1
|
Mary L, Fradin M, Pasquier L, Quelin C, Loget P, Le Lous M, Le Bouar G, Nivot-Adamiak S, Lokchine A, Dubourg C, Jauffret V, Nouyou B, Henry C, Launay E, Odent S, Jaillard S, Belaud-Rotureau MA. Role of chromosomal imbalances in the pathogenesis of DSD: A retrospective analysis of 115 prenatal samples. Eur J Med Genet 2023; 66:104748. [PMID: 36948288 DOI: 10.1016/j.ejmg.2023.104748] [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: 09/16/2022] [Revised: 03/10/2023] [Accepted: 03/18/2023] [Indexed: 03/24/2023]
Abstract
Differences of sex development (DSDs) are a group of congenital conditions characterized by a discrepancy between chromosomal, gonadal, and genital sex development of an individual, with significant impact on medical, psychological and reproductive life. The genetic heterogeneity of DSDs complicates the diagnosis and almost half of the patients remains undiagnosed. In this context, chromosomal imbalances in syndromic DSD patients may help to identify new genes implicated in DSDs. In this study, we aimed at describing the burden of chromosomal imbalances including submicroscopic ones (copy number variants or CNVs) in a cohort of prenatal syndromic DSD patients, and review their role in DSDs. Our patients carried at least one pathogenic or likely pathogenic chromosomal imbalance/CNV or low-level mosaicism for aneuploidy. Almost half of the cases resulted from an unbalanced chromosomal rearrangement. Chromosome 9p/q, 4p/q, 3q and 11q anomalies were more frequently observed. Review of the literature confirmed the causative role of CNVs in DSDs, either in disruption of known DSD-causing genes (SOX9, NR0B1, NR5A1, AR, ATRX, …) or as a tool to suspect new genes in DSDs (HOXD cluster, ADCY2, EMX2, CAMK1D, …). Recurrent CNVs of regulatory elements without coding sequence content (i.e. duplications/deletions upstream of SOX3 or SOX9) confirm detection of CNVs as a mean to explore our non-coding genome. Thus, CNV detection remains a powerful tool to explore undiagnosed DSDs, either through routine techniques or through emerging technologies such as long-read whole genome sequencing or optical genome mapping.
Collapse
Affiliation(s)
- L Mary
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, F-35033, Rennes, France; Univ Rennes, CHU Rennes, Inserm, EHESP, Irset, UMR_S, 1085, F-35000, Rennes, France.
| | - M Fradin
- Service de Génétique Clinique, Centre de Référence Anomalies Du Développement, CLAD Ouest, CHU Rennes, Rennes, France
| | - L Pasquier
- Service de Génétique Clinique, Centre de Référence Anomalies Du Développement, CLAD Ouest, CHU Rennes, Rennes, France; Université de Rennes, IGDR (Institut de Génétique et Développement), CNRS UMR 6290, INSERM ERL 1305, Rennes, France
| | - C Quelin
- Service de Génétique Clinique, Centre de Référence Anomalies Du Développement, CLAD Ouest, CHU Rennes, Rennes, France
| | - P Loget
- Service D'Anatomie Pathologique, Hôpital Pontchaillou, CHU Rennes, Rennes, France
| | - M Le Lous
- Unité de Médecine Fœtale, Service de Gynécologie-Obstétrique, CHU Rennes, Rennes, France
| | - G Le Bouar
- Unité de Médecine Fœtale, Service de Gynécologie-Obstétrique, CHU Rennes, Rennes, France
| | - S Nivot-Adamiak
- Service D'endocrinologie Pédiatrique, CHU Rennes, Rennes, France
| | - A Lokchine
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, F-35033, Rennes, France
| | - C Dubourg
- Université de Rennes, IGDR (Institut de Génétique et Développement), CNRS UMR 6290, INSERM ERL 1305, Rennes, France; Service de Génétique Moléculaire et Génomique, CHU de Rennes, Rennes, 35033, France
| | - V Jauffret
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, F-35033, Rennes, France
| | - B Nouyou
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, F-35033, Rennes, France
| | - C Henry
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, F-35033, Rennes, France
| | - E Launay
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, F-35033, Rennes, France
| | - S Odent
- Service de Génétique Clinique, Centre de Référence Anomalies Du Développement, CLAD Ouest, CHU Rennes, Rennes, France; Université de Rennes, IGDR (Institut de Génétique et Développement), CNRS UMR 6290, INSERM ERL 1305, Rennes, France
| | - S Jaillard
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, F-35033, Rennes, France; Univ Rennes, CHU Rennes, Inserm, EHESP, Irset, UMR_S, 1085, F-35000, Rennes, France
| | - M A Belaud-Rotureau
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, F-35033, Rennes, France; Univ Rennes, CHU Rennes, Inserm, EHESP, Irset, UMR_S, 1085, F-35000, Rennes, France
| |
Collapse
|
2
|
Zidoune H, Ladjouze A, Chellat-Rezgoune D, Boukri A, Dib SA, Nouri N, Tebibel M, Sifi K, Abadi N, Satta D, Benelmadani Y, Bignon-Topalovic J, El-Zaiat-Munsch M, Bashamboo A, McElreavey K. Novel Genomic Variants, Atypical Phenotypes and Evidence of a Digenic/Oligogenic Contribution to Disorders/Differences of Sex Development in a Large North African Cohort. Front Genet 2022; 13:900574. [PMID: 36110220 PMCID: PMC9468775 DOI: 10.3389/fgene.2022.900574] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
In a majority of individuals with disorders/differences of sex development (DSD) a genetic etiology is often elusive. However, new genes causing DSD are routinely reported and using the unbiased genomic approaches, such as whole exome sequencing (WES) should result in an increased diagnostic yield. Here, we performed WES on a large cohort of 125 individuals all of Algerian origin, who presented with a wide range of DSD phenotypes. The study excluded individuals with congenital adrenal hypoplasia (CAH) or chromosomal DSD. Parental consanguinity was reported in 36% of individuals. The genetic etiology was established in 49.6% (62/125) individuals of the total cohort, which includes 42.2% (35/83) of 46, XY non-syndromic DSD and 69.2% (27/39) of 46, XY syndromic DSD. No pathogenic variants were identified in the 46, XX DSD cases (0/3). Variants in the AR, HSD17B3, NR5A1 and SRD5A2 genes were the most common causes of DSD. Other variants were identified in genes associated with congenital hypogonadotropic hypogonadism (CHH), including the CHD7 and PROKR2. Previously unreported pathogenic/likely pathogenic variants (n = 30) involving 25 different genes were identified in 22.4% of the cohort. Remarkably 11.5% of the 46, XY DSD group carried variants classified as pathogenic/likely pathogenic variant in more than one gene known to cause DSD. The data indicates that variants in PLXNA3, a candidate CHH gene, is unlikely to be involved in CHH. The data also suggest that NR2F2 variants may cause 46, XY DSD.
Collapse
Affiliation(s)
- Housna Zidoune
- Human Developmental Genetics Unit, Institut Pasteur, CNRS, Paris, France
- Laboratory of Molecular and Cellular Biology, Department of Animal Biology, University Frères Mentouri Constantine 1, Constantine, Algeria
- Department of Medicine, Laboratory of Biology and Molecular Genetics, University Salah Boubnider Constantine 3, Constantine, Algeria
| | | | - Djalila Chellat-Rezgoune
- Laboratory of Molecular and Cellular Biology, Department of Animal Biology, University Frères Mentouri Constantine 1, Constantine, Algeria
- Department of Medicine, Laboratory of Biology and Molecular Genetics, University Salah Boubnider Constantine 3, Constantine, Algeria
| | - Asma Boukri
- Department of Endocrinology and Diabetology, CHU Ibn Badis Constantine, Constantine, Algeria
| | | | - Nassim Nouri
- Department of Endocrinology and Diabetology, CHU Ibn Badis Constantine, Constantine, Algeria
| | - Meryem Tebibel
- Department of Pediatric Surgery, CHU Beni Messous, Algiers, Algeria
| | - Karima Sifi
- Department of Medicine, Laboratory of Biology and Molecular Genetics, University Salah Boubnider Constantine 3, Constantine, Algeria
| | - Noureddine Abadi
- Department of Medicine, Laboratory of Biology and Molecular Genetics, University Salah Boubnider Constantine 3, Constantine, Algeria
| | - Dalila Satta
- Laboratory of Molecular and Cellular Biology, Department of Animal Biology, University Frères Mentouri Constantine 1, Constantine, Algeria
- Department of Medicine, Laboratory of Biology and Molecular Genetics, University Salah Boubnider Constantine 3, Constantine, Algeria
| | - Yasmina Benelmadani
- Department of Medicine, Laboratory of Biology and Molecular Genetics, University Salah Boubnider Constantine 3, Constantine, Algeria
| | | | | | - Anu Bashamboo
- Human Developmental Genetics Unit, Institut Pasteur, CNRS, Paris, France
| | - Ken McElreavey
- Human Developmental Genetics Unit, Institut Pasteur, CNRS, Paris, France
- *Correspondence: Ken McElreavey,
| |
Collapse
|
3
|
Maddirevula S, Alameer S, Ewida N, de Sousa MML, Bjørås M, Vågbø CB, Alkuraya FS. Insight into ALKBH8-related intellectual developmental disability based on the first pathogenic missense variant. Hum Genet 2021; 141:209-215. [PMID: 34757492 DOI: 10.1007/s00439-021-02391-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 10/20/2021] [Indexed: 12/23/2022]
Abstract
ALKBH8 is a methyltransferase that modifies tRNAs by methylating the anticodon wobble uridine residue. The syndrome of ALKBH8-related intellectual developmental disability (MRT71) has thus far been reported solely in the context of homozygous truncating variants that cluster in the last exon. This raises interesting questions about the disease mechanism, because these variants are predicted to escape nonsense mediated decay and yet they appear to be loss of function. Furthermore, the limited class of reported variants complicates the future interpretation of missense variants in ALKBH8. Here, we report a consanguineous family in which two children with MRT71-compatible phenotype are homozygous for a novel missense variant in the methyltransferase domain. We confirm the pathogenicity of this variant by demonstrating complete absence of ALKBH8-dependent modifications in patient cells. Targeted proteomics analysis of ALKBH8 indicates that the variant does not lead to loss of ALKBH8 protein expression. This report adds to the clinical delineation of MRT71, confirms loss of function of ALKBH8 as the disease mechanism and expands the repertoire of its molecular lesions.
Collapse
Affiliation(s)
- Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia
| | - Seham Alameer
- Department of Pediatrics, Ministry of the National Guard-Health Affairs, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Nour Ewida
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia
| | | | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Cathrine Broberg Vågbø
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491, Trondheim, Norway.,Proteomics and Modomics Experimental Core and St. Olavs Hospital Central Staff, Trondheim, Norway
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia. .,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, 11533, Saudi Arabia.
| |
Collapse
|
4
|
Saad AK, Marafi D, Mitani T, Du H, Rafat K, Fatih JM, Jhangiani SN, Coban-Akdemir Z, Gibbs RA, Pehlivan D, Hunter JV, Posey JE, Zaki MS, Lupski JR. Neurodevelopmental disorder in an Egyptian family with a biallelic ALKBH8 variant. Am J Med Genet A 2021; 185:1288-1293. [PMID: 33544954 DOI: 10.1002/ajmg.a.62100] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/31/2020] [Accepted: 01/12/2021] [Indexed: 12/11/2022]
Abstract
Alkylated DNA repair protein AlkB homolog 8 (ALKBH8) is a member of the AlkB family of dioxygenases. ALKBH8 is a methyltransferase of the highly variable wobble nucleoside position in the anticodon loop of tRNA and thus plays a critical role in tRNA modification by preserving codon recognition and preventing errors in amino acid incorporation during translation. Moreover, its activity catalyzes uridine modifications that are proposed to be critical for accurate protein translation. Previously, two distinct homozygous truncating variants in the final exon of ALKBH8 were described in two unrelated large Saudi Arabian kindreds with intellectual developmental disorder and autosomal recessive 71 (MRT71) syndrome (MIM# 618504). Here, we report a third family-of Egyptian descent-harboring a novel homozygous frame-shift variant in the last exon of ALKBH8. Two affected siblings in this family exhibit global developmental delay and intellectual disability as shared characteristic features of MRT71 syndrome, and we further characterize their observed dysmorphic features and brain MRI findings. This description of a third family with a truncating ALKBH8 variant from a distinct population broadens the phenotypic and genotypic spectrum of MRT71 syndrome, affirms that perturbations in tRNA biogenesis can contribute to neurogenetic disease traits, and firmly establishes ALKBH8 as a novel neurodevelopmental disease gene.
Collapse
Affiliation(s)
- Ahmed K Saad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Medical Molecular Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Karima Rafat
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA.,Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Jill V Hunter
- Department of Radiology, Baylor College of Medicine, Houston, Texas, USA.,E.B. Singleton Department of Pediatric Radiology, Texas Children's Hospital, Houston, Texas, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Maha S Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| |
Collapse
|
5
|
Kitamura H, Hashimoto M. USP2-Related Cellular Signaling and Consequent Pathophysiological Outcomes. Int J Mol Sci 2021; 22:1209. [PMID: 33530560 PMCID: PMC7865608 DOI: 10.3390/ijms22031209] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 12/13/2022] Open
Abstract
Ubiquitin specific protease (USP) 2 is a multifunctional deubiquitinating enzyme. USP2 modulates cell cycle progression, and therefore carcinogenesis, via the deubiquitination of cyclins and Aurora-A. Other tumorigenic molecules, including epidermal growth factor and fatty acid synthase, are also targets for USP2. USP2 additionally prevents p53 signaling. On the other hand, USP2 functions as a key component of the CLOCK/BMAL1 complex and participates in rhythmic gene expression in the suprachiasmatic nucleus and liver. USP2 variants influence energy metabolism by controlling hepatic gluconeogenesis, hepatic cholesterol uptake, adipose tissue inflammation, and subsequent systemic insulin sensitivity. USP2 also has the potential to promote surface expression of ion channels in renal and intestinal epithelial cells. In addition to modifying the production of cytokines in immune cells, USP2 also modulates the signaling molecules that are involved in cytokine signaling in the target cells. Usp2 knockout mice exhibit changes in locomotion and male fertility, which suggest roles for USP2 in the central nervous system and male genital tract, respectively. In this review, we summarize the cellular events with USP2 contributions and list the signaling molecules that are upstream or downstream of USP2. Additionally, we describe phenotypic differences found in the in vitro and in vivo experimental models.
Collapse
Affiliation(s)
- Hiroshi Kitamura
- Laboratory of Veterinary Physiology, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido 069-8501, Japan;
| | | |
Collapse
|