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Tonetto E, Cucci A, Follenzi A, Bernardi F, Pinotti M, Balestra D. DNA base editing corrects common hemophilia A mutations and restores factor VIII expression in in vitro and ex vivo models. J Thromb Haemost 2024; 22:2171-2183. [PMID: 38718928 DOI: 10.1016/j.jtha.2024.04.020] [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: 01/22/2024] [Revised: 04/22/2024] [Accepted: 04/22/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Replacement and nonreplacement therapies effectively control bleeding in hemophilia A (HA) but imply lifelong interventions. Authorized gene addition therapy could provide a cure but still poses questions on durability. FVIIIgene correction would definitively restore factor (F)VIII production, as shown in animal models through nuclease-mediated homologous recombination (HR). However, low efficiency and potential off-target double-strand break still limit HR translatability. OBJECTIVES To correct common model single point mutations leading to severe HA through the recently developed double-strand break/HR-independent base editing (BE) and prime editing (PE) approaches. METHODS Screening for efficacy of BE/PE systems in HEK293T cells transiently expressing FVIII variants and validation at DNA (sequencing) and protein (enzyme-linked immunosorbent assay; activated partial thromboplastin time) level in stable clones. Evaluation of rescue in engineered blood outgrowth endothelial cells by lentiviral-mediated delivery of BE. RESULTS Transient assays identified the best-performing BE/PE systems for each variant, with the highest rescue of FVIII expression (up to 25% of wild-type recombinant FVIII) for the p.R2166∗ and p.R2228Q mutations. In stable clones, we demonstrated that the mutation reversion on DNA (∼24%) was consistent with the rescue of FVIII secretion and activity of 20% to 30%. The lentiviral-mediated delivery of the selected BE systems was attempted in engineered blood outgrowth endothelial cells harboring the p.R2166∗ and p.R2228Q variants, which led to an appreciable and dose-dependent rescue of secreted functional FVIII. CONCLUSION Overall data provide the first proof-of-concept for effective BE/PE-mediated correction of HA-causing mutations, which encourage studies in mouse models to develop a personalized cure for large cohorts of patients through a single intervention.
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Affiliation(s)
- Elena Tonetto
- Department of Life Sciences and Biotechnology and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, Ferrara, Italy
| | - Alessia Cucci
- Department of Health Sciences, School of Medicine, University of Piemonte Orientale, Novara, Italy
| | - Antonia Follenzi
- Department of Health Sciences, School of Medicine, University of Piemonte Orientale, Novara, Italy
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, Ferrara, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, Ferrara, Italy.
| | - Dario Balestra
- Department of Life Sciences and Biotechnology and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, Ferrara, Italy
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Moghadam AA, Manafzadeh AR, Dajliry K, Ramezan F, Nikoonia MR, Abdolkarimi B, Hamidpour M, Tabibian S. Genotype-phenotype analyses of Iranian patients with hemophilia B (Leyden -) and hemophilia B (Leyden +): A single-center study. Transfus Apher Sci 2024; 63:103962. [PMID: 38964254 DOI: 10.1016/j.transci.2024.103962] [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: 04/16/2024] [Revised: 06/15/2024] [Accepted: 06/19/2024] [Indexed: 07/06/2024]
Abstract
BACKGROUND There is a high prevalence of inherited bleeding disorders in Iran, such as hemophilia A (HA) and hemophilia B (HB). This study aimed to analyze the molecular and clinical profiles of patients with HB. METHODS A single-center study was conducted among patients with severe HB between March 20, 2000, and June 31, 2023. The polymerase chain reaction (PCR) amplification was used for all of the major regions, such as the promoter, the exons, the adjacent intronic regions, and the untranslated regions of the F9 gene. Finally, Sanger sequencing was performed on the PCR products. RESULTS A total of 111 HB patients (17 with HB [Leyden +] and 94 with HB [Leyden -]) were enrolled in this study. Among 94 patients with HB (Leyden -), 59 (62.8 %) had missense, 21 (22.3 %) had nonsense, and 8 (8.5 %) had frameshift mutations. Moreover, the most frequent pathogenic variant in HB (Leyden +) was c.-17 A>G in this study. CONCLUSION The results of this study confirm that HB is caused by a wide range of molecular defects in Iran. Thus, by knowing the genotypes and phenotypes, we would be able to stratify the patients which is important in terms of their management and outcome.
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Affiliation(s)
- Arash Ahmadfard Moghadam
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Reza Manafzadeh
- Department of Internal Medicine, Albert Szent-Györgyi Health Centre, University of Szeged, Szeged 6726, Hungary
| | - Khadijeh Dajliry
- Blood Disease Research Center (BDRC), Iranian Comprehensive Hemophilia Care Center, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Farahnaz Ramezan
- Blood Disease Research Center (BDRC), Iranian Comprehensive Hemophilia Care Center, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Mohammad Reza Nikoonia
- Blood Disease Research Center (BDRC), Iranian Comprehensive Hemophilia Care Center, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Babak Abdolkarimi
- Pediatric Hematology-Oncology, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Mohsen Hamidpour
- Hematopoietic Stem Cell Research Centre-Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Shadi Tabibian
- Blood Disease Research Center (BDRC), Iranian Comprehensive Hemophilia Care Center, Iran University of Medical Sciences (IUMS), Tehran, Iran.
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3
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Bossio S, Perrotta ID, Lofaro D, La Russa D, Rago V, Bonofiglio R, Greco R, Andreucci M, Aversa A, La Russa A, Perri A. The Missense Variant in the Signal Peptide of α-GLA Gene, c.13 A/G, Promotes Endoplasmic Reticular Stress and the Related Pathway's Activation. Genes (Basel) 2024; 15:947. [PMID: 39062726 PMCID: PMC11276125 DOI: 10.3390/genes15070947] [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: 06/06/2024] [Revised: 07/15/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Anderson-Fabry disease (AFD) is an X-linked multisystemic disorder with a heterogeneous phenotype, resulting from deficiency of the lysosomal enzyme α-galactosidase A (α-Gal A) and leading to globotriaosylceramide systemic accumulation. Lysosomal storage is not the unique player in organ failure and different mechanisms could drive tissue damage, including endoplasmic reticulum (ER) stress and its related signaling pathway's activation. We identified a new missense variant in the signal peptide of α-GLA gene, c.13 A/G, in a 55-year-old woman affected by chronic kidney disease, acroparesthesia, hypohidrosis, and deafness and exhibiting normal values of lysoGb3 and αGLA activity. The functional study of the new variant performed by its overexpression in HEK293T cells showed an increased protein expression of a key ER stress marker, GRP78, the pro-apoptotic BAX, the negative regulator of cell cycle p21, the pro-inflammatory cytokine, IL1β, together with pNFkB, and the pro-fibrotic marker, N-cadherin. Transmission electron microscopy showed signs of ER injury and intra-lysosomal inclusions. The proband's PBMC exhibited higher expression of TGFβ 1 and pNFkB compared to control. Our findings suggest that the new variant, although it did not affect enzymatic activity, could cause cellular damage by affecting ER homeostasis and promoting apoptosis, inflammation, and fibrosis. Further studies are needed to demonstrate the variant's contribution to cellular and tissue damage.
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Affiliation(s)
- Sabrina Bossio
- Department of Experimental and Clinical Medicine, University “Magna Graecia”, 88100 Catanzaro, Italy; (S.B.); (A.A.)
| | - Ida Daniela Perrotta
- Department of Biology, Ecology and Earth Sciences, Centre for Microscopy and Microanalysis (CM2), University of Calabria, 87036 Rende, Italy;
| | - Danilo Lofaro
- e-Health Lab, Department of Mechanical, Energy, Management Engineering, University of Calabria, 87036 Rende, Italy;
| | - Daniele La Russa
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (D.L.R.); (V.R.)
| | - Vittoria Rago
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (D.L.R.); (V.R.)
| | - Renzo Bonofiglio
- Kidney and Transplantation Research Center, Annunziata Hospital, 87100 Cosenza, Italy;
| | - Rosita Greco
- Nephrology, Dialysis, and Kidney Transplant Unit, Annunziata Hospital, 87100 Cosenza, Italy;
| | - Michele Andreucci
- Department of Health Sciences, Magna Graecia University, 88100 Catanzaro, Italy; (M.A.); (A.L.R.)
| | - Antonio Aversa
- Department of Experimental and Clinical Medicine, University “Magna Graecia”, 88100 Catanzaro, Italy; (S.B.); (A.A.)
| | - Antonella La Russa
- Department of Health Sciences, Magna Graecia University, 88100 Catanzaro, Italy; (M.A.); (A.L.R.)
| | - Anna Perri
- Department of Experimental and Clinical Medicine, University “Magna Graecia”, 88100 Catanzaro, Italy; (S.B.); (A.A.)
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Turvey S, Muench SP, Issad T, Fishwick CWG, Kearney MT, Simmons KJ. Using site-directed mutagenesis to further the understanding of insulin receptor-insulin like growth factor-1 receptor heterodimer structure. Growth Horm IGF Res 2024; 77:101607. [PMID: 39033666 DOI: 10.1016/j.ghir.2024.101607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/26/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024]
Abstract
Type 2 diabetes is characterised by the disruption of insulin and insulin-like growth factor (IGF) signalling. The key hubs of these signalling cascades - the Insulin receptor (IR) and Insulin-like growth factor 1 receptor (IGF1R) - are known to form functional IR-IGF1R hybrid receptors which are insulin resistant. However, the mechanisms underpinning IR-IGF1R hybrid formation are not fully understood, hindering the ability to modulate this for future therapies targeting this receptor. To pinpoint suitable sites for intervention, computational hotspot prediction was utilised to identify promising epitopes for targeting with point mutagenesis. Specific IGF1R point mutations F450A, R391A and D555A show reduced affinity of the hybrid receptor in a BRET based donor-saturation assay, confirming hybrid formation could be modulated at this interface. These data provide the basis for rational design of more effective hybrid receptor modulators, supporting the prospect of identifying a small molecule that specifically interacts with this target.
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Affiliation(s)
- Samuel Turvey
- Leeds Institute for Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre, University of Leeds, UK
| | - Tarik Issad
- Université Paris Cité, CNRS, INSERM, Institut Cochin, F-75014 Paris, France
| | | | - Mark T Kearney
- Leeds Institute for Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - Katie J Simmons
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre, University of Leeds, UK.
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5
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Gasparini S, Balestrini S, Saccaro LF, Bacci G, Panichella G, Montomoli M, Cantalupo G, Bigoni S, Mancano G, Pellacani S, Leuzzi V, Volpi N, Mari F, Melani F, Cavallin M, Pisano T, Porcedda G, Vaglio A, Mei D, Barba C, Parrini E, Guerrini R. Multiorgan manifestations of COL4A1 and COL4A2 variants and proposal for a clinical management protocol. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2024:e32099. [PMID: 39016117 DOI: 10.1002/ajmg.c.32099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/23/2024] [Accepted: 06/28/2024] [Indexed: 07/18/2024]
Abstract
COL4A1/2 variants are associated with highly variable multiorgan manifestations. Depicting the whole clinical spectrum of COL4A1/2-related manifestations is challenging, and there is no consensus on management and preventative strategies. Based on a systematic review of current evidence on COL4A1/2-related disease, we developed a clinical questionnaire that we administered to 43 individuals from 23 distinct families carrying pathogenic variants. In this cohort, we extended ophthalmological and cardiological examinations to asymptomatic individuals and those with only limited or mild, often nonspecific, clinical signs commonly occurring in the general population (i.e., oligosymptomatic). The most frequent clinical findings emerging from both the literature review and the questionnaire included stroke (203/685, 29.6%), seizures or epilepsy (199/685, 29.0%), intellectual disability or developmental delay (168/685, 24.5%), porencephaly/schizencephaly (168/685, 24.5%), motor impairment (162/685, 23.6%), cataract (124/685, 18.1%), hematuria (63/685, 9.2%), and retinal arterial tortuosity (58/685, 8.5%). In oligosymptomatic and asymptomatic carriers, ophthalmological investigations detected retinal vascular tortuosity (5/13, 38.5%), dysgenesis of the anterior segment (4/13, 30.8%), and cataract (2/13, 15.4%), while cardiological investigations were unremarkable except for mild ascending aortic ectasia in 1/8 (12.5%). Our multimodal approach confirms highly variable penetrance and expressivity in COL4A1/2-related conditions, even at the intrafamilial level with neurological involvement being the most frequent and severe finding in both children and adults. We propose a protocol for prevention and management based on individualized risk estimation and periodic multiorgan evaluations.
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Affiliation(s)
- Simone Gasparini
- Neuroscience and Human Genetics Department, Meyer Children's Hospital IRCCS (full member of the European Reference Network EpiCARE), Florence, Italy
- University of Florence, Florence, Italy
| | - Simona Balestrini
- Neuroscience and Human Genetics Department, Meyer Children's Hospital IRCCS (full member of the European Reference Network EpiCARE), Florence, Italy
- University of Florence, Florence, Italy
| | - Luigi Francesco Saccaro
- Department of Psychiatry, Geneva University and Geneva University Hospitals, Geneva, Switzerland
| | - Giacomo Bacci
- Pediatric Ophthalmology Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Giorgia Panichella
- University of Florence, Florence, Italy
- Department of Clinical and Experimental Medicine, University Hospital Careggi, Florence, Italy
| | - Martino Montomoli
- Neuroscience and Human Genetics Department, Meyer Children's Hospital IRCCS (full member of the European Reference Network EpiCARE), Florence, Italy
| | - Gaetano Cantalupo
- Child Neuropsychiatry Unit, University Hospital of Verona (full member of the European Reference Network EpiCARE), Verona, Italy
- Department of Engineering for Innovation Medicine, Innovation Biomedicine Section, University of Verona, Verona, Italy
- Center for Research on Epilepsy in Pediatric Age (CREP), University Hospital of Verona, Verona, Italy
| | - Stefania Bigoni
- Medical Genetics Unit, Ferrara University Hospital, Ferrara, Italy
| | - Giorgia Mancano
- Neuroscience and Human Genetics Department, Meyer Children's Hospital IRCCS (full member of the European Reference Network EpiCARE), Florence, Italy
| | - Simona Pellacani
- Neuroscience and Human Genetics Department, Meyer Children's Hospital IRCCS (full member of the European Reference Network EpiCARE), Florence, Italy
- University of Florence, Florence, Italy
| | - Vincenzo Leuzzi
- Unit of Child Neurology and Psychiatry, Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
| | - Nila Volpi
- Neurology and Clinical Neurophysiology Unit, Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy
| | - Francesco Mari
- Child and Adolescent Epilepsy and Clinical Neurophysiology Departmental Unit, USL Centro Toscana, Prato, Italy
| | - Federico Melani
- Neuroscience and Human Genetics Department, Meyer Children's Hospital IRCCS (full member of the European Reference Network EpiCARE), Florence, Italy
| | - Mara Cavallin
- Neuroscience and Human Genetics Department, Meyer Children's Hospital IRCCS (full member of the European Reference Network EpiCARE), Florence, Italy
| | - Tiziana Pisano
- Neuroscience and Human Genetics Department, Meyer Children's Hospital IRCCS (full member of the European Reference Network EpiCARE), Florence, Italy
| | - Giulio Porcedda
- Department of Paediatric Cardiology, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Augusto Vaglio
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Davide Mei
- Neuroscience and Human Genetics Department, Meyer Children's Hospital IRCCS (full member of the European Reference Network EpiCARE), Florence, Italy
| | - Carmen Barba
- Neuroscience and Human Genetics Department, Meyer Children's Hospital IRCCS (full member of the European Reference Network EpiCARE), Florence, Italy
- University of Florence, Florence, Italy
| | - Elena Parrini
- Neuroscience and Human Genetics Department, Meyer Children's Hospital IRCCS (full member of the European Reference Network EpiCARE), Florence, Italy
| | - Renzo Guerrini
- Neuroscience and Human Genetics Department, Meyer Children's Hospital IRCCS (full member of the European Reference Network EpiCARE), Florence, Italy
- University of Florence, Florence, Italy
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6
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Elfatih A, Saad C, Mifsud B, Mbarek H. Analysis of 14,392 whole genomes reveals 3.5% of Qataris carry medically actionable variants. Eur J Hum Genet 2024:10.1038/s41431-024-01656-1. [PMID: 39020067 DOI: 10.1038/s41431-024-01656-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 06/05/2024] [Accepted: 06/19/2024] [Indexed: 07/19/2024] Open
Abstract
Arabic populations are underrepresented in large genome projects; therefore, the frequency of clinically actionable variants among Arabs is largely unknown. Here, we investigated genetic variation in 14,392 whole genomes from the Qatar Genome Program (QGP) across the list of 78 actionable genes (v3.1) determined by the American College of Medical Genetics and Genomics (ACMG). Variants were categorized into one of the following groups: (1) Pathogenic (P), (2) Likely pathogenic (LP), and (3) Rare variants of uncertain significance with evidence of pathogenicity. For the classification, we used variant databases, effect predictors, and the disease-relevant phenotypes available for the cohort. Data on cardiovascular disease, cancer, and hypercholesterolemia allowed us to assess the disease-relevant phenotype association of rare missense variants. We identified 248 distinct variants in 50 ACMG genes that fulfilled our criteria to be included in one of the three groups affecting 1036 genotype-positive participants of the QGP cohort. The most frequent variants were in TTN, followed by RYR1 and ATP7B. The prevalence of reportable secondary findings was 3.5%. A further 46 heterozygous variants in six genes with an autosomal recessive mode of inheritance were detected in 200 individuals, accounting for an additional 1.4%. Altogether, they affect 5% of the population. Due to the high consanguinity rate in the QGP cohort (28% in spouses and 60% in parents), P and LP variants both in genes with dominant and recessive inheritance are important for developing better treatment options and preventive strategies in Qatar and the Arabic population of the Middle East.
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Affiliation(s)
- Amal Elfatih
- Hamad Bin Khalifa University, College of Health and Life Science, Genomics and Precision Medicine, Doha, Qatar
| | - Chadi Saad
- Qatar Genome Program, Qatar Foundation, Qatar Science and Technology Park, Innovation Center, Doha, Qatar
| | - Borbala Mifsud
- Hamad Bin Khalifa University, College of Health and Life Science, Genomics and Precision Medicine, Doha, Qatar.
- William Harvey Research Institute, Queen Mary University London, London, UK.
| | - Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation, Qatar Science and Technology Park, Innovation Center, Doha, Qatar.
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Agha Gholizadeh M, Behjati F, Ghasemi Firouzabadi S, Heidari E, Razmara E, Almadani N, Sharifi Zarchi A, Garshasbi M. Novel splicing variant and gonadal mosaicism in DYRK1A gene identified by whole-genome sequencing in multiplex autism spectrum disorder families. Neurogenetics 2024:10.1007/s10048-024-00768-6. [PMID: 38976082 DOI: 10.1007/s10048-024-00768-6] [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: 05/15/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with considerable genetic heterogeneity. The disorder is clinically diagnosed based on DSM-5 criteria, featuring deficits in social communication and interaction, along with restricted and repetitive behaviours. Here, we performed whole-genome sequencing (WGS) on four individuals with ASD from two multiplex families (MPX), where more than one individual is affected, to identify potential single nucleotide variants (SNVs) and structural variants (SVs) in coding and non-coding regions. A rigorous bioinformatics pipeline was employed for variant detection, followed by segregation analysis. Our investigation revealed an unreported splicing variant in the DYRK1A gene (c.-77 + 2T > C; IVS1 + 2T > C; NM_001396.5), in heterozygote form in two affected children in one of the families (family B), which was absent in the healthy parents and siblings. This finding suggests the presence of gonadal mosaicism in one of the parents, representing the first documented instance of such inheritance for a variant in the DYRK1A gene associated with ASD. Furthermore, we identified a 50 bp deletion in intron 9 of the DLG2 gene in two affected patients from the same family, confirmed by PCR and Sanger sequencing. In Family A, we identified potential candidate variants associated with ASD shared by the two patients. These findings enhance our understanding of the genetic landscape of ASD, particularly in MPX families, and highlight the utility of WGS in uncovering novel genetic contributions to neurodevelopmental disorders.
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Affiliation(s)
- Mehdi Agha Gholizadeh
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Jalah-Al Ahmad Hwy, Tehran, 14117-1316, Iran
| | - Farkhondeh Behjati
- Genetics Research Centre, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Erfan Heidari
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Jalah-Al Ahmad Hwy, Tehran, 14117-1316, Iran
| | - Ehsan Razmara
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Jalah-Al Ahmad Hwy, Tehran, 14117-1316, Iran
| | - Navid Almadani
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Ali Sharifi Zarchi
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Jalah-Al Ahmad Hwy, Tehran, 14117-1316, Iran.
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8
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Zaka A, Yousaf M, Shahzad S, Rao HZ, Foo JN, Siddiqi S. Structural and functional insights into a novel homozygous missense pathogenic variant in CUL7 identified in consanguineous Pakistani family. J Biomol Struct Dyn 2024; 42:5092-5103. [PMID: 37345548 DOI: 10.1080/07391102.2023.2224889] [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: 01/04/2023] [Accepted: 06/08/2023] [Indexed: 06/23/2023]
Abstract
3M syndrome is a rare genetic familial disorder characterized by short stature, growth retardation, facial dysmorphism, skeletal abnormalities, fleshy protruding heels, and normal intelligence, caused by mutations in the CUL7, OBSL1 and CCDC8 genes. In the present study, a novel homozygous missense variant of CUL7 (NP_001161842.1, c.4493T > C, p.L1498P) has been identified in a consanguineous Pakistani family by whole exome sequencing. In silico structural evaluation, molecular docking and simulation studies of mutant CUL7 provides substantial evidence about its crucial role in the progression of discussed ailment. The newly discovered variant significantly altered the protein's three dimensional structure, leading to abnormal interaction with binding proteins. This computational and experimental investigation provides useful information to drug developers for the synthesis of novel therapeutics against the discussed ailment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ayesha Zaka
- Genomics Research Lab, Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan
| | - Maha Yousaf
- Genomics Research Lab, Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Shaheen Shahzad
- Genomics Research Lab, Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Hadi Zahid Rao
- Department of Oral & Maxillofacial Surgery, Bahria University Medical and Dental College Karachi, Pakistan
| | - Jia Nee Foo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Saima Siddiqi
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan
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9
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Bazgir A, Agha Gholizadeh M, Kahani SM, Tavasoli AR, Garshasbi M. Identification of a Novel Homozygous GLS Gene Variant Associated with Developmental and Epileptic Encephalopathy (DEE) Type 71. Neurogenetics 2024; 25:225-232. [PMID: 38622440 DOI: 10.1007/s10048-024-00753-z] [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: 01/30/2024] [Accepted: 03/06/2024] [Indexed: 04/17/2024]
Abstract
Developmental and epileptic encephalopathy (DEEs) (OMIM#618,328) is characterized by seizures, hypotonia, and brain abnormalities, often arising from mutations in genes crucial for brain function. Among these genes, GLS stands out due to its vital role in the central nervous system (CNS), with homozygous variants potentially causing DEE type 71. Using Whole Exome Sequencing (WES) on a patient exhibiting symptoms of epileptic encephalopathy, we identified a novel homozygous variant, NM_014905.5:c.1849G > T; p.(Asp617Tyr), in the GLS gene. The 5-year-old patient, born to consanguineous parents, presented with developmental delay, encephalopathy, frequent seizures, and hypotonia. Sanger sequencing further validated the GLS gene variant in both the patient and his family. Furthermore, our bioinformatics analysis indicated that this missense variant could lead to alteration of splicing, resulting in the activation of a cryptic donor site and potentially causing loss of protein function. Our finding highlights the pathogenic significance of the GLS gene, particularly in the context of brain disorders, specifically DEE71.
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Affiliation(s)
- Afsaneh Bazgir
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
- PardisGene Company, Tehran, Iran
| | - Mehdi Agha Gholizadeh
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
- PardisGene Company, Tehran, Iran
| | - Seyyed Mohammad Kahani
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
- PardisGene Company, Tehran, Iran
| | - Ali Reza Tavasoli
- Division of Pediatric Neurology, Myelin Disorders Clinic, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Neurology Division, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
- Department of Medical Genetics, DeNA Laboratory, Tehran, Iran.
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Yuan X, Zhang S, Shang H, Tang Y. A novel mutation in SORD gene associated with distal hereditary motor neuropathies. BMC Med Genomics 2024; 17:169. [PMID: 38915017 PMCID: PMC11194961 DOI: 10.1186/s12920-024-01940-5] [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: 09/26/2023] [Accepted: 06/18/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND Distal hereditary motor neuropathy (dHMN) is a heterogeneous group of hereditary diseases caused by the gradual degeneration of the lower motor neuron. More than 30 genes associated with dHMN have been reported, while 70-80% of those with the condition are still unable to receive a genetic diagnosis. METHODS A 26-year-old man experiencing gradual weakness in his lower limbs was referred to our hospital, and data on clinical features, laboratory tests, and electrophysiological tests were collected. To identify the disease-causing mutation, we conducted whole exome sequencing (WES) and then validated it through Sanger sequencing for the proband and his parents. Silico analysis was performed to predict the pathogenesis of the identified mutations. A literature review of all reported mutations of the related gene for the disease was performed. RESULTS The patient presented with dHMN phenotype harboring a novel homozygous variant c.361G > C (p.Ala121Pro) in SORD, inherited from his parents, respectively. A121 is a highly conserved site and the mutation was categorized as "likely pathogenic" according to the criteria and guidelines of the American College of Medical Genetics and Genomics (ACMG). A total of 13 published articles including 101 patients reported 18 SORD variants. Almost all described cases have the homozygous deletion variant c.757delG (p.A253Qfs*27) or compound heterozygous state of a combination of c.757delG (p.A253Qfs*27) with another variant. The variant c.361G > C (p.Ala121Pro) detected in our patient was the second homozygous variant in SORD-associated hereditary neuropathy. CONCLUSION One novel homozygous variant c.361G > C (p.Ala121Pro) in SORD was identified in a Chinese patient with dHMN phenotype, which expands the mutation spectrum of SORD-associated hereditary neuropathy and underscores the significance of screening for SORD variants in patients with undiagnosed hereditary neuropathy patients.
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Affiliation(s)
- Xiaoqin Yuan
- Department of Neurology, School of Medicine, Mianyang Central Hospital, University of Electronic Science and Technology of China, Mianyang, Sichuan, 621000, China
| | - Shanshan Zhang
- Department of Neurology, School of Medicine, Mianyang Central Hospital, University of Electronic Science and Technology of China, Mianyang, Sichuan, 621000, China
| | - Huifang Shang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Yufeng Tang
- Department of Neurology, School of Medicine, Mianyang Central Hospital, University of Electronic Science and Technology of China, Mianyang, Sichuan, 621000, China.
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11
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Chen R, Zhang Z, Ma J, Liu B, Huang Z, Hu G, Huang J, Xu Y, Wang GZ. Circadian-driven tissue specificity is constrained under caloric restricted feeding conditions. Commun Biol 2024; 7:752. [PMID: 38902439 PMCID: PMC11190204 DOI: 10.1038/s42003-024-06421-0] [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: 09/01/2023] [Accepted: 06/06/2024] [Indexed: 06/22/2024] Open
Abstract
Tissue specificity is a fundamental property of an organ that affects numerous biological processes, including aging and longevity, and is regulated by the circadian clock. However, the distinction between circadian-affected tissue specificity and other tissue specificities remains poorly understood. Here, using multi-omics data on circadian rhythms in mice, we discovered that approximately 35% of tissue-specific genes are directly affected by circadian regulation. These circadian-affected tissue-specific genes have higher expression levels and are associated with metabolism in hepatocytes. They also exhibit specific features in long-reads sequencing data. Notably, these genes are associated with aging and longevity at both the gene level and at the network module level. The expression of these genes oscillates in response to caloric restricted feeding regimens, which have been demonstrated to promote longevity. In addition, aging and longevity genes are disrupted in various circadian disorders. Our study indicates that the modulation of circadian-affected tissue specificity is essential for understanding the circadian mechanisms that regulate aging and longevity at the genomic level.
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Affiliation(s)
- Renrui Chen
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ziang Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Junjie Ma
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Bing Liu
- Collaborative Innovation Center for Brain Science, Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhengyun Huang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Su Genomic Resource Center, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Ganlu Hu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Ju Huang
- Collaborative Innovation Center for Brain Science, Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ying Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Su Genomic Resource Center, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Guang-Zhong Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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12
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Kraemer D, Terumalai D, Famiglietti ML, Filges I, Joset P, Koller S, Maurer F, Meier S, Nouspikel T, Sanz J, Zweier C, Abramowicz M, Berger W, Cichon S, Schaller A, Superti-Furga A, Barbié V, Rauch A. SwissGenVar: A Platform for Clinical-Grade Interpretation of Genetic Variants to Foster Personalized Healthcare in Switzerland. J Pers Med 2024; 14:648. [PMID: 38929869 PMCID: PMC11204794 DOI: 10.3390/jpm14060648] [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: 04/04/2024] [Revised: 05/28/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Large-scale next-generation sequencing (NGS) germline testing is technically feasible today, but variant interpretation represents a major bottleneck in analysis workflows. This includes extensive variant prioritization, annotation, and time-consuming evidence curation. The scale of the interpretation problem is massive, and variants of uncertain significance (VUSs) are a challenge to personalized medicine. This challenge is further compounded by the complexity and heterogeneity of the standards used to describe genetic variants and the associated phenotypes when searching for relevant information to support clinical decision making. To address this, all five Swiss academic institutions for Medical Genetics joined forces with the Swiss Institute of Bioinformatics (SIB) to create SwissGenVar as a user-friendly nationwide repository and sharing platform for genetic variant data generated during routine diagnostic procedures and research sequencing projects. Its aim is to provide a protected environment for expert evidence sharing about individual variants to harmonize and upscale their significance interpretation at the clinical grade according to international standards. To corroborate the clinical assessment, the variant-related data will be combined with consented high-quality clinical information. Broader visibility will be achieved by interfacing with international databases, thus supporting global initiatives in personalized healthcare.
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Affiliation(s)
- Dennis Kraemer
- Institute of Medical Genetics (IMG), University of Zurich (UZH), Wagistrasse 12, CH-8952 Zurich, Switzerland;
| | - Dillenn Terumalai
- Swiss Institute of Bioinformatics (SIB), Clinical Bioinformatics, CH-1202 Geneva, Switzerland; (D.T.); (V.B.)
| | | | - Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, CH-4031 Basel, Switzerland; (I.F.); (P.J.); (S.M.); (S.C.)
| | - Pascal Joset
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, CH-4031 Basel, Switzerland; (I.F.); (P.J.); (S.M.); (S.C.)
| | - Samuel Koller
- Institute of Medical Molecular Genetics (IMMG), University of Zurich (UZH), Wagistrasse 12, CH-8952 Zurich, Switzerland; (S.K.); (W.B.)
| | - Fabienne Maurer
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), CH-1011 Lausanne, Switzerland; (F.M.); (A.S.-F.)
| | - Stéphanie Meier
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, CH-4031 Basel, Switzerland; (I.F.); (P.J.); (S.M.); (S.C.)
| | - Thierry Nouspikel
- Genetic Medicine Division, Diagnostics Department/Center for Genomic Medicine, Geneva University Hospitals (HUG), 1206 Geneva, Switzerland; (T.N.); (M.A.)
| | - Javier Sanz
- Department of Human Genetics, Inselspital, Bern University Hospital, CH-3010 Bern, Switzerland; (J.S.); (C.Z.); (A.S.)
| | - Christiane Zweier
- Department of Human Genetics, Inselspital, Bern University Hospital, CH-3010 Bern, Switzerland; (J.S.); (C.Z.); (A.S.)
| | - Marc Abramowicz
- Genetic Medicine Division, Diagnostics Department/Center for Genomic Medicine, Geneva University Hospitals (HUG), 1206 Geneva, Switzerland; (T.N.); (M.A.)
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics (IMMG), University of Zurich (UZH), Wagistrasse 12, CH-8952 Zurich, Switzerland; (S.K.); (W.B.)
- Neuroscience Center Zurich (ZNZ), University and ETH Zurich, CH-8057 Zurich, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, CH-8057 Zurich, Switzerland
| | - Sven Cichon
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, CH-4031 Basel, Switzerland; (I.F.); (P.J.); (S.M.); (S.C.)
| | - André Schaller
- Department of Human Genetics, Inselspital, Bern University Hospital, CH-3010 Bern, Switzerland; (J.S.); (C.Z.); (A.S.)
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), CH-1011 Lausanne, Switzerland; (F.M.); (A.S.-F.)
| | - Valérie Barbié
- Swiss Institute of Bioinformatics (SIB), Clinical Bioinformatics, CH-1202 Geneva, Switzerland; (D.T.); (V.B.)
| | - Anita Rauch
- Institute of Medical Genetics (IMG), University of Zurich (UZH), Wagistrasse 12, CH-8952 Zurich, Switzerland;
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13
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Elaraby NM, Ahmed HA, Dawoud H, Ashaat NA, Azmy A, Galal ER, Elhusseny Y, Awady HE, Metwally AM, Ashaat EA. Clinical and molecular characterization of myotonia congenita using whole-exome sequencing in Egyptian patients. Mol Biol Rep 2024; 51:766. [PMID: 38877370 DOI: 10.1007/s11033-024-09646-8] [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: 03/28/2024] [Accepted: 05/16/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND Myotonia Congenita (MC) is a rare disease classified into two major forms; Thomsen and Becker disease caused by mutations in the CLCN1 gene, which affects muscle excitability and encodes voltage-gated chloride channels (CLC-1). While, there are no data regarding the clinical and molecular characterization of myotonia in Egyptian patients. METHODS Herein, we report seven Egyptian MC patients from six unrelated families. Following the clinical diagnosis, whole-exome sequencing (WES) was performed for genetic diagnosis. Various in silico prediction tools were utilized to interpret variant pathogenicity. The candidate variants were then validated using Sanger sequencing technique. RESULTS In total, seven cases were recruited. The ages at the examination were ranged from eight months to nineteen years. Clinical manifestations included warm-up phenomenon, hand grip, and percussion myotonia. Electromyography was performed in all patients and revealed myotonic discharges. Molecular genetic analysis revealed five different variants. Of them, we identified two novel variants in the CLCN1 gene ( c.1583G > C; p.Gly528Ala and c.2203_2216del;p.Thr735ValfsTer57) and three known variants in the CLCN1 and SCN4A gene. According to in silico tools, the identified novel variants were predicted to have deleterious effects. CONCLUSIONS As the first study to apply WES among Egyptian MC patients, our findings reported two novel heterozygous variants that expand the CLCN1 mutational spectrum for MC diagnosis. These results further confirm that genetic testing is essential for early diagnosis of MC, which affects follow-up treatment and prognostic assessment in clinical practice.
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Affiliation(s)
- Nesma M Elaraby
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Dokki, Cairo, Egypt.
| | - Hoda A Ahmed
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Dokki, Cairo, Egypt
| | - Heba Dawoud
- Pediatric Department, Tanta University, Gharbia, Egypt
| | - Neveen A Ashaat
- Professor of Human Genetics, Ain Shams University, Cairo, Egypt
| | - Ashraf Azmy
- Child Health Department, Medical Research and Clinical Studies Institute, National Research Centre, Dokki, Cairo, Egypt
| | - Eman Reda Galal
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Yasmine Elhusseny
- Lecturer of Medical Biochemistry and Molecular Biology, School of Medicine, Newgiza University, Giza, Egypt
| | - Heba El Awady
- Pediatric Department, Fayoum University Hospitals, Fayoum, Egypt
| | - Ammal M Metwally
- Community Medicine Research Department/Medical Research, Clinical Studies Institute/National Research Centre (Affiliation ID: 60014618), Dokki, Cairo, Egypt
| | - Engy A Ashaat
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
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14
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Richards T, Wilson P, Goggolidou P. Next generation sequencing identifies WNT signalling as a significant pathway in Autosomal Recessive Polycystic Kidney Disease (ARPKD) manifestation and may be linked to disease severity. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167309. [PMID: 38885798 DOI: 10.1016/j.bbadis.2024.167309] [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: 12/19/2023] [Revised: 05/28/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024]
Abstract
INTRODUCTION Autosomal Recessive Polycystic Kidney Disease (ARPKD) is a rare paediatric disease primarily caused by sequence variants in PKHD1. ARPKD presents with considerable clinical variability relating to the type of PKHD1 sequence variant, but not its position. Animal models of Polycystic Kidney Disease (PKD) suggest a complex genetic landscape, with genetic modifiers as a potential cause of disease variability. METHODS To investigate in an unbiased manner the molecular mechanisms of ARPKD and identify potential indicators of disease severity, Whole Exome Sequencing (WES) and RNA-Sequencing (RNA-Seq) were employed on human ARPKD kidneys and age-matched healthy controls. RESULTS WES confirmed the clinical diagnosis of ARPKD in our patient cohort consisting of ten ARPKD kidneys. Sequence variant type, nor position of PKHD1 sequence variants, was linked to disease severity. Sequence variants in genes associated with other ciliopathies were detected in the ARPKD cohort, but only PKD1 could be linked to disease severity. Transcriptomic analysis on a subset of four ARPKD kidneys representing severe and moderate ARPKD, identified a significant number of genes relating to WNT signalling, cellular metabolism and development. Increased expression of WNT signalling-related genes was validated by RT-qPCR in severe and moderate ARPKD kidneys. Two individuals in our cohort with the same PKHD1 sequence variants but different rates of kidney disease progression, with displayed transcriptomic differences in the expression of WNT signalling genes. CONCLUSION ARPKD kidney transcriptomics highlights changes in WNT signalling as potentially significant in ARPKD manifestation and severity, providing indicators for slowing down the progression of ARPKD.
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Affiliation(s)
- Taylor Richards
- School of Biomedical Science and Physiology, Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK
| | - Patricia Wilson
- Centre for Nephrology, UCL Medical School, Royal Free Campus, Rowland Hill, London NW3 2PF, UK
| | - Paraskevi Goggolidou
- School of Biomedical Science and Physiology, Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK.
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15
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Maggi J, Koller S, Feil S, Bachmann-Gagescu R, Gerth-Kahlert C, Berger W. Limited Added Diagnostic Value of Whole Genome Sequencing in Genetic Testing of Inherited Retinal Diseases in a Swiss Patient Cohort. Int J Mol Sci 2024; 25:6540. [PMID: 38928247 PMCID: PMC11203445 DOI: 10.3390/ijms25126540] [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: 05/06/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
The purpose of this study was to assess the added diagnostic value of whole genome sequencing (WGS) for patients with inherited retinal diseases (IRDs) who remained undiagnosed after whole exome sequencing (WES). WGS was performed for index patients in 66 families. The datasets were analyzed according to GATK's guidelines. Additionally, DeepVariant was complemented by GATK's workflow, and a novel structural variant pipeline was developed. Overall, a molecular diagnosis was established in 19/66 (28.8%) index patients. Pathogenic deletions and one deep-intronic variant contributed to the diagnostic yield in 4/19 and 1/19 index patients, respectively. The remaining diagnoses (14/19) were attributed to exonic variants that were missed during WES analysis due to bioinformatic limitations, newly described loci, or unclear pathogenicity. The added diagnostic value of WGS equals 5/66 (9.6%) for our cohort, which is comparable to previous studies. This figure would decrease further to 1/66 (1.5%) with a standardized and reliable copy number variant workflow during WES analysis. Given the higher costs and limited added value, the implementation of WGS as a first-tier assay for inherited eye disorders in a diagnostic laboratory remains untimely. Instead, progress in bioinformatic tools and communication between diagnostic and clinical teams have the potential to ameliorate diagnostic yields.
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Affiliation(s)
- Jordi Maggi
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (S.F.)
| | - Samuel Koller
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (S.F.)
| | - Silke Feil
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (S.F.)
| | | | - Christina Gerth-Kahlert
- Department of Ophthalmology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland;
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (S.F.)
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland
- Neuroscience Center Zurich (ZNZ), University and ETH Zurich, 8057 Zurich, Switzerland
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16
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Zhen XM, Twigg SM, Wu T, Tabet E, McGill MJ, Constantino M, Mallawaarachchi A, Luo C, Thillainadesan S, Rahman Y, Wong J. Diabetic ketoacidosis in an adult with beta-ketothiolase deficiency (BKD) involving a novel ACAT1 variant : first report of established diabetes in BKD and a review of the literature. Clin Diabetes Endocrinol 2024; 10:17. [PMID: 38853254 PMCID: PMC11163784 DOI: 10.1186/s40842-024-00174-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 02/02/2024] [Indexed: 06/11/2024] Open
Abstract
BACKGROUND Diabetes presenting in young adults is often challenging to classify. Diabetic ketoacidosis is typically seen in autoimmune type 1 diabetes mellitus and more rarely in young onset type 2 diabetes mellitus. Beta-ketothiolase deficiency (BKD) is a rare autosomal recessive condition affecting isoleucine catabolism and ketone body metabolism. BKD typically manifests in childhood as recurrent episodes of ketoacidosis, the frequency of which tends to reduce with age. There is a paucity of data with respect to the co-existence of persistent dysglycemia with BKD. CASE PRESENTATION AND LITERATURE REVIEW We present a novel case of diabetes presenting as diabetic ketoacidosis in a 34-year-old man with BKD, with genetically confirmed compound heterozygosity for variants in ACAT1, including a novel ACAT1 c.481T>C, p.(Tyr161His) variant. Diabetes in people with BKD presents unique diagnostic and management challenges. To further contextualize our findings, we conducted a comprehensive narrative review of the existing literature with respect to dysglycemia in those with BKD, especially in adulthood. There are no existing reports describing diabetes in adults with BKD. Stress hyperglycemia is not uncommon when children with BKD are acutely unwell, with several pediatric case reports describing short-lived hyperglycemia but normal HbA1c measurements during metabolic crises (indicating the absence of persistent hyperglycemia). CONCLUSIONS This is the first report of diabetic ketoacidosis in an adult with BKD, with an elevated HbA1c consistent with persistent hyperglycemia. This case highlights the importance of checking HbA1c in people with BKD and hyperglycemia in order to uncover potential coexisting diabetes, facilitating timely management and preventing complications. Increased reporting on the longitudinal outcomes of those with rare metabolic disorders is essential for identifying potential associations with conditions like diabetes.
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Affiliation(s)
- Xi May Zhen
- Department of Endocrinology, Royal Prince Alfred Hospital, Sydney, NSW, Australia.
- Diabetes Centre, Royal Prince Alfred Hospital, Sydney, NSW, Australia.
- Sydney Medical School (Central), Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.
- Department of Endocrinology, Blacktown Hospital, Sydney, NSW, Australia.
- School of Medicine, Western Sydney University, Sydney, NSW, Australia.
| | - Stephen M Twigg
- Department of Endocrinology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- Diabetes Centre, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- Sydney Medical School (Central), Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Ted Wu
- Department of Endocrinology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- Diabetes Centre, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Eddy Tabet
- Department of Endocrinology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- Diabetes Centre, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- Sydney Medical School (Central), Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Margaret J McGill
- Department of Endocrinology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- Diabetes Centre, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- Sydney Medical School (Central), Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Maria Constantino
- Department of Endocrinology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- Diabetes Centre, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Amali Mallawaarachchi
- Clinical Genetics Service, Institute of Precision Medicine and Bioinformatics, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Connie Luo
- Department of Endocrinology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- Diabetes Centre, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | | | - Yusof Rahman
- Department of Genetic Medicine and ICPMR Chemical Pathology, Westmead Hospital, Sydney, NSW, Australia
| | - Jencia Wong
- Department of Endocrinology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- Diabetes Centre, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- Sydney Medical School (Central), Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
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17
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Maloney KA, Mizerik E, King RH, McGinnis EM, Perkowitz S, Diamonstein CJ, Schmanski AA, Saliganan S, Shipper AG, Udler MS, Guan Y, Pollin TI. Genetic counseling in diabetes mellitus: A practice resource of the National Society of Genetic Counselors. J Genet Couns 2024; 33:493-505. [PMID: 37537905 DOI: 10.1002/jgc4.1744] [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: 03/29/2022] [Revised: 05/30/2023] [Accepted: 06/16/2023] [Indexed: 08/05/2023]
Abstract
Diabetes mellitus is a group of diseases characterized by hyperglycemia and its consequences, affecting over 34 million individuals in the United States and 422 million worldwide. While most diabetes is polygenic and is classified as type 1 (T1D), type 2 (T2D), or gestational diabetes (GDM), at least 0.4% of all diabetes is monogenic in nature. Correct diagnosis of monogenic diabetes has important implications for glycemic management and genetic counseling. We provide this Practice Resource to familiarize the genetic counseling community with (1) the existence of monogenic diabetes, (2) how it differs from more common polygenic/complex diabetes types, (3) the advantage of a correct diagnosis, and (4) guidance for identifying, counseling, and testing patients and families with suspected monogenic diabetes. This document is intended for genetic counselors and other healthcare professionals providing clinical services in any setting, with the goal of maximizing the likelihood of a correct diagnosis of monogenic diabetes and access to related care.
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Affiliation(s)
- Kristin A Maloney
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | - Robin H King
- Genetic Services, Everly Health, Austin, Texas, USA
| | - Erin M McGinnis
- Ann & Robert H. Lurie Children's Hospital, Chicago, Illinois, USA
| | | | | | - Andrew A Schmanski
- University of Arizona Cancer Center, Banner University Medicine, Tucson, Arizona, USA
| | | | - Andrea G Shipper
- Charles Library, Temple University, Philadelphia, Pennsylvania, USA
| | - Miriam S Udler
- Diabetes Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Yue Guan
- Emory University, Atlanta, Georgia, USA
| | - Toni I Pollin
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
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Du N, Wang X, Wang Z, Liu H, Liu H, Duan H, Zhao S, Banerjee S, Zhang X. Identification of a Novel Homozygous Mutation in MTMR2 Gene Causes Very Rare Charcot-Marie-Tooth Disease Type 4B1. Appl Clin Genet 2024; 17:71-84. [PMID: 38835974 PMCID: PMC11149649 DOI: 10.2147/tacg.s448084] [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: 11/26/2023] [Accepted: 05/01/2024] [Indexed: 06/06/2024] Open
Abstract
Background Charcot-Marie-Tooth disease (CMT) is a heterogeneous group of disorders involving peripheral nervous system. Charcot-Marie-Tooth disease 4B1 (CMT4B1) is a rare subtype of CMT. CMT4B1 is an axonal demyelinating polyneuropathy with an autosomal recessive mode of inheritance. Patients with CMT4B1 usually manifested with dysfunction of the motor and sensory systems which leads to gradual and progressive muscular weakness and atrophy, starting from the peroneal muscles and finally affecting the distal muscles. Germline mutations in MTMR2 gene causes CMT4B1. Material and Methods In this study, we investigated a 4-year-old Chinese boy with gradual and progressive weakness and atrophy of both proximal and distal muscles. The proband's parents did not show any abnormalities. Whole-exome sequencing and Sanger sequencing were performed. Results Whole-exome sequencing identified a novel homozygous nonsense mutation (c.118A>T; p.Lys40*) in exon 2 of MTMR2 gene in the proband. This novel mutation leads to the formation of a truncated MTMR2 protein of 39 amino acids instead of the wild- type MTMR2 protein of 643 amino acids. This mutation is predicted to cause the complete loss of the PH-GRAM domain, phosphatase domain, coiled-coil domain, and PDZ-binding motif of the MTMR2 protein. Sanger sequencing revealed that the proband's parents carried the mutation in a heterozygous state. This mutation was absent in 100 healthy control individuals. Conclusion This study reports the first mutation in MTMR2 associated with CMT4B1 in a Chinese population. Our study also showed the importance of whole-exome sequencing in identifying candidate genes and disease-causing variants in patients with CMT4B1.
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Affiliation(s)
- Nan Du
- Department of Medical Genetics, Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an, Shaanxi, 710004, People's Republic of China
| | - Xiaolei Wang
- Department of Medical Genetics, Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an, Shaanxi, 710004, People's Republic of China
| | - Zhaohui Wang
- Center for Children Health Care, Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an, Shaanxi, 710004, People's Republic of China
| | - Hongwei Liu
- Department of Medical Genetics, Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an, Shaanxi, 710004, People's Republic of China
| | - Hui Liu
- Department of Medical Genetics, Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an, Shaanxi, 710004, People's Republic of China
| | - Hongfang Duan
- Department of Medical Genetics, Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an, Shaanxi, 710004, People's Republic of China
| | - Shaozhi Zhao
- Department of Medical Genetics, Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an, Shaanxi, 710004, People's Republic of China
| | - Santasree Banerjee
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, 130021, People's Republic of China
| | - Xinwen Zhang
- Department of Medical Genetics, Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an, Shaanxi, 710004, People's Republic of China
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Sevim-Wunderlich S, Dang T, Rossius J, Schnütgen F, Kühn R. A Mouse Model of X-Linked Chronic Granulomatous Disease for the Development of CRISPR/Cas9 Gene Therapy. Genes (Basel) 2024; 15:706. [PMID: 38927642 PMCID: PMC11203339 DOI: 10.3390/genes15060706] [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: 05/07/2024] [Revised: 05/23/2024] [Accepted: 05/25/2024] [Indexed: 06/28/2024] Open
Abstract
Chronic granulomatous disease (CGD) is an inherited immunodeficiency disease mainly caused by mutations in the X-linked CYBB gene that abrogate reactive oxygen species (ROS) production in phagocytes and microbial defense. Gene repair using the CRISPR/Cas9 system in hematopoietic stem and progenitor cells (HSPCs) is a promising technology for therapy for CGD. To support the establishment of efficient and safe gene therapies for CGD, we generated a mouse model harboring a patient-derived mutation in the CYBB gene. Our CybbC517del mouse line shows the hallmarks of CGD and provides a source for Cybb-deficient HSPCs that can be used to evaluate gene-therapy approaches in vitro and in vivo. In a setup using Cas9 RNPs and an AAV repair vector in HSPCs, we show that the mutation can be repaired in 19% of treated cells and that treatment restores ROS production by macrophages. In conclusion, our CybbC517del mouse line provides a new platform for refining and evaluating novel gene therapies and studying X-CGD pathophysiology.
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Affiliation(s)
- Seren Sevim-Wunderlich
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (S.S.-W.); (T.D.); (J.R.)
| | - Tu Dang
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (S.S.-W.); (T.D.); (J.R.)
| | - Jana Rossius
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (S.S.-W.); (T.D.); (J.R.)
| | - Frank Schnütgen
- Department of Medicine, Hematology/Oncology, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany;
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Frankfurt Cancer Institute, Goethe-University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Ralf Kühn
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (S.S.-W.); (T.D.); (J.R.)
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20
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Martínez-Romero MC, Hernández-Contreras ME, Bafalliu-Vidal JA, Barreda-Sánchez M, Martínez-Menchón T, Cabello-Chaves V, Guillén-Navarro E. HELIX Syndrome, a Claudinopathy with Relevant Dermatological Manifestations: Report of Two New Cases. Genes (Basel) 2024; 15:687. [PMID: 38927623 PMCID: PMC11202757 DOI: 10.3390/genes15060687] [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: 04/17/2024] [Revised: 05/16/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
HELIX syndrome (Hypohidrosis-Electrolyte disturbances-hypoLacrimia-Ichthyosis-Xerostomia) (MIM#617671) (ORPHA:528105), described in 2017, is due to an abnormal claudin 10 b protein, secondary to pathogenic CLDN10 variants. So far, only ten families have been described. We aim to describe the phenotype in the first Spanish family identified, highlight the skin anomalies as an important clue, and expand the genotypic spectrum. Two adult brothers from consanguineous parents with suspected ectodermal dysplasia (ED) since early childhood were re-evaluated. A comprehensive phenotypic exam and an aCGH + SNP4 × 180 K microarray followed by Sanger sequencing of the CLDN10 gene were performed. They presented hypohidrosis, xerosis, mild ichthyosis, plantar keratosis, palm hyperlinearity, alacrima, and xerostomia. In adulthood, they also developed a salt-losing nephropathy with hypokalemia and hypermagnesemia. The molecular study in both patients revealed a novel pathogenic homozygous deletion of 8 nucleotides in exon 2 of the CLDN10 gene [CLDN10 (NM_0006984.4): c.322_329delGGCTCCGA, p.Gly108fs*] leading to a premature truncation of the protein. Both parents were heterozygous carriers. Hypohidrosis, ichthyosis, and plantar keratosis associated with alacrima and xerostomia should raise suspicion for HELIX syndrome, which also includes nephropathy and electrolyte disturbances in adults. Given the potential for ED misdiagnosis in infancy, it is important to include the CLDN10 gene in a specific genodermatosis next-generation sequencing (NGS) panel to provide early diagnosis, accurate management, and genetic counseling.
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Affiliation(s)
- María Carmen Martínez-Romero
- Molecular Genetics Section, Biochemistry and Clinical Genetics Center, University Clinical Hospital Virgen de la Arrixaca, 30120 Murcia, Spain; (M.C.M.-R.); (J.A.B.-V.)
- Pediatric Research, Murcian Institute for Biosanitary Research (IMIB) Pascual Parrilla, 30120 Murcia, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Carlos III Health Institute, 28029 Madrid, Spain
- Faculty of Medicine, UCAM Catholic University of Murcia, 30109 Murcia, Spain
| | | | - Juan Antonio Bafalliu-Vidal
- Molecular Genetics Section, Biochemistry and Clinical Genetics Center, University Clinical Hospital Virgen de la Arrixaca, 30120 Murcia, Spain; (M.C.M.-R.); (J.A.B.-V.)
| | - María Barreda-Sánchez
- Pediatric Research, Murcian Institute for Biosanitary Research (IMIB) Pascual Parrilla, 30120 Murcia, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Carlos III Health Institute, 28029 Madrid, Spain
- Faculty of Medicine, UCAM Catholic University of Murcia, 30109 Murcia, Spain
| | - Teresa Martínez-Menchón
- Dermatology Department, University Clinical Hospital Virgen de la Arrixaca, 30120 Murcia, Spain;
| | | | - Encarna Guillén-Navarro
- Pediatric Research, Murcian Institute for Biosanitary Research (IMIB) Pascual Parrilla, 30120 Murcia, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Carlos III Health Institute, 28029 Madrid, Spain
- Pediatrics Department, University Clinical Hospital Virgen de la Arrixaca, 30120 Murcia, Spain
- Surgery, Pediatrics, Obstetrics and Gynecology Department, University of Murcia (UMU), 30120 Murcia, Spain
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21
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Merkuryeva ES, Markova TV, Kenis VM, Agranovich OE, Dan IM, Kotalevskaya YY, Shchagina OA, Ryzhkova OP, Fomenko SS, Dadali EL, Kutsev SI. Presentation of Rare Phenotypes Associated with the FKBP10 Gene. Genes (Basel) 2024; 15:674. [PMID: 38927610 PMCID: PMC11202786 DOI: 10.3390/genes15060674] [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: 04/22/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 06/28/2024] Open
Abstract
Pathogenic variants in the FKBP10 gene lead to a spectrum of rare autosomal recessive phenotypes, including osteogenesis imperfecta (OI) Type XI, Bruck syndrome Type I (BS I), and the congenital arthrogryposis-like phenotype (AG), each with variable clinical manifestations that are crucial for diagnosis. This study analyzed the clinical-genetic characteristics of patients with these conditions, focusing on both known and newly identified FKBP10 variants. We examined data from 15 patients, presenting symptoms of OI and joint contractures. Diagnostic methods included genealogical analysis, clinical assessments, radiography, whole exome sequencing, and direct automated Sanger sequencing. We diagnosed 15 patients with phenotypes due to biallelic FKBP10 variants-4 with OI Type XI, 10 with BS I, and 1 with the AG-like phenotype-demonstrating polymorphism in disease severity. Ten pathogenic FKBP10 variants were identified, including three novel ones, c.1373C>T (p.Pro458Leu), c.21del (p.Pro7fs), and c.831_832insCG (p.Gly278Argfs), and a recurrent variant, c.831dup (p.Gly278Argfs). Variant c.1490G>A (p.Trp497Ter) was found in two unrelated patients, causing OI XI in one and BS I in the other. Additionally, two unrelated patients with BS I and epidermolysis bullosa shared identical homozygous FKBP10 and KRT14 variants. This observation illustrates the diversity of FKBP10-related pathology and the importance of considering the full spectrum of phenotypes in clinical diagnostics.
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Affiliation(s)
| | | | - Vladimir M. Kenis
- The Turner Scientific Research Institute for Children’s Orthopedics, 196603 Saint Petersburg, Russia
| | - Olga E. Agranovich
- The Turner Scientific Research Institute for Children’s Orthopedics, 196603 Saint Petersburg, Russia
| | - Ivan M. Dan
- The National Medical Research Center of Traumatology and Orthopedics Named after N.N. Priorov, 127299 Moscow, Russia
| | - Yulia Y. Kotalevskaya
- Vladimirsky Moscow Regional Research and Clinical Institute, 61/2, Schepkina St., 129110 Moscow, Russia
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 10, St. Ushaika River Embankment, 634050 Tomsk, Russia
- Charitable Foundation «BELA. Butterfly Children», Building 3, Room 1, Furmanny Lane, 105062 Moscow, Russia
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22
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Yavas Abalı Z, Guran T. Diagnosis and management of non-CAH 46,XX disorders/differences in sex development. Front Endocrinol (Lausanne) 2024; 15:1354759. [PMID: 38812815 PMCID: PMC11134272 DOI: 10.3389/fendo.2024.1354759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/01/2024] [Indexed: 05/31/2024] Open
Abstract
Prenatal-onset androgen excess leads to abnormal sexual development in 46,XX individuals. This androgen excess can be caused endogenously by the adrenals or gonads or by exposure to exogenous androgens. The most common cause of 46,XX disorders/differences in sex development (DSD) is congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency, comprising >90% of 46,XX DSD cases. Deficiencies of 11β-hydroxylase, 3β-hydroxysteroid dehydrogenase, and P450-oxidoreductase (POR) are rare types of CAH, resulting in 46,XX DSD. In all CAH forms, patients have normal ovarian development. The molecular genetic causes of 46,XX DSD, besides CAH, are uncommon. These etiologies include primary glucocorticoid resistance (PGCR) and aromatase deficiency with normal ovarian development. Additionally, 46,XX gonads can differentiate into testes, causing 46,XX testicular (T) DSD or a coexistence of ovarian and testicular tissue, defined as 46,XX ovotesticular (OT)-DSD. PGCR is caused by inactivating variants in NR3C1, resulting in glucocorticoid insensitivity and the signs of mineralocorticoid and androgen excess. Pathogenic variants in the CYP19A1 gene lead to aromatase deficiency, causing androgen excess. Many genes are involved in the mechanisms of gonadal development, and genes associated with 46,XX T/OT-DSD include translocations of the SRY; copy number variants in NR2F2, NR0B1, SOX3, SOX9, SOX10, and FGF9, and sequence variants in NR5A1, NR2F2, RSPO1, SOX9, WNT2B, WNT4, and WT1. Progress in cytogenetic and molecular genetic techniques has significantly improved our understanding of the etiology of non-CAH 46,XX DSD. Nonetheless, uncertainties about gonadal function and gender outcomes may make the management of these conditions challenging. This review explores the intricate landscape of diagnosing and managing these conditions, shedding light on the unique aspects that distinguish them from other types of DSD.
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Affiliation(s)
| | - Tulay Guran
- Department of Pediatric Endocrinology and Diabetes, School of Medicine, Marmara University, Istanbul, Türkiye
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23
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Luppino G, Wasniewska M, Coco R, Pepe G, Morabito LA, Li Pomi A, Corica D, Aversa T. Role of NR5A1 Gene Mutations in Disorders of Sex Development: Molecular and Clinical Features. Curr Issues Mol Biol 2024; 46:4519-4532. [PMID: 38785542 PMCID: PMC11119465 DOI: 10.3390/cimb46050274] [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: 03/30/2024] [Revised: 05/04/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Disorders/differences of sex development (DSDs) are defined as broad, heterogenous groups of congenital conditions characterized by atypical development of genetic, gonadal, or phenotypic sex accompanied by abnormal development of internal and/or external genitalia. NR5A1 gene mutation is one of the principal genetic alterations implicated in causing DSD. This review outlines the role of NR5A1 gene during the process of gonadal development in humans, provides an overview of the molecular and functional characteristics of NR5A1 gene, and discusses potential clinical phenotypes and additional organ diseases due to NR5A1 mutations. NR5A1 mutations were analyzed in patients with 46,XY DSD and 46,XX DSD both during the neonatal and pubertal periods. Loss of function of the NR5A1 gene causes several different phenotypes, including some associated with disease in additional organs. Clinical phenotypes may vary, even among patients carrying the same NR5A1 variant, indicating that there is no specific genotype-phenotype correlation. Genetic tests are crucial diagnostic tools that should be used early in the diagnostic pathway, as early as the neonatal period, when gonadal dysgenesis is the main manifestation of NR5A1 mutation. NR5A1 gene mutations could be mainly associated with amenorrhea, ovarian failure, hypogonadism, and infertility during puberty. Fertility preservation techniques should be considered as early as possible.
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Affiliation(s)
- Giovanni Luppino
- Department of Human Pathology of Adulthood and Childhood, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy; (R.C.); (G.P.); (A.L.P.); (D.C.); (T.A.)
| | - Malgorzata Wasniewska
- Department of Human Pathology of Adulthood and Childhood, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy; (R.C.); (G.P.); (A.L.P.); (D.C.); (T.A.)
- Pediatric Unit, AOU Policlinico G. Martino, Via Consolare Valeria 1, 98125 Messina, Italy;
| | - Roberto Coco
- Department of Human Pathology of Adulthood and Childhood, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy; (R.C.); (G.P.); (A.L.P.); (D.C.); (T.A.)
| | - Giorgia Pepe
- Department of Human Pathology of Adulthood and Childhood, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy; (R.C.); (G.P.); (A.L.P.); (D.C.); (T.A.)
- Pediatric Unit, AOU Policlinico G. Martino, Via Consolare Valeria 1, 98125 Messina, Italy;
| | - Letteria Anna Morabito
- Pediatric Unit, AOU Policlinico G. Martino, Via Consolare Valeria 1, 98125 Messina, Italy;
| | - Alessandra Li Pomi
- Department of Human Pathology of Adulthood and Childhood, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy; (R.C.); (G.P.); (A.L.P.); (D.C.); (T.A.)
| | - Domenico Corica
- Department of Human Pathology of Adulthood and Childhood, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy; (R.C.); (G.P.); (A.L.P.); (D.C.); (T.A.)
- Pediatric Unit, AOU Policlinico G. Martino, Via Consolare Valeria 1, 98125 Messina, Italy;
| | - Tommaso Aversa
- Department of Human Pathology of Adulthood and Childhood, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy; (R.C.); (G.P.); (A.L.P.); (D.C.); (T.A.)
- Pediatric Unit, AOU Policlinico G. Martino, Via Consolare Valeria 1, 98125 Messina, Italy;
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24
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Yin X, Richardson M, Laner A, Shi X, Ognedal E, Vasta V, Hansen TVO, Pineda M, Ritter D, den Dunnen JT, Hassanin E, Lyman Lin W, Borras E, Krahn K, Nordling M, Martins A, Mahmood K, Nadeau EAW, Beshay V, Tops C, Genuardi M, Pesaran T, Frayling IM, Capellá G, Latchford A, Tavtigian SV, Maj C, Plon SE, Greenblatt MS, Macrae FA, Spier I, Aretz S. Systematic large-scale application of ClinGen InSiGHT APC -specific ACMG/AMP variant classification criteria substantially alleviates the burden of variants of uncertain significance in ClinVar and LOVD databases. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.03.24306761. [PMID: 38746299 PMCID: PMC11092726 DOI: 10.1101/2024.05.03.24306761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background Pathogenic constitutional APC variants underlie familial adenomatous polyposis, the most common hereditary gastrointestinal polyposis syndrome. To improve variant classification and resolve the interpretative challenges of variants of uncertain significance (VUS), APC-specific ACMG/AMP variant classification criteria were developed by the ClinGen-InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP). Methods A streamlined algorithm using the APC -specific criteria was developed and applied to assess all APC variants in ClinVar and the InSiGHT international reference APC LOVD variant database. Results A total of 10,228 unique APC variants were analysed. Among the ClinVar and LOVD variants with an initial classification of (Likely) Benign or (Likely) Pathogenic, 94% and 96% remained in their original categories, respectively. In contrast, 41% ClinVar and 61% LOVD VUS were reclassified into clinically actionable classes, the vast majority as (Likely) Benign. The total number of VUS was reduced by 37%. In 21 out of 36 (58%) promising APC variants that remained VUS despite evidence for pathogenicity, a data mining-driven work-up allowed their reclassification as (Likely) Pathogenic. Conclusions The application of APC -specific criteria substantially reduced the number of VUS in ClinVar and LOVD. The study also demonstrated the feasibility of a systematic approach to variant classification in large datasets, which might serve as a generalisable model for other gene-/disease-specific variant interpretation initiatives. It also allowed for the prioritization of VUS that will benefit from in-depth evidence collection. This subset of APC variants was approved by the VCEP and made publicly available through ClinVar and LOVD for widespread clinical use.
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25
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Granhøj J, Nøhr TK, Hinrichs GR, Rasmussen M, Svenningsen P. Reverse Phenotypes of Patients with Genetically Confirmed Liddle Syndrome. Clin J Am Soc Nephrol 2024; 19:610-619. [PMID: 38265765 PMCID: PMC11108250 DOI: 10.2215/cjn.0000000000000430] [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: 10/17/2023] [Accepted: 01/19/2024] [Indexed: 01/25/2024]
Abstract
BACKGROUND Liddle syndrome was initially characterized by hypertension, hypokalemia, metabolic alkalosis, and suppressed plasma renin and aldosterone, resulting from gain-of-function variants in the epithelial Na + channel (ENaC). Efficient treatment with ENaC inhibitors is available, but the phenotypic spectrum of genetically confirmed Liddle syndrome is unknown, and some patients may remain undiagnosed and at risk of inefficient treatment. In this study, we used a reverse phenotyping approach to investigate the Liddle syndrome phenotypic spectrum and genotype-phenotype correlations. METHODS Pubmed, Embase, Scopus, and the Human Gene Mutation Database were searched for articles reporting Liddle syndrome variants. The genetic variants were systematically classified to identify patients with genetically confirmed Liddle syndrome. We identified 62 articles describing 45 unique variants within 86 Liddle syndrome families, and phenotypic data were pooled for 268 patients with confirmed Liddle syndrome. RESULTS The Liddle syndrome variants localized to exon 13 of SCNN1B and SCNN1G , disrupting the PPPxY motif critical for downregulating ENaC activity. Hypertension sensitive to ENaC inhibition was present in 97% of adults carrying Liddle syndrome variants while hypokalemia, metabolic alkalosis, and plasma renin and aldosterone suppression showed incomplete penetrance. In addition, 95% and 55% of patients had a family history of hypertension or cerebrovascular events, respectively. The genotype had minor phenotypic effects; however, probands compared with relatives showed significant phenotypic discrepancies consistent with selection bias for initial genetic screening. CONCLUSIONS Patients with genetically confirmed Liddle syndrome displayed a phenotypic spectrum, with ENaC-sensitive hypertension and family history of hypertension being the most common features. The phenotype seemed independent of the specific gene or variant type involved.
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Affiliation(s)
- Jeff Granhøj
- Department of Clinical Genetics, Lillebaelt Hospital, University Hospital of Southern Denmark, Vejle, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Thomas K. Nøhr
- Department of Clinical Genetics, Lillebaelt Hospital, University Hospital of Southern Denmark, Vejle, Denmark
| | - Gitte R. Hinrichs
- Department of Molecular Medicine, Cardiovascular and Renal Research, University of Southern Denmark, Odense, Denmark
- Department of Nephrology, Odense University Hospital, Odense, Denmark
| | - Maria Rasmussen
- Department of Clinical Genetics, Lillebaelt Hospital, University Hospital of Southern Denmark, Vejle, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Per Svenningsen
- Department of Molecular Medicine, Cardiovascular and Renal Research, University of Southern Denmark, Odense, Denmark
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26
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Ferrer A, Duffy P, Olson RJ, Meiners MA, Schultz-Rogers L, Macke EL, Safgren S, Morales-Rosado JA, Cousin MA, Oliver GR, Rider D, Williams M, Pichurin PN, Deyle DR, Morava E, Gavrilova RH, Dhamija R, Wierenga KJ, Lanpher BC, Babovic-Vuksanovic D, Kaiwar C, Vitek CR, McAllister TM, Wick MJ, Schimmenti LA, Lazaridis KN, Vairo FPE, Klee EW. Semiautomated approach focused on new genomic information results in time and effort-efficient reannotation of negative exome data. Hum Genet 2024; 143:649-666. [PMID: 38538918 DOI: 10.1007/s00439-024-02664-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 02/25/2024] [Indexed: 05/18/2024]
Abstract
Most rare disease patients (75-50%) undergoing genomic sequencing remain unsolved, often due to lack of information about variants identified. Data review over time can leverage novel information regarding disease-causing variants and genes, increasing this diagnostic yield. However, time and resource constraints have limited reanalysis of genetic data in clinical laboratories setting. We developed RENEW, (REannotation of NEgative WES/WGS) an automated reannotation procedure that uses relevant new information in on-line genomic databases to enable rapid review of genomic findings. We tested RENEW in an unselected cohort of 1066 undiagnosed cases with a broad spectrum of phenotypes from the Mayo Clinic Center for Individualized Medicine using new information in ClinVar, HGMD and OMIM between the date of previous analysis/testing and April of 2022. 5741 variants prioritized by RENEW were rapidly reviewed by variant interpretation specialists. Mean analysis time was approximately 20 s per variant (32 h total time). Reviewed cases were classified as: 879 (93.0%) undiagnosed, 63 (6.6%) putatively diagnosed, and 4 (0.4%) definitively diagnosed. New strategies are needed to enable efficient review of genomic findings in unsolved cases. We report on a fast and practical approach to address this need and improve overall diagnostic success in patient testing through a recurrent reannotation process.
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Affiliation(s)
- Alejandro Ferrer
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Patrick Duffy
- Bioinformatics Systems, Information Technology, Mayo Clinic, Rochester, MN, USA
| | - Rory J Olson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Michael A Meiners
- Bioinformatics Systems, Information Technology, Mayo Clinic, Rochester, MN, USA
| | - Laura Schultz-Rogers
- Department of Pathology and Lab Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Erica L Macke
- The Institute of Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Joel A Morales-Rosado
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gavin R Oliver
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - David Rider
- Bioinformatics Systems, Information Technology, Mayo Clinic, Rochester, MN, USA
| | - Megan Williams
- Bioinformatics Systems, Information Technology, Mayo Clinic, Rochester, MN, USA
| | - Pavel N Pichurin
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - David R Deyle
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eva Morava
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Radhika Dhamija
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Klass J Wierenga
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Carolyn R Vitek
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Myra J Wick
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Lisa A Schimmenti
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
- Departments of Otorhinolaryngology, Head and Neck Surgery, Ophthalmology, and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Konstantinos N Lazaridis
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.
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27
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Saravanan KS, Satish KS, Saraswathy GR, Kuri U, Vastrad SJ, Giri R, Dsouza PL, Kumar AP, Nair G. Innovative target mining stratagems to navigate drug repurposing endeavours. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 205:303-355. [PMID: 38789185 DOI: 10.1016/bs.pmbts.2024.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
The conventional theory linking a single gene with a particular disease and a specific drug contributes to the dwindling success rates of traditional drug discovery. This requires a substantial shift focussing on contemporary drug design or drug repurposing, which entails linking multiple genes to diverse physiological or pathological pathways and drugs. Lately, drug repurposing, the art of discovering new/unlabelled indications for existing drugs or candidates in clinical trials, is gaining attention owing to its success rates. The rate-limiting phase of this strategy lies in target identification, which is generally driven through disease-centric and/or drug-centric approaches. The disease-centric approach is based on exploration of crucial biomolecules such as genes or proteins underlying pathological cascades of the disease of interest. Investigating these pathological interplays aids in the identification of potential drug targets that can be leveraged for novel therapeutic interventions. The drug-centric approach involves various strategies such as exploring the mechanism of adverse drug reactions that can unearth potential targets, as these untoward reactions might be considered desirable therapeutic actions in other disease conditions. Currently, artificial intelligence is an emerging robust tool that can be used to translate the aforementioned intricate biological networks to render interpretable data for extracting precise molecular targets. Integration of multiple approaches, big data analytics, and clinical corroboration are essential for successful target mining. This chapter highlights the contemporary strategies steering target identification and diverse frameworks for drug repurposing. These strategies are illustrated through case studies curated from recent drug repurposing research inclined towards neurodegenerative diseases, cancer, infections, immunological, and cardiovascular disorders.
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Affiliation(s)
- Kamatchi Sundara Saravanan
- Department of Pharmacognosy, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Kshreeraja S Satish
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Ganesan Rajalekshmi Saraswathy
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India.
| | - Ushnaa Kuri
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Soujanya J Vastrad
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Ritesh Giri
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Prizvan Lawrence Dsouza
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Adusumilli Pramod Kumar
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Gouri Nair
- Department of Pharmacology, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
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Ha ZY, Chijiwa C, Lewis S. Clinical and Molecular Characterization of a Novel Homozygous Frameshift Variant in AEBP1-Related Classical-like Ehlers Danlos Syndrome Type 2 with Comparison to Previously Reported Rare Cases. Genes (Basel) 2024; 15:461. [PMID: 38674395 PMCID: PMC11049394 DOI: 10.3390/genes15040461] [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: 03/06/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Recently, an autosomal recessive subtype of connective tissue disorder within the spectrum of Ehlers-Danlos syndrome (EDS), named classical-like EDS type 2 (clEDS2), was identified. clEDS2 is associated with biallelic variants in the adipocyte enhancer binding protein 1 (AEBP1) gene, specifically, affecting its aortic carboxypeptidase-like protein (ACLP) isoform. We described the 15th patient (13th family) diagnosed with clEDS2. This patient presented with notable similarities in phenotype to the documented cases, along with additional characteristics such as significant prematurity and short stature. An EDS sequencing panel-based analysis revealed homozygous AEBP1: NM_001129.5:c.2923del, p.Ala975Profs*22 likely pathogenic variants, and maternally inherited heterozygous COL11A1: NM_001854.4:c.1160A>G, p.Lys387Arg variant of uncertain significance in our patient. Upon comprehensive review of all previously reported clEDS2 patients, our patient exhibited the following overlapping phenotypes, including cutaneous features: hyperextensibility, atrophic scars/delayed wound healing (100%), easy bruising (100%), excessive skin (93%); skeletal features: generalized joint hypermobility (93%), pes planus (93%), dislocation/subluxation (93%); and cardiovascular features (86%). Our patient did not display symptoms of the critical complications reported in a few individuals, including superior mesenteric artery aneurysms and ruptures, aortic root aneurysm/dissection, spontaneous pneumothoraxes, and bowel ruptures. Together, this case expands the genetic and clinical phenotypic spectrum of AEBP1-related clEDS2.
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Affiliation(s)
- Zong Yi Ha
- Department of Medical Genetics, University of British Columbia, C234-4500 Oak Street, Vancouver, BC V6H 3N1, Canada (S.L.)
| | - Chieko Chijiwa
- Department of Medical Genetics, University of British Columbia, C234-4500 Oak Street, Vancouver, BC V6H 3N1, Canada (S.L.)
- The BC Provincial Medical Genetics Program, University of British Columbia, C234-4500 Oak Street, Vancouver, BC V6H 3N1, Canada
| | - Suzanne Lewis
- Department of Medical Genetics, University of British Columbia, C234-4500 Oak Street, Vancouver, BC V6H 3N1, Canada (S.L.)
- The BC Provincial Medical Genetics Program, University of British Columbia, C234-4500 Oak Street, Vancouver, BC V6H 3N1, Canada
- BC Children’s Hospital Research Institute, University of British Columbia, C234-4500 Oak Street, Vancouver, BC V6H 3N1, Canada
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Mudau MM, Dillon B, Smal C, Feben C, Honey E, Carstens N, Krause A. Mutation analysis and clinical profile of South African patients with Neurofibromatosis type 1 (NF1) phenotype. Front Genet 2024; 15:1331278. [PMID: 38596211 PMCID: PMC11002079 DOI: 10.3389/fgene.2024.1331278] [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: 10/31/2023] [Accepted: 03/11/2024] [Indexed: 04/11/2024] Open
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant genetic condition with complete age-dependent penetrance, variable expressivity and a global prevalence of ∼1/3,000. It is characteriszed by numerous café-au-lait macules, skin freckling in the inguinal or axillary regions, Lisch nodules of the iris, optic gliomas, neurofibromas, and tumour predisposition. The diagnostic testing strategy for NF1 includes testing for DNA single nucleotide variants (SNVs), copy number variants (CNVs) as well as RNA analysis for deep intronic and splice variants, which can cumulatively identify the causative variant in 95% of patients. In the present study, NF1 patients were screened using a next-generation sequencing (NGS) assay targeting NF1 exons and intron/exon boundaries for SNV and NF1 multiple ligation-dependent probe amplification (MLPA) analysis for CNV detection. Twenty-six unrelated Southern African patients clinically suspected of having NF1, based on the clinical diagnostic criteria developed by the National Institute of Health (NIH), were included in the current study. A detection rate of 58% (15/26) was obtained, with SNVs identified in 80% (12/15) using a targeted gene panel and NF1 gene deletion in 20% (3/15) identified using MLPA. Ten patients (38%) had no variants identified, although they met NF1 diagnostic criteria. One VUS was identified in this study in a patient that met NF1 diagnostic criteria, however there was no sufficient information to classify variant as pathogenic. The clinical features of Southern African patients with NF1 are similar to that of the known NF1 phenotype, with the exception of a lower frequency of plexiform neurofibromas and a higher frequency of developmental/intellectual disability compared to other cohorts. This is the first clinical and molecular characterisation of a Southern African ancestry NF1 cohort using both next-generation sequencing and MLPA analysis. A significant number of patients remained without a diagnosis following DNA-level testing. The current study offers a potential molecular testing strategy for our low resource environment that could benefit a significant proportion of patients who previously only received a clinical diagnosis without molecular confirmation.
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Affiliation(s)
- Maria Mabyalwa Mudau
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bronwyn Dillon
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Clarice Smal
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Candice Feben
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Engela Honey
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Chandrasekhar A, Mroczkowski HJ, Urraca N, Gross A, Bluske K, Thorpe E, Hagelstrom RT, Schonberg SA, Perry DL, Taft RJ, Kesari A. Genome sequencing detects a balanced pericentric inversion with breakpoints that impact the DMD and upstream region of POU3F4 genes. Am J Med Genet A 2024; 194:e63462. [PMID: 37929330 DOI: 10.1002/ajmg.a.63462] [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: 06/30/2023] [Revised: 09/11/2023] [Accepted: 10/20/2023] [Indexed: 11/07/2023]
Abstract
We describe a family with two maternal half-brothers both of whom presented with muscular dystrophy, autism spectrum disorder, developmental delay, and sensorineural hearing loss. The elder brother had onset of features at ~3 months of age, followed by clinical confirmation of muscular dystrophy at 3 years. Skeletal biopsy staining at 4.7 years showed an absence of dystrophin protein which prompted extensive molecular testing over 4 years that included gene panels, targeted single-gene assays, arrays, and karyotyping, all of which failed to identify a clinically significant variant in the DMD gene. At 10 years of age, clinical whole-genome sequencing (cWGS) was performed, which revealed a novel hemizygous ~50.7 Mb balanced pericentric inversion on chromosome X that disrupts the DMD gene in both siblings, consistent with the muscular dystrophy phenotype. This inversion also impacts the upstream regulatory region of POU3F4, structural rearrangements which are known to cause hearing loss. The unaffected mother is a heterozygous carrier for the pericentric inversion. This finding illustrates the ability of cWGS to detect a wide breadth of disease-causing genomic variations including large genomic rearrangements.
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Affiliation(s)
| | - Henry J Mroczkowski
- Department of Pediatrics, University of Tennessee Health Science Center and Le Bonheur Children's Hospital, Memphis, Tennessee, USA
| | - Nora Urraca
- Department of Pediatrics, University of Tennessee Health Science Center and Le Bonheur Children's Hospital, Memphis, Tennessee, USA
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Sriwattanapong K, Theerapanon T, Khamwachirapitak C, Sae-Ear P, Srijunbarl A, Porntaveetus T, Shotelersuk V. Deep dental phenotyping and a novel FAM20A variant in patients with amelogenesis imperfecta type IG. Oral Dis 2024; 30:537-550. [PMID: 36650945 DOI: 10.1111/odi.14510] [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: 08/09/2022] [Revised: 12/18/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023]
Abstract
OBJECTIVES To identify etiologic variants and perform deep dental phenotyping in patients with amelogenesis imperfecta (AI). METHODS Three patients of two unrelated families were evaluated. Genetic variants were investigated by exome and Sanger sequencing. An unerupted permanent third molar (AI1) from Patient1 and a deciduous first molar (AI2) from Patient2, along with three tooth-type matched controls for each were characterized. RESULTS All three patients harbored biallelic pathogenic variants in FAM20A, indicating AI1G. Of the four identified variants, one, c.1231C > T p.(Arg411Trp), was novel. Patient1 possessed the largest deletion, 7531 bp, ever identified in FAM20A. In addition to hypoplastic enamel, multiple impacted teeth, intrapulpal calcification, pericoronal radiolucencies, malocclusion, and periodontal infections were found in all three patients, gingival hyperplasia in Patient1 and Patient2, and alveolar bone exostosis in Patient3. Surface roughness was increased in AI1 but decreased in AI2. Decreased enamel mineral density, hardness, and elastic modulus were observed in AI1 enamel and dentin and AI2 dentin, along with decreased phosphorus, increased carbon, and increased calcium/phosphorus and carbon/oxygen ratios. Severely collapsed enamel rods and disorganized dentin-enamel junction were observed. CONCLUSIONS We report a novel FAM20A variant and, for the first time, the defective mineral composition and physical/mechanical properties of AI1G teeth.
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Affiliation(s)
- Kanokwan Sriwattanapong
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Thanakorn Theerapanon
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Chompak Khamwachirapitak
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Pannagorn Sae-Ear
- Oral Biology Research Center, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Anucharte Srijunbarl
- Dental Materials R&D Center, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Thantrira Porntaveetus
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
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Mao B, Yang J, Zhao X, Jia X, Shi X, Zhao L, Banerjee S, Zhang L, Ma X. Identification and functional characterization of a novel heterozygous splice‑site mutation in the calpain 3 gene causes rare autosomal dominant limb‑girdle muscular dystrophy. Exp Ther Med 2024; 27:97. [PMID: 38356676 PMCID: PMC10865457 DOI: 10.3892/etm.2024.12385] [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: 08/30/2022] [Accepted: 11/03/2023] [Indexed: 02/16/2024] Open
Abstract
Limb-girdle muscular dystrophies are a group of extremely heterogenous neuromuscular disorders that manifest with gradual and progressive weakness of both proximal and distal muscles. Autosomal dominant limb-girdle muscular dystrophy (LGMDD4) or calpainopathy is a very rare form of myopathy characterized by weakness and atrophy of both proximal and distal muscles with a variable age of onset. LGMDD4 is caused by germline heterozygous mutations of the calpain 3 (CAPN3) gene. Patients with LGMDD4 often show extreme phenotypic heterogeneity; however, most patients present with gait difficulties, increased levels of serum creatine kinase, myalgia and back pain. In the present study, a 16-year-old male patient, clinically diagnosed with LGMDD4, was investigated. The proband had been suffering from weakness and atrophy of both of their proximal and distal muscles, and had difficulty walking and standing independently. The serum creatine kinase levels (4,754 IU/l; normal, 35-232 IU/l) of the patient were markedly elevated. The younger sister and mother of the proband were also clinically diagnosed with LGMDD4, while the father was phenotypically normal. Whole exome sequencing identified a heterozygous novel splice-site (c.2440-1G>A) mutation in intron 23 of the CAPN3 gene in the proband. Sanger sequencing confirmed that this mutation was also present in both the younger sister and mother of the proband, but the father was not a carrier of this mutation. This splice-site (c.2440-1G>A) mutation causes aberrant splicing of CAPN3 mRNA, leading to the skipping of the last exon (exon 24) of CAPN3 mRNA and resulting in the removal of eight amino acids from the C-terminal of domain IV of the CAPN3 protein. Hence, this splice site mutation causes the formation of a truncated CAPN3 protein (p.Trp814*) of 813 amino acids instead of the wild-type CAPN3 protein that consists of 821 amino acids. This mutation causes partial loss of domain IV (PEF domain) in the CAPN3 protein, which is involved in calcium binding and homodimerization; therefore, this is a loss-of-function mutation. Relative expression of the mutated CAPN3 mRNA was reduced in comparison with the wild-type CAPN3 mRNA in the proband, and their younger sister and mother. This mutation was also not present in 100 normal healthy control individuals of the same ethnicity. The present study reported the first case of CAPN3 gene-associated LGMDD4 in the Chinese population.
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Affiliation(s)
- Bin Mao
- The Reproductive Medicine Centre, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Jie Yang
- The Reproductive Medicine Centre, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Xiaodong Zhao
- The Reproductive Medicine Centre, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Xueling Jia
- The Reproductive Medicine Centre, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Xin Shi
- The Reproductive Medicine Centre, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Lihui Zhao
- The Reproductive Medicine Centre, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Santasree Banerjee
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Lili Zhang
- The Reproductive Medicine Centre, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Xiaoling Ma
- The Reproductive Medicine Centre, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
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Preisler B, Pezeshkpoor B, Merzenich A, Ohlenforst S, Rühl H, Ivaškevičius V, Scholz U, Bönigk H, Eberl W, Zieger B, Pavlova A, Oldenburg J. Genetic Landscape of Factor VII Deficiency: Insights from a Comprehensive Analysis of Pathogenic Variants and Their Impact on Coagulation Activity. Int J Mol Sci 2024; 25:2384. [PMID: 38397060 PMCID: PMC10889322 DOI: 10.3390/ijms25042384] [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: 01/10/2024] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Congenital factor VII (FVII) deficiency is a rare genetic bleeding disorder characterized by deficient or reduced activity of coagulation FVII. It is caused by genetic variants in the F7 gene. We aimed to evaluate the rate of detection of pathogenic variants in the F7 gene in a large group of patients with FVII deficiency and investigate the correlations between the F7 genotype and FVII activity (FVII:C). Moreover, the influence of the common genetic variant rs6046: c.1238G>A; p.(Arg413Gln), designated as the M2 allele, on FVII:C was investigated. Genetic analysis of the F7 gene was performed on 704 index patients (IPs) using either direct Sanger- or next-generation sequencing. Genetic variants were detected in 390 IPs, yielding a variant detection rate (VDR) of 55%. Notably, the VDR exhibited a linear decline with increasing FVII:C levels. We identified 124 genetic variants, of which 48 were not previously reported. Overall, the frequency of the M2 allele was considerably higher in patients with mild deficiency (FVII:C > 20 IU/dl). Furthermore, IPs lacking an identified pathogenic variant exhibited a significantly higher prevalence of the M2 allele (69%) compared to IPs with a disease-causing variant (47%). These results strongly support the association of the M2 allele with decreased FVII:C levels. This study shows the utility of FVII:C as a predictive marker for identifying pathogenic variants in patients with FVII deficiency. The M2 allele contributes to the reduction of FVII:C levels, particularly in cases of mild deficiency.
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Affiliation(s)
- Barbara Preisler
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Faculty of Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (S.O.); (H.R.); (V.I.); (A.P.)
| | - Behnaz Pezeshkpoor
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Faculty of Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (S.O.); (H.R.); (V.I.); (A.P.)
| | - Anja Merzenich
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Faculty of Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (S.O.); (H.R.); (V.I.); (A.P.)
| | - Sandra Ohlenforst
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Faculty of Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (S.O.); (H.R.); (V.I.); (A.P.)
| | - Heiko Rühl
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Faculty of Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (S.O.); (H.R.); (V.I.); (A.P.)
| | - Vytautas Ivaškevičius
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Faculty of Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (S.O.); (H.R.); (V.I.); (A.P.)
| | - Ute Scholz
- Center of Hemostasis, MVZ Labor Leipzig, 04289 Leipzig, Germany;
| | - Hagen Bönigk
- MVZ Limbach Magdeburg, Lab Dr. Franke, Bönigk and Colleagues, Center of Coagulation Disorders and Vascular Diseases, 39104 Magdeburg, Germany;
| | - Wolfgang Eberl
- Pediatric Hematology and Oncology, Klinikum Braunschweig, 38118 Braunschweig, Germany;
| | - Barbara Zieger
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center–University of Freiburg, Faculty of Medicine, 79110 Freiburg, Germany;
| | - Anna Pavlova
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Faculty of Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (S.O.); (H.R.); (V.I.); (A.P.)
| | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Faculty of Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (S.O.); (H.R.); (V.I.); (A.P.)
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Ali A, Tabouni M, Kizhakkedath P, Baydoun I, Allam M, John A, Busafared F, Alnuaimi A, Al-Jasmi F, Alblooshi H. Spectrum of genetic variants in bilateral sensorineural hearing loss. Front Genet 2024; 15:1314535. [PMID: 38410152 PMCID: PMC10894970 DOI: 10.3389/fgene.2024.1314535] [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: 10/10/2023] [Accepted: 01/22/2024] [Indexed: 02/28/2024] Open
Abstract
Background: Hearing loss (HL) is an impairment of auditory function with identified genetic forms that can be syndromic (30%) or non-syndromic (70%). HL is genetically heterogeneous, with more than 1,000 variants across 150 causative genes identified to date. The genetic diagnostic rate varies significantly depending on the population being tested. Countries with a considerably high rate of consanguinity provide a unique resource for studying rare forms of recessive HL. In this study, we identified genetic variants associated with bilateral sensorineural HL (SNHL) using whole-exome sequencing (WES) in 11 families residing in the United Arab Emirates (UAE). Results: We established the molecular diagnosis in six probands, with six different pathogenic or likely pathogenic variants in the genes MYO15A, SLC26A4, and GJB2. One novel nonsense variant, MYO15A:p.Tyr1962Ter*, was identified in a homozygous state in one family, which has not been reported in any public database. SLC26A4 and GJB2 were found to be the most frequently associated genes in this study. In addition, six variants of uncertain significance (VUS) were detected in five probands in the genes CDH23, COL11A1, ADGRV1, NLRP3, and GDF6. In total, 12 variants were observed in eight genes. Among these variants, eight missense variants (66.7%), three nonsense variants (25.0%), and one frameshift (8.3%) were identified. The overall diagnostic rate of this study was 54.5%. Approximately 45.5% of the patients in this study came from consanguineous families. Conclusion: Understanding the genetic basis of HL provides insight for the clinical diagnosis of hearing impairment cases through the utilization of next-generation sequencing (NGS). Our findings contribute to the knowledge of the heterogeneous genetic profile of HL, especially in a population with a high rate of consanguineous marriage in the Arab population.
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Affiliation(s)
- Amanat Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mohammed Tabouni
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Praseetha Kizhakkedath
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Ibrahim Baydoun
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mushal Allam
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Anne John
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Faiza Busafared
- Department of Otolaryngology, Al Kuwait Hospital, Dubai, United Arab Emirates
| | - Ayesha Alnuaimi
- Department of Otolaryngology, Al Kuwait Hospital, Dubai, United Arab Emirates
| | - Fatma Al-Jasmi
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- Department of Pediatrics, Tawam Hospital, Al Ain, United Arab Emirates
| | - Hiba Alblooshi
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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Liu J, Ding C, Liu X, Kang Q. Cytoskeletal Protein 4.1R in Health and Diseases. Biomolecules 2024; 14:214. [PMID: 38397451 PMCID: PMC10887211 DOI: 10.3390/biom14020214] [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: 01/09/2024] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
The protein 4.1R is an essential component of the erythrocyte membrane skeleton, serving as a key structural element and contributing to the regulation of the membrane's physical properties, including mechanical stability and deformability, through its interaction with spectrin-actin. Recent research has uncovered additional roles of 4.1R beyond its function as a linker between the plasma membrane and the membrane skeleton. It has been found to play a crucial role in various biological processes, such as cell fate determination, cell cycle regulation, cell proliferation, and cell motility. Additionally, 4.1R has been implicated in cancer, with numerous studies demonstrating its potential as a diagnostic and prognostic biomarker for tumors. In this review, we provide an updated overview of the gene and protein structure of 4.1R, as well as its cellular functions in both physiological and pathological contexts.
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Affiliation(s)
- Jiaojiao Liu
- School of Life Science, Zhengzhou University, Zhengzhou 450001, China
| | - Cong Ding
- Children's Hospital Affiliated of Zhengzhou University, Zhengzhou 450018, China
| | - Xin Liu
- School of Life Science, Zhengzhou University, Zhengzhou 450001, China
| | - Qiaozhen Kang
- School of Life Science, Zhengzhou University, Zhengzhou 450001, China
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Köroğlu M, Karakaplan M, Gündüz E, Kesriklioğlu B, Ergen E, Aslantürk O, Özdemir ZM. Cerebrotendinous Xanthomatosis patients with late diagnosed in single orthopedic clinic: two novel variants in the CYP27A1 gene. Orphanet J Rare Dis 2024; 19:53. [PMID: 38336741 PMCID: PMC10858589 DOI: 10.1186/s13023-024-03082-4] [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: 06/11/2023] [Accepted: 02/05/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Cerebrotendinous Xanthomatosis (CTX) is a rare autosomal recessive lipid storage disorder caused by loss of function variants in the CYP27A1 gene which encodes sterol 27-hydroxylase, on chromosome 2q35. Although the symptoms begin commonly in infancy, CTX diagnosis is often delayed. The aim of this study is to review the orthopedic findings of the disease by providing an overview of the clinical features of the disease. It is to raise awareness of this condition for which early diagnosis and treatment are important. METHODS We retrospectively evaluated the clinical, laboratory, radiological, and genetic findings of eight patients from four families who were admitted to our Orthopedics and Traumatology Department between 2017 and 2022 due to bilateral Achilles tendon xanthomas, were found to have high cholestanol and CYP27A1 gene mutations. RESULTS The mean age of patients was 37, and five of them were male. The mean age at the onset of symptoms was 9.25 years. The mean age of initial diagnosis was 33.75 years. Between symptom onset and clinical diagnosis, an average delay of 24.5 years was observed. All patients had bilateral Achilles tendon xanthoma. Notably, a novel variant (c.670_671delAA) in CYP27A1 gene was identified in three patients who also presented with peripheral neuropathy and bilateral pes cavus. One patient had osteoporosis and four patients had osteopenia. Five patients had a history of bilateral cataracts. Furthermore, three of the patients had early-onset chronic diarrhea and three of the patients had ataxia. Two of the patients had epilepsy and seven of the patients had behavior-personality disorder. All patients had low intelligence, but none of them had cardiac disease. CONCLUSION We present the diagnostic process and clinical features which the largest CTX case series ever reported from single orthopedic clinic. We suggest that patients with normal cholesterol levels presenting with xanthoma being genetically analyzed by testing at their serum cholestanol level, and that all siblings of patients diagnosed with CTX be examined.
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Affiliation(s)
- Muhammed Köroğlu
- Orthopaedics and Traumatology Department, Turgut Özal Medical Center, İnönü University Medical School, Malatya, 44280, Turkey
| | - Mustafa Karakaplan
- Orthopaedics and Traumatology Department, Turgut Özal Medical Center, İnönü University Medical School, Malatya, 44280, Turkey.
| | - Enes Gündüz
- Orthopaedics and Traumatology Department, Şarkışla State Hospital, Sivas, Turkey
| | - Betül Kesriklioğlu
- Department of Medical Genetics, Cerrahpaşa Faculty of Medicine, İstanbul University, Istanbul, Turkey
| | - Emre Ergen
- Orthopaedics and Traumatology Department, Turgut Özal Medical Center, İnönü University Medical School, Malatya, 44280, Turkey
| | - Okan Aslantürk
- Orthopaedics and Traumatology Department, Turgut Özal Medical Center, İnönü University Medical School, Malatya, 44280, Turkey
| | - Zeynep Maraş Özdemir
- Department of Radiology, Turgut Özal Medical Center, İnönü University Medical School, Malatya, Turkey
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Yuan X, Su J, Wang J, Dai B, Sun Y, Zhang K, Li Y, Chuan J, Tang C, Yu Y, Gong Q. Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases. Sci Rep 2024; 14:2845. [PMID: 38310124 PMCID: PMC10838329 DOI: 10.1038/s41598-024-53461-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: 01/31/2024] [Indexed: 02/05/2024] Open
Abstract
Phenotype-guided gene prioritizers have proved a highly efficient approach to identifying causal genes for Mendelian diseases. In our previous study, we preliminarily evaluated the performance of ten prioritizers. However, all the selected software was run based on default settings and singleton mode. With a large-scale family dataset from Deciphering Developmental Disorders (DDD) project (N = 305) and an in-house trio cohort (N = 152), the four optimal performers in our prior study including Exomiser, PhenIX, AMELIE, and LIRCIAL were further assessed through parameter optimization and/or the utilization of trio mode. The in-depth assessment revealed high diagnostic yields of the four prioritizers with refined preferences, each alone or together: (1) 83.3-91.8% of the causal genes were presented among the first ten candidates in the final ranking lists of the four tools; (2) Over 97.7% of the causal genes were successfully captured within the top 50 by either of the four software. Exomiser did best in directly hitting the target (ranking the causal gene at the very top) while LIRICAL displayed a predominant overall detection capability. Besides, cases affected by low-penetrance and high-frequency pathogenic variants were found misjudged during the automated prioritization process. The discovery of the limitations shed light on the specific directions of future enhancement for causal-gene ranking tools.
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Affiliation(s)
- Xiao Yuan
- Changsha Kingmed Center for Clinical Laboratory, Lutian Road 28, Changsha, 410000, Hunan, China
| | - Jieqiong Su
- Changsha Kingmed Center for Clinical Laboratory, Lutian Road 28, Changsha, 410000, Hunan, China
| | - Jing Wang
- Changsha Kingmed Center for Clinical Laboratory, Lutian Road 28, Changsha, 410000, Hunan, China
| | - Bing Dai
- Changsha Kingmed Center for Clinical Laboratory, Lutian Road 28, Changsha, 410000, Hunan, China
| | - Yanfang Sun
- Changsha Kingmed Center for Clinical Laboratory, Lutian Road 28, Changsha, 410000, Hunan, China
| | - Keke Zhang
- Changsha Kingmed Center for Clinical Laboratory, Lutian Road 28, Changsha, 410000, Hunan, China
| | - Yinghua Li
- Guangzhou Kingmed Center for Clinical Laboratory, Guangzhou, Guangdong, China
| | - Jun Chuan
- Genetalks Biotech. Co., Ltd., Changsha, Hunan, China
| | - Chunyan Tang
- Changsha Kingmed Center for Clinical Laboratory, Lutian Road 28, Changsha, 410000, Hunan, China
| | - Yan Yu
- Changsha Kingmed Center for Clinical Laboratory, Lutian Road 28, Changsha, 410000, Hunan, China.
| | - Qiang Gong
- Changsha Kingmed Center for Clinical Laboratory, Lutian Road 28, Changsha, 410000, Hunan, China.
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Ben Issa A, Kamoun F, Bouchaala W, Charfi Triki C, Fakhfakh F. Complex genotypes in family with metachromatic leukodystrophy: Effect of trans and cis mutations distribution on the phenotype variability. Int J Dev Neurosci 2024; 84:35-46. [PMID: 37848385 DOI: 10.1002/jdn.10306] [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: 05/26/2023] [Revised: 09/08/2023] [Accepted: 10/04/2023] [Indexed: 10/19/2023] Open
Abstract
Metachromatic leukodystrophy (MLD) is a severe metabolic disorder caused by the deficient activity of arylsulfatase A due to ARSA gene mutations. According to the age of onset, MLD is classified into three forms: infantile, juvenile, and adult. In our study, we aimed to perform a genetic analysis for two siblings with juvenile MLD for a better characterization of the molecular mechanisms behind the disease. A consanguineous family including two MLD patients (PII.1 and PII.2) was enrolled in our study. The diagnosis was made based on the clinical and neuroimaging investigations. The sequencing of ARSA gene was performed followed by in silico analysis. Besides, the cis/trans distribution of the variants was verified through a PCR-RFLP. The ARSA gene sequencing revealed three known variants, two exonic c.1055A > G and c.1178C > G and an intronic one (c.1524 + 95A > G) in the 3'UTR region. All variants were present at heterozygous state in the two siblings and their mother. The assessment of the cis/trans distribution showed the presence of these variants in cis within the mother, while PII.2 and PII.2 present the c.1055A > G/c.1524 + 95A > G and the c.1178C > G in trans. Additionally, PII.1 harbored a de novo novel missense variant c.1119G > T, whose pathogenicity was supported by our predictive results. Our genetic findings, supported by a clinical examination, confirmed the affection of the mother by the adult MLD. Our results proved the implication of the variable distribution of the found variants in the age of MLD onset. Besides, we described a variable severity between the two siblings due to the de novo pathogenic variant. In conclusion, we identified a complex genotype of ARSA variants within two MLD siblings with a variable severity due to a de novo variant present in one of them. Our results allowed the establishment of an adult MLD diagnosis and highlighted the importance of an assessment of the trans/cis distribution in the cases of complex genotypes.
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Affiliation(s)
- Abir Ben Issa
- Laboratory of Molecular and Functional Genetics, Faculty of Science of Sfax, University of Sfax, Sfax, Tunisia
- Research laboratory "Neuropédiatrie" (LR19ES15), Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Fatma Kamoun
- Research laboratory "Neuropédiatrie" (LR19ES15), Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
- Child Neurology Department, CHU Hedi Chaker, Sfax, Tunisia
- Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Wafa Bouchaala
- Research laboratory "Neuropédiatrie" (LR19ES15), Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
- Child Neurology Department, CHU Hedi Chaker, Sfax, Tunisia
- Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Chahnez Charfi Triki
- Research laboratory "Neuropédiatrie" (LR19ES15), Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
- Child Neurology Department, CHU Hedi Chaker, Sfax, Tunisia
- Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Faiza Fakhfakh
- Laboratory of Molecular and Functional Genetics, Faculty of Science of Sfax, University of Sfax, Sfax, Tunisia
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Daich Varela M, Schiff E, Malka S, Wright G, Mahroo OA, Webster AR, Michaelides M, Arno G. PHYH c.678+5G>T Leads to In-Frame Exon Skipping and Is Associated With Attenuated Refsum Disease. Invest Ophthalmol Vis Sci 2024; 65:38. [PMID: 38411969 PMCID: PMC10910431 DOI: 10.1167/iovs.65.2.38] [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: 11/27/2023] [Accepted: 02/02/2024] [Indexed: 02/28/2024] Open
Abstract
Purpose To investigate the molecular effect of the variant PHYH:c.678+5G>T. This variant has conflicting interpretations in the ClinVar database and a maximum allele frequency of 0.0045 in the South Asian population in gnomAD. Methods We recruited patients from Moorfields Eye Hospital (London, UK) and Buenos Aires, Argentina, who were diagnosed with retinitis pigmentosa and found to have biallelic variants in PHYH, with at least one being c.678+5G>T. Total RNA was purified from PaxGene RNA-stabilized whole-blood samples, followed by reverse transcription to cDNA, PCR amplification of the canonical PHYH transcript, Oxford Nanopore Technologies library preparation, and single-molecule amplicon sequencing. Results Four patients provided a blood sample. One patient had isolated retinitis pigmentosa and three had mild extraocular findings. Blood phytanic acid levels were normal in two patients, mildly elevated in one, and markedly high in the fourth. Retinal evaluation showed an intact ellipsoid zone as well as preserved autofluorescence in the macular region in three of the four patients. In all patients, we observed in-frame skipping of exons 5 and 6 in 31.1% to 88.4% of the amplicons and a smaller proportion (0% to 11.3% of amplicons) skipping exon 6 only. Conclusions We demonstrate a significant effect of PHYH:c.678+5G>T on splicing of the canonical transcript. The in-frame nature of this may be in keeping with a mild presentation and higher prevalence in the general population. These data support the classification of the variant as pathogenic, and patients harboring a biallelic genotype should undergo phytanic acid testing.
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Affiliation(s)
- Malena Daich Varela
- Moorfields Eye Hospital, London, United Kingdom
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | | | | | | | - Omar A. Mahroo
- Moorfields Eye Hospital, London, United Kingdom
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Andrew R. Webster
- Moorfields Eye Hospital, London, United Kingdom
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Michel Michaelides
- Moorfields Eye Hospital, London, United Kingdom
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Gavin Arno
- Moorfields Eye Hospital, London, United Kingdom
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
- Great Ormond Street Hospital for Children, London, United Kingdom
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Cunningham-Rundles C, Casanova JL, Boisson B. Genetics and clinical phenotypes in common variable immunodeficiency. Front Genet 2024; 14:1272912. [PMID: 38274105 PMCID: PMC10808799 DOI: 10.3389/fgene.2023.1272912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/09/2023] [Indexed: 01/27/2024] Open
Abstract
Common variable immunodeficiency (CVID) is one of the most common symptomatic groups of inborn errors of immunity. In addition to infections resulting from insufficient levels of immune globulins and antibodies, many patients develop inflammatory or autoimmune conditions, which are associated with increased mortality. This aspect of CVID has been the focus of many studies, and dissecting the clinical phenotypes of CVID, has had the goal of providing biomarkers to identify these subjects, potentially at the time of diagnosis. With the application of whole exome (WES) and whole genome analyses, an increasing number of monogenic causes of CVID have been elucidated. From the standpoint of the practicing physician, an important question is whether the clinical phenotype, particularly the occurrence of autoinflammation of autoimmunity, might suggest the likelihood of identifying a causative mutation, and if possible the gene most likely to underlie CVID. We addressed this question in a patient group of 405 subjects diagnosed with CVID from one medical center.
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Affiliation(s)
- Charlotte Cunningham-Rundles
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of Clinical Immunology, Departments of Medicine and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, United States
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France
- Paris Cité Université, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, NY, United States
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, United States
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France
- Paris Cité Université, Imagine Institute, Paris, France
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Sas DJ, Mara K, Mehta RA, Seide BM, Banks CJ, Danese DS, McGregor TL, Lieske JC, Milliner DS. Natural history of urine and plasma oxalate in children with primary hyperoxaluria type 1. Pediatr Nephrol 2024; 39:141-148. [PMID: 37458799 PMCID: PMC11044200 DOI: 10.1007/s00467-023-06074-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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/13/2023] [Accepted: 06/22/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND Primary hyperoxaluria type 1 (PH1) is a rare, severe genetic disease causing increased hepatic oxalate production resulting in urinary stone disease, nephrocalcinosis, and often progressive chronic kidney disease. Little is known about the natural history of urine and plasma oxalate values over time in children with PH1. METHODS For this retrospective observational study, we analyzed data from genetically confirmed PH1 patients enrolled in the Rare Kidney Stone Consortium PH Registry between 2003 and 2018 who had at least 2 measurements before age 18 years of urine oxalate-to-creatinine ratio (Uox:cr), 24-h urine oxalate excretion normalized to body surface area (24-h Uox), or plasma oxalate concentration (Pox). We compared values among 3 groups: homozygous G170R, heterozygous G170R, and non-G170R AGXT variants both before and after initiating pyridoxine (B6). RESULTS Of 403 patients with PH1 in the registry, 83 met the inclusion criteria. Uox:cr decreased rapidly over the first 5 years of life. Both before and after B6 initiation, patients with non-G170R had the highest Uox:cr, 24-h Uox, and Pox. Patients with heterozygous G170R had similar Uox:cr to homozygous G170R prior to B6. Patients with homozygous G170R had the lowest 24-h Uox and Uox:cr after B6. Urinary oxalate excretion and Pox tend to decrease over time during childhood. eGFR over time was not different among groups. CONCLUSIONS Children with PH1 under 5 years old have relatively higher urinary oxalate excretion which may put them at greater risk for nephrocalcinosis and kidney failure than older PH1 patients. Those with homozygous G170R variants may have milder disease. A higher resolution version of the Graphical abstract is available as Supplementary information.
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Affiliation(s)
- David J Sas
- Division of Pediatric Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA.
| | - Kristin Mara
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, MN, USA
| | - Ramila A Mehta
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, MN, USA
| | - Barbara M Seide
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Carly J Banks
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | | | | | - John C Lieske
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Dawn S Milliner
- Division of Pediatric Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
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Setia N, del Gaudio D, Kandikatla P, Arndt K, Tjota M, Wang P, Segal J, Alikhan M, Hart J. A novel telomere biology disease-associated gastritis identified through a whole exome sequencing-driven approach. J Pathol Clin Res 2024; 10:e349. [PMID: 37994393 PMCID: PMC10766041 DOI: 10.1002/cjp2.349] [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: 08/08/2023] [Revised: 09/20/2023] [Accepted: 10/19/2023] [Indexed: 11/24/2023]
Abstract
A whole exome sequencing (WES)-driven approach to uncover the etiology of unexplained inflammatory gastritides has been underutilized by surgical pathologists. Here, we discovered the pathobiology of an unusual chronic atrophic gastritis in two unrelated patients using this approach. The gastric biopsies were notable for an unusual pattern of gastritis with persistent dense inflammation, loss of both parietal and neuroendocrine cells in the oxyntic mucosa, and sparing of the antral mucosa. The patients were found to harbor pathogenic variants in telomeropathic genes (POT1 and DCLRE1B). Clonality testing for one of the patients showed evidence of evolving clonality of TCR-gene rearrangement. Both patients showed significantly decreased numbers of stem/progenitor cells by immunohistochemistry, which appears to be responsible for the development of mucosal atrophy. No such cases of unusual chronic atrophic gastritis in the setting of telomeropathy have been previously reported. The loss of stem/progenitor cells suggests that stem/progenitor cell exhaustion in the setting of telomere dysfunction is the likely mechanism for development of this unusual chronic atrophic gastritis. The results underscore the need for close monitoring of these gastric lesions, with special regard to their neoplastic potential. This combined WES-driven approach has promise to identify the cause and mechanism of other uncharacterized gastrointestinal inflammatory disorders.
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Affiliation(s)
- Namrata Setia
- Department of PathologyUniversity of ChicagoChicagoILUSA
| | | | | | - Kelly Arndt
- Department of PathologyUniversity of ChicagoChicagoILUSA
| | - Melissa Tjota
- Department of PathologyUniversity of ChicagoChicagoILUSA
| | - Peng Wang
- Department of PathologyUniversity of ChicagoChicagoILUSA
| | - Jeremy Segal
- Department of PathologyUniversity of ChicagoChicagoILUSA
| | - Mir Alikhan
- NorthShore University Health SystemEvanstonILUSA
| | - John Hart
- Department of PathologyUniversity of ChicagoChicagoILUSA
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Chen S, Francioli LC, Goodrich JK, Collins RL, Kanai M, Wang Q, Alföldi J, Watts NA, Vittal C, Gauthier LD, Poterba T, Wilson MW, Tarasova Y, Phu W, Grant R, Yohannes MT, Koenig Z, Farjoun Y, Banks E, Donnelly S, Gabriel S, Gupta N, Ferriera S, Tolonen C, Novod S, Bergelson L, Roazen D, Ruano-Rubio V, Covarrubias M, Llanwarne C, Petrillo N, Wade G, Jeandet T, Munshi R, Tibbetts K, O'Donnell-Luria A, Solomonson M, Seed C, Martin AR, Talkowski ME, Rehm HL, Daly MJ, Tiao G, Neale BM, MacArthur DG, Karczewski KJ. A genomic mutational constraint map using variation in 76,156 human genomes. Nature 2024; 625:92-100. [PMID: 38057664 DOI: 10.1038/s41586-023-06045-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/03/2023] [Indexed: 12/08/2023]
Abstract
The depletion of disruptive variation caused by purifying natural selection (constraint) has been widely used to investigate protein-coding genes underlying human disorders1-4, but attempts to assess constraint for non-protein-coding regions have proved more difficult. Here we aggregate, process and release a dataset of 76,156 human genomes from the Genome Aggregation Database (gnomAD)-the largest public open-access human genome allele frequency reference dataset-and use it to build a genomic constraint map for the whole genome (genomic non-coding constraint of haploinsufficient variation (Gnocchi)). We present a refined mutational model that incorporates local sequence context and regional genomic features to detect depletions of variation. As expected, the average constraint for protein-coding sequences is stronger than that for non-coding regions. Within the non-coding genome, constrained regions are enriched for known regulatory elements and variants that are implicated in complex human diseases and traits, facilitating the triangulation of biological annotation, disease association and natural selection to non-coding DNA analysis. More constrained regulatory elements tend to regulate more constrained protein-coding genes, which in turn suggests that non-coding constraint can aid the identification of constrained genes that are as yet unrecognized by current gene constraint metrics. We demonstrate that this genome-wide constraint map improves the identification and interpretation of functional human genetic variation.
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Affiliation(s)
- Siwei Chen
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
| | - Laurent C Francioli
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Julia K Goodrich
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan L Collins
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Masahiro Kanai
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Qingbo Wang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Jessica Alföldi
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Nicholas A Watts
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher Vittal
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Laura D Gauthier
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Timothy Poterba
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael W Wilson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Yekaterina Tarasova
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William Phu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Riley Grant
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mary T Yohannes
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zan Koenig
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yossi Farjoun
- Richards Lab, Lady Davis Institute, Montreal, Quebec, Canada
| | - Eric Banks
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Stacey Gabriel
- Broad Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Namrata Gupta
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Broad Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven Ferriera
- Broad Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charlotte Tolonen
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sam Novod
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Louis Bergelson
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Roazen
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Miguel Covarrubias
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nikelle Petrillo
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gordon Wade
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Thibault Jeandet
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ruchi Munshi
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathleen Tibbetts
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Matthew Solomonson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Cotton Seed
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alicia R Martin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael E Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Mark J Daly
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland
| | - Grace Tiao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Benjamin M Neale
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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44
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Kouri C, Sommer G, Martinez de Lapiscina I, Elzenaty RN, Tack LJW, Cools M, Ahmed SF, Flück CE. Clinical and genetic characteristics of a large international cohort of individuals with rare NR5A1/SF-1 variants of sex development. EBioMedicine 2024; 99:104941. [PMID: 38168586 PMCID: PMC10797150 DOI: 10.1016/j.ebiom.2023.104941] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Steroidogenic factor 1 (SF-1/NR5A1) is essential for human sex development. Heterozygous NR5A1/SF-1 variants manifest with a broad range of phenotypes of differences of sex development (DSD), which remain unexplained. METHODS We conducted a retrospective analysis on the so far largest international cohort of individuals with NR5A1/SF-1 variants, identified through the I-DSD registry and a research network. FINDINGS Among 197 individuals with NR5A1/SF-1 variants, we confirmed diverse phenotypes. Over 70% of 46, XY individuals had a severe DSD phenotype, while 90% of 46, XX individuals had female-typical sex development. Close to 100 different novel and known NR5A1/SF-1 variants were identified, without specific hot spots. Additionally, likely disease-associated variants in other genes were reported in 32 individuals out of 128 tested (25%), particularly in those with severe or opposite sex DSD phenotypes. Interestingly, 48% of these variants were found in known DSD or SF-1 interacting genes, but no frequent gene-clusters were identified. Sex registration at birth varied, with <10% undergoing reassignment. Gonadectomy was performed in 30% and genital surgery in 58%. Associated organ anomalies were observed in 27% of individuals with a DSD, mainly concerning the spleen. Intrafamilial phenotypes also varied considerably. INTERPRETATION The observed phenotypic variability in individuals and families with NR5A1/SF-1 variants is large and remains unpredictable. It may often not be solely explained by the monogenic pathogenicity of the NR5A1/SF-1 variants but is likely influenced by additional genetic variants and as-yet-unknown factors. FUNDING Swiss National Science Foundation (320030-197725) and Boveri Foundation Zürich, Switzerland.
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Affiliation(s)
- Chrysanthi Kouri
- Pediatric Endocrinology, Diabetology and Metabolism, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland; Department for BioMedical Research, University of Bern, Bern 3008, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Grit Sommer
- Pediatric Endocrinology, Diabetology and Metabolism, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland; Department for BioMedical Research, University of Bern, Bern 3008, Switzerland; Institute of Social and Preventive Medicine, University of Bern, Switzerland, University of Bern, Bern 3012, Switzerland
| | - Idoia Martinez de Lapiscina
- Pediatric Endocrinology, Diabetology and Metabolism, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland; Department for BioMedical Research, University of Bern, Bern 3008, Switzerland; Research into the Genetics and Control of Diabetes and Other Endocrine Disorders, Biobizkaia Health Research Institute, Cruces University Hospital, Barakaldo 48903, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid 28029, Spain; CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid 28029, Spain; Endo-ERN, Amsterdam 1081 HV, the Netherlands
| | - Rawda Naamneh Elzenaty
- Pediatric Endocrinology, Diabetology and Metabolism, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland; Department for BioMedical Research, University of Bern, Bern 3008, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Lloyd J W Tack
- Department of Paediatric Endocrinology, Department of Paediatrics and Internal Medicine, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Martine Cools
- Department of Paediatric Endocrinology, Department of Paediatrics and Internal Medicine, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - S Faisal Ahmed
- Developmental Endocrinology Research Group, University of Glasgow, Royal Hospital for Sick Children, Glasgow G51 4TF, UK
| | - Christa E Flück
- Pediatric Endocrinology, Diabetology and Metabolism, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland; Department for BioMedical Research, University of Bern, Bern 3008, Switzerland.
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45
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Cui H, Srinivasan S, Gao Z, Korkin D. The Extent of Edgetic Perturbations in the Human Interactome Caused by Population-Specific Mutations. Biomolecules 2023; 14:40. [PMID: 38254640 PMCID: PMC11154503 DOI: 10.3390/biom14010040] [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: 08/11/2023] [Revised: 11/30/2023] [Accepted: 12/03/2023] [Indexed: 01/24/2024] Open
Abstract
Until recently, efforts in population genetics have been focused primarily on people of European ancestry. To attenuate this bias, global population studies, such as the 1000 Genomes Project, have revealed differences in genetic variation across ethnic groups. How many of these differences can be attributed to population-specific traits? To answer this question, the mutation data must be linked with functional outcomes. A new "edgotype" concept has been proposed, which emphasizes the interaction-specific, "edgetic", perturbations caused by mutations in the interacting proteins. In this work, we performed systematic in silico edgetic profiling of ~50,000 non-synonymous SNVs (nsSNVs) from the 1000 Genomes Project by leveraging our semi-supervised learning approach SNP-IN tool on a comprehensive set of over 10,000 protein interaction complexes. We interrogated the functional roles of the variants and their impact on the human interactome and compared the results with the pathogenic variants disrupting PPIs in the same interactome. Our results demonstrated that a considerable number of nsSNVs from healthy populations could rewire the interactome. We also showed that the proteins enriched with interaction-disrupting mutations were associated with diverse functions and had implications in a broad spectrum of diseases. Further analysis indicated that distinct gene edgetic profiles among major populations could shed light on the molecular mechanisms behind the population phenotypic variances. Finally, the network analysis revealed that the disease-associated modules surprisingly harbored a higher density of interaction-disrupting mutations from healthy populations. The variation in the cumulative network damage within these modules could potentially account for the observed disparities in disease susceptibility, which are distinctly specific to certain populations. Our work demonstrates the feasibility of a large-scale in silico edgetic study, and reveals insights into the orchestrated play of population-specific mutations in the human interactome.
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Affiliation(s)
- Hongzhu Cui
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA;
- Chromatography and Mass Spectrometry Division, Thermo Fisher Scientific, San Jose, CA 95134, USA
| | - Suhas Srinivasan
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA;
- Program in Epithelial Biology, Stanford School of Medicine, Stanford, CA 94305, USA
- Center for Personal Dynamic Regulomes, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Ziyang Gao
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA;
| | - Dmitry Korkin
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA;
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA;
- Computer Science Department, Worcester Polytechnic Institute, Worcester, MA 01609, USA
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46
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Murtazina A, Borovikov A, Kuchina A, Ovsova O, Bulakh M, Chukhrova A, Braslavskaya S, Ryzhkova O, Skryabin N, Kutsev S, Dadali E. Expanding the Phenotype of Hereditary Congenital Facial Paresis Type 3. Int J Mol Sci 2023; 25:129. [PMID: 38203298 PMCID: PMC10779017 DOI: 10.3390/ijms25010129] [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: 11/26/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
The HOXB1 gene encodes a homeobox transcription factor pivotal in the development of rhombomere 4. Biallelic pathogenic variants in this gene are associated with congenital facial paresis type 3 (HCFP3). Only seven single nucleotide variants have been reported in the literature to date. Here, we report a 27-year-old female with a unique presentation of HCFP3 with two novel compound-heterozygous missense variants: c.763C>G, p.(Arg255Gly), which arose de novo and an inherited c.781C>T, p.(Arg261Cys) variant. The patient exhibited HCFP3 symptoms with mild upward esodeviation and lacked the documented ear malformations common in HCFP. For many years, she was misdiagnosed with facio-scapulo-humeral muscular dystrophy, due to complaints of shoulder girdle and neck muscle weakness. No alternative genetic or acquired causes of neck and shoulder girdle weakness were found, suggesting its potential inclusion in the phenotypic spectrum.
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Affiliation(s)
- Aysylu Murtazina
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (A.B.); (A.K.); (M.B.); (A.C.); (S.B.); (O.R.); (S.K.); (E.D.)
| | - Artem Borovikov
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (A.B.); (A.K.); (M.B.); (A.C.); (S.B.); (O.R.); (S.K.); (E.D.)
| | - Anna Kuchina
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (A.B.); (A.K.); (M.B.); (A.C.); (S.B.); (O.R.); (S.K.); (E.D.)
| | - Olga Ovsova
- Department of Neurology, Neurosurgery and Medical Genetics, Ural State Medical University, 620028 Ekaterinburg, Russia;
| | - Maria Bulakh
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (A.B.); (A.K.); (M.B.); (A.C.); (S.B.); (O.R.); (S.K.); (E.D.)
| | - Alena Chukhrova
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (A.B.); (A.K.); (M.B.); (A.C.); (S.B.); (O.R.); (S.K.); (E.D.)
| | - Svetlana Braslavskaya
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (A.B.); (A.K.); (M.B.); (A.C.); (S.B.); (O.R.); (S.K.); (E.D.)
| | - Oksana Ryzhkova
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (A.B.); (A.K.); (M.B.); (A.C.); (S.B.); (O.R.); (S.K.); (E.D.)
| | - Nikolay Skryabin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634050 Tomsk, Russia;
| | - Sergey Kutsev
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (A.B.); (A.K.); (M.B.); (A.C.); (S.B.); (O.R.); (S.K.); (E.D.)
| | - Elena Dadali
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (A.B.); (A.K.); (M.B.); (A.C.); (S.B.); (O.R.); (S.K.); (E.D.)
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47
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Maharaj AV. Familial Glucocorticoid Deficiency: the changing landscape of an eponymous syndrome. Front Endocrinol (Lausanne) 2023; 14:1268345. [PMID: 38189052 PMCID: PMC10771341 DOI: 10.3389/fendo.2023.1268345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Familial Glucocorticoid Deficiency encompasses a broad spectrum of monogenic recessive disorders that theoretically solely abrogate cortisol biosynthesis. In reality, delineating clear genotype-phenotype correlations in this disorder is made complicated by marked phenotypic heterogeneity even within kindreds harbouring identical variants. Phenotypes range from isolated glucocorticoid insufficiency to cortisol deficiency plus a variety of superimposed features including salt-wasting and hypoaldosteronism, primary hypothyroidism, hypogonadism and growth defects. Furthermore, mutation type, domain topology and perceived enzyme activity do not always predict disease severity. Given the high burden of disease and implications of a positive diagnosis, genetic testing is crucial in the management of patients warranting detailed delineation of genomic variants including viable functional studies.
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Affiliation(s)
- Avinaash V. Maharaj
- Centre for Endocrinology, William Harvey Research Institute, Queen Mary University of London (QMUL), London, United Kingdom
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48
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Fritze JS, Stiehler FF, Wolfrum U. Pathogenic Variants in USH1G/SANS Alter Protein Interaction with Pre-RNA Processing Factors PRPF6 and PRPF31 of the Spliceosome. Int J Mol Sci 2023; 24:17608. [PMID: 38139438 PMCID: PMC10744108 DOI: 10.3390/ijms242417608] [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: 11/01/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Pre-mRNA splicing is an essential process orchestrated by the spliceosome, a dynamic complex assembled stepwise on pre-mRNA. We have previously identified that USH1G protein SANS regulates pre-mRNA splicing by mediating the intranuclear transfer of the spliceosomal U4/U6.U5 tri-snRNP complex. During this process, SANS interacts with the U4/U6 and U5 snRNP-specific proteins PRPF31 and PRPF6 and regulates splicing, which is disturbed by variants of USH1G/SANS causative for human Usher syndrome (USH), the most common form of hereditary deaf-blindness. Here, we aim to gain further insights into the molecular interaction of the splicing molecules PRPF31 and PRPF6 to the CENTn domain of SANS using fluorescence resonance energy transfer assays in cells and in silico deep learning-based protein structure predictions. This demonstrates that SANS directly binds via two distinct conserved regions of its CENTn to the two PRPFs. In addition, we provide evidence that these interactions occur sequentially and a conformational change of an intrinsically disordered region to a short α-helix of SANS CENTn2 is triggered by the binding of PRPF6. Furthermore, we find that pathogenic variants of USH1G/SANS perturb the binding of SANS to both PRPFs, implying a significance for the USH1G pathophysiology.
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Affiliation(s)
| | | | - Uwe Wolfrum
- Institute of Molecular Physiology, Johannes Gutenberg University Mainz, 55128 Mainz, Germany; (J.S.F.)
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49
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Liu S, Zhong M, Huang Y, Zhang Q, Chen T, Xu X, Peng W, Wang X, Feng X, Kang L, Lu Y, Cheng J, Bu F, Yuan H. Quantitative thresholds for variant enrichment in 13,845 cases: improving pathogenicity classification in genetic hearing loss. Genome Med 2023; 15:116. [PMID: 38111038 PMCID: PMC10726519 DOI: 10.1186/s13073-023-01271-7] [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: 07/21/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND The American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) guidelines recommend using variant enrichment among cases as "strong" evidence for pathogenicity per the PS4 criterion. However, quantitative support for PS4 thresholds from real-world Mendelian case-control cohorts is lacking. METHODS To address this gap, we evaluated and established PS4 thresholds using data from the Chinese Deafness Genetics Consortium. A total of 9,050 variants from 13,845 patients with hearing loss (HL) and 6,570 ancestry-matched controls were analyzed. Positive likelihood ratio and local positive likelihood ratio values were calculated to determine the thresholds corresponding to each strength of evidence across three variant subsets. RESULTS In subset 1, consisting of variants present in both cases and controls with an allele frequency (AF) in cases ≥ 0.0005, an odds ratio (OR) ≥ 6 achieved strong evidence, while OR ≥ 3 represented moderate evidence. For subset 2, which encompassed variants present in both cases and controls with a case AF < 0.0005, and subset 3, comprising variants found only in cases and absent from controls, we defined the PS4_Supporting threshold (OR > 2.27 or allele count ≥ 3) and the PS4_Moderate threshold (allele count ≥ 6), respectively. Reanalysis applying the adjusted PS4 criteria changed the classification of 15 variants and enabled diagnosis of an additional four patients. CONCLUSIONS Our study quantified evidence strength thresholds for variant enrichment in genetic HL cases, highlighting the importance of defining disease/gene-specific thresholds to improve the precision and accuracy of clinical genetic testing.
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Affiliation(s)
- Sihan Liu
- Department of Oto-Rhino-Laryngology, West China Hospital, Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Mingjun Zhong
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Yu Huang
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Qian Zhang
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Ting Chen
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Xiaofei Xu
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Wan Peng
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Xiaolu Wang
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Xiaoshu Feng
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Lu Kang
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Yu Lu
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Jing Cheng
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Fengxiao Bu
- Department of Oto-Rhino-Laryngology, West China Hospital, Sichuan University, Chengdu, 610000, China.
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China.
| | - Huijun Yuan
- Department of Oto-Rhino-Laryngology, West China Hospital, Sichuan University, Chengdu, 610000, China.
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China.
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50
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Hogner S, Lundman E, Strand J, Ytre-Arne ME, Tangeraas T, Stray-Pedersen A. Newborn Genetic Screening-Still a Role for Sanger Sequencing in the Era of NGS. Int J Neonatal Screen 2023; 9:67. [PMID: 38132826 PMCID: PMC10743540 DOI: 10.3390/ijns9040067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/23/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
In the Norwegian newborn screening (NBS) program, genetic testing has been implemented as a second or third tier method for the majority of NBS disorders, significantly increasing positive predictive value (PPV). DNA is extracted from dried blood spot (DBS) filter cards. For monogenic disorders caused by variants in one single gene or a few genes only, Sanger sequencing has been shown to be the most time- and cost-efficient method to use. Here, we present the Sanger sequencing method, including primer sequences and the genetic test algorithms, currently used in the Norwegian newborn screening program.
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Affiliation(s)
- Silje Hogner
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (E.L.); (J.S.); (M.E.Y.-A.); (T.T.); (A.S.-P.)
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