMCID: PMC8821644 DOI: 10.1038/s41431-021-00968-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/11/2021] [Accepted: 09/09/2021] [Indexed: 02/03/2023] Open
Abstract
Intellectual disability (ID) represents an extremely heterogeneous group of disorders, characterized by significant limitations in intellectual function and adaptive behavior. Among the monogenic causes, autosomal recessive genes (ARID) are responsible for more than 50% of ID. Here, we report a novel in-frame homozygous deletion variant [c.730_753del; p.(Ala244_Gly251del)] in SOX4 (sex-determining region Y-related high-mobility group box 4), segregating with moderate to severe ID, hypotonia, and developmental delay in a Pakistani family. Our identified variant p.(Ala244_Gly251del) is predicted to remove evolutionarily conserved residues from the interdomain region and may destabilize the protein secondary structure. SOX4 belongs to group C of the SOX transcription regulating family known to be involved in early embryo development. Single-cell RNA data analysis of developing telencephalon revealed highly overlapping expression of SOX4 with SOX11 and DCX, known neurogenesis regulators. Our study expands the mutational landscape of SOX4 and the repertoire of the known genetic causes of ARID.
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Ropers HH, van Karnebeek CD. Rare diseases: human genome research is coming home. Cold Spring Harb Mol Case Stud 2022; 8:a006210. [PMID: 35332074 PMCID: PMC8958923 DOI: 10.1101/mcs.a006210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
After a long and largely disappointing detour, Genome Research has reidentified Rare Diseases as a major opportunity for improving health care and a clue to understanding gene and genome function. In this Special Issue of CSH Molecular Case Studies on Rare Diseases, several invited Perspectives, numerous Case Reports, and this Editorial itself address recent breakthroughs as well as unsolved problems in this wide field. These range from exciting prospects for gap-free diagnostic whole-genome sequencing to persisting problems related to identifying and distinguishing pathogenic and benign variants; and from the good news that soon, the United Kingdom will no longer be the only country to have introduced whole-genome sequencing into health care to the sobering conclusion that in many countries the clinical infrastructure for bringing Genome Medicine to the patient is still lacking. With less than 5000 genes firmly implicated in disease, the identification of at least twice as many disease genes is a major challenge, and the elucidation of their function is an even larger task. But given the renewed interest in rare diseases, their importance for health care, and the vast and growing spectrum of concepts and methods for studying them, the future of Human Genome Research is bright.
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Affiliation(s)
- Hans-Hilger Ropers
- Max Planck Institute for Molecular Genetics, Berlin D-14195, and Institute of Human Genetics, University Medicine, Mainz D-55131, Germany
| | - Clara D van Karnebeek
- Departments of Pediatrics and Human Genetics, Emma Children's Hospital, Amsterdam University Medical Centers, NL-1105 AZ Amsterdam, The Netherlands
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Tran V, Goyette MA, Martínez-García M, Jiménez de Domingo A, Fernández-Mayoralas DM, Fernández-Perrone AL, Tirado P, Calleja-Pérez B, Álvarez S, Côté JF, Fernández-Jaén A. Biallelic ELMO3 mutations and loss of function for DOCK-mediated RAC1 activation result in intellectual disability. Small GTPases 2022; 13:48-55. [PMID: 33660564 PMCID: PMC9707537 DOI: 10.1080/21541248.2021.1888557] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The engulfment and cell motility 3 (ELMO3) protein belongs to the ELMO-family of proteins. ELMO proteins form a tight complex with the DOCK1-5 guanine nucleotide exchange factors that regulate RAC1 spatiotemporal activation and signalling. DOCK proteins and RAC1 are known to have fundamental roles in central nervous system development. Here, we searched for homozygous or compound heterozygous mutations in the ELMO3 gene in 390 whole exomes sequenced in trio in individuals with neurodevelopmental disorders compatible with a genetic origin. We found a compound heterozygous mutation in ELMO3 (c.1153A>T, p.Ser385Cys and c.1009 G > A, p.Val337Ile) in a 5 year old male child with autism spectrum disorder (ASD) and developmental delay. These mutations did not interfere with the formation of an ELMO3/DOCK1 complex, but markedly impaired the ability of the complex to promote RAC1-GTP-loading. Consequently, cells expressing DOCK1 and either of the ELMO3 mutants displayed impaired migration and invasion. Collectively, our results suggest that biallelic loss-of-function mutations in ELMO3 may cause a developmental delay and provide new insight into the role of ELMO3 in neurodevelopmental as well as the pathological consequences of ELMO3 mutations.
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Affiliation(s)
- Viviane Tran
- Laboratory of Cytoskeletal Organization and Cell Migration, Montreal Clinical Research Institute (IRCM), Montréal, QC, Canada,Department of Biochemistry and Molecular Medicine, Université De Montréal, Montréal, QC, Canada
| | - Marie-Anne Goyette
- Laboratory of Cytoskeletal Organization and Cell Migration, Montreal Clinical Research Institute (IRCM), Montréal, QC, Canada,Molecular Biology Programs, Université De Montréal, Montréal, QC, Canada
| | | | | | | | | | - Pilar Tirado
- Department of Pediatric Neurology. Hospital Universitario La Paz. Madrid. Spain
| | | | - Sara Álvarez
- Department of Genomics and Medicine, NIMGenetics, Madrid, Spain
| | - Jean-François Côté
- Laboratory of Cytoskeletal Organization and Cell Migration, Montreal Clinical Research Institute (IRCM), Montréal, QC, Canada,Department of Biochemistry and Molecular Medicine, Université De Montréal, Montréal, QC, Canada,Molecular Biology Programs, Université De Montréal, Montréal, QC, Canada,Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada
| | - Alberto Fernández-Jaén
- Department of Pediatric Neurology. ónsalud. Madrid. Spain,Department of Pediatric Neurology, Medicine School. Universidad Europea De, Madrid, Spain,CONTACT Alberto Fernández-Jaén Cytoskeletal Organization and Cell Migration Laboratory Montreal Clinical Research Institute (IRCM)110 Avenue Des, Pins, Ouest, Canada
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40
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Family-Based Whole-Exome Analysis of Specific Language Impairment (SLI) Identifies Rare Variants in BUD13, a Component of the Retention and Splicing (RES) Complex. Brain Sci 2021; 12:brainsci12010047. [PMID: 35053791 PMCID: PMC8773923 DOI: 10.3390/brainsci12010047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/18/2021] [Accepted: 12/27/2021] [Indexed: 12/12/2022] Open
Abstract
Specific language impairment (SLI) is a common neurodevelopmental disorder (NDD) that displays high heritability estimates. Genetic studies have identified several loci, but the molecular basis of SLI remains unclear. With the aim to better understand the genetic architecture of SLI, we performed whole-exome sequencing (WES) in a single family (ID: 489; n = 11). We identified co-segregating rare variants in three new genes: BUD13, APLP2, and NDRG2. To determine the significance of these genes in SLI, we Sanger sequenced all coding regions of each gene in unrelated individuals with SLI (n = 175). We observed 13 additional rare variants in 18 unrelated individuals. Variants in BUD13 reached genome-wide significance (p-value < 0.01) upon comparison with similar variants in the 1000 Genomes Project, providing gene level evidence that BUD13 is involved in SLI. Additionally, five BUD13 variants showed cohesive variant level evidence of likely pathogenicity. Bud13 is a component of the retention and splicing (RES) complex. Additional supportive evidence from studies of an animal model (loss-of-function mutations in BUD13 caused a profound neural phenotype) and individuals with an NDD phenotype (carrying a CNV spanning BUD13), indicates BUD13 could be a target for investigation of the neural basis of language.
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41
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Hassan AY, Yousaf S, Levin MR, Saeedi OJ, Riazuddin S, Alexander JL, Ahmed ZM. Novel Homozygous Missense Variant in GJA3 Connexin Domain Causing Congenital Nuclear and Cortical Cataracts. Int J Mol Sci 2021; 23:240. [PMID: 35008666 PMCID: PMC8745576 DOI: 10.3390/ijms23010240] [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: 11/15/2021] [Revised: 12/17/2021] [Accepted: 12/24/2021] [Indexed: 11/29/2022] Open
Abstract
Congenital cataracts (CC) are responsible for approximately one-tenth of childhood blindness cases globally. Here, we report an African American family with a recessively inherited form of CC. The proband demonstrated decreased visual acuity and bilateral cataracts, with nuclear and cortical cataracts in the right and left eye, respectively. Exome sequencing revealed a novel homozygous variant (c.563A > G; p.(Asn188Ser)) in GJA3, which was predicted to be pathogenic by structural analysis. Dominantly inherited variants in GJA3 are known to cause numerous types of cataracts in various populations. Our study represents the second case of recessive GJA3 allele, and the first report in African Americans. These results validate GJA3 as a bona fide gene for recessively inherited CC in humans.
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Affiliation(s)
- Abdullah Y. Hassan
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (A.Y.H.); (S.Y.); (S.R.)
| | - Sairah Yousaf
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (A.Y.H.); (S.Y.); (S.R.)
| | - Moran R. Levin
- Department of Ophthalmology and Visual Sciences, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (M.R.L.); (O.J.S.)
| | - Osamah J. Saeedi
- Department of Ophthalmology and Visual Sciences, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (M.R.L.); (O.J.S.)
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (A.Y.H.); (S.Y.); (S.R.)
- Department of Molecular Biology and Biochemistry, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Janet L. Alexander
- Department of Ophthalmology and Visual Sciences, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (M.R.L.); (O.J.S.)
| | - Zubair M. Ahmed
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (A.Y.H.); (S.Y.); (S.R.)
- Department of Ophthalmology and Visual Sciences, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (M.R.L.); (O.J.S.)
- Department of Molecular Biology and Biochemistry, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
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42
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Pastore SF, Muhammad T, Harripaul R, Lau R, Khan MTM, Khan MI, Islam O, Kang C, Ayub M, Jelani M, Vincent JB. Biallelic inheritance in a single Pakistani family with intellectual disability implicates new candidate gene RDH14. Sci Rep 2021; 11:23113. [PMID: 34848785 PMCID: PMC8632963 DOI: 10.1038/s41598-021-02599-z] [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: 03/11/2021] [Accepted: 11/12/2021] [Indexed: 11/19/2022] Open
Abstract
In a multi-branch family from Pakistan, individuals presenting with palmoplantar keratoderma segregate in autosomal dominant fashion, and individuals with intellectual disability (ID) segregate in apparent autosomal recessive fashion. Initial attempts to identify the ID locus using homozygosity-by-descent (HBD) mapping were unsuccessful. However, following an assumption of locus heterogeneity, a reiterative HBD approach in concert with whole exome sequencing (WES) was employed. We identified a known disease-linked mutation in the polymicrogyria gene, ADGRG1, in two affected members. In the remaining two (living) affected members, HBD mapping cross-referenced with WES data identified a single biallelic frameshifting variant in the gene encoding retinol dehydrogenase 14 (RDH14). Transcription data indicate that RDH14 is expressed in brain, but not in retina. Magnetic resonance imaging for the individuals with this RDH14 mutation show no signs of polymicrogyria, however cerebellar atrophy was a notable feature. RDH14 in HEK293 cells localized mainly in the nucleoplasm. Co-immunoprecipitation studies confirmed binding to the proton-activated chloride channel 1 (PACC1/TMEM206), which is greatly diminished by the mutation. Our studies suggest RDH14 as a candidate for autosomal recessive ID and cerebellar atrophy, implicating either disrupted retinoic acid signaling, or, through PACC1, disrupted chloride ion homeostasis in the brain as a putative disease mechanism.
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Affiliation(s)
- Stephen F Pastore
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College Street, Toronto, ON, M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Tahir Muhammad
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College Street, Toronto, ON, M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Ricardo Harripaul
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College Street, Toronto, ON, M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Rebecca Lau
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College Street, Toronto, ON, M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Muhammad Tariq Masood Khan
- Department of Pathology, North-West School of Medicine, Hayatabad, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Ismail Khan
- Department of Zoology, Islamia College Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Omar Islam
- Department of Diagnostic Radiology, Queen's University, Kingston, ON, Canada
| | - Changsoo Kang
- Department of Biology and Institute of Basic Sciences, Sungshin Women's University, Seoul, Republic of Korea
| | - Muhammad Ayub
- Department of Psychiatry, Queen's University Kingston, Kingston, ON, Canada
| | - Musharraf Jelani
- Centre for Omic Sciences, Islamia College Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - John B Vincent
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College Street, Toronto, ON, M5T 1R8, Canada.
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
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43
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Pastore SF, Muhammad T, Harripaul R, Lau R, Khan MTM, Khan MI, Islam O, Kang C, Ayub M, Jelani M, Vincent JB. Biallelic inheritance in a single Pakistani family with intellectual disability implicates new candidate gene RDH14. Sci Rep 2021; 11:23113. [DOI: https:/doi.org/10.1038/s41598-021-02599-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 11/12/2021] [Indexed: 10/10/2023] Open
Abstract
AbstractIn a multi-branch family from Pakistan, individuals presenting with palmoplantar keratoderma segregate in autosomal dominant fashion, and individuals with intellectual disability (ID) segregate in apparent autosomal recessive fashion. Initial attempts to identify the ID locus using homozygosity-by-descent (HBD) mapping were unsuccessful. However, following an assumption of locus heterogeneity, a reiterative HBD approach in concert with whole exome sequencing (WES) was employed. We identified a known disease-linked mutation in the polymicrogyria gene, ADGRG1, in two affected members. In the remaining two (living) affected members, HBD mapping cross-referenced with WES data identified a single biallelic frameshifting variant in the gene encoding retinol dehydrogenase 14 (RDH14). Transcription data indicate that RDH14 is expressed in brain, but not in retina. Magnetic resonance imaging for the individuals with this RDH14 mutation show no signs of polymicrogyria, however cerebellar atrophy was a notable feature. RDH14 in HEK293 cells localized mainly in the nucleoplasm. Co-immunoprecipitation studies confirmed binding to the proton-activated chloride channel 1 (PACC1/TMEM206), which is greatly diminished by the mutation. Our studies suggest RDH14 as a candidate for autosomal recessive ID and cerebellar atrophy, implicating either disrupted retinoic acid signaling, or, through PACC1, disrupted chloride ion homeostasis in the brain as a putative disease mechanism.
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44
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Lei K, Lin S, Yuan Q. N6-methyladenosine (m6A) modification of ribosomal RNAs (rRNAs): Critical roles in mRNA translation and diseases. Genes Dis 2021; 10:126-134. [PMID: 37013049 PMCID: PMC10066336 DOI: 10.1016/j.gendis.2021.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 10/14/2021] [Accepted: 10/22/2021] [Indexed: 11/18/2022] Open
Abstract
As key components of the ribosome and the most abundant RNA species, the rRNAs are modified during ribosome formation. N6-methyladenosine (m6A) is a conserved RNA modification occurring on different RNA species including rRNAs. Recently, it has been reported that ZCCHC4 and METTL5 are methyltransferases that mediate m6A modification of human 28S and 18S rRNA, respectively. The newly discovered biological functions of the two methyltransferases include regulation of mRNA translation, cell proliferation, cell differentiation, stress response, and other biological processes. Both of them, especially METTL5, have been proved to be associated with a variety of diseases such as intellectual disability, cancer, congenital dysplasia and have potential clinical application as biomarkers and therapeutic targets.
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Affiliation(s)
- Kexin Lei
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shuibin Lin
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Quan Yuan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
- Corresponding author. State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No.14, 3rd Section, South Renmin Road, Chengdu, Sichuan 610041, China.
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45
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Nouri N, Bahreini A, Nasiri J, Salehi M. Clinical and genetic profile of children with unexplained intellectual disability/developmental delay and epilepsy. Epilepsy Res 2021; 177:106782. [PMID: 34695666 DOI: 10.1016/j.eplepsyres.2021.106782] [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: 12/09/2020] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 10/20/2022]
Abstract
OBJECTIVE This study was conducted to evaluate the validity of performing whole exome sequencing in children with unexplained intellectual disability (ID), developmental delay (DD), and epilepsy. METHODS We enrolled 61 Iranian children with unexplained DD/ID, and epilepsy with no etiologic diagnosis. 64 % of cases were male and 36 % were female, with a mean age of 6.2 years (range, 38 days to 15 years). Approximately 79 % of patients were born to consanguineous parents or had non-related parents from a highly inbred local region. Whole-exome sequencing analysis followed by Sanger sequencing was performed in all patients. RESULTS Pathogenic/likely pathogenic variants were identified in 59% (36/61) of patients, consisting of 26 novel and 14 known alterations. Variants of unknown significance were observed in 6.5 % (4/61) of patients. Variants in 28 genes have not been previously reported in Iranian patients with ID. Several additional phenotypes, mostly microcephaly, were common in 57.4 % of cases. Additionally, epilepsy was refractory in 40 % of patients. Three groups of brain anomalies consisting of brain dysgenesis, brain atrophy, and leukodystrophy were identified in our cohort. Mutations in genes implicated in cellular metabolic pathways were the most common, followed by ion channel/ion transporter and transcription pathways. DISCUSSION High-throughput DNA sequencing of the Iranian population with a high rate of parental consanguinity is a valuable strategy for identifying genetic etiology in children with unexplained ID/DD and epilepsy. Determining the genetic basis and most commonly involved pathways may help to identify novel genes and targeted antiepileptic treatments.
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Affiliation(s)
- Nayereh Nouri
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Amir Bahreini
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, PA, USA; KaryoGen, Isfahan, Iran
| | - Jafar Nasiri
- Child Growth and Development Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mansoor Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran; Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
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46
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Schymick J, Leahy P, Cowan T, Ruzhnikov MRZ, Gates R, Fernandez L, Pramanik G, Yarlagadda V, Wheeler M, Bernstein JA, Enns GM, Lee C. Variable clinical severity in TANGO2 deficiency: Case series and literature review. Am J Med Genet A 2021; 188:473-487. [PMID: 34668327 DOI: 10.1002/ajmg.a.62543] [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] [Received: 07/15/2021] [Revised: 09/21/2021] [Accepted: 09/29/2021] [Indexed: 11/10/2022]
Abstract
Biallelic pathogenic variants in the TANGO2 (transport and Golgi organization 2 homolog) gene have been identified as causing a rare metabolic disorder characterized by susceptibility to recurrent rhabdomyolysis, lactic acidosis, encephalopathy, and life-threatening tachyarrhythmias. Recently published reports suggest variable clinical severity and phenotypes. This study details five new patients from two families with biallelic pathogenic variants in the TANGO2 gene identified by whole exome sequencing and includes the largest number of affected individuals from a single family reported to date. We document significant intrafamilial variability and highlight that milder phenotypes may be underrecognized. We present biochemical and clinical data to help highlight the features that aid in consideration of this condition in the differential with disorders of fatty acid oxidation. We also present a comprehensive literature review summarizing the molecular, clinical, and biochemical findings for 92 individuals across 13 publications. Of the 27 pathogenic variants reported to date, the recurrent exons 3-9 deletion represents the most common variant seen in 42% of individuals with TANGO2 deficiency. Common clinical features seen in >70% of all individuals include acute metabolic crisis, rhabdomyolysis, neurologic abnormalities, developmental delay, and intellectual disability. Findings such as elevated creatine kinase, hypothyroidism, ketotic hypoglycemia, QT prolongation, or abnormalities of long-chain acylcarnitines and urine dicarboxylic acids should raise clinical suspicion for this life-threatening condition.
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Affiliation(s)
- Jennifer Schymick
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA.,Department of Pediatrics, Santa Clara Valley Health and Hospital System, San Jose, California, USA
| | - Peter Leahy
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA.,Cook Children's Medical Center, Fort Worth, Texas, USA
| | - Tina Cowan
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Maura R Z Ruzhnikov
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA.,Stanford Center for Undiagnosed Diseases, Stanford, California, USA
| | - Ryan Gates
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | | | - Gopal Pramanik
- Stanford Center for Undiagnosed Diseases, Stanford, California, USA
| | | | - Vamsi Yarlagadda
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Matthew Wheeler
- Stanford Center for Undiagnosed Diseases, Stanford, California, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA.,Stanford Center for Undiagnosed Diseases, Stanford, California, USA
| | - Gregory M Enns
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Chung Lee
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
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47
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Biallelic Variants in EPHA2 Identified in Three Large Inbred Families with Early-Onset Cataract. Int J Mol Sci 2021; 22:ijms221910655. [PMID: 34638995 PMCID: PMC8508826 DOI: 10.3390/ijms221910655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 11/17/2022] Open
Abstract
Hereditary congenital cataract (HCC) is clinically and genetically heterogeneous. We investigated HCC that segregates in three inbred families (LUCC03, LUCC16, and LUCC24). Ophthalmological examinations revealed cataracts with variability related to the age of onset segregating in a recessive manner in these families. Exome sequencing of probands identified a novel homozygous c.2710delG;p.(Val904Cysfs*36) EPHA2 variant in LUCC03 and a known homozygous c.2353G>A;p.(Ala785Thr) EPHA2 variant in the other two recessive families. EPHA2 encodes a transmembrane tyrosine kinase receptor, which is primarily involved in membrane-transport, cell-cell adhesion, and repulsion signaling processes. Computational structural modeling predicts that substitution of a threonine for an alanine p.(Ala785Thr) results in the formation of three new hydrogen bonds with the neighboring residues, which causes misfolding of EPHA2 in both scenarios. Insights from our study will facilitate counseling regarding the molecular and phenotypic landscape of EPHA2-related HCC.
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48
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Rasheed M, Khan V, Harripaul R, Siddiqui M, Malik MA, Ullah Z, Zahid M, Vincent JB, Ansar M. Exome sequencing identifies novel and known mutations in families with intellectual disability. BMC Med Genomics 2021; 14:211. [PMID: 34452636 PMCID: PMC8399827 DOI: 10.1186/s12920-021-01066-y] [Citation(s) in RCA: 4] [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: 02/16/2021] [Accepted: 08/25/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Intellectual disability (ID) is a phenotypically and genetically heterogeneous disorder. METHODS In this study, genome wide SNP microarray and whole exome sequencing are used for the variant identification in eight Pakistani families with ID. Beside ID, most of the affected individuals had speech delay, facial dysmorphism and impaired cognitive abilities. Repetitive behavior was observed in MRID143, while seizures were reported in affected individuals belonging to MRID137 and MRID175. RESULTS In two families (MRID137b and MRID175), we identified variants in the genes CCS and ELFN1, which have not previously been reported to cause ID. In four families, variants were identified in ARX, C5orf42, GNE and METTL4. A copy number variation (CNV) was identified in IL1RAPL1 gene in MRID165. CONCLUSION These findings expand the existing knowledge of variants and genes implicated in autosomal recessive and X linked ID.
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Affiliation(s)
- Memoona Rasheed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Valeed Khan
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Ricardo Harripaul
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Maimoona Siddiqui
- Division of Neurology, Shifa College of Medicine, H-8/1, Islamabad, Pakistan
| | - Madiha Amin Malik
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Zahid Ullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Zahid
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - John B Vincent
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan.
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49
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Khuller K, Yigit G, Martínez Grijalva C, Altmüller J, Thiele H, Nürnberg P, Elcioglu NH, Yeter B, Hehr U, Stein A, Della Marina A, Köninger A, Depienne C, Kaiser FJ, Wollnik B, Kuechler A. MFSD2A-associated primary microcephaly - Expanding the clinical and mutational spectrum of this ultra-rare disease. Eur J Med Genet 2021; 64:104310. [PMID: 34400370 DOI: 10.1016/j.ejmg.2021.104310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 04/25/2021] [Accepted: 08/12/2021] [Indexed: 01/07/2023]
Abstract
MFSD2A, a member of the major facilitator superfamily (MFS), is a transmembrane transporter responsible for the uptake of specific essential fatty acids through the blood-brain barrier (BBB) to the brain. The transporter is crucial for early embryonic brain development and a major factor in the formation and maintenance of the BBB. Mfsd2a-knockout mice show a leakage of the BBB in early embryonic stages and develop a phenotype characterized by microcephaly, cognitive impairment, and anxiety. So far, homozygous or compound heterozygous MFSD2A mutations in humans have only been reported in 13 different families with a total of 28 affected individuals. The phenotypical spectrum of patients with MFSD2A variants is rather broad but all patients present with microcephaly and severe intellectual disability, absent or limited speech, and walking difficulties. Severely affected patients develop seizures and show brain malformations and have, above all, a profound developmental delay hardly reaching any developmental motor milestones. Here, we report on two unrelated individuals with novel homozygous variants in the MFSD2A gene, presenting with severe primary microcephaly, brain malformations, profound developmental delay, and epilepsy, including hypsarrhythmia. Our findings extend the mutational spectrum of the bi-allelic MFSD2A variants causing autosomal recessive primary microcephaly type 15 and broaden the phenotypic spectrum associated with these pathogenic variants emphasizing the role of MFSD2A in early brain development.
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Affiliation(s)
| | - Gökhan Yigit
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany.
| | | | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.
| | - Nursel H Elcioglu
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul, Turkey; Eastern Mediterranean University School of Medicine, Cyprus, Mersin, 10, Turkey.
| | - Burcu Yeter
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul, Turkey.
| | - Ute Hehr
- Center for Human Genetics, and Department of Human Genetics, University of Regensburg, Regensburg, Germany.
| | - Anja Stein
- Department of Pediatrics, Neonatology, University Hospital Essen, Germany.
| | - Adela Della Marina
- Department of Neuropediatrics, Developmental Neurology and Social Pediatrics, University of Essen, Germany, University Hospital Essen, Germany.
| | - Angela Köninger
- Department of Obstetrics and Gynaecology, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
| | | | - Frank J Kaiser
- Institute for Human Genetics, University Hospital Essen, Germany.
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
| | - Alma Kuechler
- Institute for Human Genetics, University Hospital Essen, Germany.
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50
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Wood CAP, Zhang J, Aydin D, Xu Y, Andreone BJ, Langen UH, Dror RO, Gu C, Feng L. Structure and mechanism of blood-brain-barrier lipid transporter MFSD2A. Nature 2021; 596:444-448. [PMID: 34349262 PMCID: PMC8884080 DOI: 10.1038/s41586-021-03782-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/29/2021] [Indexed: 02/07/2023]
Abstract
MFSD2A is a sodium-dependent lysophosphatidylcholine symporter that is responsible for the uptake of docosahexaenoic acid into the brain1,2, which is crucial for the development and performance of the brain3. Mutations that affect MFSD2A cause microcephaly syndromes4,5. The ability of MFSD2A to transport lipid is also a key mechanism that underlies its function as an inhibitor of transcytosis to regulate the blood-brain barrier6,7. Thus, MFSD2A represents an attractive target for modulating the permeability of the blood-brain barrier for drug delivery. Here we report the cryo-electron microscopy structure of mouse MFSD2A. Our structure defines the architecture of this important transporter, reveals its unique extracellular domain and uncovers its substrate-binding cavity. The structure-together with our functional studies and molecular dynamics simulations-identifies a conserved sodium-binding site, reveals a potential lipid entry pathway and helps to rationalize MFSD2A mutations that underlie microcephaly syndromes. These results shed light on the critical lipid transport function of MFSD2A and provide a framework to aid in the design of specific modulators for therapeutic purposes.
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Affiliation(s)
- Chase A P Wood
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jinru Zhang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Deniz Aydin
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Computer Science, Stanford University, Stanford, CA, USA.,Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Yan Xu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Urs H Langen
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Ron O Dror
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Computer Science, Stanford University, Stanford, CA, USA.,Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Chenghua Gu
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Liang Feng
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
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