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Wang L, Pan P, Ma H, He C, Qin Z, He W, Huang J, Tan S, Meng D, Wei H, Yin A. Malformations of cortical development: Fetal imaging and genetics. Mol Genet Genomic Med 2024; 12:e2440. [PMID: 38634212 PMCID: PMC11024634 DOI: 10.1002/mgg3.2440] [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: 12/14/2023] [Revised: 03/04/2024] [Accepted: 03/28/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Malformations of cortical development (MCD) are a group of congenital disorders characterized by structural abnormalities in the brain cortex. The clinical manifestations include refractory epilepsy, mental retardation, and cognitive impairment. Genetic factors play a key role in the etiology of MCD. Currently, there is no curative treatment for MCD. Phenotypes such as epilepsy and cerebral palsy cannot be observed in the fetus. Therefore, the diagnosis of MCD is typically based on fetal brain magnetic resonance imaging (MRI), ultrasound, or genetic testing. The recent advances in neuroimaging have enabled the in-utero diagnosis of MCD using fetal ultrasound or MRI. METHODS The present study retrospectively reviewed 32 cases of fetal MCD diagnosed by ultrasound or MRI. Then, the chromosome karyotype analysis, single nucleotide polymorphism array or copy number variation sequencing, and whole-exome sequencing (WES) findings were presented. RESULTS Pathogenic copy number variants (CNVs) or single-nucleotide variants (SNVs) were detected in 22 fetuses (three pathogenic CNVs [9.4%, 3/32] and 19 SNVs [59.4%, 19/32]), corresponding to a total detection rate of 68.8% (22/32). CONCLUSION The results suggest that genetic testing, especially WES, should be performed for fetal MCD, in order to evaluate the outcomes and prognosis, and predict the risk of recurrence in future pregnancies.
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Affiliation(s)
- Lin‐Lin Wang
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of Jinan UniversityGuangzhouGuangdongChina
- Prenatal Diagnosis CenterMaternal & Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningGuangxiChina
| | - Ping‐Shan Pan
- Prenatal Diagnosis CenterMaternal & Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningGuangxiChina
| | - Hui Ma
- Prenatal Diagnosis CenterMaternal & Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningGuangxiChina
| | - Chun He
- Prenatal Diagnosis CenterMaternal & Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningGuangxiChina
| | - Zai‐Long Qin
- Prenatal Diagnosis CenterMaternal & Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningGuangxiChina
| | - Wei He
- Prenatal Diagnosis CenterMaternal & Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningGuangxiChina
| | - Jing Huang
- Prenatal Diagnosis CenterMaternal & Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningGuangxiChina
| | - Shu‐Yin Tan
- Prenatal Diagnosis CenterMaternal & Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningGuangxiChina
| | - Da‐Hua Meng
- Prenatal Diagnosis CenterMaternal & Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningGuangxiChina
| | - Hong‐Wei Wei
- Prenatal Diagnosis CenterMaternal & Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningGuangxiChina
| | - Ai‐Hua Yin
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of Jinan UniversityGuangzhouGuangdongChina
- Medical Genetic CenterGuangdong Women and Children HospitalGuangzhouGuangdongChina
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Aslam K, Anjum I, Aslam K, Haq R, Bashir R. Genetic susceptibility of vitamin D receptor gene polymorphisms on autosomal recessive primary microcephaly patients in Pakistani population: a case-control and in-silico study. Mol Biol Rep 2023; 50:8049-8059. [PMID: 37541996 DOI: 10.1007/s11033-023-08681-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/14/2023] [Indexed: 08/06/2023]
Abstract
BACKGROUND Autosomal recessive primary microcephaly (MCPH) is a rare genetic disorder that leads to reduced cerebral cortex caused by a mutation in corticogenesis. The expression of the Vitamin D receptor (VDR) gene is involved in the proliferation and differentiation of neural stem cells, and VDR polymorphisms have been associated with various neurological disorders. However, their relationship with MCPH has not been explored. This study aimed to investigate the association of VDR polymorphisms with MCPH due to its role in Wnt signaling pathway and its In-silico analysis. METHODS Blood samples of 64 MCPH patients and 52 controls were collected to genotype VDR SNPs (TaqI (rs731236), FokI (rs2228570) and BsmI (rs1544410). In-silico tools were also used to assess the effects of exonic SNPs on mRNA and protein structure and pathogenicity of exonic and intronic SNPs. RESULTS The study found that serum 25-OH vitamin D3 levels were significantly different in MCPH patients and healthy controls (P = 0.000). The genetic analysis showed that VDR polymorphisms of FokI and BsmI were seven times more frequent in MCPH patients than in controls (P < 0.05) and the recessive model for TaqI and dominant model for BsmI polymorphisms were also associated with the pathogenesis of MCPH. In-silico analysis showed that the pathogenicity effects of rs2228570 and rs1544410 are neutral while rs731236 causes a silent mutation which has no effect on VDR protein. CONCLUSION VDR polymorphisms of FokI and BsmI are associated with the risk of MCPH. These findings suggest that VDR polymorphisms play a role in MCPH, which could provide important insights for understanding the molecular mechanisms of the disease.
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Affiliation(s)
- Komal Aslam
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
- Department of Biotechnology, Kinnaird College for Women, Lahore, Pakistan
| | - Iram Anjum
- Department of Biotechnology, Kinnaird College for Women, Lahore, Pakistan
| | - Kanwal Aslam
- Department of Statistics, Kinnaird College for Women, Lahore, Pakistan
| | - Rukhama Haq
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
| | - Rasheeda Bashir
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan.
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Farcy S, Hachour H, Bahi-Buisson N, Passemard S. Genetic Primary Microcephalies: When Centrosome Dysfunction Dictates Brain and Body Size. Cells 2023; 12:1807. [PMID: 37443841 PMCID: PMC10340463 DOI: 10.3390/cells12131807] [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: 04/06/2023] [Revised: 06/04/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023] Open
Abstract
Primary microcephalies (PMs) are defects in brain growth that are detectable at or before birth and are responsible for neurodevelopmental disorders. Most are caused by biallelic or, more rarely, dominant mutations in one of the likely hundreds of genes encoding PM proteins, i.e., ubiquitous centrosome or microtubule-associated proteins required for the division of neural progenitor cells in the embryonic brain. Here, we provide an overview of the different types of PMs, i.e., isolated PMs with or without malformations of cortical development and PMs associated with short stature (microcephalic dwarfism) or sensorineural disorders. We present an overview of the genetic, developmental, neurological, and cognitive aspects characterizing the most representative PMs. The analysis of phenotypic similarities and differences among patients has led scientists to elucidate the roles of these PM proteins in humans. Phenotypic similarities indicate possible redundant functions of a few of these proteins, such as ASPM and WDR62, which play roles only in determining brain size and structure. However, the protein pericentrin (PCNT) is equally required for determining brain and body size. Other PM proteins perform both functions, albeit to different degrees. Finally, by comparing phenotypes, we considered the interrelationships among these proteins.
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Affiliation(s)
- Sarah Farcy
- UMR144, Institut Curie, 75005 Paris, France;
- Inserm UMR-S 1163, Institut Imagine, 75015 Paris, France
| | - Hassina Hachour
- Service de Neurologie Pédiatrique, DMU INOV-RDB, APHP, Hôpital Robert Debré, 75019 Paris, France;
| | - Nadia Bahi-Buisson
- Service de Neurologie Pédiatrique, DMU MICADO, APHP, Hôpital Necker Enfants Malades, 75015 Paris, France;
- Université Paris Cité, Inserm UMR-S 1163, Institut Imagine, 75015 Paris, France
| | - Sandrine Passemard
- Service de Neurologie Pédiatrique, DMU INOV-RDB, APHP, Hôpital Robert Debré, 75019 Paris, France;
- Université Paris Cité, Inserm UMR 1141, NeuroDiderot, 75019 Paris, France
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New Genetic Variants in CYP2B6 and SLC6A Support the Role of Oxidative Stress in Familial Ménière’s Disease. Genes (Basel) 2022; 13:genes13060998. [PMID: 35741759 PMCID: PMC9222295 DOI: 10.3390/genes13060998] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 12/10/2022] Open
Abstract
The objective was to study the genetic etiology of Ménière’s disease (MD) using next-generation sequencing in three families with three cases of MD. Whole exome sequencing was used to identify rare genetic variants co-segregating with MD in Finnish families. In silico estimations and population databases were used to estimate the frequency and pathogenicity of the variants. Variants were validated and genotyped from additional family members using capillary sequencing. A geneMANIA analysis was conducted to investigate the functional pathways and protein interactions of candidate genes. Seven rare variants were identified to co-segregate with MD in the three families: one variant in the CYP2B6 gene in family I, one variant in GUSB and EPB42 in family II, and one variant in each of the SLC6A, ASPM, KNTC1, and OVCH1 genes in family III. Four of these genes were linked to the same co-expression network with previous familial MD candidate genes. Dysfunction of CYP2B6 and SLC6A could predispose to MD via the oxidative stress pathway. Identification of ASPM and KNTC1 as candidate genes for MD suggests dysregulation of mitotic spindle formation in familial MD. The genetic etiology of familial MD is heterogenic. Our findings suggest a role for genes acting on oxidative stress and mitotic spindle formation in MD but also highlight the genetic complexity of MD.
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Fatumo S, Chikowore T, Choudhury A, Ayub M, Martin AR, Kuchenbaecker K. A roadmap to increase diversity in genomic studies. Nat Med 2022; 28:243-250. [PMID: 35145307 PMCID: PMC7614889 DOI: 10.1038/s41591-021-01672-4] [Citation(s) in RCA: 195] [Impact Index Per Article: 97.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 12/21/2021] [Indexed: 12/12/2022]
Abstract
Two decades ago, the sequence of the first human genome was published. Since then, advances in genome technologies have resulted in whole-genome sequencing and microarray-based genotyping of millions of human genomes. However, genetic and genomic studies are predominantly based on populations of European ancestry. As a result, the potential benefits of genomic research-including better understanding of disease etiology, early detection and diagnosis, rational drug design and improved clinical care-may elude the many underrepresented populations. Here, we describe factors that have contributed to the imbalance in representation of different populations and, leveraging our experiences in setting up genomic studies in diverse global populations, we propose a roadmap to enhancing inclusion and ensuring equal health benefits of genomics advances. Our Perspective highlights the importance of sincere, concerted global efforts toward genomic equity to ensure the benefits of genomic medicine are accessible to all.
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Affiliation(s)
- Segun Fatumo
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM, Entebbe, Uganda.
- The Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
| | - Tinashe Chikowore
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- MRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Muhammad Ayub
- Division of Psychiatry, University College London, London, UK
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Karoline Kuchenbaecker
- Division of Psychiatry, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
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Naqvi SF, Shabbir RMK, Tolun A, Basit S, Malik S. A Two-Base Pair Deletion in IQ Repeats in ASPM Underlies Microcephaly in a Pakistani Family. Genet Test Mol Biomarkers 2022; 26:37-42. [PMID: 35089071 DOI: 10.1089/gtmb.2021.0231] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aims: Autosomal recessive primary microcephaly (MCPH) is a clinically rare and genetically highly heterogeneous developmental disorder. Biallelic variants in the abnormal spindle-like microcephaly-associated (ASPM) gene account for 40% to 68% of all MCPH cases. This study was designed to elucidate the genetic basis of MCPH in an extended family. To highlight recurrent mutations useful in implementing genetic testing programs, we further aimed to carry out a descriptive review of the reported ASPM mutations. Materials and Methods: A large inbred kindred with seven affected members was investigated, and detailed clinical and behavioral assessments were carried out. Single nucleotide polymorphism (SNP)-based homozygosity mapping and exome sequencing were performed. Results: Affected individuals had characteristic features, including small head, receding forehead, mild to moderate intellectual disability, developmental delay, short stature, apraxia, and behavioral anomalies. We mapped the disease gene locus and detected a rare frameshift deletion c.6854_6855del (p.(Leu2285GlnfsTer32)) in exon 18 of ASPM. A total of 215 mutations in ASPM have been reported in at least 453 families, nearly 50% of which are of Pakistani origin. These mutations can be classified as recurrent, founder or private in Pakistani and other populations. Conclusion: SNP-based homozygosity mapping and exome sequencing are essential in delineating the genetically distinct microcephaly types. The highlighted recurrent mutations in ASPM could be useful in implementing genetic testing programs for MCPH.
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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
| | - Rana Muhammad Kamran Shabbir
- Human Genetics Program, Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Aslıhan Tolun
- Department of Molecular Biology and Genetics, MOBGAM, Istanbul Technical University, Istanbul, Turkey
| | - Sulman Basit
- Department of Biochemistry, College of Medicine & Center for Genetics and Inherited Diseases, Taibah University Medina, Kingdom of Saudi Arabia
| | - Sajid Malik
- Human Genetics Program, Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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