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Murali H, Wang P, Liao EC, Wang K. Genetic variant classification by predicted protein structure: A case study on IRF6. Comput Struct Biotechnol J 2024; 23:892-904. [PMID: 38370976 PMCID: PMC10869248 DOI: 10.1016/j.csbj.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/20/2024] Open
Abstract
Next-generation genome sequencing has revolutionized genetic testing, identifying numerous rare disease-associated gene variants. However, to impute pathogenicity, computational approaches remain inadequate and functional testing of gene variant is required to provide the highest level of evidence. The emergence of AlphaFold2 has transformed the field of protein structure determination, and here we outline a strategy that leverages predicted protein structure to enhance genetic variant classification. We used the gene IRF6 as a case study due to its clinical relevance, its critical role in cleft lip/palate malformation, and the availability of experimental data on the pathogenicity of IRF6 gene variants through phenotype rescue experiments in irf6-/- zebrafish. We compared results from over 30 pathogenicity prediction tools on 37 IRF6 missense variants. IRF6 lacks an experimentally derived structure, so we used predicted structures to explore associations between mutational clustering and pathogenicity. We found that among these variants, 19 of 37 were unanimously predicted as deleterious by computational tools. Comparing in silico predictions with experimental findings, 12 variants predicted as pathogenic were experimentally determined as benign. Even with the recently published AlphaMissense model, 15/18 (83%) of the predicted pathogenic variants were experimentally determined as benign. In comparison, mapping variants to the protein revealed deleterious mutation clusters around the protein binding domain, whereas N-terminal variants tend to be benign, suggesting the importance of structural information in determining pathogenicity of mutations in this gene. In conclusion, incorporating gene-specific structural features of known pathogenic/benign mutations may provide meaningful insights into pathogenicity predictions in a gene-specific manner and facilitate the interpretation of variant pathogenicity.
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Affiliation(s)
- Hemma Murali
- Graduate Program in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA 19104, United States
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Peng Wang
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Master of Biotechnology Program, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Eric C. Liao
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Center for Craniofacial Innovation, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Kai Wang
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
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2
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Carpenter KA, Altman RB. Databases of ligand-binding pockets and protein-ligand interactions. Comput Struct Biotechnol J 2024; 23:1320-1338. [PMID: 38585646 PMCID: PMC10997877 DOI: 10.1016/j.csbj.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/16/2024] [Accepted: 03/17/2024] [Indexed: 04/09/2024] Open
Abstract
Many research groups and institutions have created a variety of databases curating experimental and predicted data related to protein-ligand binding. The landscape of available databases is dynamic, with new databases emerging and established databases becoming defunct. Here, we review the current state of databases that contain binding pockets and protein-ligand binding interactions. We have compiled a list of such databases, fifty-three of which are currently available for use. We discuss variation in how binding pockets are defined and summarize pocket-finding methods. We organize the fifty-three databases into subgroups based on goals and contents, and describe standard use cases. We also illustrate that pockets within the same protein are characterized differently across different databases. Finally, we assess critical issues of sustainability, accessibility and redundancy.
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Affiliation(s)
- Kristy A. Carpenter
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Russ B. Altman
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
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Lildballe DL, Markholt S, Lyngholm CD, Hao Q, Fagerberg C, Nielsen DG, Svensmark JH, Diness BR, Gregersen PA. Reclassification of an FBN1 variant emphasizes the importance of segregation analysis, information sharing, and multidisciplinary teamwork in understanding genetic variants in health and disease. Am J Med Genet A 2024; 194:e63795. [PMID: 39394948 DOI: 10.1002/ajmg.a.63795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/25/2024] [Accepted: 06/08/2024] [Indexed: 10/14/2024]
Abstract
Marfan syndrome (MFS) is a complex connective tissue disorder characterized by considerable clinical variability. The diagnosis of MFS is based on the Ghent criteria, which require the presence of both clinical and genetic features. MFS is primarily caused by pathogenic alterations in FBN1, which encodes the fibrillin-1 protein. Fibrillin-1 comprises multiple domains rich in cysteine residues, with disulfide bonds formed between these residues. It has long been recognized that variants that alter or introduce cysteine residues damage protein function, leading to the development of MFS. In this study, we report a cysteine-introducing variant: FBN1 variant, c.6724C>T (p.[Arg2242Cys]). We have observed this variant in several individuals without MFS, challenging our previous understanding of the underlying mechanism of MFS. This finding emphasizes the importance of revisiting and reevaluating our current knowledge in light of new and unexpected observations. Moreover, our study highlights the significance of incorporating local and national data on allele frequencies, as well as employing multidisciplinary phenotyping approaches, in the classification of genetic variants. By considering a wide range of information, we can enhance the accuracy and reliability of variant classification, ultimately improving the diagnosis and management of individuals with genetic disorders like MFS.
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Affiliation(s)
- Dorte L Lildballe
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Sara Markholt
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | | | - Qin Hao
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | | | | | - Birgitte Rode Diness
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Copenhagen University, Copenhagen, Denmark
| | - Pernille A Gregersen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
- Centre for Rare Diseases, Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
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4
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Tao J, Luo J, Li K, Yang R, Lin Y, Ge J. Comprehensive genetic analysis uncovers the mutational spectrum of MFRP and its genotype-phenotype correlation in a large cohort of Chinese microphthalmia patients. Gene 2024; 926:148647. [PMID: 38848879 DOI: 10.1016/j.gene.2024.148647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/21/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
PURPOSE Microphthalmia is a severe congenital ocular disease featured by abnormal ocular development. The aim of this study was to detail the genetic and clinical characteristics of a large cohort of Chinese patients with microphthalmia related to MFRP variants, focusing on uncovering genotype-phenotype correlations. METHODS Fifty microphthalmia patients from 44 unrelated Chinese families were recruited. Whole-exome sequencing (WES) was conducted to analyze the coding regions and adjacent intronic regions of MFRP. Axial lengths (AL) were measured for all probands and available family members. Protein structures of mutations with high frequency in our cohort were predicted. The genotype-phenotype correlations were explored by statistical analysis. RESULTS Sixteen MFRP variants were detected in 17 families, accounting for 38.64 % of all microphthalmia families. There were 9 novel mutations (c.427+1G>C, c.428-2A>C, c.561_575del:p.A188_E192del, c.836G>A:p.C279Y, c.1010_1021del:p.H337_E340del:p.Y479*, c.1516_1517del:p.S506Pfs*66, c.1561T>G:p.C521G, c.1616G>A:p.R539H, and c.1735C>T:p.P579S) and six previously reported variants in MFRP, with p.E496K and p.H337_E340del being highly frequent, found in eight (47.06 %) and two families (11.76 %), respectively. Seven variants (43.75 %) were located in the C-terminal cysteine-rich frizzled-related domain (CRD) (7/16, 43.75 %). Protein prediction implicated p.E496K and p.H337_E340del mutations might lead to a destabilization of the MFRP protein. The average AL of all 42 eyes was 16.02 ± 1.05 mm, and 78.36 % of eyes with AL < 16 mm harbored p.E496K variant. Twenty-six eyes with variant variant had shorter AL than that of the other 16 eyes without this variant (p = 0.006), highlighting a novel genotype-phenotype correlation. CONCLUSIONS In this largest cohort of Chinese patients with microphthalmia, the 9 novel variants, high frequency of p.E496W, and mutation hotspots in CRD reveals unique insights into the MFRP mutation spectrum among Chinese patients, indicating ethnic variability. A new genotype-phenotype correlation that p.E496K variant associated with a shorter AL is unveiled. Our findings enhance the current knowledge of MFRP-associated microphthalmia and provide valuable information for prenatal diagnosis as well as future therapy.
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Affiliation(s)
- Jing Tao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100730, China
| | - Jingyi Luo
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Kaijing Li
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Runcai Yang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Yixiu Lin
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Jian Ge
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong 510000, China.
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Chandrasekaran FP, Nelson EJR. Molecular dynamics simulations involving different β-propeller mutations reported in Swiss and French patients correlate with their disease phenotypes. Sci Rep 2024; 14:24133. [PMID: 39406775 PMCID: PMC11480402 DOI: 10.1038/s41598-024-75070-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 10/01/2024] [Indexed: 10/19/2024] Open
Abstract
Integrin αIIbβ3 is the predominant receptor for fibrinogen which mediates platelet aggregation, an important step in hemostasis and thrombosis. Several mutations have been reported in the genes encoding αIIb and β3 subunits among patients with Glanzmann thrombasthenia, of which 177 are in the β-propeller domain. The two subunits form a heterodimer at the interface between β-propeller and β-I domains of αIIb and β3, respectively with their stability critical for intracellular trafficking, surface expression, and ligand binding. Our study was aimed at retrieving the β-propeller mutations from various databases and studying structural variations due to select mutations upon interaction with fibrinogen using molecular docking and molecular dynamics. Mutations were studied for their impact on phenotypic severity, structural stability, and evolutionary conservation. Molecular docking analysis and molecular dynamics simulations were carried out for αIIb-β3 complexes as well as αIIbβ3-fibrinogen complexes; in particular, E355K structure had more deviations, fluctuations, and other changes which compromised its structural stability and binding affinity when compared to both wild-type and G401C structures. Our comprehensive in silico analysis clearly reiterates that mutations in the β-propeller are not only responsible for structural changes in this domain but also have implications on the overall structure and function of integrin αIIbβ3.
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Affiliation(s)
- Finola Priyadharshini Chandrasekaran
- Gene Therapy Laboratory, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632 014, India
| | - Everette Jacob Remington Nelson
- Gene Therapy Laboratory, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632 014, India.
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D'Abrusco F, Serpieri V, Taccagni CM, Garau J, Cattaneo L, Boggioni M, Gana S, Battini R, Bertini E, Zanni G, Boltshauser E, Borgatti R, Romaniello R, Signorini S, Leuzzi V, Caputi C, Manti F, D'Arrigo S, De Laurentiis A, Graziano C, Lemke JR, Morelli F, Petković Ramadža D, Sirchia F, Giorgio E, Valente EM. Pathogenic cryptic variants detectable through exome data reanalysis significantly increase the diagnostic yield in Joubert syndrome. Eur J Hum Genet 2024:10.1038/s41431-024-01703-x. [PMID: 39394465 DOI: 10.1038/s41431-024-01703-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 09/02/2024] [Accepted: 09/25/2024] [Indexed: 10/13/2024] Open
Abstract
Joubert syndrome (JS) is a genetically heterogeneous neurodevelopmental ciliopathy. Despite exome sequencing (ES), several patients remain undiagnosed. This study aims to increase the diagnostic yield by uncovering cryptic variants through targeted ES reanalysis. We first focused on 26 patients in whom ES only disclosed heterozygous pathogenic coding variants in a JS gene. We reanalyzed raw ES data searching for copy number variants (CNVs) and intronic variants affecting splicing. We validated CNVs through real-time PCR or chromosomal microarray, and splicing variants through RT-PCR or minigenes. Cryptic variants were then searched in additional 44 ES-negative JS individuals. We identified cryptic "second hits" in 14 of 26 children (54%) and biallelic cryptic variants in 3 of 44 (7%), reaching a definite diagnosis in 17 of 70 (overall diagnostic gain 24%). We show that CNVs and intronic splicing variants are a common mutational mechanism in JS; more importantly, we demonstrate that a significant proportion of such variants can be disclosed simply through a focused reanalysis of available ES data, with a significantly increase of the diagnostic yield especially among patients previously found to carry heterozygous coding variants in the KIAA0586, CC2D2A and CPLANE1 genes.
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Affiliation(s)
- Fulvio D'Abrusco
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | | | | | - Jessica Garau
- Neurogenetics Research Centre, IRCCS Mondino Foundation, Pavia, Italy
| | - Luca Cattaneo
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Monica Boggioni
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Simone Gana
- Neurogenetics Research Centre, IRCCS Mondino Foundation, Pavia, Italy
| | - Roberta Battini
- IRCCS Stella Maris Foundation, Pisa, Italy
- Department of Clinical ad Experimental Medicine, University of Pisa, Pisa, Italy
| | - Enrico Bertini
- Research Unit of Neuromuscular and Neurodegenerative Disorders, IRCCS Bambino Gesù Pediatric Hospital, Rome, Italy
| | - Ginevra Zanni
- Research Unit of Neuromuscular and Neurodegenerative Disorders, IRCCS Bambino Gesù Pediatric Hospital, Rome, Italy
| | | | - Renato Borgatti
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Child Neurology and Psychiatry Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Romina Romaniello
- Child Neurology and Psychiatry Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Sabrina Signorini
- Child Neurology and Psychiatry Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Vincenzo Leuzzi
- Department of Human Neuroscience, Unit of Child Neurology and Psychiatry, Sapienza University of Rome, Rome, Italy
| | - Caterina Caputi
- Developmental Age Rehabilitation Service, Trasimeno District, Magione (PG), Italy
| | - Filippo Manti
- Department of Human Neuroscience, Unit of Child Neurology and Psychiatry, Sapienza University of Rome, Rome, Italy
| | - Stefano D'Arrigo
- Department of Developmental Neurology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Arianna De Laurentiis
- Department of Developmental Neurology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Claudio Graziano
- Medical Genetics Unit, MeLabeT Department, AUSL Romagna, Cesena, Italy
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig, Leipzig, Germany
| | - Federica Morelli
- Department of Psychiatry, Autism Spectrum Disorders and Related Conditions Service, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Danijela Petković Ramadža
- Department of Pediatrics, University Hospital Centre Zagreb and University of Zagreb School of Medicine, Zagreb, Croatia
| | - Fabio Sirchia
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Medical Genetics Unit, IRCCS San Matteo Foundation, Pavia, Italy
| | - Elisa Giorgio
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Neurogenetics Research Centre, IRCCS Mondino Foundation, Pavia, Italy
| | - Enza Maria Valente
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.
- Neurogenetics Research Centre, IRCCS Mondino Foundation, Pavia, Italy.
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Choi HS, Kwon OI, Kim SS, Cho JY, Bae EH, Ma SK, Kim SW, Kim CS. Fabry disease in female monozygotic twins with complex intronic haplotype variants: a case report. BMC Med Genomics 2024; 17:245. [PMID: 39375654 PMCID: PMC11460125 DOI: 10.1186/s12920-024-02021-3] [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: 06/02/2024] [Accepted: 09/27/2024] [Indexed: 10/09/2024] Open
Abstract
BACKGROUND Fabry disease is an X-linked lysosomal storage disease caused by the impairment of α-galactosidase A. The complex intronic haplotype (CIH) variants, located in promoter and intronic regulatory lesions, has been found in patients with classical forms of Fabry disease. We present a case of Fabry disease in female monozygotic twins exhibiting the CIH mutation and classical manifestations. CASE PRESENTATION A 61-year-old woman with a history of stroke, carotid artery occlusion, hypertrophic cardiomyopathy, and chronic kidney disease was referred to the nephrology clinic for management of her chronic kidney disease. Her monozygotic twin sister also presented with hypertrophic cardiomyopathy, atrial flutter, carotid stenosis, and proteinuria. Clinical symptoms and a comprehensive family history strongly suggested the presence of Fabry disease. Genetic analysis revealed the presence of 5 variants within a complex intronic haplotype (CIH): c.-10 C > T, c.369 + 990 C > A, c.370 - 81_370-77delCAGCC, c.640-16 A > G, and c.1000-22 C > T. We conducted a review of the patient's previous kidney biopsy findings, which demonstrated the presence of lamellated inclusion bodies in electron microscopy. Remarkably, both the monozygotic twin sister and her son exhibited the same genetic mutation. Enzyme replacement therapy was initiated for the patient. Her kidney function decreased throughout a thorough 2-year follow-up period, while there was a slight decrease in the left ventricular mass index. CONCLUSIONS This is the first reported case of female monozygotic twins with the CIH variants representing cardiac, cerebrovascular, and renal manifestations suggestive of Fabry disease.
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Affiliation(s)
- Hong Sang Choi
- Department of Internal Medicine, Chonnam National University Medical School, 160, Baekseo‑ro, Dong‑gu, Gwangju, 61469, Republic of Korea
- Department of Internal Medicine, Chonnam National University Hospital, Gwangju, Korea
| | - Oh Il Kwon
- Department of Internal Medicine, Chonnam National University Hospital, Gwangju, Korea
| | - Sung Sun Kim
- Department of Pathology, Chonnam National University Medical School and Hospital, Gwangju, South Korea
| | - Jae Yeong Cho
- Department of Internal Medicine, Chonnam National University Hospital, Gwangju, Korea
- Department of Cardiovascular Medicine, Chonnam National University Medical School and Hospital, Gwangju, Korea
| | - Eun Hui Bae
- Department of Internal Medicine, Chonnam National University Medical School, 160, Baekseo‑ro, Dong‑gu, Gwangju, 61469, Republic of Korea
- Department of Internal Medicine, Chonnam National University Hospital, Gwangju, Korea
| | - Seong Kwon Ma
- Department of Internal Medicine, Chonnam National University Medical School, 160, Baekseo‑ro, Dong‑gu, Gwangju, 61469, Republic of Korea
- Department of Internal Medicine, Chonnam National University Hospital, Gwangju, Korea
| | - Soo Wan Kim
- Department of Internal Medicine, Chonnam National University Medical School, 160, Baekseo‑ro, Dong‑gu, Gwangju, 61469, Republic of Korea
- Department of Internal Medicine, Chonnam National University Hospital, Gwangju, Korea
| | - Chang Seong Kim
- Department of Internal Medicine, Chonnam National University Medical School, 160, Baekseo‑ro, Dong‑gu, Gwangju, 61469, Republic of Korea.
- Department of Internal Medicine, Chonnam National University Hospital, Gwangju, Korea.
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Singh S, Badiger VA, Balan S, Nampoothiri S, Rao AP, Shah H, Bhavani GS, Narayanan DL, Girisha KM. Thirteen Indians with camptodactyly-arthropathy-coxa vara-pericarditis syndrome. Clin Dysmorphol 2024; 33:152-159. [PMID: 38856641 DOI: 10.1097/mcd.0000000000000500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Camptodactyly-arthropathy-coxa vara-pericarditis (CACP) syndrome (MIM# 208250) is a rare monogenic disorder, characterized by early onset of camptodactyly, progressive coxa vara, bilateral arthropathy and constrictive pericarditis. The syndrome is caused by biallelic loss-of-function variants in PRG4 . Deficiency of PRG4 results in progressive worsening of joint deformity with age. Thirteen individuals with CACP syndrome from eight consanguineous Indian families were evaluated. We used exome sequencing to elucidate disease-causing variants in all the probands. These variants were further validated and segregated by Sanger sequencing, confirming the diagnosis of CACP syndrome in them. Seven females and six males aged 2-23 years were studied. Camptodactyly (13/13), coxa vara (11/13), short femoral neck (11/13) and arthritis in large joints (12/13) [wrists (11/13), ankle (11/13), elbow (10/13) and knee (10/13)] were observed commonly. Five novel disease-causing variants (c.3636G>T, c.1935del, c.1134dup, c.1699del and c.962T>A) and two previously reported variants (c.1910_1911del and c.2816_2817del) were identified in homozygous state in PRG4 . We describe the phenotype and mutations in one of the large cohorts of patients with CACP syndrome, from India.
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Affiliation(s)
- Swati Singh
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka
| | - Vaishnavi Ashok Badiger
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka
| | - Suma Balan
- Department of Rheumatology and Clinical Immunology, Amrita Institute of Medical Sciences and Research Centre
| | - Sheela Nampoothiri
- Department of Paediatric Genetics, Amrita Institute of Medical Sciences and Research Centre, Kochi, Kerala
| | - Anand Prahalad Rao
- Department of Paediatric Rheumatology, Indira Gandhi Institute of Child Health, Bangalore
| | - Hitesh Shah
- Department of Paediatric Orthopaedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka
| | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka
- DBT-Wellcome Trust India Alliance Early Career Clinical and Public Health Research Fellow, Hyderabad, Telangana, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
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9
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Dulski J, Baker M, Banks SA, Bayat M, Bruffaerts R, Ortiz Cruz G, Disserol CC, Fisher KS, Jose JN, Kalman B, Kantarci OH, Maltsev D, Middleton C, Novotni G, Plaseska-Karanfilska D, Raskin S, Souza J, Teive HA, Wszolek ZK. Global Presence and Penetrance of CSF1R-Related Disorder. Neurol Genet 2024; 10:e200187. [PMID: 39280886 PMCID: PMC11398975 DOI: 10.1212/nxg.0000000000200187] [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: 03/11/2024] [Accepted: 07/17/2024] [Indexed: 09/18/2024]
Abstract
Objectives To highlight the worldwide presence of CSF1R-related disorder (CSF1R-RD), discuss its penetrance, and provide the first haplotype analysis. Methods Data on patients worldwide were collected, including demographics, genotype, family history, and clinical status. For haplotype analysis, polymorphisms of short tandem repeats in 3 distinct families with CSF1R p.Ile794Thr variant were examined. Results Nineteen new patients were included, at a mean age of 38.7 years (ranging from 11 to 74 years), from 14 families from the Americas, Asia, Australia, and Europe, including the first from Mexico, North Macedonia, and Ukraine. Fifteen CSF1R variants were found, including 8 novel. Three patients were compound heterozygotes with disease onset at 1, 4, and 22 years. Patients with heterozygous CSF1R variants developed symptoms at a mean of 39.0 years (range 8-71 years). Four patients died at a mean of 3.3 years from onset (range 2-5 years). Negative family history was noted in 7 patients. In haplotype analysis, 2 families exhibited shared haplotype encompassing ∼6-Mb region downstream of the CSF1R while the third family displayed a different haplotype. Discussion CSF1R-RD has a global prevalence. The reasons for negative family history include de novo variants (as shown by the haplotype analysis), mosaicism, and incomplete penetrance, which are possibly modulated by environmental and genetic factors.
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Affiliation(s)
- Jaroslaw Dulski
- From the Department of Neurology (J.D., Z.K.W.), Mayo Clinic, Jacksonville, FL; Division of Neurological and Psychiatric Nursing (J.D.), Faculty of Health Sciences, Medical University of Gdansk; Neurology Department (J.D.), St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland; Department of Neuroscience (M. Baker), Mayo Clinic, Jacksonville, FL; Department of Neurology (S.A.B., O.H.K.), Mayo Clinic, Rochester, MN; Department of Neurology (M. Bayat); Centre for Rare Diseases (M. Bayat), Aarhus University Hospital, Aarhus, Denmark; Experimental Neurobiology Unit (R.B.), Department of Biomedical Sciences, University of Antwerp; Department of Neurology, Antwerp University Hospital, Belgium; Center for Research in Genetics and Genomics (CIGEN) (G.O.C.), Autonomous University of Coahuila, México; Universidade Federal do Paraná (C.C.D.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Curitiba, Brazil; Department of Pediatrics (K.S.F.), Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, TX; Department of Paediatrics (J.N.J.), St. Johns Medical College, Bangalore, Karnataka, India; Office of the Dean (B.K.), University of Pécs, School of Medicine; Molecular Medicine (B.K.), Markusovszky University Teaching Hospital, Szombathely, Hungary; Immunology and Molecular Biology Laboratory of Experimental and Clinical Medicine Institute at the O'Bogomolets National Medical University (D.M.), Kyiv, Ukraine; General Practice (C.M.), Brisbane, Queensland, Australia; Department of Cognitive Neurology and Neurodegenerative Diseases (G.N.), University Clinic of Neurology, Medical Faculty, University "Ss. Cyril and Methodius", Institute for Alzheimer's Disease and Neuroscience-Skopje; Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov" (D.P.-K.), Macedonian Academy of Sciences and Arts, Skopje, North Macedonia; Postgraduate Program in Child and Adolescent (S.R.), Department of Pediatrics, Federal University of Paraná, Curitiba; School of Medicine (J.S.), Pontificia Universidade Católica do Paraná (PUCPR); Department of Genetics (J.S.), Hospital Infantil Pequeno Príncipe; and Universidade Federal do Paraná (H.A.T.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Setor de Distúrbios do Movimento, Curitiba, Brazil
| | - Matthew Baker
- From the Department of Neurology (J.D., Z.K.W.), Mayo Clinic, Jacksonville, FL; Division of Neurological and Psychiatric Nursing (J.D.), Faculty of Health Sciences, Medical University of Gdansk; Neurology Department (J.D.), St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland; Department of Neuroscience (M. Baker), Mayo Clinic, Jacksonville, FL; Department of Neurology (S.A.B., O.H.K.), Mayo Clinic, Rochester, MN; Department of Neurology (M. Bayat); Centre for Rare Diseases (M. Bayat), Aarhus University Hospital, Aarhus, Denmark; Experimental Neurobiology Unit (R.B.), Department of Biomedical Sciences, University of Antwerp; Department of Neurology, Antwerp University Hospital, Belgium; Center for Research in Genetics and Genomics (CIGEN) (G.O.C.), Autonomous University of Coahuila, México; Universidade Federal do Paraná (C.C.D.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Curitiba, Brazil; Department of Pediatrics (K.S.F.), Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, TX; Department of Paediatrics (J.N.J.), St. Johns Medical College, Bangalore, Karnataka, India; Office of the Dean (B.K.), University of Pécs, School of Medicine; Molecular Medicine (B.K.), Markusovszky University Teaching Hospital, Szombathely, Hungary; Immunology and Molecular Biology Laboratory of Experimental and Clinical Medicine Institute at the O'Bogomolets National Medical University (D.M.), Kyiv, Ukraine; General Practice (C.M.), Brisbane, Queensland, Australia; Department of Cognitive Neurology and Neurodegenerative Diseases (G.N.), University Clinic of Neurology, Medical Faculty, University "Ss. Cyril and Methodius", Institute for Alzheimer's Disease and Neuroscience-Skopje; Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov" (D.P.-K.), Macedonian Academy of Sciences and Arts, Skopje, North Macedonia; Postgraduate Program in Child and Adolescent (S.R.), Department of Pediatrics, Federal University of Paraná, Curitiba; School of Medicine (J.S.), Pontificia Universidade Católica do Paraná (PUCPR); Department of Genetics (J.S.), Hospital Infantil Pequeno Príncipe; and Universidade Federal do Paraná (H.A.T.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Setor de Distúrbios do Movimento, Curitiba, Brazil
| | - Samantha A Banks
- From the Department of Neurology (J.D., Z.K.W.), Mayo Clinic, Jacksonville, FL; Division of Neurological and Psychiatric Nursing (J.D.), Faculty of Health Sciences, Medical University of Gdansk; Neurology Department (J.D.), St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland; Department of Neuroscience (M. Baker), Mayo Clinic, Jacksonville, FL; Department of Neurology (S.A.B., O.H.K.), Mayo Clinic, Rochester, MN; Department of Neurology (M. Bayat); Centre for Rare Diseases (M. Bayat), Aarhus University Hospital, Aarhus, Denmark; Experimental Neurobiology Unit (R.B.), Department of Biomedical Sciences, University of Antwerp; Department of Neurology, Antwerp University Hospital, Belgium; Center for Research in Genetics and Genomics (CIGEN) (G.O.C.), Autonomous University of Coahuila, México; Universidade Federal do Paraná (C.C.D.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Curitiba, Brazil; Department of Pediatrics (K.S.F.), Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, TX; Department of Paediatrics (J.N.J.), St. Johns Medical College, Bangalore, Karnataka, India; Office of the Dean (B.K.), University of Pécs, School of Medicine; Molecular Medicine (B.K.), Markusovszky University Teaching Hospital, Szombathely, Hungary; Immunology and Molecular Biology Laboratory of Experimental and Clinical Medicine Institute at the O'Bogomolets National Medical University (D.M.), Kyiv, Ukraine; General Practice (C.M.), Brisbane, Queensland, Australia; Department of Cognitive Neurology and Neurodegenerative Diseases (G.N.), University Clinic of Neurology, Medical Faculty, University "Ss. Cyril and Methodius", Institute for Alzheimer's Disease and Neuroscience-Skopje; Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov" (D.P.-K.), Macedonian Academy of Sciences and Arts, Skopje, North Macedonia; Postgraduate Program in Child and Adolescent (S.R.), Department of Pediatrics, Federal University of Paraná, Curitiba; School of Medicine (J.S.), Pontificia Universidade Católica do Paraná (PUCPR); Department of Genetics (J.S.), Hospital Infantil Pequeno Príncipe; and Universidade Federal do Paraná (H.A.T.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Setor de Distúrbios do Movimento, Curitiba, Brazil
| | - Michael Bayat
- From the Department of Neurology (J.D., Z.K.W.), Mayo Clinic, Jacksonville, FL; Division of Neurological and Psychiatric Nursing (J.D.), Faculty of Health Sciences, Medical University of Gdansk; Neurology Department (J.D.), St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland; Department of Neuroscience (M. Baker), Mayo Clinic, Jacksonville, FL; Department of Neurology (S.A.B., O.H.K.), Mayo Clinic, Rochester, MN; Department of Neurology (M. Bayat); Centre for Rare Diseases (M. Bayat), Aarhus University Hospital, Aarhus, Denmark; Experimental Neurobiology Unit (R.B.), Department of Biomedical Sciences, University of Antwerp; Department of Neurology, Antwerp University Hospital, Belgium; Center for Research in Genetics and Genomics (CIGEN) (G.O.C.), Autonomous University of Coahuila, México; Universidade Federal do Paraná (C.C.D.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Curitiba, Brazil; Department of Pediatrics (K.S.F.), Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, TX; Department of Paediatrics (J.N.J.), St. Johns Medical College, Bangalore, Karnataka, India; Office of the Dean (B.K.), University of Pécs, School of Medicine; Molecular Medicine (B.K.), Markusovszky University Teaching Hospital, Szombathely, Hungary; Immunology and Molecular Biology Laboratory of Experimental and Clinical Medicine Institute at the O'Bogomolets National Medical University (D.M.), Kyiv, Ukraine; General Practice (C.M.), Brisbane, Queensland, Australia; Department of Cognitive Neurology and Neurodegenerative Diseases (G.N.), University Clinic of Neurology, Medical Faculty, University "Ss. Cyril and Methodius", Institute for Alzheimer's Disease and Neuroscience-Skopje; Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov" (D.P.-K.), Macedonian Academy of Sciences and Arts, Skopje, North Macedonia; Postgraduate Program in Child and Adolescent (S.R.), Department of Pediatrics, Federal University of Paraná, Curitiba; School of Medicine (J.S.), Pontificia Universidade Católica do Paraná (PUCPR); Department of Genetics (J.S.), Hospital Infantil Pequeno Príncipe; and Universidade Federal do Paraná (H.A.T.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Setor de Distúrbios do Movimento, Curitiba, Brazil
| | - Rose Bruffaerts
- From the Department of Neurology (J.D., Z.K.W.), Mayo Clinic, Jacksonville, FL; Division of Neurological and Psychiatric Nursing (J.D.), Faculty of Health Sciences, Medical University of Gdansk; Neurology Department (J.D.), St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland; Department of Neuroscience (M. Baker), Mayo Clinic, Jacksonville, FL; Department of Neurology (S.A.B., O.H.K.), Mayo Clinic, Rochester, MN; Department of Neurology (M. Bayat); Centre for Rare Diseases (M. Bayat), Aarhus University Hospital, Aarhus, Denmark; Experimental Neurobiology Unit (R.B.), Department of Biomedical Sciences, University of Antwerp; Department of Neurology, Antwerp University Hospital, Belgium; Center for Research in Genetics and Genomics (CIGEN) (G.O.C.), Autonomous University of Coahuila, México; Universidade Federal do Paraná (C.C.D.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Curitiba, Brazil; Department of Pediatrics (K.S.F.), Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, TX; Department of Paediatrics (J.N.J.), St. Johns Medical College, Bangalore, Karnataka, India; Office of the Dean (B.K.), University of Pécs, School of Medicine; Molecular Medicine (B.K.), Markusovszky University Teaching Hospital, Szombathely, Hungary; Immunology and Molecular Biology Laboratory of Experimental and Clinical Medicine Institute at the O'Bogomolets National Medical University (D.M.), Kyiv, Ukraine; General Practice (C.M.), Brisbane, Queensland, Australia; Department of Cognitive Neurology and Neurodegenerative Diseases (G.N.), University Clinic of Neurology, Medical Faculty, University "Ss. Cyril and Methodius", Institute for Alzheimer's Disease and Neuroscience-Skopje; Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov" (D.P.-K.), Macedonian Academy of Sciences and Arts, Skopje, North Macedonia; Postgraduate Program in Child and Adolescent (S.R.), Department of Pediatrics, Federal University of Paraná, Curitiba; School of Medicine (J.S.), Pontificia Universidade Católica do Paraná (PUCPR); Department of Genetics (J.S.), Hospital Infantil Pequeno Príncipe; and Universidade Federal do Paraná (H.A.T.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Setor de Distúrbios do Movimento, Curitiba, Brazil
| | - Gabriela Ortiz Cruz
- From the Department of Neurology (J.D., Z.K.W.), Mayo Clinic, Jacksonville, FL; Division of Neurological and Psychiatric Nursing (J.D.), Faculty of Health Sciences, Medical University of Gdansk; Neurology Department (J.D.), St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland; Department of Neuroscience (M. Baker), Mayo Clinic, Jacksonville, FL; Department of Neurology (S.A.B., O.H.K.), Mayo Clinic, Rochester, MN; Department of Neurology (M. Bayat); Centre for Rare Diseases (M. Bayat), Aarhus University Hospital, Aarhus, Denmark; Experimental Neurobiology Unit (R.B.), Department of Biomedical Sciences, University of Antwerp; Department of Neurology, Antwerp University Hospital, Belgium; Center for Research in Genetics and Genomics (CIGEN) (G.O.C.), Autonomous University of Coahuila, México; Universidade Federal do Paraná (C.C.D.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Curitiba, Brazil; Department of Pediatrics (K.S.F.), Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, TX; Department of Paediatrics (J.N.J.), St. Johns Medical College, Bangalore, Karnataka, India; Office of the Dean (B.K.), University of Pécs, School of Medicine; Molecular Medicine (B.K.), Markusovszky University Teaching Hospital, Szombathely, Hungary; Immunology and Molecular Biology Laboratory of Experimental and Clinical Medicine Institute at the O'Bogomolets National Medical University (D.M.), Kyiv, Ukraine; General Practice (C.M.), Brisbane, Queensland, Australia; Department of Cognitive Neurology and Neurodegenerative Diseases (G.N.), University Clinic of Neurology, Medical Faculty, University "Ss. Cyril and Methodius", Institute for Alzheimer's Disease and Neuroscience-Skopje; Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov" (D.P.-K.), Macedonian Academy of Sciences and Arts, Skopje, North Macedonia; Postgraduate Program in Child and Adolescent (S.R.), Department of Pediatrics, Federal University of Paraná, Curitiba; School of Medicine (J.S.), Pontificia Universidade Católica do Paraná (PUCPR); Department of Genetics (J.S.), Hospital Infantil Pequeno Príncipe; and Universidade Federal do Paraná (H.A.T.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Setor de Distúrbios do Movimento, Curitiba, Brazil
| | - Caio C Disserol
- From the Department of Neurology (J.D., Z.K.W.), Mayo Clinic, Jacksonville, FL; Division of Neurological and Psychiatric Nursing (J.D.), Faculty of Health Sciences, Medical University of Gdansk; Neurology Department (J.D.), St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland; Department of Neuroscience (M. Baker), Mayo Clinic, Jacksonville, FL; Department of Neurology (S.A.B., O.H.K.), Mayo Clinic, Rochester, MN; Department of Neurology (M. Bayat); Centre for Rare Diseases (M. Bayat), Aarhus University Hospital, Aarhus, Denmark; Experimental Neurobiology Unit (R.B.), Department of Biomedical Sciences, University of Antwerp; Department of Neurology, Antwerp University Hospital, Belgium; Center for Research in Genetics and Genomics (CIGEN) (G.O.C.), Autonomous University of Coahuila, México; Universidade Federal do Paraná (C.C.D.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Curitiba, Brazil; Department of Pediatrics (K.S.F.), Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, TX; Department of Paediatrics (J.N.J.), St. Johns Medical College, Bangalore, Karnataka, India; Office of the Dean (B.K.), University of Pécs, School of Medicine; Molecular Medicine (B.K.), Markusovszky University Teaching Hospital, Szombathely, Hungary; Immunology and Molecular Biology Laboratory of Experimental and Clinical Medicine Institute at the O'Bogomolets National Medical University (D.M.), Kyiv, Ukraine; General Practice (C.M.), Brisbane, Queensland, Australia; Department of Cognitive Neurology and Neurodegenerative Diseases (G.N.), University Clinic of Neurology, Medical Faculty, University "Ss. Cyril and Methodius", Institute for Alzheimer's Disease and Neuroscience-Skopje; Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov" (D.P.-K.), Macedonian Academy of Sciences and Arts, Skopje, North Macedonia; Postgraduate Program in Child and Adolescent (S.R.), Department of Pediatrics, Federal University of Paraná, Curitiba; School of Medicine (J.S.), Pontificia Universidade Católica do Paraná (PUCPR); Department of Genetics (J.S.), Hospital Infantil Pequeno Príncipe; and Universidade Federal do Paraná (H.A.T.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Setor de Distúrbios do Movimento, Curitiba, Brazil
| | - Kristen S Fisher
- From the Department of Neurology (J.D., Z.K.W.), Mayo Clinic, Jacksonville, FL; Division of Neurological and Psychiatric Nursing (J.D.), Faculty of Health Sciences, Medical University of Gdansk; Neurology Department (J.D.), St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland; Department of Neuroscience (M. Baker), Mayo Clinic, Jacksonville, FL; Department of Neurology (S.A.B., O.H.K.), Mayo Clinic, Rochester, MN; Department of Neurology (M. Bayat); Centre for Rare Diseases (M. Bayat), Aarhus University Hospital, Aarhus, Denmark; Experimental Neurobiology Unit (R.B.), Department of Biomedical Sciences, University of Antwerp; Department of Neurology, Antwerp University Hospital, Belgium; Center for Research in Genetics and Genomics (CIGEN) (G.O.C.), Autonomous University of Coahuila, México; Universidade Federal do Paraná (C.C.D.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Curitiba, Brazil; Department of Pediatrics (K.S.F.), Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, TX; Department of Paediatrics (J.N.J.), St. Johns Medical College, Bangalore, Karnataka, India; Office of the Dean (B.K.), University of Pécs, School of Medicine; Molecular Medicine (B.K.), Markusovszky University Teaching Hospital, Szombathely, Hungary; Immunology and Molecular Biology Laboratory of Experimental and Clinical Medicine Institute at the O'Bogomolets National Medical University (D.M.), Kyiv, Ukraine; General Practice (C.M.), Brisbane, Queensland, Australia; Department of Cognitive Neurology and Neurodegenerative Diseases (G.N.), University Clinic of Neurology, Medical Faculty, University "Ss. Cyril and Methodius", Institute for Alzheimer's Disease and Neuroscience-Skopje; Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov" (D.P.-K.), Macedonian Academy of Sciences and Arts, Skopje, North Macedonia; Postgraduate Program in Child and Adolescent (S.R.), Department of Pediatrics, Federal University of Paraná, Curitiba; School of Medicine (J.S.), Pontificia Universidade Católica do Paraná (PUCPR); Department of Genetics (J.S.), Hospital Infantil Pequeno Príncipe; and Universidade Federal do Paraná (H.A.T.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Setor de Distúrbios do Movimento, Curitiba, Brazil
| | - Jainy N Jose
- From the Department of Neurology (J.D., Z.K.W.), Mayo Clinic, Jacksonville, FL; Division of Neurological and Psychiatric Nursing (J.D.), Faculty of Health Sciences, Medical University of Gdansk; Neurology Department (J.D.), St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland; Department of Neuroscience (M. Baker), Mayo Clinic, Jacksonville, FL; Department of Neurology (S.A.B., O.H.K.), Mayo Clinic, Rochester, MN; Department of Neurology (M. Bayat); Centre for Rare Diseases (M. Bayat), Aarhus University Hospital, Aarhus, Denmark; Experimental Neurobiology Unit (R.B.), Department of Biomedical Sciences, University of Antwerp; Department of Neurology, Antwerp University Hospital, Belgium; Center for Research in Genetics and Genomics (CIGEN) (G.O.C.), Autonomous University of Coahuila, México; Universidade Federal do Paraná (C.C.D.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Curitiba, Brazil; Department of Pediatrics (K.S.F.), Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, TX; Department of Paediatrics (J.N.J.), St. Johns Medical College, Bangalore, Karnataka, India; Office of the Dean (B.K.), University of Pécs, School of Medicine; Molecular Medicine (B.K.), Markusovszky University Teaching Hospital, Szombathely, Hungary; Immunology and Molecular Biology Laboratory of Experimental and Clinical Medicine Institute at the O'Bogomolets National Medical University (D.M.), Kyiv, Ukraine; General Practice (C.M.), Brisbane, Queensland, Australia; Department of Cognitive Neurology and Neurodegenerative Diseases (G.N.), University Clinic of Neurology, Medical Faculty, University "Ss. Cyril and Methodius", Institute for Alzheimer's Disease and Neuroscience-Skopje; Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov" (D.P.-K.), Macedonian Academy of Sciences and Arts, Skopje, North Macedonia; Postgraduate Program in Child and Adolescent (S.R.), Department of Pediatrics, Federal University of Paraná, Curitiba; School of Medicine (J.S.), Pontificia Universidade Católica do Paraná (PUCPR); Department of Genetics (J.S.), Hospital Infantil Pequeno Príncipe; and Universidade Federal do Paraná (H.A.T.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Setor de Distúrbios do Movimento, Curitiba, Brazil
| | - Bernadette Kalman
- From the Department of Neurology (J.D., Z.K.W.), Mayo Clinic, Jacksonville, FL; Division of Neurological and Psychiatric Nursing (J.D.), Faculty of Health Sciences, Medical University of Gdansk; Neurology Department (J.D.), St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland; Department of Neuroscience (M. Baker), Mayo Clinic, Jacksonville, FL; Department of Neurology (S.A.B., O.H.K.), Mayo Clinic, Rochester, MN; Department of Neurology (M. Bayat); Centre for Rare Diseases (M. Bayat), Aarhus University Hospital, Aarhus, Denmark; Experimental Neurobiology Unit (R.B.), Department of Biomedical Sciences, University of Antwerp; Department of Neurology, Antwerp University Hospital, Belgium; Center for Research in Genetics and Genomics (CIGEN) (G.O.C.), Autonomous University of Coahuila, México; Universidade Federal do Paraná (C.C.D.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Curitiba, Brazil; Department of Pediatrics (K.S.F.), Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, TX; Department of Paediatrics (J.N.J.), St. Johns Medical College, Bangalore, Karnataka, India; Office of the Dean (B.K.), University of Pécs, School of Medicine; Molecular Medicine (B.K.), Markusovszky University Teaching Hospital, Szombathely, Hungary; Immunology and Molecular Biology Laboratory of Experimental and Clinical Medicine Institute at the O'Bogomolets National Medical University (D.M.), Kyiv, Ukraine; General Practice (C.M.), Brisbane, Queensland, Australia; Department of Cognitive Neurology and Neurodegenerative Diseases (G.N.), University Clinic of Neurology, Medical Faculty, University "Ss. Cyril and Methodius", Institute for Alzheimer's Disease and Neuroscience-Skopje; Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov" (D.P.-K.), Macedonian Academy of Sciences and Arts, Skopje, North Macedonia; Postgraduate Program in Child and Adolescent (S.R.), Department of Pediatrics, Federal University of Paraná, Curitiba; School of Medicine (J.S.), Pontificia Universidade Católica do Paraná (PUCPR); Department of Genetics (J.S.), Hospital Infantil Pequeno Príncipe; and Universidade Federal do Paraná (H.A.T.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Setor de Distúrbios do Movimento, Curitiba, Brazil
| | - Orhun H Kantarci
- From the Department of Neurology (J.D., Z.K.W.), Mayo Clinic, Jacksonville, FL; Division of Neurological and Psychiatric Nursing (J.D.), Faculty of Health Sciences, Medical University of Gdansk; Neurology Department (J.D.), St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland; Department of Neuroscience (M. Baker), Mayo Clinic, Jacksonville, FL; Department of Neurology (S.A.B., O.H.K.), Mayo Clinic, Rochester, MN; Department of Neurology (M. Bayat); Centre for Rare Diseases (M. Bayat), Aarhus University Hospital, Aarhus, Denmark; Experimental Neurobiology Unit (R.B.), Department of Biomedical Sciences, University of Antwerp; Department of Neurology, Antwerp University Hospital, Belgium; Center for Research in Genetics and Genomics (CIGEN) (G.O.C.), Autonomous University of Coahuila, México; Universidade Federal do Paraná (C.C.D.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Curitiba, Brazil; Department of Pediatrics (K.S.F.), Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, TX; Department of Paediatrics (J.N.J.), St. Johns Medical College, Bangalore, Karnataka, India; Office of the Dean (B.K.), University of Pécs, School of Medicine; Molecular Medicine (B.K.), Markusovszky University Teaching Hospital, Szombathely, Hungary; Immunology and Molecular Biology Laboratory of Experimental and Clinical Medicine Institute at the O'Bogomolets National Medical University (D.M.), Kyiv, Ukraine; General Practice (C.M.), Brisbane, Queensland, Australia; Department of Cognitive Neurology and Neurodegenerative Diseases (G.N.), University Clinic of Neurology, Medical Faculty, University "Ss. Cyril and Methodius", Institute for Alzheimer's Disease and Neuroscience-Skopje; Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov" (D.P.-K.), Macedonian Academy of Sciences and Arts, Skopje, North Macedonia; Postgraduate Program in Child and Adolescent (S.R.), Department of Pediatrics, Federal University of Paraná, Curitiba; School of Medicine (J.S.), Pontificia Universidade Católica do Paraná (PUCPR); Department of Genetics (J.S.), Hospital Infantil Pequeno Príncipe; and Universidade Federal do Paraná (H.A.T.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Setor de Distúrbios do Movimento, Curitiba, Brazil
| | - Dmytro Maltsev
- From the Department of Neurology (J.D., Z.K.W.), Mayo Clinic, Jacksonville, FL; Division of Neurological and Psychiatric Nursing (J.D.), Faculty of Health Sciences, Medical University of Gdansk; Neurology Department (J.D.), St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland; Department of Neuroscience (M. Baker), Mayo Clinic, Jacksonville, FL; Department of Neurology (S.A.B., O.H.K.), Mayo Clinic, Rochester, MN; Department of Neurology (M. Bayat); Centre for Rare Diseases (M. Bayat), Aarhus University Hospital, Aarhus, Denmark; Experimental Neurobiology Unit (R.B.), Department of Biomedical Sciences, University of Antwerp; Department of Neurology, Antwerp University Hospital, Belgium; Center for Research in Genetics and Genomics (CIGEN) (G.O.C.), Autonomous University of Coahuila, México; Universidade Federal do Paraná (C.C.D.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Curitiba, Brazil; Department of Pediatrics (K.S.F.), Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, TX; Department of Paediatrics (J.N.J.), St. Johns Medical College, Bangalore, Karnataka, India; Office of the Dean (B.K.), University of Pécs, School of Medicine; Molecular Medicine (B.K.), Markusovszky University Teaching Hospital, Szombathely, Hungary; Immunology and Molecular Biology Laboratory of Experimental and Clinical Medicine Institute at the O'Bogomolets National Medical University (D.M.), Kyiv, Ukraine; General Practice (C.M.), Brisbane, Queensland, Australia; Department of Cognitive Neurology and Neurodegenerative Diseases (G.N.), University Clinic of Neurology, Medical Faculty, University "Ss. Cyril and Methodius", Institute for Alzheimer's Disease and Neuroscience-Skopje; Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov" (D.P.-K.), Macedonian Academy of Sciences and Arts, Skopje, North Macedonia; Postgraduate Program in Child and Adolescent (S.R.), Department of Pediatrics, Federal University of Paraná, Curitiba; School of Medicine (J.S.), Pontificia Universidade Católica do Paraná (PUCPR); Department of Genetics (J.S.), Hospital Infantil Pequeno Príncipe; and Universidade Federal do Paraná (H.A.T.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Setor de Distúrbios do Movimento, Curitiba, Brazil
| | - Catherine Middleton
- From the Department of Neurology (J.D., Z.K.W.), Mayo Clinic, Jacksonville, FL; Division of Neurological and Psychiatric Nursing (J.D.), Faculty of Health Sciences, Medical University of Gdansk; Neurology Department (J.D.), St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland; Department of Neuroscience (M. Baker), Mayo Clinic, Jacksonville, FL; Department of Neurology (S.A.B., O.H.K.), Mayo Clinic, Rochester, MN; Department of Neurology (M. Bayat); Centre for Rare Diseases (M. Bayat), Aarhus University Hospital, Aarhus, Denmark; Experimental Neurobiology Unit (R.B.), Department of Biomedical Sciences, University of Antwerp; Department of Neurology, Antwerp University Hospital, Belgium; Center for Research in Genetics and Genomics (CIGEN) (G.O.C.), Autonomous University of Coahuila, México; Universidade Federal do Paraná (C.C.D.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Curitiba, Brazil; Department of Pediatrics (K.S.F.), Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, TX; Department of Paediatrics (J.N.J.), St. Johns Medical College, Bangalore, Karnataka, India; Office of the Dean (B.K.), University of Pécs, School of Medicine; Molecular Medicine (B.K.), Markusovszky University Teaching Hospital, Szombathely, Hungary; Immunology and Molecular Biology Laboratory of Experimental and Clinical Medicine Institute at the O'Bogomolets National Medical University (D.M.), Kyiv, Ukraine; General Practice (C.M.), Brisbane, Queensland, Australia; Department of Cognitive Neurology and Neurodegenerative Diseases (G.N.), University Clinic of Neurology, Medical Faculty, University "Ss. Cyril and Methodius", Institute for Alzheimer's Disease and Neuroscience-Skopje; Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov" (D.P.-K.), Macedonian Academy of Sciences and Arts, Skopje, North Macedonia; Postgraduate Program in Child and Adolescent (S.R.), Department of Pediatrics, Federal University of Paraná, Curitiba; School of Medicine (J.S.), Pontificia Universidade Católica do Paraná (PUCPR); Department of Genetics (J.S.), Hospital Infantil Pequeno Príncipe; and Universidade Federal do Paraná (H.A.T.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Setor de Distúrbios do Movimento, Curitiba, Brazil
| | - Gabriela Novotni
- From the Department of Neurology (J.D., Z.K.W.), Mayo Clinic, Jacksonville, FL; Division of Neurological and Psychiatric Nursing (J.D.), Faculty of Health Sciences, Medical University of Gdansk; Neurology Department (J.D.), St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland; Department of Neuroscience (M. Baker), Mayo Clinic, Jacksonville, FL; Department of Neurology (S.A.B., O.H.K.), Mayo Clinic, Rochester, MN; Department of Neurology (M. Bayat); Centre for Rare Diseases (M. Bayat), Aarhus University Hospital, Aarhus, Denmark; Experimental Neurobiology Unit (R.B.), Department of Biomedical Sciences, University of Antwerp; Department of Neurology, Antwerp University Hospital, Belgium; Center for Research in Genetics and Genomics (CIGEN) (G.O.C.), Autonomous University of Coahuila, México; Universidade Federal do Paraná (C.C.D.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Curitiba, Brazil; Department of Pediatrics (K.S.F.), Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, TX; Department of Paediatrics (J.N.J.), St. Johns Medical College, Bangalore, Karnataka, India; Office of the Dean (B.K.), University of Pécs, School of Medicine; Molecular Medicine (B.K.), Markusovszky University Teaching Hospital, Szombathely, Hungary; Immunology and Molecular Biology Laboratory of Experimental and Clinical Medicine Institute at the O'Bogomolets National Medical University (D.M.), Kyiv, Ukraine; General Practice (C.M.), Brisbane, Queensland, Australia; Department of Cognitive Neurology and Neurodegenerative Diseases (G.N.), University Clinic of Neurology, Medical Faculty, University "Ss. Cyril and Methodius", Institute for Alzheimer's Disease and Neuroscience-Skopje; Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov" (D.P.-K.), Macedonian Academy of Sciences and Arts, Skopje, North Macedonia; Postgraduate Program in Child and Adolescent (S.R.), Department of Pediatrics, Federal University of Paraná, Curitiba; School of Medicine (J.S.), Pontificia Universidade Católica do Paraná (PUCPR); Department of Genetics (J.S.), Hospital Infantil Pequeno Príncipe; and Universidade Federal do Paraná (H.A.T.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Setor de Distúrbios do Movimento, Curitiba, Brazil
| | - Dijana Plaseska-Karanfilska
- From the Department of Neurology (J.D., Z.K.W.), Mayo Clinic, Jacksonville, FL; Division of Neurological and Psychiatric Nursing (J.D.), Faculty of Health Sciences, Medical University of Gdansk; Neurology Department (J.D.), St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland; Department of Neuroscience (M. Baker), Mayo Clinic, Jacksonville, FL; Department of Neurology (S.A.B., O.H.K.), Mayo Clinic, Rochester, MN; Department of Neurology (M. Bayat); Centre for Rare Diseases (M. Bayat), Aarhus University Hospital, Aarhus, Denmark; Experimental Neurobiology Unit (R.B.), Department of Biomedical Sciences, University of Antwerp; Department of Neurology, Antwerp University Hospital, Belgium; Center for Research in Genetics and Genomics (CIGEN) (G.O.C.), Autonomous University of Coahuila, México; Universidade Federal do Paraná (C.C.D.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Curitiba, Brazil; Department of Pediatrics (K.S.F.), Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, TX; Department of Paediatrics (J.N.J.), St. Johns Medical College, Bangalore, Karnataka, India; Office of the Dean (B.K.), University of Pécs, School of Medicine; Molecular Medicine (B.K.), Markusovszky University Teaching Hospital, Szombathely, Hungary; Immunology and Molecular Biology Laboratory of Experimental and Clinical Medicine Institute at the O'Bogomolets National Medical University (D.M.), Kyiv, Ukraine; General Practice (C.M.), Brisbane, Queensland, Australia; Department of Cognitive Neurology and Neurodegenerative Diseases (G.N.), University Clinic of Neurology, Medical Faculty, University "Ss. Cyril and Methodius", Institute for Alzheimer's Disease and Neuroscience-Skopje; Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov" (D.P.-K.), Macedonian Academy of Sciences and Arts, Skopje, North Macedonia; Postgraduate Program in Child and Adolescent (S.R.), Department of Pediatrics, Federal University of Paraná, Curitiba; School of Medicine (J.S.), Pontificia Universidade Católica do Paraná (PUCPR); Department of Genetics (J.S.), Hospital Infantil Pequeno Príncipe; and Universidade Federal do Paraná (H.A.T.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Setor de Distúrbios do Movimento, Curitiba, Brazil
| | - Salmo Raskin
- From the Department of Neurology (J.D., Z.K.W.), Mayo Clinic, Jacksonville, FL; Division of Neurological and Psychiatric Nursing (J.D.), Faculty of Health Sciences, Medical University of Gdansk; Neurology Department (J.D.), St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland; Department of Neuroscience (M. Baker), Mayo Clinic, Jacksonville, FL; Department of Neurology (S.A.B., O.H.K.), Mayo Clinic, Rochester, MN; Department of Neurology (M. Bayat); Centre for Rare Diseases (M. Bayat), Aarhus University Hospital, Aarhus, Denmark; Experimental Neurobiology Unit (R.B.), Department of Biomedical Sciences, University of Antwerp; Department of Neurology, Antwerp University Hospital, Belgium; Center for Research in Genetics and Genomics (CIGEN) (G.O.C.), Autonomous University of Coahuila, México; Universidade Federal do Paraná (C.C.D.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Curitiba, Brazil; Department of Pediatrics (K.S.F.), Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, TX; Department of Paediatrics (J.N.J.), St. Johns Medical College, Bangalore, Karnataka, India; Office of the Dean (B.K.), University of Pécs, School of Medicine; Molecular Medicine (B.K.), Markusovszky University Teaching Hospital, Szombathely, Hungary; Immunology and Molecular Biology Laboratory of Experimental and Clinical Medicine Institute at the O'Bogomolets National Medical University (D.M.), Kyiv, Ukraine; General Practice (C.M.), Brisbane, Queensland, Australia; Department of Cognitive Neurology and Neurodegenerative Diseases (G.N.), University Clinic of Neurology, Medical Faculty, University "Ss. Cyril and Methodius", Institute for Alzheimer's Disease and Neuroscience-Skopje; Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov" (D.P.-K.), Macedonian Academy of Sciences and Arts, Skopje, North Macedonia; Postgraduate Program in Child and Adolescent (S.R.), Department of Pediatrics, Federal University of Paraná, Curitiba; School of Medicine (J.S.), Pontificia Universidade Católica do Paraná (PUCPR); Department of Genetics (J.S.), Hospital Infantil Pequeno Príncipe; and Universidade Federal do Paraná (H.A.T.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Setor de Distúrbios do Movimento, Curitiba, Brazil
| | - Josiane Souza
- From the Department of Neurology (J.D., Z.K.W.), Mayo Clinic, Jacksonville, FL; Division of Neurological and Psychiatric Nursing (J.D.), Faculty of Health Sciences, Medical University of Gdansk; Neurology Department (J.D.), St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland; Department of Neuroscience (M. Baker), Mayo Clinic, Jacksonville, FL; Department of Neurology (S.A.B., O.H.K.), Mayo Clinic, Rochester, MN; Department of Neurology (M. Bayat); Centre for Rare Diseases (M. Bayat), Aarhus University Hospital, Aarhus, Denmark; Experimental Neurobiology Unit (R.B.), Department of Biomedical Sciences, University of Antwerp; Department of Neurology, Antwerp University Hospital, Belgium; Center for Research in Genetics and Genomics (CIGEN) (G.O.C.), Autonomous University of Coahuila, México; Universidade Federal do Paraná (C.C.D.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Curitiba, Brazil; Department of Pediatrics (K.S.F.), Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, TX; Department of Paediatrics (J.N.J.), St. Johns Medical College, Bangalore, Karnataka, India; Office of the Dean (B.K.), University of Pécs, School of Medicine; Molecular Medicine (B.K.), Markusovszky University Teaching Hospital, Szombathely, Hungary; Immunology and Molecular Biology Laboratory of Experimental and Clinical Medicine Institute at the O'Bogomolets National Medical University (D.M.), Kyiv, Ukraine; General Practice (C.M.), Brisbane, Queensland, Australia; Department of Cognitive Neurology and Neurodegenerative Diseases (G.N.), University Clinic of Neurology, Medical Faculty, University "Ss. Cyril and Methodius", Institute for Alzheimer's Disease and Neuroscience-Skopje; Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov" (D.P.-K.), Macedonian Academy of Sciences and Arts, Skopje, North Macedonia; Postgraduate Program in Child and Adolescent (S.R.), Department of Pediatrics, Federal University of Paraná, Curitiba; School of Medicine (J.S.), Pontificia Universidade Católica do Paraná (PUCPR); Department of Genetics (J.S.), Hospital Infantil Pequeno Príncipe; and Universidade Federal do Paraná (H.A.T.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Setor de Distúrbios do Movimento, Curitiba, Brazil
| | - Helio A Teive
- From the Department of Neurology (J.D., Z.K.W.), Mayo Clinic, Jacksonville, FL; Division of Neurological and Psychiatric Nursing (J.D.), Faculty of Health Sciences, Medical University of Gdansk; Neurology Department (J.D.), St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland; Department of Neuroscience (M. Baker), Mayo Clinic, Jacksonville, FL; Department of Neurology (S.A.B., O.H.K.), Mayo Clinic, Rochester, MN; Department of Neurology (M. Bayat); Centre for Rare Diseases (M. Bayat), Aarhus University Hospital, Aarhus, Denmark; Experimental Neurobiology Unit (R.B.), Department of Biomedical Sciences, University of Antwerp; Department of Neurology, Antwerp University Hospital, Belgium; Center for Research in Genetics and Genomics (CIGEN) (G.O.C.), Autonomous University of Coahuila, México; Universidade Federal do Paraná (C.C.D.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Curitiba, Brazil; Department of Pediatrics (K.S.F.), Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, TX; Department of Paediatrics (J.N.J.), St. Johns Medical College, Bangalore, Karnataka, India; Office of the Dean (B.K.), University of Pécs, School of Medicine; Molecular Medicine (B.K.), Markusovszky University Teaching Hospital, Szombathely, Hungary; Immunology and Molecular Biology Laboratory of Experimental and Clinical Medicine Institute at the O'Bogomolets National Medical University (D.M.), Kyiv, Ukraine; General Practice (C.M.), Brisbane, Queensland, Australia; Department of Cognitive Neurology and Neurodegenerative Diseases (G.N.), University Clinic of Neurology, Medical Faculty, University "Ss. Cyril and Methodius", Institute for Alzheimer's Disease and Neuroscience-Skopje; Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov" (D.P.-K.), Macedonian Academy of Sciences and Arts, Skopje, North Macedonia; Postgraduate Program in Child and Adolescent (S.R.), Department of Pediatrics, Federal University of Paraná, Curitiba; School of Medicine (J.S.), Pontificia Universidade Católica do Paraná (PUCPR); Department of Genetics (J.S.), Hospital Infantil Pequeno Príncipe; and Universidade Federal do Paraná (H.A.T.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Setor de Distúrbios do Movimento, Curitiba, Brazil
| | - Zbigniew K Wszolek
- From the Department of Neurology (J.D., Z.K.W.), Mayo Clinic, Jacksonville, FL; Division of Neurological and Psychiatric Nursing (J.D.), Faculty of Health Sciences, Medical University of Gdansk; Neurology Department (J.D.), St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland; Department of Neuroscience (M. Baker), Mayo Clinic, Jacksonville, FL; Department of Neurology (S.A.B., O.H.K.), Mayo Clinic, Rochester, MN; Department of Neurology (M. Bayat); Centre for Rare Diseases (M. Bayat), Aarhus University Hospital, Aarhus, Denmark; Experimental Neurobiology Unit (R.B.), Department of Biomedical Sciences, University of Antwerp; Department of Neurology, Antwerp University Hospital, Belgium; Center for Research in Genetics and Genomics (CIGEN) (G.O.C.), Autonomous University of Coahuila, México; Universidade Federal do Paraná (C.C.D.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Curitiba, Brazil; Department of Pediatrics (K.S.F.), Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, TX; Department of Paediatrics (J.N.J.), St. Johns Medical College, Bangalore, Karnataka, India; Office of the Dean (B.K.), University of Pécs, School of Medicine; Molecular Medicine (B.K.), Markusovszky University Teaching Hospital, Szombathely, Hungary; Immunology and Molecular Biology Laboratory of Experimental and Clinical Medicine Institute at the O'Bogomolets National Medical University (D.M.), Kyiv, Ukraine; General Practice (C.M.), Brisbane, Queensland, Australia; Department of Cognitive Neurology and Neurodegenerative Diseases (G.N.), University Clinic of Neurology, Medical Faculty, University "Ss. Cyril and Methodius", Institute for Alzheimer's Disease and Neuroscience-Skopje; Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov" (D.P.-K.), Macedonian Academy of Sciences and Arts, Skopje, North Macedonia; Postgraduate Program in Child and Adolescent (S.R.), Department of Pediatrics, Federal University of Paraná, Curitiba; School of Medicine (J.S.), Pontificia Universidade Católica do Paraná (PUCPR); Department of Genetics (J.S.), Hospital Infantil Pequeno Príncipe; and Universidade Federal do Paraná (H.A.T.), Hospital de Clínicas, Departamento de Medicina Interna, Serviço de Neurologia, Setor de Distúrbios do Movimento, Curitiba, Brazil
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10
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Kwon S, Safer J, Nguyen DT, Hoksza D, May P, Arbesfeld JA, Rubin AF, Campbell AJ, Burgin A, Iqbal S. Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures. Nat Methods 2024; 21:1947-1957. [PMID: 39294369 PMCID: PMC11466821 DOI: 10.1038/s41592-024-02409-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 08/09/2024] [Indexed: 09/20/2024]
Abstract
Recent advances in AI-based methods have revolutionized the field of structural biology. Concomitantly, high-throughput sequencing and functional genomics have generated genetic variants at an unprecedented scale. However, efficient tools and resources are needed to link disparate data types-to 'map' variants onto protein structures, to better understand how the variation causes disease, and thereby design therapeutics. Here we present the Genomics 2 Proteins portal ( https://g2p.broadinstitute.org/ ): a human proteome-wide resource that maps 20,076,998 genetic variants onto 42,413 protein sequences and 77,923 structures, with a comprehensive set of structural and functional features. Additionally, the Genomics 2 Proteins portal allows users to interactively upload protein residue-wise annotations (for example, variants and scores) as well as the protein structure beyond databases to establish the connection between genomics to proteins. The portal serves as an easy-to-use discovery tool for researchers and scientists to hypothesize the structure-function relationship between natural or synthetic variations and their molecular phenotypes.
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Affiliation(s)
- Seulki Kwon
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jordan Safer
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Duyen T Nguyen
- PATTERN, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Hoksza
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jeremy A Arbesfeld
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Alan F Rubin
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Arthur J Campbell
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alex Burgin
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sumaiya Iqbal
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Cancer Data Sciences, Dana-Farber/Harvard Cancer Center, Boston, MA, USA.
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11
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Samarasinghe SR, Lee SB, Corpas M, Fatumo S, Guchelaar HJ, Nagaraj SH. Mapping the Pharmacogenetic Landscape in a Ugandan Population: Implications for Personalized Medicine in an Underrepresented Population. Clin Pharmacol Ther 2024; 116:980-995. [PMID: 38837390 DOI: 10.1002/cpt.3309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/27/2024] [Indexed: 06/07/2024]
Abstract
Africans are extremely underrepresented in global genomic research. African populations face high burdens of communicable and non-communicable diseases and experience widespread polypharmacy. As population-specific genetic studies are crucial to understanding unique genetic profiles and optimizing treatments to reduce medication-related complications in this diverse population, the present study aims to characterize the pharmacogenomics profile of a rural Ugandan population. We analyzed low-pass whole genome sequencing data from 1998 Ugandans to investigate 18 clinically actionable pharmacogenes in this population. We utilized PyPGx to identify star alleles (haplotype patterns) and compared allele frequencies across populations using the Pharmacogenomics Knowledgebase PharmGKB. Clinical interpretations of the identified alleles were conducted following established dosing guidelines. Over 99% of participants displayed actionable phenotypes across the 18 pharmacogenes, averaging 3.5 actionable genotypes per individual. Several variant alleles known to affect drug metabolism (i.e., CYP3A5*1, CYP2B6*9, CYP3A5*6, CYP2D6*17, CYP2D6*29, and TMPT*3C)-which are generally more prevalent in African individuals-were notably enriched in the Ugandan cohort, beyond reported frequencies in other African peoples. More than half of the cohort exhibited a predicted impaired drug response associated with CFTR, IFNL3, CYP2B6, and CYP2C19, and approximately 31% predicted altered CYP2D6 metabolism. Potentially impaired CYP2C9, SLCO1B1, TPMT, and DPYD metabolic phenotypes were also enriched in Ugandans compared with other African populations. Ugandans exhibit distinct allele profiles that could impact drug efficacy and safety. Our findings have important implications for pharmacogenomics in Uganda, particularly with respect to the treatment of prevalent communicable and non-communicable diseases, and they emphasize the potential of pharmacogenomics-guided therapies to optimize healthcare outcomes and precision medicine in Uganda.
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Affiliation(s)
- Sumudu Rangika Samarasinghe
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | | | - Manuel Corpas
- College of Liberal Arts and Sciences, University of Westminster, London, UK
| | - Segun Fatumo
- Department of Non-communicable Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Shivashankar H Nagaraj
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, Queensland, Australia
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12
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Wang D, Liu XY, He QF, Zheng FZ, Chen L, Zheng Y, Zeng MH, Lin YH, Lin X, Chen HZ, Lin MT, Wang N, Wang ZQ, Lin F. Comprehensive Proteomic Analysis of Dysferlinopathy Unveiling Molecular Mechanisms and Biomarkers Linked to Pathological Progression. CNS Neurosci Ther 2024; 30:e70065. [PMID: 39350328 PMCID: PMC11442333 DOI: 10.1111/cns.70065] [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: 04/11/2024] [Revised: 08/23/2024] [Accepted: 09/13/2024] [Indexed: 10/04/2024] Open
Abstract
AIMS Previous proteomics studies in dysferlinopathy muscle have been limited in scope, often utilizing 2D-electrophoresis and yielding only a small number of differential expression calls. To address this gap, this study aimed to employ high-resolution proteomics to explore the proteomic landscapes of dysferlinopathy and analyze the correlation between muscle pathological changes and alterations in protein expression in muscle biopsies. METHODS We conducted a comprehensive approach to investigate the proteomic profile and disease-associated changes in the muscle tissue proteome from 15 patients with dysferlinopathy, exhibiting varying degrees of dystrophic pathology, alongside age-matched controls. Our methodology encompasses tandem mass tag (TMT)-labeled liquid chromatography-mass spectrometry (LC-MS/MS)-based proteomics, protein-protein interaction (PPI) network analysis, weighted gene co-expression network analysis, and differential expression analysis. Subsequently, we examined the correlation between the expression of key proteins and the clinical characteristics of the patients to identify pathogenic targets associated with DYSF mutations in dysferlinopathy. RESULTS A total of 1600 differentially expressed proteins were identified, with 1321 showing high expression levels and 279 expressed at lower levels. Our investigation yields a molecular profile delineating the altered protein networks in dysferlinopathy-afflicted skeletal muscle, uncovering dysregulation across numerous cellular pathways and molecular processes, including mRNA metabolic processes, regulated exocytosis, immune response, muscle system processes, energy metabolic processes, and calcium transmembrane transport. Moreover, we observe significant associations between the protein expression of ANXA1, ANXA2, ANXA4, ANXA5, LMNA, PYGM, and the extent of histopathologic changes in muscle biopsies from patients with dysferlinopathy, validated through immunoblotting and immunofluorescence assays. CONCLUSIONS Through the aggregation of expression data from dysferlinopathy-impacted muscles exhibiting a range of pathological alterations, we identified multiple key proteins associated with the dystrophic pathology of patients with dysferlinopathy. These findings provide novel insights into the pathogenesis of dysferlinopathy and propose promising targets for future therapeutic endeavors.
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Affiliation(s)
- Di Wang
- Department of Molecular Pathology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
- Center for Bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine and Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin-Yi Liu
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Qi-Fang He
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Fu-Ze Zheng
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Long Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Ying Zheng
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Ming-Hui Zeng
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Yu-Hua Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Xin Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Hai-Zhu Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Min-Ting Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ning Wang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zhi-Qiang Wang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Feng Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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13
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Sebastiano MR, Hadano S, Cesca F, Ermondi G. Preclinical alternative drug discovery programs for monogenic rare diseases. Should small molecules or gene therapy be used? The case of hereditary spastic paraplegias. Drug Discov Today 2024; 29:104138. [PMID: 39154774 DOI: 10.1016/j.drudis.2024.104138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/28/2024] [Accepted: 08/13/2024] [Indexed: 08/20/2024]
Abstract
Patients diagnosed with rare diseases and their and families search desperately to organize drug discovery campaigns. Alternative models that differ from default paradigms offer real opportunities. There are, however, no clear guidelines for the development of such models, which reduces success rates and raises costs. We address the main challenges in making the discovery of new preclinical treatments more accessible, using rare hereditary paraplegia as a paradigmatic case. First, we discuss the necessary expertise, and the patients' clinical and genetic data. Then, we revisit gene therapy, de novo drug development, and drug repurposing, discussing their applicability. Moreover, we explore a pool of recommended in silico tools for pathogenic variant and protein structure prediction, virtual screening, and experimental validation methods, discussing their strengths and weaknesses. Finally, we focus on successful case applications.
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Affiliation(s)
- Matteo Rossi Sebastiano
- University of Torino, Molecular Biotechnology and Health Sciences Department, CASSMedChem, Piazza Nizza, 10138 Torino, Italy
| | - Shinji Hadano
- Molecular Neuropathobiology Laboratory, Department of Physiology, Tokai University School of Medicine, Isehara, Japan
| | - Fabrizia Cesca
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Giuseppe Ermondi
- University of Torino, Molecular Biotechnology and Health Sciences Department, CASSMedChem, Piazza Nizza, 10138 Torino, Italy.
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14
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Wu C, Shazeeb MS, Mangkalaphiban K, Han G, Peker A, Rentiya ZS, Gounis MJ, Jacobson A. Investigating therapeutic nonsense suppression in a neurofibromatosis mouse model. Exp Neurol 2024; 380:114914. [PMID: 39106942 DOI: 10.1016/j.expneurol.2024.114914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 07/15/2024] [Accepted: 07/31/2024] [Indexed: 08/09/2024]
Abstract
Neurofibromatosis type 1 (NF1) is a human genetic disorder caused by variants in the NF1 gene. Plexiform neurofibromas, one of many NF1 manifestations, are benign peripheral nerve sheath tumors occurring in up to 50% of NF1 patients. A substantial fraction of NF1 pathogenetic variants are nonsense mutations, which result in the synthesis of truncated non-functional NF1 protein (neurofibromin). To date, no therapeutics have restored neurofibromin expression or addressed the consequences of this protein's absence in NF1 nonsense mutation patients, but nonsense suppression is a potential approach to the problem. Ataluren is a small molecule drug that has been shown to stimulate functional nonsense codon readthrough in several models of nonsense mutation diseases, as well as in Duchenne muscular dystrophy patients. To test ataluren's potential applicability in nonsense mutation NF1 patients, we evaluated its therapeutic effects using three treatment regimens in a previously established NF1 patient-derived (c.2041C > T; p.Arg681X) nonsense mutation mouse model. Collectively, our experiments indicate that: i) ataluren appeared to slow the growth of neurofibromas and alleviate some paralysis phenotypes, ii) female Nf1-nonsense mutation mice manifested more severe paralysis and neurofibroma phenotypes than male mice, iii) ataluren doses with apparent effectiveness were lower in female mice than in male mice, and iv) age factors also influenced ataluren's effectiveness.
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Affiliation(s)
- Chan Wu
- Department of Microbiology, UMass Chan Medical School, Worcester, MA, USA
| | | | | | - George Han
- Department of Radiology, UMass Chan Medical School, Worcester, MA, USA; Department of Medicine, Beth Israel Deaconess Medical Center, Brockton, MA, USA
| | - Ahmet Peker
- Department of Radiology, UMass Chan Medical School, Worcester, MA, USA; Koç University Hospital, Istanbul, Türkiye
| | - Zubir S Rentiya
- Department of Radiology, UMass Chan Medical School, Worcester, MA, USA; Department of Radiation Oncology & Radiology, University of Virginia, Charlottesville, VA, USA
| | - Matthew J Gounis
- Department of Radiology, UMass Chan Medical School, Worcester, MA, USA
| | - Allan Jacobson
- Department of Microbiology, UMass Chan Medical School, Worcester, MA, USA; Li Weibo Institute for Rare Disease Research, UMass Chan Medical School, Worcester, MA, USA.
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15
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Green DJ, Michaud V, Lasseaux E, Plaisant C, Fitzgerald T, Birney E, Black GC, Arveiler B, Sergouniotis PI. The co-occurrence of genetic variants in the TYR and OCA2 genes confers susceptibility to albinism. Nat Commun 2024; 15:8436. [PMID: 39349469 PMCID: PMC11443028 DOI: 10.1038/s41467-024-52763-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 09/19/2024] [Indexed: 10/02/2024] Open
Abstract
Although rare genetic conditions are mostly caused by DNA sequence alterations that functionally disrupt individual genes, large-scale studies using genome sequencing have started to unmask additional complexity. Understanding how combinations of variants in different genes shape human phenotypes is expected to provide important insights into the clinical and genetic heterogeneity of rare disorders. Here, we use albinism, an archetypal rare condition associated with hypopigmentation, as an exemplar for the study of genetic interactions. We analyse data from the Genomics England 100,000 Genomes Project alongside a cohort of 1120 individuals with albinism, and investigate the effect of dual heterozygosity for the combination of two established albinism-related variants: TYR:c.1205 G > A (p.Arg402Gln) [rs1126809] and OCA2:c.1327 G > A (p.Val443Ile) [rs74653330]. As each of these changes alone is insufficient to cause disease when present in the heterozygous state, we sought evidence of synergistic effects. We show that, when both variants are present, the probability of receiving a diagnosis of albinism is significantly increased (odds ratio 12.8; 95% confidence interval 6.0 - 24.7; p-value 2.1 ×10-8). Further analyses in an independent cohort, the UK Biobank, support this finding and highlight that heterozygosity for the TYR:c.1205 G > A and OCA2:c.1327 G > A variant combination is associated with statistically significant alterations in visual acuity and central retinal thickness (traits that are considered albinism endophenotypes). The approach discussed in this report opens up new avenues for the investigation of oligogenic patterns in apparently Mendelian disorders.
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Affiliation(s)
- David J Green
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Vincent Michaud
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
- INSERM U1211, Rare Diseases, Genetics and Metabolism, University of Bordeaux, Bordeaux, France
| | - Eulalie Lasseaux
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
| | - Claudio Plaisant
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
| | - Tomas Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL- EBI), Wellcome Genome Campus, Cambridge, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL- EBI), Wellcome Genome Campus, Cambridge, UK
| | - Graeme C Black
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Benoît Arveiler
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
- INSERM U1211, Rare Diseases, Genetics and Metabolism, University of Bordeaux, Bordeaux, France
| | - Panagiotis I Sergouniotis
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL- EBI), Wellcome Genome Campus, Cambridge, UK.
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK.
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, UK.
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16
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Yang Y, Wang Y, Qin M, Zhao Y, Has C, Wang X. An intronic variant in LAMB3 contributes to junctional epidermolysis bullosa and enamel hypoplasia via translational attenuation. Arch Oral Biol 2024; 169:106101. [PMID: 39357391 DOI: 10.1016/j.archoralbio.2024.106101] [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: 08/15/2024] [Revised: 09/22/2024] [Accepted: 09/26/2024] [Indexed: 10/04/2024]
Abstract
OBJECTIVES This study aimed to investigate the genetic etiology of a family affected by junctional epidermolysis bullosa (JEB) and generalized enamel hypoplasia, and to explore how an intronic variant influenced the 5' untranslated region (5'UTR), thereby affecting LAMB3 expression and contributing to the pathogenesis of the disease. DESIGN Whole-exome and whole-genome sequencing were used to screen for genetic defects in the patient. Mutational consequences were characterized through luciferase assays, splice assay, in silico analyses, and verification using the patient's gingival sample. RESULTS A nonsense variant (c.2983 C>T; p.Gln995*) and an intronic variant (c.-38+2 T>C) of LAMB3 were identified. In vitro assays demonstrated that the intronic variant activated a cryptic splice site, resulting in a 120 bp intronic inclusion. This splicing alteration significantly reduced the translation efficiency of the downstream coding sequence, while overall mRNA expression remained unaffected. Bioinformatic analysis unveiled the creation of three upstream AUG codons, leading to the presence of two upstream open reading frames (uORFs) and one overlapping ORF. The longer uORF's AUG exhibited a moderate Kozak strength similar to that of the main ORF's AUG. Structural analysis of the mutant 5'UTR sequence revealed a more complex secondary structure, characterized by a large branch loop and a stem-loop preceding the coding sequence's start codon. CONCLUSION This study suggests that variants affecting the 5'UTR may contribute to the genetic etiology of JEB. These findings could help enhance the diagnostic accuracy and efficiency in JEB patients.
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Affiliation(s)
- Yi Yang
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology & National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, PR China
| | - Yao Wang
- Department of Dermatology, Medical Faculty and Medical Center, University of Freiburg, Freiburg, Germany
| | - Man Qin
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology & National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, PR China
| | - Yuming Zhao
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology & National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, PR China
| | - Cristina Has
- Department of Dermatology, Medical Faculty and Medical Center, University of Freiburg, Freiburg, Germany
| | - Xin Wang
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology & National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, PR China.
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17
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Feng M, Wei X, Zheng X, Liu L, Lin L, Xia M, He G, Shi Y, Lu Q. Decoding Missense Variants by Incorporating Phase Separation via Machine Learning. Nat Commun 2024; 15:8279. [PMID: 39333476 PMCID: PMC11436885 DOI: 10.1038/s41467-024-52580-3] [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: 12/28/2023] [Accepted: 09/12/2024] [Indexed: 09/29/2024] Open
Abstract
Computational models have made significant progress in predicting the effect of protein variants. However, deciphering numerous variants of uncertain significance (VUS) located within intrinsically disordered regions (IDRs) remains challenging. To address this issue, we introduce phase separation, which is tightly linked to IDRs, into the investigation of missense variants. Phase separation is vital for multiple physiological processes. By leveraging missense variants that alter phase separation propensity, we develop a machine learning approach named PSMutPred to predict the impact of missense mutations on phase separation. PSMutPred demonstrates robust performance in predicting missense variants that affect natural phase separation. In vitro experiments further underscore its validity. By applying PSMutPred on over 522,000 ClinVar missense variants, it significantly contributes to decoding the pathogenesis of disease variants, especially those in IDRs. Our work provides insights into the understanding of a vast number of VUSs in IDRs, expediting clinical interpretation and diagnosis.
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Affiliation(s)
- Mofan Feng
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, Shanghai, China
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoxi Wei
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, Shanghai, China
| | - Xi Zheng
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, Shanghai, China
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Liangjie Liu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, Shanghai, China
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Lin Lin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, Shanghai, China
| | - Manying Xia
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, Shanghai, China
| | - Guang He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, Shanghai, China.
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China.
| | - Yi Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, Shanghai, China.
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China.
| | - Qing Lu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, Shanghai, China.
- Department of Otorhinolaryngology-Head and Neck Surgery, Chongqing General Hospital, Chongqing, China.
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China.
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18
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Jiao K, Zhang J, Li Q, Lv X, Yu Y, Zhu B, Zhong H, Yu X, Song J, Ke Q, Qian F, Luan X, Zhang X, Chang X, Wang L, Liu M, Dong J, Zou Z, Bu B, Jiang H, Liu L, Li Y, Yue D, Chang X, Zheng Y, Wang N, Gao M, Xia X, Cheng N, Wang T, Luo SS, Xi J, Lin J, Lu J, Zhao C, Yang H, Lin P, Hong D, Zhao Z, Wang Z, Zhu W. Novel variants and genotype-phenotype correlation in a multicentre cohort of GNE myopathy in China. J Med Genet 2024:jmg-2024-110149. [PMID: 39332896 DOI: 10.1136/jmg-2024-110149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 09/11/2024] [Indexed: 09/29/2024]
Abstract
BACKGROUND GlcNAc2-epimerase (GNE) myopathy is a rare autosomal recessive disorder caused by pathogenic variants in the GNE gene, which is essential for the sialic acid biosynthesis pathway. OBJECTIVE This multi-centre study aimed to delineate the clinical phenotype and GNE variant spectrum in Chinese patients, enhancing our understanding of the genetic diversity and clinical manifestation across different populations. METHODS We retrospectively analysed GNE variants from 113 patients, integrating these data with external GNE variants from online databases for a global perspective, examining their consequences, distribution, ethnicity and severity. RESULTS This study revealed 97 distinct GNE variants, including 35 (36.08%) novel variants. Two more patients with deep intronic variant c.862+870C>T were identified, while whole genome sequencing (WGS) uncovered another two novel intronic variants: c.52-8924G>T and c.1505-12G>A. Nanopore long reads sequencing (LRS) and further PCR analysis verified a 639 bp insertion at chr9:36249241. Missense variants predominantly located in the epimerase/kinase domain coding region, indicating the impairment of catalytic function as a key pathogenic consequence. Comparative studies with Japanese, Korean and Jewish, our cohorts showed later onset ages by 2 years. The high allele frequency of the non-catalytic GNE variant, c.620A>T, might underlie the milder phenotype of Chinese patients. CONCLUSIONS Comprehensive techniques such as WGS and Nanopore LRS warrants the identifying of GNE variants. Patients with the non-catalytic GNE variant, c.620A>T, had a milder disease progression and later wheelchair use.
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Affiliation(s)
- Kexin Jiao
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, Shanghai, China
| | - Jialong Zhang
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, Shanghai, China
| | - Qiuxiang Li
- Department of Neurology and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital Central South University, Changsha, Hunan, China
| | - Xiaoqing Lv
- Department of Neurology and Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Yanyan Yu
- Department of Neurology and Department of Medical Genetics, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Bochen Zhu
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, Shanghai, China
| | - Huahua Zhong
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, Shanghai, China
| | - Xu'en Yu
- Department of Neurology, The Affiliated Hospital of Institute of Neurology, Anhui University of Chinese Medicine, Hefei, China
| | - Jia Song
- Department of Neurology, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Qing Ke
- Department of Neurology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Fangyuan Qian
- Department of Neurology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
| | - Xinghua Luan
- Department of Neurology, Shanghai Sixth People's Hospital, Shanghai, China
| | - Xiaojie Zhang
- Department of Neurology, Shanghai Sixth People's Hospital, Shanghai, China
| | - Xueli Chang
- Department of Neurology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Liang Wang
- Department of Neurology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
| | - Meirong Liu
- Department of Neurology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Jihong Dong
- Department of Neurology, Zhongshan Hospital Fudan University, Shanghai, Shanghai, China
| | - Zhangyu Zou
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Bitao Bu
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haishan Jiang
- Department of Neurology, Southern Medical University Nanfang Hospital, Guangzhou, China, China
| | - LingChun Liu
- Department of Neurology, First People's Hospital of Yunnan, Kunming, Yunnan, China
| | - Yue Li
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dongyue Yue
- Department of Neurology, Jing'an District Centre Hospital of Shanghai, Shanghai, Shanghai, China
| | - Xuechun Chang
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Yongsheng Zheng
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, Shanghai, China
| | - Ningning Wang
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, Shanghai, China
| | - Mingshi Gao
- Department of Pathology, Huashan Hospital Fudan University, Shanghai, Shanghai, China
| | - Xingyu Xia
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, Shanghai, China
| | - Nachuan Cheng
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, Shanghai, China
| | - Tao Wang
- Department of Anesthesiology, Zhongshan hospital, Shanghai, China
- Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science,Fudan University, Shanghai, China
| | - Su-Shan Luo
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, Shanghai, China
| | - Jianying Xi
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, Shanghai, China
| | - Jie Lin
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, Shanghai, China
| | - Jiahong Lu
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, Shanghai, China
| | - Chongbo Zhao
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, Shanghai, China
| | - Huan Yang
- Department of Neurology and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital Central South University, Changsha, Hunan, China
| | - Pengfei Lin
- Department of Neurology and Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Daojun Hong
- Department of Neurology and Department of Medical Genetics, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Zhe Zhao
- Department of Neuromuscular Disease, Third Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zhiqiang Wang
- The Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Xiamen, Fujian, China
| | - Wenhua Zhu
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, Shanghai, China
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19
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İhtiyar MN, Özgür A. Generative language models on nucleotide sequences of human genes. Sci Rep 2024; 14:22204. [PMID: 39333252 PMCID: PMC11437190 DOI: 10.1038/s41598-024-72512-x] [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: 10/17/2023] [Accepted: 09/09/2024] [Indexed: 09/29/2024] Open
Abstract
Language models, especially transformer-based ones, have achieved colossal success in natural language processing. To be precise, studies like BERT for natural language understanding and works like GPT-3 for natural language generation are very important. If we consider DNA sequences as a text written with an alphabet of four letters representing the nucleotides, they are similar in structure to natural languages. This similarity has led to the development of discriminative language models such as DNABERT in the field of DNA-related bioinformatics. To our knowledge, however, the generative side of the coin is still largely unexplored. Therefore, we have focused on the development of an autoregressive generative language model such as GPT-3 for DNA sequences. Since working with whole DNA sequences is challenging without extensive computational resources, we decided to conduct our study on a smaller scale and focus on nucleotide sequences of human genes, i.e. unique parts of DNA with specific functions, rather than the whole DNA. This decision has not significantly changed the structure of the problem, as both DNA and genes can be considered as 1D sequences consisting of four different nucleotides without losing much information and without oversimplification. First of all, we systematically studied an almost entirely unexplored problem and observed that recurrent neural networks (RNNs) perform best, while simple techniques such as N-grams are also promising. Another beneficial point was learning how to work with generative models on languages we do not understand, unlike natural languages. The importance of using real-world tasks beyond classical metrics such as perplexity was noted. In addition, we examined whether the data-hungry nature of these models can be altered by selecting a language with minimal vocabulary size, four due to four different types of nucleotides. The reason for reviewing this was that choosing such a language might make the problem easier. However, in this study, we found that this did not change the amount of data required very much.
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Affiliation(s)
- Musa Nuri İhtiyar
- Department of Computer Engineering, Boğaziçi University, 34342, Istanbul, Turkey.
| | - Arzucan Özgür
- Department of Computer Engineering, Boğaziçi University, 34342, Istanbul, Turkey.
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20
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Lacoste J, Haghighi M, Haider S, Reno C, Lin ZY, Segal D, Qian WW, Xiong X, Teelucksingh T, Miglietta E, Shafqat-Abbasi H, Ryder PV, Senft R, Cimini BA, Murray RR, Nyirakanani C, Hao T, McClain GG, Roth FP, Calderwood MA, Hill DE, Vidal M, Yi SS, Sahni N, Peng J, Gingras AC, Singh S, Carpenter AE, Taipale M. Pervasive mislocalization of pathogenic coding variants underlying human disorders. Cell 2024:S0092-8674(24)01021-3. [PMID: 39353438 DOI: 10.1016/j.cell.2024.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 07/22/2024] [Accepted: 09/04/2024] [Indexed: 10/04/2024]
Abstract
Widespread sequencing has yielded thousands of missense variants predicted or confirmed as disease causing. This creates a new bottleneck: determining the functional impact of each variant-typically a painstaking, customized process undertaken one or a few genes and variants at a time. Here, we established a high-throughput imaging platform to assay the impact of coding variation on protein localization, evaluating 3,448 missense variants of over 1,000 genes and phenotypes. We discovered that mislocalization is a common consequence of coding variation, affecting about one-sixth of all pathogenic missense variants, all cellular compartments, and recessive and dominant disorders alike. Mislocalization is primarily driven by effects on protein stability and membrane insertion rather than disruptions of trafficking signals or specific interactions. Furthermore, mislocalization patterns help explain pleiotropy and disease severity and provide insights on variants of uncertain significance. Our publicly available resource extends our understanding of coding variation in human diseases.
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Affiliation(s)
- Jessica Lacoste
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Shahan Haider
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Chloe Reno
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Dmitri Segal
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Wesley Wei Qian
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Xueting Xiong
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Tanisha Teelucksingh
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | | | - Pearl V Ryder
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Rebecca Senft
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Beth A Cimini
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ryan R Murray
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Chantal Nyirakanani
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gregory G McClain
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Frederick P Roth
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada; Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - S Stephen Yi
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA; Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, USA; Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, USA; Interdisciplinary Life Sciences Graduate Programs (ILSGP), College of Natural Sciences, The University of Texas at Austin, Austin, TX, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Quantitative and Computational Biosciences Program, Baylor College of Medicine, Houston, TX, USA
| | - Jian Peng
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | | | | | - Mikko Taipale
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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21
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Bandres-Ciga S, Faghri F, Majounie E, Koretsky MJ, Kim J, Levine KS, Leonard H, Makarious MB, Iwaki H, Crea PW, Hernandez DG, Arepalli S, Billingsley K, Lohmann K, Klein C, Lubbe SJ, Jabbari E, Saffie-Awad P, Narendra D, Reyes-Palomares A, Quinn JP, Schulte C, Morris HR, Traynor BJ, Scholz SW, Houlden H, Hardy J, Dumanis S, Riley E, Blauwendraat C, Singleton A, Nalls M, Jeff J, Vitale D. NeuroBooster Array: A Genome-Wide Genotyping Platform to Study Neurological Disorders Across Diverse Populations. Mov Disord 2024. [PMID: 39283294 DOI: 10.1002/mds.29902] [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: 03/28/2024] [Revised: 05/28/2024] [Accepted: 06/06/2024] [Indexed: 09/25/2024] Open
Abstract
BACKGROUND Commercial genome-wide genotyping arrays have historically neglected coverage of genetic variation across populations. OBJECTIVE We aimed to create a multi-ancestry genome-wide array that would include a wide range of neuro-specific genetic content to facilitate genetic research in neurological disorders across multiple ancestral groups, fostering diversity and inclusivity in research studies. METHODS We developed the Illumina NeuroBooster Array (NBA), a custom high-throughput and cost-effective platform on a backbone of 1,914,934 variants from the Infinium Global Diversity Array and added custom content comprising 95,273 variants associated with more than 70 neurological conditions or traits, and we further tested its performance on more than 2000 patient samples. This novel platform includes approximately 10,000 tagging variants to facilitate imputation and analyses of neurodegenerative disease-related genome-wide association study loci across diverse populations. RESULTS In this article, we describe NBA's potential as an efficient means for researchers to assess known and novel disease genetic associations in a multi-ancestry framework. The NBA can identify rare genetic variants and accurately impute more than 15 million common variants across populations. Apart from enabling sample prioritization for further whole-genome sequencing studies, we envisage that NBA will play a pivotal role in recruitment for interventional studies in the precision medicine space. CONCLUSIONS From a broader perspective, the NBA serves as a promising means to foster collaborative research endeavors in the field of neurological disorders worldwide. Ultimately, this carefully designed tool is poised to make a substantial contribution to uncovering the genetic etiology underlying these debilitating conditions. © 2024 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Sara Bandres-Ciga
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Faraz Faghri
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- Data Tecnica, Washington, District of Columbia, USA
| | | | - Mathew J Koretsky
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Jeffrey Kim
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Kristin S Levine
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- Data Tecnica, Washington, District of Columbia, USA
| | - Hampton Leonard
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- Data Tecnica, Washington, District of Columbia, USA
| | - Mary B Makarious
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Hirotaka Iwaki
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- Data Tecnica, Washington, District of Columbia, USA
| | - Peter Wild Crea
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Sampath Arepalli
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Kimberley Billingsley
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Steven J Lubbe
- Ken and Ruth Davee Department of Neurology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Edwin Jabbari
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Paula Saffie-Awad
- Programa de Pós-Graduação em Ciências Médicas, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Centro de Trastornos del Movimiento, Santiago, Chile
- Clínica Santa María, Santiago, Chile
| | - Derek Narendra
- Inherited Movement Disorders Unit, Neurogenetics Branch, Division of Intramural Research, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Armando Reyes-Palomares
- Department of Molecular Biology and Biochemistry, Faculty of Sciences, University of Málaga, Málaga, Spain
| | - John P Quinn
- Department of Pharmacology & Therapeutics, University of Liverpool, Liverpool, United Kingdom
| | - Claudia Schulte
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tuebingen and German Center for Neurodegenerative Diseases, University of Tuebingen, Tuebingen, Germany
| | - Huw R Morris
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, United Kingdom
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, Maryland, USA
| | - Bryan J Traynor
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, Maryland, USA
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA
| | - Henry Houlden
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, Maryland, USA
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - John Hardy
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, Maryland, USA
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Sonya Dumanis
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, Maryland, USA
| | - Ekemini Riley
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, Maryland, USA
| | - Cornelis Blauwendraat
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew Singleton
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Mike Nalls
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- Data Tecnica, Washington, District of Columbia, USA
| | | | - Dan Vitale
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- Data Tecnica, Washington, District of Columbia, USA
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Mustafa A, Shabbir M, Badshah Y, Khan K, Abid F, Trembley JH, Afsar T, Almajwal A, Razak S. Genetic polymorphism in untranslated regions of PRKCZ influences mRNA structure, stability and binding sites. BMC Cancer 2024; 24:1147. [PMID: 39272077 PMCID: PMC11401371 DOI: 10.1186/s12885-024-12900-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 09/04/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND Variations in untranslated regions (UTR) alter regulatory pathways impacting phenotype, disease onset, and course of disease. Protein kinase C Zeta (PRKCZ), a serine-threonine kinase, is implicated in cardiovascular, neurological and oncological disorders. Due to limited research on PRKCZ, this study aimed to investigate the impact of UTR genetic variants' on binding sites for transcription factors and miRNA. RNA secondary structure, eQTLs, and variation tolerance analysis were also part of the study. METHODS The data related to PRKCZ gene variants was downloaded from the Ensembl genome browser, COSMIC and gnomAD. The RegulomeDB database was used to assess the functional impact of 5' UTR and 3'UTR variants. The analysis of the transcription binding sites (TFBS) was done through the Alibaba tool, and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) was employed to identify pathways associated with PRKCZ. To predict the effect of variants on microRNA binding sites, PolymiRTS was utilized for 3' UTR variants, and the SNPinfo tool was used for 5' UTR variants. RESULTS The results obtained indicated that a total of 24 variants present in the 3' UTR and 25 variants present in the 5' UTR were most detrimental. TFBS analysis revealed that 5' UTR variants added YY1, repressor, and Oct1, whereas 3' UTR variants added AP-2alpha, AhR, Da, GR, and USF binding sites. The study predicted TFs that influenced PRKCZ expression. RNA secondary structure analysis showed that eight 5' UTR and six 3' UTR altered the RNA structure by either removal or addition of the stem-loop. The microRNA binding site analysis highlighted that seven 3' UTR and one 5' UTR variant altered the conserved site and also created new binding sites. eQTLs analysis showed that one variant was associated with PRKCZ expression in the lung and thyroid. The variation tolerance analysis revealed that PRKCZ was an intolerant gene. CONCLUSION This study laid the groundwork for future studies aimed at targeting PRKCZ as a therapeutic target.
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Affiliation(s)
- Aneela Mustafa
- Department of Healthcare BiotechnologyAtta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan
| | - Maria Shabbir
- Department of Healthcare BiotechnologyAtta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan.
| | - Yasmin Badshah
- Department of Healthcare BiotechnologyAtta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan
| | | | - Fizzah Abid
- Department of Healthcare BiotechnologyAtta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan
| | - Janeen H Trembley
- Minneapolis VA Health Care System Research Service, Minneapolis, MN, USA
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ali Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.
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23
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Vieira Neto E, Wang M, Szuminsky AJ, Ferraro L, Koppes E, Wang Y, Van't Land C, Mohsen AW, Zanatta G, El-Gharbawy AH, Anthonymuthu TS, Tyurina YY, Tyurin VA, Kagan V, Bayır H, Vockley J. Mitochondrial bioenergetics and cardiolipin remodeling abnormalities in mitochondrial trifunctional protein deficiency. JCI Insight 2024; 9:e176887. [PMID: 39088276 PMCID: PMC11385086 DOI: 10.1172/jci.insight.176887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 07/25/2024] [Indexed: 08/03/2024] Open
Abstract
Mitochondrial trifunctional protein (TFP) deficiency is an inherited metabolic disorder leading to a block in long-chain fatty acid β-oxidation. Mutations in HADHA and HADHB, which encode the TFP α and β subunits, respectively, usually result in combined TFP deficiency. A single common mutation, HADHA c.1528G>C (p.E510Q), leads to isolated 3-hydroxyacyl-CoA dehydrogenase deficiency. TFP also catalyzes a step in the remodeling of cardiolipin (CL), a phospholipid critical to mitochondrial membrane stability and function. We explored the effect of mutations in TFP subunits on CL and other phospholipid content and composition and the consequences of these changes on mitochondrial bioenergetics in patient-derived fibroblasts. Abnormalities in these parameters varied extensively among different fibroblasts, and some cells were able to maintain basal oxygen consumption rates similar to controls. Although CL reduction was universally identified, a simultaneous increase in monolysocardiolipins was discrepant among cells. A similar profile was seen in liver mitochondria isolates from a TFP-deficient mouse model. Response to new potential drugs targeting CL metabolism might be dependent on patient genotype.
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Affiliation(s)
- Eduardo Vieira Neto
- Genetic and Genomic Medicine Division, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh
- Children's Neuroscience Institute, Department of Pediatrics, School of Medicine, and
| | - Meicheng Wang
- Genetic and Genomic Medicine Division, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh
| | - Austin J Szuminsky
- Department of Biological Sciences, Kenneth P. Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lethicia Ferraro
- Genetic and Genomic Medicine Division, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh
- School of Medicine and
| | - Erik Koppes
- Genetic and Genomic Medicine Division, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh
| | - Yudong Wang
- Genetic and Genomic Medicine Division, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh
| | - Clinton Van't Land
- Genetic and Genomic Medicine Division, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh
| | - Al-Walid Mohsen
- Genetic and Genomic Medicine Division, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh
| | - Geancarlo Zanatta
- Department of Biophysics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Areeg H El-Gharbawy
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Yulia Y Tyurina
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, School of Public Health
| | - Vladimir A Tyurin
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, School of Public Health
| | - Valerian Kagan
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, School of Public Health
- Department of Pharmacology and Chemical Biology, School of Medicine; Department of Chemistry, Kenneth P. Dietrich School of Arts and Sciences; and Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Hülya Bayır
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Redox Health Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Jerry Vockley
- Genetic and Genomic Medicine Division, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh
- Department of Human Genetics, School of Public Health, Center for Rare Disease Therapy, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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24
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Toledano I, Supek F, Lehner B. Genome-scale quantification and prediction of pathogenic stop codon readthrough by small molecules. Nat Genet 2024; 56:1914-1924. [PMID: 39174735 PMCID: PMC11387191 DOI: 10.1038/s41588-024-01878-5] [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: 08/01/2023] [Accepted: 07/23/2024] [Indexed: 08/24/2024]
Abstract
Premature termination codons (PTCs) cause ~10-20% of inherited diseases and are a major mechanism of tumor suppressor gene inactivation in cancer. A general strategy to alleviate the effects of PTCs would be to promote translational readthrough. Nonsense suppression by small molecules has proven effective in diverse disease models, but translation into the clinic is hampered by ineffective readthrough of many PTCs. Here we directly tackle the challenge of defining drug efficacy by quantifying the readthrough of ~5,800 human pathogenic stop codons by eight drugs. We find that different drugs promote the readthrough of complementary subsets of PTCs defined by local sequence context. This allows us to build interpretable models that accurately predict drug-induced readthrough genome-wide, and we validate these models by quantifying endogenous stop codon readthrough. Accurate readthrough quantification and prediction will empower clinical trial design and the development of personalized nonsense suppression therapies.
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Affiliation(s)
- Ignasi Toledano
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Fran Supek
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Ben Lehner
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
- University Pompeu Fabra (UPF), Barcelona, Spain.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
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25
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Reis LM, Seese SE, Costakos D, Semina EV. Congenital anterior segment ocular disorders: Genotype-phenotype correlations and emerging novel mechanisms. Prog Retin Eye Res 2024; 102:101288. [PMID: 39097141 PMCID: PMC11392650 DOI: 10.1016/j.preteyeres.2024.101288] [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: 03/30/2023] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024]
Abstract
Development of the anterior segment of the eye requires reciprocal sequential interactions between the arising tissues, facilitated by numerous genetic factors. Disruption of any of these processes results in congenital anomalies in the affected tissue(s) leading to anterior segment disorders (ASD) including aniridia, Axenfeld-Rieger anomaly, congenital corneal opacities (Peters anomaly, cornea plana, congenital primary aphakia), and primary congenital glaucoma. Current understanding of the genetic factors involved in ASD remains incomplete, with approximately 50% overall receiving a genetic diagnosis. While some genes are strongly associated with a specific clinical diagnosis, the majority of known factors are linked with highly variable phenotypic presentations, with pathogenic variants in FOXC1, CYP1B1, and PITX2 associated with the broadest spectrum of ASD conditions. This review discusses typical clinical presentations including associated systemic features of various forms of ASD; the latest functional data and genotype-phenotype correlations related to 25 ASD factors including newly identified genes; promising novel candidates; and current and emerging treatments for these complex conditions. Recent developments of interest in the genetics of ASD include identification of phenotypic expansions for several factors, discovery of multiple modes of inheritance for some genes, and novel mechanisms including a growing number of non-coding variants and alleles affecting specific domains/residues and requiring further studies.
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Affiliation(s)
- Linda M Reis
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Sarah E Seese
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Deborah Costakos
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Elena V Semina
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA; Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
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26
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Tikhonova TB, Sharkov AA, Zhorov BS, Vassilevski AA. Diverse biophysical mechanisms in voltage-gated sodium channel Na v1.4 variants associated with myotonia. FASEB J 2024; 38:e23883. [PMID: 39150825 DOI: 10.1096/fj.202400867r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/14/2024] [Accepted: 07/31/2024] [Indexed: 08/18/2024]
Abstract
Mutations in SCN4A gene encoding Nav1.4 channel α-subunit, are known to cause neuromuscular disorders such as myotonia or paralysis. Here, we study the effect of two amino acid replacements, K1302Q and G1306E, in the DIII-IV loop of the channel, corresponding to mutations found in patients with myotonia. We combine clinical, electrophysiological, and molecular modeling data to provide a holistic picture of the molecular mechanisms operating in mutant channels and eventually leading to pathology. We analyze the existing clinical data for patients with the K1302Q substitution, which was reported for adults with or without myotonia phenotypes, and report two new unrelated patients with the G1306E substitution, who presented with severe neonatal episodic laryngospasm and childhood-onset myotonia. We provide a functional analysis of the mutant channels by expressing Nav1.4 α-subunit in Xenopus oocytes in combination with β1 subunit and recording sodium currents using two-electrode voltage clamp. The K1302Q variant exhibits abnormal voltage dependence of steady-state fast inactivation, being the likely cause of pathology. K1302Q does not lead to decelerated fast inactivation, unlike several other myotonic mutations such as G1306E. For both mutants, we observe increased window currents corresponding to a larger population of channels available for activation. To elaborate the structural rationale for our experimental data, we explore the contacts involving K/Q1302 and E1306 in the AlphaFold2 model of wild-type Nav1.4 and Monte Carlo-minimized models of mutant channels. Our data provide the missing evidence to support the classification of K1302Q variant as likely pathogenic and may be used by clinicians.
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Affiliation(s)
- Tatiana B Tikhonova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Artem A Sharkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University, Moscow, Russia
- Genomed Ltd., Moscow, Russia
| | - Boris S Zhorov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Sechenov Institute of Evolutionary Physiology & Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Alexander A Vassilevski
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, State University, Dolgoprudny, Russia
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Lin YJ, Menon AS, Hu Z, Brenner SE. Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors. Hum Genomics 2024; 18:90. [PMID: 39198917 PMCID: PMC11360829 DOI: 10.1186/s40246-024-00663-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Accepted: 08/19/2024] [Indexed: 09/01/2024] Open
Abstract
BACKGROUND Variant interpretation is essential for identifying patients' disease-causing genetic variants amongst the millions detected in their genomes. Hundreds of Variant Impact Predictors (VIPs), also known as Variant Effect Predictors (VEPs), have been developed for this purpose, with a variety of methodologies and goals. To facilitate the exploration of available VIP options, we have created the Variant Impact Predictor database (VIPdb). RESULTS The Variant Impact Predictor database (VIPdb) version 2 presents a collection of VIPs developed over the past three decades, summarizing their characteristics, ClinGen calibrated scores, CAGI assessment results, publication details, access information, and citation patterns. We previously summarized 217 VIPs and their features in VIPdb in 2019. Building upon this foundation, we identified and categorized an additional 190 VIPs, resulting in a total of 407 VIPs in VIPdb version 2. The majority of the VIPs have the capacity to predict the impacts of single nucleotide variants and nonsynonymous variants. More VIPs tailored to predict the impacts of insertions and deletions have been developed since the 2010s. In contrast, relatively few VIPs are dedicated to the prediction of splicing, structural, synonymous, and regulatory variants. The increasing rate of citations to VIPs reflects the ongoing growth in their use, and the evolving trends in citations reveal development in the field and individual methods. CONCLUSIONS VIPdb version 2 summarizes 407 VIPs and their features, potentially facilitating VIP exploration for various variant interpretation applications. VIPdb is available at https://genomeinterpretation.org/vipdb.
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Affiliation(s)
- Yu-Jen Lin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
- Center for Computational Biology, University of California, Berkeley, CA, 94720, USA
| | - Arul S Menon
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
- College of Computing, Data Science, and Society, University of California, Berkeley, CA, 94720, USA
| | - Zhiqiang Hu
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall #3102, Berkeley, CA, 94720-3102, USA
- Illumina, Foster City, CA, 94404, USA
| | - Steven E Brenner
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
- Center for Computational Biology, University of California, Berkeley, CA, 94720, USA.
- College of Computing, Data Science, and Society, University of California, Berkeley, CA, 94720, USA.
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall #3102, Berkeley, CA, 94720-3102, USA.
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28
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Chacon-Camacho OF, Xilotl-de Jesús N, Calderón-Martínez E, Ordoñez-Labastida V, Neria-Gonzalez MI, Villafuerte-de la Cruz R, Martinez-Rojas A, Zenteno JC. Genotypic spectrum of ABCA4-associated retinal degenerations in 211 unrelated Mexican patients: identification of 22 novel disease-causing variants. Mol Genet Genomics 2024; 299:79. [PMID: 39162841 PMCID: PMC11335775 DOI: 10.1007/s00438-024-02174-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: 07/19/2023] [Accepted: 08/02/2024] [Indexed: 08/21/2024]
Abstract
The purpose of this study was to analyze and molecularly describe the largest group of patients with ABCA4-associated retinal degeneration in Latin America. Pathogenic variants in ABCA4, a member of the ATP Binding Cassette (ABC) transporters superfamily, is one of the most common causes of inherited visual deficiency in humans. Retinal phenotypes associated with genetic defects in ABCA4 are collectively known as ABCA4-associated retinal degenerations (ABCA4R), a group of recessively inherited disorders associated with a high allelic heterogeneity. While large groups of Caucasian and Asiatic individuals suffering from ABCA4R have been well characterized, molecular information from certain ethnic groups is limited or unavailable, precluding a more realistic knowledge of ABCA4-related mutational profile worldwide. In this study, we describe the molecular findings of a large group of 211 ABCA4R index cases from Mexico. Genotyping was performed using either next generation sequencing (NGS) of a retinal dystrophy genes panel or exome. ABCA4 targeted mutation testing was applied to a subgroup of subjects in whom founder mutations were suspected. A total of 128 different ABCA4 pathogenic variants were identified, including 22 previously unpublished variants. The most common type of genetic variation was single nucleotide substitutions which occurred in 92.7% (408/440 alleles). According to the predicted protein effect, the most frequent variant type was missense, occurring in 83.5% of disease-causing alleles (368/440). Mutations such as p.Ala1773Val are fully demonstrated as a founder effect in native inhabitants of certain regions of Mexico. This study also gives us certain indications of other founder effects that need to be further studied in the near future. This is the largest molecularly characterized ABCA4R Latin American cohort, and our results supports the value of conducting genetic screening in underrepresented populations for a better knowledge of the mutational profile leading to monogenic diseases.
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Affiliation(s)
- Oscar F Chacon-Camacho
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Chimalpopoca 14, Col. Obrera, Cuauhtemoc, Mexico City, CP06800, Mexico
- Laboratorio 5, Edificio A-4, Carrera de Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Laboratorio 5, Edificio A-4, Mexico City, Mexico
| | - Nancy Xilotl-de Jesús
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Chimalpopoca 14, Col. Obrera, Cuauhtemoc, Mexico City, CP06800, Mexico
| | - Ernesto Calderón-Martínez
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Chimalpopoca 14, Col. Obrera, Cuauhtemoc, Mexico City, CP06800, Mexico
- Department of Biomedical Informatics, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Vianey Ordoñez-Labastida
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Chimalpopoca 14, Col. Obrera, Cuauhtemoc, Mexico City, CP06800, Mexico
- Rare Disease Diagnostic Unit, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- Faculty of Medicine, Autonomous University of the State of Morelos (UAEM), Morelos, Mexico
| | - M Isabel Neria-Gonzalez
- Laboratory of Integrative Microbiology and Molecular Biology, Division of Chemical and Biochemical Engineering, TecNm: Tecnológico de Estudios Superiores de Ecatepec. Ecatepec de Morelos, Morelos, Edo. México, Mexico
| | | | | | - Juan Carlos Zenteno
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Chimalpopoca 14, Col. Obrera, Cuauhtemoc, Mexico City, CP06800, Mexico.
- Rare Disease Diagnostic Unit, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico.
- Biochemistry Department, Faculty of Medicine, UNAM, Mexico City, Mexico.
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29
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Lancaster NM, Sinitcyn P, Forny P, Peters-Clarke TM, Fecher C, Smith AJ, Shishkova E, Arrey TN, Pashkova A, Robinson ML, Arp N, Fan J, Hansen J, Galmozzi A, Serrano LR, Rojas J, Gasch AP, Westphall MS, Stewart H, Hock C, Damoc E, Pagliarini DJ, Zabrouskov V, Coon JJ. Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer. Nat Commun 2024; 15:7016. [PMID: 39147754 PMCID: PMC11327265 DOI: 10.1038/s41467-024-51274-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 08/02/2024] [Indexed: 08/17/2024] Open
Abstract
Owing to its roles in cellular signal transduction, protein phosphorylation plays critical roles in myriad cell processes. That said, detecting and quantifying protein phosphorylation has remained a challenge. We describe the use of a novel mass spectrometer (Orbitrap Astral) coupled with data-independent acquisition (DIA) to achieve rapid and deep analysis of human and mouse phosphoproteomes. With this method, we map approximately 30,000 unique human phosphorylation sites within a half-hour of data collection. The technology is benchmarked to other state-of-the-art MS platforms using both synthetic peptide standards and with EGF-stimulated HeLa cells. We apply this approach to generate a phosphoproteome multi-tissue atlas of the mouse. Altogether, we detect 81,120 unique phosphorylation sites within 12 hours of measurement. With this unique dataset, we examine the sequence, structural, and kinase specificity context of protein phosphorylation. Finally, we highlight the discovery potential of this resource with multiple examples of phosphorylation events relevant to mitochondrial and brain biology.
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Affiliation(s)
- Noah M Lancaster
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Patrick Forny
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Caroline Fecher
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrew J Smith
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI, USA
| | | | - Anna Pashkova
- Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany
| | - Margaret Lea Robinson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Nicholas Arp
- Morgridge Institute for Research, Madison, WI, USA
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Jing Fan
- Morgridge Institute for Research, Madison, WI, USA
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Juli Hansen
- Department of Medicine, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - Andrea Galmozzi
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medicine, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
- University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - Lia R Serrano
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Julie Rojas
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
| | - Audrey P Gasch
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael S Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI, USA
| | | | | | - Eugen Damoc
- Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany
| | - David J Pagliarini
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Morgridge Institute for Research, Madison, WI, USA.
- National Center for Quantitative Biology of Complex Systems, Madison, WI, USA.
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA.
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30
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Lazareva TE, Barbitoff YA, Nasykhova YA, Glotov AS. Major Causes of Conflicting Interpretations of Variant Pathogenicity in Rare Disease: A Systematic Analysis. J Pers Med 2024; 14:864. [PMID: 39202055 PMCID: PMC11355203 DOI: 10.3390/jpm14080864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/31/2024] [Accepted: 08/12/2024] [Indexed: 09/03/2024] Open
Abstract
The identification of the genetic causes of inherited disorders from next-generation sequencing (NGS) data remains a complicated process, in particular due to challenges in interpretation of the vast amount of generated data and hundreds of candidate variants identified. Inconsistencies in variant classification, where genetic centers classify the same variant differently, can hinder accurate diagnoses for rare diseases. Publicly available databases that collect data on human genetic variations and their association with diseases provide ample opportunities to discover conflicts in variant interpretation worldwide. In this study, we explored patterns of variant classification discrepancies using data from ClinVar, a public archive of variant interpretations. We found that 5.7% of variants have conflicting interpretations (COIs) reported, and the vast majority of interpretation conflicts arise for variants of uncertain significance (VUS). As many as 78% of clinically relevant genes harbor variants with COIs, and genes with high COI rates tended to have more exons and longer transcripts, with a greater proportion of genes linked to several distinct conditions. The enrichment analysis of COI-enriched genes revealed that the products of these genes are involved in cardiac disorders, muscle development, and function. To improve diagnoses, we believe that specific variant interpretation rules could be developed for such genes. Additionally, our findings underscore the need for the publication of variant pathogenicity evidence and the importance of considering every variant as VUS unless proven otherwise.
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Affiliation(s)
- Tatyana E. Lazareva
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia
| | - Yury A. Barbitoff
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia
- Bioinformatics Institute, Kantemirovskaya St. 2A, 197342 St. Petersburg, Russia
| | - Yulia A. Nasykhova
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia
| | - Andrey S. Glotov
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia
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31
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Gjorgjievski N, Karanfilovski V, Arsov T, Vidimliski PD, Andreevska GS, Selim G, Dejanov P, Jordanova V, Marinova I, Paskalev E, Nikolov IG. Case report: First diagnosis of Fabry disease in North Macedonia in a patient presenting with kidney failure on hemodialysis. Front Genet 2024; 15:1415906. [PMID: 39205943 PMCID: PMC11349674 DOI: 10.3389/fgene.2024.1415906] [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: 04/11/2024] [Accepted: 07/18/2024] [Indexed: 09/04/2024] Open
Abstract
Introduction Fabry disease is a rare X-linked lysosomal storage disorder caused by α-galactosidase A (α-Gal A) deficiency. Reduced or absent enzyme activity causes progressive lysosomal accumulation of globotriaosylceramide (Lyso-Gb3) in various cells throughout the body to trigger inflammation and fibrosis. Case description We present the first familial case of Fabry Disease in North Macedonia identified based on clinical manifestations and confirmed through enzyme, biomarker, and genetic tests. The index case in the family was a 45-year-old male undergoing hemodialysis therapy. He has had chronic burning uncontrolled limb pain since childhood, intermittent abdominal cramps, anhidrosis, and hypertension. The constellation of clinical presentations accompanied by similar symptoms in close family members prompted the enzyme, biomarker, and genetic analyses for Fabry disease. Genetic testing identified a known pathogenic GLA missense variant c.443G>A or p.(Ser148Asn) in the hemizygous state. Subsequent family studies allowed identification of another hemizygous male and five heterozygous female carriers affected by this X-linked disorder. Conclusion We report identification of the first familial case of Fabry disease in North Macedonia and describe the phenotype associated with the Ser148Asn GLA variant. Greater awareness of this rare disease linked to continuous medical education is crucial for timely diagnosis and treatment.
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Affiliation(s)
- Nikola Gjorgjievski
- Faculty of Medicine Ss. Cyril and Methodius in Skopje, University Hospital of Nephrology, Skopje, North Macedonia
| | - Vlatko Karanfilovski
- Faculty of Medicine Ss. Cyril and Methodius in Skopje, University Hospital of Nephrology, Skopje, North Macedonia
| | - Todor Arsov
- Faculty of Medical Sciences, University Goce Delcev in Shtip, Stip, North Macedonia
| | - Pavlina Dzekova Vidimliski
- Faculty of Medicine Ss. Cyril and Methodius in Skopje, University Hospital of Nephrology, Skopje, North Macedonia
| | - Galisna Severeova Andreevska
- Faculty of Medicine Ss. Cyril and Methodius in Skopje, University Hospital of Nephrology, Skopje, North Macedonia
| | - Gjulshen Selim
- Faculty of Medicine Ss. Cyril and Methodius in Skopje, University Hospital of Nephrology, Skopje, North Macedonia
| | - Petar Dejanov
- Faculty of Medicine Ss. Cyril and Methodius in Skopje, University Hospital of Nephrology, Skopje, North Macedonia
| | - Vasilena Jordanova
- Department of Nephrology and Transplantation University Hospital "Alexandrovska", Sofia, Bulgaria
| | - Ivelina Marinova
- Department of Nephrology and Transplantation University Hospital "Alexandrovska", Sofia, Bulgaria
| | - Emil Paskalev
- Department of Nephrology and Transplantation University Hospital "Alexandrovska", Sofia, Bulgaria
| | - Igor G Nikolov
- Faculty of Medicine Ss. Cyril and Methodius in Skopje, University Hospital of Nephrology, Skopje, North Macedonia
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32
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do Nascimento RRNR, Quaio CRDC, Chung CH, de Moraes Vasconcelos D, Sztajnbok FR, Rosa Neto NS, Perazzio SF. Principles of clinical genetics for rheumatologists: clinical indications and interpretation of broad-based genetic testing. Adv Rheumatol 2024; 64:59. [PMID: 39143637 DOI: 10.1186/s42358-024-00400-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 08/05/2024] [Indexed: 08/16/2024] Open
Abstract
Advances in DNA sequencing technologies, especially next-generation sequencing (NGS), which is the basis for whole-exome sequencing (WES) and whole-genome sequencing (WGS), have profoundly transformed immune-mediated rheumatic disease diagnosis. Recently, substantial cost reductions have facilitated access to these diagnostic tools, expanded the capacity of molecular diagnostics and enabled the pursuit of precision medicine in rheumatology. Understanding the fundamental principles of genetics and diversity in genetic variant classification is a crucial milestone in rheumatology. However, despite the growing availability of DNA sequencing platforms, a significant number of autoinflammatory diseases (AIDs), neuromuscular disorders, hereditary collagen diseases, and monogenic bone diseases remain unsolved, and variants of uncertain significance (VUS) pose a formidable challenge to addressing these unmet needs in the coming decades. This article aims to provide an overview of the clinical indications and interpretation of comprehensive genetic testing in the medical field, addressing the related complexities and implications.
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Affiliation(s)
| | | | | | | | | | | | - Sandro Félix Perazzio
- Disciplina de Reumatologia, Universidade Federal de Sao Paulo, Escola Paulista de Medicina, Rua Otonis, 863, Sao Paulo, SP, 04025-002, Brazil.
- Fleury Medicina e Saude, Sao Paulo, Brazil.
- Universidade de Sao Paulo Faculdade de Medicina (USP FM), Sao Paulo, Brazil.
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33
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Torices L, Nunes-Xavier CE, Pulido R. Potentiation by Protein Synthesis Inducers of Translational Readthrough of Pathogenic Premature Termination Codons in PTEN Isoforms. Cancers (Basel) 2024; 16:2836. [PMID: 39199607 PMCID: PMC11352852 DOI: 10.3390/cancers16162836] [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: 06/22/2024] [Revised: 08/05/2024] [Accepted: 08/12/2024] [Indexed: 09/01/2024] Open
Abstract
The PTEN tumor suppressor is frequently targeted in tumors and patients with PTEN hamartoma tumor syndrome (PHTS) through nonsense mutations generating premature termination codons (PTC) that may cause the translation of truncated non-functional PTEN proteins. We have previously described a global analysis of the readthrough reconstitution of the protein translation and function of the human canonical PTEN isoform by aminoglycosides. Here, we report the efficient functional readthrough reconstitution of the PTEN translational isoform PTEN-L, which displays a minimal number of PTC in its specific N-terminal extension in association with disease. We illustrate the importance of the specific PTC and its nucleotide proximal sequence for optimal readthrough and show that the more frequent human PTEN PTC variants and their mouse PTEN PTC equivalents display similar patterns of readthrough efficiency. The heterogeneous readthrough response of the different PTEN PTC variants was independent of the length of the PTEN protein being reconstituted, and we found a correlation between the amount of PTEN protein being synthesized and the PTEN readthrough efficiency. Furthermore, combination of aminoglycosides and protein synthesis inducers increased the readthrough response of specific PTEN PTC. Our results provide insights with which to improve the functional reconstitution of human-disease-related PTC pathogenic variants from PTEN isoforms by increasing protein synthesis coupled to translational readthrough.
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Affiliation(s)
- Leire Torices
- Biobizkaia Health Research Institute, 48903 Barakaldo, Spain; (L.T.); (C.E.N.-X.)
| | - Caroline E. Nunes-Xavier
- Biobizkaia Health Research Institute, 48903 Barakaldo, Spain; (L.T.); (C.E.N.-X.)
- Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway
- Centro de Investigación Biomédica en Red de Enfermedades Raras, CIBERER, ISCIII, 28029 Madrid, Spain
| | - Rafael Pulido
- Biobizkaia Health Research Institute, 48903 Barakaldo, Spain; (L.T.); (C.E.N.-X.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras, CIBERER, ISCIII, 28029 Madrid, Spain
- Ikerbasque, The Basque Foundation for Science, 48009 Bilbao, Spain
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34
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Nicolas-Martinez EC, Robinson O, Pflueger C, Gardner A, Corbett MA, Ritchie T, Kroes T, van Eyk CL, Scheffer IE, Hildebrand MS, Barnier JV, Rousseau V, Genevieve D, Haushalter V, Piton A, Denommé-Pichon AS, Bruel AL, Nambot S, Isidor B, Grigg J, Gonzalez T, Ghedia S, Marchant RG, Bournazos A, Wong WK, Webster RI, Evesson FJ, Jones KJ, Cooper ST, Lister R, Gecz J, Jolly LA. RNA variant assessment using transactivation and transdifferentiation. Am J Hum Genet 2024; 111:1673-1699. [PMID: 39084224 PMCID: PMC11339655 DOI: 10.1016/j.ajhg.2024.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 08/02/2024] Open
Abstract
Understanding the impact of splicing and nonsense variants on RNA is crucial for the resolution of variant classification as well as their suitability for precision medicine interventions. This is primarily enabled through RNA studies involving transcriptomics followed by targeted assays using RNA isolated from clinically accessible tissues (CATs) such as blood or skin of affected individuals. Insufficient disease gene expression in CATs does however pose a major barrier to RNA based investigations, which we show is relevant to 1,436 Mendelian disease genes. We term these "silent" Mendelian genes (SMGs), the largest portion (36%) of which are associated with neurological disorders. We developed two approaches to induce SMG expression in human dermal fibroblasts (HDFs) to overcome this limitation, including CRISPR-activation-based gene transactivation and fibroblast-to-neuron transdifferentiation. Initial transactivation screens involving 40 SMGs stimulated our development of a highly multiplexed transactivation system culminating in the 6- to 90,000-fold induction of expression of 20/20 (100%) SMGs tested in HDFs. Transdifferentiation of HDFs directly to neurons led to expression of 193/516 (37.4%) of SMGs implicated in neurological disease. The magnitude and isoform diversity of SMG expression following either transactivation or transdifferentiation was comparable to clinically relevant tissues. We apply transdifferentiation and/or gene transactivation combined with short- and long-read RNA sequencing to investigate the impact that variants in USH2A, SCN1A, DMD, and PAK3 have on RNA using HDFs derived from affected individuals. Transactivation and transdifferentiation represent rapid, scalable functional genomic solutions to investigate variants impacting SMGs in the patient cell and genomic context.
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Affiliation(s)
- Emmylou C Nicolas-Martinez
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; School of Biomedicine, University of Adelaide, Adelaide, SA 5005, Australia
| | - Olivia Robinson
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; School of Biomedicine, University of Adelaide, Adelaide, SA 5005, Australia
| | - Christian Pflueger
- Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia; Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - Alison Gardner
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
| | - Mark A Corbett
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - Tarin Ritchie
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
| | - Thessa Kroes
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
| | - Clare L van Eyk
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia; Murdoch Children's Research Institute, Parkville, VIC 3052, Australia; Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - Jean-Vianney Barnier
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
| | - Véronique Rousseau
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
| | - David Genevieve
- Montpellier University, Inserm U1183, Reference Center for Rare Diseases Developmental Anomaly and Malformative Syndromes, Genetics Department, Montpellier Hospital, Montpellier, France
| | - Virginie Haushalter
- Genetic Diagnosis Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Amélie Piton
- Genetic Diagnosis Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Anne-Sophie Denommé-Pichon
- CRMRs "Anomalies du Développement et syndromes malformatifs" et "Déficiences Intellectuelles de causes rares", Centre de Génétique, CHU Dijon, Dijon, France; INSERM UMR1231, GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Ange-Line Bruel
- CRMRs "Anomalies du Développement et syndromes malformatifs" et "Déficiences Intellectuelles de causes rares", Centre de Génétique, CHU Dijon, Dijon, France; INSERM UMR1231, GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Sophie Nambot
- CRMRs "Anomalies du Développement et syndromes malformatifs" et "Déficiences Intellectuelles de causes rares", Centre de Génétique, CHU Dijon, Dijon, France; INSERM UMR1231, GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Bertrand Isidor
- CRMRs "Anomalies du Développement et syndromes malformatifs" et "Déficiences Intellectuelles de causes rares", Centre de Génétique, CHU Dijon, Dijon, France; INSERM UMR1231, GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - John Grigg
- Speciality of Ophthalmology, Save Sight Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2000, Australia
| | - Tina Gonzalez
- Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
| | - Sondhya Ghedia
- Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
| | - Rhett G Marchant
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2000, Australia
| | - Adam Bournazos
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Wui-Kwan Wong
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Children's Medical Research Institute, Westmead, NSW 2145, Australia; Department of Paediatric Neurology, Children's Hospital at Westmead, Sydney, NSW 2000, Australia
| | - Richard I Webster
- Department of Paediatric Neurology, Children's Hospital at Westmead, Sydney, NSW 2000, Australia
| | - Frances J Evesson
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2000, Australia; Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Kristi J Jones
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Children's Medical Research Institute, Westmead, NSW 2145, Australia; Department of Clinical Genetics, Children's Hospital at Westmead, Sydney, NSW 2000, Australia
| | - Sandra T Cooper
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2000, Australia; Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Ryan Lister
- Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia; Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Jozef Gecz
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia.
| | - Lachlan A Jolly
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; School of Biomedicine, University of Adelaide, Adelaide, SA 5005, Australia.
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Andhika NS, Biswas S, Hardcastle C, Green DJ, Ramsden SC, Birney E, Black GC, Sergouniotis PI. Using computational approaches to enhance the interpretation of missense variants in the PAX6 gene. Eur J Hum Genet 2024; 32:1005-1013. [PMID: 38849599 PMCID: PMC11292026 DOI: 10.1038/s41431-024-01638-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/12/2024] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Abstract
The PAX6 gene encodes a highly-conserved transcription factor involved in eye development. Heterozygous loss-of-function variants in PAX6 can cause a range of ophthalmic disorders including aniridia. A key molecular diagnostic challenge is that many PAX6 missense changes are presently classified as variants of uncertain significance. While computational tools can be used to assess the effect of genetic alterations, the accuracy of their predictions varies. Here, we evaluated and optimised the performance of computational prediction tools in relation to PAX6 missense variants. Through inspection of publicly available resources (including HGMD, ClinVar, LOVD and gnomAD), we identified 241 PAX6 missense variants that were used for model training and evaluation. The performance of ten commonly used computational tools was assessed and a threshold optimization approach was utilized to determine optimal cut-off values. Validation studies were subsequently undertaken using PAX6 variants from a local database. AlphaMissense, SIFT4G and REVEL emerged as the best-performing predictors; the optimized thresholds of these tools were 0.967, 0.025, and 0.772, respectively. Combining the prediction from these top-three tools resulted in lower performance compared to using AlphaMissense alone. Tailoring the use of computational tools by employing optimized thresholds specific to PAX6 can enhance algorithmic performance. Our findings have implications for PAX6 variant interpretation in clinical settings.
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Affiliation(s)
- Nadya S Andhika
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Susmito Biswas
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Claire Hardcastle
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - David J Green
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Simon C Ramsden
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Graeme C Black
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Panagiotis I Sergouniotis
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, UK.
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK.
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Misaki M, Takeichi T, Omi M, Ito Y, Ogi T, Muro Y, Akiyama M. Localized epidermolysis bullosa simplex caused by a previously unreported substitution in the linker 12 domain of keratin 14. J Dermatol 2024; 51:e264-e265. [PMID: 38362638 DOI: 10.1111/1346-8138.17165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 02/17/2024]
Affiliation(s)
- Miyu Misaki
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takuya Takeichi
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Nagoya University Institute for Advanced Research, Nagoya, Japan
| | - Michiya Omi
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasutoshi Ito
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshinao Muro
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masashi Akiyama
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Alary B, Cintas P, Claude C, Dellis O, Thèze C, Van Goethem C, Cossée M, Krahn M, Delague V, Bartoli M. Store-operated calcium entry dysfunction in CRAC channelopathy: Insights from a novel STIM1 mutation. Clin Immunol 2024; 265:110306. [PMID: 38977117 DOI: 10.1016/j.clim.2024.110306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/19/2024] [Accepted: 07/05/2024] [Indexed: 07/10/2024]
Abstract
Store-operated calcium entry (SOCE) plays a crucial role in maintaining cellular calcium homeostasis. This mechanism involves proteins, such as stromal interaction molecule 1 (STIM1) and ORAI1. Mutations in the genes encoding these proteins, especially STIM1, can lead to various diseases, including CRAC channelopathies associated with severe combined immunodeficiency. Herein, we describe a novel homozygous mutation, NM_003156 c.792-3C > G, in STIM1 in a patient with a clinical profile of CRAC channelopathy, including immune system deficiencies and muscle weakness. Functional analyses revealed three distinct spliced forms in the patient cells: wild-type, exon 7 skipping, and intronic retention. Calcium influx analysis revealed impaired SOCE in the patient cells, indicating a loss of STIM1 function. We developed an antisense oligonucleotide treatment that improves STIM1 splicing and highlighted its potential as a therapeutic approach. Our findings provide insights into the complex effects of STIM1 mutations and shed light on the multifaceted clinical presentation of the patient.
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Affiliation(s)
| | - Pascal Cintas
- Centre de Référence Maladies Rares Neuromusculaire, CHU Toulouse, Toulouse, France
| | | | | | - Corinne Thèze
- Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | | | - Mireille Cossée
- Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France; PhyMedExp (Physiologie et Médecine Expérimentale du Cœur et des Muscles), Université de Montpellier, Inserm U1046, CNRS UMR9214, Montpellier, France
| | - Martin Krahn
- Aix Marseille Univ, INSERM, MMG, U1251 Marseille, France; Département de Génétique Médicale, Hôpital Timone Enfants, APHM, Marseille, France
| | | | - Marc Bartoli
- Aix Marseille Univ, INSERM, MMG, U1251 Marseille, France; CNRS, Marseille, France
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Bozkurt B, Bağcı O, Üzüm S, Çora T. A novel LTBP2 gene variant in a Turkish family with juvenile-onset open-angle glaucoma. Ophthalmic Genet 2024; 45:384-389. [PMID: 38557215 DOI: 10.1080/13816810.2024.2331540] [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: 10/17/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND Juvenile-onset open-angle glaucoma (JOAG) is a rare form of primary open-angle glaucoma (POAG) with an early age of onset before 40 years. Latent transforming growth factor-beta binding protein 2 (LTBP-2) is an extracellular matrix protein with a multi-domain structure and homology to fibrillins. LTBP2 gene variants have been associated with JOAG in a small number of patients. Herein, we report a novel missense variant in the LTBP2 gene in a Turkish family with JOAG. MATERIALS AND METHODS Blood samples were obtained from three siblings (a 20-year-old woman with JOAG, 26-year-old man with JOAG, and 15-year-old girl with posterior embryotoxon) for genetic analysis. Their father had moderate-severe POAG and the 24-year-old brother had JOAG. The mother and 32-year-old sister were healthy. Although the parents reported no consanguinity, they come from the same village. RESULTS Clinical exome sequencing analysis of the two siblings with JOAG revealed a novel c.607C>T p.(R203C) (rs777450651) homozygous LTBP2 variant, while the variant was heterozygous in their 15-year-old sister. There were no mutations in the MYOC, CYP1B1, or FBN1 genes. CONCLUSION We documented a novel missense mutation in the LTBP2 gene leading to a severe form of JOAG with refractory IOP and progressive optic nerve damage, which seems to show autosomal recessive inheritance.
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Affiliation(s)
- Banu Bozkurt
- Department of Ophthalmology, Selçuk University Faculty of Medicine, Konya, Türkiye
| | - Ozkan Bağcı
- Department of Medical Genetics, Selçuk University Faculty of Medicine, Konya, Türkiye
| | - Sema Üzüm
- Department of Ophthalmology, Selçuk University Faculty of Medicine, Konya, Türkiye
| | - Tülin Çora
- Department of Medical Genetics, Selçuk University Faculty of Medicine, Konya, Türkiye
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Madhana Priya N, Archana Pai P, Thirumal Kumar D, Gnanasambandan R, Magesh R. Elucidating the functional impact of G137V and G144R variants in Maroteaux Lamy's Syndrome by Molecular Dynamics Simulation. Mol Divers 2024; 28:2049-2063. [PMID: 37458922 DOI: 10.1007/s11030-023-10694-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/03/2023] [Indexed: 10/05/2024]
Abstract
Mucopolysaccharidoses VI (Maroteaux Lamy syndrome) is a metabolic disorder due to the loss of enzyme activity of N-acetyl galactosamine-4-sulphatase arising from mutations in the ARSB gene. The mutated ARSB is the origin for the accumulation of GAGs within the lysosome leading to severe growth deformities, causing lysosomal storage disease. The main focus of this study is to identify the deleterious variants by applying bioinformatics tools to predict the conservation, pathogenicity, stability, and effect of the ARSB variants. We examined 170 missense variants, of which G137V and G144R were the resultant variants predicted detrimental to the progression of the disease. The native along with G137V and G144R structures were fixed as the receptors and subjected to Molecular docking with the small molecule Odiparcil to analyze the binding efficiency and the varied interactions of the receptors towards the drug. The interaction resulted in similar docking scores of - 7.3 kcal/mol indicating effective binding and consistent interactions of the drug with residues CYS117, GLN118, THR182, and GLN517 for native, along with G137V and G144R structures. Molecular Dynamics were conducted to validate the stability and flexibility of the native and variant structures on ligand binding. The overall study indicates that the drug has similar therapeutic towards the native and variant based on the higher binding affinity and also the complexes show stability with an average of 0.2 nm RMS value. This can aid in the future development therapeutics for the Maroteaux Lamy syndrome.
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Affiliation(s)
- N Madhana Priya
- Department of Biotechnology, Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, Tamil Nadu, 600116, India
| | - P Archana Pai
- Department of Biotechnology, Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, Tamil Nadu, 600116, India
| | - D Thirumal Kumar
- Faculty of Allied Health Sciences, Meenakshi Academy of Higher Education, Chennai, India
| | - R Gnanasambandan
- Department of Biomedical Genetics, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Vellore, India
| | - R Magesh
- Department of Biotechnology, Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, Tamil Nadu, 600116, India.
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Jiang Y, Yi Z, Zheng Y, Ouyang J, Guo D, Li S, Xiao X, Wang P, Sun W, Zhang Q. The Systemic Genotype-Phenotype Characterization of PAX6-Related Eye Disease in 164 Chinese Families. Invest Ophthalmol Vis Sci 2024; 65:46. [PMID: 39212610 PMCID: PMC11364179 DOI: 10.1167/iovs.65.10.46] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 08/11/2024] [Indexed: 09/04/2024] Open
Abstract
Purpose This study aims to evaluate the genetic and phenotypic characteristics and elucidate the genotype-phenotype correlations of a large Chinese cohort with PAX6-related disorders. Methods Variants detected with exome sequencing were filtered through multistep bioinformatic and co-segregation analyses, and validated by Sanger sequencing. The related clinical data were collected, and cluster analysis and statistical analysis of the PAX6-related phenotypes across different variant groups were carried out. Parental mosaicism was investigated using cloning analysis and Droplet digital PCR. Results A total of 119 pathogenic or likely pathogenic PAX6 variants, including 74 truncation, 31 missense, and 14 others, were identified in 228 patients from 164 unrelated families. The most common phenotypes were foveal hypoplasia (97.8%), nystagmus (92.6%), aniridia (76.7%), cataract (36.8%), and iris hypoplasia (22.4%). Mosaicism ranging from 13.9% to 18.8% was identified in 3 unrelated patients' parents with relatively mild phenotypes. Missense variants in the linker region of the paired domain were associated with high myopia, whereas truncation variants in the homeodomain and proline-serine-threonine-rich domain were associated with hyperopia. Similarly, the degree of iris defects, visual acuity, and associated ocular comorbidity varied among the different types and locations of PAX6 variants. Conclusions Our data indicate that foveal hypoplasia but not aniridia is the most common sign of PAX6-related disorders, contributing to subtle iris changes that might easily be overlooked in clinical practice. Recognition of mosaicism in atypical cases or parents with very mild phenotypes is important in genetic counseling as their offspring are at increased risk of typical aniridia. Recognition of the genotype-phenotype relationship emphasizes involvement of PAX6 regulation in shaping complex ocular phenotypes.
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Affiliation(s)
- Yi Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Zhen Yi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yuxi Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Jiamin Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Dongwei Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
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Chen X, Yu X. Toward a universal approach for predicting variant pathogenicity in diverse disease landscapes. J Genet Genomics 2024:S1673-8527(24)00193-0. [PMID: 39043334 DOI: 10.1016/j.jgg.2024.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Revised: 07/02/2024] [Accepted: 07/14/2024] [Indexed: 07/25/2024]
Affiliation(s)
- Xiang Chen
- Liangzhu Laboratory of Zhejiang University, Hangzhou, Zhejiang 310058, China; Department of Rheumatology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xiaomin Yu
- Liangzhu Laboratory of Zhejiang University, Hangzhou, Zhejiang 310058, China; Department of Rheumatology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.
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Bekele BM, Gazzerro E, Schoenrath F, Falk V, Rost S, Hoerning S, Jelting Y, Zaum AK, Spuler S, Knierim J. Undetected Neuromuscular Disease in Patients after Heart Transplantation. Int J Mol Sci 2024; 25:7819. [PMID: 39063061 PMCID: PMC11277526 DOI: 10.3390/ijms25147819] [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: 06/08/2024] [Revised: 07/10/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
(1) Heart transplantation (HTX) improves the overall survival and functional status of end-stage heart failure patients with cardiomyopathies (CMPs). The majority of CMPs have genetic causes, and the overlap between CMPs and inherited myopathies is well documented. However, the long-term outcome in skeletal muscle function and possibility of an undiagnosed underlying genetic cause of both a cardiac and skeletal pathology remain unknown. (2) Thirty-nine patients were assessed using open and standardized interviews on muscle function, a quality-of-life (EuroQol EQ-5D-3L) questionnaire, and a physical examination (Medical Research Council Muscle scale). Whole-exome sequencing was completed in three stages for those with skeletal muscle weakness. (3) Seven patients (17.9%) reported new-onset muscle weakness and motor limitations. Objective muscle weakness in the upper and lower extremities was seen in four patients. In three of them, exome sequencing revealed pathogenic/likely pathogenic variants in the genes encoding nexilin, myosin heavy chain, titin, and SPG7. (4) Our findings support a positive long-term outcome of skeletal muscle function in HTX patients. However, 10% of patients showed clinical signs of myopathy due to a possible genetic cause. The integration of genetic testing and standardized neurological assessment of motor function during the peri-HTX period should be considered.
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Affiliation(s)
- Biniam Melese Bekele
- Muscle Research Unit, ECRC Experimental and Clinical Research Center, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Lindenberger Weg 80, 13125 Berlin, Germany; (B.M.B.); (E.G.)
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany (J.K.)
- Deutsches Herzzentrum der Charité—Medical Heart Center of Charité and German Heart Institute Berlin, Department of Cardiothoracic and Vascular Surgery, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Elisabetta Gazzerro
- Muscle Research Unit, ECRC Experimental and Clinical Research Center, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Lindenberger Weg 80, 13125 Berlin, Germany; (B.M.B.); (E.G.)
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Felix Schoenrath
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany (J.K.)
- Deutsches Herzzentrum der Charité—Medical Heart Center of Charité and German Heart Institute Berlin, Department of Cardiothoracic and Vascular Surgery, Augustenburger Platz 1, 13353 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner site Berlin, 13125 Berlin, Germany
| | - Volkmar Falk
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany (J.K.)
- Deutsches Herzzentrum der Charité—Medical Heart Center of Charité and German Heart Institute Berlin, Department of Cardiothoracic and Vascular Surgery, Augustenburger Platz 1, 13353 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner site Berlin, 13125 Berlin, Germany
- Translational Cardiovascular Technologies, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Simone Rost
- Institute for Human Genetics, University of Würzburg, 97074 Würzburg, Germany
| | - Selina Hoerning
- Institute for Human Genetics, University of Würzburg, 97074 Würzburg, Germany
| | - Yvonne Jelting
- Institute for Human Genetics, University of Würzburg, 97074 Würzburg, Germany
| | - Ann-Kathrin Zaum
- Institute for Human Genetics, University of Würzburg, 97074 Würzburg, Germany
| | - Simone Spuler
- Muscle Research Unit, ECRC Experimental and Clinical Research Center, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Lindenberger Weg 80, 13125 Berlin, Germany; (B.M.B.); (E.G.)
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jan Knierim
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany (J.K.)
- Sana Paulinenkrankenhaus, Department of Internal Medicine and Cardiology, Dickensweg 25-39, 14055 Berlin, Germany
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Vinci M, Treccarichi S, Galati Rando R, Musumeci A, Todaro V, Federico C, Saccone S, Elia M, Calì F. A de novo ARIH2 gene mutation was detected in a patient with autism spectrum disorders and intellectual disability. Sci Rep 2024; 14:15848. [PMID: 38982159 PMCID: PMC11233510 DOI: 10.1038/s41598-024-66475-2] [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: 02/20/2024] [Accepted: 07/01/2024] [Indexed: 07/11/2024] Open
Abstract
E3 ubiquitin protein ligase encoded by ARIH2 gene catalyses the ubiquitination of target proteins and plays a crucial role in posttranslational modifications across various cellular processes. As prior documented, mutations in genes involved in the ubiquitination process are often associated with autism spectrum disorder (ASD) and/or intellectual disability (ID). In the current study, a de novo heterozygous mutation was identified in the splicing intronic region adjacent to the last exon of the ARIH2 gene using whole exome sequencing (WES). We hypothesize that this mutation, found in an ASD/ID patient, disrupts the protein Ariadne domain which is involved in the autoinhibition of ARIH2 enzyme. Predictive analyses elucidated the implications of the novel mutation in the splicing process and confirmed its autosomal dominant inheritance model. Nevertheless, we cannot exclude the possibility that other genetic factors, undetectable by WES, such as mutations in non-coding regions and polygenic risk in inter-allelic complementation, may contribute to the patient's phenotype. This work aims to suggest potential relationship between the detected mutation in ARIH2 gene and both ASD and ID, even though functional studies combined with new sequencing approaches will be necessary to validate this hypothesis.
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Affiliation(s)
| | | | | | | | - Valeria Todaro
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", University of Catania, Catania, Italy
| | - Concetta Federico
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124, Catania, Italy
| | - Salvatore Saccone
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124, Catania, Italy.
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44
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Taylor J, Ayres-Galhardo PH, Brown BL. Elucidating the Role of Human ALAS2 C-terminal Mutations Resulting in Loss of Function and Disease. Biochemistry 2024; 63:1636-1646. [PMID: 38888931 PMCID: PMC11223264 DOI: 10.1021/acs.biochem.4c00066] [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: 02/03/2024] [Revised: 06/07/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024]
Abstract
The conserved enzyme aminolevulinic acid synthase (ALAS) initiates heme biosynthesis in certain bacteria and eukaryotes by catalyzing the condensation of glycine and succinyl-CoA to yield aminolevulinic acid. In humans, the ALAS isoform responsible for heme production during red blood cell development is the erythroid-specific ALAS2 isoform. Owing to its essential role in erythropoiesis, changes in human ALAS2 (hALAS2) function can lead to two different blood disorders. X-linked sideroblastic anemia results from loss of ALAS2 function, while X-linked protoporphyria results from gain of ALAS2 function. Interestingly, mutations in the ALAS2 C-terminal extension can be implicated in both diseases. Here, we investigate the molecular basis for enzyme dysfunction mediated by two previously reported C-terminal loss-of-function variants, hALAS2 V562A and M567I. We show that the mutations do not result in gross structural perturbations, but the enzyme stability for V562A is decreased. Additionally, we show that enzyme stability moderately increases with the addition of the pyridoxal 5'-phosphate (PLP) cofactor for both variants. The variants display differential binding to PLP and the individual substrates compared to wild-type hALAS2. Although hALAS2 V562A is a more active enzyme in vitro, it is less efficient concerning succinyl-CoA binding. In contrast, the M567I mutation significantly alters the cooperativity of substrate binding. In combination with previously reported cell-based studies, our work reveals the molecular basis by which hALAS2 C-terminal mutations negatively affect ALA production necessary for proper heme biosynthesis.
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Affiliation(s)
- Jessica
L. Taylor
- Department
of Biochemistry, Center for Structural Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Pedro H. Ayres-Galhardo
- Department
of Biochemistry, Center for Structural Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Breann L. Brown
- Department
of Biochemistry, Center for Structural Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
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45
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Chen Y, Lee K, Woo J, Kim DW, Keum C, Babbi G, Casadio R, Martelli PL, Savojardo C, Manfredi M, Shen Y, Sun Y, Katsonis P, Lichtarge O, Pejaver V, Seward DJ, Kamandula A, Bakolitsa C, Brenner SE, Radivojac P, O’Donnell-Luria A, Mooney SD, Jain S. Evaluating predictors of kinase activity of STK11 variants identified in primary human non-small cell lung cancers. RESEARCH SQUARE 2024:rs.3.rs-4587317. [PMID: 39011112 PMCID: PMC11247923 DOI: 10.21203/rs.3.rs-4587317/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Critical evaluation of computational tools for predicting variant effects is important considering their increased use in disease diagnosis and driving molecular discoveries. In the sixth edition of the Critical Assessment of Genome Interpretation (CAGI) challenge, a dataset of 28 STK11 rare variants (27 missense, 1 single amino acid deletion), identified in primary non-small cell lung cancer biopsies, was experimentally assayed to characterize computational methods from four participating teams and five publicly available tools. Predictors demonstrated a high level of performance on key evaluation metrics, measuring correlation with the assay outputs and separating loss-of-function (LoF) variants from wildtype-like (WT-like) variants. The best participant model, 3Cnet, performed competitively with well-known tools. Unique to this challenge was that the functional data was generated with both biological and technical replicates, thus allowing the assessors to realistically establish maximum predictive performance based on experimental variability. Three out of the five publicly available tools and 3Cnet approached the performance of the assay replicates in separating LoF variants from WT-like variants. Surprisingly, REVEL, an often-used model, achieved a comparable correlation with the real-valued assay output as that seen for the experimental replicates. Performing variant interpretation by combining the new functional evidence with computational and population data evidence led to 16 new variants receiving a clinically actionable classification of likely pathogenic (LP) or likely benign (LB). Overall, the STK11 challenge highlights the utility of variant effect predictors in biomedical sciences and provides encouraging results for driving research in the field of computational genome interpretation.
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Affiliation(s)
- Yile Chen
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, 98105, WA, USA
| | - Kyoungyeul Lee
- 3billion, 3billion Biotechnology company, Seoul, South Korea
| | - Junwoo Woo
- 3billion, 3billion Biotechnology company, Seoul, South Korea
| | - Dong-wook Kim
- 3billion, 3billion Biotechnology company, Seoul, South Korea
| | - Changwon Keum
- 3billion, 3billion Biotechnology company, Seoul, South Korea
| | - Giulia Babbi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Rita Casadio
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Pier Luigi Martelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Castrense Savojardo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Matteo Manfredi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, 77843, TX, USA
| | - Yuanfei Sun
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, 77843, TX, USA
| | - Panagiotis Katsonis
- Molecular and Human Genetics, Baylor College of Medicine, Houston, 77030, TX, USA
| | - Olivier Lichtarge
- Molecular and Human Genetics, Baylor College of Medicine, Houston, 77030, TX, USA
| | - Vikas Pejaver
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
| | - David J. Seward
- Department of Pathology, University of Vermont, Burlington, 5445, VT, USA
| | - Akash Kamandula
- Khoury College of Computer Sciences, Northeastern University, Boston, 02115, MA, USA
| | | | | | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, 02115, MA, USA
| | - Anne O’Donnell-Luria
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, 02115, MA, USA
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA
| | - Sean D. Mooney
- Center for Information Technology, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Shantanu Jain
- Khoury College of Computer Sciences, Northeastern University, Boston, 02115, MA, USA
- The Institute for Experiential AI, Northeastern University, Boston, 02115, MA, USA
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46
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Arunachalam AK, Aboobacker FN, Sampath E, Devasia AJ, Korula A, George B, Edison ES. Molecular Heterogeneity of Osteopetrosis in India: Report of 17 Novel Variants. Indian J Hematol Blood Transfus 2024; 40:494-503. [PMID: 39011244 PMCID: PMC11246401 DOI: 10.1007/s12288-023-01732-4] [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: 03/07/2023] [Accepted: 12/26/2023] [Indexed: 07/17/2024] Open
Abstract
Osteopetrosis is a clinically and genetically heterogeneous group of inherited bone disorders that is caused by defects in osteoclast formation or function. Treatment options vary with the disease severity and an accurate molecular diagnosis helps in prognostication and treatment decisions. We investigated the genetic causes of osteopetrosis in 31 unrelated patients of Indian origin. Screening for the genetic variants was done by Sanger sequencing or next generation sequencing in 48 samples that included 31 samples from index patients, 16 from parents' and 1 chorionic villus sample. A total of 30 variants, including 29 unique variants, were identified in 26 of the 31 patients in the study. TCIRG1 was the most involved gene (n = 14) followed by TNFRSF11A (n = 4) and CLCN7 (n = 3). A total of 17 novel variants were identified. Prenatal diagnosis was done in one family and the foetus showed homozygous c.807 + 2T > G variant in TCIRG1. Molecular diagnosis of osteopetrosis aids in therapeutic decisions including the need for a stem cell transplantation and gives a possible option of performing prenatal diagnosis in affected families. Further studies would help in understanding the genetic etiology in patients where no variants were identified. Supplementary Information The online version contains supplementary material available at 10.1007/s12288-023-01732-4.
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Affiliation(s)
| | - Fouzia N. Aboobacker
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu 632517 India
| | - Eswari Sampath
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu 632517 India
| | - Anup J. Devasia
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu 632517 India
| | - Anu Korula
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu 632517 India
| | - Biju George
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu 632517 India
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Tsuchiya KD, Funke B, Hegde M, Santani A, Souers RJ, Szelinger S, Halley J, Zhao Q, Mot N, Roy A, Smith VL, Zhang BM, Voelkerding K, Moyer AM. Implementation, Evolution, and Laboratory Performance of Methods-Based Proficiency Testing for Next-Generation Sequencing Detection of Germline Sequence Variants. Arch Pathol Lab Med 2024; 148:775-783. [PMID: 37852169 DOI: 10.5858/arpa.2023-0090-cp] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2023] [Indexed: 10/20/2023]
Abstract
CONTEXT.— Next-generation sequencing (NGS)-based assays are used for diagnosis of diverse inherited disorders. Limited data are available pertaining to interlaboratory analytical performance of these assays. OBJECTIVE.— To report on the College of American Pathologists (CAP) NGS Germline Program, which is methods based, and explore the evolution in laboratory testing practices. DESIGN.— Results from the NGS Germline Program from 2016-2020 were analyzed for interlaboratory analytical performance. Self-reported laboratory testing practices were also evaluated. RESULTS.— From 2016-2020, a total of 297 laboratories participated in at least 1 program mailing. Of the 289 laboratories that provided information on tests offered, 138 (47.8%) offered only panel testing throughout their enrollment, while 35 (12.1%) offered panels and exome testing, 30 (10.4%) offered only exomes, 9 (3.1%) offered only genomes, and 15 (5.2%) offered panels, exomes, and genomes. The remainder (62 laboratories, 21.4%) changed their test offerings during the 2016-2020 timeframe. Considering each genomic position/interval, the median detection percentage at variant positions across the 2016-2020 mailings ranged from 94.3% to 100%, while at reference positions (no variant detected), the median correct response percentage was 100% across all mailings. When considering performance of individual laboratories, 89.5% (136 of 152) to 98.0% (149 of 152) of laboratories successfully met the detection threshold (≥90% of the variants present), while 94.6% (87 of 92) to 100% (163 of 163) of laboratories met the 95% specificity threshold across mailings. CONCLUSIONS.— Since the inception of this program, laboratories have consistently performed well. The median sensitivity and specificity of detection of sequence variants included in this program (eg, single nucleotide variants, insertions, and deletions) were 100.0%.
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Affiliation(s)
- Karen D Tsuchiya
- From the Department of Laboratory Medicine and Pathology, University of Washington, Seattle (Tsuchiya)
| | - Birgit Funke
- Sema4, Stamford, Connecticut, Children's Hospital of Philadelphia, Pennsylvania(Funke)
| | - Madhuri Hegde
- Revvity Omics, Pittsburgh, Pennsylvania, Children's Hospital of Philadelphia, Pennsylvania(Hegde)
| | - Avni Santani
- Center for Applied Genomics, Children's Hospital of Philadelphia, Pennsylvania (Santani)
- LetsGetChecked, Monrovia, California (Santani)
| | - Rhona J Souers
- Biostatistics Department, College of American Pathologists, Northfield, Illinois(Souers)
| | - Szabolcs Szelinger
- Proficiency Testing, College of American Pathologists, Northfield, Illinois(Szelinger, Halley, Zhao, Mot)
| | - Jaimie Halley
- Proficiency Testing, College of American Pathologists, Northfield, Illinois(Szelinger, Halley, Zhao, Mot)
| | - Qin Zhao
- Proficiency Testing, College of American Pathologists, Northfield, Illinois(Szelinger, Halley, Zhao, Mot)
| | - Nicole Mot
- Proficiency Testing, College of American Pathologists, Northfield, Illinois(Szelinger, Halley, Zhao, Mot)
| | - Angshumoy Roy
- the Departments of Pathology & Immunology and Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston (Roy)
| | - Vanessa L Smith
- the Department of Pathology, Duke University School of Medicine, Durham, North Carolina (Smith)
| | - Bing M Zhang
- the Department of Pathology, Stanford University School of Medicine, Stanford, California (Zhang)
| | | | - Ann M Moyer
- the Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota (Moyer)
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48
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Karchin R, Radivojac P, O'Donnell-Luria A, Greenblatt MS, Tolstorukov MY, Sonkin D. Improving transparency of computational tools for variant effect prediction. Nat Genet 2024; 56:1324-1326. [PMID: 38956207 PMCID: PMC11330584 DOI: 10.1038/s41588-024-01821-8] [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] [Indexed: 07/04/2024]
Abstract
Efforts to integrate computational tools for variant effect prediction into the process of clinical decision-making are in progress. However, for such efforts to succeed and help to provide more informed clinical decisions, it is necessary to enhance transparency and address the current limitations of computational predictors.
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Affiliation(s)
- Rachel Karchin
- The Institute for Computational Medicine, The Johns Hopkins University, Baltimore, MD, USA.
- Departments of Biomedical Engineering, Oncology, and Computer Science, The Johns Hopkins University, Baltimore, MD, USA.
| | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Marc S Greenblatt
- Department of Medicine and University of Vermont Cancer Center, University of Vermont, Larner College of Medicine, Burlington, VT, USA
| | - Michael Y Tolstorukov
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dmitriy Sonkin
- National Cancer Institute, Division of Cancer Treatment and Diagnosis, Rockville, MD, USA.
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49
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Mandler JM, Härtl J, Cordts I, Sturm M, Hedderich DM, Bafligil C, Baki E, Becker B, Machetanz G, Haack TB, Berthele A, Hemmer B, Deschauer M. Uncovering genetic mimics in multiple sclerosis: A single-center clinical exome sequencing study. Mult Scler J Exp Transl Clin 2024; 10:20552173241263491. [PMID: 39072298 PMCID: PMC11273569 DOI: 10.1177/20552173241263491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/05/2024] [Indexed: 07/30/2024] Open
Abstract
Background Multiple sclerosis (MS) shares clinical/radiological features with several monogenic diseases that can mimic MS. Objective We aimed to determine if exome sequencing can identify monogenic diseases in patients diagnosed with MS according to the McDonald criteria thus uncovering them as being misdiagnosed. Methods We performed whole exome sequencing in a cohort of 278 patients with MS, clinically or radiologically isolated syndrome without cerebrospinal fluid-specific oligoclonal bands (CSF-OCBs) (n = 228), a positive family history of MS (n = 44), or both (n = 6), thereby focusing on individuals potentially more likely to have underlying monogenic conditions mimicking MS. We prioritized 495 genes associated with monogenic diseases sharing features with MS. Results A disease-causing variant in NOTCH3 was identified in one patient without CSF-OCBs, no spinal lesions, with non-response to immunotherapy, and a family history of dementia, thereby converting the diagnosis to cerebral autosomal-dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL). Moreover, 18 patients (6.5% of total) carried variants of unclear significance. Conclusion Monogenic diseases being misdiagnosed as MS seem rare in patients diagnosed with MS according to the McDonald criteria, even in CSF-OCB negative cases. The detected pathogenic NOTCH3 variant emphasizes CADASIL as a rare differential diagnosis and highlights the relevance of genetic testing in selected MS cases with atypical presentations.
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Affiliation(s)
- Julia M Mandler
- Department of Neurology, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, München, Germany
| | - Johanna Härtl
- Department of Neurology, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, München, Germany
| | - Isabell Cordts
- Department of Neurology, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, München, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Dennis M Hedderich
- Department of Neuroradiology, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, München, Germany
| | - Cemsel Bafligil
- Department of Neurology, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, München, Germany
| | - Enayatullah Baki
- Department of Neurology, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, München, Germany
| | - Benedikt Becker
- Department of Neurology, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, München, Germany
| | - Gerrit Machetanz
- Department of Neurology, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, München, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Achim Berthele
- Department of Neurology, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, München, Germany
| | - Bernhard Hemmer
- Department of Neurology, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, München, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Marcus Deschauer
- Department of Neurology, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, München, Germany
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50
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Bromberg Y, Prabakaran R, Kabir A, Shehu A. Variant Effect Prediction in the Age of Machine Learning. Cold Spring Harb Perspect Biol 2024; 16:a041467. [PMID: 38621825 PMCID: PMC11216171 DOI: 10.1101/cshperspect.a041467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Over the years, many computational methods have been created for the analysis of the impact of single amino acid substitutions resulting from single-nucleotide variants in genome coding regions. Historically, all methods have been supervised and thus limited by the inadequate sizes of experimentally curated data sets and by the lack of a standardized definition of variant effect. The emergence of unsupervised, deep learning (DL)-based methods raised an important question: Can machines learn the language of life from the unannotated protein sequence data well enough to identify significant errors in the protein "sentences"? Our analysis suggests that some unsupervised methods perform as well or better than existing supervised methods. Unsupervised methods are also faster and can, thus, be useful in large-scale variant evaluations. For all other methods, however, their performance varies by both evaluation metrics and by the type of variant effect being predicted. We also note that the evaluation of method performance is still lacking on less-studied, nonhuman proteins where unsupervised methods hold the most promise.
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Affiliation(s)
- Yana Bromberg
- Department of Biology, Emory University, Atlanta 30322, Georgia, USA
- Department of Computer Science, Emory University, Atlanta 30322, Georgia, USA
| | - R Prabakaran
- Department of Biology, Emory University, Atlanta 30322, Georgia, USA
| | - Anowarul Kabir
- Department of Computer Science, George Mason University, Fairfax 22030, Virginia, USA
| | - Amarda Shehu
- Department of Computer Science, George Mason University, Fairfax 22030, Virginia, USA
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