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de Wagenaar NP, van den Bersselaar LM, Odijk HJHM, Stefens SJM, Reinhardt DP, Roos-Hesselink JW, Kanaar R, Verhagen JMA, Brüggenwirth HT, van de Laar IMBH, van der Pluijm I, Essers J. Functional analysis of cell lines derived from SMAD3-related Loeys-Dietz syndrome patients provides insights into genotype-phenotype relation. Hum Mol Genet 2024; 33:1090-1104. [PMID: 38538566 PMCID: PMC11153339 DOI: 10.1093/hmg/ddae044] [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: 02/01/2024] [Revised: 02/23/2024] [Accepted: 03/06/2024] [Indexed: 06/07/2024] Open
Abstract
RATIONALE Pathogenic (P)/likely pathogenic (LP) SMAD3 variants cause Loeys-Dietz syndrome type 3 (LDS3), which is characterized by arterial aneurysms, dissections and tortuosity throughout the vascular system combined with osteoarthritis. OBJECTIVES Investigate the impact of P/LP SMAD3 variants with functional tests on patient-derived fibroblasts and vascular smooth muscle cells (VSMCs), to optimize interpretation of SMAD3 variants. METHODS A retrospective analysis on clinical data from individuals with a P/LP SMAD3 variant and functional analyses on SMAD3 patient-derived VSMCs and SMAD3 patient-derived fibroblasts, differentiated into myofibroblasts. RESULTS Individuals with dominant negative (DN) SMAD3 variant in the MH2 domain exhibited more major events (66.7% vs. 44.0%, P = 0.054), occurring at a younger age compared to those with haploinsufficient (HI) variants. The age at first major event was 35.0 years [IQR 29.0-47.0] in individuals with DN variants in MH2, compared to 46.0 years [IQR 40.0-54.0] in those with HI variants (P = 0.065). Fibroblasts carrying DN SMAD3 variants displayed reduced differentiation potential, contrasting with increased differentiation potential in HI SMAD3 variant fibroblasts. HI SMAD3 variant VSMCs showed elevated SMA expression and altered expression of alternative MYH11 isoforms. DN SMAD3 variant myofibroblasts demonstrated reduced extracellular matrix formation compared to control cell lines. CONCLUSION Distinguishing between P/LP HI and DN SMAD3 variants can be achieved by assessing differentiation potential, and SMA and MYH11 expression. The differences between DN and HI SMAD3 variant fibroblasts and VSMCs potentially contribute to the differences in disease manifestation. Notably, myofibroblast differentiation seems a suitable alternative in vitro test system compared to VSMCs.
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Affiliation(s)
- Nathalie P de Wagenaar
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
- Department of Cardiology and European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Lisa M van den Bersselaar
- Department of Clinical Genetics and European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Hanny J H M Odijk
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Sanne J M Stefens
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Dieter P Reinhardt
- Faculty of Medicine and Health Sciences, McGill University, 3640 University Street, Montreal, QC H3A 0C7, Canada
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, 3640 University Street, Montreal, QC H3A 0C7, Canada
| | - Jolien W Roos-Hesselink
- Department of Cardiology and European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Judith M A Verhagen
- Department of Clinical Genetics and European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Hennie T Brüggenwirth
- Department of Clinical Genetics and European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Ingrid M B H van de Laar
- Department of Clinical Genetics and European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Ingrid van der Pluijm
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
- Department of Vascular Surgery, Cardiovascular Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Jeroen Essers
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
- Department of Vascular Surgery, Cardiovascular Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
- Department of Radiotherapy, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
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George AM, Viswanathan A, Best LG, Monahan C, Limmina M, Ganguly A, Kalish JM. Expanded phenotype and cancer risk in patients with Beckwith-Wiedemann spectrum caused by CDKN1C variants. Am J Med Genet A 2024:e63777. [PMID: 38822599 DOI: 10.1002/ajmg.a.63777] [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: 03/26/2024] [Revised: 05/03/2024] [Accepted: 05/19/2024] [Indexed: 06/03/2024]
Abstract
Beckwith-Wiedemann spectrum (BWSp) is caused by genetic and epigenetic alterations on chromosome 11 that regulate cell growth and division. Considering the diverse phenotypic landscape in BWSp, the characterization of the CDKN1C molecular subtype remains relatively limited. Here, we investigate the role of CDKN1C in the broader BWSp phenotype. Notably, patients with CDKN1C variants appear to exhibit a different tumor risk than other BWSp molecular subtypes. We performed a comprehensive literature review using the search term "CDKN1C Beckwith" to identify 113 cases of patients with molecularly confirmed CDKN1C-BWSp. We then assessed the genotype and phenotype in a novel cohort of patients with CDKN1C-BWSp enrolled in the BWS Research Registry. Cardinal and suggestive features were evaluated for all patients reported, and tumor risk was established based on available reports. The most common phenotypes included macroglossia, omphalocele, and ear creases/pits. Tumor types reported from the literature included neuroblastoma, acute lymphocytic leukemia, superficial spreading melanoma, and intratubular germ cell neoplasia. Overall, this study identifies unique features associated with CDKN1C variants in BWSp, enabling more accurate clinical management. The absence of Wilms tumor and hepatoblastoma suggests that screening for these tumors may not be necessary, while the neuroblastoma risk warrants appropriate screening recommendations.
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Affiliation(s)
- Andrew M George
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Aravind Viswanathan
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lyle G Best
- Department of Pathology, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota, USA
| | - Caitlin Monahan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Maria Limmina
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arupa Ganguly
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jennifer M Kalish
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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3
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Cowan QT, Gu S, Gu W, Ranzau BL, Simonson TS, Komor AC. Development of multiplexed orthogonal base editor (MOBE) systems. Nat Biotechnol 2024:10.1038/s41587-024-02240-0. [PMID: 38773305 DOI: 10.1038/s41587-024-02240-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 04/10/2024] [Indexed: 05/23/2024]
Abstract
Base editors (BEs) enable efficient, programmable installation of point mutations while avoiding the use of double-strand breaks. Simultaneous application of two or more different BEs, such as an adenine BE (which converts A·T base pairs to G·C) and a cytosine BE (which converts C·G base pairs to T·A), is not feasible because guide RNA crosstalk results in non-orthogonal editing, with all BEs modifying all target loci. Here we engineer both adenine BEs and cytosine BEs that can be orthogonally multiplexed by using RNA aptamer-coat protein systems to recruit the DNA-modifying enzymes directly to the guide RNAs. We generate four multiplexed orthogonal BE systems that enable rates of precise co-occurring edits of up to 7.1% in the same DNA strand without enrichment or selection strategies. The addition of a fluorescent enrichment strategy increases co-occurring edit rates up to 24.8% in human cells. These systems are compatible with expanded protospacer adjacent motif and high-fidelity Cas9 variants, function well in multiple cell types, have equivalent or reduced off-target propensities compared with their parental systems and can model disease-relevant point mutation combinations.
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Affiliation(s)
- Quinn T Cowan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Sifeng Gu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Wanjun Gu
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of California San Diego, La Jolla, CA, USA
| | - Brodie L Ranzau
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Tatum S Simonson
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of California San Diego, La Jolla, CA, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
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Stone SI, Balasubramanyam A, Posey JE. Atypical Diabetes: What Have We Learned and What Does the Future Hold? Diabetes Care 2024; 47:770-781. [PMID: 38329838 PMCID: PMC11043229 DOI: 10.2337/dci23-0038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/21/2023] [Indexed: 02/10/2024]
Abstract
As our understanding of the pathophysiology of diabetes evolves, we increasingly recognize that many patients may have a form of diabetes that does not neatly fit with a diagnosis of either type 1 or type 2 diabetes. The discovery and description of these forms of "atypical diabetes" have led to major contributions to our collective understanding of the basic biology that drives insulin secretion, insulin resistance, and islet autoimmunity. These discoveries now pave the way to a better classification of diabetes based on distinct endotypes. In this review, we highlight the key biological and clinical insights that can be gained from studying known forms of atypical diabetes. Additionally, we provide a framework for identification of patients with atypical diabetes based on their clinical, metabolic, and molecular features. Helpful clinical and genetic resources for evaluating patients suspected of having atypical diabetes are provided. Therefore, appreciating the various endotypes associated with atypical diabetes will enhance diagnostic accuracy and facilitate targeted treatment decisions.
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Affiliation(s)
- Stephen I. Stone
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO
| | - Ashok Balasubramanyam
- Division of Diabetes, Endocrinology and Metabolism, Baylor College of Medicine, Houston, TX
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
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5
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Yuan S, Chen Y, Zou L, Lu X, Liu R, Zhang S, Zhang Y, Chen C, Cheng D, Chen L, Sun G. Functional prediction of the potential NGLY1 mutations associated with rare disease CDG. Heliyon 2024; 10:e28787. [PMID: 38628705 PMCID: PMC11016977 DOI: 10.1016/j.heliyon.2024.e28787] [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: 08/01/2023] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
Genetic diseases are currently diagnosed by functional mutations. However, only some mutations are associated with disease. It is necessary to establish a quick prediction model for clinical screening. Pathogenic mutations in NGLY1 cause a rare autosomal recessive disease known as congenital disorder of deglycosylation (NGLY1-CDDG). Although NGLY1-CDDG can be diagnosed through gene sequencing, clinical relevance of a detected mutation in NGLY1 needs to be further confirmed. In this study, taken NGLY1-CDDG as an example, a comprehensive and practical predictive model for pathogenic mutations on NGLY1 through an NGLY1/Glycopeptide complex model was constructed, the binding sites of NGLY1 and glycopeptides were simulated, and an in vitro enzymatic assay system was established to facilitate quick clinical decisions for NGLY1-CDDG patients. The docking model covers 42 % of reported NGLY1-CDDG missense mutations (5/12). All reported mutations were subjected to in vitro enzymatic assay in which 18 mutations were dysfunctional (18/30). In addition, a full spectrum of functional R328 mutations was assayed and 11 mutations were dysfunctional (11/19). In this study, a model of NGLY1 and glycopeptides was built for potential functional mutations in NGLY1. In addition, the effect of potential regulatory compounds, including N-acetyl-l-cysteine and dithiothreitol, on NGLY1 was examined. The established in vitro assay may serve as a standard protocol to facilitate rapid diagnosis of all mutations in NGLY1-CDDG. This method could also be applied as a comprehensive and practical predictive model for the other rare genetic diseases.
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Affiliation(s)
- Shuying Yuan
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Yanwen Chen
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Lin Zou
- Department of Medical Microbiology and Parasitology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Xinrong Lu
- Department of Medical Microbiology and Parasitology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Ruijie Liu
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Shaoxing Zhang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Yuxin Zhang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Cuiying Chen
- Department of Research and Development, SysDiagno Biotech, Nanjing, 211800, Jiangsu Province, China
| | - Dongqing Cheng
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Li Chen
- Department of Medical Microbiology and Parasitology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Guiqin Sun
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
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Mohar NP, Cox EM, Adelizzi E, Moore SA, Mathews KD, Darbro BW, Wallrath LL. The Influence of a Genetic Variant in CCDC78 on LMNA-Associated Skeletal Muscle Disease. Int J Mol Sci 2024; 25:4930. [PMID: 38732148 PMCID: PMC11084688 DOI: 10.3390/ijms25094930] [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: 03/13/2024] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Mutations in the LMNA gene-encoding A-type lamins can cause Limb-Girdle muscular dystrophy Type 1B (LGMD1B). This disease presents with weakness and wasting of the proximal skeletal muscles and has a variable age of onset and disease severity. This variability has been attributed to genetic background differences among individuals; however, such variants have not been well characterized. To identify such variants, we investigated a multigeneration family in which affected individuals are diagnosed with LGMD1B. The primary genetic cause of LGMD1B in this family is a dominant mutation that activates a cryptic splice site, leading to a five-nucleotide deletion in the mature mRNA. This results in a frame shift and a premature stop in translation. Skeletal muscle biopsies from the family members showed dystrophic features of variable severity, with the muscle fibers of some family members possessing cores, regions of sarcomeric disruption, and a paucity of mitochondria, not commonly associated with LGMD1B. Using whole genome sequencing (WGS), we identified 21 DNA sequence variants that segregate with the family members possessing more profound dystrophic features and muscle cores. These include a relatively common variant in coiled-coil domain containing protein 78 (CCDC78). This variant was given priority because another mutation in CCDC78 causes autosomal dominant centronuclear myopathy-4, which causes cores in addition to centrally positioned nuclei. Therefore, we analyzed muscle biopsies from family members and discovered that those with both the LMNA mutation and the CCDC78 variant contain muscle cores that accumulated both CCDC78 and RyR1. Muscle cores containing mislocalized CCDC78 and RyR1 were absent in the less profoundly affected family members possessing only the LMNA mutation. Taken together, our findings suggest that a relatively common variant in CCDC78 can impart profound muscle pathology in combination with a LMNA mutation and accounts for variability in skeletal muscle disease phenotypes.
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Affiliation(s)
- Nathaniel P. Mohar
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA; (N.P.M.); (E.A.)
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Efrem M. Cox
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA (S.A.M.)
- Department of Neurosurgery, UNLV School of Medicine, Las Vegas, NV 89106, USA
| | - Emily Adelizzi
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA; (N.P.M.); (E.A.)
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Steven A. Moore
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA (S.A.M.)
| | - Katherine D. Mathews
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA;
| | - Benjamin W. Darbro
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA; (N.P.M.); (E.A.)
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA;
| | - Lori L. Wallrath
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA; (N.P.M.); (E.A.)
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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Farhat NY, Alexander D, McKee K, Iben J, Rodriguez-Gil JL, Wassif CA, Cawley NX, Balch WE, Porter FD. Sterol O-Acyltransferase 1 ( SOAT1): A Genetic Modifier of Niemann-Pick Disease, Type C1. Int J Mol Sci 2024; 25:4217. [PMID: 38673803 PMCID: PMC11050712 DOI: 10.3390/ijms25084217] [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: 03/20/2024] [Revised: 04/02/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
Niemann-Pick disease type C1 (NPC1) is a lysosomal disorder due to impaired intracellular cholesterol transport out of the endolysosomal compartment.. Marked heterogeneity has been observed in individuals with the same NPC1 genotype, thus suggesting a significant effect of modifier genes. Prior work demonstrated that decreased SOAT1 activity decreased disease severity in an NPC1 mouse model. Thus, we hypothesized that a polymorphism associated with decreased SOAT1 expression might influence the NPC1 phenotype. Phenotyping and genomic sequencing of 117 individuals with NPC1 was performed as part of a Natural History trial. Phenotyping included determination of disease severity and disease burden. Significant clinical heterogeneity is present in individuals homozygous for the NPC1I1061T variant and in siblings. Analysis of the SOAT1 polymorphism, rs1044925 (A>C), showed a significant association of the C-allele with earlier age of neurological onset. The C-allele may be associated with a higher Annualized Severity Index Score as well as increased frequency of liver disease and seizures. A polymorphism associated with decreased expression of SOAT1 appears to be a genetic modifier of the NPC1 phenotype. This finding is consistent with prior data showing decreased phenotypic severity in Npc1-/-:Soat1-/- mice and supports efforts to investigate the potential of SOAT1 inhibitors as a potential therapy for NPC1.
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Affiliation(s)
- Nicole Y. Farhat
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (N.Y.F.); (D.A.); (K.M.); (C.A.W.); (N.X.C.)
| | - Derek Alexander
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (N.Y.F.); (D.A.); (K.M.); (C.A.W.); (N.X.C.)
| | - Kyli McKee
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (N.Y.F.); (D.A.); (K.M.); (C.A.W.); (N.X.C.)
| | - James Iben
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Jorge L. Rodriguez-Gil
- Division of Medical Genetics, Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University, Palo Alto, CA 94304, USA;
| | - Christopher A. Wassif
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (N.Y.F.); (D.A.); (K.M.); (C.A.W.); (N.X.C.)
| | - Niamh X. Cawley
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (N.Y.F.); (D.A.); (K.M.); (C.A.W.); (N.X.C.)
| | - William E. Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA;
| | - Forbes D. Porter
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (N.Y.F.); (D.A.); (K.M.); (C.A.W.); (N.X.C.)
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8
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Mackay TFC, Anholt RRH. Pleiotropy, epistasis and the genetic architecture of quantitative traits. Nat Rev Genet 2024:10.1038/s41576-024-00711-3. [PMID: 38565962 DOI: 10.1038/s41576-024-00711-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 04/04/2024]
Abstract
Pleiotropy (whereby one genetic polymorphism affects multiple traits) and epistasis (whereby non-linear interactions between genetic polymorphisms affect the same trait) are fundamental aspects of the genetic architecture of quantitative traits. Recent advances in the ability to characterize the effects of polymorphic variants on molecular and organismal phenotypes in human and model organism populations have revealed the prevalence of pleiotropy and unexpected shared molecular genetic bases among quantitative traits, including diseases. By contrast, epistasis is common between polymorphic loci associated with quantitative traits in model organisms, such that alleles at one locus have different effects in different genetic backgrounds, but is rarely observed for human quantitative traits and common diseases. Here, we review the concepts and recent inferences about pleiotropy and epistasis, and discuss factors that contribute to similarities and differences between the genetic architecture of quantitative traits in model organisms and humans.
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Affiliation(s)
- Trudy F C Mackay
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
| | - Robert R H Anholt
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
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9
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Chrzanowski S, Batra R. CRISPR-Based Gene Editing Techniques in Pediatric Neurological Disorders. Pediatr Neurol 2024; 153:166-174. [PMID: 38394831 DOI: 10.1016/j.pediatrneurol.2024.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 01/15/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024]
Abstract
The emergence of gene editing technologies offers a unique opportunity to develop mutation-specific treatments for pediatric neurological disorders. Gene editing systems can potentially alter disease trajectory by correcting dysfunctional mutations or therapeutically altering gene expression. Clustered regularly interspaced short palindromic repeats (CRISPR)-based approaches are attractive gene therapy platforms to personalize treatments because of their specificity, ease of design, versatility, and cost. However, many such approaches remain in the early stages of development, with ongoing efforts to optimize editing efficiency, minimize unintended off-target effects, and mitigate pathologic immune responses. Given the rapid evolution of CRISPR-based therapies, it is prudent for the clinically based child neurologist to have a conceptual understanding of what such therapies may entail, including both benefits and risks and how such therapies may be clinically applied. In this review, we describe the fundamentals of CRISPR-based therapies, discuss the opportunities and challenges that have arisen, and highlight preclinical work in several pediatric neurological diseases.
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Affiliation(s)
- Stephen Chrzanowski
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts; Division of Neuromuscular Medicine, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts; Division of Neuromuscular Medicine, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts.
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10
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Rodrigues Alves Barbosa V, Maroilley T, Diao C, Colvin-James L, Perrier R, Tarailo-Graovac M. Single variant, yet "double trouble": TSC and KBG syndrome because of a large de novo inversion. Life Sci Alliance 2024; 7:e202302115. [PMID: 38253421 PMCID: PMC10803213 DOI: 10.26508/lsa.202302115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Despite the advances in high-throughput sequencing, many rare disease patients remain undiagnosed. In particular, the patients with well-defined clinical phenotypes and established clinical diagnosis, yet missing or partial genetic diagnosis, may hold a clue to more complex genetic mechanisms of a disease that could be missed by available clinical tests. Here, we report a patient with a clinical diagnosis of Tuberous sclerosis, combined with unusual secondary features, but negative clinical tests including TSC1 and TSC2 Short-read whole-genome sequencing combined with advanced bioinformatics analyses were successful in uncovering a de novo pericentric 87-Mb inversion with breakpoints in TSC2 and ANKRD11, which explains the TSC clinical diagnosis, and confirms a second underlying monogenic disorder, KBG syndrome. Our findings illustrate how complex variants, such as large inversions, may be missed by clinical tests and further highlight the importance of well-defined clinical diagnoses in uncovering complex molecular mechanisms of a disease, such as complex variants and "double trouble" effects.
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Affiliation(s)
- Victoria Rodrigues Alves Barbosa
- https://ror.org/03yjb2x39 Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Tatiana Maroilley
- https://ror.org/03yjb2x39 Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Catherine Diao
- https://ror.org/03yjb2x39 Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Leslie Colvin-James
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Renee Perrier
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Maja Tarailo-Graovac
- https://ror.org/03yjb2x39 Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
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11
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Brlek P, Bulić L, Bračić M, Projić P, Škaro V, Shah N, Shah P, Primorac D. Implementing Whole Genome Sequencing (WGS) in Clinical Practice: Advantages, Challenges, and Future Perspectives. Cells 2024; 13:504. [PMID: 38534348 DOI: 10.3390/cells13060504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/04/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
The integration of whole genome sequencing (WGS) into all aspects of modern medicine represents the next step in the evolution of healthcare. Using this technology, scientists and physicians can observe the entire human genome comprehensively, generating a plethora of new sequencing data. Modern computational analysis entails advanced algorithms for variant detection, as well as complex models for classification. Data science and machine learning play a crucial role in the processing and interpretation of results, using enormous databases and statistics to discover new and support current genotype-phenotype correlations. In clinical practice, this technology has greatly enabled the development of personalized medicine, approaching each patient individually and in accordance with their genetic and biochemical profile. The most propulsive areas include rare disease genomics, oncogenomics, pharmacogenomics, neonatal screening, and infectious disease genomics. Another crucial application of WGS lies in the field of multi-omics, working towards the complete integration of human biomolecular data. Further technological development of sequencing technologies has led to the birth of third and fourth-generation sequencing, which include long-read sequencing, single-cell genomics, and nanopore sequencing. These technologies, alongside their continued implementation into medical research and practice, show great promise for the future of the field of medicine.
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Affiliation(s)
- Petar Brlek
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Luka Bulić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Matea Bračić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Petar Projić
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
| | | | - Nidhi Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Parth Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Dragan Primorac
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Split, 21000 Split, Croatia
- Eberly College of Science, The Pennsylvania State University, State College, PA 16802, USA
- The Henry C. Lee College of Criminal Justice and Forensic Sciences, University of New Haven, West Haven, CT 06516, USA
- REGIOMED Kliniken, 96450 Coburg, Germany
- Medical School, University of Rijeka, 51000 Rijeka, Croatia
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
- National Forensic Sciences University, Gujarat 382007, India
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12
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Gao J, Skidmore JM, Cimerman J, Ritter KE, Qiu J, Wilson LMQ, Raphael Y, Kwan KY, Martin DM. CHD7 and SOX2 act in a common gene regulatory network during mammalian semicircular canal and cochlear development. Proc Natl Acad Sci U S A 2024; 121:e2311720121. [PMID: 38408234 DOI: 10.1073/pnas.2311720121] [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: 07/29/2023] [Accepted: 01/19/2024] [Indexed: 02/28/2024] Open
Abstract
Inner ear morphogenesis requires tightly regulated epigenetic and transcriptional control of gene expression. CHD7, an ATP-dependent chromodomain helicase DNA-binding protein, and SOX2, an SRY-related HMG box pioneer transcription factor, are known to contribute to vestibular and auditory system development, but their genetic interactions in the ear have not been explored. Here, we analyzed inner ear development and the transcriptional regulatory landscapes in mice with variable dosages of Chd7 and/or Sox2. We show that combined haploinsufficiency for Chd7 and Sox2 results in reduced otic cell proliferation, severe malformations of semicircular canals, and shortened cochleae with ectopic hair cells. Examination of mice with conditional, inducible Chd7 loss by Sox2CreER reveals a critical period (~E9.5) of susceptibility in the inner ear to combined Chd7 and Sox2 loss. Data from genome-wide RNA-sequencing and CUT&Tag studies in the otocyst show that CHD7 regulates Sox2 expression and acts early in a gene regulatory network to control expression of key otic patterning genes, including Pax2 and Otx2. CHD7 and SOX2 directly bind independently and cooperatively at transcription start sites and enhancers to regulate otic progenitor cell gene expression. Together, our findings reveal essential roles for Chd7 and Sox2 in early inner ear development and may be applicable for syndromic and other forms of hearing or balance disorders.
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Affiliation(s)
- Jingxia Gao
- Department of Pediatrics, The University of Michigan, Ann Arbor, MI 48109
| | | | - Jelka Cimerman
- Department of Pediatrics, The University of Michigan, Ann Arbor, MI 48109
| | - K Elaine Ritter
- Department of Pediatrics, The University of Michigan, Ann Arbor, MI 48109
| | - Jingyun Qiu
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854
- Keck Center for Collaborative Neuroscience, Stem Cell Research Center, Rutgers University, Piscataway, NJ 08854
| | - Lindsey M Q Wilson
- Medical Scientist Training Program, The University of Michigan, Ann Arbor, MI 48109
| | - Yehoash Raphael
- Department of Otolaryngology-Head and Neck Surgery, The University of Michigan, Ann Arbor, MI 48109
| | - Kelvin Y Kwan
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854
- Keck Center for Collaborative Neuroscience, Stem Cell Research Center, Rutgers University, Piscataway, NJ 08854
| | - Donna M Martin
- Department of Pediatrics, The University of Michigan, Ann Arbor, MI 48109
- Department of Human Genetics, The University of Michigan, Ann Arbor, MI 48109
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13
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Rahit KMTH, Avramovic V, Chong JX, Tarailo-Graovac M. GPAD: a natural language processing-based application to extract the gene-disease association discovery information from OMIM. BMC Bioinformatics 2024; 25:84. [PMID: 38413851 PMCID: PMC10898068 DOI: 10.1186/s12859-024-05693-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: 08/15/2023] [Accepted: 02/09/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Thousands of genes have been associated with different Mendelian conditions. One of the valuable sources to track these gene-disease associations (GDAs) is the Online Mendelian Inheritance in Man (OMIM) database. However, most of the information in OMIM is textual, and heterogeneous (e.g. summarized by different experts), which complicates automated reading and understanding of the data. Here, we used Natural Language Processing (NLP) to make a tool (Gene-Phenotype Association Discovery (GPAD)) that could syntactically process OMIM text and extract the data of interest. RESULTS GPAD applies a series of language-based techniques to the text obtained from OMIM API to extract GDA discovery-related information. GPAD can inform when a particular gene was associated with a specific phenotype, as well as the type of validation-whether through model organisms or cohort-based patient-matching approaches-for such an association. GPAD extracted data was validated with published reports and was compared with large language model. Utilizing GPAD's extracted data, we analysed trends in GDA discoveries, noting a significant increase in their rate after the introduction of exome sequencing, rising from an average of about 150-250 discoveries each year. Contrary to hopes of resolving most GDAs for Mendelian disorders by now, our data indicate a substantial decline in discovery rates over the past five years (2017-2022). This decline appears to be linked to the increasing necessity for larger cohorts to substantiate GDAs. The rising use of zebrafish and Drosophila as model organisms in providing evidential support for GDAs is also observed. CONCLUSIONS GPAD's real-time analyzing capacity offers an up-to-date view of GDA discovery and could help in planning and managing the research strategies. In future, this solution can be extended or modified to capture other information in OMIM and scientific literature.
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Affiliation(s)
- K M Tahsin Hassan Rahit
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Vladimir Avramovic
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Jessica X Chong
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
- Brotman-Baty Institute, Seattle, WA, 98195, USA
| | - Maja Tarailo-Graovac
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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14
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Hay Mele B, Rossetti F, Cubellis MV, Monticelli M, Andreotti G. Drug Repurposing and Lysosomal Storage Disorders: A Trick to Treat. Genes (Basel) 2024; 15:290. [PMID: 38540351 PMCID: PMC10970111 DOI: 10.3390/genes15030290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 06/14/2024] Open
Abstract
Rare diseases, or orphan diseases, are defined as diseases affecting a small number of people compared to the general population. Among these, we find lysosomal storage disorders (LSDs), a cluster of rare metabolic diseases characterized by enzyme mutations causing abnormal glycolipid storage. Drug repositioning involves repurposing existing approved drugs for new therapeutic applications, offering advantages in cost, time savings, and a lower risk of failure. We present a comprehensive analysis of existing drugs, their repurposing potential, and their clinical implications in the context of LSDs, highlighting the necessity of mutation-specific approaches. Our review systematically explores the landscape of drug repositioning as a means to enhance LSDs therapies. The findings advocate for the strategic repositioning of drugs, accentuating its role in expediting the discovery of effective treatments. We conclude that drug repurposing represents a viable pathway for accelerating therapeutic discovery for LSDs, emphasizing the need for the careful evaluation of drug efficacy and toxicity in disease-specific contexts.
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Affiliation(s)
- Bruno Hay Mele
- Department of Biology, University of Napoli “Federico II”, Complesso Universitario Monte Sant’Angelo, Via Cinthia, 80126 Napoli, Italy; (B.H.M.); (F.R.); (M.V.C.)
| | - Federica Rossetti
- Department of Biology, University of Napoli “Federico II”, Complesso Universitario Monte Sant’Angelo, Via Cinthia, 80126 Napoli, Italy; (B.H.M.); (F.R.); (M.V.C.)
| | - Maria Vittoria Cubellis
- Department of Biology, University of Napoli “Federico II”, Complesso Universitario Monte Sant’Angelo, Via Cinthia, 80126 Napoli, Italy; (B.H.M.); (F.R.); (M.V.C.)
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy;
- Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy
| | - Maria Monticelli
- Department of Biology, University of Napoli “Federico II”, Complesso Universitario Monte Sant’Angelo, Via Cinthia, 80126 Napoli, Italy; (B.H.M.); (F.R.); (M.V.C.)
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy;
| | - Giuseppina Andreotti
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy;
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15
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Panis B, Vos EN, Barić I, Bosch AM, Brouwers MCGJ, Burlina A, Cassiman D, Coman DJ, Couce ML, Das AM, Demirbas D, Empain A, Gautschi M, Grafakou O, Grunewald S, Kingma SDK, Knerr I, Leão-Teles E, Möslinger D, Murphy E, Õunap K, Pané A, Paci S, Parini R, Rivera IA, Scholl-Bürgi S, Schwartz IVD, Sdogou T, Shakerdi LA, Skouma A, Stepien KM, Treacy EP, Waisbren S, Berry GT, Rubio-Gozalbo ME. Brain function in classic galactosemia, a galactosemia network (GalNet) members review. Front Genet 2024; 15:1355962. [PMID: 38425716 PMCID: PMC10902464 DOI: 10.3389/fgene.2024.1355962] [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: 12/14/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Classic galactosemia (CG, OMIM #230400, ORPHA: 79,239) is a hereditary disorder of galactose metabolism that, despite treatment with galactose restriction, affects brain function in 85% of the patients. Problems with cognitive function, neuropsychological/social emotional difficulties, neurological symptoms, and abnormalities in neuroimaging and electrophysiological assessments are frequently reported in this group of patients, with an enormous individual variability. In this review, we describe the role of impaired galactose metabolism on brain dysfunction based on state of the art knowledge. Several proposed disease mechanisms are discussed, as well as the time of damage and potential treatment options. Furthermore, we combine data from longitudinal, cross-sectional and retrospective studies with the observations of specialist teams treating this disease to depict the brain disease course over time. Based on current data and insights, the majority of patients do not exhibit cognitive decline. A subset of patients, often with early onset cerebral and cerebellar volume loss, can nevertheless experience neurological worsening. While a large number of patients with CG suffer from anxiety and depression, the increased complaints about memory loss, anxiety and depression at an older age are likely multifactorial in origin.
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Affiliation(s)
- Bianca Panis
- Department of Pediatrics, MosaKids Children’s Hospital, Maastricht University Medical Centre, Maastricht, Netherlands
- European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member, Padova, Italy
- United for Metabolic Diseases (UMD), Amsterdam, Netherlands
| | - E. Naomi Vos
- Department of Pediatrics, MosaKids Children’s Hospital, Maastricht University Medical Centre, Maastricht, Netherlands
- European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member, Padova, Italy
- United for Metabolic Diseases (UMD), Amsterdam, Netherlands
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, Netherlands
- GROW School for Oncology and Reproduction, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
| | - Ivo Barić
- Department of Pediatrics, University Hospital Center Zagreb, Croatia, and School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Annet M. Bosch
- European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member, Padova, Italy
- United for Metabolic Diseases (UMD), Amsterdam, Netherlands
- Department of Pediatrics, Division of Metabolic Diseases, Emma Children’s Hospital, Amsterdam University Medical Center, Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, Netherlands
| | - Martijn C. G. J. Brouwers
- European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member, Padova, Italy
- Department of Internal Medicine, Division of Endocrinology and Metabolic Disease, Maastricht University Medical Centre, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, Netherlands
| | - Alberto Burlina
- European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member, Padova, Italy
- Division of Inherited Metabolic Diseases, Reference Centre Expanded Newborn Screening, University Hospital Padova, Padova, Italy
| | - David Cassiman
- Laboratory of Hepatology, Department of Chronic Diseases, Metabolism and Ageing, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - David J. Coman
- Queensland Children’s Hospital, Children’s Health Queensland, Brisbane, QLD, Australia
| | - María L. Couce
- European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member, Padova, Italy
- Department of Pediatrics, Diagnosis and Treatment Unit of Congenital Metabolic Diseases, University Clinical Hospital of Santiago de Compostela, IDIS-Health Research Institute of Santiago de Compostela, CIBERER, RICORS Instituto Salud Carlos III, Santiago de Compostela, Spain
| | - Anibh M. Das
- European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member, Padova, Italy
- Department of Paediatrics, Pediatric Metabolic Medicine, Hannover Medical School, Hannover, Germany
| | - Didem Demirbas
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Manton Center for Orphan Disease Research, Boston, MA, United States
| | - Aurélie Empain
- European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member, Padova, Italy
- Department of Paediatrics, Metabolic and Nutrition Unit, Division of Endocrinology, Diabetes and Metabolism, University Hospital for Children Queen Fabiola, Bruxelles, Belgium
| | - Matthias Gautschi
- Department of Paediatrics, Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Swiss Reference Centre for Inborn Errors of Metabolism, Site Bern, Division of Pediatric Endocrinology, Diabetes and Metabolism, University of Bern, Bern, Switzerland
| | - Olga Grafakou
- European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member, Padova, Italy
- IEM Clinic, Arch Makarios III Hospital, Nicosia, Cyprus
| | - Stephanie Grunewald
- Metabolic Unit Great Ormond Street Hospital and Institute for Child Health, University College London, London, United Kingdom
| | - Sandra D. K. Kingma
- European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member, Padova, Italy
- Centre for Metabolic Diseases, University Hospital Antwerp, University of Antwerp, Antwerp, Belgium
| | - Ina Knerr
- National Centre for Inherited Metabolic Disorders, Children’s Health Ireland at Temple Street, University College Dublin, Dublin, Ireland
| | - Elisa Leão-Teles
- European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member, Padova, Italy
- Reference Centre of Inherited Metabolic Diseases, Centro Hospitalar Universitário São João, Porto, Portugal
| | - Dorothea Möslinger
- European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member, Padova, Italy
- Department of Paediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Elaine Murphy
- Charles Dent Metabolic Unit, National Hospital for Neurology and Neurosurgery (NHNN), London, United Kingdom
| | - Katrin Õunap
- European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member, Padova, Italy
- Genetics and Personalized Medicine Clinic, Faculty of Medicine, Tartu University Hospital, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Adriana Pané
- European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member, Padova, Italy
- Endocrinology and Nutrition Department, Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Sabrina Paci
- European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member, Padova, Italy
- Inborn Errors of Metabolism, Clinical Department of Pediatrics, San Paolo Hospital - ASST Santi Paolo e Carlo, University of Milan, Milan, Italy
| | - Rossella Parini
- European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member, Padova, Italy
- Rare Diseases Unit, Department of Internal Medicine, San Gerardo Hospital IRCCS, Monza, Italy
| | - Isabel A. Rivera
- iMed.ULisboa–Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Sabine Scholl-Bürgi
- Department of Child and Adolescent Health, Division of Pediatrics I-Inherited Metabolic Disorders, Medical University Innsbruck, Innsbruck, Austria
| | - Ida V. D. Schwartz
- Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Porto Alegre, Brazil
| | - Triantafyllia Sdogou
- European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member, Padova, Italy
- Newborn Screening Department, Institute of Child Health, Athens, Greece
| | - Loai A. Shakerdi
- Adult Metabolics/Genetics, National Centre for Inherited Metabolic Disorders, The Mater Misericordiae University Hospital, Dublin, Ireland
| | - Anastasia Skouma
- European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member, Padova, Italy
- Newborn Screening Department, Institute of Child Health, Athens, Greece
| | - Karolina M. Stepien
- Salford Royal Organisation, Northern Care Alliance NHS Foundation Trust, Salford, United Kingdom
| | - Eileen P. Treacy
- School of Medicine, Trinity College Dublin, National Rare Diseases Office, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Susan Waisbren
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Manton Center for Orphan Disease Research, Boston, MA, United States
| | - Gerard T. Berry
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Manton Center for Orphan Disease Research, Boston, MA, United States
| | - M. Estela Rubio-Gozalbo
- Department of Pediatrics, MosaKids Children’s Hospital, Maastricht University Medical Centre, Maastricht, Netherlands
- European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member, Padova, Italy
- United for Metabolic Diseases (UMD), Amsterdam, Netherlands
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, Netherlands
- GROW School for Oncology and Reproduction, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
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16
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Fenner BJ, Whitmore SS, DeLuca AP, Andorf JL, Daggett HT, Luse MA, Haefeli LM, Riley JB, Critser DB, Wilkinson ME, Dumitrescu AV, Drack AV, Boyce TM, Russell JF, Binkley EM, Sohn EH, Russell SR, Boldt HC, Mullins RF, Tucker BA, Scheetz TE, Han IC, Stone EM. A Retrospective Longitudinal Study of 460 Patients with ABCA4-Associated Retinal Disease. Ophthalmology 2024:S0161-6420(24)00096-4. [PMID: 38309476 DOI: 10.1016/j.ophtha.2024.01.035] [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: 08/05/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024] Open
Abstract
PURPOSE To investigate the distribution of genotypes and natural history of ABCA4-associated retinal disease in a large cohort of patients seen at a single institution. DESIGN Retrospective, single-institution cohort review. PARTICIPANTS Patients seen at the University of Iowa between November 1986 and August 2022 clinically suspected to have disease caused by sequence variations in ABCA4. METHODS DNA samples from participants were subjected to a tiered testing strategy progressing from allele-specific screening to whole genome sequencing. Charts were reviewed, and clinical data were tabulated. The pathogenic severity of the most common alleles was estimated by studying groups of patients who shared 1 allele. Groups of patients with shared genotypes were reviewed for evidence of modifying factor effects. MAIN OUTCOME MEASURES Age at first uncorrectable vision loss, best-corrected visual acuity, and the area of the I2e isopter of the Goldmann visual field. RESULTS A total of 460 patients from 390 families demonstrated convincing clinical features of ABCA4-associated retinal disease. Complete genotypes were identified in 399 patients, and partial genotypes were identified in 61. The median age at first vision loss was 16 years (range, 4-76 years). Two hundred sixty-five families (68%) harbored a unique genotype, and no more than 10 patients shared any single genotype. Review of the patients with shared genotypes revealed evidence of modifying factors that in several cases resulted in a > 15-year difference in age at first vision loss. Two hundred forty-one different alleles were identified among the members of this cohort, and 161 of these (67%) were found in only a single individual. CONCLUSIONS ABCA4-associated retinal disease ranges from a very severe photoreceptor disease with an onset before 5 years of age to a late-onset retinal pigment epithelium-based condition resembling pattern dystrophy. Modifying factors frequently impact the ABCA4 disease phenotype to a degree that is similar in magnitude to the detectable ABCA4 alleles themselves. It is likely that most patients in any cohort will harbor a unique genotype. The latter observations taken together suggest that patients' clinical findings in most cases will be more useful for predicting their clinical course than their genotype. FINANCIAL DISCLOSURE(S) Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Beau J Fenner
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa; Singapore National Eye Centre; Singapore Eye Research Institute; and Ophthalmology and Visual Sciences Academic Clinical Programme, SingHealth Duke-NUS Academic Medical Centre, Duke-NUS Graduate Medical School, Singapore, Republic of Singapore
| | - S Scott Whitmore
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Adam P DeLuca
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Jean L Andorf
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Heather T Daggett
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Meagan A Luse
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Lorena M Haefeli
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Janet B Riley
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Douglas B Critser
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Mark E Wilkinson
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Alina V Dumitrescu
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Arlene V Drack
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Timothy M Boyce
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Jonathan F Russell
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Elaine M Binkley
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Elliott H Sohn
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Stephen R Russell
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - H Culver Boldt
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Robert F Mullins
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Budd A Tucker
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Todd E Scheetz
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Ian C Han
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Edwin M Stone
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa.
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17
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Monson E, Cideciyan AV, Roman AJ, Sumaroka A, Swider M, Wu V, Viarbitskaya I, Jacobson SG, Fliesler SJ, Pittler SJ. Inherited Retinal Degeneration Caused by Dehydrodolichyl Diphosphate Synthase Mutation-Effect of an ALG6 Modifier Variant. Int J Mol Sci 2024; 25:1004. [PMID: 38256083 PMCID: PMC10816542 DOI: 10.3390/ijms25021004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Modern advances in disease genetics have uncovered numerous modifier genes that play a role in the severity of disease expression. One such class of genetic conditions is known as inherited retinal degenerations (IRDs), a collection of retinal degenerative disorders caused by mutations in over 300 genes. A single missense mutation (K42E) in the gene encoding the enzyme dehydrodolichyl diphosphate synthase (DHDDS), which is required for protein N-glycosylation in all cells and tissues, causes DHDDS-IRD (retinitis pigmentosa type 59 (RP59; OMIM #613861)). Apart from a retinal phenotype, however, DHDDS-IRD is surprisingly non-syndromic (i.e., without any systemic manifestations). To explore disease pathology, we selected five glycosylation-related genes for analysis that are suggested to have disease modifier variants. These genes encode glycosyltransferases (ALG6, ALG8), an ER resident protein (DDOST), a high-mannose oligosaccharyl transferase (MPDU1), and a protein N-glycosylation regulatory protein (TNKS). DNA samples from 11 confirmed DHDDS (K42E)-IRD patients were sequenced at the site of each candidate genetic modifier. Quantitative measures of retinal structure and function were performed across five decades of life by evaluating foveal photoreceptor thickness, visual acuity, foveal sensitivity, macular and extramacular rod sensitivity, and kinetic visual field extent. The ALG6 variant, (F304S), was correlated with greater macular cone disease severity and less peripheral rod disease severity. Thus, modifier gene polymorphisms may account for a significant portion of phenotypic variation observed in human genetic disease. However, the consequences of the polymorphisms may be counterintuitively complex in terms of rod and cone populations affected in different regions of the retina.
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Affiliation(s)
- Elisha Monson
- Department of Optometry and Vision Science, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Artur V. Cideciyan
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Alejandro J. Roman
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Alexander Sumaroka
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Malgorzata Swider
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Vivian Wu
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Iryna Viarbitskaya
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Samuel G. Jacobson
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Steven J. Fliesler
- Departments of Ophthalmology and Biochemistry, and Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York—University at Buffalo, Buffalo, NY 14203, USA;
- Research Service, VA Western NY Healthcare System, Buffalo, NY 14215, USA
| | - Steven J. Pittler
- Department of Optometry and Vision Science, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
- Vision Science Research Center, School of Optometry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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18
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Derrick CJ, Szenker-Ravi E, Santos-Ledo A, Alqahtani A, Yusof A, Eley L, Coleman AHL, Tohari S, Ng AYJ, Venkatesh B, Alharby E, Mansard L, Bonnet-Dupeyron MN, Roux AF, Vaché C, Roume J, Bouvagnet P, Almontashiri NAM, Henderson DJ, Reversade B, Chaudhry B. Functional analysis of germline VANGL2 variants using rescue assays of vangl2 knockout zebrafish. Hum Mol Genet 2024; 33:150-169. [PMID: 37815931 PMCID: PMC10772043 DOI: 10.1093/hmg/ddad171] [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: 07/27/2023] [Revised: 09/11/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023] Open
Abstract
Developmental studies have shown that the evolutionarily conserved Wnt Planar Cell Polarity (PCP) pathway is essential for the development of a diverse range of tissues and organs including the brain, spinal cord, heart and sensory organs, as well as establishment of the left-right body axis. Germline mutations in the highly conserved PCP gene VANGL2 in humans have only been associated with central nervous system malformations, and functional testing to understand variant impact has not been performed. Here we report three new families with missense variants in VANGL2 associated with heterotaxy and congenital heart disease p.(Arg169His), non-syndromic hearing loss p.(Glu465Ala) and congenital heart disease with brain defects p.(Arg135Trp). To test the in vivo impact of these and previously described variants, we have established clinically-relevant assays using mRNA rescue of the vangl2 mutant zebrafish. We show that all variants disrupt Vangl2 function, although to different extents and depending on the developmental process. We also begin to identify that different VANGL2 missense variants may be haploinsufficient and discuss evidence in support of pathogenicity. Together, this study demonstrates that zebrafish present a suitable pipeline to investigate variants of unknown significance and suggests new avenues for investigation of the different developmental contexts of VANGL2 function that are clinically meaningful.
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Affiliation(s)
- Christopher J Derrick
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | | | - Adrian Santos-Ledo
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Ahlam Alqahtani
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Amirah Yusof
- Genome Institute of Singapore (GIS), A*STAR, 60 Biopolis St, 138672, Singapore
| | - Lorraine Eley
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Alistair H L Coleman
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Sumanty Tohari
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Dr, Proteos, 138673, Singapore
| | - Alvin Yu-Jin Ng
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Dr, Proteos, 138673, Singapore
- MGI Tech Singapore Pte Ltd, 21 Biopolis Rd, 138567, Singapore
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Dr, Proteos, 138673, Singapore
| | - Essa Alharby
- Center for Genetics and Inherited Diseases, Taibah University, 7534 Abdul Muhsin Ibn Abdul Aziz, Al Ihn, Al-Madinah al-Munawwarah 42318, Saudi Arabia
- Faculty of Applied Medical Sciences, Taibah University, Janadah Bin Umayyah Road, Tayba, Al-Madinah al-Munawwarah 42353, Saudi Arabia
| | - Luke Mansard
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, 80 Av. Augustin Fliche, 34000 Montpellier, France
| | | | - Anne-Francoise Roux
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, 80 Av. Augustin Fliche, 34000 Montpellier, France
| | - Christel Vaché
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, 80 Av. Augustin Fliche, 34000 Montpellier, France
| | - Joëlle Roume
- Département de Génétique, CHI Poissy, St Germain-en-Laye, 10 Rue du Champ Gaillard, 78300 Poissy, France
| | - Patrice Bouvagnet
- CPDPN, Hôpital MFME, CHU de Martinique, Fort de France, Fort-de-France 97261, Martinique, France
| | - Naif A M Almontashiri
- Center for Genetics and Inherited Diseases, Taibah University, 7534 Abdul Muhsin Ibn Abdul Aziz, Al Ihn, Al-Madinah al-Munawwarah 42318, Saudi Arabia
- Faculty of Applied Medical Sciences, Taibah University, Janadah Bin Umayyah Road, Tayba, Al-Madinah al-Munawwarah 42353, Saudi Arabia
| | - Deborah J Henderson
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Bruno Reversade
- Genome Institute of Singapore (GIS), A*STAR, 60 Biopolis St, 138672, Singapore
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Dr, Proteos, 138673, Singapore
- Smart-Health Initiative, BESE, KAUST, Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Medical Genetics Department, Koç Hospital Davutpaşa Caddesi 34010 Topkapı Istanbul, Istanbul, Turkey
| | - Bill Chaudhry
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
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19
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Audet S, Triassi V, Gelinas M, Legault-Cadieux N, Ferraro V, Duquette A, Tetreault M. Integration of multi-omics technologies for molecular diagnosis in ataxia patients. Front Genet 2024; 14:1304711. [PMID: 38239855 PMCID: PMC10794629 DOI: 10.3389/fgene.2023.1304711] [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: 09/29/2023] [Accepted: 11/27/2023] [Indexed: 01/22/2024] Open
Abstract
Background: Episodic ataxias are rare neurological disorders characterized by recurring episodes of imbalance and coordination difficulties. Obtaining definitive molecular diagnoses poses challenges, as clinical presentation is highly heterogeneous, and literature on the underlying genetics is limited. While the advent of high-throughput sequencing technologies has significantly contributed to Mendelian disorders genetics, interpretation of variants of uncertain significance and other limitations inherent to individual methods still leaves many patients undiagnosed. This study aimed to investigate the utility of multi-omics for the identification and validation of molecular candidates in a cohort of complex cases of ataxia with episodic presentation. Methods: Eight patients lacking molecular diagnosis despite extensive clinical examination were recruited following standard genetic testing. Whole genome and RNA sequencing were performed on samples isolated from peripheral blood mononuclear cells. Integration of expression and splicing data facilitated genomic variants prioritization. Subsequently, long-read sequencing played a crucial role in the validation of those candidate variants. Results: Whole genome sequencing uncovered pathogenic variants in four genes (SPG7, ATXN2, ELOVL4, PMPCB). A missense and a nonsense variant, both previously reported as likely pathogenic, configured in trans in individual #1 (SPG7: c.2228T>C/p.I743T, c.1861C>T/p.Q621*). An ATXN2 microsatellite expansion (CAG32) in another late-onset case. In two separate individuals, intronic variants near splice sites (ELOVL4: c.541 + 5G>A; PMPCB: c.1154 + 5G>C) were predicted to induce loss-of-function splicing, but had never been reported as disease-causing. Long-read sequencing confirmed the compound heterozygous variants configuration, repeat expansion length, as well as splicing landscape for those pathogenic variants. A potential genetic modifier of the ATXN2 expansion was discovered in ZFYVE26 (c.3022C>T/p.R1008*). Conclusion: Despite failure to identify pathogenic variants through clinical genetic testing, the multi-omics approach enabled the molecular diagnosis in 50% of patients, also giving valuable insights for variant prioritization in remaining cases. The findings demonstrate the value of long-read sequencing for the validation of candidate variants in various scenarios. Our study demonstrates the effectiveness of leveraging complementary omics technologies to unravel the underlying genetics in patients with unresolved rare diseases such as ataxia. Molecular diagnoses not only hold significant promise in improving patient care management, but also alleviates the burden of diagnostic odysseys, more broadly enhancing quality of life.
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Affiliation(s)
- Sebastien Audet
- University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada
- Department of Neurosciences, University of Montreal, Montreal, QC, Canada
| | - Valerie Triassi
- University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada
| | - Myriam Gelinas
- Department of Medicine, University of Montreal Hospital Centre (CHUM), Montreal, QC, Canada
| | - Nab Legault-Cadieux
- University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada
- Department of Neurosciences, University of Montreal, Montreal, QC, Canada
| | - Vincent Ferraro
- Department of Medicine, University of Montreal Hospital Centre (CHUM), Montreal, QC, Canada
| | - Antoine Duquette
- University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada
- Department of Neurosciences, University of Montreal, Montreal, QC, Canada
- Neurology Service, Department of Medicine, André-Barbeau Movement Disorders Unit, University of Montreal Hospital (CHUM), Montreal, QC, Canada
- Genetic Service, Department of Medicine, University of Montreal Hospital (CHUM), Montreal, QC, Canada
| | - Martine Tetreault
- University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada
- Department of Neurosciences, University of Montreal, Montreal, QC, Canada
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20
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Hashemi Sheikhshabani S, Ghafouri-Fard S, Hosseini E, Omrani MD. A novel homozygote nonsense variant of MSH4 leads to primary ovarian insufficiency and non-obstructive azoospermia. Mol Biol Rep 2024; 51:68. [PMID: 38175272 DOI: 10.1007/s11033-023-09000-4] [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: 09/08/2023] [Accepted: 11/02/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Both non-obstructive azoospermia (NOA) and primary ovarian insufficiency (POI) are pathological conditions characterized by premature and frequently complete gametogenesis failure. Considering that the conserved meiosis I steps are the same between oogenesis and spermatogenesis, inherited defects in meiosis I may result in common causes for both POI and NOA. The present research is a retrospective investigation on an Iranian family with four siblings of both genders who were affected by primary gonadal failure. METHODS Proband, an individual with NOA, was subjected to clinical examination, hormonal assessment, and genetic consultation. After reviewing the medical history of other infertile members of the family, patients with NOA went through genetic investigations including karyotyping and assessment of Y chromosome microdeletions, followed by Whole exome sequencing (WES) on the proband. After analyzing WES data, the candidate variant was validated using Sanger sequencing and traced in the family. RESULTS WES analysis of the proband uncovered a novel homozygote nonsense variant, namely c.118C>T in MSH4. This variant resulted in the occurrence of a premature stop codon in residue 40 of MSH4. Notably, the variant was absent in all public exome databases and in the exome data of 400 fertile Iranian individuals. Additionally, the variant was found to co-segregate with infertility in the family. It was also observed that all affected members had homozygous mutations, while their parents were heterozygous and the fertile sister had no mutant allele, corresponding to autosomal recessive inheritance. In addition, we conducted a review of variants reported so far in MSH4, as well as available clinical features related to these variants. The results show that the testicular sperm retrieval and ovarian stimulation cycles have not been successful yet. CONCLUSION Overall, the results of this study indicate that the identification of pathogenic variants in this gene will be beneficial in selecting proper therapeutic strategies. Also, the findings of this study demonstrate that clinicians should obtain the history of other family members of the opposite sex when diagnosing for POI and/or NOA.
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Affiliation(s)
- Somayeh Hashemi Sheikhshabani
- Student Research Committee, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elham Hosseini
- Department of Obstetrics and Gynecology, Mousavi Hospital, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mir Davood Omrani
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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21
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Na D, Lim DH, Hong JS, Lee HM, Cho D, Yu MS, Shaker B, Ren J, Lee B, Song JG, Oh Y, Lee K, Oh KS, Lee MY, Choi MS, Choi HS, Kim YH, Bui JM, Lee K, Kim HW, Lee YS, Gsponer J. A multi-layered network model identifies Akt1 as a common modulator of neurodegeneration. Mol Syst Biol 2023; 19:e11801. [PMID: 37984409 DOI: 10.15252/msb.202311801] [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: 06/05/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/22/2023] Open
Abstract
The accumulation of misfolded and aggregated proteins is a hallmark of neurodegenerative proteinopathies. Although multiple genetic loci have been associated with specific neurodegenerative diseases (NDs), molecular mechanisms that may have a broader relevance for most or all proteinopathies remain poorly resolved. In this study, we developed a multi-layered network expansion (MLnet) model to predict protein modifiers that are common to a group of diseases and, therefore, may have broader pathophysiological relevance for that group. When applied to the four NDs Alzheimer's disease (AD), Huntington's disease, and spinocerebellar ataxia types 1 and 3, we predicted multiple members of the insulin pathway, including PDK1, Akt1, InR, and sgg (GSK-3β), as common modifiers. We validated these modifiers with the help of four Drosophila ND models. Further evaluation of Akt1 in human cell-based ND models revealed that activation of Akt1 signaling by the small molecule SC79 increased cell viability in all models. Moreover, treatment of AD model mice with SC79 enhanced their long-term memory and ameliorated dysregulated anxiety levels, which are commonly affected in AD patients. These findings validate MLnet as a valuable tool to uncover molecular pathways and proteins involved in the pathophysiology of entire disease groups and identify potential therapeutic targets that have relevance across disease boundaries. MLnet can be used for any group of diseases and is available as a web tool at http://ssbio.cau.ac.kr/software/mlnet.
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Affiliation(s)
- Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Do-Hwan Lim
- College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
- School of Systems Biomedical Science, Soongsil University, Seoul, Republic of Korea
| | - Jae-Sang Hong
- College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Hyang-Mi Lee
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Daeahn Cho
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Myeong-Sang Yu
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Bilal Shaker
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Jun Ren
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Bomi Lee
- College of Life Sciences, Sejong University, Seoul, Republic of Korea
| | - Jae Gwang Song
- College of Life Sciences, Sejong University, Seoul, Republic of Korea
| | - Yuna Oh
- Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Kyungeun Lee
- Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Kwang-Seok Oh
- Information-based Drug Research Center, Korea Research Institute of Chemical Technology, Deajeon, Republic of Korea
| | - Mi Young Lee
- Information-based Drug Research Center, Korea Research Institute of Chemical Technology, Deajeon, Republic of Korea
| | - Min-Seok Choi
- College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Han Saem Choi
- College of Life Sciences, Sejong University, Seoul, Republic of Korea
| | - Yang-Hee Kim
- College of Life Sciences, Sejong University, Seoul, Republic of Korea
| | - Jennifer M Bui
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Hyung Wook Kim
- College of Life Sciences, Sejong University, Seoul, Republic of Korea
| | - Young Sik Lee
- College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Jörg Gsponer
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
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22
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Maroilley T, Rahit KMTH, Chida AR, Cotra F, Rodrigues Alves Barbosa V, Tarailo-Graovac M. Model Organism Modifier (MOM): a user-friendly Galaxy workflow to detect modifiers from genome sequencing data using Caenorhabditis elegans. G3 (BETHESDA, MD.) 2023; 13:jkad184. [PMID: 37585487 PMCID: PMC10627290 DOI: 10.1093/g3journal/jkad184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 04/21/2023] [Accepted: 08/05/2023] [Indexed: 08/18/2023]
Abstract
Genetic modifiers are variants modulating phenotypic outcomes of a primary detrimental variant. They contribute to rare diseases phenotypic variability, but their identification is challenging. Genetic screening with model organisms is a widely used method for demystifying genetic modifiers. Forward genetics screening followed by whole genome sequencing allows the detection of variants throughout the genome but typically produces thousands of candidate variants making the interpretation and prioritization process very time-consuming and tedious. Despite whole genome sequencing is more time and cost-efficient, usage of computational pipelines specific to modifier identification remains a challenge for biological-experiment-focused laboratories doing research with model organisms. To facilitate a broader implementation of whole genome sequencing in genetic screens, we have developed Model Organism Modifier or MOM, a pipeline as a user-friendly Galaxy workflow. Model Organism Modifier analyses raw short-read whole genome sequencing data and implements tailored filtering to provide a Candidate Variant List short enough to be further manually curated. We provide a detailed tutorial to run the Galaxy workflow Model Organism Modifier and guidelines to manually curate the Candidate Variant Lists. We have tested Model Organism Modifier on published and validated Caenorhabditis elegans modifiers screening datasets. As whole genome sequencing facilitates high-throughput identification of genetic modifiers in model organisms, Model Organism Modifier provides a user-friendly solution to implement the bioinformatics analysis of the short-read datasets in laboratories without expertise or support in Bioinformatics.
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Affiliation(s)
- Tatiana Maroilley
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - K M Tahsin Hassan Rahit
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Afiya Razia Chida
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Filip Cotra
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Victoria Rodrigues Alves Barbosa
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Maja Tarailo-Graovac
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
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23
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Jo HS, Yang M, Ahn SY, Sung SI, Park WS, Jang JH, Chang YS. Optimal Protocols and Management of Clinical and Genomic Data Collection to Assist in the Early Diagnosis and Treatment of Multiple Congenital Anomalies. CHILDREN (BASEL, SWITZERLAND) 2023; 10:1673. [PMID: 37892336 PMCID: PMC10605914 DOI: 10.3390/children10101673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/01/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023]
Abstract
Standardized protocols have been designed and developed specifically for clinical information collection and obtaining trio genomic information from infants affected with congenital anomalies (CA) and their parents, as well as securing human biological resources. The protocols include clinical and genomic information collection on multiple CA that were difficult to diagnose using pre-existing screening methods. We obtained human-derived resources and genomic information from 138 cases, including 45 families of infants with CA and their parent trios. For the clinical information collection protocol, criteria for target patient selection and a consent system for collecting and utilizing research resources are crucial. Whole genome sequencing data were generated for all participants, and standardized protocols were developed for resource collection and manufacturing. We recorded the phenotype information according to the Human Phenotype Ontology term, and epidemiological information was collected through an environmental factor questionnaire. Updating and recording of clinical symptoms and genetic information that have been newly added or changed over time are significant. The protocols enabled long-term tracking by including the growth and development status that reflect the important characteristics of newborns. Using these clinical and genetic information collection protocols for CA, an essential platform for early genetic diagnosis and diagnostic research can be established, and new genetic diagnostic guidelines can be presented in the near future.
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Affiliation(s)
- Heui Seung Jo
- Department of Pediatrics, Kangwon National University Hospital, Kangwon National University School of Medicine, Kangwon 24289, Republic of Korea
| | - Misun Yang
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - So Yoon Ahn
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Se In Sung
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Won Soon Park
- Department of Pediatrics, CHA Gangnam Medical Center, CHA University, Seoul 06135, Republic of Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Yun Sil Chang
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Republic of Korea
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24
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Zhu S, Deen MC, Zhu Y, Gilormini PA, Chen X, Davis OB, Chin MY, Henry AG, Vocadlo DJ. A Fixable Fluorescence-Quenched Substrate for Quantitation of Lysosomal Glucocerebrosidase Activity in Both Live and Fixed Cells. Angew Chem Int Ed Engl 2023; 62:e202309306. [PMID: 37582679 DOI: 10.1002/anie.202309306] [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: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 08/17/2023]
Abstract
Fluorogenic substrates are emerging tools that enable studying enzymatic processes within their native cellular environments. However, fluorogenic substrates that function within live cells are generally incompatible with cellular fixation, preventing their tandem application with fundamental cell biology methods such as immunocytochemistry. Here we report a simple approach to enable the chemical fixation of a dark-to-light substrate, LysoFix-GBA, which enables quantification of glucocerebrosidase (GCase) activity in both live and fixed cells. LysoFix-GBA enables measuring responses to both chemical and genetic perturbations to lysosomal GCase activity. Further, LysoFix-GBA permits simple multiplexed co-localization studies of GCase activity with subcellular protein markers. This tool will aid studying the role of GCase activity in Parkinson's Disease, creating new therapeutic approaches targeting the GCase pathway. This approach also lays the foundation for an approach to create fixable substrates for other lysosomal enzymes.
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Affiliation(s)
- Sha Zhu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Matthew C Deen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Yanping Zhu
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Pierre-André Gilormini
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Xi Chen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Oliver B Davis
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - Marcus Y Chin
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - Anastasia G Henry
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
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25
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Richardson K, Wessells R. A novel panel of Drosophila TAFAZZIN mutants in distinct genetic backgrounds as a resource for therapeutic testing. PLoS One 2023; 18:e0286380. [PMID: 37756350 PMCID: PMC10529581 DOI: 10.1371/journal.pone.0286380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/16/2023] [Indexed: 09/29/2023] Open
Abstract
Barth Syndrome is a rare, X-linked disorder caused by mutation of the gene TAFAZZIN (TAZ). The corresponding Tafazzin protein is involved in the remodeling of cardiolipin, a phospholipid with critical roles in mitochondrial function. While recent clinical trials have been promising, there is still no cure for Barth Syndrome. Because TAZ is highly conserved, multiple animal and cell culture models exist for pre-clinical testing of therapeutics. However, since the same mutation in different patients can lead to different symptoms and responses to treatment, isogenized experimental models can't fully account for human disease conditions. On the other hand, isogenized animal models allow for sufficient numbers to thoroughly establish efficacy for a given genetic background. Therefore, a combined method for testing treatments in a panel of isogenized cohorts that are genetically distinct from each other would be transformative for testing emerging pre-clinical therapies. To aid in this effort, we've created a novel panel of 10 Drosophila lines, each with the same TAZ mutation in highly diverse genetic backgrounds, to serve as a helpful resource to represent natural variation in background genetics in pre-clinical studies. As a proof of principle, we test our panel here using nicotinamide riboside (NR), a treatment with established therapeutic value, to evaluate how robust this therapy is across the 10 genetic backgrounds in this novel reference panel. We find substantial variation in the response to NR across backgrounds. We expect this resource will be valuable in pre-clinical testing of emerging therapies for Barth Syndrome.
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Affiliation(s)
- Kristin Richardson
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, United States of America
| | - Robert Wessells
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, United States of America
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26
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Cengiz Winter N, Karakaya M, Mosen P, Brusius I, Anlar B, Haliloglu G, Winter D, Wirth B. Proteomic Investigation of Differential Interactomes of Glypican 1 and a Putative Disease-Modifying Variant of Ataxia. J Proteome Res 2023; 22:3081-3095. [PMID: 37585105 PMCID: PMC10476613 DOI: 10.1021/acs.jproteome.3c00402] [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: 07/05/2023] [Indexed: 08/17/2023]
Abstract
In a currently 13-year-old girl of consanguineous Turkish parents, who developed unsteady gait and polyneuropathy at the ages of 3 and 6 years, respectively, we performed whole genome sequencing and identified a biallelic missense variant c.424C>T, p.R142W in glypican 1 (GPC1) as a putative disease-associated variant. Up to date, GPC1 has not been associated with a neuromuscular disorder, and we hypothesized that this variant, predicted as deleterious, may be causative for the disease. Using mass spectrometry-based proteomics, we investigated the interactome of GPC1 WT and the missense variant. We identified 198 proteins interacting with GPC1, of which 16 were altered for the missense variant. This included CANX as well as vacuolar ATPase (V-ATPase) and the mammalian target of rapamycin complex 1 (mTORC1) complex members, whose dysregulation could have a potential impact on disease severity in the patient. Importantly, these proteins are novel interaction partners of GPC1. At 10.5 years, the patient developed dilated cardiomyopathy and kyphoscoliosis, and Friedreich's ataxia (FRDA) was suspected. Given the unusually severe phenotype in a patient with FRDA carrying only 104 biallelic GAA repeat expansions in FXN, we currently speculate that disturbed GPC1 function may have exacerbated the disease phenotype. LC-MS/MS data are accessible in the ProteomeXchange Consortium (PXD040023).
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Affiliation(s)
- Nur Cengiz Winter
- Institute
of Human Genetics, University Hospital Cologne, 50931 Cologne, Germany
- Center
for Molecular Medicine Cologne, University
of Cologne, 50931 Cologne, Germany
| | - Mert Karakaya
- Institute
of Human Genetics, University Hospital Cologne, 50931 Cologne, Germany
- Center
for Molecular Medicine Cologne, University
of Cologne, 50931 Cologne, Germany
- Center
for Rare Diseases Cologne, University Hospital
of Cologne, 50931 Cologne, Germany
| | - Peter Mosen
- Institute
for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, 53115 Bonn, Germany
| | - Isabell Brusius
- Institute
of Human Genetics, University Hospital Cologne, 50931 Cologne, Germany
| | - Banu Anlar
- Department
of Pediatrics, Division of Pediatric Neurology, Hacettepe University Faculty of Medicine, 06230 Ankara, Turkey
| | - Goknur Haliloglu
- Department
of Pediatrics, Division of Pediatric Neurology, Hacettepe University Faculty of Medicine, 06230 Ankara, Turkey
| | - Dominic Winter
- Institute
for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, 53115 Bonn, Germany
| | - Brunhilde Wirth
- Institute
of Human Genetics, University Hospital Cologne, 50931 Cologne, Germany
- Center
for Molecular Medicine Cologne, University
of Cologne, 50931 Cologne, Germany
- Center
for Rare Diseases Cologne, University Hospital
of Cologne, 50931 Cologne, Germany
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27
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Renaux A, Terwagne C, Cochez M, Tiddi I, Nowé A, Lenaerts T. A knowledge graph approach to predict and interpret disease-causing gene interactions. BMC Bioinformatics 2023; 24:324. [PMID: 37644440 PMCID: PMC10463539 DOI: 10.1186/s12859-023-05451-5] [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: 06/07/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Understanding the impact of gene interactions on disease phenotypes is increasingly recognised as a crucial aspect of genetic disease research. This trend is reflected by the growing amount of clinical research on oligogenic diseases, where disease manifestations are influenced by combinations of variants on a few specific genes. Although statistical machine-learning methods have been developed to identify relevant genetic variant or gene combinations associated with oligogenic diseases, they rely on abstract features and black-box models, posing challenges to interpretability for medical experts and impeding their ability to comprehend and validate predictions. In this work, we present a novel, interpretable predictive approach based on a knowledge graph that not only provides accurate predictions of disease-causing gene interactions but also offers explanations for these results. RESULTS We introduce BOCK, a knowledge graph constructed to explore disease-causing genetic interactions, integrating curated information on oligogenic diseases from clinical cases with relevant biomedical networks and ontologies. Using this graph, we developed a novel predictive framework based on heterogenous paths connecting gene pairs. This method trains an interpretable decision set model that not only accurately predicts pathogenic gene interactions, but also unveils the patterns associated with these diseases. A unique aspect of our approach is its ability to offer, along with each positive prediction, explanations in the form of subgraphs, revealing the specific entities and relationships that led to each pathogenic prediction. CONCLUSION Our method, built with interpretability in mind, leverages heterogenous path information in knowledge graphs to predict pathogenic gene interactions and generate meaningful explanations. This not only broadens our understanding of the molecular mechanisms underlying oligogenic diseases, but also presents a novel application of knowledge graphs in creating more transparent and insightful predictors for genetic research.
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Affiliation(s)
- Alexandre Renaux
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles - Vrije Universiteit Brussel, Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
- Artificial Intelligence lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Chloé Terwagne
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles - Vrije Universiteit Brussel, Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
| | - Michael Cochez
- Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Discovery Lab, Elsevier, Amsterdam, The Netherlands
| | - Ilaria Tiddi
- Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ann Nowé
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles - Vrije Universiteit Brussel, Brussels, Belgium
- Artificial Intelligence lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles - Vrije Universiteit Brussel, Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
- Artificial Intelligence lab, Vrije Universiteit Brussel, Brussels, Belgium
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28
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Foreman J, Perrett D, Mazaika E, Hunt SE, Ware JS, Firth HV. DECIPHER: Improving Genetic Diagnosis Through Dynamic Integration of Genomic and Clinical Data. Annu Rev Genomics Hum Genet 2023; 24:151-176. [PMID: 37285546 PMCID: PMC7615097 DOI: 10.1146/annurev-genom-102822-100509] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DECIPHER (Database of Genomic Variation and Phenotype in Humans Using Ensembl Resources) shares candidate diagnostic variants and phenotypic data from patients with genetic disorders to facilitate research and improve the diagnosis, management, and therapy of rare diseases. The platform sits at the boundary between genomic research and the clinical community. DECIPHER aims to ensure that the most up-to-date data are made rapidly available within its interpretation interfaces to improve clinical care. Newly integrated cardiac case-control data that provide evidence of gene-disease associations and inform variant interpretation exemplify this mission. New research resources are presented in a format optimized for use by a broad range of professionals supporting the delivery of genomic medicine. The interfaces within DECIPHER integrate and contextualize variant and phenotypic data, helping to determine a robust clinico-molecular diagnosis for rare-disease patients, which combines both variant classification and clinical fit. DECIPHER supports discovery research, connecting individuals within the rare-disease community to pursue hypothesis-driven research.
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Affiliation(s)
- Julia Foreman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom; ,
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Daniel Perrett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom; ,
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Erica Mazaika
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; ,
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom; ,
| | - James S Ware
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; ,
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Helen V Firth
- Wellcome Sanger Institute, Hinxton, United Kingdom
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom;
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29
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Tilemis FN, Marinakis NM, Veltra D, Svingou M, Kekou K, Mitrakos A, Tzetis M, Kosma K, Makrythanasis P, Traeger-Synodinos J, Sofocleous C. Germline CNV Detection through Whole-Exome Sequencing (WES) Data Analysis Enhances Resolution of Rare Genetic Diseases. Genes (Basel) 2023; 14:1490. [PMID: 37510394 PMCID: PMC10379589 DOI: 10.3390/genes14071490] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/14/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Whole-Exome Sequencing (WES) has proven valuable in the characterization of underlying genetic defects in most rare diseases (RDs). Copy Number Variants (CNVs) were initially thought to escape detection. Recent technological advances enabled CNV calling from WES data with the use of accurate and highly sensitive bioinformatic tools. Amongst 920 patients referred for WES, 454 unresolved cases were further analysed using the ExomeDepth algorithm. CNVs were called, evaluated and categorized according to ACMG/ClinGen recommendations. Causative CNVs were identified in 40 patients, increasing the diagnostic yield of WES from 50.7% (466/920) to 55% (506/920). Twenty-two CNVs were available for validation and were all confirmed; of these, five were novel. Implementation of the ExomeDepth tool promoted effective identification of phenotype-relevant and/or novel CNVs. Among the advantages of calling CNVs from WES data, characterization of complex genotypes comprising both CNVs and SNVs minimizes cost and time to final diagnosis, while allowing differentiation between true or false homozygosity, as well as compound heterozygosity of variants in AR genes. The use of a specific algorithm for calling CNVs from WES data enables ancillary detection of different types of causative genetic variants, making WES a critical first-tier diagnostic test for patients with RDs.
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Affiliation(s)
- Faidon-Nikolaos Tilemis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Nikolaos M Marinakis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Research University Institute for the Study and Prevention of Genetic and Malignant Disease of Childhood, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Danai Veltra
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Research University Institute for the Study and Prevention of Genetic and Malignant Disease of Childhood, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Maria Svingou
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Kyriaki Kekou
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Anastasios Mitrakos
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Research University Institute for the Study and Prevention of Genetic and Malignant Disease of Childhood, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Maria Tzetis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Konstantina Kosma
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Periklis Makrythanasis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Department of Genetic Medicine and Development, Medical School, University of Geneva, 1211 Geneva, Switzerland
- Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Joanne Traeger-Synodinos
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Christalena Sofocleous
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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30
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Nurchis MC, Altamura G, Riccardi MT, Radio FC, Chillemi G, Bertini ES, Garlasco J, Tartaglia M, Dallapiccola B, Damiani G. Whole genome sequencing diagnostic yield for paediatric patients with suspected genetic disorders: systematic review, meta-analysis, and GRADE assessment. Arch Public Health 2023; 81:93. [PMID: 37231492 DOI: 10.1186/s13690-023-01112-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 05/18/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND About 80% of the roughly 7,000 known rare diseases are single gene disorders, about 85% of which are ultra-rare, affecting less than one in one million individuals. NGS technologies, in particular whole genome sequencing (WGS) in paediatric patients suffering from severe disorders of likely genetic origin improve the diagnostic yield allowing targeted, effective care and management. The aim of this study is to perform a systematic review and meta-analysis to assess the effectiveness of WGS, with respect to whole exome sequencing (WES) and/or usual care, for the diagnosis of suspected genetic disorders among the paediatric population. METHODS A systematic review of the literature was conducted querying relevant electronic databases, including MEDLINE, EMBASE, ISI Web of Science, and Scopus from January 2010 to June 2022. A random-effect meta-analysis was run to inspect the diagnostic yield of different techniques. A network meta-analysis was also performed to directly assess the comparison between WGS and WES. RESULTS Of the 4,927 initially retrieved articles, thirty-nine met the inclusion criteria. Overall results highlighted a significantly higher pooled diagnostic yield for WGS, 38.6% (95% CI: [32.6 - 45.0]), in respect to WES, 37.8% (95% CI: [32.9 - 42.9]) and usual care, 7.8% (95% CI: [4.4 - 13.2]). The meta-regression output suggested a higher diagnostic yield of the WGS compared to WES after controlling for the type of disease (monogenic vs non-monogenic), with a tendency to better diagnostic performances for Mendelian diseases. The network meta-analysis showed a higher diagnostic yield for WGS compared to WES (OR = 1.54, 95%CI: [1.11 - 2.12]). CONCLUSIONS Although whole genome sequencing for the paediatric population with suspected genetic disorders provided an accurate and early genetic diagnosis in a high proportion of cases, further research is needed for evaluating costs, effectiveness, and cost-effectiveness of WGS and achieving an informed decision-making process. TRIAL REGISTRATION This systematic review has not been registered.
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Grants
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
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Affiliation(s)
- Mario Cesare Nurchis
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
- School of Economics, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Gerardo Altamura
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy.
| | - Maria Teresa Riccardi
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Giovanni Chillemi
- Department for Innovation in Biological Agro-Food and Forest Systems (DIBAF), University of Tuscia, 01100, Viterbo, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Centro Nazionale Delle Ricerche, 70126, Bari, Italy
| | - Enrico Silvio Bertini
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Jacopo Garlasco
- Department of Public Health Sciences and Paediatrics, University of Turin, 10126, Turin, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Gianfranco Damiani
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
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31
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Versbraegen N, Gravel B, Nachtegael C, Renaux A, Verkinderen E, Nowé A, Lenaerts T, Papadimitriou S. Faster and more accurate pathogenic combination predictions with VarCoPP2.0. BMC Bioinformatics 2023; 24:179. [PMID: 37127601 PMCID: PMC10152795 DOI: 10.1186/s12859-023-05291-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/14/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND The prediction of potentially pathogenic variant combinations in patients remains a key task in the field of medical genetics for the understanding and detection of oligogenic/multilocus diseases. Models tailored towards such cases can help shorten the gap of missing diagnoses and can aid researchers in dealing with the high complexity of the derived data. The predictor VarCoPP (Variant Combinations Pathogenicity Predictor) that was published in 2019 and identified potentially pathogenic variant combinations in gene pairs (bilocus variant combinations), was the first important step in this direction. Despite its usefulness and applicability, several issues still remained that hindered a better performance, such as its False Positive (FP) rate, the quality of its training set and its complex architecture. RESULTS We present VarCoPP2.0: the successor of VarCoPP that is a simplified, faster and more accurate predictive model identifying potentially pathogenic bilocus variant combinations. Results from cross-validation and on independent data sets reveal that VarCoPP2.0 has improved in terms of both sensitivity (95% in cross-validation and 98% during testing) and specificity (5% FP rate). At the same time, its running time shows a significant 150-fold decrease due to the selection of a simpler Balanced Random Forest model. Its positive training set now consists of variant combinations that are more confidently linked with evidence of pathogenicity, based on the confidence scores present in OLIDA, the Oligogenic Diseases Database ( https://olida.ibsquare.be ). The improvement of its performance is also attributed to a more careful selection of up-to-date features identified via an original wrapper method. We show that the combination of different variant and gene pair features together is important for predictions, highlighting the usefulness of integrating biological information at different levels. CONCLUSIONS Through its improved performance and faster execution time, VarCoPP2.0 enables a more accurate analysis of larger data sets linked to oligogenic diseases. Users can access the ORVAL platform ( https://orval.ibsquare.be ) to apply VarCoPP2.0 on their data.
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Affiliation(s)
- Nassim Versbraegen
- Machine Learning Group, Université Libre de Bruxelles, 1050, Brussels, Belgium.
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050, Brussels, Belgium.
| | - Barbara Gravel
- Machine Learning Group, Université Libre de Bruxelles, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050, Brussels, Belgium
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, 1050, Brussels, Belgium
| | - Charlotte Nachtegael
- Machine Learning Group, Université Libre de Bruxelles, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050, Brussels, Belgium
| | - Alexandre Renaux
- Machine Learning Group, Université Libre de Bruxelles, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050, Brussels, Belgium
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, 1050, Brussels, Belgium
| | - Emma Verkinderen
- Machine Learning Group, Université Libre de Bruxelles, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050, Brussels, Belgium
| | - Ann Nowé
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050, Brussels, Belgium
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, 1050, Brussels, Belgium
| | - Tom Lenaerts
- Machine Learning Group, Université Libre de Bruxelles, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050, Brussels, Belgium
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, 1050, Brussels, Belgium
| | - Sofia Papadimitriou
- Machine Learning Group, Université Libre de Bruxelles, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050, Brussels, Belgium
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, 1050, Brussels, Belgium
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Baalmann N, Spielmann M, Gillessen-Kaesbach G, Hanker B, Schmidt J, Lill CM, Hellenbroich Y, Greiten B, Lohmann K, Trinh J, Hüning I. Phenotypic specificity in patients with neurodevelopmental delay does not correlate with diagnostic yield of trio-exome sequencing. Eur J Med Genet 2023; 66:104774. [PMID: 37120078 DOI: 10.1016/j.ejmg.2023.104774] [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: 10/24/2022] [Revised: 03/12/2023] [Accepted: 04/26/2023] [Indexed: 05/01/2023]
Abstract
In this study, we aimed to examine the diagnostic yield achieved by applying a trio approach in exome sequencing (ES) and the interdependency between the clinical specificity in families with neurodevelopmental delay. Thirty-seven families were recruited and trio-ES as well as three criteria for estimating the clinical phenotypic specificity were suggested and applied to the underaged children. All our patients showed neurodevelopmental delay and most of them a large spectrum of congenital anomalies. Applying the pathogenicity guidelines of the American College of Medical Genetics (ACMG), likely pathogenic (29.7%) and pathogenic variants (8.1%) were found in 40,5% of our index patients. Additionally, we found four variants of uncertain significance (VUS; according to ACMG) and two genes of interest (GOI; going beyond ACMG classification) (GLRA4, NRXN2). Spastic Paraplegia 4 (SPG4) caused by a formerly known SPAST variant was diagnosed in a patient with a complex phenotype, in whom a second genetic disorder may be present. A potential pathogenic variant linked to severe intellectual disability in GLRA4 requires further investigation. No interdependency between the diagnostic yield and the clinical specificity of the phenotypes could be observed. In consequence, trio-ES should be used early in the diagnostic process, independently from the specificity of the patient.
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Affiliation(s)
- Nadja Baalmann
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany.
| | - Malte Spielmann
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany.
| | | | - Britta Hanker
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany.
| | - Julia Schmidt
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany; Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany.
| | - Christina M Lill
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany; Institute of Neurogenetics, University of Lübeck, Lübeck, Germany; Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Germany; Ageing Epidemiology Research Unit (AGE), School of Public Health, Imperial College London, London, UK.
| | | | - Bianca Greiten
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany.
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.
| | - Joanne Trinh
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.
| | - Irina Hüning
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany.
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Alonso-Luna O, Mercado-Celis GE, Melendez-Zajgla J, Zapata-Tarres M, Mendoza-Caamal E. The genetic era of childhood cancer: Identification of high-risk patients and germline sequencing approaches. Ann Hum Genet 2023; 87:81-90. [PMID: 36896780 DOI: 10.1111/ahg.12502] [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: 10/14/2022] [Revised: 02/10/2023] [Accepted: 02/12/2023] [Indexed: 03/11/2023]
Abstract
Childhood cancer is a leading cause of death by disease in children ages 5-14, for which there are no preventive strategies. Due to early-age of diagnosis and short period of exposure to environmental factors, increasing evidence suggests childhood cancer could have strong association with germline alterations in predisposition cancer genes but, their frequency and distribution are largely unknown. Several efforts have been made to develop tools to identify children with increased risk of cancer who may benefit from genetic testing but their validation and application on a large scale is necessary. Research on genetic bases of childhood cancer is ongoing, in which several approaches for the identification of genetic variants related to cancer predisposition have been used. In this paper, we discuss the updated efforts, strategies, molecular mechanisms and clinical implications for germline predisposition gene alterations and the characterization of risk variants in childhood cancer.
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Affiliation(s)
- Oscar Alonso-Luna
- Programa de Maestría y Doctorado en Ciencias Médicas, Odontológicas y de la Salud, UNAM, Ciudad de México, CDMX, México
| | - Gabriela E Mercado-Celis
- Laboratorio de Genómica Clínica, División de Estudios de Posgrado e Investigación, Facultad de Odontologia, UNAM, Ciudad de México, CDMX, México
| | | | - Marta Zapata-Tarres
- Coordinación de Investigación, Fundación IMSS A.C., Juárez, Ciudad de México, CDMX, México
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Asif M, Abdullah U, Nürnberg P, Tinschert S, Hussain MS. Congenital Microcephaly: A Debate on Diagnostic Challenges and Etiological Paradigm of the Shift from Isolated/Non-Syndromic to Syndromic Microcephaly. Cells 2023; 12:cells12040642. [PMID: 36831309 PMCID: PMC9954724 DOI: 10.3390/cells12040642] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Congenital microcephaly (CM) exhibits broad clinical and genetic heterogeneity and is thus categorized into several subtypes. However, the recent bloom of disease-gene discoveries has revealed more overlaps than differences in the underlying genetic architecture for these clinical sub-categories, complicating the differential diagnosis. Moreover, the mechanism of the paradigm shift from a brain-restricted to a multi-organ phenotype is only vaguely understood. This review article highlights the critical factors considered while defining CM subtypes. It also presents possible arguments on long-standing questions of the brain-specific nature of CM caused by a dysfunction of the ubiquitously expressed proteins. We argue that brain-specific splicing events and organ-restricted protein expression may contribute in part to disparate clinical manifestations. We also highlight the role of genetic modifiers and de novo variants in the multi-organ phenotype of CM and emphasize their consideration in molecular characterization. This review thus attempts to expand our understanding of the phenotypic and etiological variability in CM and invites the development of more comprehensive guidelines.
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Affiliation(s)
- Maria Asif
- Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Uzma Abdullah
- University Institute of Biochemistry and Biotechnology (UIBB), PMAS-Arid Agriculture University, Rawalpindi, Rawalpindi 46300, Pakistan
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Sigrid Tinschert
- Zentrum Medizinische Genetik, Medizinische Universität, 6020 Innsbruck, Austria
| | - Muhammad Sajid Hussain
- Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Correspondence:
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Yao Q, Gorevic P, Shen B, Gibson G. Genetically transitional disease: a new concept in genomic medicine. Trends Genet 2023; 39:98-108. [PMID: 36564319 DOI: 10.1016/j.tig.2022.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/02/2022] [Accepted: 11/27/2022] [Indexed: 12/24/2022]
Abstract
Traditional classification of genetic diseases as monogenic and polygenic has lagged far behind scientific progress. In this opinion article, we propose and define a new terminology, genetically transitional disease (GTD), referring to cases where a large-effect mutation is necessary, but not sufficient, to cause disease. This leads to a working disease nosology based on gradients of four types of genetic architecture: monogenic, polygenic, GTD, and mixed. We present four scenarios under which GTD may occur; namely, subsets of traditionally Mendelian disease, modifiable Tier 1 monogenic conditions, variable penetrance, and situations where a genetic mutational spectrum produces qualitatively divergent pathologies. The implications of the new nosology in precision medicine are discussed, in which therapeutic options may target the molecular cause or the disease phenotype.
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Affiliation(s)
- Qingping Yao
- Division of Rheumatology, Allergy, and Immunology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY, USA.
| | - Peter Gorevic
- Division of Rheumatology, Allergy, and Immunology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY, USA
| | - Bo Shen
- Center for Inflammatory Bowel Diseases, New York-Presbyterian/Columbia University Irving Medical Center, New York, NY, USA
| | - Greg Gibson
- Center for Integrative Genomics, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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Ghorbani F, de Boer EN, Benjamins-Stok M, Verschuuren-Bemelmans CC, Knapper J, de Boer-Bergsma J, de Vries JJ, Sikkema-Raddatz B, Verbeek DS, Westers H, van Diemen CC. Copy Number Variant Analysis of Spinocerebellar Ataxia Genes in a Cohort of Dutch Patients With Cerebellar Ataxia. Neurol Genet 2023; 9:e200050. [PMID: 38058854 PMCID: PMC10696507 DOI: 10.1212/nxg.0000000000200050] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/27/2022] [Indexed: 12/08/2023]
Abstract
Background and Objectives The spinocerebellar ataxias (SCAs) are a genetically heterogeneous group of neurodegenerative disorders generally caused by single nucleotide variants (SNVs) or indels in coding regions or by repeat expansions in coding and noncoding regions of SCA genes. Copy number variants (CNVs) have now also been reported for 3 genes-ITPR1, FGF14, and SPTBN2-but not all SCA genes have been screened for CNVs as the underlying cause of the disease in patients. In this study, we aim to assess the prevalence of CNVs encompassing 36 known SCA genes. Methods A cohort of patients with cerebellar ataxia who were referred to the University Medical Center Groningen for SCA genetic diagnostics was selected for this study. Genome-wide single nucleotide polymorphism (SNP) genotyping was performed using the Infinium Global Screening Array. Following data processing, genotyping data were uploaded into NxClinical software to perform CNV analysis per patient and to visualize identified CNVs in 36 genes with allocated SCA symbols. The clinical relevance of detected CNVs was determined using evidence from studies based on PubMed literature searches for similar CNVs and phenotypic features. Results Of the 338 patients with cerebellar ataxia, we identified putative clinically relevant CNV deletions in 3 patients: an identical deletion encompassing ITPR1 in 2 patients, who turned out to be related, and a deletion involving PPP2R2B in another patient. Although the CNV deletion in ITPR1 was clearly the underlying cause of SCA15 in the 2 related patients, the clinical significance of the deletion in PPP2R2B remained unknown. Discussion We showed that CNVs detectable with the limited resolution of SNP array are a very rare cause of SCA. Nevertheless, we suggest adding CNV analysis alongside SNV analysis to SCA gene diagnostics using next-generation sequencing approaches, at least for ITPR1, to improve the genetic diagnostics for patients.
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Affiliation(s)
- Fatemeh Ghorbani
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Eddy N de Boer
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Marloes Benjamins-Stok
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Corien C Verschuuren-Bemelmans
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Jurjen Knapper
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Jelkje de Boer-Bergsma
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Jeroen J de Vries
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Birgit Sikkema-Raddatz
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Dineke S Verbeek
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Helga Westers
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Cleo C van Diemen
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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Best LG, Duffy KA, George AM, Ganguly A, Kalish JM. Familial Beckwith-Wiedemann syndrome in a multigenerational family: Forty years of careful phenotyping. Am J Med Genet A 2023; 191:348-356. [PMID: 36322462 DOI: 10.1002/ajmg.a.63026] [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: 06/27/2022] [Revised: 09/22/2022] [Accepted: 10/15/2022] [Indexed: 01/11/2023]
Abstract
Beckwith-Wiedemann Spectrum (BWSp) is an overgrowth and cancer predisposition disorder characterized by a wide spectrum of phenotypic manifestations including macroglossia, abdominal wall defects, neonatal hypoglycemia, and predisposition to embryonal tumors. In 1981, Best and Hoekstra reported four patients with BWSp in a single family which suggested autosomal dominant inheritance, but standard clinical testing for BWSp was not available during this time. Meticulous phenotyping of this family has occurred over the past 40 years of follow-up with additional family members being identified and samples collected for genetic testing. Genetic testing revealed a pathogenic mutation in CDKN1C, consistent with the most common cause of familial BWSp. CDKN1C mutations account for just 5% of sporadic cases of BWSp. Here, we report the variable presentation of BWSp across the individuals affected by the CDKN1C mutation and other extended family members spanning multiple generations, all examined by the same physician. Additional phenotypes thought to be atypical in patients with BWSp were reported which included cardiac abnormalities. The incidence of tumors was documented in extended family members and included rhabdomyosarcoma, astrocytoma, and thyroid carcinoma, which have previously been reported in patients with BWSp. These observations suggest that in addition to the inheritance of the CDKN1C variant, there are modifying factors in this family driving the phenotypic spectrum observed. Alternative theories are suggested to explain the etiology of clinical variability including diffused mosaicism, anticipation, and the presence of additional variants tracking in the family. This study highlights the necessity of long-term follow-up in patients with BWSp and consideration of individual familial characteristics in the context of phenotype and/or (epi)genotype associations.
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Affiliation(s)
- Lyle G Best
- Department of Pathology, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota, USA
| | - Kelly A Duffy
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Andrew M George
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Arupa Ganguly
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jennifer M Kalish
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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38
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Quelhas D, Jaeken J, Azevedo L. Genetic modifiers in glycosylation pathways: Is there a link between PMM2 and PGM1? J Inherit Metab Dis 2023; 46:1-2. [PMID: 36451346 DOI: 10.1002/jimd.12576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/24/2022] [Indexed: 12/04/2022]
Affiliation(s)
- Dulce Quelhas
- Unidade de Bioquímica Genética, Centro de Genética Médica, Centro Hospitalar Universitário do Porto, Porto, Portugal
- UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- Centro Referência Doenças Hereditárias do Metabolismo, Centro Hospitalar Universitário do Porto, Porto, Portugal
| | - Jaak Jaeken
- Center for Metabolic Diseases, KU Leuven, Leuven, Belgium
| | - Luisa Azevedo
- UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR-Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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Giacomozzi C, Martin A, Fernández MC, Gutiérrez M, Iascone M, Domené HM, Dominici FP, Bergadá I, Cangiano B, Persani L, Pennisi PA. Novel Insulin-Like Growth Factor 1 Gene Mutation: Broadening of the Phenotype and Implications for Insulin Resistance. J Clin Endocrinol Metab 2022; 108:1355-1369. [PMID: 36546343 DOI: 10.1210/clinem/dgac738] [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: 05/26/2022] [Revised: 11/23/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE Insulin-like Growth Factor (IGF)1 gene mutations are extremely rare causes of pre- and post-natal growth retardation. Phenotype can be heterogenous with varying degrees of neurosensory deafness, cognitive defects, glucose metabolism impairment and short stature. This study describes a 12.6-year-old girl presenting severe short stature and insulin resistance, but with normal hearing and neurological development at the lower limit of normal. METHODS DNA was obtained from the proband and both parents for whole exome sequencing (WES). In silico analysis was performed to predict the impact of the IGF1 variant on IGF1 and insulin receptors (IGF1R and IR) signalling. Phosphorylation of the IGF1R at activating Tyr residues and cell proliferation analyses were used to assess the ability of each subject's IGF1 to bind and activate IGF1R. RESULTS The proband had low immunoreactive IGF1 in serum and WES revealed a novel homozygous IGF1 missense variant (c.247A > T), causing a change of serine 83 for cysteine (p.Ser83Cys; p.Ser35Cys in mature peptide). The proband's parents were heterozygous for this mutation. In silico analyses indicated the pathogenic potential of the variant with electrostatic variations with the potential of hampering the interaction with the IGF1R but strengthening the binding to IR. The mutant IGF1 protein had a significantly reduced activity on in vitro bioassays. MAIN CONCLUSIONS We describe a novel IGF1 mutation leading to severe loss of circulating IGF1 immunoreactivity and bioactivity, In silico modelling predicts that the mutant IGF1 could interfere with IR signalling, providing a possible explanation for the severe insulin resistance observed in the patient. The absence of significant hearing and neurodevelopmental involvement in the present case is unusual and broadens the clinical spectrum of IGF1 mutations.
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Affiliation(s)
- Claudio Giacomozzi
- Unit of Pediatrics, Department of Maternal and Child Health, Carlo Poma Hospital, ASST-Mantova, Mantua, Italy
| | - Ayelen Martin
- Centro de Investigaciones Endocrinológicas 'Dr César Bergadá' (CEDIE) CONICET - FEI - División de Endocrinología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina
| | - María Celia Fernández
- Centro de Investigaciones Endocrinológicas 'Dr César Bergadá' (CEDIE) CONICET - FEI - División de Endocrinología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Mariana Gutiérrez
- Centro de Investigaciones Endocrinológicas 'Dr César Bergadá' (CEDIE) CONICET - FEI - División de Endocrinología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Maria Iascone
- Department of Medical Genetics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Horacio M Domené
- Centro de Investigaciones Endocrinológicas 'Dr César Bergadá' (CEDIE) CONICET - FEI - División de Endocrinología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Fernando P Dominici
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica (IQUIFIB-CONICET), Buenos Aires, Argentina
| | - Ignacio Bergadá
- Centro de Investigaciones Endocrinológicas 'Dr César Bergadá' (CEDIE) CONICET - FEI - División de Endocrinología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Biagio Cangiano
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20100 Milan, Italy
- Department of Endocrine and Metabolic Diseases, IRCCS Istituto Auxologico Italiano, 20100 Milan, Italy
| | - Luca Persani
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20100 Milan, Italy
- Department of Endocrine and Metabolic Diseases, IRCCS Istituto Auxologico Italiano, 20100 Milan, Italy
| | - Patricia A Pennisi
- Centro de Investigaciones Endocrinológicas 'Dr César Bergadá' (CEDIE) CONICET - FEI - División de Endocrinología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina
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Zepeda-Romero LC, Zenker M, Schanze D, Schanze I, Peña-Padilla C, Quezada-Salazar CA, Pacheco-Torres PA, Rivera-Montellano ML, Aguirre-Guillén RL, Bobadilla-Morales L, Corona-Rivera A, Corona-Rivera JR. Intrafamilial phenotypic variability in autosomal recessive DOCK6-related Adams-Oliver syndrome. Eur J Med Genet 2022; 65:104653. [DOI: 10.1016/j.ejmg.2022.104653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 09/15/2022] [Accepted: 10/20/2022] [Indexed: 11/03/2022]
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Liu X, Zhao Y, Zhu J. A novel mutation in the collagen domain of
EDA
results in hypohidrotic ectodermal dysplasia by impacting the receptor‐binding capability. Mol Genet Genomic Med 2022; 11:e2119. [PMID: 36448232 PMCID: PMC10094068 DOI: 10.1002/mgg3.2119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 11/05/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Hypohidrotic ectodermal dysplasia (HED) mainly results from gene mutations in the EDA/EDAR/NF-κB pathway. Function analysis of the mutations in the collagen domain of ectodysplasin A (EDA)result in HED has been rarely studied. This study aimed at determining the mechanism by which the novel collagen domain mutation of EDA results in HED. METHODS We analyzed the DNAs from a Chinese family with HED and performed bioinformatics analysis. A new three-dimensional structure model of the EDA trimer was built and used to predict the effect of the mutations on EDA. We performed a western blot to detect EDA1 proteins in cell lysates and supernatants. We then performed coimmunoprecipitation to determine whether the mutation would affect the interaction of EDA1 with the EDA receptor (EDAR). Dual luciferase reporter assay and immunofluorescence were performed to detect the effect of the mutant EDA1 protein on nuclear factor kappa B (NF-κB) activation. RESULTS A novel missense mutation (c.593G > A, p. Gly198Glu) in the collagen domain of EDA was detected. The mutation was predicted to be disease-causing. A three-dimensional structure model of the EDA trimer was first built in this study, in which the mutation site is located around the receptor binding domain. Functional studies showed that there was no difference in the secretion activity between the mutant EDA1 and the wild-type EDA1. However, the receptor-binding activity and the transcription activation of NF-κB were impaired by the mutation. CONCLUSION We identified a novel mutation (c.593G > A, p. Gly198Glu) in the collagen domain of EDA. Bioinformatics analysis and functional studies showed this mutation was damaging, indicating that mutations in the collagen domain of EDA could result in HED by affecting the receptor-binding activity of EDA and the transcriptional activity of NF-κB.
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Affiliation(s)
- Xingyu Liu
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Central Laboratory Peking University School and Hospital of Stomatology Beijing China
| | - Yuming Zhao
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Central Laboratory Peking University School and Hospital of Stomatology Beijing China
| | - Junxia Zhu
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Central Laboratory Peking University School and Hospital of Stomatology Beijing China
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Han Q, Fu H, Chu X, Wen R, Zhang M, You T, Fu P, Qin J, Cui T. Research advances in treatment methods and drug development for rare diseases. Front Pharmacol 2022; 13:971541. [PMID: 36313320 PMCID: PMC9597619 DOI: 10.3389/fphar.2022.971541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/05/2022] [Indexed: 11/22/2022] Open
Abstract
As the incidence of rare diseases increases each year, the total number of rare disease patients worldwide is nearly 400 million. Orphan medications are drugs used to treat rare diseases. Orphan drugs, however, are rare and patients often struggle to utilize them and expensive medications during treatment. Orphan drugs have been the focus of new drug research and development for both domestic and international pharmaceutical companies as a result of the substantial investment being made in the field of rare diseases. Clinical breakthroughs have been made in every field, from traditional antibodies and small molecule drugs to gene therapy, stem cell therapy and small nucleic acid drugs. We here review the therapeutic means of rare diseases and drug development of rare diseases to show the progress of treatment of rare diseases in order to provide a reference for clinical use and new drug development of rare diseases in China.
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Affiliation(s)
- Qiaoqiao Han
- School of Pharmacy, Anhui Medical University, Hefei, Anhui, China
| | - Hengtao Fu
- Hefei Kualai Biomedical Technology Co., Ltd., Hefei, Anhui, China
| | - Xiaoyue Chu
- Hefei Kualai Biomedical Technology Co., Ltd., Hefei, Anhui, China
| | - Ruixin Wen
- School of Pharmacy, Anhui Medical University, Hefei, Anhui, China
| | - Miao Zhang
- School of Pharmacy, Anhui Medical University, Hefei, Anhui, China
| | - Tao You
- The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Peng Fu
- Guoke Saifu (Shenzhen) New Drug Research and Development Technology Co., Ltd., Shenzhen, China
- *Correspondence: Peng Fu, ; Jian Qin, ; Tao Cui,
| | - Jian Qin
- Hefei Anyaohui Health Industry Co., Ltd., Hefei, China
- *Correspondence: Peng Fu, ; Jian Qin, ; Tao Cui,
| | - Tao Cui
- State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, China
- Research Unit for Drug Metabolism, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Peng Fu, ; Jian Qin, ; Tao Cui,
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Zhang Z, Fang T, Chen L, Qiu B, Lv Y. Thyroid Function and COVID-19 Susceptibility and Its Severity: A Two-Sample Mendelian Randomization Study. Endocrinology 2022; 163:6681113. [PMID: 36048436 DOI: 10.1210/endocr/bqac139] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Indexed: 11/19/2022]
Abstract
Several observational studies have confirmed the relationship between thyroid hormones and coronavirus disease 2019 (COVID-19), but this correlation remains controversial. We performed a two-sample Mendelian randomization (MR) analysis based on the largest publicly available summary datasets. Summary statistics with 49 269 individuals for free thyroxine (FT4) and 54 288 for thyroid stimulating hormone (TSH) were used as exposure instruments. Genome-wide association studies of susceptibility (cases = 38 984; controls = 1 644 784), hospitalization (cases: 9986 = controls = 1 877 672), and very severe disease (cases = 5101; controls = 1 383 241) of COVID-19 were used as the outcome. We used the inverse-variance weighted (IVW) method as the primary analysis, and utilized MR-Egger regression, weighted median, and robust adjusted profile score (RAPS) for sensitivity analysis. Genetic predisposition to higher serum levels of FT4 within the normal range was negatively associated with the risk of COVID-19 hospitalization (odds ratio [OR] = 0.818; 95% CI, 0.718-0.932; P = 2.6 × 10-3) and very severe disease (OR = 0.758; 95% CI, 0.626-0.923; P = 5.8 × 10-3), but not susceptibility. There is no evidence that genetically predicted circulating TSH levels are associated with COVID-19 susceptibility and severity risk. Neither apparent pleiotropy nor heterogeneity were detected in the sensitivity analysis. In summary, we found that higher FT4 levels may reduce the risk of COVID-19 severity, suggesting that thyroid function testing may be required for patients with COVID-19.
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Affiliation(s)
- Zhihao Zhang
- Department of Thyroid Breast Surgery, Xi'an NO.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, P.R. China
| | - Tian Fang
- Department of Medical Oncology, Cancer Center, West China Hospital of Sichuan University, Chengdu, China
| | - Lanlan Chen
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Binxu Qiu
- Department of Gastrocolorectal and Surgery, The First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Yonggang Lv
- Department of Thyroid Breast Surgery, Xi'an NO.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, P.R. China
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Crosstalk between Glycogen-Selective Autophagy, Autophagy and Apoptosis as a Road towards Modifier Gene Discovery and New Therapeutic Strategies for Glycogen Storage Diseases. Life (Basel) 2022; 12:life12091396. [PMID: 36143432 PMCID: PMC9504455 DOI: 10.3390/life12091396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/23/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022] Open
Abstract
Glycogen storage diseases (GSDs) are rare metabolic monogenic disorders characterized by an excessive accumulation of glycogen in the cell. However, monogenic disorders are not simple regarding genotype–phenotype correlation. Genes outside the major disease-causing locus could have modulatory effect on GSDs, and thus explain the genotype–phenotype inconsistencies observed in these patients. Nowadays, when the sequencing of all clinically relevant genes, whole human exomes, and even whole human genomes is fast, easily available and affordable, we have a scientific obligation to holistically analyze data and draw smarter connections between genotype and phenotype. Recently, the importance of glycogen-selective autophagy for the pathophysiology of disorders of glycogen metabolism have been described. Therefore, in this manuscript, we review the potential role of genes involved in glycogen-selective autophagy as modifiers of GSDs. Given the small number of genes associated with glycogen-selective autophagy, we also include genes, transcription factors, and non-coding RNAs involved in autophagy. A cross-link with apoptosis is addressed. All these genes could be analyzed in GSD patients with unusual discrepancies between genotype and phenotype in order to discover genetic variants potentially modifying their phenotype. The discovery of modifier genes related to glycogen-selective autophagy and autophagy will start a new chapter in understanding of GSDs and enable the usage of autophagy-inducing drugs for the treatment of this group of rare-disease patients.
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Prediction of Regulatory SNPs in Putative Minor Genes of the Neuro-Cardiovascular Variant in Fabry Reveals Insights into Autophagy/Apoptosis and Fibrosis. BIOLOGY 2022; 11:biology11091287. [PMID: 36138766 PMCID: PMC9495465 DOI: 10.3390/biology11091287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022]
Abstract
Even though a mutation in monogenic diseases leads to a “classic” manifestation, many disorders exhibit great clinical variability that could be due to modifying genes also called minor genes. Fabry disease (FD) is an X-linked inborn error resulting from the deficient or absent activity of alpha-galactosidase A (α-GAL) enzyme, that leads to deposits of globotriaosylceramide. With our proprietary software SNPclinic v.1.0, we analyzed 110 single nucleotide polymorphisms (SNPs) in the proximal promoter of 14 genes that could modify the FD phenotype FD. We found seven regulatory-SNP (rSNPs) in three genes (IL10, TGFB1 and EDN1) in five cell lines relevant to FD (Cardiac myocytes and fibroblasts, Astrocytes-cerebellar, endothelial cells and T helper cells 1-TH1). Each SNP was confirmed as a true rSNP in public eQTL databases, and additional software suggested the prediction of variants. The two proposed rSNPs in IL10, could explain components for the regulation of active B cells that influence the fibrosis process. The three predicted rSNPs in TGFB1, could act in apoptosis-autophagy regulation. The two putative rSNPs in EDN1, putatively regulate chronic inflammation. The seven rSNPs described here could act to modulate Fabry’s clinical phenotype so we propose that IL10, TGFB1 and EDN1 be considered minor genes in FD.
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Olguín V, Durán A, Las Heras M, Rubilar JC, Cubillos FA, Olguín P, Klein AD. Genetic Background Matters: Population-Based Studies in Model Organisms for Translational Research. Int J Mol Sci 2022; 23:ijms23147570. [PMID: 35886916 PMCID: PMC9316598 DOI: 10.3390/ijms23147570] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 02/01/2023] Open
Abstract
We are all similar but a bit different. These differences are partially due to variations in our genomes and are related to the heterogeneity of symptoms and responses to treatments that patients exhibit. Most animal studies are performed in one single strain with one manipulation. However, due to the lack of variability, therapies are not always reproducible when treatments are translated to humans. Panels of already sequenced organisms are valuable tools for mimicking human phenotypic heterogeneities and gene mapping. This review summarizes the current knowledge of mouse, fly, and yeast panels with insightful applications for translational research.
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Affiliation(s)
- Valeria Olguín
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile; (V.O.); (A.D.); (M.L.H.); (J.C.R.)
| | - Anyelo Durán
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile; (V.O.); (A.D.); (M.L.H.); (J.C.R.)
| | - Macarena Las Heras
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile; (V.O.); (A.D.); (M.L.H.); (J.C.R.)
| | - Juan Carlos Rubilar
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile; (V.O.); (A.D.); (M.L.H.); (J.C.R.)
| | - Francisco A. Cubillos
- Departamento de Biología, Santiago, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 9170022, Chile;
- Millennium Institute for Integrative Biology (iBio), Santiago 7500565, Chile
| | - Patricio Olguín
- Program in Human Genetics, Institute of Biomedical Sciences, Biomedical Neurosciences Institute, Department of Neuroscience, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile;
| | - Andrés D. Klein
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile; (V.O.); (A.D.); (M.L.H.); (J.C.R.)
- Correspondence:
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Kingdom R, Tuke M, Wood A, Beaumont RN, Frayling TM, Weedon MN, Wright CF. Rare genetic variants in genes and loci linked to dominant monogenic developmental disorders cause milder related phenotypes in the general population. Am J Hum Genet 2022; 109:1308-1316. [PMID: 35700724 PMCID: PMC9300873 DOI: 10.1016/j.ajhg.2022.05.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/19/2022] [Indexed: 12/02/2022] Open
Abstract
Many rare monogenic diseases are known to be caused by deleterious variants in thousands of genes, however the same variants can also be found in people without the associated clinical phenotypes. The penetrance of these monogenic variants is generally unknown in the wider population, as they are typically identified in small clinical cohorts of affected individuals and families with highly penetrant variants. Here, we investigated the phenotypic effect of rare, potentially deleterious variants in genes and loci where similar variants are known to cause monogenic developmental disorders (DDs) in a large population cohort. We used UK Biobank to investigate phenotypes associated with rare protein-truncating and missense variants in 599 monoallelic DDG2P genes by using whole-exome-sequencing data from ∼200,000 individuals and rare copy-number variants overlapping known DD loci by using SNP-array data from ∼500,000 individuals. We found that individuals with these likely deleterious variants had a mild DD-related phenotype, including lower fluid intelligence, slower reaction times, lower numeric memory scores, and longer pairs matching times compared to the rest of the UK Biobank cohort. They were also shorter, had a higher BMI, and had significant socioeconomic disadvantages: they were less likely to be employed or be able to work and had a lower income and higher deprivation index. Our findings suggest that many genes routinely tested within pediatric genetics have deleterious variants with intermediate penetrance that may cause lifelong sub-clinical phenotypes in the general adult population.
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Affiliation(s)
- Rebecca Kingdom
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Marcus Tuke
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Andrew Wood
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Robin N Beaumont
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Timothy M Frayling
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Michael N Weedon
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK.
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Blair DR, Hoffmann TJ, Shieh JT. Common genetic variation associated with Mendelian disease severity revealed through cryptic phenotype analysis. Nat Commun 2022; 13:3675. [PMID: 35760791 PMCID: PMC9237040 DOI: 10.1038/s41467-022-31030-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 05/30/2022] [Indexed: 11/09/2022] Open
Abstract
Clinical heterogeneity is common in Mendelian disease, but small sample sizes make it difficult to identify specific contributing factors. However, if a disease represents the severely affected extreme of a spectrum of phenotypic variation, then modifier effects may be apparent within a larger subset of the population. Analyses that take advantage of this full spectrum could have substantially increased power. To test this, we developed cryptic phenotype analysis, a model-based approach that infers quantitative traits that capture disease-related phenotypic variability using qualitative symptom data. By applying this approach to 50 Mendelian diseases in two cohorts, we identify traits that reliably quantify disease severity. We then conduct genome-wide association analyses for five of the inferred cryptic phenotypes, uncovering common variation that is predictive of Mendelian disease-related diagnoses and outcomes. Overall, this study highlights the utility of computationally-derived phenotypes and biobank-scale cohorts for investigating the complex genetic architecture of Mendelian diseases.
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Affiliation(s)
- David R Blair
- Division of Medical Genetics, Department of Pediatrics, Benioff Children's Hospital, San Francisco, CA, USA.
| | - Thomas J Hoffmann
- Institute for Human Genetics, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Joseph T Shieh
- Division of Medical Genetics, Department of Pediatrics, Benioff Children's Hospital, San Francisco, CA, USA. .,Institute for Human Genetics, San Francisco, CA, USA.
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New Developments and Possibilities in Reanalysis and Reinterpretation of Whole Exome Sequencing Datasets for Unsolved Rare Diseases Using Machine Learning Approaches. Int J Mol Sci 2022; 23:ijms23126792. [PMID: 35743235 PMCID: PMC9224427 DOI: 10.3390/ijms23126792] [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: 04/30/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 11/21/2022] Open
Abstract
Rare diseases impact the lives of 300 million people in the world. Rapid advances in bioinformatics and genomic technologies have enabled the discovery of causes of 20–30% of rare diseases. However, most rare diseases have remained as unsolved enigmas to date. Newer tools and availability of high throughput sequencing data have enabled the reanalysis of previously undiagnosed patients. In this review, we have systematically compiled the latest developments in the discovery of the genetic causes of rare diseases using machine learning methods. Importantly, we have detailed methods available to reanalyze existing whole exome sequencing data of unsolved rare diseases. We have identified different reanalysis methodologies to solve problems associated with sequence alterations/mutations, variation re-annotation, protein stability, splice isoform malfunctions and oligogenic analysis. In addition, we give an overview of new developments in the field of rare disease research using whole genome sequencing data and other omics.
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50
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Musicante M, Kim HH, Chen Y, Liao F, Bhattacharya SK, Lu L, Sun Y. Regulation of endothelial nitric oxide synthase in cardiac remodeling. Int J Cardiol 2022; 364:96-101. [PMID: 35654172 DOI: 10.1016/j.ijcard.2022.05.013] [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: 11/11/2021] [Revised: 03/25/2022] [Accepted: 05/06/2022] [Indexed: 11/05/2022]
Abstract
OBJECTIVES Our previous study demonstrated that endothelial nitric oxide synthase (eNOS) gene serves as a candidate for modifiers of hypertrophic cardiomyopathy (HCM), which alters severity of HCM phenotypes. Herein, we sought to further elucidate the role of eNOS on cardiac myocyte hypertrophy and fibrosis, the major phenotypes of HCM. METHODS Male eNOS-deficient mice (eNOS-/-) and wild type control mice (eNOS+/+, C57B1/6 J) were used in this study. Myocyte size was analyzed in hematoxylin/eosin stained sections using an image analyzing system. Cardiac β-myosin heavy chain (β-MHC) and α-skeletal actin (α-SKA) levels, markers of myocyte hypertrophy were evaluated by Western blot. Cardiac collagen volume fraction (CVF) was examined in picrosirius red stained section using an image analyzing system. Cardiac expression of tissue inhibitor of metalloproteinase 1 (TIMP-1) and transforming growth factor beta 1 (TGF-β1), markers of fibrosis, were determined by Western blot. RESULTS Compared to eNOS+/+ mice, we found that; 1) myocyte size was significantly increased in eNOS-/- mice; 2) cardiac expression of β-MHC was markedly elevated, while α-SKA levels remained unchanged in eNOS-/- mice; 3) cardiac total and interstitial CVF levels were significantly higher in eNOS-/- mice; and 4) cardiac TIMP-1 levels were significantly greater in eNOS-/- mice, however, cardiac TGF-β1 was not differently expressed between the two groups. CONCLUSION The current study revealed that eNOS plays a beneficial role in cardiac remodeling, preventing the heart from development of myocyte hypertrophy and cardiac fibrosis. These findings support our previous report that eNOS may modify the severity of HCM phenotypes.
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Affiliation(s)
- Meryl Musicante
- University of Tennessee Health Science Center, United States of America
| | - Hannah H Kim
- University of Tennessee Health Science Center, United States of America
| | - Yuanjian Chen
- Division of Cardiovascular Diseases, Department of Medicine(,) University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Fang Liao
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Syamal K Bhattacharya
- Division of Cardiovascular Diseases, Department of Medicine(,) University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States of America.
| | - Yao Sun
- Division of Cardiovascular Diseases, Department of Medicine(,) University of Tennessee Health Science Center, Memphis, TN, United States of America.
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