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Garrido-Sanchez L, Leiva-Badosa E, Llop-Talaveron J, Pintó-Sala X, Lozano-Andreu T, Corbella-Inglés E, Alia-Ramos P, Arias-Barquet L, Ramon-Torrel JM, Badía-Tahull MB. Blood Phytosterol Concentration and Genetic Variant Associations in a Sample Population. Nutrients 2024; 16:1067. [PMID: 38613098 PMCID: PMC11013666 DOI: 10.3390/nu16071067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024] Open
Abstract
The main objective of this study was to determine plasma levels of PS and to study SNVs rs41360247, rs4245791, rs4148217, and rs11887534 of ABCG8 and the r657152 SNV at the ABO blood group locus in a sample of a population treated at our hospital, and to determine whether these SNVs are related to plasma PS concentrations. The secondary objective was to establish the variables associated with plasma PS concentrations in adults. Participants completed a dietary habit questionnaire and a blood sample was collected to obtain the following variables: campesterol, sitosterol, sitostanol, lanosterol, stigmasterol, biochemical parameters, and the SNVs. In addition, biometric and demographic variables were also recorded. In the generalized linear model, cholesterol and age were positively associated with total PS levels, while BMI was negatively related. For rs4245791, homozygous T allele individuals showed a significantly lower campesterol concentration compared with C homozygotes, and the GG alleles of rs657152 had the lowest levels of campesterol compared with the other alleles of the SNV. Conclusions: The screening of certain SNVs could help prevent the increase in plasma PS and maybe PNALD in some patients. However, further studies on the determinants of plasma phytosterol concentrations are needed.
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Affiliation(s)
- Leticia Garrido-Sanchez
- Pharmacy Department, Hospital Universitari Bellvitge, IDIBELL, Universitat Barcelona, 08907 L’Hospitalet de Llobregat, Spain
| | - Elisabet Leiva-Badosa
- Pharmacy Department, Hospital Universitari Bellvitge, IDIBELL, Universitat Barcelona, 08907 L’Hospitalet de Llobregat, Spain
| | - Josep Llop-Talaveron
- Pharmacy Department, Hospital Universitari Bellvitge, IDIBELL, Universitat Barcelona, 08907 L’Hospitalet de Llobregat, Spain
| | - Xavier Pintó-Sala
- Cardiovascular Risk Unit, Internal Medicine, Hospital Universitari de Bellvitge, IDIBELL, Universitat Barcelona, 08907 L’Hospitalet de Llobregat, Spain; (X.P.-S.)
| | - Toni Lozano-Andreu
- Pharmacy Department, Institut Català d’Oncologia, IDIBELL, Universitat Barcelona, 08907 L’Hospitalet de Llobregat, Spain
| | - Emili Corbella-Inglés
- Cardiovascular Risk Unit, Internal Medicine, Hospital Universitari de Bellvitge, IDIBELL, Universitat Barcelona, 08907 L’Hospitalet de Llobregat, Spain; (X.P.-S.)
| | - Pedro Alia-Ramos
- Clinical Laboratory Department, Hospital Universitari Bellvitge, IDIBELL, Universitat Barcelona, 08907 L’Hospitalet de Llobregat, Spain
| | - Lluis Arias-Barquet
- Ophthalmology Department, Hospital Universitari Bellvitge, IDIBELL, Universitat Barcelona, 08907 L’Hospitalet de Llobregat, Spain
| | - Josep Maria Ramon-Torrel
- Preventive Medicine Department, Hospital Universitari Bellvitge, IDIBELL, Universitat Barcelona, 08907 L’Hospitalet de Llobregat, Spain
| | - Maria B. Badía-Tahull
- Pharmacy Department, Hospital Universitari Bellvitge, IDIBELL, Universitat Barcelona, 08907 L’Hospitalet de Llobregat, Spain
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Camps-Vilaró A, Pinsach-Abuin ML, Degano IR, Ramos R, Martí-Lluch R, Elosua R, Subirana I, Solà-Richarte C, Puigmulé M, Pérez A, Vilaró I, Cruz R, Diz-de Almeida S, Nogues X, Masclans JR, Güerri-Fernández R, Marin J, Tizon-Marcos H, Vaquerizo B, Brugada R, Marrugat J. Genetic characteristics involved in COVID-19 severity. The CARGENCORS case-control study and meta-analysis. J Med Virol 2024; 96:e29404. [PMID: 38293834 DOI: 10.1002/jmv.29404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/30/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024]
Abstract
Pre-existing coronary artery disease (CAD), and thrombotic, inflammatory, or virus infectivity response phenomena have been associated with COVID-19 disease severity. However, the association of candidate single nucleotide variants (SNVs) related to mechanisms of COVID-19 complications has been seldom analysed. Our aim was to test and validate the effect of candidate SNVs on COVID-19 severity. CARGENCORS (CARdiovascular GENetic risk score for Risk Stratification of patients positive for SARS-CoV-2 [COVID-19] virus) is an age- and sex-matched case-control study with 818 COVID-19 cases hospitalized with hypoxemia, and 1636 controls with COVID-19 treated at home. The association between severity and SNVs related to CAD (n = 32), inflammation (n = 19), thrombosis (n = 14), virus infectivity (n = 11), and two published to be related to COVID-19 severity was tested with adjusted logistic regression models. Two external independent cohorts were used for meta-analysis (SCOURGE and UK Biobank). After adjustment for potential confounders, 14 new SNVs were associated with COVID-19 severity in the CARGENCORS Study. These SNVs were related to CAD (n = 10), thrombosis (n = 2), and inflammation (n = 2). We also confirmed eight SNVs previously related to severe COVID-19 and virus infectivity. The meta-analysis showed five SNVs associated with severe COVID-19 in adjusted analyses (rs11385942, rs1561198, rs6632704, rs6629110, and rs12329760). We identified 14 novel SNVs and confirmed eight previously related to COVID-19 severity in the CARGENCORS data. In the meta-analysis, five SNVs were significantly associated to COVID-19 severity, one of them previously related to CAD.
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Affiliation(s)
- Anna Camps-Vilaró
- Registre Gironí del Cor (REGICOR) Study Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Doctoral College, University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
| | - Mel Lina Pinsach-Abuin
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IdIBGi), Salt, Spain
| | - Irene R Degano
- Registre Gironí del Cor (REGICOR) Study Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- Institute for Research and Innovation in Life Sciences and Health in Central Catalonia (IRIS-CC), Vic, Spain
| | - Rafel Ramos
- Medical Science Department, School of Medicine, University of Girona, Girona, Spain
- Vascular Health Research Group, Institut Universitari per a la Recerca en Atenció Primària Jordi Gol i Gurina, Girona, Spain
- Girona Biomedical Research Institute, Girona, Spain
- Primary Care Services, Catalan Institute of Health, Girona, Spain
| | - Ruth Martí-Lluch
- Vascular Health Research Group, Institut Universitari per a la Recerca en Atenció Primària Jordi Gol i Gurina, Girona, Spain
- Girona Biomedical Research Institute, Girona, Spain
| | - Roberto Elosua
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- Cardiovascular Epidemiology and Genetics Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Isaac Subirana
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Cardiovascular Epidemiology and Genetics Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Clàudia Solà-Richarte
- Registre Gironí del Cor (REGICOR) Study Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Marta Puigmulé
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
| | - Alexandra Pérez
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IdIBGi), Salt, Spain
| | | | - Raquel Cruz
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - Silvia Diz-de Almeida
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - Xavier Nogues
- Musculoskeletal Research Unit, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Internal Medicine, Hospital del Mar, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable, Instituto de Salud Carlos III, Madrid, Spain
- Department of Medicine, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Joan R Masclans
- Critical Illness Research Group (GREPAC), Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Critical Care, Hospital del Mar, Barcelona, Spain
- Medicine and Life Sciences department, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Roberto Güerri-Fernández
- Department of Medicine, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Department of Infectious Diseases, Hospital del Mar Research Institute, Barcelona, Spain
| | - Judith Marin
- Critical Illness Research Group (GREPAC), Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Critical Care, Hospital del Mar, Barcelona, Spain
| | - Helena Tizon-Marcos
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Biomedical Research in Heart Diseases Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Cardiology, Hospital del Mar, Barcelona, Spain
| | - Beatriz Vaquerizo
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Department of Medicine, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- Biomedical Research in Heart Diseases Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Cardiology, Hospital del Mar, Barcelona, Spain
| | - Ramon Brugada
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IdIBGi), Salt, Spain
- Medical Science Department, School of Medicine, University of Girona, Girona, Spain
- Department of Cardiology, Hospital Josep Trueta & University of Girona, Girona, Spain
| | - Jaume Marrugat
- Registre Gironí del Cor (REGICOR) Study Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
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Campos ACS, Araújo TM, Moraes L, Corrêa dos Santos RA, Goldman GH, Riano-Pachon DM, Oliveira JVDC, Squina FM, Castro IDM, Trópia MJM, da Cunha AC, Rosse IC, Brandão RL. Selected cachaça yeast strains share a genomic profile related to traits relevant to industrial fermentation processes. Appl Environ Microbiol 2024; 90:e0175923. [PMID: 38112453 PMCID: PMC10807443 DOI: 10.1128/aem.01759-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/01/2023] [Indexed: 12/21/2023] Open
Abstract
The isolation and selection of yeast strains to improve the quality of the cachaça-Brazilian Spirit-have been studied in our research group. Our strategy considers Saccharomyces cerevisiae as the predominant species involved in sugarcane juice fermentation and the presence of different stressors (osmolarity, temperature, ethanol content, and competition with other microorganisms). It also considers producing balanced concentrations of volatile compounds (higher alcohols and acetate and/or ethyl esters), flocculation capacity, and ethanol production. Since the genetic bases behind these traits of interest are not fully established, the whole genome sequencing of 11 different Saccharomyces cerevisiae strains isolated and selected from different places was analyzed to identify the presence of a specific genetic variation common to cachaça yeast strains. We have identified 20,128 single-nucleotide variants shared by all genomes. Of these shared variants, 37 were new variants (being six missenses), and 4,451 were identified as missenses. We performed a detailed functional annotation (using enrichment analysis, protein-protein interaction network analysis, and database and in-depth literature searches) of these new and missense variants. Many genes carrying these variations were involved in the phenotypes of flocculation, tolerance to fermentative stresses, and production of volatile compounds and ethanol. These results demonstrate the existence of a genetic profile shared by the 11 strains under study that could be associated with the applied selective strategy. Thus, this study points out genes and variants that may be used as molecular markers for selecting strains well suited to the fermentation process, including genetic improvement by genome editing, ultimately producing high-quality beverages and adding value.IMPORTANCEThis work demonstrates the existence of new genetic markers related to different phenotypes used to select yeast strains and mutations in genes directly involved in producing flavoring compounds and ethanol, and others related to flocculation and stress resistance.
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Affiliation(s)
- Anna Clara Silva Campos
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
| | - Thalita Macedo Araújo
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
- Área de Ciências Biológicas, Instituto Federal de Minas Gerais, Campus Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Lauro Moraes
- Laboratório Multiusuário de Bioinformática, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Renato Augusto Corrêa dos Santos
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
- Laboratório de Biologia Computacional, Evolutiva e de Sistemas, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Diego Maurício Riano-Pachon
- Laboratório de Biologia Computacional, Evolutiva e de Sistemas, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | | | | | - Ieso de Miranda Castro
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
| | - Maria José Magalhães Trópia
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
| | - Aureliano Claret da Cunha
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
- Laboratório de Engenharia de Alimentos, Departamento de Alimentos, Escola de Nutrição, Salvador, Brazil
| | - Izinara C. Rosse
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
- Laboratório Multiusuário de Bioinformática, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Rogelio Lopes Brandão
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
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Shah PW, Reinberger T, Hashmi S, Aherrahrou Z, Erdmann J. MRAS in coronary artery disease-Unchartered territory. IUBMB Life 2024. [PMID: 38251784 DOI: 10.1002/iub.2805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 12/03/2023] [Indexed: 01/23/2024]
Abstract
Genome-wide association studies (GWAS) have identified coronary artery disease (CAD) susceptibility locus on chromosome 3q22.3. This locus contains a cluster of several genes that includes muscle rat sarcoma virus (MRAS). Common MRAS variants are also associated with CAD causing risk factors such as hypertension, dyslipidemia, obesity, and type II diabetes. The MRAS gene is an oncogene that encodes a membrane-bound small GTPase. It is involved in a variety of signaling pathways, regulating cell differentiation and cell survival (mitogen-activated protein kinase [MAPK]/extracellular signal-regulated kinase and phosphatidylinositol 3-kinase) as well as acute phase response signaling (tumor necrosis factor [TNF] and interleukin 6 [IL6] signaling). In this review, we will summarize the role of genetic MRAS variants in the etiology of CAD and its comorbidities with the focus on tissue distribution of MRAS isoforms, cell type/tissue specificity, and mode of action of single nucleotide variants in MRAS associated complex traits. Finally, we postulate that CAD risk variants in the MRAS locus are specific to smooth muscle cells and lead to higher levels of MRAS, particularly in arterial and cardiac tissue, resulting in MAPK-dependent tissue hypertrophy or hyperplasia.
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Affiliation(s)
- Pashmina Wiqar Shah
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
- DZHK (German Research Centre for Cardiovascular Research), Lübeck, Germany
- University Heart Center Lübeck, Lübeck, Germany
| | - Tobias Reinberger
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
- DZHK (German Research Centre for Cardiovascular Research), Lübeck, Germany
- University Heart Center Lübeck, Lübeck, Germany
| | - Satwat Hashmi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Zouhair Aherrahrou
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
- DZHK (German Research Centre for Cardiovascular Research), Lübeck, Germany
- University Heart Center Lübeck, Lübeck, Germany
| | - Jeanette Erdmann
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
- DZHK (German Research Centre for Cardiovascular Research), Lübeck, Germany
- University Heart Center Lübeck, Lübeck, Germany
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Jiménez-Ortega RF, Aparicio-Bautista DI, Becerra-Cervera A, López-Montoya P, León-Reyes G, Flores-Morales J, Castillejos-López M, Hidalgo-Bravo A, Salmerón J, Rivera-Paredez B, Velázquez-Cruz R. Association Study between Antioxidant Nutrient Intake and Low Bone Mineral Density with Oxidative Stress-Single Nucleotide Variants: GPX1 (rs1050450 and rs17650792), SOD2 (rs4880) and CAT (rs769217) in Mexican Women. Antioxidants (Basel) 2023; 12:2089. [PMID: 38136209 PMCID: PMC10740963 DOI: 10.3390/antiox12122089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/29/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Oxidative stress is essential in developing multiple bone metabolism diseases, including osteoporosis. Single-nucleotide variants (SNVs) have been associated with oxidative stress, promoting an imbalance between the production of reactive oxygen species and the ability to neutralize them, and it has been reported that antioxidant nutrient intake can influence bone mineral density (BMD). This work reports the association between oxidative stress-related SNVs (GPX1-rs1050450, rs17650792, SOD2-rs4880, and CAT-rs769217), BMD, and antioxidant nutrient intake. The study included 1269 Mexican women from the Health Workers Cohort Study. Genotyping was performed using predesigned TaqMan assays. Dietary data were collected using a 116-item semi-quantitative food frequency questionnaire. A dietary antioxidant quality score (DAQS) was used to estimate antioxidant-nutrient intake. Association analysis was estimated via linear, logistic, or quantile regression models. The results showed an association of the rs1050450-A and rs17650792-A alleles with femoral neck BMD (p = 0.038 and p = 0.017, respectively) and the SNV rs4880-A allele with total hip BMD (p = 0.026) in respondents aged 45 years or older. In addition, antioxidant-nutrient intake was associated with the rs4880-GG genotype, being significant for fiber (p = 0.007), riboflavin (p = 0.005), vitamin B6 (p = 0.034), and vitamin D (p = 0.002). The study showed an association between oxidative stress-related SNVs, BMD, and antioxidant-nutrient intake in Mexican women. Therefore, treatments for low BMD could be developed based on antioxidant supplementation.
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Affiliation(s)
- Rogelio F. Jiménez-Ortega
- Laboratorio de Genómica del Metabolismo Óseo, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (R.F.J.-O.); (D.I.A.-B.); (A.B.-C.); (P.L.-M.); (G.L.-R.); (J.F.-M.)
| | - Diana I. Aparicio-Bautista
- Laboratorio de Genómica del Metabolismo Óseo, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (R.F.J.-O.); (D.I.A.-B.); (A.B.-C.); (P.L.-M.); (G.L.-R.); (J.F.-M.)
| | - Adriana Becerra-Cervera
- Laboratorio de Genómica del Metabolismo Óseo, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (R.F.J.-O.); (D.I.A.-B.); (A.B.-C.); (P.L.-M.); (G.L.-R.); (J.F.-M.)
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT), Mexico City 03940, Mexico
| | - Priscilla López-Montoya
- Laboratorio de Genómica del Metabolismo Óseo, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (R.F.J.-O.); (D.I.A.-B.); (A.B.-C.); (P.L.-M.); (G.L.-R.); (J.F.-M.)
| | - Guadalupe León-Reyes
- Laboratorio de Genómica del Metabolismo Óseo, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (R.F.J.-O.); (D.I.A.-B.); (A.B.-C.); (P.L.-M.); (G.L.-R.); (J.F.-M.)
| | - Jeny Flores-Morales
- Laboratorio de Genómica del Metabolismo Óseo, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (R.F.J.-O.); (D.I.A.-B.); (A.B.-C.); (P.L.-M.); (G.L.-R.); (J.F.-M.)
| | - Manuel Castillejos-López
- Unidad de Epidemiología Hospitalaria e Infectología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas (INER), Mexico City 14080, Mexico;
| | - Alberto Hidalgo-Bravo
- Departamento de Medicina Genómica, Instituto Nacional de Rehabilitación (INR), Mexico City 14389, Mexico;
| | - Jorge Salmerón
- Centro de Investigación en Políticas, Población y Salud, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (J.S.); (B.R.-P.)
| | - Berenice Rivera-Paredez
- Centro de Investigación en Políticas, Población y Salud, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (J.S.); (B.R.-P.)
| | - Rafael Velázquez-Cruz
- Laboratorio de Genómica del Metabolismo Óseo, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (R.F.J.-O.); (D.I.A.-B.); (A.B.-C.); (P.L.-M.); (G.L.-R.); (J.F.-M.)
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6
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Abdi M, Aliyev E, Trost B, Kohailan M, Aamer W, Syed N, Shaath R, Gandhi GD, Engchuan W, Howe J, Thiruvahindrapuram B, Geng M, Whitney J, Syed A, Lakshmi J, Hussein S, Albashir N, Hussein A, Poggiolini I, Elhag SF, Palaniswamy S, Kambouris M, de Fatima Janjua M, Tahir MOE, Nazeer A, Shahwar D, Azeem MW, Mokrab Y, Aati NA, Akil A, Scherer SW, Kamal M, Fakhro KA. Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study. Genome Med 2023; 15:81. [PMID: 37805537 PMCID: PMC10560429 DOI: 10.1186/s13073-023-01228-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/04/2023] [Indexed: 10/09/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by impaired social and communication skills, restricted interests, and repetitive behaviors. The prevalence of ASD among children in Qatar was recently estimated to be 1.1%, though the genetic architecture underlying ASD both in Qatar and the greater Middle East has been largely unexplored. Here, we describe the first genomic data release from the BARAKA-Qatar Study-a nationwide program building a broadly consented biorepository of individuals with ASD and their families available for sample and data sharing and multi-omics research. METHODS In this first release, we present a comprehensive analysis of whole-genome sequencing (WGS) data of the first 100 families (372 individuals), investigating the genetic architecture, including single-nucleotide variants (SNVs), copy number variants (CNVs), tandem repeat expansions (TREs), as well as mitochondrial DNA variants (mtDNA) segregating with ASD in local families. RESULTS Overall, we identify potentially pathogenic variants in known genes or regions in 27 out of 100 families (27%), of which 11 variants (40.7%) were classified as pathogenic or likely-pathogenic based on American College of Medical Genetics (ACMG) guidelines. Dominant variants, including de novo and inherited, contributed to 15 (55.6%) of these families, consisting of SNVs/indels (66.7%), CNVs (13.3%), TREs (13.3%), and mtDNA variants (6.7%). Moreover, homozygous variants were found in 7 families (25.9%), with a sixfold increase in homozygous burden in consanguineous versus non-consanguineous families (13.6% and 1.8%, respectively). Furthermore, 28 novel ASD candidate genes were identified in 20 families, 23 of which had recurrent hits in MSSNG and SSC cohorts. CONCLUSIONS This study illustrates the value of ASD studies in under-represented populations and the importance of WGS as a comprehensive tool for establishing a molecular diagnosis for families with ASD. Moreover, it uncovers a significant role for recessive variation in ASD architecture in consanguineous settings and provides a unique resource of Middle Eastern genomes for future research to the global ASD community.
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Affiliation(s)
- Mona Abdi
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | - Elbay Aliyev
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | - Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Waleed Aamer
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | - Najeeb Syed
- Genomics Data Science Core, Sidra Medicine, Doha, Qatar
| | - Rulan Shaath
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | | | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jennifer Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Melissa Geng
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Joe Whitney
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Amira Syed
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | | | - Sura Hussein
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | | | - Amal Hussein
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | | | - Saba F Elhag
- Department of Genetics, Sidra Medicine, Doha, Qatar
- Hamad Medical Corporation, Doha, Qatar
| | | | - Marios Kambouris
- Pathology and Laboratory Medicine Department, Genetics Division, Sidra Medicine, Doha, Qatar
| | | | | | - Ahsan Nazeer
- Department of Psychiatry, Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine, Doha, Qatar
| | - Durre Shahwar
- Department of Psychiatry, Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine, Doha, Qatar
| | - Muhammad Waqar Azeem
- Department of Psychiatry, Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine, Doha, Qatar
| | - Younes Mokrab
- Department of Genetics, Sidra Medicine, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine, Doha, Qatar
- Qatar University, Doha, Qatar
| | | | - Ammira Akil
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Madeeha Kamal
- Department of Pediatrics, Sidra Medicine, Doha, Qatar
| | - Khalid A Fakhro
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
- Department of Genetics, Sidra Medicine, Doha, Qatar.
- Department of Genetic Medicine, Weill Cornell Medicine, Doha, Qatar.
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7
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Temilola DO, Wium M, Paccez J, Salukazana AS, Rotimi SO, Otu HH, Carbone GM, Kaestner L, Cacciatore S, Zerbini LF. Detection of Cancer-Associated Gene Mutations in Urinary Cell-Free DNA among Prostate Cancer Patients in South Africa. Genes (Basel) 2023; 14:1884. [PMID: 37895233 PMCID: PMC10606409 DOI: 10.3390/genes14101884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Prostate cancer (PCa) is the most common cause of cancer death among African men. The presence of tumor-specific variations in cell-free DNA (cfDNA), such as mutations, microsatellite instability, and DNA methylation, has been explored as a source of biomarkers for cancer diagnosis. In this study, we investigated the diagnostic role of cfDNA among South African PCa patients. We performed whole exome sequencing (WES) of urinary cfDNA. We identified a novel panel of 31 significantly deregulated somatic mutated genes between PCa and benign prostatic hyperplasia (BPH). Additionally, we performed whole-genome sequencing (WGS) on matching PCa and normal prostate tissue in an independent PCa cohort from South Africa. Our results suggest that the mutations are of germline origin as they were also found in the normal prostate tissue. In conclusion, our study contributes to the knowledge of cfDNA as a biomarker for diagnosing PCa in the South African population.
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Affiliation(s)
- Dada Oluwaseyi Temilola
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (D.O.T.); (M.W.); (J.P.); (S.C.)
- Integrative Biomedical Sciences Division, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Martha Wium
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (D.O.T.); (M.W.); (J.P.); (S.C.)
| | - Juliano Paccez
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (D.O.T.); (M.W.); (J.P.); (S.C.)
| | - Azola Samkele Salukazana
- Division of Urology, University of Cape Town, Groote Schuur Hospital, Cape Town 7925, South Africa; (A.S.S.); (L.K.)
| | | | - Hasan H. Otu
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Giuseppina M. Carbone
- Institute of Oncology Research (IOR), Università della Svizzera italiana, 6900 Bellinzona, Switzerland;
| | - Lisa Kaestner
- Division of Urology, University of Cape Town, Groote Schuur Hospital, Cape Town 7925, South Africa; (A.S.S.); (L.K.)
| | - Stefano Cacciatore
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (D.O.T.); (M.W.); (J.P.); (S.C.)
| | - Luiz Fernando Zerbini
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (D.O.T.); (M.W.); (J.P.); (S.C.)
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8
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Fatemeh S, Mahboobeh Z, Khadijeh A, Amirhossein MK, Pegah M. An in-silico study to determine susceptibility to cancer by evaluating the coding and non-coding non-synonymous single nucleotide variants in the SOCS3 gene. J Biomol Struct Dyn 2023:1-12. [PMID: 37753777 DOI: 10.1080/07391102.2023.2256408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Single Nucleotide Variant (SNVs) affect gene expression as well as protein structure and activity, leading to reduced signaling capabilities and ultimately, increasing cancer risk. SOCS3 (suppressor of cytokine signaling 3), a critical tumor suppressor providing a substantial part in the feedback loop of the JAK/STAT pathway, is abnormally suppressed in various cancer. This study aims to screen non-coding and potentially deleterious coding SNVs in the SOCS3 gene. We performed six programs: PredictSNP1.0 (predicting Deleterious nsSNVs), ConSurf (analyzing sequence conservation), ModPred (analyzing SNVS in PTMs sites), I-Mutant and MUpro (to analyze SNVs effecting protein stability), and molecular docking and molecular dynamics (MD) (to assess the consequences of SOCS3 genetic variations on JAK interactions) for coding regions and three programs (UTRSite, SNP2TFBS, miRNA SNP) (to analyze SNVs effecting the gene expression) in non-coding regions, respectively. After screening 2786 SOCS3 SNVs, we found 10 SNVs, as well as 49 SNPs that change the function of non-coding areas. Out of 10 selected nsSNVs, 3 SNVs (W48R, R71C, N198S) predicted to be the most damaging by all the software programs, as well as one nsSNV (R194W) could be highly deleterious from Molecular Docking analysis combined with MD Simulations. Our findings propose a procedure for studying the structure-related consequences of SNVs on protein function in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sadri Fatemeh
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Zarei Mahboobeh
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Ahmadi Khadijeh
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | | | - Mousavi Pegah
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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9
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Huang L, Yang C, Chen Y, Deng H, Liao Z, Xiao H. CRISPR-Mediated Base Editing: Promises and Challenges for a Viable Oncotherapy Strategy. Hum Gene Ther 2023; 34:669-681. [PMID: 37276175 DOI: 10.1089/hum.2023.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023] Open
Abstract
Base editing technology, developed from the CRISPR/Cas9 system, is able to efficiently implement single-base substitutions at specific DNA or RNA sites without generating double-strand breaks with precision and efficiency. Point mutations account for 58% of disease-causing genetic mutations in humans, and single nucleotide variants are an important cause of tumorigenesis, and the advent of base editors offers new hope for the study or treatment of such diseases. Although it has some limitations, base editors have been continuously improved in terms of editing efficiency, specificity, and product purity since their development. In this review, we examine the main base editing technologies and discuss their applications and prospects in tumor research and therapy, as well as elaborate on their mode of delivery.
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Affiliation(s)
- Lu Huang
- Department of Pharmacy, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Center, Sichuan Cancer Hospital and Institute, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, China
| | - Chao Yang
- Department of Traditional Chinese Medicine Surgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
| | - Yan Chen
- Department of Pharmacy, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Center, Sichuan Cancer Hospital and Institute, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Han Deng
- Department of Pharmacy, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Center, Sichuan Cancer Hospital and Institute, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, China
| | - Zhi Liao
- Department of Gynecology and Obstetrics, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
| | - Hongtao Xiao
- Department of Pharmacy, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Center, Sichuan Cancer Hospital and Institute, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, China
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10
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Omolaoye TS, Cardona Maya WD, du Plessis SS. Could exposure to spaceflight cause mutations in genes that affect male fertility? Life Sci Space Res (Amst) 2023; 37:15-17. [PMID: 37087174 DOI: 10.1016/j.lssr.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 05/03/2023]
Abstract
Recently, a study reported that upon analyzing blood samples from 14 astronauts that flew Space Transportation System missions between 1998 and 2001, 34 somatic nonsynonymous single nucleotide variants were detected in 17 CH-driver genes. Of interest is that the cohort consisted of relatively young astronauts, 85% of which were males of reproductive age. Having investigated the genes with nonsynonymous substitutes from the literature, it was found that twelve of these 17 genes appear to play essential roles in male reproduction. Changes in telomere length and gene regulation were also reported in another study conducted on an astronaut during a long duration stay on the International Space Station. Realizing the impact of spaceflight on gene sequence with potential influence on male fertility, it is important that more studies are conducted in this field. Specifically, in light of ultimately colonizing space, multi-generational survival is crucial and strategies to mitigate or counteract such effects should be explored.
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Affiliation(s)
- Temidayo S Omolaoye
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Walter D Cardona Maya
- Reproduction Group, Department of Microbiology and Parasitology, Faculty of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Stefan S du Plessis
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates; Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa.
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11
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Rosic J, Miladinov M, Dragicevic S, Eric K, Bogdanovic A, Krivokapic Z, Nikolic A. Genetic analysis and allele-specific expression of SMAD7 3'UTR variants in human colorectal cancer reveal a novel somatic variant exhibiting allelic imbalance. Gene 2023; 859:147217. [PMID: 36690223 DOI: 10.1016/j.gene.2023.147217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023]
Abstract
BACKGROUND Considering the impact of SMAD7 deregulation in colorectal cancer (CRC) progression and the significance of single nucleotide variant (SNV)-mediated disruptions of microRNA (miRNA)-dependent regulation for cancer susceptibility, our study aimed to analyze genetic variation in the SMAD7 3' untranslated region ( 3'UTR) in CRC, measure differences in allelic mRNA expression, and evaluate its interference with miRNA-mediated post-transcriptional regulation. PATIENTS AND METHODS This study included 80 patients with different CRC stages and six human colon cancer cell lines of various histological origins. SMAD7 3'UTR was analyzed by direct sequencing, followed by the relative quantification of differential allelic expression of detected variants by allele-specific qRT-PCR. In silico tools were employed for predictions of regulatory consequences of detected variants. RESULTS A total of four different SNVs in one cell line and nine patients were found, among which were a novel somatic point variant and three already known germline variants (rs16950113, rs1050799536, and rs1043778717). All evaluated SNVs exhibited variable extents of allelic imbalance in expression. In silico analysis predicted significant effects of SNVs on miRNA binding efficiency, with each SNV disrupting existing and creating new target sites for one or more miRNAs. CONCLUSION Imbalance observed in the expression of SNV alleles altering miRNA binding suggests that all investigated SNVs are potential contributing factors impacting SMAD7 expression regulation in CRC that further studies should investigate.
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Affiliation(s)
- Jovana Rosic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.
| | - Marko Miladinov
- Clinic for Digestive Surgery - First Surgical Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | - Sandra Dragicevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Katarina Eric
- Department of Patohistology, University Clinical Center of Serbia, Belgrade, Serbia
| | - Aleksandar Bogdanovic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia; Clinic for Digestive Surgery - First Surgical Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | - Zoran Krivokapic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia; Clinic for Digestive Surgery - First Surgical Clinic, University Clinical Center of Serbia, Belgrade, Serbia; Serbian Academy of Sciences and Arts, Belgrade, Serbia
| | - Aleksandra Nikolic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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12
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Wang S, Li Y, Du X, Li Q. Two single nucleotide variants in the miR-23a promoter affect granulosa cell apoptosis. Anim Genet 2023; 54:207-210. [PMID: 36478437 DOI: 10.1111/age.13284] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022]
Abstract
microRNAs (miRNAs) are well known to be important in mammalian female fertility. However, the genetic regulation of miRNAs associated with female fertility remains largely unknown. Here, we report that two single-nucleotide variants (SNVs) in the miR-23a promoter strongly influence miR-23a transcription and function in granulosa cell (GC) apoptosis. Two novel SNVs, g.-283G>C and g.-271C>T, were detected in the porcine miR-23a promoter by pooled-DNA sequencing. Furthermore, SNVs in the promoter region influenced miR-23a transcription in porcine GCs by altering its promoter activity. Functionally, SNVs in the promoter strongly influenced miR-23a regulation of early apoptosis in porcine GCs cultured in vitro. In addition, a preliminary association analysis showed that the combined genotypes of the two SNVs, rather than a single SNV, were tentatively associated with sow fertility traits in a Large White population. Overall, our findings suggest that the SNVs g.-283G>C and g.-271C>T in the miR-23a promoter are causal variants affecting GC apoptosis and miR-23a may be a potential small-molecule nonhormonal drug for regulating female fertility.
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Affiliation(s)
- Siqi Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yuqi Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xing Du
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Qifa Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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13
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da Silva Menezes E, de Moraes FCA, de Nazaré Cohen-Paes A, Wanderley AV, Pereira EEB, Pastana LF, Modesto AAC, de Assumpção PP, Burbano RMR, dos Santos SEB, dos Santos NPC, Fernandes MR. Influence of Genetic Variations in miRNA and Genes Encoding Proteins in the miRNA Synthesis Complex on Toxicity of the Treatment of Pediatric B-Cell ALL in the Brazilian Amazon. Int J Mol Sci 2023; 24:ijms24054431. [PMID: 36901860 PMCID: PMC10003057 DOI: 10.3390/ijms24054431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/24/2022] [Accepted: 12/29/2022] [Indexed: 02/25/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer in the world. Single nucleotide variants (SNVs) in miRNA and genes encoding proteins of the miRNA synthesis complex (SC) may affect the processing of drugs used in the treatment of ALL, resulting in treatment-related toxicities (TRTs). We investigated the role of 25 SNVs in microRNA genes and genes encoding proteins of the miRNA SC, in 77 patients treated for ALL-B from the Brazilian Amazon. The 25 SNVs were investigated using the TaqMan® OpenArray™ Genotyping System. SNVs rs2292832 (MIR149), rs2043556 (MIR605), and rs10505168 (MIR2053) were associated with an increased risk of developing Neurological Toxicity, while rs2505901 (MIR938) was associated with protection from this toxicity. MIR2053 (rs10505168) and MIR323B (rs56103835) were associated with protection from gastrointestinal toxicity, while DROSHA (rs639174) increased the risk of development. The rs2043556 (MIR605) variant was related to protection from infectious toxicity. SNVs rs12904 (MIR200C), rs3746444 (MIR499A), and rs10739971 (MIRLET7A1) were associated with a lower risk for severe hematologic toxicity during ALL treatment. These findings reveal the potential for the use of these genetic variants to understand the development of toxicities related to the treatment of ALL in patients from the Brazilian Amazon region.
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Affiliation(s)
| | | | | | - Alayde Vieira Wanderley
- Otávio Lobo Children’s Cancer Hospital, Belém 66063-005, PA, Brazil
- State Department of Public Health (SESPA), Belém 66093-677, PA, Brazil
| | - Esdras Edgar Batista Pereira
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil
- State Department of Public Health (SESPA), Belém 66093-677, PA, Brazil
- Laboratory of Human and Medical Genetics, Institute of Biological Science, Federal University of Pará, Belém 66077-830, PA, Brazil
- Instituto Tocantinense Presidente Antônio Carlos (ITPAC), Abaetetuba 68440-000, PA, Brazil
| | | | | | | | - Rommel Mario Rodríguez Burbano
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil
- Ophir Loyola Hospital, Molecular Biology Laboratory, Belém 66063-240, PA, Brazil
| | - Sidney Emanuel Batista dos Santos
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil
- Laboratory of Human and Medical Genetics, Institute of Biological Science, Federal University of Pará, Belém 66077-830, PA, Brazil
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14
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Arizmendi A, Rudd Garces G, Crespi JA, Olivera LH, Barrientos LS, Peral García P, Giovambattista G. Analysis of Doberman Pinscher and Toy Poodle samples with targeted next-generation sequencing. Gene 2023; 853:147069. [PMID: 36427679 DOI: 10.1016/j.gene.2022.147069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/04/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022]
Abstract
Next-generation sequencing (NGS) technologies have enabled the identification of many causal variants of genetic disorders, the development of parentage tests and the analysis of multiple traits in domestic animals. In this study, we evaluated the performance of a Canine Targeted Genotyping-by-Sequencing (GBS) custom panel (Thermo Fisher Scientific, Waltham, Ma, USA) in a cohort of 95 dog DNA samples, comprising 76 Doberman Pinschers and 19 Toy Poodles from Argentina. The used panel included 383 targets (228 parentage SNVs, 137 genetic disorder markers and 18 trait markers). While paternity analysis showed correct duo (97.4%; LOD > 2.98E+13) and trio (100%; LOD > 2.20E+15) parentage assignment, the panel resulted still insufficient for excluding close relatives in inbred populations. In this sense, close relatives were wrongly assigned as parents in 12.6% of duos and 0.3% of trios. We detected 17 polymorphic markers (genetic disorders, n = 4; hair type, n = 3; coat color, n = 10) and estimated their allele frequencies in the studied breeds. The accuracy of targeted GBS results were evaluated for three markers that were associated with Progressive rod-cone degeneration, von Willebrand disease type 1 and dilated cardiomyopathy by pyrosequencing and Sanger sequencing genotyping, showing 94-100% concordance among assays. The targeted GBS custom panel resulted cost-effective strategy to study the prevalence of genetic disorders and traits in a large number of samples and to analyze genetic interactions between previously reported variants. Once assays based on AgriSeq technology were standardized, their uses are a good strategy for large-scale routine genetic evaluation of animal populations.
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Affiliation(s)
- A Arizmendi
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando N. Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 S/N, 1900 La Plata, Buenos Aires, Argentina; Servicio de Cardiología, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 S/N, 1900 La Plata, Buenos Aires, Argentina
| | - G Rudd Garces
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando N. Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 S/N, 1900 La Plata, Buenos Aires, Argentina
| | - J A Crespi
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando N. Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 S/N, 1900 La Plata, Buenos Aires, Argentina
| | - L H Olivera
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando N. Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 S/N, 1900 La Plata, Buenos Aires, Argentina
| | - L S Barrientos
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando N. Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 S/N, 1900 La Plata, Buenos Aires, Argentina
| | - P Peral García
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando N. Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 S/N, 1900 La Plata, Buenos Aires, Argentina
| | - G Giovambattista
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando N. Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 S/N, 1900 La Plata, Buenos Aires, Argentina.
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15
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Block V, Sevdali E, Recher M, Abolhassani H, Hammarstrom L, Smulski CR, Baronio M, Plebani A, Proietti M, Speletas M, Warnatz K, Voll RE, Lougaris V, Schneider P, Eibel H. CVID-Associated B Cell Activating Factor Receptor Variants Change Receptor Oligomerization, Ligand Binding, and Signaling Responses. J Clin Immunol 2023; 43:391-405. [PMID: 36308663 PMCID: PMC9616699 DOI: 10.1007/s10875-022-01378-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 09/23/2022] [Indexed: 02/07/2023]
Abstract
PURPOSE Binding of the B cell activating factor (BAFF) to its receptor (BAFFR) activates in mature B cells many essential pro-survival functions. Null mutations in the BAFFR gene result in complete BAFFR deficiency and cause a block in B cell development at the transition from immature to mature B cells leading therefore to B lymphopenia and hypogammaglobulinemia. In addition to complete BAFFR deficiency, single nucleotide variants encoding BAFFR missense mutations were found in patients suffering from common variable immunodeficiency (CVID), autoimmunity, or B cell lymphomas. As it remained unclear to which extent such variants disturb the activity of BAFFR, we performed genetic association studies and developed a cellular system that allows the unbiased analysis of BAFFR variants regarding oligomerization, signaling, and ectodomain shedding. METHODS In addition to genetic association studies, the BAFFR variants P21R, A52T, G64V, DUP92-95, P146S, and H159Y were expressed by lentiviral gene transfer in DG-75 Burkitt's lymphoma cells and analyzed for their impacts on BAFFR function. RESULTS Binding of BAFF to BAFFR was affected by P21R and A52T. Spontaneous oligomerization of BAFFR was disturbed by P21R, A52T, G64V, and P146S. BAFF-dependent activation of NF-κB2 was reduced by P21R and P146S, while interactions between BAFFR and the B cell antigen receptor component CD79B and AKT phosphorylation were impaired by P21R, A52T, G64V, and DUP92-95. P21R, G64V, and DUP92-95 interfered with phosphorylation of ERK1/2, while BAFF-induced shedding of the BAFFR ectodomain was only impaired by P21R. CONCLUSION Although all variants change BAFFR function and have the potential to contribute as modifiers to the development of primary antibody deficiencies, autoimmunity, and lymphoma, P21R is the only variant that was found to correlate positively with CVID.
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Affiliation(s)
- Violeta Block
- Department of Rheumatology and Clinical Immunology, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medial Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eirini Sevdali
- Department of Rheumatology and Clinical Immunology, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medial Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Mike Recher
- Immunodeficiency Clinic and Laboratory, Medical Outpatient Unit and Department Biomedicine, University Hospital and University of Basel, Basel, Switzerland
| | - Hassan Abolhassani
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Lennart Hammarstrom
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Cristian R Smulski
- Department of Rheumatology and Clinical Immunology, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Medical Physics Department, Centro Atómico Bariloche, Comisión Nacional de Energía Atómica (CNEA), Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), San Carlos de Bariloche, Río Negro, Argentina
| | - Manuela Baronio
- Department of Clinical and Exp. Sciences, University of Brescia, Brescia, Italy
| | - Alessandro Plebani
- Department of Clinical and Exp. Sciences, University of Brescia, Brescia, Italy
| | - Michele Proietti
- Center for Chronic Immunodeficiency, Medial Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute for Immunodeficiency, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matthaios Speletas
- Department of Immunology & Histocompatibility, Faculty of Medicine, University of Thessaly, Larissa, Greece
| | - Klaus Warnatz
- Department of Rheumatology and Clinical Immunology, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medial Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Reinhard E Voll
- Department of Rheumatology and Clinical Immunology, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medial Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Vassilios Lougaris
- Department of Clinical and Exp. Sciences, University of Brescia, Brescia, Italy
| | - Pascal Schneider
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Hermann Eibel
- Department of Rheumatology and Clinical Immunology, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- Center for Chronic Immunodeficiency, Medial Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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Hassan MM, Hussain MA, Ali SS, Mahdi MA. In Silico Analysis: HLA-DRB1 Gene's Variants and Their Clinical Impact. Cell Transplant 2023; 32:9636897231184473. [PMID: 37387418 DOI: 10.1177/09636897231184473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
The HLA-DRB1 gene encodes a protein that is essential for the immune system. This gene is important in organ transplant rejection and acceptance, as well as multiple sclerosis, systemic lupus erythematosus, Addison's disease, rheumatoid arthritis, caries susceptibility, and Aspirin-exacerbated respiratory disease. The following Homo sapiens variants were investigated: single-nucleotide variants (SNVs), multi-nucleotide variants (MNVs), and small insertions-deletions (Indels) in the HLA-DRB1 gene via coding and untranslated regions. The current study sought to identify functional variants that could affect gene expression and protein product function/structure. ALL target variants available until April 14, 2022, were obtained from the Single Nucleotide Polymorphism database (dbSNP). Out of all the variants in the coding region, 91 nsSNVs were considered highly deleterious by seven prediction tools and instability index; 25 of them are evolutionary conserved and located in domain regions. Furthermore, 31 indels were predicted as harmful, potentially affecting a few amino acids or even the entire protein. Last, within the coding sequence (CDS), 23 stop-gain variants (SNVs/indels) were predicted as high impact. High impact refers to the assumption that the variant will have a significant (disruptive) effect on the protein, likely leading to protein truncation or loss of function. For untranslated regions, functional 55 single-nucleotide polymorphisms (SNPs), and 16 indels located within microRNA binding sites, furthermore, 10 functionally verified SNPs were predicted at transcription factor-binding sites. The findings demonstrate that employing in silico methods in biomedical research is extremely successful and has a major influence on the capacity to identify the source of genetic variation in diverse disorders. In conclusion, these previously functional identified variants could lead to gene alteration, which may directly or indirectly contribute to the occurrence of many diseases. The study's results could be an important guide in the research of potential diagnostic and therapeutic interventions that require experimental mutational validation and large-scale clinical trials.
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Affiliation(s)
- Mohamed M Hassan
- Faculty of Medical Laboratory Sciences, National University, Khartoum, Sudan
| | - Mohamed A Hussain
- Faculty of Pharmacy, International University of Africa, Khartoum, Sudan
| | - Sababil S Ali
- Faculty of Medical Laboratory Sciences, National University, Khartoum, Sudan
| | - Mohammed A Mahdi
- Faculty of Medical Laboratory Sciences, National University, Khartoum, Sudan
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Chen B, Wang Y, Tang W, Chen Y, Liu C, Kang M, Xie J. Association between PPARγ, PPARGC1A, and PPARGC1B genetic variants and susceptibility of gastric cancer in an Eastern Chinese population. BMC Med Genomics 2022; 15:274. [PMID: 36587194 PMCID: PMC9805199 DOI: 10.1186/s12920-022-01428-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/26/2022] [Indexed: 01/01/2023] Open
Abstract
PURPOSE Previous studies showed that peroxisome proliferator-activated receptor gamma (PPARγ) and PPARγ coactivator1 family (PPARGC1A and PPARGC1B) gene single nucleotide variants (SNVs)were strongly associated with cancer susceptibility. The purpose of this study was to investigate the association of PPARγ, PPARGC1A, and PPARGC1B variants with the risk of gastric cancer (GC). PATIENTS AND METHODS We performed a case-control study of 490 GC cases and 1,476 healthy controls from eastern China. PPARγ rs1801282 C > G, rs3856806 C > T, PPARGC1A rs2970847 C > T, rs8192678 C > T and PPARGC1B rs7732671 G > C, rs17572019 G > A SNVs were selected to investigate the association between these SNVs and GC susceptibility. Genotypes of the SNVs were assessed by multiplex fluorescent PCR using a custom-by-design 48-Plex SNPscantm Kit. RESULTS The PPARγ rs1801282 SNV was associated with a decreased risk for GC (GC vs. CC: odds ratio (OR) = 0.62, 95% confidence interval (95%CI) = 0.42-0.93, adjusted P = 0.019; GC + GG vs. GG: OR = 0.63 95%CI = 0.42-0.93, adjusted P = 0.019; respectively). In addition, stratified analysis revealed that the PPARγ rs1801282 SNV was correlated with the risk of GC in subgroups of age ≥ 61, no smoking, and no alcohol consuming. We also confirmed that the PPARγ rs3856806 C > T SNV promoted the risk of GC in women. The PPARGC1A rs8192678 TT genotype decreased the susceptibility of GC in men. The PPARGC1A rs2970847 C > T SNV decreased the susceptibility of GC in the subgroup of BMI ≥ 24 kg/m2. The PPARGC1B rs7732671 G > C and rs17572019 G > A SNVs promoted the risk of GC in the subgroup of BMI ≥ 24 kg/m2. CONCLUSION This study indicates that the PPARγ, PPARGC1A, and PPARGC1B SNVs may be associated with the susceptibility of GC in eastern Chinese population. Future studies with larger populations, detailed H. pylori infection status for subgroup analysis, and functional study are needed to further clarify the relationship between these SNVs and GC risk.
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Affiliation(s)
- Boyang Chen
- grid.440618.f0000 0004 1757 7156Department of Cardiothoracic Surgery, The Affiliated Hospital of Putian University, Putian, 351100 Fujian Province China
| | - Yafeng Wang
- Department of Cardiology, The People’s Hospital of Xishuangbanna Dai Autonomous Prefecture, Jinghong, Yunnan Province China
| | - Weifeng Tang
- grid.428392.60000 0004 1800 1685Department of Cardiothoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province China
| | - Yu Chen
- grid.415110.00000 0004 0605 1140Department of Medical Oncology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, Fujian Province China
| | - Chao Liu
- grid.452247.2Department of Cardiothoracic Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu Province China
| | - Mingqiang Kang
- grid.440618.f0000 0004 1757 7156Department of Cardiothoracic Surgery, The Affiliated Hospital of Putian University, Putian, 351100 Fujian Province China ,grid.411176.40000 0004 1758 0478Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001 Fujian Province China
| | - Jinbiao Xie
- grid.440618.f0000 0004 1757 7156Department of Cardiothoracic Surgery, The Affiliated Hospital of Putian University, Putian, 351100 Fujian Province China
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Moser AI, Campos-Madueno EI, Perreten V, Endimiani A. Genome stability during serial subculturing in hyperepidemic multidrug-resistant Klebsiella pneumoniae and Escherichia coli. J Glob Antimicrob Resist 2022; 31:152-61. [PMID: 36049731 DOI: 10.1016/j.jgar.2022.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/19/2022] [Accepted: 08/09/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES Core-genome single nucleotide variant (cgSNV) analysis represents a powerful tool for epidemiological investigations of multidrug-resistant (MDR) bacteria. However, cgSNV thresholds to confirm whether isolates are the same clone are not formally defined. METHODS We implemented hybrid whole-genome sequencing to study the genomic changes of four MDR isolates belonging to hyperepidemic sequence types (STs) during 20 propagation steps (T20) on MacConkey and CHROMID(R) ESBL plates. The following strains were analyzed: Klebsiella pneumoniae AE-2247421 (OXA-48/NDM-1-producing, ST101), K. pneumoniae MCL-2017-2 (CTX-M-15-producing, ST307), Escherichia coli Ec-042 (OXA-181-producing, ST410), and E. coli Ec-050 (NDM-5-producing, ST167). The genome assembly at T5 and T20 was compared to that at time point zero (T0) and to two reference genomes. RESULTS At T20, AE-2247421 lost the IncL blaOXA-48-carrying plasmid when grown on CHROMID(R) ESBL plates, while a large fragment encompassing blaNDM-1 was lost from its IncC plasmid when grown on both plates. In contrast, no structural changes were noted for the other three strains. Regarding the cgSNVs, the following results were obtained at T5 and T20 (ranges considering the different agar plates and reference genomes): AE-2247421 (1-8 and 2-12 cgSNVs), MCL-2017-2 (both 1-2 cgSNVs), Ec-042 (both 0 cgSNVs), and Ec-050 (0-6 and 0-9 cgSNVs). CONCLUSION We showed that structural changes and accumulation of cgSNVs can occur in few propagation steps under laboratory conditions. These changes might also arise in the clinical context in a short time, especially under antibiotics treatment. This phenomenon should be carefully considered because it might affect the final interpretation of epidemiological genomic analyses.
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Shen Y, Liu X, Xu L, Zhu W, Zhang Z, Liu J, Jiang L, Mao Y, Xu J, Yan X, Sun J, Liu F, Xiong X, Chen X, Che Y, Du J. Whole-exome sequencing reveals novel variants associated with abnormal uterine bleeding caused by copper intrauterine device. Per Med 2022; 19:523-534. [PMID: 36250535 DOI: 10.2217/pme-2022-0060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Aim: This study aimed to explore the genetic risk factors and validate variants of abnormal uterine bleeding after copper intrauterine device insertion. Methods: Whole-exome sequencing was performed and several variants were validated by Sequenom MassARRAY. Results: Eight variants showed potential clinical damage according to American College of Medical Genetics and Genomics criteria. By combined analysis of screening and validation, NFASC RS2802808 C>G p.Ile971Met (Pallele = 0.009 and Pgenotype = 0.027) and PIGR RS2275531 C>T p.Gly365Ser (Pallele = 0.009 and Pgenotype = 0.013) variants were identified as significantly associated with abnormal uterine bleeding with a false discovery rate <0.05. NFASC and PIGR may play a role in abnormal uterine bleeding by regulating coagulation fibrinolysis and endometrial epithelium inflammation functions. Conclusion: These findings provide a genetic basis for clinical individualization and precision of intrauterine device implantation.
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Affiliation(s)
- Yupei Shen
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Fudan University, Shanghai, China
| | - Xiaoli Liu
- Chongqing Health Center for Women & Children, Chongqing, China
| | - Linfen Xu
- Fujian Maternity & Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian, China
| | - Weiqiang Zhu
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Fudan University, Shanghai, China
| | - Zhaofeng Zhang
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Fudan University, Shanghai, China
| | - Junwei Liu
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Fudan University, Shanghai, China
| | - Lifang Jiang
- NHC Key Laboratory of Birth Defects Prevention, Henan Institute of Reproduction Health Science & Technology, Zhengzhou, Henan, China
| | - Yanyan Mao
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Fudan University, Shanghai, China
| | - Jianhua Xu
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Fudan University, Shanghai, China
| | - Xiaoqin Yan
- Maternal & Child Health & Family Planning Service Center of Huixian City, Henan, China
| | - Junjie Sun
- Chongqing Health Center for Women & Children, Chongqing, China
| | - Fang Liu
- Chongqing Health Center for Women & Children, Chongqing, China
| | - Xiumei Xiong
- Fujian Maternity & Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian, China
| | - Xiujuan Chen
- Fujian Maternity & Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian, China
| | - Yan Che
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Fudan University, Shanghai, China
| | - Jing Du
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Fudan University, Shanghai, China
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Kong Y, Li J, Lin H, Liang X, Zhou X. Landscapes of synchronous multiple primary cancers detected by next-generation sequencing. FEBS Open Bio 2022; 12:1996-2005. [PMID: 36128740 PMCID: PMC9623518 DOI: 10.1002/2211-5463.13491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/13/2022] [Accepted: 09/20/2022] [Indexed: 01/25/2023] Open
Abstract
An increase in the detection rate of multiple primary cancers has been accompanied with declining cancer death rates over the past few decades. However, synchronous multiple primary tumors have gradually increased, and the molecular mechanisms involved in the synchronous occurrence of multiple primary cancers of different origins are unclear. To investigate these mechanisms, we sequenced cancer tissues by FoundationOne CDx. Data were annotated with annovar, and we then performed pathway enrichment analysis. A total of 109 genes that were mutated in all samples were clustered into different diseases, biological processes, and molecular functions. GO and KEGG analyses indicated that the P53 and PKB signaling pathways may be relevant to the occurrence of synchronous multiple primary cancers. In summary, patients with a concordance of mutations in pathogenetic genes may have a higher risk of developing a second cancer. Our research may provide a basis for the development of individualized treatments for synchronous multiple primary cancers.
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Affiliation(s)
- Yiru Kong
- Department of OncologyHuashan Hospital Fudan UniversityShanghaiChina,Department of OncologyShanghai Medical College Fudan UniversityChina
| | - Jing Li
- Department of OncologyHuashan Hospital Fudan UniversityShanghaiChina
| | - Hao Lin
- Department of OncologyHuashan Hospital Fudan UniversityShanghaiChina
| | - Xiaohua Liang
- Department of OncologyHuashan Hospital Fudan UniversityShanghaiChina
| | - Xinli Zhou
- Department of OncologyHuashan Hospital Fudan UniversityShanghaiChina
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Chakraborty C, Bhattacharya M, Sharma AR, Dhama K, Agoramoorthy G. A comprehensive analysis of the mutational landscape of the newly emerging Omicron (B.1.1.529) variant and comparison of mutations with VOCs and VOIs. GeroScience 2022; 44:2393-2425. [PMID: 35989365 PMCID: PMC9393103 DOI: 10.1007/s11357-022-00631-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/20/2022] [Indexed: 01/18/2023] Open
Abstract
The Omicron variant is spreading rapidly throughout several countries. Thus, we comprehensively analyzed Omicron's mutational landscape and compared mutations with VOC/VOI. We analyzed SNVs throughout the genome, and AA variants (NSP and SP) in VOC/VOI, including Omicron. We generated heat maps to illustrate the AA variants with high mutation prevalence (> 75% frequency) of Omicron, which demonstrated eight mutations with > 90% prevalence in ORF1a and 29 mutations with > 75% prevalence in S-glycoprotein. A scatter plot for Omicron and VOC/VOI's cluster evaluation was computed. We performed a risk analysis of the antibody-binding risk among four mutations (L452, F490, P681, D614) and observed three mutations (L452R, F490S, D614G) destabilized antibody interactions. Our comparative study evaluated the properties of 28 emerging mutations of the S-glycoprotein of Omicron, and the ΔΔG values. Our results showed K417N with minimum and Q954H with maximum ΔΔG value. Furthermore, six important RBD mutations (G339D, S371L, N440K, G446S, T478K, Q498R) were chosen for comprehensive analysis for stabilizing/destabilizing properties and molecular flexibility. The G339D, S371L, N440K, and T478K were noted as stable mutations with 0.019 kcal/mol, 0.127 kcal/mol, 0.064 kcal/mol, and 1.009 kcal/mol. While, G446S and Q498R mutations showed destabilizing results. Simultaneously, among six RBD mutations, G339D, G446S, and Q498R mutations increased the molecular flexibility of S-glycoprotein. This study depicts the comparative mutational pattern of Omicron and other VOC/VOI, which will help researchers to design and deploy novel vaccines and therapeutic antibodies to fight against VOC/VOI, including Omicron.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Rd, Kolkata, West Bengal, 700126, India.
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, 756020, Odisha, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252, Gangwon-do, Republic of Korea
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
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Hattori T, Saito T, Okuya K, Takahashi Y, Miyamoto H, Kajihara M, Igarashi M, Takada A. Human ACE2 Genetic Polymorphism Affecting SARS-CoV and SARS-CoV-2 Entry into Cells. Microbiol Spectr 2022; 10:e0087022. [PMID: 35862965 PMCID: PMC9430119 DOI: 10.1128/spectrum.00870-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/27/2022] [Indexed: 11/29/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 have a single envelope glycoprotein (S protein) that binds to human angiotensin-converting enzyme 2 (ACE2) on the host cell membrane. Previous mutational scanning studies have suggested that some substitutions corresponding to single nucleotide variants (SNVs) in human ACE2 affect the binding affinity to the receptor binding domain (RBD) of the SARS-CoV-2 S protein. However, the importance of these substitutions in actual virus infection is still unclear. In this study, we investigated the effects of the reported ACE2 SNV substitutions on the entry of SARS-CoV and SARS-CoV-2 into cells, using vesicular stomatitis Indiana virus (VSIV) pseudotyped with S proteins of these coronaviruses (CoVs). HEK293T cells transfected with plasmids expressing ACE2 having each SNV substitution were infected with the pseudotyped VSIVs and relative infectivities were determined compared to the cells expressing wild-type ACE2. We found that some of the SNV substitutions positively or negatively affected the infectivities of the pseudotyped viruses. Particularly, the H505R substitution significantly enhanced the infection with the pseudotyped VSIVs, including those having the substitutions found in the S protein RBD of SARS-CoV-2 variants of concern. Our findings suggest that human ACE2 SNVs may potentially affect cell susceptibilities to SARS-CoV and SARS-CoV-2. IMPORTANCE SARS-CoV and SARS-CoV-2 are known to cause severe pneumonia in humans. The S protein of these CoVs binds to the ACE2 molecule on the plasma membrane and mediates virus entry into cells. The interaction between the S protein and ACE2 is thought to be important for host susceptibility to these CoVs. Although previous studies suggested that some SNV substitutions in ACE2 might affect the binding to the S protein, it remains elusive whether these SNV substitutions actually alter the efficiency of the entry of SARS CoVs into cells. We analyzed the impact of the ACE2 SNVs on the cellular entry of SARS CoVs using pseudotyped VSIVs having the S protein on the viral surface. We found that some of the SNV substitutions positively or negatively affected the infectivities of the viruses. Our data support the notion that genetic polymorphisms of ACE2 may potentially influence cell susceptibilities to SARS CoVs.
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Affiliation(s)
- Takanari Hattori
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Takeshi Saito
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kosuke Okuya
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yuji Takahashi
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hiroko Miyamoto
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Masahiro Kajihara
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Manabu Igarashi
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
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Furuuchi K, Seto S, Nakamura H, Hikichi H, Miyabayashi A, Wakabayashi K, Mizuno K, Oka T, Morimoto K, Hijikata M, Keicho N. Novel Screening System of Virulent Strains for the Establishment of a Mycobacterium avium Complex Lung Disease Mouse Model Using Whole-Genome Sequencing. Microbiol Spectr 2022;:e0045122. [PMID: 35579455 DOI: 10.1128/spectrum.00451-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The establishment of animal models reflecting human Mycobacterium avium complex (MAC) lung disease (LD) pathology has the potential to expand our understanding of the disease pathophysiology. However, inducing sustained infection in immunocompetent mice is difficult since MAC generally shows less virulence and higher genetic variability than M. tuberculosis. To overcome this hurdle, we developed a screening system for identifying virulent MAC strains using whole-genome sequencing (WGS). We obtained nine clinical strains from Mycobacterium avium complex lung disease (MAC-LD) patients and divided them into two groups to make the mixed strain inocula for infection. Intranasal infection with the strain mixture of both groups in BALB/c mice resulted in progressive infection and extensive granuloma formation in the lungs, suggesting the existence of highly pathogenic strains in each group. We hypothesized that the change in the abundance of strain-specific single-nucleotide variants (SNVs) reflects the change in bacterial number of each strain in infected lungs. Based on this hypothesis, we quantified individual strain-specific SNVs in bacterial DNA from infected lungs. Specific SNVs for four strains were detected, suggesting the pathogenicity of these four strains. Consistent with these results, individual infection with these four strains induced a high lung bacterial burden, forming extensive peribronchial granuloma, while the other strains showed a decreased lung bacterial burden. The current method combining mixed infection and WGS accurately identified virulent strains that induced sustained infection in mice. This method will contribute to the establishment of mouse models that reflect human MAC-LD and lead to antimycobacterial drug testing. IMPORTANCE To promote research on Mycobacterium avium complex (MAC) pathogenicity, animal models reflecting human progressive MAC lung disease (MAC-LD) are needed. Because there is high genetic and virulence diversity among clinical MAC strains, choosing a suitable strain is an important process for developing a mouse model. In this study, we developed a screening system for virulent strains in mice by combining mixed infection and whole-genome sequencing analysis. This approach is designed on the hypothesis that in vivo virulence of MAC strains can be examined simultaneously by comparing changes in the abundance of strain-specific single-nucleotide variants in the mouse lungs after infection with mixed strains. The identified strains were shown to induce high bacterial burdens and cause extensive peribronchial granuloma resembling the pulmonary pathology of human MAC-LD. The current method will help researchers develop mouse models that reflect human MAC-LD and will lead to further investigation of MAC pathogenicity.
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González-Barrios R, Alcaraz N, Montalvo-Casimiro M, Cervera A, Arriaga-Canon C, Munguia-Garza P, Hinojosa-Ugarte D, Sobrevilla-Moreno N, Torres-Arciga K, Mendoza-Perez J, Diaz-Chavez J, Cortes-González CC, Castro-Hernández C, Martínez-Cedillo J, Scavuzzo A, Pérez-Montiel D, Jiménez-Ríos MA, Herrera LA. Genomic Profile in a Non-Seminoma Testicular Germ-Cell Tumor Cohort Reveals a Potential Biomarker of Sensitivity to Platinum-Based Therapy. Cancers (Basel) 2022; 14:cancers14092065. [PMID: 35565196 PMCID: PMC9101377 DOI: 10.3390/cancers14092065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/07/2022] [Accepted: 04/17/2022] [Indexed: 11/16/2022] Open
Abstract
Despite having a favorable response to platinum-based chemotherapies, ~15% of Testicular Germ-Cell Tumor (TGCT) patients are platinum-resistant. Mortality rates among Latin American countries have remained constant over time, which makes the study of this population of particular interest. To gain insight into this phenomenon, we conducted whole-exome sequencing, microarray-based comparative genomic hybridization, and copy number analysis of 32 tumors from a Mexican cohort, of which 18 were platinum-sensitive and 14 were platinum-resistant. We incorporated analyses of mutational burden, driver mutations, and SNV and CNV signatures. DNA breakpoints in genes were also investigated and might represent an interesting research opportunity. We observed that sensitivity to chemotherapy does not seem to be explained by any of the mutations detected. Instead, we uncovered CNVs, particularly amplifications on segment 2q11.1 as a novel variant with chemosensitivity biomarker potential. Our data shed light into understanding platinum resistance in a Latin-origin population.
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Affiliation(s)
- Rodrigo González-Barrios
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico; (R.G.-B.); (M.M.-C.); (C.A.-C.); (P.M.-G.); (K.T.-A.); (J.D.-C.); (C.C.C.-G.); (C.C.-H.)
| | - Nicolás Alcaraz
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark;
- Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico;
| | - Michel Montalvo-Casimiro
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico; (R.G.-B.); (M.M.-C.); (C.A.-C.); (P.M.-G.); (K.T.-A.); (J.D.-C.); (C.C.C.-G.); (C.C.-H.)
| | | | - Cristian Arriaga-Canon
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico; (R.G.-B.); (M.M.-C.); (C.A.-C.); (P.M.-G.); (K.T.-A.); (J.D.-C.); (C.C.C.-G.); (C.C.-H.)
| | - Paulina Munguia-Garza
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico; (R.G.-B.); (M.M.-C.); (C.A.-C.); (P.M.-G.); (K.T.-A.); (J.D.-C.); (C.C.C.-G.); (C.C.-H.)
| | - Diego Hinojosa-Ugarte
- Departamento de Cirugía, Hospital Regional de Alta Especialidad del Bajío, Leon 37660, Mexico;
| | - Nora Sobrevilla-Moreno
- Departamento de Oncología Médica, Clínica de Tumores Genitourinarios, Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (N.S.-M.); (J.M.-C.)
| | - Karla Torres-Arciga
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico; (R.G.-B.); (M.M.-C.); (C.A.-C.); (P.M.-G.); (K.T.-A.); (J.D.-C.); (C.C.C.-G.); (C.C.-H.)
| | - Julia Mendoza-Perez
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - José Diaz-Chavez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico; (R.G.-B.); (M.M.-C.); (C.A.-C.); (P.M.-G.); (K.T.-A.); (J.D.-C.); (C.C.C.-G.); (C.C.-H.)
| | - Carlo Cesar Cortes-González
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico; (R.G.-B.); (M.M.-C.); (C.A.-C.); (P.M.-G.); (K.T.-A.); (J.D.-C.); (C.C.C.-G.); (C.C.-H.)
| | - Clementina Castro-Hernández
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico; (R.G.-B.); (M.M.-C.); (C.A.-C.); (P.M.-G.); (K.T.-A.); (J.D.-C.); (C.C.C.-G.); (C.C.-H.)
| | - Jorge Martínez-Cedillo
- Departamento de Oncología Médica, Clínica de Tumores Genitourinarios, Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (N.S.-M.); (J.M.-C.)
| | - Ana Scavuzzo
- Departamento de Urología, Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (A.S.); (M.A.J.-R.)
| | - Delia Pérez-Montiel
- Departamento de Patología, Instituto Nacional de Cancerología, Mexico City 14080, Mexico;
| | - Miguel A. Jiménez-Ríos
- Departamento de Urología, Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (A.S.); (M.A.J.-R.)
| | - Luis A. Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico; (R.G.-B.); (M.M.-C.); (C.A.-C.); (P.M.-G.); (K.T.-A.); (J.D.-C.); (C.C.C.-G.); (C.C.-H.)
- Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico;
- Correspondence: ; Tel.: +52-55-5350-1900
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Zhou S, Liu S, Zhao L, Sun HX. A Comprehensive Survey of Genomic Mutations in Breast Cancer Reveals Recurrent Neoantigens as Potential Therapeutic Targets. Front Oncol 2022; 12:786438. [PMID: 35387130 PMCID: PMC8978336 DOI: 10.3389/fonc.2022.786438] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/25/2022] [Indexed: 12/12/2022] Open
Abstract
Neoantigens are mutated antigens specifically generated by cancer cells but absent in normal cells. With high specificity and immunogenicity, neoantigens are considered as an ideal target for immunotherapy. This study was aimed to investigate the signature of neoantigens in breast cancer. Somatic mutations, including SNVs and indels, were obtained from cBioPortal of 5991 breast cancer patients. 738 non-silent somatic variants present in at least 3 patients for neoantigen prediction were selected. PIK3CA (38%), the highly mutated gene in breast cancer, could produce the highest number of neoantigens per gene. Some pan-cancer hotspot mutations, such as PIK3CA E545K (6.93%), could be recognized by at least one HLA molecule. Since there are more SNVs than indels in breast cancer, SNVs are the major source of neoantigens. Patients with hormone receptor-positive or HER2 negative are more competent to produce neoantigens. Age, but not the clinical stage, is a significant contributory factor of neoantigen production. We believe a detailed description of breast cancer neoantigen signatures could contribute to neoantigen-based immunotherapy development.
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Affiliation(s)
- Si Zhou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Songming Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lijian Zhao
- College of Medical Technology, Hebei Medical University, Shijiazhuang, China
| | - Hai-Xi Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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El Menshawy N, El-Ashwah S, Ebrahim MA, Mortada MI, Ramez A, Attia DM. TERT Genotype Polymorphism: A Glance of Change Egyptian MDS Outcomes. Asian Pac J Cancer Prev 2021; 22:1547-1555. [PMID: 34048184 PMCID: PMC8408390 DOI: 10.31557/apjcp.2021.22.5.1547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Indexed: 12/02/2022] Open
Abstract
Background: Myelodysplastic Syndromes (MDS)are clonal hematologic disorders characterized by genetic instability and ineffective hematopoiesis associated with telomere dysfunction. We aimed at investigating the association between the rs2242652 single nucleotide variant of the TERT gene and susceptibility for MDS, as well as its prognostic impact and relation to disease phenotype. Methods: Genotyping analysis was carried on 100 MDS patients recruited at Mansoura Oncology center, in addition to 100 healthy subjects for detection of rs2242652 variant of TERT gene on chromosome 5 by real time PCR following the protocol of Custom TaqMan® SNP Genotyping. Results: The rs2242652 TERT genetic polymorphism was associated with an increased risk of MDS (odds ratios 2.6 for genotype GA, 6.4 for genotype AA). The majority of AA homozygous mutant variant were associated pancytopenia (88%), poor risk cytogenetics (92%) and High/very high IPSS-R score (88%). At the end of follow-up (median 30 months), 14% of the cases transformed to secondary AML. The rate of leukemic transformation was significantly associated with the mutant AA genotype (93% of transformed cases, 52% of AA genotype cases; P< 0.0001). Survival outcome was inferior in AA mutant genotype (median 14 months, 95% CI: 12-16 months) to the GA genotype (median 30 months, 95% CI: 26-33 months) and those of the GG genotype (median not reached), P<0.001. Conclusion: Our study shows an intriguing and previously unrecognized association between rs2242652 TERT mutation and MDS risk. The presence of rs2242652 mutation defines a subgroup of patients with aggressive disease phenotype and dismal outcome. Further research is recommended to elucidate underlying pathologic mechanisms and to define an efficient therapeutic target.
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Affiliation(s)
- Nadia El Menshawy
- Department of Clinical Pathology, Hematology Unit, Faculty of Medicine, Mansoura University, Egypt
| | - Shaimaa El-Ashwah
- Clinical Hematology Unit, Department of Internal Medicine, Faculty of Medicine, Mansoura University, Egypt
| | - Mohamed A Ebrahim
- Medical Oncology Unit, Department of Internal Medicine, Faculty of Medicine, Mansoura University, Egypt
| | - Metwally Ibrahem Mortada
- Department of Clinical Pathology, Hematology Unit, Faculty of Medicine, Mansoura University, Egypt
| | - Ahmed Ramez
- Medical Oncology Unit, Department of Internal Medicine, Faculty of Medicine, Mansoura University, Egypt
| | - Doaa M Attia
- Department of Clinical Pathology, Hematology Unit, Faculty of Medicine, Mansoura University, Egypt
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Zamariolli M, Burssed B, Moysés-Oliveira M, Colovati M, Bellucco FTDS, Dos Santos LC, Alvarez Perez AB, Bragagnolo S, Melaragno MI. Novel MYT1 variants expose the complexity of oculo-auriculo-vertebral spectrum genetic mechanisms. Am J Med Genet A 2021; 185:2056-2064. [PMID: 33880880 DOI: 10.1002/ajmg.a.62217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/10/2021] [Accepted: 03/22/2021] [Indexed: 12/17/2022]
Abstract
Oculo-auriculo-vertebral spectrum (OAVS) is a developmental disorder characterized by anomalies mainly involving the structures derived from the first and second pharyngeal arches. The spectrum presents with heterogeneous clinical features and complex etiology with genetic factors not yet completely understood. To date, MYT1 is the most important gene unambiguously associated with the spectrum and with functional data confirmation. In this work, we aimed to identify new single nucleotide variants (SNVs) affecting MYT1 in a cohort of 73 Brazilian patients diagnosed with OAVS. In addition, we investigated copy number variations (CNVs) encompassing this gene or its cis-regulatory elements and compared the frequency of these events in patients versus a cohort of 455 Brazilian control individuals. A new SNV, predicted as likely deleterious, was identified in five unrelated patients with OAVS. All five patients presented hearing impairment and orbital asymmetry suggesting an association with the variant. CNVs near MYT1, located in its neighboring topologically associating domain (TAD), were found to be enriched in patients when compared to controls, indicating a possible involvement of this region with OAVS pathogenicity. Our findings highlight the genetic complexity of the spectrum that seems to involve more than one variant type and inheritance patterns.
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Affiliation(s)
- Malú Zamariolli
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Bruna Burssed
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mariana Moysés-Oliveira
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mileny Colovati
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Leonardo Caires Dos Santos
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana Beatriz Alvarez Perez
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Silvia Bragagnolo
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
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Assis-Mendonça GR, Fattori A, Rocha RM, Lourenço GJ, Delamain MT, Nonogaki S, de Lima VCC, Colleoni GWB, de Souza CA, Soares FA, Lima CSP, Vassallo J. Single nucleotide variants in immune-response genes and the tumor microenvironment composition predict progression of mantle cell lymphoma. BMC Cancer 2021; 21:209. [PMID: 33648463 PMCID: PMC7919095 DOI: 10.1186/s12885-021-07891-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 02/08/2021] [Indexed: 11/20/2022] Open
Abstract
Background There is evidence to consider that the tumor microenvironment (TME) composition associates with antitumor immune response, and may predict the outcome of various non-Hodgkin lymphoma subtypes. However, in the case of mantle cell lymphoma (MCL), a rare and aggressive disease, there is lacking a detailed study of the TME components, as well as an integrative approach among them in patients’ samples. Also, from the genetic point of view, it is known that single nucleotide variants (SNVs) in immune-response genes are among important regulators of immunity. At present, it is uncertain whether SNVs in candidate immune-response genes and the TME composition are able to alter the prognosis in MCL. Methods We assessed a detailed TME composition in 88 MCL biopsies using immunohistochemistry, which was automatically analyzed by pixel counting (Aperio system). We also genotyped SNVs located in candidate immune-response genes (IL12A, IL2, IL10, TGFB1, TGFBR1, TGFBR2, IL17A, IL17F) in 95 MCL patients. We tested whether the SNVs could modulate the respective protein expression and TME composition in the tumor compartment. Finally, we proposed survival models in rituximab-treated patients, considering immunohistochemical and SNV models. Results High FOXP3/CD3 ratios (p = 0.001), high IL17A levels (p = 0.003) and low IL2 levels (p = 0.03) were individual immunohistochemical predictors of poorer survival. A principal component, comprising high quantities of macrophages and high Ki-67 index, also worsened outcome (p = 0.02). In the SNV model, the CC haplotype of IL10 (p < 0.01), the GG genotype of IL2 rs2069762 (p = 0.02) and the AA+AG genotypes of TGFBR2 rs3087465 (p < 0.01) were independent predictors of outcome. Finally, the GG genotype of TGFB1 rs6957 associated with lower tumor TGFβ levels (p = 0.03) and less CD163+ macrophages (p = 0.01), but did not modulate patients’ survival. Conclusions Our results indicate that the TME composition has relevant biological roles in MCL. In this setting, immunohistochemical detection of T-reg cells, IL17A and IL2, coupled with SNV genotyping in IL10, TGFBR2 and IL2, may represent novel prognostic factors in this disease, following future validations. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-07891-9.
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Affiliation(s)
- Guilherme Rossi Assis-Mendonça
- Department of Pathology, Faculty of Medical Sciences, University of Campinas, Distrito de Barão Geraldo, Campinas, SP, Brazil.
| | - André Fattori
- Department of Internal Medicine, Faculty of Medical Sciences, University of Campinas, Campinas, SP, Brazil
| | - Rafael Malagoli Rocha
- Molecular Gynecology Laboratory, Department of Gynecology, Federal University of São Paulo, São Paulo, Brazil
| | - Gustavo Jacob Lourenço
- Laboratory of Cancer Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, SP, Brazil
| | | | - Suely Nonogaki
- Instituto Adolfo Lutz, Secretaria de Estado da Saúde, São Paulo, SP, Brazil
| | | | | | - Cármino Antonio de Souza
- Department of Internal Medicine, Faculty of Medical Sciences, University of Campinas, Campinas, SP, Brazil.,Hematology and Hemotherapy Center, University of Campinas, Campinas, Brazil
| | | | - Carmen Silvia Passos Lima
- Department of Internal Medicine, Faculty of Medical Sciences, University of Campinas, Campinas, SP, Brazil.,Laboratory of Cancer Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, SP, Brazil
| | - José Vassallo
- Department of Pathology, Faculty of Medical Sciences, University of Campinas, Distrito de Barão Geraldo, Campinas, SP, Brazil.,Rede D'Or Hospitals Network - Pathology Division, São Paulo, SP, Brazil.,Laboratory of Investigative and Molecular Pathology (LIP), CIPED, Faculty of Medical Sciences, University of Campinas, Campinas, SP, Brazil
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Liu F, Huang Y, Wang Q, Li J, Shan H. Rescue of Senecavirus A to uncover mutation profiles of its progenies during 80 serial passages in vitro. Vet Microbiol 2021; 253:108969. [PMID: 33450657 DOI: 10.1016/j.vetmic.2020.108969] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 12/20/2020] [Indexed: 02/07/2023]
Abstract
Senecavirus A (SVA), also known as Seneca Valley virus, belongs to the genus Senecavirus in the family Picornaviridae. In this study, a China SVA isolate (CH-LX-01-2016) was rescued from its cDNA clone, and then identified by RT-PCR, indirect immunofluorescence assay and mass spectrometry. The rescued SVA could separately induce typical plaque formations and cytopathic effects in cell monolayers. In order to uncover its evolutionary dynamics, the SVA was subjected to eighty serial passages in vitro. Its progenies per ten passages were analyzed by next-generation sequencing (NGS). The NGS analyses showed that neither sequence-deleting nor -inserting phenotype was detectable in eight progenies, within which a total of forty-one intra-host single-nucleotide variations (SNVs) arose with passaging. Almost all SNVs were identified as the single-nucleotide polymorphism with mixture of two nucleotides. SNVs led to eighteen nonsynonymous mutations, out of which sixteen could directly reflect their own frequencies of amino acid mutation, due to only one SNV occurring in their individual codons. Compared with its parental virus without passaging, the passage-80 SVA progeny had formed a viral quasispecies, as evidenced by a total of twenty-eight SNVs identified in it.
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Carron J, Torricelli C, Silva JK, Queiroz GSR, Ortega MM, Lima CSP, Lourenço GJ. microRNAs deregulation in head and neck squamous cell carcinoma. Head Neck 2020; 43:645-667. [PMID: 33159410 DOI: 10.1002/hed.26533] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 09/30/2020] [Accepted: 10/23/2020] [Indexed: 12/24/2022] Open
Abstract
Head and neck (HN) squamous cell carcinoma (SCC) is the eighth most common human cancer worldwide. Besides tobacco and alcohol consumption, genetic and epigenetic alterations play an important role in HNSCC occurrence and progression. microRNAs (miRNAs) are small noncoding RNAs that regulate cell cycle, proliferation, development, differentiation, and apoptosis by interfering in gene expression. Expression profiling of miRNAs showed that some miRNAs are upregulated or downregulated in tumor cells when compared with the normal cells. The present review focuses on the role of miRNAs deregulations in HNSCC, enrolled in risk, development, outcome, and therapy sensitivity. Moreover, the influence of single nucleotide variants in miRNAs target sites, miRNAs seed sites, and miRNAs-processing genes in HNSCC was also revised. Due to its potential for cancer diagnosis, progression, and as a therapeutic target, miRNAs may bring new perspectives in HNSCC understanding and therapy, especially for those patients with no or insufficient treatment options.
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Affiliation(s)
- Juliana Carron
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, Brazil
| | - Caroline Torricelli
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, Brazil
| | - Janet K Silva
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, Brazil
| | - Gabriela S R Queiroz
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, Brazil
| | - Manoela M Ortega
- Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, São Francisco University, Bragança Paulista, Brazil
| | - Carmen S P Lima
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, Brazil
| | - Gustavo J Lourenço
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, Brazil
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Crooks L, Cooper-Knock J, Heath PR, Bouhouche A, Elfahime M, Azzouz M, Bakri Y, Adnaoui M, Ibrahimi A, Amzazi S, Tazi-Ahnini R. Identification of single nucleotide variants in the Moroccan population by whole-genome sequencing. BMC Genet 2020; 21:111. [PMID: 32957965 PMCID: PMC7507649 DOI: 10.1186/s12863-020-00917-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 09/08/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Large-scale human sequencing projects have described around a hundred-million single nucleotide variants (SNVs). These studies have predominately involved individuals with European ancestry despite the fact that genetic diversity is expected to be highest in Africa where Homo sapiens evolved and has maintained a large population for the longest time. The African Genome Variation Project examined several African populations but these were all located south of the Sahara. Morocco is on the northwest coast of Africa and mostly lies north of the Sahara, which makes it very attractive for studying genetic diversity. The ancestry of present-day Moroccans is unknown and may be substantially different from Africans found South of the Sahara desert, Recent genomic data of Taforalt individuals in Eastern Morocco revealed 15,000-year-old modern humans and suggested that North African individuals may be genetically distinct from previously studied African populations. RESULTS We present SNVs discovered by whole genome sequencing (WGS) of three Moroccans. From a total of 5.9 million SNVs detected, over 200,000 were not identified by 1000G and were not in the extensive gnomAD database. We summarise the SNVs by genomic position, type of sequence gene context and effect on proteins encoded by the sequence. Analysis of the overall genomic information of the Moroccan individuals to individuals from 1000G supports the Moroccan population being distinct from both sub-Saharan African and European populations. CONCLUSIONS We conclude that Moroccan samples are genetically distinct and lie in the middle of the previously observed cline between populations of European and African ancestry. WGS of Moroccan individuals can identify a large number of novel SNVs and aid in functional characterisation of the genome.
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Affiliation(s)
- Lucy Crooks
- Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Howard Street, Sheffield,, S1 1WB, UK
| | - Johnathan Cooper-Knock
- Neuroscience (SITraN), Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, UK
| | - Paul R Heath
- Neuroscience (SITraN), Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, UK
| | - Ahmed Bouhouche
- Neurology and Neurogenetics, Genomic of Human Pathlogies Center, Medical School and Pharmacy, Mohammed-V University, Rabat, Morocco
| | | | - Mimoun Azzouz
- Neuroscience (SITraN), Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, UK
| | - Youssef Bakri
- Laboratory of human pathologies Biology BioPatH-Faculty of science-Center of human pathologies Genomics, GenoPatH- Faculty of Medicine- Mohammed V University in Rabat, Rabat, Morocco
| | - Mohammed Adnaoui
- Medical School and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Lab (MedBiotech), Medical School and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Saaïd Amzazi
- Laboratory of human pathologies Biology BioPatH-Faculty of science-Center of human pathologies Genomics, GenoPatH- Faculty of Medicine- Mohammed V University in Rabat, Rabat, Morocco
| | - Rachid Tazi-Ahnini
- Medical School and Pharmacy, Mohammed V University, Rabat, Morocco.
- Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, S10 2RX, UK.
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Landero-Huerta DA, Vigueras-Villaseñor RM, Yokoyama-Rebollar E, García-Andrade F, Rojas-Castañeda JC, Herrera-Montalvo LA, Díaz-Chávez J, Pérez-Añorve IX, Aréchaga-Ocampo E, Chávez-Saldaña MD. Cryptorchidism and Testicular Tumor: Comprehensive Analysis of Common Clinical Features and Search of SNVs in the KIT and AR Genes. Front Cell Dev Biol 2020; 8:762. [PMID: 32850863 PMCID: PMC7426638 DOI: 10.3389/fcell.2020.00762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/21/2020] [Indexed: 11/17/2022] Open
Abstract
Allelic variants in genes implicated in the development of testicular germ cell tumor (TGCT) could be present in patients with cryptorchidism (CO). Currently; the mechanisms explaining this relationship are still unknown. In this study the common clinical features in patients with CO and TGCT and 6 variants of KIT and AR genes associated to TGCT were analyzed. Population analyzed included 328 individuals: 91 patients with CO; 79 with TGCT, 13 of them with previous CO diagnosis, and 158 healthy males. Of the 13 patients with TGCT and history of CO, one patient (7.7%) presented the heterozygous form of the variant rs121913507 and two patients (15.4%) presented homozygote genotype for the variant rs121913506 in KIT gene. Interestingly, the heterozygous form for the variant rs121913506 of KIT gene was identifying in all of 13 patients. The rs201934623, rs774171864, and rs12014709 variants of the AR gene did not show any clinical association. Our results strongly support that genetic component in CO could be conditioning for the development of TGCT. Notably, KIT gene variants might be determinants in the pathological association between TGCT and CO.
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Affiliation(s)
- Daniel Adrian Landero-Huerta
- Laboratorio de Biología de la Reproducción, Instituto Nacional de Pediatría, Mexico City, Mexico.,Posgrado en Ciencias Naturales e Ingeniería, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | | | | | - Fabiola García-Andrade
- Laboratorio de Biología de la Reproducción, Instituto Nacional de Pediatría, Mexico City, Mexico
| | | | - Luis Alonso Herrera-Montalvo
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | | | - Isidro Xavier Pérez-Añorve
- Posgrado en Ciencias Naturales e Ingeniería, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Elena Aréchaga-Ocampo
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Mexico City, Mexico
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33
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Nath N, Hagenau L, Weiss S, Tzvetkova A, Jensen LR, Kaderali L, Port M, Scherthan H, Kuss AW. Genome-Wide DNA Alterations in X-Irradiated Human Gingiva Fibroblasts. Int J Mol Sci 2020; 21:E5778. [PMID: 32806598 PMCID: PMC7460866 DOI: 10.3390/ijms21165778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 01/04/2023] Open
Abstract
While ionizing radiation (IR) is a powerful tool in medical diagnostics, nuclear medicine, and radiology, it also is a serious threat to the integrity of genetic material. Mutagenic effects of IR to the human genome have long been the subject of research, yet still comparatively little is known about the genome-wide effects of IR exposure on the DNA-sequence level. In this study, we employed high throughput sequencing technologies to investigate IR-induced DNA alterations in human gingiva fibroblasts (HGF) that were acutely exposed to 0.5, 2, and 10 Gy of 240 kV X-radiation followed by repair times of 16 h or 7 days before whole-genome sequencing (WGS). Our analysis of the obtained WGS datasets revealed patterns of IR-induced variant (SNV and InDel) accumulation across the genome, within chromosomes as well as around the borders of topologically associating domains (TADs). Chromosome 19 consistently accumulated the highest SNVs and InDels events. Translocations showed variable patterns but with recurrent chromosomes of origin (e.g., Chr7 and Chr16). IR-induced InDels showed a relative increase in number relative to SNVs and a characteristic signature with respect to the frequency of triplet deletions in areas without repetitive or microhomology features. Overall experimental conditions and datasets the majority of SNVs per genome had no or little predicted functional impact with a maximum of 62, showing damaging potential. A dose-dependent effect of IR was surprisingly not apparent. We also observed a significant reduction in transition/transversion (Ti/Tv) ratios for IR-dependent SNVs, which could point to a contribution of the mismatch repair (MMR) system that strongly favors the repair of transitions over transversions, to the IR-induced DNA-damage response in human cells. Taken together, our results show the presence of distinguishable characteristic patterns of IR-induced DNA-alterations on a genome-wide level and implicate DNA-repair mechanisms in the formation of these signatures.
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Affiliation(s)
- Neetika Nath
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; (N.N.); (L.H.); (S.W.); (A.T.); (L.R.J.)
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany;
| | - Lisa Hagenau
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; (N.N.); (L.H.); (S.W.); (A.T.); (L.R.J.)
| | - Stefan Weiss
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; (N.N.); (L.H.); (S.W.); (A.T.); (L.R.J.)
| | - Ana Tzvetkova
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; (N.N.); (L.H.); (S.W.); (A.T.); (L.R.J.)
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany;
| | - Lars R. Jensen
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; (N.N.); (L.H.); (S.W.); (A.T.); (L.R.J.)
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany;
| | - Matthias Port
- Bundeswehr Institute for Radiobiology Affiliated to the University of Ulm, 80937 München, Germany; (M.P.); (H.S.)
| | - Harry Scherthan
- Bundeswehr Institute for Radiobiology Affiliated to the University of Ulm, 80937 München, Germany; (M.P.); (H.S.)
| | - Andreas W. Kuss
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; (N.N.); (L.H.); (S.W.); (A.T.); (L.R.J.)
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Galvão AA, de Araújo Sena F, Andrade Belitardo EMMD, de Santana MBR, Costa GNDO, Cruz ÁA, Barreto ML, Costa RDS, Alcantara-Neves NM, Figueiredo CA. Genetic polymorphisms in vitamin D pathway influence 25(OH)D levels and are associated with atopy and asthma. Allergy Asthma Clin Immunol 2020; 16:62. [PMID: 32834827 PMCID: PMC7386242 DOI: 10.1186/s13223-020-00460-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/26/2020] [Indexed: 12/28/2022] Open
Abstract
Background Vitamin D deficiency or insufficiency, has been associated with atopy and lack of asthma control. Our objective was to investigate associations between variants in genes of vitamin D pathway with serum levels of 25-hydroxyvitamin D (25(OH)D), atopy, asthma and asthma severity in teenagers from Northeast Brazil. Methods This is a cross sectional study nested in a cohort population of asthma. 25(OH)D was quantified from 968 of 11–17 years old individuals by ELISA. Asthma diagnosis was obtained by using the ISAAC Phase III questionnaire. Specific IgE was determined by ImmunoCAP; genotyping was performed using the 2.5 HumanOmni Biochip from Illumina. Statistical analyses were performed in PLINK 1.07 and SPSS 22.1. Results After quality control, 104 Single Nucleotides Variants (SNVs) in vitamin D pathway genes, typed in 792 individuals, were included in the analysis. The allele A of rs10875694 on VDR was positively associated with atopy (OR = 1.35; 95% CI 1.01–1.81). The allele C of rs9279 on VDR, was negatively associated with asthma risk (OR = 0.66; 95% CI 0.45–0.97), vitamin D insufficiency (OR = 0.78; 95% CI 0.70–0.96) and higher VDR expression. Two variants in VDR were associated with asthma severity, the allele A of rs2189480 (OR = 0.34; 95% CI 0.13–0.89) and the allele G of rs4328262 (OR = 3.18; 95% CI 1.09–9.28). The combination of variants in CYP2R1 and CYP24A1 (GAC, to rs10500804, rs12794714 and rs3886163, respectively) was negatively associated with vitamin D production (β = − 1.24; 95% CI − 2.42 to − 0.06). Conclusions Genetic variants in the vitamin D pathway affect vitamin D serum levels and, thus, atopy and asthma.
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Affiliation(s)
- Alana Alcântara Galvão
- Instituto de Ciências da Saúde, Universidade Federal da Bahia (UFBA), Salvador, Bahia, Brazil.,Programa de Pós Graduação em Imunologia (PPGIm), Bahia, Brazil
| | - Flávia de Araújo Sena
- Instituto de Ciências da Saúde, Universidade Federal da Bahia (UFBA), Salvador, Bahia, Brazil.,Programa de Pós Graduação em Imunologia (PPGIm), Bahia, Brazil
| | | | - Maria Borges Rabelo de Santana
- Instituto de Ciências da Saúde, Universidade Federal da Bahia (UFBA), Salvador, Bahia, Brazil.,Programa de Pós Graduação em Imunologia (PPGIm), Bahia, Brazil
| | - Gustavo Nunes de Oliveira Costa
- Instituto de Saúde Coletiva, Universidade Federal da Bahia (UFBA), Salvador, Bahia, Brazil.,Universidade Salvador (UNIFACS), Salvador, Bahia, Brazil
| | - Álvaro Augusto Cruz
- ProAR, Faculdade de Medicina, Universidade Federal da Bahia (UFBA), Salvador, Bahia, Brazil
| | - Maurício Lima Barreto
- Instituto de Saúde Coletiva, Universidade Federal da Bahia (UFBA), Salvador, Bahia, Brazil.,Centro de Integração de dados e Conhecimentos para Saúde(CIDACS), Fiocruz, Bahia Brazil
| | - Ryan Dos Santos Costa
- Instituto de Ciências da Saúde, Universidade Federal da Bahia (UFBA), Salvador, Bahia, Brazil.,Programa de Pós Graduação em Imunologia (PPGIm), Bahia, Brazil
| | - Neuza Maria Alcantara-Neves
- Instituto de Ciências da Saúde, Universidade Federal da Bahia (UFBA), Salvador, Bahia, Brazil.,Programa de Pós Graduação em Imunologia (PPGIm), Bahia, Brazil
| | - Camila Alexandrina Figueiredo
- Instituto de Ciências da Saúde, Universidade Federal da Bahia (UFBA), Salvador, Bahia, Brazil.,Programa de Pós Graduação em Imunologia (PPGIm), Bahia, Brazil.,Departamento de Ciências da Biorregulação, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Canela, CEP 41110-100 Salvador, BA Brazil
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35
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Yao H, Wu C, Chen Y, Guo L, Chen W, Pan Y, Fu X, Wang G, Ding Y. Spectrum of gene mutations identified by targeted next-generation sequencing in Chinese leukemia patients. Mol Genet Genomic Med 2020; 8:e1369. [PMID: 32638549 PMCID: PMC7507579 DOI: 10.1002/mgg3.1369] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 05/23/2020] [Accepted: 05/28/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Despite targeted sequencing have identified several mutations for leukemia, there is still a limit of mutation screening for Chinese leukemia. Here, we used targeted next-generation sequencing for testing the mutation patterns of Chinese leukemia patients. METHODS We performed targeted sequencing of 504 tumor-related genes in 109 leukemia samples to identify single-nucleotide variants (SNVs) and insertions and deletions (INDELs). Pathogenic variants were assessed based on the American College of Medical Genetics and Genomics (ACMG) guidelines. The functional impact of pathogenic genes was explored through gene ontology (GO), pathway analysis, and protein-protein interaction network in silico. RESULTS We identified a total of 4,655 SNVs and 614 INDELs in 419 genes, in which PDE4DIP, NOTCH2, FANCA, BCR, and ROS1 emerged as the highly mutated genes. Of note, we were the first to demonstrate an association of PDE4DIP mutation and leukemia. Based on ACMG guidelines, 39 pathogenic and likely pathogenic mutations in 27 genes were found. GO annotation showed that the biological process including gland development, leukocyte differentiation, respiratory system development, myeloid leukocyte differentiation, mesenchymal to epithelial transition, and so on were involved. CONCLUSION Our study provided a map of gene mutations in Chinese patients with leukemia and gave insights into the molecular pathogenesis of leukemia.
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Affiliation(s)
- Hongxia Yao
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Congming Wu
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Yueqing Chen
- Hainan General Hospital, University of South China, Haikou, Hainan, China
| | - Li Guo
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Wenting Chen
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Yanping Pan
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Xiangjun Fu
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Guyun Wang
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Yipeng Ding
- Department of General Practice, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
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36
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Meyerson W, Leisman J, Navarro FCP, Gerstein M. Origins and characterization of variants shared between databases of somatic and germline human mutations. BMC Bioinformatics 2020; 21:227. [PMID: 32498674 PMCID: PMC7273669 DOI: 10.1186/s12859-020-3508-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/20/2020] [Indexed: 01/26/2023] Open
Abstract
Background Mutations arise in the human genome in two major settings: the germline and the soma. These settings involve different inheritance patterns, time scales, chromatin structures, and environmental exposures, all of which impact the resulting distribution of substitutions. Nonetheless, many of the same single nucleotide variants (SNVs) are shared between germline and somatic mutation databases, such as between the gnomAD database of 120,000 germline exomes and the TCGA database of 10,000 somatic exomes. Here, we sought to explain this overlap. Results After strict filtering to exclude common germline polymorphisms and sites with poor coverage or mappability, we found 336,987 variants shared between the somatic and germline databases. A uniform statistical model explains 34% of these shared variants; a model that incorporates the varying mutation rates of the basic mutation types explains another 50% of shared variants; and a model that includes extended nucleotide contexts (e.g. surrounding 3 bases on either side) explains an additional 4% of shared variants. Analysis of read depth finds mixed evidence that up to 4% of the shared variants may represent germline variants leaked into somatic call sets. 9% of the shared variants are not explained by any model. Sequencing errors and convergent evolution did not account for these. We surveyed other factors as well: Cancers driven by endogenous mutational processes share a greater fraction of variants with the germline, and recently derived germline variants were more likely to be somatically shared than were ancient germline ones. Conclusions Overall, we find that shared variants largely represent bona fide biological occurrences of the same variant in the germline and somatic setting and arise primarily because DNA has some of the same basic chemical vulnerabilities in either setting. Moreover, we find mixed evidence that somatic call-sets leak appreciable numbers of germline variants, which is relevant to genomic privacy regulations. In future studies, the similar chemical vulnerability of DNA between the somatic and germline settings might be used to help identify disease-related genes by guiding the development of background-mutation models that are informed by both somatic and germline patterns of variation.
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Affiliation(s)
- William Meyerson
- Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06511, USA. .,Yale School of Medicine, Yale University, New Haven, CT, 06510, USA.
| | - John Leisman
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06510, USA
| | - Fabio C P Navarro
- Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06511, USA.,Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06511, USA
| | - Mark Gerstein
- Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06511, USA. .,Yale School of Medicine, Yale University, New Haven, CT, 06510, USA. .,Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06511, USA. .,Department of Computer Science, Yale University, New Haven, CT, 06511, USA.
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37
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Farkas C, Fuentes-Villalobos F, Garrido JL, Haigh J, Barría MI. Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions. PeerJ 2020; 8:e9255. [PMID: 32509472 PMCID: PMC7246029 DOI: 10.7717/peerj.9255] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/08/2020] [Indexed: 01/12/2023] Open
Abstract
Here we aim to describe early mutational events across samples from publicly available SARS-CoV-2 sequences from the sequence read archive and GenBank repositories. Up until 27 March 2020, we downloaded 50 illumina datasets, mostly from China, USA (WA State) and Australia (VIC). A total of 30 datasets (60%) contain at least a single founder mutation and most of the variants are missense (over 63%). Five-point mutations with clonal (founder) effect were found in USA next-generation sequencing samples. Sequencing samples from North America in GenBank (22 April 2020) present this signature with up to 39% allele frequencies among samples (n = 1,359). Australian variant signatures were more diverse than USA samples, but still, clonal events were found in these samples. Mutations in the helicase, encoded by the ORF1ab gene in SARS-CoV-2 were predominant, among others, suggesting that these regions are actively evolving. Finally, we firmly urge that primer sets for diagnosis be carefully designed, since rapidly occurring variants would affect the performance of the reverse transcribed quantitative PCR (RT-qPCR) based viral testing.
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Affiliation(s)
- Carlos Farkas
- Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB, Canada.,Department of Pharmacology and Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Francisco Fuentes-Villalobos
- Faculty of Biological Sciences, Department of Microbiology, Center of Biotechnology, Universidad de Concepción, Universidad de Concepción, Concepción, Chile
| | | | - Jody Haigh
- Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB, Canada.,Department of Pharmacology and Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - María Inés Barría
- Faculty of Biological Sciences, Department of Microbiology, Center of Biotechnology, Universidad de Concepción, Universidad de Concepción, Concepción, Chile
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38
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Bieder A, Einarsdottir E, Matsson H, Nilsson HE, Eisfeldt J, Dragomir A, Paucar M, Granberg T, Li TQ, Lindstrand A, Kere J, Tapia-Páez I. Rare variants in dynein heavy chain genes in two individuals with situs inversus and developmental dyslexia: a case report. BMC Med Genet 2020; 21:87. [PMID: 32357925 PMCID: PMC7193346 DOI: 10.1186/s12881-020-01020-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 04/05/2020] [Indexed: 02/08/2023]
Abstract
Background Developmental dyslexia (DD) is a neurodevelopmental learning disorder with high heritability. A number of candidate susceptibility genes have been identified, some of which are linked to the function of the cilium, an organelle regulating left-right asymmetry development in the embryo. Furthermore, it has been suggested that disrupted left-right asymmetry of the brain may play a role in neurodevelopmental disorders such as DD. However, it is unknown whether there is a common genetic cause to DD and laterality defects or ciliopathies. Case presentation Here, we studied two individuals with co-occurring situs inversus (SI) and DD using whole genome sequencing to identify genetic variants of importance for DD and SI. Individual 1 had primary ciliary dyskinesia (PCD), a rare, autosomal recessive disorder with oto-sino-pulmonary phenotype and SI. We identified two rare nonsynonymous variants in the dynein axonemal heavy chain 5 gene (DNAH5): a previously reported variant c.7502G > C; p.(R2501P), and a novel variant c.12043 T > G; p.(Y4015D). Both variants are predicted to be damaging. Ultrastructural analysis of the cilia revealed a lack of outer dynein arms and normal inner dynein arms. MRI of the brain revealed no significant abnormalities. Individual 2 had non-syndromic SI and DD. In individual 2, one rare variant (c.9110A > G;p.(H3037R)) in the dynein axonemal heavy chain 11 gene (DNAH11), coding for another component of the outer dynein arm, was identified. Conclusions We identified the likely genetic cause of SI and PCD in one individual, and a possibly significant heterozygosity in the other, both involving dynein genes. Given the present evidence, it is unclear if the identified variants also predispose to DD and further studies into the association between laterality, ciliopathies and DD are needed.
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Affiliation(s)
- Andrea Bieder
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, 141 83, Huddinge, Sweden.
| | - Elisabet Einarsdottir
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, 141 83, Huddinge, Sweden.,Stem Cells and Metabolism Research Program (STEMM), University of Helsinki, Helsinki, Finland.,Folkhälsan Institute of Genetics, Helsinki, Finland.,Science for Life Laboratory, Department of Gene Technology, KTH-Royal Institute of Technology, Solna, Sweden
| | - Hans Matsson
- Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Harriet E Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, 141 83, Huddinge, Sweden.,Department of Biomedical Engineering and Health Systems, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Huddinge, Sweden
| | - Jesper Eisfeldt
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Anca Dragomir
- Department of Pathology, Uppsala University Hospital, Uppsala, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Martin Paucar
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Tobias Granberg
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.,Department of Radiology, Karolinska University Hospital, Stockholm, Sweden
| | - Tie-Qiang Li
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Anna Lindstrand
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, 141 83, Huddinge, Sweden.,Stem Cells and Metabolism Research Program (STEMM), University of Helsinki, Helsinki, Finland.,School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Isabel Tapia-Páez
- Department of Medicine, Solna, Karolinska Institutet, Solnavägen 30, 171 76 Solna, Stockholm, Sweden.
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Kreimer A, Yan Z, Ahituv N, Yosef N. Meta-analysis of massively parallel reporter assays enables prediction of regulatory function across cell types. Hum Mutat 2019; 40:1299-1313. [PMID: 31131957 PMCID: PMC6771677 DOI: 10.1002/humu.23820] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/18/2019] [Accepted: 05/24/2019] [Indexed: 01/01/2023]
Abstract
Deciphering the potential of noncoding loci to influence gene regulation has been the subject of intense research, with important implications in understanding genetic underpinnings of human diseases. Massively parallel reporter assays (MPRAs) can measure regulatory activity of thousands of DNA sequences and their variants in a single experiment. With increasing number of publically available MPRA data sets, one can now develop data-driven models which, given a DNA sequence, predict its regulatory activity. Here, we performed a comprehensive meta-analysis of several MPRA data sets in a variety of cellular contexts. We first applied an ensemble of methods to predict MPRA output in each context and observed that the most predictive features are consistent across data sets. We then demonstrate that predictive models trained in one cellular context can be used to predict MPRA output in another, with loss of accuracy attributed to cell-type-specific features. Finally, we show that our approach achieves top performance in the Fifth Critical Assessment of Genome Interpretation "Regulation Saturation" Challenge for predicting effects of single-nucleotide variants. Overall, our analysis provides insights into how MPRA data can be leveraged to highlight functional regulatory regions throughout the genome and can guide effective design of future experiments by better prioritizing regions of interest.
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Affiliation(s)
- Anat Kreimer
- Department of Electrical Engineering and Computer Sciences, Center for Computational BiologyUniversity of CaliforniaBerkeleyCalifornia
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCalifornia
| | - Zhongxia Yan
- Department of Electrical Engineering and Computer Sciences, Center for Computational BiologyUniversity of CaliforniaBerkeleyCalifornia
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCalifornia
| | - Nir Yosef
- Department of Electrical Engineering and Computer Sciences, Center for Computational BiologyUniversity of CaliforniaBerkeleyCalifornia
- Ragon Institute of MGH MIT and HarvardCambridgeMassachusetts
- Chan Zuckerberg BiohubSan FranciscoCalifornia
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Zamariolli M, Colovati M, Moysés-Oliveira M, Nunes N, Caires Dos Santos L, Alvarez Perez AB, Bragagnolo S, Melaragno MI. Rare single-nucleotide variants in oculo-auriculo-vertebral spectrum (OAVS). Mol Genet Genomic Med 2019; 7:e00959. [PMID: 31469246 PMCID: PMC6785430 DOI: 10.1002/mgg3.959] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/07/2019] [Indexed: 01/13/2023] Open
Abstract
Background Oculo‐auriculo‐vertebral spectrum (OAVS) is a craniofacial developmental disorder that affects structures derived from the first and second pharyngeal arches. The clinically heterogeneous phenotype involves mandibular, oral, and ear development anomalies. Etiology is complex and poorly understood. Genetic factors have been associated, evidenced by chromosomal abnormalities affecting different genomic regions and genes. However, known pathogenic single‐nucleotide variants (SNVs) have only been identified in MYT1 in a restricted number of patients. Therefore, investigations of SNVs on candidate genes may reveal other pathogenic mechanisms. Methods In a cohort of 73 patients, coding and untranslated regions (UTR) of 10 candidate genes (CRKL, YPEL1, MAPK1, NKX3‐2, HMX1, MYT1, OTX2, GSC, PUF60, HOXA2) were sequenced. Rare SNVs were selected and in silico predictions were performed to ascertain pathogenicity. Likely pathogenic variants were validated by Sanger sequencing and heritability was assessed when possible. Results Four likely pathogenic variants in heterozygous state were identified in different patients. Two SNVs were located in the 5’UTR of YPEL1; one in the 3’UTR of CRKL and one in the 3’UTR of OTX2. Conclusion Our work described variants in candidate genes for OAVS and supported the genetic heterogeneity of the spectrum.
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Affiliation(s)
- Malú Zamariolli
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mileny Colovati
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mariana Moysés-Oliveira
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Natália Nunes
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Leonardo Caires Dos Santos
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana B Alvarez Perez
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Silvia Bragagnolo
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
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41
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Monteiro LLS, Franco OL, Alencar SA, Porto WF. Deciphering the structural basis for glucocorticoid resistance caused by missense mutations in the ligand binding domain of glucocorticoid receptor. J Mol Graph Model 2019; 92:216-226. [PMID: 31401440 DOI: 10.1016/j.jmgm.2019.07.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/01/2019] [Accepted: 07/31/2019] [Indexed: 11/25/2022]
Abstract
The glucocorticoid resistance hereditary condition may emerge from the occurrence of point mutations in the glucocorticoid receptor (GR), which could impair its functionality. Because the main feature of such pathology is the resistance of the hypothalamic-pituitary-adrenal axis to the hormone cortisol, we used the GR ligand binding domain three-dimensional structure to perform computational analysis for eight variants known to cause this clinical condition (I559 N, V571A, D641V, G679S, F737L, I747 M, L753F and L773P), aiming to understand, on the atom scale, how they cause glucocorticoid resistance. We observed that the mutations generated a reduced affinity to cortisol and they alter some loop conformations, which could be a consequence from changes in protein motion, which in turn could result from the reduced stability of mutant GR structures. Therefore, the analyzed mutations compromise the GR ligand binding domain structure and cortisol binding, which could characterize the glucocorticoid resistance phenotype.
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Affiliation(s)
- L L S Monteiro
- Programa de Pós-Graduação Em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - O L Franco
- Programa de Pós-Graduação Em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação Em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-Inova Biotech, Pós-Graduação Em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - S A Alencar
- Programa de Pós-Graduação Em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - W F Porto
- Porto Reports, Brasília, DF, Brazil; S-Inova Biotech, Pós-Graduação Em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil.
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Abstract
Objectives Current developments in sequencing techniques have enabled rapid and high-throughput generation of sequence data. However, there is a growing gap between the generation of raw sequencing data and the extraction of meaningful biological information. Variant annotation is a crucial step in the analysis of genome sequencing data. Incorrect or incomplete annotations can cause researchers to dilute interesting variants in a pool of false positives. We require consistent, accurate and reliable annotation of variants for making diagnostic and treatment decisions. Current annotation depends on the set of transcripts, and software used can be managed, with sufficient care, in the research context. Careful thought needs to be given to the choice of transcript sets and software packages for variant annotation in sequencing studies. In this project, the main objective is to analyze the genetic variants observed in Pakistani population data within the 1000 genomes project (1KGP). Results We characterized only SNVs and InDels types of genetic variations, in total ~ 1.4 million variants. Besides this, we also annotated the genetic variants with multiple annotations tools, ANNOVAR and SnpEff and compared the differential results. Our population-specific catalogue will enhance future studies on the functional impact at protein level. Electronic supplementary material The online version of this article (10.1186/s13104-019-4508-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Waqasuddin Khan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
| | - Aisha Ghani
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Bilal Azmi
- Department of Biochemistry, Dow Medical College, Dow University of Health Sciences, Baba-E-Urdu Road, Karachi, 74200, Pakistan
| | - Safina Abdul Razzak
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
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Eaaswarkhanth M, Melhem M, Sharma P, Nizam R, Al Madhoun A, Chaubey G, Alsmadi O, AlOzairi E, Al-Mulla F. Mitochondrial DNA D-loop sequencing reveals obesity variants in an Arab population. Appl Clin Genet 2019; 12:63-70. [PMID: 31213875 PMCID: PMC6541754 DOI: 10.2147/tacg.s198593] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/13/2019] [Indexed: 01/11/2023]
Abstract
Background: The association of mitochondrial DNA (mtDNA) variations with obesity has been investigated in diverse populations across the world. However, such obesity-associated mtDNA examinations are rarely conducted in Arab populations. Materials and methods: We re-sequenced mtDNA displacement loop (D-loop) region of 395 Arab individuals of Kuwait. We categorized the individuals based on their BMI scores as obese (n=232; BMI ≥30 kg/m2), overweight (n=110; BMI ≥25 kg/m2 and <30 kg/m2), and lean (n=53; BMI <25 kg/m2). We performed all the statistical tests by combining obese and overweight individuals in one group. Association analyses were conducted applying Fisher's exact test and logistic regression model. Results: We identified that the mtDNA variations m.73A>G, and m.523delAC were positively correlated with obesity, while m.310T>C, and m.16318A>T were negatively associated. All these variants, except m.16318A>T, remain statistically significant after adjusting for age and gender. We found that the variant m.73A>G increases the likelihood of being obese by 6-fold, whereas haplogroup H decreases the probability of being obese in Arab individuals of Kuwait. Haplotype analysis revealed that a haplotype, A263G-C309CT-T310C, defining the H2a clade of H haplogroup, reduces the probability of being obese. Conclusion: Our study reports, for the first time, the obesity-related mtDNA variants in Arabs of Kuwait. Based on the mtDNA D-loop region variations, we detected particular variants and haplogroup that are related with increased and decreased probability of being obese in the Kuwait Arab population.
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Affiliation(s)
| | - Motasem Melhem
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Dasman, 15462, Kuwait
| | - Prem Sharma
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Dasman, 15462, Kuwait
| | - Rasheeba Nizam
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Dasman, 15462, Kuwait
| | - Ashraf Al Madhoun
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Dasman, 15462, Kuwait
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Osama Alsmadi
- Department of Cell Therapy & Applied Genomics, King Hussein Cancer Center, Amman, Jordan
| | - Ebaa AlOzairi
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Dasman, 15462, Kuwait
| | - Fahd Al-Mulla
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Dasman, 15462, Kuwait
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Li J, Fan Z, Sun T, Peng C, Yue B, Li J. Comparative genome-wide survey of single nucleotide variation uncovers the genetic diversity and potential biomedical applications among six Macaca species. Int J Mol Sci 2018; 19:E3123. [PMID: 30314376 DOI: 10.3390/ijms19103123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/21/2018] [Accepted: 10/08/2018] [Indexed: 12/30/2022] Open
Abstract
Macaca is of great importance in evolutionary and biomedical research. Aiming at elucidating genetic diversity patterns and potential biomedical applications of macaques, we characterized single nucleotide variations (SNVs) of six Macaca species based on the reference genome of Macaca mulatta. Using eight whole-genome sequences, representing the most comprehensive genomic SNV study in Macaca to date, we focused on discovery and comparison of nonsynonymous SNVs (nsSNVs) with bioinformatic tools. We observed that SNV distribution patterns were generally congruent among the eight individuals. Outlier tests of nsSNV distribution patterns detected 319 bins with significantly distinct genetic divergence among macaques, including differences in genes associated with taste transduction, homologous recombination, and fat and protein digestion. Genes with specific nsSNVs in various macaques were differentially enriched for metabolism pathways, such as glycolysis, protein digestion and absorption. On average, 24.95% and 11.67% specific nsSNVs were putatively deleterious according to PolyPhen2 and SIFT4G, respectively, among which the shared deleterious SNVs were located in 564–1981 genes. These genes displayed enrichment signals in the ‘obesity-related traits’ disease category for all surveyed macaques, confirming that they were suitable models for obesity related studies. Additional enriched disease categories were observed in some macaques, exhibiting promising potential for biomedical application. Positively selected genes identified by PAML in most tested Macaca species played roles in immune and nervous system, growth and development, and fat metabolism. We propose that metabolism and body size play important roles in the evolutionary adaptation of macaques.
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Abstract
Current human whole genome sequencing projects produce massive amounts of data, often creating significant computational challenges. Different approaches have been developed for each type of genome variant and method of its detection, necessitating users to run multiple algorithms to find variants. We present Genome Rearrangement OmniMapper (GROM), a novel comprehensive variant detection algorithm accepting aligned read files as input and finding SNVs, indels, structural variants (SVs), and copy number variants (CNVs). We show that GROM outperforms state-of-the-art methods on 7 validated benchmarks using 2 whole genome sequencing (WGS) data sets. Additionally, GROM boasts lightning-fast run times, analyzing a 50× WGS human data set (NA12878) on commonly available computer hardware in 11 minutes, more than an order of magnitude (up to 72 times) faster than tools detecting a similar range of variants. Addressing the needs of big data analysis, GROM combines in 1 algorithm SNV, indel, SV, and CNV detection, providing superior speed, sensitivity, and precision. GROM is also able to detect CNVs, SNVs, and indels in non-paired-read WGS libraries, as well as SNVs and indels in whole exome or RNA sequencing data sets.
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Affiliation(s)
- Sean D Smith
- Department of Biology, Center for Computational and Integrative Biology, Rutgers University, 315 Penn St, Camden 08102, NJ, USA
| | - Joseph K Kawash
- Department of Biology, Center for Computational and Integrative Biology, Rutgers University, 315 Penn St, Camden 08102, NJ, USA
| | - Andrey Grigoriev
- Department of Biology, Center for Computational and Integrative Biology, Rutgers University, 315 Penn St, Camden 08102, NJ, USA
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Chen J, Ye L, Jin L, Xu X, Xu P, Wang X, Li H. Application of next-generation sequencing to characterize novel mutations in clarithromycin-susceptible Helicobacter pylori strains with A2143G of 23S rRNA gene. Ann Clin Microbiol Antimicrob 2018; 17:10. [PMID: 29562911 PMCID: PMC5863438 DOI: 10.1186/s12941-018-0259-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 03/08/2018] [Indexed: 12/22/2022] Open
Abstract
Background Clarithromycin (CLR) resistance has become a predominant factor for treatment failure of Helicobacter pylori eradication. Although the molecular mechanism of CLR resistance has been clearly understood in H. pylori, it is lack of evidence of other genes involved in drug resistance. Furthermore, the molecular mechanism of phenotype susceptible to CLR while genotype of 23S rRNA is mutant with A2143G is unclear. Here, we characterized the mutations of CLR-resistant and -susceptible H. pylori strains to explore bacterial resistance. Methods In the present study, the whole genomes of twelve clinical isolated H. pylori strains were sequenced, including two CLR-susceptible strains with mutation of A2143G. Single nucleotide variants (SNVs) were extracted and analyzed from multidrug efflux transporter genes. Results We did not find mutations associated with known CLR-resistant sites except for controversial T2182C outside of A2143G in the 23S rRNA gene. Although total SNVs of multidrug efflux transporter gene and the SNVs of HP0605 were significant differences (P ≤ 0.05) between phenotype resistant and susceptible strains. There is no significant difference in SNVs of RND or MFS (HP1181) family. However, the number of mutations in the RND family was significantly higher in the mutant strain (A2143G) than in the wild type. In addition, three special variations from two membrane proteins of mtrC and hefD were identified in both CLR-susceptible strains with A2143G. Conclusions Next-generation sequencing is a practical strategy for analyzing genomic variation associated with antibiotic resistance in H. pylori. The variations of membrane proteins of the RND family may be able to participate in the regulation of clinical isolated H. pylori susceptibility profiles.
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Affiliation(s)
- Jiaoe Chen
- Department of Gastroenterology, Sanmen People's Hospital, No. 117, Renmin Road, Sanmen, 317100, Zhejiang, People's Republic of China
| | - Liping Ye
- Department of Gastroenterology, Zhejiang Taizhou Hospital, Taizhou, 31700, People's Republic of China
| | - Liangmin Jin
- Department of Gastroenterology, Sanmen People's Hospital, No. 117, Renmin Road, Sanmen, 317100, Zhejiang, People's Republic of China
| | - Xuehua Xu
- Department of Gastroenterology, Sanmen People's Hospital, No. 117, Renmin Road, Sanmen, 317100, Zhejiang, People's Republic of China
| | - Peisong Xu
- Department of Research Service, Zhiyuan Inspection Medical Institute, Hangzhou, Zhejiang, 310006, People's Republic of China
| | - Xianjun Wang
- Clinical Laboratory, Hangzhou First People's Hospital, Hangzhou, 310006, Zhejiang, People's Republic of China
| | - Hongzhang Li
- Department of Gastroenterology, Sanmen People's Hospital, No. 117, Renmin Road, Sanmen, 317100, Zhejiang, People's Republic of China.
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Sun J, Meng Z, Wu K, Liu B, Zhang S, Liu Y, Wang Y, Zheng H, Huang J, Zhou P. Tracing the origin of Treponema pallidum in China using next-generation sequencing. Oncotarget 2018; 7:42904-42918. [PMID: 27344187 PMCID: PMC5189996 DOI: 10.18632/oncotarget.10154] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 06/01/2016] [Indexed: 12/29/2022] Open
Abstract
Syphilis is a systemic sexually transmitted disease caused by Treponema pallidum ssp. pallidum (TPA). The origin and genetic background of Chinese TPA strains remain unclear. We identified a total of 329 single-nucleotide variants (SNVs) in eight Chinese TPA strains using next-generation sequencing. All of the TPA strains were clustered into three lineages, and Chinese TPA strains were grouped in Lineage 2 based on phylogenetic analysis. The phylogeographical data showed that TPA strains originated earlier than did T. pallidum ssp. pertenue (TPE) and T. pallidum ssp. endemicum (TPN) strains and that Chinese TPA strains might be derived from recombination between Lineage 1 and Lineage 3. Moreover, we found through a homology modeling analysis that a nonsynonymous substitution (I415F) in the PBP3 protein might affect the structural flexibility of PBP3 and the binding constant for substrates based on its possible association with penicillin resistance in T. pallidum. Our findings provide new insight into the molecular foundation of the evolutionary origin of TPA and support the development of novel diagnostic/therapeutic technology for syphilis.
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Affiliation(s)
- Jun Sun
- STD Institute, Shanghai Skin Disease Hospital, Shanghai, China
| | - Zhefeng Meng
- Oncology Bioinformatics Center, Minhang Hospital, Fudan University, Shanghai, China
| | - Kaiqi Wu
- School of Laboratory Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Biao Liu
- School of Laboratory Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Sufang Zhang
- Shanghai Skin Disease Hospital, Clinical School of Anhui Medical University, Shanghai, China
| | - Yudan Liu
- Shanghai Skin Disease Hospital, Clinical School of Anhui Medical University, Shanghai, China
| | - Yuezhu Wang
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center and National Engineering Center for Biochip at Shanghai, Shanghai, China
| | - Huajun Zheng
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center and National Engineering Center for Biochip at Shanghai, Shanghai, China
| | - Jian Huang
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center and National Engineering Center for Biochip at Shanghai, Shanghai, China.,Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Pingyu Zhou
- STD Institute, Shanghai Skin Disease Hospital, Shanghai, China.,Shanghai Skin Disease Hospital, Clinical School of Anhui Medical University, Shanghai, China
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Wolff A, Perera-Bel J, Schildhaus HU, Homayounfar K, Schatlo B, Bleckmann A, Beißbarth T. Using RNA-Seq Data for the Detection of a Panel of Clinically Relevant Mutations. Stud Health Technol Inform 2018; 253:217-221. [PMID: 30147077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Somatic single nucleotide variants (SNVs) are genomic events with increasing implications in cancer treatment. The clinical standard for SNVs detection is whole genome/exome sequencing (WGS/WES) in matched tumor-normal samples. Yet, this is a very costly approach both economically and biologically and very often only tumor samples are sequenced. On the other hand, RNA sequencing (RNA-Seq) is the most popular technology to study gene expression, and has also the potential for a cost-effective identification of SNVs as an alternative to tumor-only WES. Here we present a method for the identification of SNVs in tumor-only RNA-Seq data putting a special focus on a small panel of clinically relevant SNVs. For evaluation purposeswe analyzed matched tumor-normal WEStumor-only RNA-Seq data from 14 cancer patients. We compared SNVs detected in i) RNA-Seq by our method, ii) WES tumor-only by Mutect2 and iii) WES matched tumor-normal by Mutect2. We did a detailed evaluation for a reduced panel of clinically relevant SNVs and reliably identified in RNA-Seq data a subset of mutations for which we had pathological annotation. Hence, RNA-Seq rises as a cost-effective option to detect in parallel gene expression as well as a small panel of clinically relevant SNVs in research.
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Affiliation(s)
- Alexander Wolff
- Department of Medical Statistics, University Medical Center Göttingen
| | - Júlia Perera-Bel
- Department of Medical Statistics, University Medical Center Göttingen
| | | | - Kia Homayounfar
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen
| | | | - Annalen Bleckmann
- Department of Medical Statistics, University Medical Center Göttingen
| | - Tim Beißbarth
- Department of Medical Statistics, University Medical Center Göttingen
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Henriksen MG, Nordgaard J, Jansson LB. Genetics of Schizophrenia: Overview of Methods, Findings and Limitations. Front Hum Neurosci 2017; 11:322. [PMID: 28690503 PMCID: PMC5480258 DOI: 10.3389/fnhum.2017.00322] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 06/06/2017] [Indexed: 01/12/2023] Open
Abstract
Genetics constitute a crucial risk factor to schizophrenia. In the last decade, molecular genetic research has produced novel findings, infusing optimism about discovering the biological roots of schizophrenia. However, the complexity of the object of inquiry makes it almost impossible for non-specialists in genetics (e.g., many clinicians and researchers) to get a proper understanding and appreciation of the genetic findings and their limitations. This study aims at facilitating such an understanding by providing a brief overview of some of the central methods and findings in schizophrenia genetics, from its historical origins to its current status, and also by addressing some limitations and challenges that confront this field of research. In short, the genetic architecture of schizophrenia has proven to be highly complex, heterogeneous and polygenic. The disease risk is constituted by numerous common genetic variants of only very small individual effect and by rare, highly penetrant genetic variants of larger effects. In spite of recent advances in molecular genetics, our knowledge of the etiopathogenesis of schizophrenia and the genotype-environment interactions remain limited.
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Affiliation(s)
- Mads G. Henriksen
- Mental Health Center Glostrup, University Hospital of CopenhagenCopenhagen, Denmark
- Faculty of Health and Medical Sciences, Institute of Clinical Medicine, University of CopenhagenCopenhagen, Denmark
- Center for Subjectivity Research, University of CopenhagenCopenhagen, Denmark
| | - Julie Nordgaard
- Faculty of Health and Medical Sciences, Institute of Clinical Medicine, University of CopenhagenCopenhagen, Denmark
- Early Psychosis Intervention Center, Region Zealand Psychiatry Roskilde, University of CopenhagenCopenhagen, Denmark
| | - Lennart B. Jansson
- Mental Health Center Glostrup, University Hospital of CopenhagenCopenhagen, Denmark
- Faculty of Health and Medical Sciences, Institute of Clinical Medicine, University of CopenhagenCopenhagen, Denmark
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Lipka A, Majewska M, Panasiewicz G, Bieniek-Kobuszewska M, Szafranska B. Gene structure of the pregnancy-associated glycoprotein-like (PAG-L) in the Eurasian beaver (Castor fiber L.). Funct Integr Genomics 2017; 17:599-605. [PMID: 28353203 DOI: 10.1007/s10142-017-0557-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 03/14/2017] [Accepted: 03/15/2017] [Indexed: 11/01/2022]
Abstract
The pregnancy-associated glycoprotein-like family (PAG-L) is a large group of chorionic products, expressed in the pre-placental trophoblast and later in the post-implantational chorionic epithelium, and are involved in proper placenta development and embryo-maternal interaction in eutherians. This study describes identification of the PAG-L family in the genome of the Eurasian beaver (Castor fiber L.), named CfPAG-L. We identified 7657 bp of the CfPAG-L gDNA sequence (Acc. No. KX377932), encompassing nine exons (1-9) and eight introns (A-H). The length of the CfPAG-L exons (59-200 bp) was equivalently similar to the only known counterparts of bPAG1, bPAG2, and pPAG2. The length of the CfPAG-L introns ranged 288-1937 bp and was completely different from previously known PAG introns. The exonic CfPAG-L regions revealed 50.3-72.9% homology with equivalent segments of bPAG1 and pPAG2 structure. The intronic CfPAG-L regions alignments revealed a lack of homology. Within the entire CfPAG-L gene, 31 potential single nucleotide variants (SNV: 7 transversions and 24 transitions) were predicted. The identified exonic polymorphic loci did not affect the amino acid sequence of the CfPAG-L polypeptide precursor. This is the first report describing the CfPAG-L gene sequence, structural organization, and SNVs in the Eurasian beaver, one of the largest rodents.
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