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Silva S, Rosas M, Guerra B, Muñoz M, Fujita A, Sakamoto M, Matsumoto N. Adolescent-onset epilepsy and deterioration associated with CAD deficiency: A case report. Brain Dev 2024; 46:250-253. [PMID: 38641466 DOI: 10.1016/j.braindev.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 04/21/2024]
Abstract
INTRODUCTION CAD (MIM*114010) encodes a large multifunctional protein with the enzymatic activity of the first three enzymes initiating and controlling the de novo pyrimidine biosynthesis pathway. Biallelic pathogenic variants in CAD cause the autosomal recessive developmental and epileptic encephalopathy 50 (MIM #616457) or CAD deficiency presenting with epilepsy, status epilepticus (SE), neurological deterioration and anemia with anisopoikilocytosis. Mortality is around 9% of patients, mainly related to the no use of its specific treatment with uridine. Majority of reported cases have an early onset during infancy, with some few starting later in childhood. CASE REPORT Here we report a deceased female patient with CAD deficiency whose epilepsy started at 14 years. She showed a rapid neurologic deterioration including cognitive decline, electroencephalographic background slowing which later evolved to a fatal refractory SE and supra and infratentorial atrophy on neuroimaging. Anemia developed after SE onset. METHODS AND RESULTS her post-mortem whole exome sequencing identified biallelic missense variants in CAD (NM_004341.5): c.[2944G > A];[5366G > A] p.[(Asp982Asn)];[(Arg1789Gln)]. Our review of twenty-eight reported cases (2015-2023) revealed an epilepsy age onset from neonatal period to 7 years and the SE prevalence of 46 %. DISCUSSION With our case, we highlight the relevance of suspecting this treatable condition in older patients and in SE with no evident etiology.
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Affiliation(s)
- Sebastián Silva
- Child Neurology Service, Hospital de Puerto Montt, Puerto Montt, Chile; Escuela de Medicina, Universidad San Sebastián, Sede Patagonia, Puerto Montt, Chile
| | - Mónica Rosas
- Adult Neurology Service, Hospital de Puerto Montt, Puerto Montt, Chile
| | - Benjamín Guerra
- Escuela de Medicina, Universidad San Sebastián, Sede Patagonia, Puerto Montt, Chile
| | - Marión Muñoz
- Child Neurology Service, Hospital de Puerto Montt, Puerto Montt, Chile
| | - Atsushi Fujita
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Masamune Sakamoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.
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Luo Y, Li J, Li X, Lin H, Mao Z, Xu Z, Li S, Nie C, Zhou XA, Liao J, Xiong Y, Xu X, Wang J. The ARK2N-CK2 complex initiates transcription-coupled repair through enhancing the interaction of CSB with lesion-stalled RNAPII. Proc Natl Acad Sci U S A 2024; 121:e2404383121. [PMID: 38843184 PMCID: PMC11181095 DOI: 10.1073/pnas.2404383121] [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: 03/04/2024] [Accepted: 05/08/2024] [Indexed: 06/19/2024] Open
Abstract
Transcription is extremely important for cellular processes but can be hindered by RNA polymerase II (RNAPII) pausing and stalling. Cockayne syndrome protein B (CSB) promotes the progression of paused RNAPII or initiates transcription-coupled nucleotide excision repair (TC-NER) to remove stalled RNAPII. However, the specific mechanism by which CSB initiates TC-NER upon damage remains unclear. In this study, we identified the indispensable role of the ARK2N-CK2 complex in the CSB-mediated initiation of TC-NER. The ARK2N-CK2 complex is recruited to damage sites through CSB and then phosphorylates CSB. Phosphorylation of CSB enhances its binding to stalled RNAPII, prolonging the association of CSB with chromatin and promoting CSA-mediated ubiquitination of stalled RNAPII. Consistent with this finding, Ark2n-/- mice exhibit a phenotype resembling Cockayne syndrome. These findings shed light on the pivotal role of the ARK2N-CK2 complex in governing the fate of RNAPII through CSB, bridging a critical gap necessary for initiating TC-NER.
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Affiliation(s)
- Yefei Luo
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Jia Li
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Xiaoman Li
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Haodong Lin
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Zuchao Mao
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Zhanzhan Xu
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Shiwei Li
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Chen Nie
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Xiao Albert Zhou
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Junwei Liao
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Yundong Xiong
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen518055, China
| | - Jiadong Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
- Department of Gastrointestinal Translational Research, Peking University Cancer Hospital, Beijing100142, China
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Harrington CN, Morales A, Bernstein JA, Calderwood L. Implications of Provider Specialty, Test Type, and Demographic Factors on Genetic Testing Outcomes for Patients with Autism Spectrum Disorder. J Autism Dev Disord 2024:10.1007/s10803-024-06423-1. [PMID: 38858309 DOI: 10.1007/s10803-024-06423-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2024] [Indexed: 06/12/2024]
Abstract
A minority of patients with autism spectrum disorder (ASD) are offered genetic testing by their providers or referred for genetics evaluation despite published guidelines and consensus statements supporting genetics-informed care for this population. This study aimed to investigate the ordering habits of providers of different specialties and to additionally assess the diagnostic utility of genetic testing by test type, patient sex, and race and ethnicity. We retrospectively analyzed data associated with orders for the indication of ASD from a large clinical laboratory over 6 years (2017-2022). Geneticists and neurologists were more likely than other specialists to order exome sequencing and neurodevelopmental (NDD) panel testing while other providers were more likely to order chromosomal microarray (CMA) and Fragile X testing. Exome had the highest diagnostic yield (24.5%), followed by NDD panel (6.4%), CMA (6.2%), and Fragile X testing (0.4%). Females were 1.4x (95% CI: 1.2-1.7) more likely than males to receive a genetic diagnosis. However, for Fragile X, males had a higher diagnostic yield than females (0.4% vs 0.2%). Our findings highlight the need to enable non-genetics providers to order comprehensive genetic testing or promote referral to genetics following negative CMA and/or Fragile X testing. Our data supports that ASD testing should include exome, CMA, and other clinically indicated tests, as first-tier tests, with the consideration of panel testing, in cases where exome sequencing is not an option. Lastly, our study helps to inform expectations for genetic testing yield by test type and patient presentation.
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Affiliation(s)
- Caitlin N Harrington
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Medicine Children's Health, Stanford, CA, USA.
| | - Ana Morales
- Translational Health Sciences Program, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Medicine Children's Health, Stanford, CA, USA
| | - Laurel Calderwood
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Medicine Children's Health, Stanford, CA, USA
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Bao YK, Situ BA, Runner M, Moshfeghi A, Ameri H. Comparison of The Results of Sponsored Genetic Testing Panels for Inherited Retinal Diseases. J Clin Med 2024; 13:3118. [PMID: 38892829 PMCID: PMC11172676 DOI: 10.3390/jcm13113118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Background/Objectives: Gene therapy's emergence has made molecular diagnosis for inherited retinal diseases clinically significant. Free genetic testing panels have improved testing access in clinical practice, yet the interpretation of results, especially variants of unknown significance (VUS), remains challenging and requires expertise. This study shares our experience in utilizing sponsored IRD panel tests by Invitae and Blueprint Genetics (BG), reporting their positivity rates, and comparing their reclassification of variants through amendments. Methods: This retrospective study analyzed genetic test reports from patients who underwent testing via Invitae or BG panels. A positive test was determined if there was a pathogenic mutation in an autosomal dominant gene, two pathogenic mutations in an autosomal recessive gene, or a pathogenic mutation in an X-linked gene in a male patient. Results: The testing positivity rates were 34.9% for Invitae (n = 109) and 42.1% for BG (n = 107). Invitae had more pathogenic variants per report (0.87 vs. 0.58 variants, p = 0.0038) and issued more amendments than BG (0.54 vs. 0.03 amendments; p < 0.01). Of the Invitae variant classification changes, 66.2% switched a VUS to benign. In the BG group, 75% of variant reclassifications changed a VUS to pathogenic. As a result of the Invitae amendments, 88% did not change the overall report result. Conclusions: While free-of-charge genetic testing panels offer valuable insights for diagnosing IRD, limitations such as low diagnostic yield and variant classification discrepancies persist between Invitae and BG. VUS should not be considered pathogenic in the clinical decision-making process. Careful interpretation of genetic testing is required.
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Affiliation(s)
- Yicheng K. Bao
- Department of Ophthalmology, USC Roski Eye Institute, Keck School of Medicine, University of Southern California, 1450 San Pablo Street, Los Angeles, CA 90033, USA; (Y.K.B.); (B.A.S.); (A.M.)
| | - Betty A. Situ
- Department of Ophthalmology, USC Roski Eye Institute, Keck School of Medicine, University of Southern California, 1450 San Pablo Street, Los Angeles, CA 90033, USA; (Y.K.B.); (B.A.S.); (A.M.)
| | | | - Andrew Moshfeghi
- Department of Ophthalmology, USC Roski Eye Institute, Keck School of Medicine, University of Southern California, 1450 San Pablo Street, Los Angeles, CA 90033, USA; (Y.K.B.); (B.A.S.); (A.M.)
| | - Hossein Ameri
- Department of Ophthalmology, USC Roski Eye Institute, Keck School of Medicine, University of Southern California, 1450 San Pablo Street, Los Angeles, CA 90033, USA; (Y.K.B.); (B.A.S.); (A.M.)
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Xu Z, Sadleir L, Goel H, Jiao X, Niu Y, Zhou Z, de Valles-Ibáñez G, Poke G, Hildebrand M, Lieffering N, Qin J, Yang Z. Genotype and phenotype correlation of PHACTR1-related neurological disorders. J Med Genet 2024; 61:536-542. [PMID: 38272663 DOI: 10.1136/jmg-2023-109638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024]
Abstract
BACKGROUND PHACTR1 (phosphatase and actin regulators) plays a key role in cortical migration and synaptic activity by binding and regulating G-actin and PPP1CA. This study aimed to expand the genotype and phenotype of patients with de novo variants in PHACTR1 and analyse the impact of variants on protein-protein interaction. METHODS We identified seven patients with PHACTR1 variants by trio-based whole-exome sequencing. Additional two subjects were ascertained from two centres through GeneMatcher. The genotype-phenotype correlation was determined, and AlphaFold-Multimer was used to predict protein-protein interactions and interfaces. RESULTS Eight individuals carried missense variants and one had CNV in the PHACTR1. Infantile epileptic spasms syndrome (IESS) was the unifying phenotype in eight patients with missense variants of PHACTR1. They could present with other types of seizures and often exhibit drug-resistant epilepsy with a poor prognosis. One patient with CNV displayed a developmental encephalopathy phenotype. Using AlphaFold-Multimer, our findings indicate that PHACTR1 and G-actin-binding sequences overlap with PPP1CA at the RPEL3 domain, which suggests possible competition between PPP1CA and G-actin for binding to PHACTR1 through a similar polymerisation interface. In addition, patients carrying missense variants located at the PHACTR1-PPP1CA or PHACTR1-G-actin interfaces consistently exhibit the IESS phenotype. These missense variants are mostly concentrated in the overlapping sequence (RPEL3 domain). CONCLUSIONS Patients with variants in PHACTR1 can have a phenotype of developmental encephalopathy in addition to IESS. Moreover, our study confirmed that the variants affect the binding of PHACTR1 to G-actin or PPP1CA, resulting in neurological disorders in patients.
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Affiliation(s)
- Zhao Xu
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Lynette Sadleir
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington, New Zealand
| | - Himanshu Goel
- Hunter Genetics, Waratah, New South Wales, Australia
| | - Xianru Jiao
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Yue Niu
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Zongpu Zhou
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Guillem de Valles-Ibáñez
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington, New Zealand
| | - Gemma Poke
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington, New Zealand
| | - Michael Hildebrand
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Heidelberg, Victoria, Australia
- Neuroscience Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, South Brisbane, Queensland, Australia
| | - Nico Lieffering
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington, New Zealand
| | - Jiong Qin
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Zhixian Yang
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
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Grigore LG, Radoi VE, Serban A, Mihai AD, Stoica I. The Molecular Detection of Germline Mutations in the BRCA1 and BRCA2 Genes Associated with Breast and Ovarian Cancer in a Romanian Cohort of 616 Patients. Curr Issues Mol Biol 2024; 46:4630-4645. [PMID: 38785549 PMCID: PMC11119367 DOI: 10.3390/cimb46050281] [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: 04/15/2024] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
The objective of this study was to identify and classify the spectrum of mutations found in the BRCA1 and BRCA2 genes associated with breast and ovarian cancer in female patients in Romania. Germline BRCA1 and BRCA2 mutations were investigated in a cohort of 616 female patients using NGS and/or MLPA methods followed by software-based data analysis and classification according to international guidelines. Out of the 616 female patients included in this study, we found that 482 patients (78.2%) did not have any mutation present in the two genes investigated; 69 patients (11.2%) had a BRCA1 mutation, 34 (5.5%) had a BRCA2 mutation, and 31 (5%) presented different type of mutations with uncertain clinical significance, moderate risk or a large mutation in the BRCA1 gene. Our investigation indicates the most common mutations in the BRCA1 and BRCA2 genes, associated with breast and ovarian cancer in the Romanian population. Our results also bring more data in support of the frequency of the c.5266 mutation in the BRCA1 gene, acknowledged in the literature as a founder mutation in Eastern Europe. We consider that the results of our study will provide necessary data regarding BRCA1 and BRCA2 mutations that would help to create a genetic database for the Romanian population.
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Affiliation(s)
- Liliana-Georgiana Grigore
- Doctoral School of Biology, Faculty of Biology, University of Bucharest, 030018 Bucharest, Romania
- Personal Genetics, 010987 Bucharest, Romania
| | - Viorica-Elena Radoi
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
- “Alessandrescu-Rusescu” National Institute for Maternal and Child Health, 20382 Bucharest, Romania
| | | | | | - Ileana Stoica
- Department of Genetics, Faculty of Biology, University of Bucharest, 030018 Bucharest, Romania
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Elgaali E, Mezzavilla M, Ahmed I, Elanbari M, Ali A, Abdelaziz G, Fakhro KA, Saleh A, Ben-Omran T, Almulla N, Cugno C. Genetic background of primary and familial HLH in Qatar: registry data and population study. Front Pediatr 2024; 12:1326489. [PMID: 38808104 PMCID: PMC11130942 DOI: 10.3389/fped.2024.1326489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 04/08/2024] [Indexed: 05/30/2024] Open
Abstract
Background Familial hemophagocytic lymphohistiocytosis (FHLH) is an inherited life-threatening disease. Five types are identified, with the addition of congenital immunodeficiency syndromes in which HLH is a typical manifestation. The literature on this disease is very scarce in the Middle East, with only a few scattered reports. Methods We report detailed demographic, clinical, and genomic data from 28 patients diagnosed with primary and familial HLH over the last decade in Qatar. An evaluation was performed of allele frequencies of deleterious variants from 12 primary and familial HLH causative genes on the Qatar Genome Programme (QGP) cohort of 14,669 Qatari individuals. Results The genetic diagnosis was obtained in 15 patients, and four novel mutations in Perforin 1 (PRF1), UNC13D, LYST, and RAB27A genes were found. We identified 22,945 low/high/moderate/modifier impact variants significantly enriched in the QGP in those 12 genes. The variants rs1271079313 in PRF1 and rs753966933 in RAB27A found in our patient cohort were significantly more prevalent in the QGP compared to the Genome Aggregation Database (gnomAD) database, with a high carrier frequency in the Qatari population. Conclusions We established the first primary and familial HLH Registry in the Gulf Region and identified novel possibly pathogenic variants present at higher frequency in the Qatari population, which could be used for screening purposes. Raising awareness about primary and familial HLH and implementing screening activities in the Qatari highly inbred population could stem into more comprehensive premarital and prenatal evaluations and faster diagnosis.
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Affiliation(s)
- Elkhansa Elgaali
- Pediatric Hematology and Oncology Department, Sidra Medicine, Doha, Qatar
| | | | - Ikhlak Ahmed
- Research Department, Sidra Medicine, Doha, Qatar
| | | | - Aesha Ali
- Research Department, Sidra Medicine, Doha, Qatar
| | | | | | - Ayman Saleh
- Pediatric Hematology and Oncology Department, Sidra Medicine, Doha, Qatar
| | - Tawfeg Ben-Omran
- Division of Genetic and Genomic Medicine, Sidra Medicine, Doha, Qatar
- Department of Medical Genetics, Hamad Medical Corporation, Doha, Qatar
| | - Naima Almulla
- Pediatric Hematology and Oncology Department, Sidra Medicine, Doha, Qatar
| | - Chiara Cugno
- Pediatric Hematology and Oncology Department, Sidra Medicine, Doha, Qatar
- Research Department, Sidra Medicine, Doha, Qatar
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Kiel MJ, Kozaric A. Correspondence on "Comparison of literature mining tools for variant classification: Through the lens of 50 RYR1 variants" by Wermers et al. Genet Med 2024:101161. [PMID: 38726794 DOI: 10.1016/j.gim.2024.101161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 04/23/2024] [Indexed: 06/06/2024] Open
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MacCarrick G, Aradhya S, Bailey M, Chu D, Hunt A, Izzo E, Krakow D, Mackenzie W, Poll S, Raggio C, Shediac R, White KK, McLaughlin HM, Seratti G. Clinical utility of comprehensive gene panel testing for common and rare causes of skeletal dysplasia and other skeletal disorders: Results from the largest cohort to date. Am J Med Genet A 2024:e63646. [PMID: 38702915 DOI: 10.1002/ajmg.a.63646] [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: 08/16/2023] [Revised: 04/03/2024] [Accepted: 04/18/2024] [Indexed: 05/06/2024]
Abstract
Molecular genetics enables more precise diagnoses of skeletal dysplasia and other skeletal disorders (SDs). We investigated the clinical utility of multigene panel testing for 5011 unrelated individuals with SD in the United States (December 2019-April 2022). Median (range) age was 8 (0-90) years, 70.5% had short stature and/or disproportionate growth, 27.4% had a positive molecular diagnosis (MDx), and 30 individuals received two MDx. Genes most commonly contributing to MDx were FGFR3 (16.9%), ALPL (13.0%), and COL1A1 (10.3%). Most of the 112 genes associated with ≥1 MDx were primarily involved in signal transduction (n = 35), metabolism (n = 23), or extracellular matrix organization (n = 17). There were implications associated with specific care/treatment options for 84.4% (1158/1372) of MDx-positive individuals; >50% were linked to conditions with targeted therapy approved or in clinical development, including osteogenesis imperfecta, achondroplasia, hypophosphatasia, and mucopolysaccharidosis. Forty individuals with initially inconclusive results became MDx-positive following family testing. Follow-up mucopolysaccharidosis enzyme activity testing was positive in 14 individuals (10 of these were not MDx-positive). Our findings showed that inclusion of metabolic genes associated with SD increased the clinical utility of a gene panel and confirmed that integrated use of comprehensive gene panel testing with orthogonal testing reduced the burden of inconclusive results.
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Affiliation(s)
- Gretchen MacCarrick
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Mitch Bailey
- BioMarin Pharmaceutical Inc, Novato, California, USA
| | - Dorna Chu
- BioMarin Pharmaceutical Inc, Novato, California, USA
| | - Abigail Hunt
- BioMarin Pharmaceutical Inc, Novato, California, USA
| | - Emanuela Izzo
- BioMarin Pharmaceutical Inc, Novato, California, USA
| | - Deborah Krakow
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - William Mackenzie
- Department of Orthopaedic Surgery, Nemours Children's Hospital, Wilmington, Delaware, USA
| | - Sarah Poll
- Invitae Corporation, San Francisco, California, USA
| | - Cathleen Raggio
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, New York, USA
| | - Renée Shediac
- BioMarin Pharmaceutical Inc, Novato, California, USA
| | - Klane K White
- Department of Pediatric Orthopedic Surgery, Children's Hospital Colorado, Aurora, Colorado, USA
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Miyanohara I, Ohori J, Tabuchi M, Nishio SY, Yamashita M, Usami SI. Comprehensive Genetic Evaluation in Patients with Special Reference to Late-Onset Sensorineural Hearing Loss. Genes (Basel) 2024; 15:571. [PMID: 38790200 PMCID: PMC11120787 DOI: 10.3390/genes15050571] [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: 03/30/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 05/26/2024] Open
Abstract
Hearing loss (HL) is a common and multi-complex etiological deficit that can occur at any age and can be caused by genetic variants, aging, toxic drugs, noise, injury, viral infection, and other factors. Recently, a high incidence of genetic etiologies in congenital HL has been reported, and the usefulness of genetic testing has been widely accepted in congenital-onset or early-onset HL. In contrast, there have been few comprehensive reports on the relationship between late-onset HL and genetic causes. In this study, we performed next-generation sequencing analysis for 91 HL patients mainly consisting of late-onset HL patients. As a result, we identified 23 possibly disease-causing variants from 29 probands, affording a diagnostic rate for this study of 31.9%. The highest diagnostic rate was observed in the congenital/early-onset group (42.9%), followed by the juvenile/young adult-onset group (31.7%), and the middle-aged/aged-onset group (21.4%). The diagnostic ratio decreased with age; however, genetic etiologies were involved to a considerable degree even in late-onset HL. In particular, the responsible gene variants were found in 19 (55.9%) of 34 patients with a familial history and progressive HL. Therefore, this phenotype is considered to be a good candidate for genetic evaluation based on this diagnostic panel.
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Affiliation(s)
- Ikuyo Miyanohara
- Department of Otolaryngology-Head and Neck Surgery, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1, Sakuragaoka, Kagoshima 890-8520, Japan; (J.O.); (M.T.); (M.Y.)
| | - Junichiro Ohori
- Department of Otolaryngology-Head and Neck Surgery, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1, Sakuragaoka, Kagoshima 890-8520, Japan; (J.O.); (M.T.); (M.Y.)
| | - Minako Tabuchi
- Department of Otolaryngology-Head and Neck Surgery, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1, Sakuragaoka, Kagoshima 890-8520, Japan; (J.O.); (M.T.); (M.Y.)
| | - Shin-ya Nishio
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto 390-8621, Japan;
| | - Masaru Yamashita
- Department of Otolaryngology-Head and Neck Surgery, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1, Sakuragaoka, Kagoshima 890-8520, Japan; (J.O.); (M.T.); (M.Y.)
| | - Shin-ichi Usami
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto 390-8621, Japan;
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Abu-Hijlih R, Sharaf B, Salah S, Bani Hani H, Alqaisieh M, Alzibdeh A, Ababneh L, Mahafdah S, Abdel-Razeq H. Germline Genetic Mutations in Adult Patients with Sarcoma: Insight into the Middle East Genetic Landscape. Cancers (Basel) 2024; 16:1668. [PMID: 38730621 PMCID: PMC11083501 DOI: 10.3390/cancers16091668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Data on germline mutations in soft tissue and bone sarcomas are scarce. We sought to identify the prevalence of germline mutations in adult sarcoma patients treated at a tertiary cancer center. Newly diagnosed patients were offered germline genetic testing via an 84-gene panel. The prevalence of pathogenic germline variants (PGVs) and their association with disease-, and patient- related factors are reported. A total of 87 patients were enrolled, the median age was 48 (19-78) years, and 47 (54%) were females. Gastrointestinal stromal tumors (n = 12, 13.8%), liposarcoma (n = 10, 11.5%), and Ewing sarcoma (n = 10, 11.5%) were the main subtypes. A total of 20 PGVs were detected in 18 (20.7%) patients. Variants of uncertain significance, in the absence of PGVs, were detected in 40 (45.9%) patients. Young age (p = 0.031), presence of a second primary cancer (p = 0.019), and female gender (p = 0.042) were correlated with the presence of PGVs. All identified PGVs have potential clinical actionability and cascade testing, and eight (44.44%) suggested eligibility for a targeted therapy. Almost one in five adult patients with soft tissue and bone sarcomas harbor pathogenic or likely pathogenic variants. Many of these variants are potentially actionable, and almost all have implications on cancer screening and family counselling. In this cohort from the Middle East, younger age, presence of a second primary tumor, and female gender were significantly associated with higher PGVs rates. Larger studies able to correlate treatment outcomes with genetic variants are highly needed.
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Affiliation(s)
- Ramiz Abu-Hijlih
- Department of Radiation Oncology, King Hussein Cancer Center, Amman 11941, Jordan; (R.A.-H.); (A.A.)
| | - Baha Sharaf
- Department of Internal Medicine, King Hussein Cancer Center, Amman 11941, Jordan; (B.S.); (S.S.); (H.B.H.); (M.A.)
| | - Samer Salah
- Department of Internal Medicine, King Hussein Cancer Center, Amman 11941, Jordan; (B.S.); (S.S.); (H.B.H.); (M.A.)
| | - Hira Bani Hani
- Department of Internal Medicine, King Hussein Cancer Center, Amman 11941, Jordan; (B.S.); (S.S.); (H.B.H.); (M.A.)
| | - Mohammad Alqaisieh
- Department of Internal Medicine, King Hussein Cancer Center, Amman 11941, Jordan; (B.S.); (S.S.); (H.B.H.); (M.A.)
| | - Abdulla Alzibdeh
- Department of Radiation Oncology, King Hussein Cancer Center, Amman 11941, Jordan; (R.A.-H.); (A.A.)
| | - Layan Ababneh
- School of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Suleiman Mahafdah
- Department of Surgery, Royal Jordanian Medical Services, Amman 11855, Jordan;
| | - Hikmat Abdel-Razeq
- Department of Internal Medicine, King Hussein Cancer Center, Amman 11941, Jordan; (B.S.); (S.S.); (H.B.H.); (M.A.)
- School of Medicine, The University of Jordan, Amman 11942, Jordan
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Dias MQ, Gouveia N, Félix R, Estrela-Silva S, Cabral D, Carvalho AL, Murta J, Silva R, Marques JP. Mutational spectrum and deep phenotyping in Pseudoxanthoma Elasticum: Findings from a Portuguese cohort. Eur J Ophthalmol 2024:11206721241247676. [PMID: 38602027 DOI: 10.1177/11206721241247676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
INTRODUCTION Pseudoxanthoma Elasticum (PXE) is a rare autosomal recessive disorder originated by disease-causing variants in ABCC6 gene. The purpose of this study was to characterize the genetic landscape, phenotypic spectrum and genotype-phenotype correlations in a Portuguese cohort of PXE patients. METHODS Multicentric cross-sectional study conducted in patients with a clinical and genetic diagnosis of PXE. Patients were identified using the IRD-PT registry (www.retina.com.pt). Genotypes were classified into 3 groups: (1) two truncating variants, (2) two non-truncating variants, or (3) mixed variants. Deep phenotyping comprised a comprehensive ophthalmologic and systemic evaluation using the updated Phenodex Score (PS). RESULTS Twenty-seven patients (23 families) were included. Sixteen different ABCC6 variants were identified, 7 of which are novel. The most prevalent variant was the nonsense variant c.3421C > T p.(Arg1141*) with an allele frequency of 18.5%. All patients exhibited ocular manifestations. Cutaneous manifestations were present in most patients (88.9%, n = 24/27). A PS score > E2 was strongly associated with worse visual acuity (B = -29.02; p = 0.001). No association was found between genotypic groups and cutaneous, vascular or cardiac manifestations. CONCLUSIONS This study describes the genetic spectrum of patients with PXE for the first time in a Portuguese cohort. A total of 16 different variants in ABCC6 were found (7 of which are novel), thus highlighting the genotypic heterogeneity associated with this condition and expanding its mutational spectrum. Still, no major genotype-phenotype associations could be established.
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Affiliation(s)
- Margarida Q Dias
- Ophthalmology Unit, Centro Hospitalar e Universitário de Coimbra, (CHUC), Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
| | - Nuno Gouveia
- Ophthalmology Unit, Centro Hospitalar e Universitário de Coimbra, (CHUC), Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
| | - Raquel Félix
- Ophthalmology Unit, Centro Hospitalar e Universitário de Coimbra, (CHUC), Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
| | - Sérgio Estrela-Silva
- Ophthalmology Unit, Centro Hospitalar e Universitário de São João (CHUSJ), Porto, Portugal
- Department of Surgery and Physiology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Diogo Cabral
- Ophthalmology Unit, Hospital Garcia de Orta (HGO), Lisbon, Portugal
| | - Ana Luísa Carvalho
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
- Medical Genetics Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
- University Clinic of Medical Genetics, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
| | - Joaquim Murta
- Ophthalmology Unit, Centro Hospitalar e Universitário de Coimbra, (CHUC), Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
- University Clinic of Ophthalmology, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
| | - Rufino Silva
- Ophthalmology Unit, Centro Hospitalar e Universitário de Coimbra, (CHUC), Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
- University Clinic of Ophthalmology, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
| | - João Pedro Marques
- Ophthalmology Unit, Centro Hospitalar e Universitário de Coimbra, (CHUC), Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
- University Clinic of Ophthalmology, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
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Durward-Akhurst SA, Marlowe JL, Schaefer RJ, Springer K, Grantham B, Carey WK, Bellone RR, Mickelson JR, McCue ME. Predicted genetic burden and frequency of phenotype-associated variants in the horse. Sci Rep 2024; 14:8396. [PMID: 38600096 PMCID: PMC11006912 DOI: 10.1038/s41598-024-57872-8] [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: 12/20/2023] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Disease-causing variants have been identified for less than 20% of suspected equine genetic diseases. Whole genome sequencing (WGS) allows rapid identification of rare disease causal variants. However, interpreting the clinical variant consequence is confounded by the number of predicted deleterious variants that healthy individuals carry (predicted genetic burden). Estimation of the predicted genetic burden and baseline frequencies of known deleterious or phenotype associated variants within and across the major horse breeds have not been performed. We used WGS of 605 horses across 48 breeds to identify 32,818,945 variants, demonstrate a high predicted genetic burden (median 730 variants/horse, interquartile range: 613-829), show breed differences in predicted genetic burden across 12 target breeds, and estimate the high frequencies of some previously reported disease variants. This large-scale variant catalog for a major and highly athletic domestic animal species will enhance its ability to serve as a model for human phenotypes and improves our ability to discover the bases for important equine phenotypes.
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Affiliation(s)
- S A Durward-Akhurst
- Department of Veterinary Clinical Sciences, University of Minnesota, C339 VMC, 1353 Boyd Avenue, St. Paul, MN, 55108, USA.
| | - J L Marlowe
- Department of Veterinary Clinical Sciences, University of Minnesota, C339 VMC, 1353 Boyd Avenue, St. Paul, MN, 55108, USA
| | - R J Schaefer
- Department of Veterinary Population Medicine, University of Minnesota, 225 VMC, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
| | - K Springer
- Department of Veterinary Population Medicine, University of Minnesota, 225 VMC, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
| | - B Grantham
- Interval Bio LLC, 408 Stierline Road, Mountain View, CA, 94043, USA
| | - W K Carey
- Interval Bio LLC, 408 Stierline Road, Mountain View, CA, 94043, USA
| | - R R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
- Population Health and Reproduction and Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - J R Mickelson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 295F Animal Science Veterinary Medicine Building, 1988 Fitch Avenue, St. Paul, MN, 55108, USA
| | - M E McCue
- Department of Veterinary Population Medicine, University of Minnesota, 225 VMC, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
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Gao S, Zhang Q, Ding Y, Wang L, Li Z, Hu F, Yao RE, Yu T, Chang G, Wang X. Molecular and phenotypic characteristics of Bardet-Biedl syndrome in Chinese patients. Orphanet J Rare Dis 2024; 19:149. [PMID: 38584252 PMCID: PMC11000329 DOI: 10.1186/s13023-024-03150-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 03/27/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUND Bardet-Biedl syndrome (BBS) is a type of non-motile ciliopathy. To date, 26 genes have been reported to be associated with BBS. However, BBS is genetically heterogeneous, with significant clinical overlap with other ciliopathies, which complicates diagnosis. Disability and mortality rates are high in BBS patients; therefore, it is urgent to improve our understanding of BBS. Thus, our study aimed to describe the genotypic and phenotypic spectra of BBS in China and to elucidate genotype-phenotype correlations. METHODS Twenty Chinese patients diagnosed with BBS were enrolled in this study. We compared the phenotypes of Chinese BBS patients in this study with those from other countries to analyze the phenotypic differences across patients worldwide. In addition, genotype-phenotype correlations were described for our cohort. We also summarized all previously reported cases of BBS in Chinese patients (71 patients) and identified common and specific genetic variants in the Chinese population. RESULTS Twenty-eight variants, of which 10 are novel, in 5 different BBS-associated genes were identified in 20 Chinese BBS patients. By comparing the phenotypes of BBSome-coding genes (BBS2,7,9) with those of chaperonin-coding genes (BBS10,12), we found that patients with mutations in BBS10 and 12 had an earlier age of onset (1.10 Vs. 2.20, p < 0.01) and diagnosis (4.64 Vs. 13.17, p < 0.01), whereas patients with mutations in BBS2, 7, and 9 had a higher body mass index (28.35 Vs. 24.21, p < 0.05) and more vision problems (p < 0.05). Furthermore, in 91 Chinese BBS patients, mutations were predominant in BBS2 (28.89%) and BBS7 (15.56%), and the most frequent variants were in BBS2: c.534 + 1G > T (10/182 alleles) and BBS7: c.1002delT (7/182 alleles), marking a difference from the genotypic spectra of BBS reported abroad. CONCLUSIONS We recruited 20 Chinese patients with BBS for genetic and phenotypic analyses, and identified common clinical manifestations, pathogenic genes, and variants. We also described the phenotypic differences across patients worldwide and among different BBS-associated genes. This study involved the largest cohort of Chinese patients with BBS, and provides new insights into the distinctive clinical features of specific pathogenic variants.
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Affiliation(s)
- Shiyang Gao
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Qianwen Zhang
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yu Ding
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Libo Wang
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Zhiying Li
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Feihan Hu
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Ru-En Yao
- Department of Genetic Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Tingting Yu
- Department of Genetic Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Guoying Chang
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
| | - Xiumin Wang
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
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Lin ZJ, He JW, Zhu SY, Xue LH, Zheng JF, Zheng LQ, Huang BX, Chen GZ, Lin PX. Gene-gene interaction network analysis indicates CNTN2 is a candidate gene for idiopathic generalized epilepsy. Neurogenetics 2024; 25:131-139. [PMID: 38460076 DOI: 10.1007/s10048-024-00748-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 01/19/2024] [Indexed: 03/11/2024]
Abstract
Twin and family studies have established the genetic contribution to idiopathic generalized epilepsy (IGE). The genetic architecture of IGE is generally complex and heterogeneous, and the majority of the genetic burden in IGE remains unsolved. We hypothesize that gene-gene interactions contribute to the complex inheritance of IGE. CNTN2 (OMIM* 615,400) variants have been identified in cases with familial adult myoclonic epilepsy and other epilepsies. To explore the gene-gene interaction network in IGE, we took the CNTN2 gene as an example and investigated its co-occurrent genetic variants in IGE cases. We performed whole-exome sequencing in 114 unrelated IGE cases and 296 healthy controls. Variants were qualified with sequencing quality, minor allele frequency, in silico prediction, genetic phenotype, and recurrent case numbers. The STRING_TOP25 gene interaction network analysis was introduced with the bait gene CNTN2 (denoted as A). The gene-gene interaction pair mode was presumed to be A + c, A + d, A + e, with a leading gene A, or A + B + f, A + B + g, A + B + h, with a double-gene A + B, or other combinations. We compared the number of gene interaction pairs between the case and control groups. We identified three pairs in the case group, CNTN2 + PTPN18, CNTN2 + CNTN1 + ANK2 + ANK3 + SNTG2, and CNTN2 + PTPRZ1, while we did not discover any pairs in the control group. The number of gene interaction pairs in the case group was much more than in the control group (p = 0.021). Taking together the genetic bioinformatics, reported epilepsy cases, and statistical evidence in the study, we supposed CNTN2 as a candidate pathogenic gene for IGE. The gene interaction network analysis might help screen candidate genes for IGE or other complex genetic disorders.
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Affiliation(s)
- Zhi-Jian Lin
- Department of Neurology, School of Clinical Medicine, the Affiliated Hospital of Putian UniversityFujian Medical UniversityBrain Science Institute of Putian University, 999 Dongzhen East Road, Licheng District, Putian, 351100, China
| | - Jun-Wei He
- Department of Neurology, School of Clinical Medicine, the Affiliated Hospital of Putian UniversityFujian Medical UniversityBrain Science Institute of Putian University, 999 Dongzhen East Road, Licheng District, Putian, 351100, China
| | - Sheng-Yin Zhu
- Department of Neurology, School of Clinical Medicine, the Affiliated Hospital of Putian UniversityFujian Medical UniversityBrain Science Institute of Putian University, 999 Dongzhen East Road, Licheng District, Putian, 351100, China
| | - Li-Hong Xue
- Department of Neurology, School of Clinical Medicine, the Affiliated Hospital of Putian UniversityFujian Medical UniversityBrain Science Institute of Putian University, 999 Dongzhen East Road, Licheng District, Putian, 351100, China
| | - Jian-Feng Zheng
- Department of Neurology, School of Clinical Medicine, the Affiliated Hospital of Putian UniversityFujian Medical UniversityBrain Science Institute of Putian University, 999 Dongzhen East Road, Licheng District, Putian, 351100, China
| | - Li-Qin Zheng
- Department of Neurology, School of Clinical Medicine, the Affiliated Hospital of Putian UniversityFujian Medical UniversityBrain Science Institute of Putian University, 999 Dongzhen East Road, Licheng District, Putian, 351100, China
| | - Bi-Xia Huang
- Department of Neurology, School of Clinical Medicine, the Affiliated Hospital of Putian UniversityFujian Medical UniversityBrain Science Institute of Putian University, 999 Dongzhen East Road, Licheng District, Putian, 351100, China
| | - Guo-Zhang Chen
- Department of Neurology, School of Clinical Medicine, the Affiliated Hospital of Putian UniversityFujian Medical UniversityBrain Science Institute of Putian University, 999 Dongzhen East Road, Licheng District, Putian, 351100, China
| | - Peng-Xing Lin
- Department of Neurology, School of Clinical Medicine, the Affiliated Hospital of Putian UniversityFujian Medical UniversityBrain Science Institute of Putian University, 999 Dongzhen East Road, Licheng District, Putian, 351100, China.
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16
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Hozhabrpour A, Mojbafan M, Palizban F, Vahidnezhad F, Talebi S, Amani M, Garshasbi M, Naghavi A, Khalesi R, Mansouri P, Sotoudeh S, Mahmoudi H, Varghaei A, Daneshpazhooh M, Karimi F, Zeinali S, Kalamati E, Uitto J, Youssefian L, Vahidnezhad H. DNA repair-related heritable photosensitivity syndromes: Mutation landscape in a multiethnic cohort of 17 multigenerational families with high degree of consanguinity. DNA Repair (Amst) 2024; 136:103633. [PMID: 38422792 DOI: 10.1016/j.dnarep.2024.103633] [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: 03/27/2023] [Revised: 12/30/2023] [Accepted: 01/19/2024] [Indexed: 03/02/2024]
Abstract
Inherited photosensitivity syndromes are a heterogeneous group of genetic skin disorders with tremendous phenotypic variability, characterized by photosensitivity and defective DNA repair, especially nucleotide excision repair. A cohort of 17 Iranian families with heritable photosensitivity syndromes was evaluated to identify their genetic defect. The patients' DNA was analyzed with either whole-exome sequencing or RNA sequencing (RNA-Seq). The interpretations of the genomic results were guided by genome-wide homozygosity mapping. Haplotype analysis was performed for cases with recurrent mutations. RNA-Seq, in addition to mutation detection, was also utilized to confirm the pathogenicity. Thirteen sequence variants, including six previously unreported pathogenic variants, were disclosed in 17 Iranian families, with XPC as the most common mutated gene in 10 families (59%). In one patient, RNA-Seq, as a first-tier diagnostic approach, revealed a non-canonical homozygous germline variant: XPC:c.413-9 T > A. The Sashimi plot showed skipping of exon 4 with dramatic XPC down-expression. Haplotype analysis of XPC:c.2251-1 G>C and XPC:1243 C>T in four families showed common haplotypes of 1.7 Mb and 2.6 Mb, respectively, denoting a founder effect. Lastly, two extremely rare cases were presented in this report: a homozygous UVSSA:c .1990 C>T was disclosed, and ERCC2-related cerebro-oculo-facio-skeletal (COFS) syndrome with an early childhood death. A direct comparison of our data with the results of previously reported cohorts demonstrates the international mutation landscape of DNA repair-related photosensitivity disorders, although population-specific differences were observed.
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Affiliation(s)
- Amir Hozhabrpour
- Department of Medical Genetics, School of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Marzieh Mojbafan
- Department of Medical Genetics, School of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Fahimeh Palizban
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Saeed Talebi
- Department of Medical Genetics, School of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Maliheh Amani
- Clinical Research Development Unit of Allameh Bohlool Gonabadi Hospital, Gonabad University of Medical Sciences, Gonabad, Iran; Department of Dermatology, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Anoosh Naghavi
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Raziyeh Khalesi
- Department of Medical Genetics, DeNA Laboratory, Tehran, Iran
| | - Parvin Mansouri
- Skin and Stem Cell Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Soheila Sotoudeh
- Department of Dermatology, Children's Medical Center, Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamidreza Mahmoudi
- Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Aida Varghaei
- Department of Dermatology, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Maryam Daneshpazhooh
- Department of Dermatology, Autoimmune Bullous Diseases Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | | | - Elnaz Kalamati
- Department of Obstetrics and Gynecology, Imam Zaman Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA; Department of Dermatology and Cutaneous Biology, Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Leila Youssefian
- Department of Pathology and Laboratory Medicine, UCLA Clinical Genomics Center, University of California, Los Angeles, David Geffen School of Medicine, Los Angeles, CA, USA.
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA; Department of Dermatology and Cutaneous Biology, Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA; Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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17
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Ren B, Wu X, Zhou Y, Chen L, Jiang J. SYN1 variant causes X-linked neurodevelopmental disorders: a case report of variable clinical phenotypes in siblings. Front Neurol 2024; 15:1359287. [PMID: 38576531 PMCID: PMC10991737 DOI: 10.3389/fneur.2024.1359287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/08/2024] [Indexed: 04/06/2024] Open
Abstract
The SYN1 gene encodes synapsin I, variants within the SYN1 gene are linked to X-linked neurodevelopmental disorders with high clinical heterogeneity, with reflex epilepsies (REs) being a representative clinical manifestation. This report analyzes a Chinese pedigree affected by seizures associated with SYN1 variants and explores the genotype-phenotype correlation. The proband, a 9-year-old boy, experienced seizures triggered by bathing at the age of 3, followed by recurrent absence seizures, behavioral issues, and learning difficulties. His elder brother exhibited a distinct clinical phenotype, experiencing sudden seizures during sleep at the age of 16, accompanied by hippocampal sclerosis. Whole exome sequencing (WES) confirmed a pathogenic SYN1 variant, c.1647_1650dup (p. Ser551Argfs*134), inherited in an X-linked manner from their mother. Notably, this variant displayed diverse clinical phenotypes in the two brothers and one previously reported case in the literature. Retrospective examination of SYN1 variants revealed an association between truncating variants and the pathogenicity of REs, and non-truncating variants are more related to developmental delay/intellectual disability (DD/ID). In summary, this study contributes to understanding complex neurodevelopmental disorders associated with SYN1, highlighting the clinical heterogeneity of gene variants and emphasizing the necessity for comprehensive genetic analysis in elucidating the pathogenic mechanisms of such diseases.
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Affiliation(s)
- Bin Ren
- Shanghai Nyuen Biotechnology Co., Ltd., Shanghai, China
| | - Xiaoyan Wu
- Shanghai Nyuen Biotechnology Co., Ltd., Shanghai, China
| | - Yuqiang Zhou
- Shanghai Nyuen Biotechnology Co., Ltd., Shanghai, China
| | - Lijuan Chen
- Shanghai Nyuen Biotechnology Co., Ltd., Shanghai, China
| | - Jingzi Jiang
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin, China
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18
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Takaiso N, Imoto I, Yoshimura A, Ouchi A, Komori K, Iwata H, Shimizu Y. BARD1 deletion in a patient with suspected hereditary colorectal cancer. Hum Genome Var 2024; 11:11. [PMID: 38485918 PMCID: PMC10940602 DOI: 10.1038/s41439-024-00267-y] [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: 10/25/2023] [Revised: 01/28/2024] [Accepted: 02/06/2024] [Indexed: 03/18/2024] Open
Abstract
Deleterious germline variants in the BRCA1-associated ring domain (BARD1) gene moderately elevate breast cancer risk; however, their potential association with other neoplasms remains unclear. Here, we present the case of a 43-year-old female patient diagnosed with sigmoid colon adenocarcinoma whose maternal family members met the Amsterdam Criteria II for Lynch syndrome. Comprehensive multigene panel testing revealed a heterozygous BARD1 exon 3 deletion.
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Affiliation(s)
- Nobue Takaiso
- Risk Assessment Unit, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Issei Imoto
- Risk Assessment Unit, Aichi Cancer Center Hospital, Nagoya, Japan.
- Aichi Cancer Center Research Institute, Nagoya, Japan.
| | - Akiyo Yoshimura
- Risk Assessment Unit, Aichi Cancer Center Hospital, Nagoya, Japan
- Department of Breast Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Akira Ouchi
- Department of Gastroenterological Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Koji Komori
- Department of Gastroenterological Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Hiroji Iwata
- Department of Breast Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Yasuhiro Shimizu
- Department of Gastroenterological Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
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Balla C, Margutti A, De Carolis B, Canovi L, Di Domenico A, Vivaldi I, Vitali F, De Raffele M, Malagù M, Sassone B, Biffi M, Selvatici R, Ferlini A, Gualandi F, Bertini M. Cardiac conduction disorders in young adults: Clinical characteristics and genetic background of an underestimated population. Heart Rhythm 2024:S1547-5271(24)00243-1. [PMID: 38467355 DOI: 10.1016/j.hrthm.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/13/2024]
Abstract
BACKGROUND Cardiac conduction disorder (CCD) in patients <50 years old is a rare and mostly unknown condition. OBJECTIVE We aimed to assess clinical characteristics and genetic background of patients <50 years old with CCD of unknown origin. METHODS We retrospectively reviewed a consecutive series of patients with a diagnosis of CCD before the age of 50 years referred to our center between January 2019 and December 2021. Patients underwent complete clinical examination and genetic evaluation. RESULTS We enrolled 39 patients with a median age of 40 years (28-47 years) at the onset of symptoms. A cardiac implantable electronic device was implanted in 69% of the patients. In 15 of 39 CCD index patients (38%), we found a total of 13 different gene variations (3 pathogenic, 6 likely pathogenic, and 4 variants of uncertain significance), mostly in 3 genes (SCN5A, TRPM4, and LMNA). In our cohort, genetic testing led to the decision to implant an implantable cardioverter-defibrillator in 2 patients for the increased risk of sudden cardiac death. CONCLUSION Patients with the occurrence of CCD before the age of 50 years present with a high rate of pathologic gene variations, mostly in 3 genes (SCN5A, TRPM4, and LMNA). The presence of pathogenic variations may add information about the prognosis and lead to an individualized therapeutic approach.
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Affiliation(s)
- Cristina Balla
- Cardiology Unit, Azienda Ospedaliero-Universitaria di Ferrara, Cona (Ferrara), Italy.
| | - Alice Margutti
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Beatrice De Carolis
- Cardiology Unit, Azienda Ospedaliero-Universitaria di Ferrara, Cona (Ferrara), Italy
| | - Luca Canovi
- Cardiology Unit, Azienda Ospedaliero-Universitaria di Ferrara, Cona (Ferrara), Italy
| | - Assunta Di Domenico
- Cardiology Unit, Azienda Ospedaliero-Universitaria di Ferrara, Cona (Ferrara), Italy
| | - Ilaria Vivaldi
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Francesco Vitali
- Cardiology Unit, Azienda Ospedaliero-Universitaria di Ferrara, Cona (Ferrara), Italy
| | - Martina De Raffele
- Cardiology Unit, Azienda Ospedaliero-Universitaria di Ferrara, Cona (Ferrara), Italy
| | - Michele Malagù
- Cardiology Unit, Azienda Ospedaliero-Universitaria di Ferrara, Cona (Ferrara), Italy
| | - Biagio Sassone
- Division of Cardiology, SS.ma Annunziata Hospital, Department of Emergency, AUSL Ferrara, Cento (Ferrara), Italy
| | - Mauro Biffi
- Cardiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Rita Selvatici
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Alessandra Ferlini
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Francesca Gualandi
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Matteo Bertini
- Cardiology Unit, Azienda Ospedaliero-Universitaria di Ferrara, Cona (Ferrara), Italy
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Chia SPS, Pang JKS, Soh BS. Current RNA strategies in treating cardiovascular diseases. Mol Ther 2024; 32:580-608. [PMID: 38291757 PMCID: PMC10928165 DOI: 10.1016/j.ymthe.2024.01.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/22/2023] [Accepted: 01/23/2024] [Indexed: 02/01/2024] Open
Abstract
Cardiovascular disease (CVD) continues to impose a significant global health burden, necessitating the exploration of innovative treatment strategies. Ribonucleic acid (RNA)-based therapeutics have emerged as a promising avenue to address the complex molecular mechanisms underlying CVD pathogenesis. We present a comprehensive review of the current state of RNA therapeutics in the context of CVD, focusing on the diverse modalities that bring about transient or permanent modifications by targeting the different stages of the molecular biology central dogma. Considering the immense potential of RNA therapeutics, we have identified common gene targets that could serve as potential interventions for prevalent Mendelian CVD caused by single gene mutations, as well as acquired CVDs developed over time due to various factors. These gene targets offer opportunities to develop RNA-based treatments tailored to specific genetic and molecular pathways, presenting a novel and precise approach to address the complex pathogenesis of both types of cardiovascular conditions. Additionally, we discuss the challenges and opportunities associated with delivery strategies to achieve targeted delivery of RNA therapeutics to the cardiovascular system. This review highlights the immense potential of RNA-based interventions as a novel and precise approach to combat CVD, paving the way for future advancements in cardiovascular therapeutics.
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Affiliation(s)
- Shirley Pei Shan Chia
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
| | - Jeremy Kah Sheng Pang
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Boon-Seng Soh
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore.
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21
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Jolfayi AG, Kohansal E, Ghasemi S, Naderi N, Hesami M, MozafaryBazargany M, Moghadam MH, Fazelifar AF, Maleki M, Kalayinia S. Exploring TTN variants as genetic insights into cardiomyopathy pathogenesis and potential emerging clues to molecular mechanisms in cardiomyopathies. Sci Rep 2024; 14:5313. [PMID: 38438525 PMCID: PMC10912352 DOI: 10.1038/s41598-024-56154-7] [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: 11/22/2023] [Accepted: 03/01/2024] [Indexed: 03/06/2024] Open
Abstract
The giant protein titin (TTN) is a sarcomeric protein that forms the myofibrillar backbone for the components of the contractile machinery which plays a crucial role in muscle disorders and cardiomyopathies. Diagnosing TTN pathogenic variants has important implications for patient management and genetic counseling. Genetic testing for TTN variants can help identify individuals at risk for developing cardiomyopathies, allowing for early intervention and personalized treatment strategies. Furthermore, identifying TTN variants can inform prognosis and guide therapeutic decisions. Deciphering the intricate genotype-phenotype correlations between TTN variants and their pathologic traits in cardiomyopathies is imperative for gene-based diagnosis, risk assessment, and personalized clinical management. With the increasing use of next-generation sequencing (NGS), a high number of variants in the TTN gene have been detected in patients with cardiomyopathies. However, not all TTN variants detected in cardiomyopathy cohorts can be assumed to be disease-causing. The interpretation of TTN variants remains challenging due to high background population variation. This narrative review aimed to comprehensively summarize current evidence on TTN variants identified in published cardiomyopathy studies and determine which specific variants are likely pathogenic contributors to cardiomyopathy development.
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Affiliation(s)
- Amir Ghaffari Jolfayi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Erfan Kohansal
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Serwa Ghasemi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Niloofar Naderi
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mahshid Hesami
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | | | - Maryam Hosseini Moghadam
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Amir Farjam Fazelifar
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Maleki
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Kalayinia
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran.
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22
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Yoganathan S, Whitney R, Thomas M, Danda S, Chettali AM, Prasad AN, Farhan SMK, AlSowat D, Abukhaled M, Aldhalaan H, Gowda VK, Kinhal UV, Bylappa AY, Konanki R, Lingappa L, Parchuri BM, Appendino JP, Scantlebury MH, Cunningham J, Hadjinicolaou A, El Achkar CM, Kamate M, Menon RN, Jose M, Riordan G, Kannan L, Jain V, Manokaran RK, Chau V, Donner EJ, Costain G, Minassian BA, Jain P. KCTD7-related progressive myoclonic epilepsy: Report of 42 cases and review of literature. Epilepsia 2024; 65:709-724. [PMID: 38231304 DOI: 10.1111/epi.17880] [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: 07/14/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/18/2024]
Abstract
OBJECTIVE KCTD7-related progressive myoclonic epilepsy (PME) is a rare autosomal-recessive disorder. This study aimed to describe the clinical details and genetic variants in a large international cohort. METHODS Families with molecularly confirmed diagnoses of KCTD7-related PME were identified through international collaboration. Furthermore, a systematic review was done to identify previously reported cases. Salient demographic, epilepsy, treatment, genetic testing, electroencephalographic (EEG), and imaging-related variables were collected and summarized. RESULTS Forty-two patients (36 families) were included. The median age at first seizure was 14 months (interquartile range = 11.75-22.5). Myoclonic seizures were frequently the first seizure type noted (n = 18, 43.9%). EEG and brain magnetic resonance imaging findings were variable. Many patients exhibited delayed development with subsequent progressive regression (n = 16, 38.1%). Twenty-one cases with genetic testing available (55%) had previously reported variants in KCTD7, and 17 cases (45%) had novel variants in KCTD7 gene. Six patients died in the cohort (age range = 1.5-21 years). The systematic review identified 23 eligible studies and further identified 59 previously reported cases of KCTD7-related disorders from the literature. The phenotype for the majority of the reported cases was consistent with a PME (n = 52, 88%). Other reported phenotypes in the literature included opsoclonus myoclonus ataxia syndrome (n = 2), myoclonus dystonia (n = 2), and neuronal ceroid lipofuscinosis (n = 3). Eight published cases died over time (14%, age range = 3-18 years). SIGNIFICANCE This study cohort and systematic review consolidated the phenotypic spectrum and natural history of KCTD7-related disorders. Early onset drug-resistant epilepsy, relentless neuroregression, and severe neurological sequalae were common. Better understanding of the natural history may help future clinical trials.
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Affiliation(s)
- Sangeetha Yoganathan
- Department of Neurological Sciences, Christian Medical College, Vellore, Tamil Nadu, India
| | - Robyn Whitney
- Comprehensive Pediatric Epilepsy Program, Division of Neurology, Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Maya Thomas
- Department of Neurological Sciences, Christian Medical College, Vellore, Tamil Nadu, India
| | - Sumita Danda
- Department of Medical Genetics, Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Asuri N Prasad
- Division of Pediatric Neurology and Clinical Neurosciences, Department of Pediatrics, Children's Hospital, London Health Sciences Centre, London, Ontario, Canada
| | - Sali M K Farhan
- Department of Neurology and Neurosurgery, and Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Daad AlSowat
- Division of Pediatric Neurology, Neurosciences Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Musaad Abukhaled
- Division of Pediatric Neurology, Neurosciences Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hesham Aldhalaan
- Division of Pediatric Neurology, Neurosciences Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Vykuntaraju K Gowda
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, Karnataka, India
| | - Uddhava V Kinhal
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, Karnataka, India
| | - Arun Y Bylappa
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, Karnataka, India
| | - Ramesh Konanki
- Department of Pediatric Neurology, Rainbow Children's Hospital, Hyderabad, Telangana, India
| | - Lokesh Lingappa
- Department of Pediatric Neurology, Rainbow Children's Hospital, Hyderabad, Telangana, India
| | | | - Juan P Appendino
- Pediatric Neurology Service, Department of Pediatrics, Cumming School of Medicine, University of Calgary, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Morris H Scantlebury
- Departments of Pediatrics and Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jessie Cunningham
- Hospital Library and Archives, Learning Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Aristides Hadjinicolaou
- Division of Neurology, Department of Pediatrics, CHU (Centre Hospitalier Universitaire) Sainte-Justine, Université de Montréal, Montreal, Quebec, Canada
| | - Christelle Moufawad El Achkar
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mahesh Kamate
- Department of Pediatric Neurology, Jawaharlal Nehru Medical College, KLE (Karnataka Lingayat Education) Academy of Higher Education and Research, KLE's Dr Prabhakar Kore (PK) Hospital, Belagavi, Karnataka, India
| | - Ramshekhar N Menon
- Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram, Kerala, India
| | - Manna Jose
- Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram, Kerala, India
| | - Gillian Riordan
- Department of Paediatric Neurology, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
| | | | - Vivek Jain
- Department of Pediatric Neurology, Neoclinic Children's Hospital, Jaipur, Rajasthan, India
| | - Ranjith Kumar Manokaran
- Division of Pediatric neurology, Department of Neurology, Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - Vann Chau
- Division of Neurology, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Elizabeth J Donner
- Epilepsy Program, Division of Neurology, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Gregory Costain
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, and Program in Genetics & Genome Biology, SickKids Research Institute, Toronto, Ontario, Canada
| | - Berge A Minassian
- Division of Neurology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Puneet Jain
- Epilepsy Program, Division of Neurology, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
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Chen HA, Hsu RH, Chen LC, Lee NC, Chiu PC, Hwu WL, Chien YH. Twelve-year review of galactosemia newborn screening in Taiwan: Evolving methods and insights. Mol Genet Metab Rep 2024; 38:101048. [PMID: 38469088 PMCID: PMC10926206 DOI: 10.1016/j.ymgmr.2024.101048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 03/13/2024] Open
Abstract
Background Galactosemia was introduced into Taiwan's routine newborn screening (NBS) program in 1985. This study presents a 12-year experience, emphasizing disease diagnosis and screening performance. Method NBS for galactosemia utilized dried blood spot samples taken 48-72 h post-delivery, with total galactose (TGal) level as the primary marker. Newborns with critical TGal levels were referred immediately, while those with borderline TGal underwent a recall test. GALT activity measurement was applied simultaneously as the second-tier marker. Further confirmatory tests, such as whole exome sequencing (WES), were conducted upon referral. Results From January 1st, 2011, to December 31st, 2022, 51 cases were identified from 817,906 newborns. Of these, nine individuals had persistently elevated TGal. Diagnoses included one case of GALT deficiency, one of GALM deficiency, and seven of GALE deficiencies. Notably, the classic galactosemia patient (GALT deficiency) presented with extreme high TGal and was referred to the hospital for diet management immediately. All affected patients were instructed to adopt a galactose-restricted diet. By the median age of 2.5 years, all exhibited normal development and liver function. Conclusion The incidence of classical galactosemia and its variants is extremely low in Taiwan. Incorporating WES into NBS has improved our ability to detect various galactosemia forms, enriching our understanding of the genetic underpinnings. While these newly discovered forms often present with milder initial elevations in TGal, specific biochemical investigations and regular monitoring are essential to understanding the long-term implications and outcomes.
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Affiliation(s)
- Hui-An Chen
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Rai-Hseng Hsu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Li-Chu Chen
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Ni-Chung Lee
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Pao-Chin Chiu
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Wuh-Liang Hwu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Integrated Medicine, China Medical University, Taichung City, Taiwan
| | - Yin-Hsiu Chien
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
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Schlegel A. Diagnostic challenge of an APOB variant of uncertain significance resolved by transheterozygosity with a pathological LDLR variant and clinical response to therapy. Atherosclerosis 2024; 390:117460. [PMID: 38290940 DOI: 10.1016/j.atherosclerosis.2024.117460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 01/19/2024] [Indexed: 02/01/2024]
Affiliation(s)
- Amnon Schlegel
- Division of Endocrinology, Metabolism and Diabetes, Department of Internal Medicine, Spencer Fox Eccles School of Medicine, University of Utah, Salt Lake City, UT, 84112, USA.
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Karimi K, Mol MO, Haghshenas S, Relator R, Levy MA, Kerkhof J, McConkey H, Brooks A, Zonneveld-Huijssoon E, Gerkes EH, Tedder ML, Vissers L, Salzano E, Piccione M, Asaftei SD, Carli D, Mussa A, Shukarova-Angelovska E, Trajkova S, Brusco A, Merla G, Alders MM, Bouman A, Sadikovic B. Identification of DNA methylation episignature for the intellectual developmental disorder, autosomal dominant 21 syndrome, caused by variants in the CTCF gene. Genet Med 2024; 26:101041. [PMID: 38054406 DOI: 10.1016/j.gim.2023.101041] [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: 06/09/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023] Open
Abstract
PURPOSE The main objective of this study was to assess clinical features and genome-wide DNA methylation profiles in individuals affected by intellectual developmental disorder, autosomal dominant 21 (IDD21) syndrome, caused by variants in the CCCTC-binding factor (CTCF) gene. METHODS DNA samples were extracted from peripheral blood of 16 individuals with clinical features and genetic findings consistent with IDD21. DNA methylation analysis was performed using the Illumina Infinium Methylation EPIC Bead Chip microarrays. The methylation levels were fitted in a multivariate linear regression model to identify the differentially methylated probes. A binary support vector machine classification model was constructed to differentiate IDD21 samples from controls. RESULTS We identified a highly specific, reproducible, and sensitive episignature associated with CTCF variants. Six variants of uncertain significance were tested, of which 2 mapped to the IDD21 episignature and clustered alongside IDD21 cases in both heatmap and multidimensional scaling plots. Comparison of the genomic DNA methylation profile of IDD21 with that of 56 other neurodevelopmental disorders provided insights into the underlying molecular pathophysiology of this disorder. CONCLUSION The robust and specific CTCF/IDD21 episignature expands the growing list of neurodevelopmental disorders with distinct DNA methylation profiles, which can be applied as supporting evidence in variant classification.
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Affiliation(s)
- Karim Karimi
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Merel O Mol
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Alice Brooks
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Erica H Gerkes
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Lisenka Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Emanuela Salzano
- Medical Genetics Unit, AOOR Villa Sofia-Cervello Hospitals, Palermo, Italy
| | - Maria Piccione
- Medical Genetics Unit, AOOR Villa Sofia-Cervello Hospitals, Palermo, Italy; Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Sebastian Dorin Asaftei
- Pediatric Onco-Hematology, Regina Margherita Children's Hospital, Città della Salute e della Scienza di Torino, Torino, Italy
| | - Diana Carli
- Department of Medical Sciences, University of Turin, Turin, Italy; Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Alessandro Mussa
- Department of Public Health and Pediatrics, University of Turin, Turin, Italy
| | - Elena Shukarova-Angelovska
- Department of Endocrinology and Genetics, University Clinic for Children's Diseases, Medical Faculty, University Sv. Kiril i Metodij, Skopje, North Macedonia
| | - Slavica Trajkova
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, Turin, Italy; Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Giuseppe Merla
- Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy; Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Marielle M Alders
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Arjan Bouman
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Canada.
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Liu K, Fu J, Guo K, Maghsoudloo M, Cheng J, Fu J. The ENG/VEGFα Pathway Is Likely Affected by a Nonsense Variant of Endoglin (ENG)/CD105, Causing Hereditary Hemorrhagic Telangiectasia Type 1 (HHT1) in a Chinese Family. Genes (Basel) 2024; 15:304. [PMID: 38540362 PMCID: PMC10970080 DOI: 10.3390/genes15030304] [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: 02/02/2024] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 06/14/2024] Open
Abstract
Hereditary hemorrhagic telangiectasia (HHT), also called Rendu-Osler syndrome, is a group of rare genetic diseases characterized by autosomal dominance, multisystemic vascular dysplasia, and age-related penetrance. This includes arteriovenous malformations (AVMs) in the skin, brain, lung, liver, and mucous membranes. The correlations between the phenotype and genotype for HHT are not clear. An HHT Chinese pedigree was recruited. Whole exome sequencing (WES) analysis, Sanger verification, and co-segregation were conducted. Western blotting was performed for monitoring ENG/VEGFα signaling. As a result, a nonsense, heterozygous variant for ENG/CD105: c.G1169A:p. Trp390Ter of the proband with hereditary hemorrhagic telangiectasia type 1 (HHT1) was identified, which co-segregated with the disease in the M666 pedigree. Western blotting found that, compared with the normal levels associated with non-carrier family members, the ENG protein levels in the proband showed approximately a one-half decrease (47.4% decrease), while levels of the VEGFα protein, in the proband, showed approximately a one-quarter decrease (25.6% decrease), implying that ENG haploinsufficiency, displayed in the carrier of this variant, may affect VEGFα expression downregulation. Pearson and Spearman correlation analyses further supported TGFβ/ENG/VEGFα signaling, implying ENG regulation in the blood vessels. Thus, next-generation sequencing including WES should provide an accurate strategy for gene diagnosis, therapy, genetic counseling, and clinical management for rare genetic diseases including that in HHT1 patients.
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Affiliation(s)
- Kemeng Liu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (K.L.); (J.F.); (K.G.); (M.M.); (J.C.)
| | - Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (K.L.); (J.F.); (K.G.); (M.M.); (J.C.)
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Kan Guo
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (K.L.); (J.F.); (K.G.); (M.M.); (J.C.)
| | - Mazaher Maghsoudloo
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (K.L.); (J.F.); (K.G.); (M.M.); (J.C.)
| | - Jingliang Cheng
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (K.L.); (J.F.); (K.G.); (M.M.); (J.C.)
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (K.L.); (J.F.); (K.G.); (M.M.); (J.C.)
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Clausen L, Voutsinos V, Cagiada M, Johansson KE, Grønbæk-Thygesen M, Nariya S, Powell RL, Have MKN, Oestergaard VH, Stein A, Fowler DM, Lindorff-Larsen K, Hartmann-Petersen R. A mutational atlas for Parkin proteostasis. Nat Commun 2024; 15:1541. [PMID: 38378758 PMCID: PMC10879094 DOI: 10.1038/s41467-024-45829-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Abstract
Proteostasis can be disturbed by mutations affecting folding and stability of the encoded protein. An example is the ubiquitin ligase Parkin, where gene variants result in autosomal recessive Parkinsonism. To uncover the pathological mechanism and provide comprehensive genotype-phenotype information, variant abundance by massively parallel sequencing (VAMP-seq) is leveraged to quantify the abundance of Parkin variants in cultured human cells. The resulting mutational map, covering 9219 out of the 9300 possible single-site amino acid substitutions and nonsense Parkin variants, shows that most low abundance variants are proteasome targets and are located within the structured domains of the protein. Half of the known disease-linked variants are found at low abundance. Systematic mapping of degradation signals (degrons) reveals an exposed degron region proximal to the so-called "activation element". This work provides examples of how missense variants may cause degradation either via destabilization of the native protein, or by introducing local signals for degradation.
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Affiliation(s)
- Lene Clausen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Vasileios Voutsinos
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Matteo Cagiada
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer E Johansson
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Grønbæk-Thygesen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Snehal Nariya
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Rachel L Powell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Magnus K N Have
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Amelie Stein
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Rasmus Hartmann-Petersen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Garcia ABDM, Viola GD, Corrêa BDS, Fischer TDS, Pinho MCDF, Rodrigues GM, Ashton-Prolla P, Rosset C. An overview of actionable and potentially actionable TSC1 and TSC2 germline variants in an online Database. Genet Mol Biol 2024; 46:e20230132. [PMID: 38373162 PMCID: PMC10876083 DOI: 10.1590/1678-4685-gmb-2023-0132] [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: 05/03/2023] [Accepted: 11/26/2023] [Indexed: 02/21/2024] Open
Abstract
Tuberous Sclerosis Complex (TSC) is caused by loss of function germline variants in the TSC1 or TSC2 tumor suppressor genes. Genetic testing for the detection of pathogenic variants in either TSC1 or TSC2 was implemented as a diagnostic criterion for TSC. However, TSC molecular diagnosis can be challenging due to the absence of variant hotspots and the high number of variants described. This review aimed to perform an overview of TSC1/2 variants submitted in the ClinVar database. Variants of uncertain significance (VUS), missense and single nucleotide variants were the most frequent in clinical significance (37-40%), molecular consequence (37%-39%) and variation type (82%-83%) categories in ClinVar in TSC1 and TSC2 variants, respectively. Frameshift and nonsense VUS have potential for pathogenic reclassification if further functional and segregation studies were performed. Indeed, there were few functional assays deposited in the database and literature. In addition, we did not observe hotspots for variation and many variants presented conflicting submissions regarding clinical significance. This study underscored the importance of disseminating molecular diagnostic results in a public database to render the information largely accessible and promote accurate diagnosis. We encourage the performance of functional studies evaluating the pathogenicity of TSC1/2 variants.
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Affiliation(s)
- Arthur Bandeira de Mello Garcia
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Guilherme Danielski Viola
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Bruno da Silveira Corrêa
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Taís da Silveira Fischer
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Maria Clara de Freitas Pinho
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Centro Universitário CESUCA, Cachoeirinha, RS, Brazil
| | - Grazielle Motta Rodrigues
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
| | - Patricia Ashton-Prolla
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Serviço de Genética Médica, Porto Alegre, RS, Brazil
| | - Clévia Rosset
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
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29
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Dursun F, Turan İ, Bitkin EÇ, Bayramoğlu E, Çayır A, Erdeve ŞS, Çakır EDP, Çamtosun E, Dilek SO, Kırmızıbekmez H, Eser M, Türkyılmaz A, Karagüzel G. Natural history of ENPP1 deficiency: Nationwide Turkish Cohort Study of autosomal-recessive hypophosphataemic rickets type 2. Clin Endocrinol (Oxf) 2024. [PMID: 38324408 DOI: 10.1111/cen.15028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/09/2023] [Accepted: 01/24/2024] [Indexed: 02/09/2024]
Abstract
OBJECTIVE Autosomal-recessive hypophosphataemic rickets type 2 (ARHR2) is a rare disease that is reported in survivors of generalized arterial calcification of infancy (GACI). DESIGN, PATIENTS AND MEASUREMENT The objective of this study was to characterize a multicenter paediatric cohort with ARHR2 due to ectonucleotide pyrophosphatase/phosphodiesterase family member 1 (ENPP1) deficiency and with a diagnosis of GACI or GACI-related findings. The clinical, biochemical and genetic characteristics of the patients were retrospectively retrieved. RESULTS We identified 18 patients from 13 families diagnosed with ARHR2. Fifteen of the patients had an ENPP1 variation confirmed with genetic analyses, and three were siblings of one of these patients, who had clinically diagnosed hypophosphataemic rickets (HRs) with the same presentation. From nine centres, 18 patients, of whom 12 (66.7%) were females, were included in the study. The mean age at diagnosis was 4.2 ± 2.2 (1.6-9) years. The most frequently reported clinical findings on admission were limb deformities (66.6%) and short stature (44.4%). At diagnosis, the mean height SD was -2.2 ± 1.3. Five of the patients were diagnosed with GACI in the neonatal period and treated with bisphosphonates. Other patients were initially diagnosed with ARHR2, but after the detection of a biallelic variant in the ENPP1 gene, it was understood that they previously had clinical findings associated with GACI. Three patients had hearing loss, and two had cervical fusion. After the treatment of HRs, one patient developed calcification, and one developed intimal proliferation. CONCLUSION ARHR2 represents one manifestation of ENPP1 deficiency that usually manifests later in life than GACI. The history of calcifications or comorbidities that might be associated with GACI will facilitate the diagnosis in patients with ARHR2, and patients receiving calcitriol and phosphate medication should be carefully monitored for signs of calcification or intimal proliferation.
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Affiliation(s)
- Fatma Dursun
- Department of Pediatric Endocrinology, SBU Umraniye Training and Research Hospital, University of Health Science, Istanbul, Türkiye
| | - İhsan Turan
- Department of Pediatric Endocrinology, Faculty of Medicine, Cukurova University, Adana, Türkiye
| | - Eda Çelebi Bitkin
- Department of Pediatric Endocrinology, Bakırkoy Dr Sadi Konuk Training and Research Hospital, Istanbul, Türkiye
| | - Elvan Bayramoğlu
- Department of Pediatric Endocrinology, Cerrahpaşa Faculty of Medicine, Istanbul University, İstanbul, Türkiye
| | - Atilla Çayır
- Department of Pediatric Endocrinology and Diabetes, Erzurum Education and Research Hospital, University of Health Science, Erzurum, Türkiye
| | - Şenay Savaş Erdeve
- Department of Pediatric Endocrinology, Ankara Etlik City Hospital, University of Health Science, Ankara, Türkiye
| | - Esra Deniz Papatya Çakır
- Department of Pediatric Endocrinology, Bakırkoy Dr Sadi Konuk Training and Research Hospital, Istanbul, Türkiye
| | - Emine Çamtosun
- Department of Pediatric Endocrinology, Faculty of Medicine, Inönü University, Malatya, Türkiye
| | - Semine Ozdemir Dilek
- Department of Pediatric Endocrinology, Adana City Training and Research Hospital, University of Health Science, Adana, Türkiye
| | - Heves Kırmızıbekmez
- Department of Pediatric Endocrinology, SBU Umraniye Training and Research Hospital, University of Health Science, Istanbul, Türkiye
| | - Metin Eser
- Department of Medical Genetic, Umraniye Training and Research Hospital, Istanbul, Türkiye
| | - Ayberk Türkyılmaz
- Department of Medical Genetic, Faculty of Medicine, Karadeniz Technical University, Trabzon, Türkiye
| | - Gülay Karagüzel
- Department of Pediatric Endocrinology, Faculty of Medicine, Karadeniz Technical University, Trabzon, Türkiye
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30
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Ul Mudassir B, Agha Z. Novel and known minor alleles of CNTNAP2 gene variants are associated with comorbidity of intellectual disability and epilepsy phenotypes: a case-control association study reveals potential biomarkers. Mol Biol Rep 2024; 51:276. [PMID: 38315301 DOI: 10.1007/s11033-023-09176-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 12/18/2023] [Indexed: 02/07/2024]
Abstract
BACKGROUND Neurodevelopmental disorders are heterogeneous due to underlying multiple shared genetic pathways and risk factors. Intellectual disability, epilepsy and autism spectrum disorder phenotypes overlap which indicates the diverse effects of common genes. Recent studies suggested the probable contribution of CNTNAP2 gene polymorphisms to the comorbidity of these neurological conditions. METHODS AND RESULTS This study was conducted to investigate the role of CNTNAP2 polymorphisms rs147815978 (G>T) and rs2710102 (A>G) as a risk factor for comorbidity of intellectual disability and epilepsy in a group of 345 individuals including 170 patients and 175 healthy controls recruited from various ethnic groups of Pakistani population. Our case-control study group was genotyped by tetra primer ARMS-PCR technique and results were analysed to know the effects of CNTNAP2 rs147815978 (G>T) and rs2710102 (A>G) polymorphisms in the group. The frequency of risk allele T (rs147815978) and risk allele G (rs2710102) for homozygous recessive genotypes (TT/GG) in our study group was 36.47% while odds ratios for risk allele T (rs147815978) was 5.45 (3.90-7.61: 95% CI, P = 0.000) and that for risk allele G (rs2710102) was 2.39 (1.76-3.24: 95% CI, P = 0.0001). Homozygous recessive genotypes (TT/GG) appeared only in cases and not in control group which indicated these as suspected risk genotypes and the significant association (p < 0.05%) of CNTNAP2 gene polymorphisms rs147815978 (G>T) and rs2710102 (A>G) with co-occurrence of intellectual disability and epilepsy phenotypes in our study group which is in HWE (χ2 = 174, P < 0.0001). Logistic regression analysis shows additive (p < 0.0001) and multiplicative (p < 0.001) models which confirms significant association of both the polymorphisms in our data, which are closely located on same haplotype (D' = - 0.168). CONCLUSIONS We propose that CNTNAP2 rs147815978 (G>T) and rs2710102 (A>G) polymorphisms are possible risk loci for overlapping neurodevelopmental disorders in Pakistani population. We propose the role of a previously reported common SNP rs2710102 (A>G) with a rarely reported novel SNP rs147815978 (G>T) for CNTNAP2 gene association with neurodevelopmental disorders in our data. Our study has expanded the knowledge of CNTNAP2 gene polymorphisms as probable biomarkers for susceptibility of co-occurrence of intellectual disability and epilepsy phenotypes in Pakistani population. We hope that our study will open new horizons of CNTNAP2 gene variants research to cure the neurological conditions in Pakistani population where consanguinity is a tradition and prevalence of neurodevelopmental disorders has increased from 1 to 2% during last 5 years.
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Affiliation(s)
- Behjat Ul Mudassir
- Translational Genomics Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Zehra Agha
- Translational Genomics Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan.
- Department of Psychiatry, State University of New York at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA.
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31
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Ghaedi H, Davey SK, Feilotter H. Variant Classification Discordance: Contributing Factors and Predictive Models. J Mol Diagn 2024; 26:115-126. [PMID: 38008287 DOI: 10.1016/j.jmoldx.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/04/2023] [Accepted: 11/07/2023] [Indexed: 11/28/2023] Open
Abstract
An ever-growing catalog of human variants is hosted in the ClinVar database. In this database, submissions on a variant are combined into a multisubmitter record; and in the case of discordance in variant classification between submitters, the record is labeled as conflicting. The current study used ClinVar data to identify characteristics that would make variants more likely to be associated with the conflict class of variants. Furthermore, the Extreme Gradient Boosting algorithm was used to train classifier models to provide prediction of classification discordance for single submission variants in ClinVar database. Population allele frequency, the gene harboring the variant, variant type, consequence on protein, variant deleteriousness score, first submitter identity, and submission count were associated with conflict in variant classification. Using such features, the optimized classifier showed accuracy on the test set of 88% with the weighted average of precision, recall, and f1-score of 0.84, 0.88, and 0.85, respectively. There were pronounced associations between variant classification discordance and allele frequency, gene type, and the identity of the first submitter. The study provides the predicted discordance status for single-submitter variants deposited in ClinVar. This approach can be used to assess whether single-submitter variants are likely to be supported, or in conflict with, future entries; this knowledge may help laboratories with clinical variant assessment.
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Affiliation(s)
- Hamid Ghaedi
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Scott K Davey
- Division of Cancer Biology and Genetics, Department of Pathology and Molecular Medicine, Queen's University Cancer Research Institute, Kingston, Ontario, Canada
| | - Harriet Feilotter
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada.
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32
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Morales A, Moretz C, Ren S, Smith E, Callis TE, Hall T, Hatchell KE, Nussbaum RL, Regalado E, Rojahn S, Vatta M, Esplin ED, Murillo J. Real-World Genetic Testing Utilization Among Patients With Cardiomyopathy. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2024; 17:e004028. [PMID: 38088168 DOI: 10.1161/circgen.122.004028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Affiliation(s)
- Ana Morales
- Invitae Corporation, San Francisco, CA (A.M., C.M., T.E.C., K.E.H., R.L.N., E.R., S. Rojahn, M.V., E.D.E.)
| | - Chad Moretz
- Invitae Corporation, San Francisco, CA (A.M., C.M., T.E.C., K.E.H., R.L.N., E.R., S. Rojahn, M.V., E.D.E.)
| | - Sheng Ren
- Optum Labs, Eden Prairie, MN (S. Ren, E.S., T.H., J.M.)
| | | | - Thomas E Callis
- Invitae Corporation, San Francisco, CA (A.M., C.M., T.E.C., K.E.H., R.L.N., E.R., S. Rojahn, M.V., E.D.E.)
| | - Taryn Hall
- Optum Labs, Eden Prairie, MN (S. Ren, E.S., T.H., J.M.)
| | - Kathryn E Hatchell
- Invitae Corporation, San Francisco, CA (A.M., C.M., T.E.C., K.E.H., R.L.N., E.R., S. Rojahn, M.V., E.D.E.)
| | - Robert L Nussbaum
- Invitae Corporation, San Francisco, CA (A.M., C.M., T.E.C., K.E.H., R.L.N., E.R., S. Rojahn, M.V., E.D.E.)
| | - Ellen Regalado
- Invitae Corporation, San Francisco, CA (A.M., C.M., T.E.C., K.E.H., R.L.N., E.R., S. Rojahn, M.V., E.D.E.)
| | - Susan Rojahn
- Invitae Corporation, San Francisco, CA (A.M., C.M., T.E.C., K.E.H., R.L.N., E.R., S. Rojahn, M.V., E.D.E.)
| | - Matteo Vatta
- Invitae Corporation, San Francisco, CA (A.M., C.M., T.E.C., K.E.H., R.L.N., E.R., S. Rojahn, M.V., E.D.E.)
| | - Edward D Esplin
- Invitae Corporation, San Francisco, CA (A.M., C.M., T.E.C., K.E.H., R.L.N., E.R., S. Rojahn, M.V., E.D.E.)
| | - Jaime Murillo
- Optum Labs, Eden Prairie, MN (S. Ren, E.S., T.H., J.M.)
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Terkelsen T, Mikkelsen NS, Bak EN, Vad-Nielsen J, Blechingberg J, Weiss S, Drue SO, Andersen H, Andresen BS, Bak RO, Jensen UB. CRISPR activation to characterize splice-altering variants in easily accessible cells. Am J Hum Genet 2024; 111:309-322. [PMID: 38272032 PMCID: PMC10870130 DOI: 10.1016/j.ajhg.2023.12.024] [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: 07/10/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/27/2024] Open
Abstract
Genetic variants that affect mRNA splicing are a major cause of hereditary disorders, but the spliceogenicity of variants is challenging to predict. RNA diagnostics of clinically accessible tissues enable rapid functional characterization of splice-altering variants within their natural genetic context. However, this analysis cannot be offered to all individuals as one in five human disease genes are not expressed in easily accessible cell types. To overcome this problem, we have used CRISPR activation (CRISPRa) based on a dCas9-VPR mRNA-based delivery platform to induce expression of the gene of interest in skin fibroblasts from individuals with suspected monogenic disorders. Using this ex vivo splicing assay, we characterized the splicing patterns associated with germline variants in the myelin protein zero gene (MPZ), which is exclusively expressed in Schwann cells of the peripheral nerves, and the spastin gene (SPAST), which is predominantly expressed in the central nervous system. After overnight incubation, CRISPRa strongly upregulated MPZ and SPAST transcription in skin fibroblasts, which enabled splice variant profiling using reverse transcription polymerase chain reaction, next-generation sequencing, and long-read sequencing. Our investigations show proof of principle of a promising genetic diagnostic tool that involves CRISPRa to activate gene expression in easily accessible cells to study the functional impact of genetic variants. The procedure is easy to perform in a diagnostic laboratory with equipment and reagents all readily available.
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Affiliation(s)
- Thorkild Terkelsen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark; Department of Biomedicine, Aarhus University, Aarhus, Denmark.
| | | | - Ebbe Norskov Bak
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Johan Vad-Nielsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Jenny Blechingberg
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Simone Weiss
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Simon Opstrup Drue
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Henning Andersen
- Department of Neurology, Aarhus University Hospital, Aarhus, Denmark
| | - Brage Storstein Andresen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Uffe Birk Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark; Department of Biomedicine, Aarhus University, Aarhus, Denmark.
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34
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Shlomovitz O, Atias-Varon D, Yagel D, Barel O, Shasha-Lavsky H, Skorecki K, Eliyahu A, Bathish Y, Frajewicki V, Kushnir D, Zaid R, Paperna T, Ofir A, Tchirkov M, Hassan K, Kruzel E, Khazim K, Geron R, Weisman I, Hanut A, Nakhoul F, Kenig-Kozlovsky Y, Refael G, Antebi A, Storch S, Leiba M, Kagan M, Shukrun R, Rechavi G, Dekel B, Ben Moshe Y, Weiss K, Assady S, Vivante A. Genetic Markers Among the Israeli Druze Minority Population With End-Stage Kidney Disease. Am J Kidney Dis 2024; 83:183-195. [PMID: 37717846 DOI: 10.1053/j.ajkd.2023.06.006] [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: 12/31/2022] [Revised: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 09/19/2023]
Abstract
RATIONALE & OBJECTIVE Genetic etiologies have been identified among approximately 10% of adults with chronic kidney disease (CKD). However, data are lacking regarding the prevalence of monogenic etiologies especially among members of minority groups. This study characterized the genetic markers among members of an Israeli minority group with end-stage kidney disease (ESKD). STUDY DESIGN A national-multicenter cross-sectional study of Israeli Druze patients (an Arabic-speaking Near-Eastern transnational population isolate) who are receiving maintenance dialysis for ESKD. All study participants underwent exome sequencing. SETTING & PARTICIPANTS We recruited 94 adults with ESKD, comprising 97% of the total 97 Druze individuals throughout Israel being treated with dialysis during the study period. PREDICTORS Demographics and clinical characteristics of kidney disease. OUTCOME Genetic markers. ANALYTICAL APPROACH Whole-exome sequencing and the relationship of markers to clinical phenotypes. RESULTS We identified genetic etiologies in 17 of 94 participants (18%). None had a previous molecular diagnosis. A novel, population-specific, WDR19 homozygous pathogenic variant (p.Cys293Tyr) was the most common genetic finding. Other monogenic etiologies included PKD1, PKD2, type IV collagen mutations, and monogenic forms of noncommunicable diseases. The pre-exome clinical diagnosis corresponded to the final molecular diagnosis in fewer than half of the participants. LIMITATIONS This study was limited to Druze individuals, so its generalizability may be limited. CONCLUSIONS Exome sequencing identified a genetic diagnosis in approximately 18% of Druze individuals with ESKD. These results support conducting genetic analyses in minority populations with high rates of CKD and for whom phenotypic disease specificity may be low. PLAIN-LANGUAGE SUMMARY Chronic kidney disease (CKD) affects many people worldwide and has multiple genetic causes. However, there is limited information on the prevalence of genetic etiologies, especially among minority populations. Our national-multicenter study focused on Israeli Druze patients. Using exome-sequencing, we identified previously undetected genetic causes in nearly 20% of patients, including a new and population-specific WDR19 homozygous pathogenic variant. This mutation has not been previously described; it is extremely rare globally but is common among the Druze, which highlights the importance of studying minority populations with high rates of CKD. Our findings provide insights into the genetic basis of end-stage kidney disease in the Israeli Druze, expand the WDR19 phenotypic spectrum, and emphasize the potential value of genetic testing in such populations.
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Affiliation(s)
- Omer Shlomovitz
- Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Safed
| | - Danit Atias-Varon
- Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Safed
| | - Dina Yagel
- Genomics Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel
| | - Ortal Barel
- Genomics Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel; The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel-Hashomer, Israel
| | - Hadas Shasha-Lavsky
- Azrieili Faculty of Medicine in Galilee, Bar-Ilan University, Safed, Israel; Department of Pediatric Nephrology, Galilee Medical Center, Nahariya, Israel
| | - Karl Skorecki
- Azrieili Faculty of Medicine in Galilee, Bar-Ilan University, Safed, Israel
| | - Aviva Eliyahu
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Safed; The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel-Hashomer, Israel
| | | | - Victor Frajewicki
- Institute of Nephrology and Hypertension, Carmel Medical Center, Haifa, Israel
| | - Daniel Kushnir
- Institute of Nephrology and Hypertension, Carmel Medical Center, Haifa, Israel
| | - Rinat Zaid
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | - Tamar Paperna
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | - Ayala Ofir
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | - Marina Tchirkov
- Department of Nephrology and Hypertension, Rambam Health Care campus, Haifa, Israel
| | - Kamal Hassan
- Nephrology Unit, Galilee Medical Center, Nahariya, Israel
| | - Etty Kruzel
- Nephrology Unit, Galilee Medical Center, Nahariya, Israel
| | - Khaled Khazim
- Nephrology Unit, Galilee Medical Center, Nahariya, Israel
| | - Ronit Geron
- Nephrology Unit, Galilee Medical Center, Nahariya, Israel
| | - Irit Weisman
- Nephrology Unit, Galilee Medical Center, Nahariya, Israel
| | - Anaam Hanut
- Division of Nephrology and Hypertension Baruch Padeh Medical Center Poriya, Tiberias, Israel
| | - Farid Nakhoul
- Division of Nephrology and Hypertension Baruch Padeh Medical Center Poriya, Tiberias, Israel
| | - Yael Kenig-Kozlovsky
- Department of Nephrology and Hypertension, Rambam Health Care campus, Haifa, Israel
| | - Gery Refael
- Nephrology Unit, Mayanei HaYeshua Medical Center, Bnei Brak, Israel
| | - Alon Antebi
- Institute of Nephrology and Hypertension, Carmel Medical Center, Haifa, Israel
| | - Shimon Storch
- Nephrology and Hypertension Unit, Bnai-Zion Medical Center, Haifa, Israel
| | | | - Maayan Kagan
- Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Safed
| | - Rachel Shukrun
- Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Safed
| | - Gidi Rechavi
- Genomics Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel; The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel-Hashomer, Israel; Azrieili Faculty of Medicine in Galilee, Bar-Ilan University, Safed, Israel
| | - Benjamin Dekel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Safed; Pediatric Stem Cell Research Institute, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel; Division of Pediatric Nephrology, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Yishay Ben Moshe
- Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Safed
| | - Karin Weiss
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel; The Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Suheir Assady
- Department of Nephrology and Hypertension, Rambam Health Care campus, Haifa, Israel; The Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Asaf Vivante
- Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Safed; Division of Pediatric Nephrology, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel.
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Manoubi W, Mahdouani M, Hmida D, Kdissa A, Rouissi A, Turki I, Gueddiche N, Soyah N, Saad A, Bouwkamp C, Elgersma Y, Mougou-Zerelli S, Gribaa M. Genetic investigation of the ubiquitin-protein ligase E3A gene as putative target in Angelman syndrome. World J Clin Cases 2024; 12:503-516. [PMID: 38322471 PMCID: PMC10841941 DOI: 10.12998/wjcc.v12.i3.503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/12/2023] [Accepted: 01/04/2024] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Angelman syndrome (AS) is caused by maternal chromosomal deletions, imprinting defects, paternal uniparental disomy involving chromosome 15 and the ubiquitin-protein ligase UBE3A gene mutations. However the genetic basis remains unclear for several patients. AIM To investigate the involvement of UBE3A gene in AS and identifying new potential genes using exome sequencing. METHODS We established a cohort study in 50 patients referred to Farhat Hached University Hospital between 2006 and 2021, with a strong suspicion of AS and absence of chromosomal aberrations. The UBE3A gene was screened for mutation detection. Two unrelated patients issued from consanguineous families were subjected to exome analysis. RESULTS We describe seven UBE3A variants among them 3 none previously described including intronic variants c.2220+14T>C (intron14), c.2507+43T>A (Exon15) and insertion in Exon7: c.30-47_30-46. The exome sequencing revealed 22 potential genes that could be involved in AS-like syndromes that should be investigated further. CONCLUSION Screening for UBE3A mutations in AS patients has been proven to be useful to confirm the diagnosis. Our exome findings could rise to new potential alternative target genes for genetic counseling.
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Affiliation(s)
- Wiem Manoubi
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse 4000, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir 3000, Tunisia
| | - Marwa Mahdouani
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse 4000, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir 3000, Tunisia
| | - Dorra Hmida
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse 4000, Tunisia
| | - Ameni Kdissa
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse 4000, Tunisia
| | - Aida Rouissi
- Department of Neuropediatry, La Rabta Hospital, Tunis 2000, Tunisia
| | - Ilhem Turki
- Department of Neuropediatry, La Rabta Hospital, Tunis 2000, Tunisia
| | - Neji Gueddiche
- Department of Pediatric, Fattouma Bourguiba Hospital Monastir, Monastir 2003, Tunisia
| | - Najla Soyah
- Department of Pediatric, Farhat Hached University Hospital, Sousse 4000, Tunisia
| | - Ali Saad
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse 4000, Tunisia
| | - Christian Bouwkamp
- Department of Neuroscience, Erasmus MC, the Netherlands, Rotterdam 3112 td, Netherlands
| | - Ype Elgersma
- Department of Neuroscience, Erasmus MC, the Netherlands, Rotterdam 3112 td, Netherlands
| | - Soumaya Mougou-Zerelli
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse 4000, Tunisia
| | - Moez Gribaa
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse 4000, Tunisia
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Barbitoff YA, Ushakov MO, Lazareva TE, Nasykhova YA, Glotov AS, Predeus AV. Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges. Brief Bioinform 2024; 25:bbad508. [PMID: 38271481 PMCID: PMC10810331 DOI: 10.1093/bib/bbad508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/18/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024] Open
Abstract
Next-generation sequencing (NGS) has revolutionized the field of rare disease diagnostics. Whole exome and whole genome sequencing are now routinely used for diagnostic purposes; however, the overall diagnosis rate remains lower than expected. In this work, we review current approaches used for calling and interpretation of germline genetic variants in the human genome, and discuss the most important challenges that persist in the bioinformatic analysis of NGS data in medical genetics. We describe and attempt to quantitatively assess the remaining problems, such as the quality of the reference genome sequence, reproducible coverage biases, or variant calling accuracy in complex regions of the genome. We also discuss the prospects of switching to the complete human genome assembly or the human pan-genome and important caveats associated with such a switch. We touch on arguably the hardest problem of NGS data analysis for medical genomics, namely, the annotation of genetic variants and their subsequent interpretation. We highlight the most challenging aspects of annotation and prioritization of both coding and non-coding variants. Finally, we demonstrate the persistent prevalence of pathogenic variants in the coding genome, and outline research directions that may enhance the efficiency of NGS-based disease diagnostics.
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Affiliation(s)
- Yury A Barbitoff
- Dpt. of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, Mendeleevskaya line 3, 199034, St. Petersburg, Russia
- Bioinformatics Institute, Kentemirovskaya st. 2A, 197342, St. Petersburg, Russia
| | - Mikhail O Ushakov
- Dpt. of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, Mendeleevskaya line 3, 199034, St. Petersburg, Russia
| | - Tatyana E Lazareva
- Dpt. of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, Mendeleevskaya line 3, 199034, St. Petersburg, Russia
| | - Yulia A Nasykhova
- Dpt. of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, Mendeleevskaya line 3, 199034, St. Petersburg, Russia
| | - Andrey S Glotov
- Dpt. of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, Mendeleevskaya line 3, 199034, St. Petersburg, Russia
| | - Alexander V Predeus
- Bioinformatics Institute, Kentemirovskaya st. 2A, 197342, St. Petersburg, Russia
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Andreotti V, Vanni I, Pastorino L, Ghiorzo P, Bruno W. Germline POT1 Variants: A Critical Perspective on POT1 Tumor Predisposition Syndrome. Genes (Basel) 2024; 15:104. [PMID: 38254993 PMCID: PMC10815363 DOI: 10.3390/genes15010104] [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: 12/18/2023] [Revised: 01/10/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
The Protection of Telomere 1 (POT1) gene was identified as a melanoma predisposition candidate nearly 10 years ago. Thereafter, various cancers have been proposed as associated with germline POT1 variants in the context of the so-called POT1 Predisposition Tumor Syndrome (POT1-TPD). While the key role, and related risks, of the alterations in POT1 in melanoma are established, the correlation between germline POT1 variants and the susceptibility to other cancers partially lacks evidence, due also to the rarity of POT1-TPD. Issues range from the absence of functional or segregation studies to biased datasets or the need for a revised classification of variants. Furthermore, a proposal of a surveillance protocol related to the cancers associated with POT1 pathogenic variants requires reliable data to avoid an excessive, possibly unjustified, burden for POT1 variant carriers. We propose a critical perspective regarding data published over the last 10 years that correlate POT1 variants to various types of cancer, other than cutaneous melanoma, to offer food for thought for the specialists who manage cancer predisposition syndromes and to stimulate a debate on the grey areas that have been exposed.
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Affiliation(s)
- Virginia Andreotti
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genoa, Italy; (V.A.); (I.V.); (L.P.); (P.G.)
| | - Irene Vanni
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genoa, Italy; (V.A.); (I.V.); (L.P.); (P.G.)
| | - Lorenza Pastorino
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genoa, Italy; (V.A.); (I.V.); (L.P.); (P.G.)
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132 Genoa, Italy
| | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genoa, Italy; (V.A.); (I.V.); (L.P.); (P.G.)
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132 Genoa, Italy
| | - William Bruno
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genoa, Italy; (V.A.); (I.V.); (L.P.); (P.G.)
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132 Genoa, Italy
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Badura-Stronka M, Wołyńska K, Winczewska-Wiktor A, Marcinkowska J, Karolewska D, Tomkowiak-Kędzia D, Piechota M, Przyborska M, Kochalska N, Steinborn B. Validation of targeted next-generation sequencing panels in a cohort of Polish patients with epilepsy: assessing variable performance across clinical endophenotypes and uncovering novel genetic variants. Front Neurol 2024; 14:1316933. [PMID: 38328757 PMCID: PMC10849089 DOI: 10.3389/fneur.2023.1316933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/26/2023] [Indexed: 02/09/2024] Open
Abstract
Introduction Targeted Next-Generation Sequencing Panels (TNGSP) have become a standard in global clinical practice. Instead of questioning the necessity of next-generation sequencing in epilepsy patients, contemporary large-scale research focuses on factors such as the size of TNGSP, the comparative advantages of exome or genome-wide sequencing over TNGSP, and the impact of clinical, electrophysiological, and demographic variables on genetic test performance. This study aims to elucidate the demographic and clinical factors influencing the performance of TNGSP in 138 Polish patients with epilepsy, recognizing the pivotal role of genetic testing in guiding patient management and therapy. Methods A retrospective analysis was conducted on patients from a genetic clinic in Poznań, Poland, who underwent commercial gene panel studies at Invitae Corporation (USA) between 2020 and 2022. Patient groups were defined based on the age of onset of the first epileptic seizures, seizure type, gender, fever dependence of seizures, presence of intellectual disability or developmental delay, abnormalities in MRI, and the presence of dysmorphic features or congenital malformations. Seizure classification followed the 2017 ILAE criteria. Results Among the 138 patients, 30 (21.7%) exhibited a pathogenic or likely pathogenic variant, with a distribution of 20.7% in males and 22.5% in females. Diagnostic performance correlated with the patient's age at the onset of the first seizure and the type of seizure. Predominant variants were identified in the SCN1A, PRRT2, CDKL5, DEPDC5, TSC2, and SLC2A1 genes. Additionally, 12 genes (CACNA1A, SCN2A, GRIN2A, KCNQ2, CHD2, DYNC1H1, NEXMIF, SCN1B, DDX3X, EEF1A2, NPRL3, UBE3A) exhibited single instances of damage. Notably, novel variants were discovered in DEPDC5, SCN1A, TSC2, CDKL5, NPRL3, DYNC1H1, CHD2, and DDX3X. Discussion Identified variants were present in genes previously recognized in both European and non-European populations. A thorough examination of Variants of Uncertain Significance (VUSs), specifically focusing on gene copy number changes, may unveil more extensive chromosomal aberrations. The relatively frequent occurrence of pathological variants in X chromosome-linked genes in girls warrants further investigation, challenging the prevailing notion of male predominance in X-linked epilepsy.
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Affiliation(s)
- Magdalena Badura-Stronka
- Chair and Department of Medical Genetics, Poznan University of Medical Sciences, Poznań, Poland
- Centers for Medical Genetics GENESIS, Poznań, Poland
| | - Katarzyna Wołyńska
- Chair and Department of Medical Genetics, Poznan University of Medical Sciences, Poznań, Poland
| | - Anna Winczewska-Wiktor
- Chair and Department of Developmental Neurology, Poznan University of Medical Sciences, Poznań, Poland
| | - Justyna Marcinkowska
- Chair and Department of Informatics and Statistics, Poznan University of Medical Sciences, Poznań, Poland
| | | | | | | | | | | | - Barbara Steinborn
- Chair and Department of Developmental Neurology, Poznan University of Medical Sciences, Poznań, Poland
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Ciesielski TH, Sirugo G, Iyengar SK, Williams SM. Characterizing the pathogenicity of genetic variants: the consequences of context. NPJ Genom Med 2024; 9:3. [PMID: 38195641 PMCID: PMC10776585 DOI: 10.1038/s41525-023-00386-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Affiliation(s)
- Timothy H Ciesielski
- The Department of Population and Quantitative Health Sciences at Case Western Reserve University School of Medicine, Cleveland, OH, USA.
- Mary Ann Swetland Center for Environmental Health at Case Western Reserve University School of Medicine, Cleveland, OH, USA.
- Ronin Institute, Montclair, NJ, USA.
| | - Giorgio Sirugo
- The Department of Population and Quantitative Health Sciences at Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Institute of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Translational Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sudha K Iyengar
- The Department of Population and Quantitative Health Sciences at Case Western Reserve University School of Medicine, Cleveland, OH, USA
- The Department of Genetics and Genome Sciences at Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Cleveland, OH, USA
| | - Scott M Williams
- The Department of Population and Quantitative Health Sciences at Case Western Reserve University School of Medicine, Cleveland, OH, USA
- The Department of Genetics and Genome Sciences at Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Cleveland, OH, USA
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Cheng J, Li T, Tan Q, Fu J, Zhang L, Yang L, Zhou B, Yang L, Fu S, Linehan AG, Fu J. Novel, pathogenic insertion variant of GSDME associates with autosomal dominant hearing loss in a large Chinese pedigree. J Cell Mol Med 2024; 28:e18004. [PMID: 37864300 PMCID: PMC10805510 DOI: 10.1111/jcmm.18004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 09/15/2023] [Accepted: 10/10/2023] [Indexed: 10/22/2023] Open
Abstract
Nonsyndromic hearing loss (NSHL) is a genetically diverse, highly heterogeneous condition characterised by deafness, and Gasdermin E (GSDME) variants have been identified as directly inducing autosomal dominant NSHL. While many NSHL cases associated with GSDME involve the skipping of exon 8, there is another, less understood pathogenic insertion variant specifically found in Chinese pedigrees that causes deafness, known as autosomal dominant 5 (DFNA5) hearing loss. In this study, we recruited a large Chinese pedigree, conducted whole-exome and Sanger sequencing to serve as a comprehensive clinical examination, and extracted genomic DNA samples for co-segregation analysis of the members. Conservation and expression analyses for GSDME were also conducted. Our clinical examinations revealed an autosomal dominant phenotype of hearing loss in the family. Genetic analysis identified a novel insertion variant in GSDME exon 8 (GSDME: NM_004403.3: c.1113_1114insGGGGTGCAGCTTACAGGGTGGGTGT: p. P372fs*36). This variant is segregated with the deafness phenotype of this pedigree. The GSDME gene was highly conserved in the different species we analysed, and its mRNA expression was ubiquitously low in different human tissues. In conclusion, we have successfully identified a novel pathogenic insertion variant of GSDME in a Chinese pedigree that causes deafness, shedding light on the genetic basis of hearing loss within this specific family. Our findings expand the spectrum of known variants associated with GSDME-related deafness and may further support both the underlying gain-of-function mechanism and functional associations of GSDME hearing loss variants.
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Affiliation(s)
- Jingliang Cheng
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical MedicineSouthwest Medical UniversityLuzhouChina
| | - Ting Li
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical MedicineSouthwest Medical UniversityLuzhouChina
| | - Qi Tan
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical MedicineSouthwest Medical UniversityLuzhouChina
| | - Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical MedicineSouthwest Medical UniversityLuzhouChina
| | - Lianmei Zhang
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical MedicineSouthwest Medical UniversityLuzhouChina
- Department of PathologyThe Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical UniversityHuai'anChina
| | - Luquan Yang
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical MedicineSouthwest Medical UniversityLuzhouChina
| | - Baixu Zhou
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical MedicineSouthwest Medical UniversityLuzhouChina
- Department of Gynecology and ObstetricsGuangdong Women and Children HospitalGuangzhouChina
| | - Lisha Yang
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical MedicineSouthwest Medical UniversityLuzhouChina
- Department of ObstetricsThe Affiliated Hospital of Southwest Medical UniversityLuzhouChina
| | - Shangyi Fu
- Department of Molecular and Human GeneticsHuman Genome Sequencing Center, Baylor College of MedicineHoustonTexasUSA
| | | | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical MedicineSouthwest Medical UniversityLuzhouChina
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Zemorshidi F, Töpf A, Claeys KG, McFarlane A, Patton A, Nafissi S, Straub V. Novel OBSCN variants associated with a risk to exercise-intolerance and rhabdomyolysis. Neuromuscul Disord 2024; 34:83-88. [PMID: 38159459 DOI: 10.1016/j.nmd.2023.10.013] [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: 03/26/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 01/03/2024]
Abstract
Obscurin, encoded by the OBSCN gene, is a muscle protein consisting of three main splice isoforms, obscurin-A, obscurin-B, and obscurin kinase-only protein (also known as KIAA1639 or Obsc-kin). Obscurin is located at the M-band and Z-disks and interacts with titin and myomesin. It plays an important role in the stability and maintenance of the A- and M-bands and the subsarcolemmal organization of the microtubule network. Furthermore, obscurin is involved in Ca2+ regulation and sarcoplasmic reticulum function and is connected to several other muscle proteins. OBSCN gene variants have been reported to be relatively common in inherited cardiomyopathies. Here we reported two young patients with a history of cramps, myalgia, exercise intolerance, rhabdomyolysis, and myoglobinuria without any evidence of concomitant cardiomyopathy in association with novel OBSCN variants (c.24822C>A and c.2653+1G>C). Obscurin-deficient muscle fibers seem to have increased susceptibility to damage triggered by exercise that may lead to rhabdomyolysis. More studies are needed to clarify the diverse clinical phenotypes and the pathophysiology of OBSCN gene variants.
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Affiliation(s)
- Fariba Zemorshidi
- Neuromuscular Research Center, Tehran University of Medical Sciences, Iran; Department of Neurology, Shariati Hospital,Tehran University of Medical Sciences, Tehran, Iran; Department of Neurology, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Kristl G Claeys
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium; Laboratory for Muscle Diseases and Neuropathies, Department of Neurosciences, KU Leuven, and Leuven Brain Institute (LBI), Leuven, Belgium
| | - Adam McFarlane
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Annabel Patton
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Shahriar Nafissi
- Neuromuscular Research Center, Tehran University of Medical Sciences, Iran; Department of Neurology, Shariati Hospital,Tehran University of Medical Sciences, Tehran, Iran.
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
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Alonso‐Luna O, Mercado‐Celis GE, Melendez‐Zajgla J, Barquera R, Zapata‐Tarres M, Juárez‐Villegas LE, Mendoza‐Caamal EC, Rey‐Helo E, Borges‐Yañez SA. Germline mutations in pediatric cancer cohort with mixed-ancestry Mexicans. Mol Genet Genomic Med 2024; 12:e2332. [PMID: 38093606 PMCID: PMC10767611 DOI: 10.1002/mgg3.2332] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/11/2023] [Accepted: 11/28/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND Childhood cancer is one of the primary causes of disease-related death in 5- to 14-year-old children and currently no prevention strategies exist to reduce the incidence of this disease. Childhood cancer has a larger hereditary component compared with cancer in adults. Few genetic studies have been conducted on children with cancer. Additionally, Latin American populations are underrepresented in genomic studies compared with other populations. Therefore, the aim of this study is to analyze germline mutations in a group of mixed-ancestry Mexican pediatric patients with solid and hematological cancers. METHODS We analyzed genetic variants from 40 Mexican childhood cancer patients and their relatives. DNA from saliva or blood samples was used for whole-exome sequencing. All variants were identified following GATK best practices. RESULTS We found that six patients (15%) were carriers of germline mutations in CDKN2A, CHEK2, DICER1, FANCA, MSH6, MUTYH, NF1, and SBDS cancer predisposition genes, and additional new variants predicted to be deleterious by in silico algorithms. A population genetics analysis detected five components consistent with the demographic models assumed for modern mixed-ancestry Mexicans. CONCLUSIONS This report identifies potential genetic risk factors and provides a better understanding of the underlying mechanisms of childhood cancer in this population.
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Grants
- 365882 Consejo Nacional de Ciencia y Tecnología, CONACyT, Mexico
- 253316 Consejo Nacional de Ciencia y Tecnología, CONACyT, Mexico
- Fundacion Carlos Slim as part of the inaugural phase of Slim Initiative in Genomic Medicine for the Americas, SIGMA
- Broad Institute of MIT and Harvard
- Instituto Nacional de Medicina Genomica (INMEGEN)
- Division de Estudios de Posgrado e Investigacion de la Facultad de Odontologia
- Programa de Maestria y Doctorado en Ciencias Medicas, Odontologicas y de la Salud, UNAM
- "Aqui nadie se rinde, ANSER (I.A.P)
- Max Planck Institute for Evolutionary Anthropology (MPI-EVA)
- Consejo Nacional de Ciencia y Tecnología, CONACyT, Mexico
- Max Planck Institute for Evolutionary Anthropology (MPI‐EVA)
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Affiliation(s)
- Oscar Alonso‐Luna
- Programa de Maestria y Doctorado en Ciencias Medicas, Odontologicas y de la SaludCiudad Universitaria, Universidad Nacional Autonoma de MexicoMexico CityMexico
| | | | - Jorge Melendez‐Zajgla
- Laboratorio de Genomica Funcional del CancerInstituto Nacional de Medicina GenomicaMexico CityMexico
| | - Rodrigo Barquera
- Department of ArchaeogeneticsMax Plank Institute for Evolutionary Anthropology (MPI‐EVA)LeipzigGermany
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Hurník P, Režnarová J, Chyra Z, Motyka O, Putnová BM, Čermáková Z, Blažek T, Fománek M, Gaykalova D, Buchtová M, Ševčíková T, Štembírek J. Enhancing oral squamous cell carcinoma prediction: the prognostic power of the worst pattern of invasion and the limited impact of molecular resection margins. Front Oncol 2023; 13:1287650. [PMID: 38188288 PMCID: PMC10766711 DOI: 10.3389/fonc.2023.1287650] [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: 09/02/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Objective Oral squamous cell carcinoma (OSCC) originates from the mucosal lining of the oral cavity. Almost half of newly diagnosed cases are classified as advanced stage IV disease, which makes resection difficult. In this study, we investigated the pathological features and mutation profiles of tumor margins in OSCC. Methods We performed hierarchical clustering of principal components to identify distinct patterns of tumor growth and their association with patient prognosis. We also used next-generation sequencing to analyze somatic mutations in tumor and marginal tissue samples. Results Our analyses uncovered that the grade of worst pattern of invasion (WPOI) is strongly associated with depth of invasion and patient survival in multivariable analysis. Mutations were primarily detected in the DNA isolated from tumors, but several mutations were also identified in marginal tissue. In total, we uncovered 29 mutated genes, mainly tumor suppressor genes involved in DNA repair including BRCA genes; however none of these mutations significantly correlated with a higher chance of relapse in our medium-size cohort. Some resection margins that appeared histologically normal harbored tumorigenic mutations in TP53 and CDKN2A genes. Conclusion Even histologically normal margins may contain molecular alterations that are not detectable by conventional histopathological methods, but NCCN classification system still outperforms other methods in the prediction of the probability of disease relapse.
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Affiliation(s)
- Pavel Hurník
- Institute of Clinical and Molecular Pathology, University Hospital Ostrava, Ostrava, Czechia
- Institute of Clinical and Molecular Pathology, Faculty of Medicine, University of Ostrava, Ostrava, Czechia
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Jana Režnarová
- Department of Oral and Maxillofacial Surgery, University Hospital Ostrava, Ostrava, Czechia
- Department of Craniofacial Surgery, Faculty of Medicine, Ostrava University, Ostrava, Ostrava, Czechia
| | - Zuzana Chyra
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czechia
| | - Oldřich Motyka
- Department of Environmental Engineering, VSB-Technical University of Ostrava, Ostrava, Czechia
| | - Barbora Moldovan Putnová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia
- Department of Pathological Morphology and Parasitology, University of Veterinary Sciences Brno, Brno, Czechia
| | - Zuzana Čermáková
- Department of Oncology, University Hospital Ostrava, Ostrava, Czechia
| | - Tomáš Blažek
- Department of Oncology, University Hospital Ostrava, Ostrava, Czechia
| | - Martin Fománek
- Department of Otorhinolaryngology, University Hospital Ostrava, Ostrava, Czechia
| | - Daria Gaykalova
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Otorhinolaryngology-Head and Neck Surgery, Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, United States
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, United States
| | - Marcela Buchtová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Tereza Ševčíková
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czechia
| | - Jan Štembírek
- Department of Oral and Maxillofacial Surgery, University Hospital Ostrava, Ostrava, Czechia
- Department of Craniofacial Surgery, Faculty of Medicine, Ostrava University, Ostrava, Ostrava, Czechia
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia
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Tirendi S, Domenicotti C, Bassi AM, Vernazza S. Genetics and Glaucoma: the state of the art. Front Med (Lausanne) 2023; 10:1289952. [PMID: 38152303 PMCID: PMC10751926 DOI: 10.3389/fmed.2023.1289952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023] Open
Abstract
Glaucoma is the second leading cause of irreversible blindness worldwide. Although genetic background contributes differently to rare early-onset glaucoma (before age 40) or common adult-onset glaucoma, it is now considered an important factor in all major forms of the disease. Genetic and genomic studies, including GWAS, are contributing to identifying novel loci associated with glaucoma or to endophenotypes across ancestries to enrich the knowledge about glaucoma genetic susceptibility. Moreover, new high-throughput functional genomics contributes to defining the relevance of genetic results in the biological pathways and processes involved in glaucoma pathogenesis. Such studies are expected to advance significantly our understanding of glaucoma's genetic basis and provide new druggable targets to treat glaucoma. This review gives an overview of the role of genetics in the pathogenesis or risk of glaucoma.
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Affiliation(s)
- Sara Tirendi
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
- Inter-University Center for the Promotion of the 3Rs Principles in Teaching & Research (Centro 3R), Genoa, Italy
| | - Cinzia Domenicotti
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
- Inter-University Center for the Promotion of the 3Rs Principles in Teaching & Research (Centro 3R), Genoa, Italy
| | - Anna Maria Bassi
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
- Inter-University Center for the Promotion of the 3Rs Principles in Teaching & Research (Centro 3R), Genoa, Italy
| | - Stefania Vernazza
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
- Inter-University Center for the Promotion of the 3Rs Principles in Teaching & Research (Centro 3R), Genoa, Italy
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45
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Joris S, Denys H, Collignon J, Rasschaert M, T'Kint de Roodenbeke D, Duhoux FP, Canon JL, Tejpar S, Mebis J, Decoster L, Aftimos P, De Grève J. Efficacy of olaparib in advanced cancers with germline or somatic mutations in BRCA1, BRCA2, CHEK2 and ATM, a Belgian Precision tumor-agnostic phase II study. ESMO Open 2023; 8:102041. [PMID: 37852034 PMCID: PMC10774963 DOI: 10.1016/j.esmoop.2023.102041] [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: 06/29/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/20/2023] Open
Abstract
BACKGROUND The Belgian Precision initiative aims to maximize the implementation of tumor-agnostic next-generation sequencing in patients with advanced cancer and enhance access to molecularly guided treatment options. Academic tumor-agnostic basket phase II studies are part of this initiative. The current investigator-driven trial aimed to investigate the efficacy of olaparib in advanced cancers with a (likely) pathogenic mutation (germline or somatic) in a gene that plays a role in homologous recombination (HR). PATIENTS AND METHODS This open-label, multi-cohort, phase II study examines the efficacy of olaparib in patients with an HR gene mutation in their tumor and disease progression on standard of care. Patients with a somatic or germline mutation in the same gene define a cohort. For each cohort, a Simon minimax two-stage design was used. If a response was observed in the first 13 patients, 14 additional patients were included. Here, we report the results on four completed cohorts: patients with a BRCA1, BRCA2, CHEK2 or ATM mutation. RESULTS The overall objective response rate across different tumor types was 11% in the BRCA1-mutated (n = 27) and 21% in the BRCA2-mutated (n = 27) cohorts. Partial responses were seen in pancreatic cancer, gallbladder cancer, endocrine carcinoma of the pancreas and parathyroid cancer. One patient with a BRCA2 germline-mutated colon cancer has an ongoing complete response with 19+ months on treatment. Median progression-free survival in responding patients was 14+ months (5-34+ months). The clinical benefit rate was 63% in the BRCA1-mutated and 46% in the BRCA2-mutated cohorts. No clinical activity was observed in the ATM (n = 13) and CHEK2 (n = 14) cohorts. CONCLUSION Olaparib showed efficacy in different cancer types harboring somatic or germline mutations in the BRCA1/2 genes but not in ATM and CHEK2. Patients with any cancer type harboring BRCA1/2 mutations should have access to olaparib.
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Affiliation(s)
- S Joris
- Department of Medical Oncology, UZ Brussel, Brussels.
| | - H Denys
- Department of Medical Oncology, University Hospital Ghent, Ghent
| | | | | | | | - F P Duhoux
- Cliniques universitaires Saint-Luc, Brussels
| | | | | | | | - L Decoster
- Department of Medical Oncology, UZ Brussel, Brussels
| | - P Aftimos
- Institut Jules Bordet-Université libre de Bruxelles, Brussels
| | - J De Grève
- Department of Medical Oncology, UZ Brussel, Brussels; Department of Medical Genetics, UZ Brussel, Brussels, Belgium
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46
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Civelek Ürey B, Ceylan AC, Çavdarlı B, Çıtak Kurt AN, Kıreker Köylü O, Yürek B, Kasapkara ÇS. Laboratory and Genotype Relationship of Patients with SDHA-Related Mitochondrial Disease. Mol Syndromol 2023; 14:459-460. [PMID: 38058758 PMCID: PMC10697767 DOI: 10.1159/000531668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 12/08/2023] Open
Affiliation(s)
| | | | | | | | | | - Burak Yürek
- Pediatric Metabolism, Ankara City Hospital, Ankara, Turkey
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47
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Li L, Xie Y, Zeng S, Li X, Lin Z, Huang S, Zhao H, Cao W, Liu L, Liu J, Rong P, Zhang R. Expanding the genetic and clinical spectrum of SORD-related peripheral neuropathy by reporting a novel variant c.210T>G and evidence of subclinical muscle involvement. J Peripher Nerv Syst 2023; 28:608-613. [PMID: 37584201 DOI: 10.1111/jns.12591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 08/08/2023] [Accepted: 08/11/2023] [Indexed: 08/17/2023]
Abstract
BACKGROUND AND AIMS Biallelic variants in the sorbitol dehydrogenase (SORD) gene have been identified as the genetic cause of autosomal recessive (AR) peripheral neuropathy (PN) manifesting as Charcot-Marie-Tooth disease type 2 (CMT2) or distal hereditary motor neuropathy (dHMN). We aim to observe the genetic and clinical spectrum of a cohort of patients with SORD-related PN (SORD-PN). METHODS A total of 107 patients with AR or sporadic CMT2/dHMN underwent molecular diagnosis by whole-exome sequencing and subsequent Sanger sequencing validation. Available phenotypic data for SORD-PN were collected and analyzed. RESULTS Eleven (10.28%) of 107 patients were identified as SORD-PN, including four with CMT2 and seven with dHMN. The SORD variant c.210 T > G;p.His70Gln in F-d3 was firstly reported and subsequent analysis showed that it resulted in loss of SORD enzyme function. Evidence of subclinical muscle involvement was frequently detected in patients with SORD-PN, including mildly to moderately elevated serum creatine kinase (CK) levels in 10 patients, myogenic electrophysiological changes in one patient, and muscle edema in five patients undergoing lower extremity MRI. Fasting serum sorbitol level was 88-fold higher in SORD-PN patients (9.69 ± 1.07 mg/L) than in healthy heterozygous subjects (0.11 ± 0.01 mg/L) and 138-fold higher than in healthy controls (0.07 ± 0.02 mg/L). INTERPRETATION The novel SORD variant c.210 T > G;p.His70Gln and evidence of subclinical muscle involvement were identified, which expanded the genetic and clinical spectrum of SORD-PN. Subclinical muscle involvement might be a common but easily overlooked clinical feature. The serum CK and fasting serum sorbitol levels were expected to be sensitive biomarkers confirmed by follow-up cohort study.
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Affiliation(s)
- Lu Li
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yongzhi Xie
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Sen Zeng
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiaobo Li
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhiqiang Lin
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Shunxiang Huang
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Huadong Zhao
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Wanqian Cao
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Lei Liu
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Jun Liu
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Pengfei Rong
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ruxu Zhang
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
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48
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Sutinen A, Jones NC, Hoffmann SV, Ruskamo S, Kursula P. Conformational analysis of membrane-proximal segments of GDAP1 in a lipidic environment using synchrotron radiation suggests a mode of assembly at the mitochondrial outer membrane. Biophys Chem 2023; 303:107113. [PMID: 37778197 DOI: 10.1016/j.bpc.2023.107113] [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: 07/10/2023] [Revised: 09/19/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
The mitochondrial outer membrane creates a diffusion barrier between the cytosol and the mitochondrial intermembrane space, allowing the exchange of metabolic products, important for efficient mitochondrial function in neurons. The ganglioside-induced differentiation-associated protein 1 (GDAP1) is a mitochondrial outer membrane protein with a critical role in mitochondrial dynamics and metabolic balance in neurons. Missense mutations in the GDAP1 gene are linked to the most common human peripheral neuropathy, Charcot-Marie-Tooth disease (CMT). GDAP1 is a distant member of the glutathione-S-transferase (GST) superfamily, with unknown enzymatic properties or functions at the molecular level. The structure of the cytosol-facing GST-like domain has been described, but there is no consensus on how the protein interacts with the mitochondrial outer membrane. Here, we describe a model for GDAP1 assembly on the membrane using peptides vicinal to the GDAP1 transmembrane domain. We used oriented circular dichroism spectroscopy (OCD) with synchrotron radiation to study the secondary structure and orientation of GDAP1 segments at the outer and inner surfaces of the outer mitochondrial membrane. These experiments were complemented by small-angle X-ray scattering, providing the first experimental structural models for full-length human GDAP1. The results indicate that GDAP1 is bound into the membrane via a single transmembrane helix, flanked by two peripheral helices interacting with the outer and inner leaflets of the mitochondrial outer membrane in different orientations. Impairment of these interactions could be a mechanism for CMT in the case of missense mutations affecting these segments instead of the GST-like domain.
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Affiliation(s)
- Aleksi Sutinen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | | | - Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland; Department of Biomedicine, University of Bergen, Bergen, Norway.
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49
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Abstract
Calcium ions (Ca2+) are the basis of a unique and potent array of cellular responses. Calmodulin (CaM) is a small but vital protein that is able to rapidly transmit information about changes in Ca2+ concentrations to its regulatory targets. CaM plays a critical role in cellular Ca2+ signaling, and interacts with a myriad of target proteins. Ca2+-dependent modulation by CaM is a major component of a diverse array of processes, ranging from gene expression in neurons to the shaping of the cardiac action potential in heart cells. Furthermore, the protein sequence of CaM is highly evolutionarily conserved, and identical CaM proteins are encoded by three independent genes (CALM1-3) in humans. Mutations within any of these three genes may lead to severe cardiac deficits including severe long QT syndrome (LQTS) and/or catecholaminergic polymorphic ventricular tachycardia (CPVT). Research into disease-associated CaM variants has identified several proteins modulated by CaM that are likely to underlie the pathogenesis of these calmodulinopathies, including the cardiac L-type Ca2+ channel (LTCC) CaV1.2, and the sarcoplasmic reticulum Ca2+ release channel, ryanodine receptor 2 (RyR2). Here, we review the research that has been done to identify calmodulinopathic CaM mutations and evaluate the mechanisms underlying their role in disease.
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Affiliation(s)
- John W. Hussey
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Worawan B. Limpitikul
- Department of Medicine, Division of Cardiology, Massachusetts General Hospital, Boston, MA, USA
| | - Ivy E. Dick
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, USA
- CONTACT Ivy E. Dick School of Medicine, University of Maryland, Baltimore, MD21210
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50
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Gurnari C, Robin M, Godley LA, Drozd-Sokołowska J, Włodarski MW, Raj K, Onida F, Worel N, Ciceri F, Carbacioglu S, Kenyon M, Aljurf M, Bonfim C, Makishima H, Niemeyer C, Fenaux P, Zebisch A, Hamad N, Chalandon Y, Hellström-Lindberg E, Voso MT, Mecucci C, Duarte FB, Sebert M, Sicre de Fontbrune F, Soulier J, Shimamura A, Lindsley RC, Maciejewski JP, Calado RT, Yakoub-Agha I, McLornan DP. Germline predisposition traits in allogeneic hematopoietic stem-cell transplantation for myelodysplastic syndromes: a survey-based study and position paper on behalf of the Chronic Malignancies Working Party of the EBMT. Lancet Haematol 2023; 10:e994-e1005. [PMID: 37898151 DOI: 10.1016/s2352-3026(23)00265-x] [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: 05/24/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 10/30/2023]
Abstract
The recent application of whole exome or whole genome sequencing unveiled a plethora of germline variants predisposing to myeloid disorders, particularly myelodysplastic neoplasms. The presence of such variants in patients with myelodysplastic syndromes has important clinical repercussions for haematopoietic stem-cell transplantation, from donor selection and conditioning regimen to graft-versus-host disease prophylaxis and genetic counselling for relatives. No international guidelines exist to harmonise management approaches to this particular clinical scenario. Moreover, the application of germline testing, and how this informs clinical decisions, differs according to the expertise of individual clinical practices and according to different countries, health-care systems, and legislations. Leveraging the global span of the European Society for Blood and Marrow Transplantation (EBMT) network, we took a snapshot of the current European situation on these matters by disseminating an electronic survey to EBMT centres experienced in myelodysplastic syndromes transplantation. An international group of haematologists, transplantation physicians, paediatricians, nurses, and experts in molecular biology and constitutional genetics with experience in myelodysplastic syndromes contributed to this Position Paper. The panel met during multiple online meetings to discuss the results of the EBMT survey and to establish suggested harmonised guidelines for such clinical situations, which are presented here.
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Affiliation(s)
- Carmelo Gurnari
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy; Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Marie Robin
- Department of Hematology and Bone Marrow Transplantation, Hôpital Saint-Louis, AP-HP, University Paris, Paris, France
| | - Lucy A Godley
- Section of Hematology and Oncology, Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Joanna Drozd-Sokołowska
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Marcin W Włodarski
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Kavita Raj
- University College London NHS Foundation Trust, London, UK
| | - Francesco Onida
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Nina Worel
- Department of Transfusion Medicine and Cell Therapy, Medical University of Vienna, Vienna, Austria
| | | | - Selim Carbacioglu
- Department of Paediatric Oncology, Haematology and Stem Cell Transplantation, University Children's Hospital Regensburg, Regensburg, Germany
| | - Michelle Kenyon
- Department of Haematological Medicine, King's College Hospital NHS Foundation Trust, London, UK
| | - Mahmoud Aljurf
- Division of Hematology, Stem Cell Transplantation and Cellular Therapy, Oncology Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Carmem Bonfim
- Pediatric Blood and Marrow Transplantation Division and Pele Pequeno Principe Research Institute, Hospital Pequeno Principe, Curitiba, Brazil
| | - Hideki Makishima
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Charlotte Niemeyer
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Pierre Fenaux
- Department of Hematology and Bone Marrow Transplantation, Hôpital Saint-Louis, AP-HP, University Paris, Paris, France; INSERM U944, CNRS UMR7212, Paris, France; Saint-Louis Hospital, Hematology Laboratory, AP-HP, Paris, France
| | - Armin Zebisch
- Division of Hematology and Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Division of Pharmacology, Medical University of Graz, Graz, Austria
| | - Nada Hamad
- Department of Hematology, St Vincent's Hospital Sydney, NSW, Australia
| | - Yves Chalandon
- Division of Hematology, Bone Marrow Transplant Unit, University Hospital of Geneva and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Eva Hellström-Lindberg
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet and Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Teresa Voso
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Cristina Mecucci
- Institute of Hematology and Center for Hemato-Oncology Research, University and Hospital of Perugia, Perugia, Italy
| | | | - Marie Sebert
- Department of Hematology and Bone Marrow Transplantation, Hôpital Saint-Louis, AP-HP, University Paris, Paris, France; INSERM U944, CNRS UMR7212, Paris, France; Saint-Louis Hospital, Hematology Laboratory, AP-HP, Paris, France
| | - Flore Sicre de Fontbrune
- Department of Hematology and Bone Marrow Transplantation, Hôpital Saint Louis, AP-HP, Université Paris Cité, Centre National de Reference des Aplasies Médullaires Acquises et Constitutionnelles, Paris, France
| | - Jean Soulier
- INSERM U944, CNRS UMR7212, Paris, France; Saint-Louis Hospital, Hematology Laboratory, AP-HP, Paris, France
| | - Akiko Shimamura
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | | | - Jarosław P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Rodrigo T Calado
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Brazil
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