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Wang K, Hu T, Tai M, Shen Y, Chai H, Lin S, Chen X. LDLR c.415G > A causes familial hypercholesterolemia by weakening LDLR binding to LDL. Lipids Health Dis 2024; 23:85. [PMID: 38515137 PMCID: PMC10956282 DOI: 10.1186/s12944-024-02068-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 02/28/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Familial hypercholesterolemia (FH) is a prevalent hereditary disease that can cause aberrant cholesterol metabolism. In this study, we confirmed that c.415G > A in low-density lipoprotein receptor (LDLR), an FH-related gene, is a pathogenic variant in FH by in silico analysis and functional experiments. METHODS The proband and his family were evaluated using the diagnostic criteria of the Dutch Lipid Clinic Network. Whole-exome and Sanger sequencing were used to explore and validate FH-related variants. In silico analyses were used to evaluate the pathogenicity of the candidate variant and its impact on protein stability. Molecular and biochemical methods were performed to examine the effects of the LDLR c.415G > A variant in vitro. RESULTS Four of six participants had a diagnosis of FH. It was estimated that the LDLR c.415G > A variant in this family was likely pathogenic. Western blotting and qPCR suggested that LDLR c.415G > A does not affect protein expression. Functional studies showed that this variant may lead to dyslipidemia by impairing the binding and absorption of LDLR to low-density lipoprotein ( LDL). CONCLUSION LDLR c.415G > A is a pathogenic variant in FH; it causes a significant reduction in LDLR's capacity to bind LDL, resulting in impaired LDL uptake. These findings expand the spectrum of variants associated with FH.
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Affiliation(s)
- Kaihan Wang
- Department of Cardiology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Tingting Hu
- Department of Cardiology, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, Zhejiang, China
| | - Mengmeng Tai
- Department of Cardiology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Yan Shen
- Department of Cardiology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Haocheng Chai
- Department of Gastroenterology, Ningbo Ninth Hospital, Ningbo, Zhejiang, China
| | - Shaoyi Lin
- Department of Cardiology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China.
| | - Xiaomin Chen
- Department of Cardiology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China.
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Larrea-Sebal A, Jebari-Benslaiman S, Galicia-Garcia U, Jose-Urteaga AS, Uribe KB, Benito-Vicente A, Martín C. Predictive Modeling and Structure Analysis of Genetic Variants in Familial Hypercholesterolemia: Implications for Diagnosis and Protein Interaction Studies. Curr Atheroscler Rep 2023; 25:839-859. [PMID: 37847331 PMCID: PMC10618353 DOI: 10.1007/s11883-023-01154-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2023] [Indexed: 10/18/2023]
Abstract
PURPOSE OF REVIEW Familial hypercholesterolemia (FH) is a hereditary condition characterized by elevated levels of low-density lipoprotein cholesterol (LDL-C), which increases the risk of cardiovascular disease if left untreated. This review aims to discuss the role of bioinformatics tools in evaluating the pathogenicity of missense variants associated with FH. Specifically, it highlights the use of predictive models based on protein sequence, structure, evolutionary conservation, and other relevant features in identifying genetic variants within LDLR, APOB, and PCSK9 genes that contribute to FH. RECENT FINDINGS In recent years, various bioinformatics tools have emerged as valuable resources for analyzing missense variants in FH-related genes. Tools such as REVEL, Varity, and CADD use diverse computational approaches to predict the impact of genetic variants on protein function. These tools consider factors such as sequence conservation, structural alterations, and receptor binding to aid in interpreting the pathogenicity of identified missense variants. While these predictive models offer valuable insights, the accuracy of predictions can vary, especially for proteins with unique characteristics that might not be well represented in the databases used for training. This review emphasizes the significance of utilizing bioinformatics tools for assessing the pathogenicity of FH-associated missense variants. Despite their contributions, a definitive diagnosis of a genetic variant necessitates functional validation through in vitro characterization or cascade screening. This step ensures the precise identification of FH-related variants, leading to more accurate diagnoses. Integrating genetic data with reliable bioinformatics predictions and functional validation can enhance our understanding of the genetic basis of FH, enabling improved diagnosis, risk stratification, and personalized treatment for affected individuals. The comprehensive approach outlined in this review promises to advance the management of this inherited disorder, potentially leading to better health outcomes for those affected by FH.
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Affiliation(s)
- Asier Larrea-Sebal
- Department of Biochemistry and Molecular Biology, Universidad del País Vasco UPV/EHU, 48080, Bilbao, Spain
- Department of Molecular Biophysics, Biofisika Institute, University of Basque Country and Consejo Superior de Investigaciones Científicas (UPV/EHU, CSIC), 48940, Leioa, Spain
- Fundación Biofisika Bizkaia, 48940, Leioa, Spain
| | - Shifa Jebari-Benslaiman
- Department of Biochemistry and Molecular Biology, Universidad del País Vasco UPV/EHU, 48080, Bilbao, Spain
- Department of Molecular Biophysics, Biofisika Institute, University of Basque Country and Consejo Superior de Investigaciones Científicas (UPV/EHU, CSIC), 48940, Leioa, Spain
| | - Unai Galicia-Garcia
- Department of Biochemistry and Molecular Biology, Universidad del País Vasco UPV/EHU, 48080, Bilbao, Spain
- Department of Molecular Biophysics, Biofisika Institute, University of Basque Country and Consejo Superior de Investigaciones Científicas (UPV/EHU, CSIC), 48940, Leioa, Spain
| | - Ane San Jose-Urteaga
- Department of Biochemistry and Molecular Biology, Universidad del País Vasco UPV/EHU, 48080, Bilbao, Spain
| | - Kepa B Uribe
- Department of Biochemistry and Molecular Biology, Universidad del País Vasco UPV/EHU, 48080, Bilbao, Spain
| | - Asier Benito-Vicente
- Department of Biochemistry and Molecular Biology, Universidad del País Vasco UPV/EHU, 48080, Bilbao, Spain
- Department of Molecular Biophysics, Biofisika Institute, University of Basque Country and Consejo Superior de Investigaciones Científicas (UPV/EHU, CSIC), 48940, Leioa, Spain
| | - César Martín
- Department of Biochemistry and Molecular Biology, Universidad del País Vasco UPV/EHU, 48080, Bilbao, Spain.
- Department of Molecular Biophysics, Biofisika Institute, University of Basque Country and Consejo Superior de Investigaciones Científicas (UPV/EHU, CSIC), 48940, Leioa, Spain.
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3
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Graça R, Zimon M, Alves AC, Pepperkok R, Bourbon M. High-Throughput Microscopy Characterization of Rare LDLR Variants. JACC Basic Transl Sci 2023; 8:1010-1021. [PMID: 37719435 PMCID: PMC10504398 DOI: 10.1016/j.jacbts.2023.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 09/19/2023]
Abstract
Familial hypercholesterolemia (FH) is the most common inherited life-threatening disorder of lipid metabolism. Early diagnosis and treatment are the key to reduce the cumulative life-long cardiovascular burden of patients with FH. The high number of LDLR variants described as variants of unknown significance is the largest obstacle to achieve a definitive FH diagnosis. This study established a time- and cost-effective high-throughput cell-based assay to functionally profile LDLR variants, which allowed us to discriminate disruptive rare variants from silent ones. This work generated a valuable resource for systematic functional characterization of LDLR variants solving 1 of the major issues to achieve a definitive FH diagnosis.
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Affiliation(s)
- Rafael Graça
- Unidade de Investigação e Desenvolvimento, Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal
- BioISI—Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Magdalena Zimon
- Roche Diabetes Care GmbH, Mannheim, Germany
- Cell Biology and Cell Biophysics Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, Heidelberg, Germany
| | - Ana C. Alves
- Unidade de Investigação e Desenvolvimento, Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal
- BioISI—Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Rainer Pepperkok
- Cell Biology and Cell Biophysics Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, Heidelberg, Germany
- Advanced Light Microscopy Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Mafalda Bourbon
- Unidade de Investigação e Desenvolvimento, Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal
- BioISI—Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
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4
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Li M, Ma L, Chen Y, Li J, Wang Y, You W, Yuan H, Tang X, Ouyang H, Pang D. Large-Scale CRISPR Screen of LDLR Pathogenic Variants. RESEARCH (WASHINGTON, D.C.) 2023; 6:0203. [PMID: 37496633 PMCID: PMC10368174 DOI: 10.34133/research.0203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 07/04/2023] [Indexed: 07/28/2023]
Abstract
Familial hypercholesterolemia (FH) is a frequently occurring genetic disorder that is linked to early-onset cardiovascular disease. If left untreated, patients with this condition can develop severe cardiovascular complications. Unfortunately, many patients remain undiagnosed, and even when diagnosed, the treatment is often not optimal. Although mutations in the LDLR gene are the primary cause of FH, predicting whether novel variants are pathogenic is not a straightforward task. Understanding the functionality of LDLR variants is crucial in uncovering the genetic basis of FH. Our study utilized CRISPR/Cas9 cytosine base editors in pooled screens to establish a novel approach for functionally assessing tens of thousands of LDLR variants on a large scale. A total of more than 100 single guide RNAs (sgRNAs) targeting LDLR pathogenic mutations were successfully screened with relatively high accuracy. Out of these, 5 sgRNAs were further subjected to functional verification studies, including 1 in the promoter, 1 in the antisense RNA, 1 in the exon, and 2 in the intron. Except for the variant caused by the sgRNA located at intron 16, the functionalities of the other LDLR variants were all downregulated. The high similarity of LDLR intron sequences may lead to some false positives. Overall, these results confirm the reliability of the large-scale screening strategy for functional analysis of LDLR variants, and the screened candidate pathogenic mutations could be used as an auxiliary means of clinical gene detection to prevent FH-induced heart disease.
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Affiliation(s)
- Mengjing Li
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center,
College of Animal Sciences, Jilin University, Changchun, Jilin Province 130062, China
- The Institute of Translational Medicine,
Tianjin Union Medical Center of Nankai University, Tianjin 300071, China
| | - Lerong Ma
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center,
College of Animal Sciences, Jilin University, Changchun, Jilin Province 130062, China
- Chongqing Research Institute,
Jilin University, Chongqing 401123, China
- Chongqing Jitang Biotechnology Research Institute Co. Ltd., Chongqing, China
| | - Yiwu Chen
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center,
College of Animal Sciences, Jilin University, Changchun, Jilin Province 130062, China
- Chongqing Research Institute,
Jilin University, Chongqing 401123, China
- Chongqing Jitang Biotechnology Research Institute Co. Ltd., Chongqing, China
| | - Jianing Li
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center,
College of Animal Sciences, Jilin University, Changchun, Jilin Province 130062, China
| | - Yanbing Wang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center,
College of Animal Sciences, Jilin University, Changchun, Jilin Province 130062, China
| | - Wenni You
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center,
College of Animal Sciences, Jilin University, Changchun, Jilin Province 130062, China
| | - Hongming Yuan
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center,
College of Animal Sciences, Jilin University, Changchun, Jilin Province 130062, China
- Chongqing Research Institute,
Jilin University, Chongqing 401123, China
- Chongqing Jitang Biotechnology Research Institute Co. Ltd., Chongqing, China
| | - Xiaochun Tang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center,
College of Animal Sciences, Jilin University, Changchun, Jilin Province 130062, China
- Chongqing Research Institute,
Jilin University, Chongqing 401123, China
- Chongqing Jitang Biotechnology Research Institute Co. Ltd., Chongqing, China
| | - Hongsheng Ouyang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center,
College of Animal Sciences, Jilin University, Changchun, Jilin Province 130062, China
- Chongqing Research Institute,
Jilin University, Chongqing 401123, China
- Chongqing Jitang Biotechnology Research Institute Co. Ltd., Chongqing, China
| | - Daxin Pang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center,
College of Animal Sciences, Jilin University, Changchun, Jilin Province 130062, China
- Chongqing Research Institute,
Jilin University, Chongqing 401123, China
- Chongqing Jitang Biotechnology Research Institute Co. Ltd., Chongqing, China
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5
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Graça R, Alves AC, Zimon M, Pepperkok R, Bourbon M. Functional profiling of LDLR variants: important evidence for variant classification. J Clin Lipidol 2022; 16:516-524. [DOI: 10.1016/j.jacl.2022.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 04/20/2022] [Accepted: 04/25/2022] [Indexed: 10/18/2022]
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6
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Chora JR, Iacocca MA, Tichý L, Wand H, Kurtz CL, Zimmermann H, Leon A, Williams M, Humphries SE, Hooper AJ, Trinder M, Brunham LR, Costa Pereira A, Jannes CE, Chen M, Chonis J, Wang J, Kim S, Johnston T, Soucek P, Kramarek M, Leigh SE, Carrié A, Sijbrands EJ, Hegele RA, Freiberger T, Knowles JW, Bourbon M. The Clinical Genome Resource (ClinGen) Familial Hypercholesterolemia Variant Curation Expert Panel consensus guidelines for LDLR variant classification. Genet Med 2021; 24:293-306. [PMID: 34906454 DOI: 10.1016/j.gim.2021.09.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/06/2021] [Accepted: 09/15/2021] [Indexed: 01/02/2023] Open
Abstract
PURPOSE In 2015, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published consensus standardized guidelines for sequence-level variant classification in Mendelian disorders. To increase accuracy and consistency, the Clinical Genome Resource Familial Hypercholesterolemia (FH) Variant Curation Expert Panel was tasked with optimizing the existing ACMG/AMP framework for disease-specific classification in FH. In this study, we provide consensus recommendations for the most common FH-associated gene, LDLR, where >2300 unique FH-associated variants have been identified. METHODS The multidisciplinary FH Variant Curation Expert Panel met in person and through frequent emails and conference calls to develop LDLR-specific modifications of ACMG/AMP guidelines. Through iteration, pilot testing, debate, and commentary, consensus among experts was reached. RESULTS The consensus LDLR variant modifications to existing ACMG/AMP guidelines include (1) alteration of population frequency thresholds, (2) delineation of loss-of-function variant types, (3) functional study criteria specifications, (4) cosegregation criteria specifications, and (5) specific use and thresholds for in silico prediction tools, among others. CONCLUSION Establishment of these guidelines as the new standard in the clinical laboratory setting will result in a more evidence-based, harmonized method for LDLR variant classification worldwide, thereby improving the care of patients with FH.
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Affiliation(s)
- Joana R Chora
- Department of Health Promotion and Prevention of Noncommunicable Diseases, Nacional Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal; BioISI - BioSystems & Integrative Sciences Institute, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Michael A Iacocca
- Departments of Biomedical Data Science and Pathology, School of Medicine, Stanford University, Stanford, CA; Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto Ontario, Canada
| | - Lukáš Tichý
- Centre of Molecular Biology and Gene Therapy, University Hospital Brno, Brno, Czech Republic
| | - Hannah Wand
- Departments of Biomedical Data Science and Pathology, School of Medicine, Stanford University, Stanford, CA; Center for Inherited Cardiovascular Disease, Stanford Health Care, Stanford University, Stanford, CA
| | - C Lisa Kurtz
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | - Maggie Williams
- Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, United Kingdom
| | - Steve E Humphries
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Amanda J Hooper
- Department of Clinical Biochemistry, PathWest Laboratory Medicine WA, Royal Perth Hospital and Fiona Stanley Hospital Network, University of Western Australia, Perth, Western Australia, Australia
| | - Mark Trinder
- Department of Medicine, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Liam R Brunham
- Department of Medicine, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexandre Costa Pereira
- Laboratory of Genetics and Molecular Cardiology, Institute of the Hearth (InCor), Faculty of Medicine, São Paulo University, São Paulo, Brazil
| | - Cinthia E Jannes
- Laboratory of Genetics and Molecular Cardiology, Institute of the Hearth (InCor), Faculty of Medicine, São Paulo University, São Paulo, Brazil
| | | | | | - Jian Wang
- Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | | | | | - Premysl Soucek
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic; Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michal Kramarek
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic; Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | | | - Alain Carrié
- University Hospitals Pitié-Salpêtrière/Charles-Foix, Molecular and Chromosomal Genetics Center, Obesity and Dyslipidemia Genetics Unit, Sorbonne University, Paris, France
| | - Eric J Sijbrands
- Academic Medical Center, Erasmus University, Rotterdam, Netherlands
| | - Robert A Hegele
- Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Tomáš Freiberger
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic; Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Joshua W Knowles
- Division of Cardiovascular Medicine, Stanford Cardiovascular Institute, Prevention Research Center, and Diabetes Research Center, School of Medicine, Stanford University, Stanford, CA; FH Foundation, Pasadena, CA
| | - Mafalda Bourbon
- Department of Health Promotion and Prevention of Noncommunicable Diseases, Nacional Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal; BioISI - BioSystems & Integrative Sciences Institute, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, Lisbon, Portugal.
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7
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Santos RD. Advancing Prediction of Pathogenicity of Familial Hypercholesterolemia LDL Receptor Commonest Variants With Machine Learning Models. JACC Basic Transl Sci 2021; 6:828-830. [PMID: 34869945 PMCID: PMC8617596 DOI: 10.1016/j.jacbts.2021.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Raul D. Santos
- Address for correspondence: Dr Raul D. Santos, Heart Institute (InCor) University of Sao Paulo, Avenida Dr Eneas C. Aguiar 44, 05403-000 São Paulo, Brazil. @rauldsf_santos
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Graça R, Fernandes R, Alves AC, Menezes J, Romão L, Bourbon M. Characterization of Two Variants at Met 1 of the Human LDLR Gene Encoding the Same Amino Acid but Causing Different Functional Phenotypes. Biomedicines 2021; 9:1219. [PMID: 34572405 PMCID: PMC8467959 DOI: 10.3390/biomedicines9091219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 12/12/2022] Open
Abstract
Familial hypercholesterolemia (FH) is the most common genetic disorder of lipid metabolism, characterized by increased levels of total and LDL plasma cholesterol, which leads to premature atherosclerosis and coronary heart disease. FH phenotype has considerable genetic heterogeneity and phenotypic variability, depending on LDL receptor activity and lifestyle. To improve diagnosis and patient management, here, we characterized two single nucleotide missense substitutions at Methionine 1 of the human LDLR gene (c.1A>T/p.(Met1Leu) and c.1A>C/p.(Met1Leu)). We used a combination of Western blot, flow cytometry, and luciferase assays to determine the effects of both variants on the expression, activity, and synthesis of LDLR. Our data show that both variants can mediate translation initiation, although the expression of variant c.1A>T is very low. Both variants are in the translation initiation codon and codify for the same amino acid p.(Met1Leu), yet they lead to different levels of impairment on LDLR expression and activity, corroborating different efficiencies of the translation initiation at these non-canonical initiation codons. The functional data of these variants allowed for an improved American College of Medical Genetics (ACMG) classification for both variants, which can allow a more personalized choice of the lipid-lowering treatment and dyslipidemia management, ultimately improving patients' prognosis.
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Affiliation(s)
- Rafael Graça
- Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1600-609 Lisbon, Portugal; (R.G.); (A.C.A.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (R.F.); (J.M.); (L.R.)
| | - Rafael Fernandes
- BioISI—Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (R.F.); (J.M.); (L.R.)
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1600-609 Lisbon, Portugal
| | - Ana Catarina Alves
- Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1600-609 Lisbon, Portugal; (R.G.); (A.C.A.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (R.F.); (J.M.); (L.R.)
| | - Juliane Menezes
- BioISI—Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (R.F.); (J.M.); (L.R.)
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1600-609 Lisbon, Portugal
| | - Luísa Romão
- BioISI—Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (R.F.); (J.M.); (L.R.)
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1600-609 Lisbon, Portugal
| | - Mafalda Bourbon
- Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1600-609 Lisbon, Portugal; (R.G.); (A.C.A.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (R.F.); (J.M.); (L.R.)
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Abstract
Dyslipidemias are a group of diseases, which are characterized by abnormal blood concentrations of cholesterol, triglycerides and/or low-density lipoprotein-cholesterol (LDL-c). Dyslipidemia is a determinant condition for the progress of an atherosclerotic plaque formation. The resulting atherogenicity is due to at least two mechanisms: first, to the accumulation in the plasma of lipid particles that have the capacity to alter the function of the endothelium and deposit at the atheromatous plaque, and second, at an insufficient concentration of multifactorial type of high density lipoprotein-cholesterol (HDL-c), whose function is to protect against the development of atherosclerosis. Its highest prevalence is encountered among individuals with diabetes, hypertension or overweight. Hyperlipidemia is one of the main predisposing factors for the development of cardiovascular disease. Hyperlipidemia can be the result of a genetic condition, the secondary expression of a primary process or the consequence of exogenous factors (food, cultural, socio-economic, etc.), all of which lead to the elevation of plasma lipid levels. The objective of this study was to carry out an analysis of the genes involved in the development of dyslipidemias that lead to cardiovascular disease with special emphasis on the proprotein convertase subtilin/kexin type 9 (PCSK9) gene. The PCSK9 gene participates in the development of primary dyslipidemias, mainly familial hypercholesterolemia, currently the pharmacological treatment of choice to reduce LDL-c are statins, however, it has been observed that these have been insufficient to eliminate cardiovascular risk, especially in subjects with primary forms of hypercholesterolemia related to genetic mutations, or statin intolerance.
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Tada H, Hori M, Matsuki K, Ogura M, Nohara A, Kawashiri MA, Harada-Shiba M. Achilles Tendon Thickness Assessed by X-ray Predicting a Pathogenic Mutation in Familial Hypercholesterolemia Gene. J Atheroscler Thromb 2021; 29:816-824. [PMID: 34193720 PMCID: PMC9174093 DOI: 10.5551/jat.62869] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
AIM The 2017 Japan Atherosclerosis Society (JAS) familial hypercholesterolemia (FH) criteria adopt a cut-off value of ≥ 9 mm of Achilles tendon thickness (ATT) detected by X-ray as one of the three key items. This threshold was determined based on an old data evaluating the ATT of 36 non-FH individuals that was published in 1977. Although the specificity of these clinical criteria is extremely high due to a strict threshold, there are a significant number of patients with FH whose ATT <9 mm. We aimed to determine a cut-off value of ATT detected by X-ray to differentiate FH and non-FH based on genetic diagnosis. METHODS The individuals (male/female=486/501) with full assessments of genetic analyses for FH-genes (LDLR and PCSK9), serum lipids, and ATT detected by X-ray at the Kanazawa University Hospital and National Cerebral and Cardiovascular Center Research Institute were included in this study. Receiver operating characteristic (ROC) analyses were conducted to determine a better cut-off value of ATT that predicts the pathogenic mutation of FH. RESULTS The ROC analyses revealed that the best cut-off values of ATT are 7.6 mm for male and 7.0 mm for female, with the sensitivities/specificities of 0.83/0.83 for male and 0.86/0.85 for female, respectively. If the thresholds of ATT of 8.0/7.5 mm and 7.5/7.0 mm were applied to the diagnosis of male/female FH, the sensitivities/specificities predicting the pathogenic mutation of FH by the 2017 JAS FH clinical criteria would be 0.82/0.90 and 0.85/0.88, respectively. CONCLUSIONS These results suggest that the cut-off value of ATT detected by X-ray is obviously lower than 9.0 mm, which was adopted by the 2017 JAS FH clinical criteria.
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Affiliation(s)
- Hayato Tada
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences
| | - Mika Hori
- Department of Endocrinology, Research Institute of Environmental Medicine, Nagoya University.,Department of Endocrinology, Nagoya University Graduate School of Medicine.,Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute
| | - Kota Matsuki
- Department of Endocrinology and Metabolism, Hirosaki University Graduate School of Medicine
| | - Masatsune Ogura
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute
| | - Atsushi Nohara
- Department of Genetics, Ishikawa Prefectural Central Hospital
| | - Masa-Aki Kawashiri
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences
| | - Mariko Harada-Shiba
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute
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11
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Yu H. The Ongoing Efforts Toward a Definite Diagnosis of Familial Hypercholesterolemia. JACC. ASIA 2021; 1:90-92. [PMID: 36338369 PMCID: PMC9627824 DOI: 10.1016/j.jacasi.2021.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Affiliation(s)
- Haojie Yu
- Precision Medicine Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Cardiovascular Disease Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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12
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Camacho OFC, Molina GP, Catalá CFM, Reali JR, Cruz RM, Zenteno JC. Familial Hypercholesterolemia: Update and Review. Endocr Metab Immune Disord Drug Targets 2021; 22:198-211. [PMID: 33563162 DOI: 10.2174/1871530321666210208212148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 11/22/2022]
Abstract
Knowledge of epidemiology, genetic etiopathogenesis, diagnostic criteria, and management of familial hypercholesterolemia have increased in the last two decades. Several population studies have shown that familial hypercholesterolemia is more frequent than previously thought, making this entity the most common metabolic disease with monogenic inheritence in the world. Identification of causal heterozygous pathogenic variants in LDLR, APOB, and PCSK9 genes have increased diagnostic accuracy of classical criteria (extreme hypercholesterolemia, personal / family history of premature coronary artery disease or other cardiovascular disease). Genetic screening has been recently introduced in many European countries to detect patients with familial hypercholesterolemia, mainly affected pediatric subjects, asymptomatic or those at the beggining of their disease, with the purpose of increasing surveillance and avoiding complications such as cardiovascular diseases. Cholesterol-lowering drugs should be started as soon as the diagnosis is made. Various combinations between drugs can be used when the goal is not achieved. New therapies, including small interference ribonucleic acids (siRNA) are being tested in different clinical trials.
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Affiliation(s)
| | - Glustein Pozo Molina
- Carrera de Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, . Mexico
| | - Claudia Fabiola Méndez Catalá
- Carrera de Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, . Mexico
| | - Julia Reyes Reali
- Carrera de Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, . Mexico
| | - René Méndez Cruz
- Carrera de Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, . Mexico
| | - Juan Carlos Zenteno
- Biochemistry Department, Faculty Medicine, National Autonomous University of Mexico, Mexico City,. Mexico
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13
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Vasilyev V, Zakharova F, Bogoslovskay T, Mandelshtam M. Familial Hypercholesterolemia in Russia: Three Decades of Genetic Studies. Front Genet 2020; 11:550591. [PMID: 33391333 PMCID: PMC7773754 DOI: 10.3389/fgene.2020.550591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/16/2020] [Indexed: 12/31/2022] Open
Abstract
The first studies of familial hypercholesterolemia (FH) in Russia go back to late 1980-ies. For more than 10 years the research in this field was carried out in Saint-Petersburg, the megapolis in the North-West Russia. Studies were focused on the search for causative mutations in low-density lipoprotein receptor gene (LDLR). Gradually the research was spread to Petrozavodsk in Karelia and in the XXI century two more centers contributed in investigations of genetics of FH, i.e., in Moscow and Novosibirsk. The best studied is the spectrum of mutations in LDLR, though genetic abnormalities in APOB and PCSK9 genes were also considered. Despite that some 40% mutations in LDLR found in Saint-Petersburg and Moscow are referred to as specific for Russian population, and this proportion is even higher in Karelia (ca. 70%), rapid introduction of NGS and intensifying genetic research all over the world result in continuous decrease of these numbers as "Slavic" mutations become documented in other countries. The samplings of genetically characterized patients in Russia were relatively small, which makes difficult to specify major mutations reflecting the national specificity of FH. Moreover, the majority of studies accomplished so far did not explore possible associations of certain mutations with ethnic origin of patients. By now the only exception is the study of Karelian population showing the absence of typical Finnish mutations in the region that borders on Finland. It can be concluded that the important primary research partly characterizing the mutation spectrum in FH patients both in the European and Siberian parts of Russia has been done. However, it seems likely that the most interesting and comprehensive genetic studies of FH in Russia, concerning various mutations in different genes and the variety of ethnic groups in this multi-national country, are still to be undertaken.
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Affiliation(s)
- Vadim Vasilyev
- Institute of Experimental Medicine, Saint Petersburg, Russia
- St. Petersburg State University, Saint Petersburg, Russia
| | - Faina Zakharova
- Institute of Experimental Medicine, Saint Petersburg, Russia
- St. Petersburg State University, Saint Petersburg, Russia
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14
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Wang H, Yang H, Liu Z, Cui K, Zhang Y, Zhang Y, Zhao K, Yin K, Li W, Zhou Z. Targeted Genetic Analysis in a Chinese Cohort of 208 Patients Related to Familial Hypercholesterolemia. J Atheroscler Thromb 2020; 27:1288-1298. [PMID: 32759540 PMCID: PMC7840166 DOI: 10.5551/jat.54593] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
AIM Familial hypercholesterolemia (FH) is the most commonly encountered genetic condition that predisposes individuals to severe autosomal dominant lipid metabolism dysfunction. Although more than 75% of the European population has been scrutinized for FH-causing mutations, the genetic diagnosis proportion among Chinese people remains very low (less than 0.5%). The aim of this study was to identify genetic mutations and help make a precise diagnosis in Chinese FH patients. METHODS We designed a gene panel containing 20 genes responsible for FH and tested 208 unrelated Chinese possible/probable or definite FH probands. In addition, we called LDLR copy number variation (CNVs) with the panel data by panelcn.MOPS, and multiple ligation-dependent probe amplification (MLPA) was used to search for CNVs in LDLR, APOB, and PCSK9. RESULTS A total of 79 probands (38.0%) tested positive for a (likely) pathogenic mutation, most of which were LDLR mutations, and three LDLR CNVs called from the panel data were all successfully confirmed by MLPA analysis. In total, 48 different mutations were identified, including 45 LDLR mutations, 1 APOB mutation, 1 ABCG5 mutation, and 1 APOE mutation. Among them, the five most frequent mutations (LDLR c.1879G>A, c.1747C>T, c.313+1G>A, c.400T>C, and APOB c.10579C>T) were detected. Moreover, we also found that patients with LDLR variants of CNVs and splicing and nonsense had increased low-density lipoprotein cholesterol levels when compared with those who carried missense variants. CONCLUSIONS The spectrum of FH-causing mutations in the Chinese population is refined and expanded. Analyses of FH causal genes have been a great help in clinical diagnosis and have deep implications in disease treatment. These data can serve as a considerable dataset for next-generation sequencing analysis of the Chinese population with FH and contribute to the genetic diagnosis and counseling of FH patients.
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Affiliation(s)
- Hao Wang
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College
| | - Hang Yang
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College
| | - Zhaohui Liu
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College
| | - Kai Cui
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College
| | - Yinhui Zhang
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College
| | - Yujing Zhang
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College
| | - Kun Zhao
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College
| | - Kunlun Yin
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College
| | - Wenke Li
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College
| | - Zhou Zhou
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College
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15
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Vargas-Alarcon G, Perez-Mendez O, Ramirez-Bello J, Posadas-Sanchez R, Gonzalez-Pacheco H, Escobedo G, Nieto-Lima B, Carreon-Torres E, Fragoso JM. The c.*52 A/G and c.*773 A/G Genetic Variants in the UTR'3 of the LDLR Gene Are Associated with the Risk of Acute Coronary Syndrome and Lower Plasma HDL-Cholesterol Concentration. Biomolecules 2020; 10:biom10101381. [PMID: 33003376 PMCID: PMC7599626 DOI: 10.3390/biom10101381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/10/2020] [Accepted: 09/24/2020] [Indexed: 01/07/2023] Open
Abstract
Dyslipidemia has a substantial role in the development of acute coronary syndrome (ACS). Low-density lipoprotein receptor (LDLR) plays a critical role in plasma lipoprotein hemostasis, which is involved in the formation of atherosclerotic plaque. This study aimed to evaluate whether LDLR gene polymorphisms are significantly associated with ACS and the plasma lipids profile. Three LDLR gene polymorphisms located in the UTR′3 region (c.*52 A/G, c.*504 A/G, and c.* 773 A/G) were determined using TaqMan genotyping assays in a group of 618 ACS patients and 666 healthy controls. Plasma lipids profile concentrations were determined by enzymatic/colorimetric assays. Under co-dominant and recessive models, the c.*52 A allele of the c.*52 A/G polymorphism was associated with a higher risk of ACS (OR = 2.02, pCCo-dom = 0.033, and OR = 2.00, pCRes = 0.009, respectively). In the same way, under co-dominant and recessive models, the c.*773 G allele of the c.*773 A/G polymorphism was associated with a high risk of ACS (OR = 2.04, pCCo-dom = 0.027, and OR = 2.01, pCRes = 0.007, respectively). The “AAG” haplotype was associated with a high risk of ACS (OR = 1.22, pC = 0.016). The c.*52 AA genotype showed a lower HDL-C concentration than individuals with the GG genotype. In addition, carriers of c.*773 GG genotype carriers had a lower concentration of the high-density lipoprotein-cholesterol (HDL-C) than subjects with the AA genotype. Our data suggest the association of the LDLRc.*773 A/G and LDLR c.*52 A/G polymorphisms with both the risk of developing ACS and with a lower concentration of HDL-C in the study population.
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Affiliation(s)
- Gilberto Vargas-Alarcon
- Department of Molecular Biology, Instituto Nacional de Cardiología Ignacio Chavez, Mexico City 14080, Mexico; (G.V.-A.); (O.P.-M.); (B.N.-L.); (E.C.-T.)
| | - Oscar Perez-Mendez
- Department of Molecular Biology, Instituto Nacional de Cardiología Ignacio Chavez, Mexico City 14080, Mexico; (G.V.-A.); (O.P.-M.); (B.N.-L.); (E.C.-T.)
- School of Engineering and Scienses, Tecnologico de Monterrey, Campus Ciudad de Mexico, Mexico City 14380, Mexico
| | - Julian Ramirez-Bello
- Research Unit on Endocrine and Metabolic Diseases, Hospital Juarez de México, Mexico City 01460, Mexico;
| | - Rosalinda Posadas-Sanchez
- Department of Endocrinology, Instituto Nacional de Cardiología Ignacio Chavez, Mexico City 14080, Mexico;
| | | | - Galileo Escobedo
- Unit of the Experimental Medicine, Hospital General de Mexico, Dr. Eduardo Liceaga, Mexico City 06726, Mexico;
| | - Betzabe Nieto-Lima
- Department of Molecular Biology, Instituto Nacional de Cardiología Ignacio Chavez, Mexico City 14080, Mexico; (G.V.-A.); (O.P.-M.); (B.N.-L.); (E.C.-T.)
| | - Elizabeth Carreon-Torres
- Department of Molecular Biology, Instituto Nacional de Cardiología Ignacio Chavez, Mexico City 14080, Mexico; (G.V.-A.); (O.P.-M.); (B.N.-L.); (E.C.-T.)
| | - Jose Manuel Fragoso
- Department of Molecular Biology, Instituto Nacional de Cardiología Ignacio Chavez, Mexico City 14080, Mexico; (G.V.-A.); (O.P.-M.); (B.N.-L.); (E.C.-T.)
- Correspondence: ; Tel.: +52-5573-2911 (ext. 26302); Fax: +52-5573-0926
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16
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A systematic review of LDLR, PCSK9, and APOB variants in Asia. Atherosclerosis 2020; 305:50-57. [DOI: 10.1016/j.atherosclerosis.2020.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 04/18/2020] [Accepted: 05/07/2020] [Indexed: 01/08/2023]
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17
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Page MM, Bell DA, Watts GF. Widening the spectrum of genetic testing in familial hypercholesterolaemia: Will it translate into better patient and population outcomes? Clin Genet 2019; 97:543-555. [PMID: 31833051 DOI: 10.1111/cge.13685] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/25/2019] [Accepted: 12/03/2019] [Indexed: 12/14/2022]
Abstract
Familial hypercholesterolaemia (FH) is caused by pathogenic variants in LDLR, APOB or PCSK9. Impaired low-density lipoprotein (LDL) receptor function leads to decreased LDL catabolism and premature atherosclerotic cardiovascular disease (ASCVD). Thousands of LDLR variants are known, but assignation of pathogenicity requires accurate phenotyping, family studies and assessment of LDL receptor function. Precise, genetic diagnosis of FH using targeted next generation sequencing allows for optimal treatment, distinguishing FH from pathogenically distinct disorders requiring different treatment. Polygenic hypercholesterolaemia resulting from an accumulation of LDL cholesterol-raising single nucleotide polymorphisms (SNPs) could also be suspected by this approach. Similarly, ASCVD risk could be estimated by broader sequencing of cholesterol and non-cholesterol-related genes. Both of these areas require further research. The clinical management of FH, focusing on the primary or secondary prevention of ASCVD, has been boosted by PCSK9 inhibitor therapy. The efficacy of PCSK9 inhibitors in homozygous FH may be partly predicted by the LDLR variants. While expanded genetic testing in FH is clinically useful in providing an accurate diagnosis and enabling cost-effective testing of relatives, further research is needed to establish its value in improving clinical outcomes.
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Affiliation(s)
- Michael M Page
- School of Medicine, Faculty of Medicine and Health Sciences, The University of Western Australia, Perth, Australia.,Department of Clinical Biochemistry, Western Diagnostic Pathology, Perth, Australia
| | - Damon A Bell
- School of Medicine, Faculty of Medicine and Health Sciences, The University of Western Australia, Perth, Australia.,Department of Clinical Biochemistry, PathWest Fiona Stanley Hospital and Royal Perth Hospital, Perth, Australia.,Lipid Disorders Clinic, Department of Cardiology, Royal Perth Hospital, Perth, Australia.,Department of Clinical Biochemistry, Clinipath Pathology, Perth, Australia
| | - Gerald F Watts
- School of Medicine, Faculty of Medicine and Health Sciences, The University of Western Australia, Perth, Australia.,Lipid Disorders Clinic, Department of Cardiology, Royal Perth Hospital, Perth, Australia
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18
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Gomez A, Colombo R, Pontoglio A, Helman L, Kaeser L, Giunta G, Parolin ML, Toscanini U, Cuniberti L. Functional analysis of six uncharacterised mutations in LDLR gene. Atherosclerosis 2019; 291:44-51. [PMID: 31689621 DOI: 10.1016/j.atherosclerosis.2019.10.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 01/12/2023]
Abstract
BACKGROUND AND AIMS Familial hypercholesterolemia (FH) is a primary hyperlipemia. It is an autosomal dominant genetic disorder of lipoproteins metabolism mainly caused by mutations in the low density lipoprotein receptor gene (LDLR). We aimed to investigate the functional impact on the low density lipoprotein receptor (LDLR) activity of six uncharacterised variants located in the coding region of the LDLR gene, namely c.428G > T, c.640T > C, c.1708C > T, c.1736A > T, c.1981C > G and c.2114C > G (NM_000527.4) and to attempt to define their clinical status. METHODS Functional studies were carried out using site-directed mutagenesis techniques and expression of LDLR protein in vitro. Results were correlated with clinical data and in silico analyses in order to assess the physiopathological role of these variants. RESULTS This work provides functional information about 6 uncharacterised mutations in LDLR. CONCLUSIONS The six variants studied here appeared to affect the LDLR function in vitro to different degrees, ranging from receptors with normal to slightly reduced activity to receptors exhibiting less than 10% of the wild-type activity. According to these studies and The American College of Medical Genetics and Genomics (ACMG) Standards and Guidelines, two variants could be classified as "Likely Benign" (p.(Ala705Gly) and p.(Leu570Phe)), three variants as "Pathogenic" (p.(Asp579Val), p.(Cys143Phe) and p.(Trp214Arg)) and one variant as "Likely Pathogenic" (p.(Pro661Ala)).
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Affiliation(s)
- Andrea Gomez
- Favaloro University, Lipids and Atherosclerosis Laboratory - IMETTyB - CONICET, Buenos Aires, Argentina; PRICAI-Favaloro Foundation, Buenos Aires, Argentina.
| | - Roberto Colombo
- Niguarda Ca' Granda Metropolitan Hospital, Center for the Study of Rare Hereditary Diseases, Milan, Italy; Faculty of Medicine Catholic University of the Sacred Heart, IRCCS "Agostino Gemelli" University Hospital, Rome, Italy
| | - Alessandro Pontoglio
- Niguarda Ca' Granda Metropolitan Hospital, Center for the Study of Rare Hereditary Diseases, Milan, Italy
| | - Lorena Helman
- Favaloro Foundation University Hospital, Metabolic Unit Service, Buenos Aires, Argentina
| | | | - Gustavo Giunta
- Favaloro University, Lipids and Atherosclerosis Laboratory - IMETTyB - CONICET, Buenos Aires, Argentina; Favaloro Foundation University Hospital, Metabolic Unit Service, Buenos Aires, Argentina
| | - Maria L Parolin
- Instituto de Diversidad y Evolución Austral. CCT Centpat-CONICET, Puerto Madryn, Argentina
| | | | - Luis Cuniberti
- Favaloro University, Lipids and Atherosclerosis Laboratory - IMETTyB - CONICET, Buenos Aires, Argentina
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19
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily G, Member 5/blood
- ATP Binding Cassette Transporter, Subfamily G, Member 5/genetics
- ATP Binding Cassette Transporter, Subfamily G, Member 8/blood
- ATP Binding Cassette Transporter, Subfamily G, Member 8/genetics
- Adaptor Proteins, Signal Transducing/blood
- Adaptor Proteins, Signal Transducing/genetics
- Apolipoprotein B-100/blood
- Apolipoprotein B-100/genetics
- Apolipoproteins E/blood
- Apolipoproteins E/genetics
- Cholesterol, LDL/blood
- Databases, Genetic
- Gene Expression
- Genomics/methods
- Humans
- Hyperlipoproteinemia Type II/blood
- Hyperlipoproteinemia Type II/genetics
- Hyperlipoproteinemia Type II/pathology
- Lipid Metabolism/genetics
- Lipoproteins/blood
- Lipoproteins/genetics
- Mutation
- Proprotein Convertase 9/blood
- Proprotein Convertase 9/genetics
- Receptors, LDL/blood
- Receptors, LDL/genetics
- Sterol Esterase/blood
- Sterol Esterase/genetics
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Affiliation(s)
- Ana C Alves
- Unidade de I&D, Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Joana R Chora
- Unidade de I&D, Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Mafalda Bourbon
- Unidade de I&D, Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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20
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Predictable and precise template-free CRISPR editing of pathogenic variants. Nature 2018; 563:646-651. [PMID: 30405244 DOI: 10.1038/s41586-018-0686-x] [Citation(s) in RCA: 325] [Impact Index Per Article: 54.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 09/10/2018] [Indexed: 12/26/2022]
Abstract
Following Cas9 cleavage, DNA repair without a donor template is generally considered stochastic, heterogeneous and impractical beyond gene disruption. Here, we show that template-free Cas9 editing is predictable and capable of precise repair to a predicted genotype, enabling correction of disease-associated mutations in humans. We constructed a library of 2,000 Cas9 guide RNAs paired with DNA target sites and trained inDelphi, a machine learning model that predicts genotypes and frequencies of 1- to 60-base-pair deletions and 1-base-pair insertions with high accuracy (r = 0.87) in five human and mouse cell lines. inDelphi predicts that 5-11% of Cas9 guide RNAs targeting the human genome are 'precise-50', yielding a single genotype comprising greater than or equal to 50% of all major editing products. We experimentally confirmed precise-50 insertions and deletions in 195 human disease-relevant alleles, including correction in primary patient-derived fibroblasts of pathogenic alleles to wild-type genotype for Hermansky-Pudlak syndrome and Menkes disease. This study establishes an approach for precise, template-free genome editing.
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21
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Affiliation(s)
- Jacqueline S Dron
- From the Department of Biochemistry (J.S.D., J.L., R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Robarts Research Institute (J.S.D., J.L., R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Julieta Lazarte
- From the Department of Biochemistry (J.S.D., J.L., R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Robarts Research Institute (J.S.D., J.L., R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Medicine (J.L., R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Robert A Hegele
- From the Department of Biochemistry (J.S.D., J.L., R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Robarts Research Institute (J.S.D., J.L., R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Medicine (J.L., R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
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22
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Iacocca MA, Wang J, Sarkar S, Dron JS, Lagace T, McIntyre AD, Lau P, Robinson JF, Yang P, Knoll JH, Cao H, McPherson R, Hegele RA. Whole-Gene Duplication of PCSK9 as a Novel Genetic Mechanism for Severe Familial Hypercholesterolemia. Can J Cardiol 2018; 34:1316-1324. [DOI: 10.1016/j.cjca.2018.07.479] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 07/30/2018] [Accepted: 07/31/2018] [Indexed: 01/23/2023] Open
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23
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Zhang X, Sessa WC, Fernández-Hernando C. Endothelial Transcytosis of Lipoproteins in Atherosclerosis. Front Cardiovasc Med 2018; 5:130. [PMID: 30320124 PMCID: PMC6167422 DOI: 10.3389/fcvm.2018.00130] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/03/2018] [Indexed: 12/12/2022] Open
Abstract
Seminal studies from Nikolai Anichckov identified the accumulation of cholesterol in the arteries as the initial event that lead to the formation of atherosclerotic plaques. Further studies by Gofman and colleagues demonstrated that high levels of circulating low-density lipoprotein cholesterol (LDL-C) was responsible for the accelerated atherosclerosis observed in humans. These findings were confirmed by numerous epidemiological studies which identified elevated LDL-C levels as a major risk factor for cardiovascular disease. LDL infiltrates in the arterial wall and interacts with the proteoglycan matrix promoting the retention and modification of LDL to a toxic form, which results in endothelial cell (EC) activation and vascular inflammation. Despite the relevance of LDL transport across the endothelium during atherogenesis, the molecular mechanism that control this process is still not fully understood. A number of studies have recently demonstrated that low density lipoprotein (LDL) transcytosis across the endothelium is dependent on the function of caveolae, scavenger receptor B1 (SR-B1), activin receptor-like kinase 1 (ALK1), and LDL receptor (LDLR), whereas high-density lipoproteins (HDL) and its major protein component apolipoprotein AI transcytose ECs through SR-B1, ATP-Binding cassette transporter A1 (ABCA1) and ABCG1. In this review article, we briefly summarize the function of the EC barrier in regulating lipoprotein transport, and its relevance during the progression of atherosclerosis. A better understanding of the mechanisms that mediate lipoprotein transcytosis across ECs will help to develop therapies targeting the early events of atherosclerosis and thus exert potential benefits for treating atherosclerotic vascular disease.
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Affiliation(s)
- Xinbo Zhang
- Vascular Biology and Therapeutics Program, Integrative Cell Signaling and Neurobiology of Metabolism Program, Department of Comparative Medicine and Department of Pathology, Yale University School of Medicine, New Haven, CT, United States
| | - William C Sessa
- Vascular Biology and Therapeutics Program, Department of Pharmacology, Yale University School of Medicine, New Haven, CT, United States
| | - Carlos Fernández-Hernando
- Vascular Biology and Therapeutics Program, Integrative Cell Signaling and Neurobiology of Metabolism Program, Department of Comparative Medicine and Department of Pathology, Yale University School of Medicine, New Haven, CT, United States
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24
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Dyslipidemias in clinical practice. Clin Chim Acta 2018; 487:117-125. [PMID: 30201369 DOI: 10.1016/j.cca.2018.09.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 09/06/2018] [Accepted: 09/06/2018] [Indexed: 01/14/2023]
Abstract
Most dyslipidemic conditions have been linked to an increased risk of cardiovascular disease. Over the past few years major advances have been made regarding the genetic and metabolic basis of dyslipidemias. Detailed characterization of the genetic basis of familial lipid disorders and knowledge concerning the effects of environmental factors on the expression of dyslipidemias have increased substantially, contributing to a better diagnosis in individual patients. In addition to these developments, therapeutic options to lower cholesterol levels in clinical practice have expanded even further in patients with familial hypercholesterolemia and in subjects with cardiovascular disease. Finally, promising upcoming therapeutic lipid lowering strategies will be reviewed. All these advances will be discussed in relation to current clinical practice with special focus on common lipid disorders including familial dyslipidemias.
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Zhuo JC, Cai DK, Xie KF, Gan HN, Li SS, Huang XJ, Huang D, Zhang CZ, Li RY, Chen YX, Zeng XH. Mechanism of YLTZ on glycolipid metabolism based on UPLC/TOF/MS metabolomics. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1097-1098:128-141. [PMID: 30241074 DOI: 10.1016/j.jchromb.2018.08.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/20/2018] [Accepted: 08/21/2018] [Indexed: 12/21/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is a metabolic disease characterized by dysfunction of glycolipid metabolism. YLTZ is used to treat hyperlipidemia, yet its hypolipidemic and hypoglycemic mechanism on T2DM are unknown. Thus, UPLC/TOF/MS was applied in this study to identify the potential bio-markers, and deduce the possible metabolic pathways. According to bio-indexes, the increased blood lipid levels, including TC, TG, LDL and FA, and the decreased HDL, the elevated glucose, reduced insulin level and impaired OGTT were observed in diabetic rat model. While YLTZ can decrease the lipid levels and glucose content, as well as increased insulin standards and improve OGTT. After data from UPLC/TOF/MS processed, 17 metabolites were obtained, including phospholipids (LPCs, PCs and PGP (18:1)), beta-oxidation production (HAA, VAG and CNE) and precursors (THA), bile acid (CA, CDCA and IDCA), hydrolysate of TG (MG (22:4)), glycometabolism (G6P), cholesterol-driven synthetics (ADO) and production of arachidonate acid (THETA). As a result, YLTZ was able to reduce LPCs, PCs, PGP (18:1), HAA, VAG, CNE, CA, ADO and THETA, as well as enhance MG (22:4) and G6P. After analyzing results, several metabolic pathways were deduced, which containing, cholesterol synthesis and elimination, FA beta-oxidation, TG hydrolysis, phospholipids synthesis, glycolysis, gluconeogenesis and inflammation. Consequently, YLTZ performed to prohibit the FA beta-oxidation, synthesis of cholesterol and phospholipids, gluconeogenesis and inflammation level, as well as promote TG hydrolysis, glycolysis and blood circulation. Hence, applying metabonomics in TCM research can uncover its pharmacological edges, elucidating comprehensively that YLTZ has capacity of hypolipidemic, hypoglycemic and promoting blood circulation, matching the effect of removing blood stasis, eliminating phlegm and dampness.
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Affiliation(s)
- Jun-Cheng Zhuo
- Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Guangdong Province Engineering Technology Research Institute of T.C.M., Guangzhou 510095, China; Guangdong Second Traditional Chinese Medicine Hospital, Guangzhou, Guangdong 510095, China
| | - Da-Ke Cai
- Guangdong Province Engineering Technology Research Institute of T.C.M., Guangzhou 510095, China; Guangdong Second Traditional Chinese Medicine Hospital, Guangzhou, Guangdong 510095, China
| | - Kai-Feng Xie
- Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Guangdong Province Engineering Technology Research Institute of T.C.M., Guangzhou 510095, China; Guangdong Second Traditional Chinese Medicine Hospital, Guangzhou, Guangdong 510095, China
| | - Hai-Ning Gan
- Guangdong Province Engineering Technology Research Institute of T.C.M., Guangzhou 510095, China; Guangdong Second Traditional Chinese Medicine Hospital, Guangzhou, Guangdong 510095, China
| | - Sha-Sha Li
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xue-Jun Huang
- Guangdong Province Engineering Technology Research Institute of T.C.M., Guangzhou 510095, China; Guangdong Second Traditional Chinese Medicine Hospital, Guangzhou, Guangdong 510095, China
| | - Dane Huang
- Guangdong Province Engineering Technology Research Institute of T.C.M., Guangzhou 510095, China; Guangdong Second Traditional Chinese Medicine Hospital, Guangzhou, Guangdong 510095, China
| | - Cheng-Zhe Zhang
- Guangdong Province Engineering Technology Research Institute of T.C.M., Guangzhou 510095, China; Guangdong Second Traditional Chinese Medicine Hospital, Guangzhou, Guangdong 510095, China
| | - Ru-Yue Li
- Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Guangdong Province Engineering Technology Research Institute of T.C.M., Guangzhou 510095, China; Guangdong Second Traditional Chinese Medicine Hospital, Guangzhou, Guangdong 510095, China
| | - Yu-Xing Chen
- Guangdong Province Engineering Technology Research Institute of T.C.M., Guangzhou 510095, China; Guangdong Second Traditional Chinese Medicine Hospital, Guangzhou, Guangdong 510095, China.
| | - Xiao-Hui Zeng
- Guangdong Province Engineering Technology Research Institute of T.C.M., Guangzhou 510095, China; Guangdong Second Traditional Chinese Medicine Hospital, Guangzhou, Guangdong 510095, China.
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Abstract
PURPOSE OF REVIEW DNA copy number variations (CNVs) are quantitative structural rearrangements that include deletions, duplications, and higher order amplifications. Because of technical limitations, the contribution of this common form of genetic variation to regulation of lipid metabolism and dyslipidemia has been underestimated. RECENT FINDINGS Recent literature involving CNVs and dyslipidemias has focused mainly on rare CNVs causing familial hypercholesterolemia, and a common CNV polymorphism as the major determinant of lipoprotein(a) plasma concentrations. Additionally, there is tantalizing evidence of largely uninvestigated but plausible presence of CNVs underlying other dyslipidemias. We also discuss the future role of improved technologies in facilitating more economic, routine CNV assessment in dyslipidemias. SUMMARY CNVs account for large proportion of human genetic variation and are already known to contribute to susceptibility of dyslipidemias, particularly in about 10% of familial hypercholesterolemia patients. Increasing availability of clinical next-generation sequencing and bioinformatics presents a cost-effective opportunity for novel CNV discoveries in dyslipidemias.
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Defesche JC, Gidding SS, Harada-Shiba M, Hegele RA, Santos RD, Wierzbicki AS. Familial hypercholesterolaemia. Nat Rev Dis Primers 2017; 3:17093. [PMID: 29219151 DOI: 10.1038/nrdp.2017.93] [Citation(s) in RCA: 278] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Familial hypercholesterolaemia is a common inherited disorder characterized by abnormally elevated serum levels of low-density lipoprotein (LDL) cholesterol from birth, which in time can lead to cardiovascular disease (CVD). Most cases are caused by autosomal dominant mutations in LDLR, which encodes the LDL receptor, although mutations in other genes coding for proteins involved in cholesterol metabolism or LDLR function and processing, such as APOB and PCSK9, can also be causative, although less frequently. Several sets of diagnostic criteria for familial hypercholesterolaemia are available; common diagnostic features are an elevated LDL cholesterol level and a family history of hypercholesterolaemia or (premature) CVD. DNA-based methods to identify the underlying genetic defect are desirable but not essential for diagnosis. Cascade screening can contribute to early diagnosis of the disease in family members of an affected individual, which is crucial because familial hypercholesterolaemia can be asymptomatic for decades. Clinical severity depends on the nature of the gene that harbours the causative mutation, among other factors, and is further modulated by the type of mutation. Lifelong LDL cholesterol-lowering treatment substantially improves CVD-free survival and longevity. Statins are the first-line therapy, but additional drugs, such as ezetimibe, bile acid sequestrants, PCSK9 inhibitors and other emerging therapies, are often required.
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Affiliation(s)
- Joep C Defesche
- Department of Clinical Genetics, Academic Medical Centre, PO Box 22 660, University of Amsterdam, 1100 DD Amsterdam, The Netherlands
| | - Samuel S Gidding
- Nemours Cardiac Center, Alfred I. DuPont Hospital for Children, Wilmington, Delaware, USA
| | - Mariko Harada-Shiba
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan
| | - Robert A Hegele
- Department of Medicine, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,Robarts Research Institute, 4288A 1151 Richmond Street North, University of Western Ontario, N6A 5B7 London, Ontario, Canada
| | - Raul D Santos
- Lipid Clinic Heart Institute (Incor), University of São Paulo, Medical School Hospital, São Paulo, Brazil.,Preventive Medicine Centre and Cardiology Program Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Anthony S Wierzbicki
- Metabolic Medicine and Chemical Pathology, Guy's and St. Thomas' Hospitals, London, UK
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Lima-Martínez MM, Paoli M, Vázquez-Cárdenas A, Magaña-Torres MT, Guevara O, Muñoz MC, Parrilla-Alvarez A, Márquez Y, Medeiros A, Bourbon M. Frecuencia, aspectos clínicos y moleculares de la hipercolesterolemia familiar en una unidad de endocrinología de Ciudad Bolívar, Venezuela. ENDOCRINOL DIAB NUTR 2017; 64:432-439. [DOI: 10.1016/j.endinu.2017.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/28/2017] [Accepted: 05/29/2017] [Indexed: 10/19/2022]
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Iacocca MA, Wang J, Dron JS, Robinson JF, McIntyre AD, Cao H, Hegele RA. Use of next-generation sequencing to detect LDLR gene copy number variation in familial hypercholesterolemia. J Lipid Res 2017; 58:2202-2209. [PMID: 28874442 PMCID: PMC5665663 DOI: 10.1194/jlr.d079301] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/31/2017] [Indexed: 12/14/2022] Open
Abstract
Familial hypercholesterolemia (FH) is a heritable condition of severely elevated LDL cholesterol, caused predominantly by autosomal codominant mutations in the LDL receptor gene (LDLR). In providing a molecular diagnosis for FH, the current procedure often includes targeted next-generation sequencing (NGS) panels for the detection of small-scale DNA variants, followed by multiplex ligation-dependent probe amplification (MLPA) in LDLR for the detection of whole-exon copy number variants (CNVs). The latter is essential because ∼10% of FH cases are attributed to CNVs in LDLR; accounting for them decreases false negative findings. Here, we determined the potential of replacing MLPA with bioinformatic analysis applied to NGS data, which uses depth-of-coverage analysis as its principal method to identify whole-exon CNV events. In analysis of 388 FH patient samples, there was 100% concordance in LDLR CNV detection between these two methods: 38 reported CNVs identified by MLPA were also successfully detected by our NGS method, while 350 samples negative for CNVs by MLPA were also negative by NGS. This result suggests that MLPA can be removed from the routine diagnostic screening for FH, significantly reducing associated costs, resources, and analysis time, while promoting more widespread assessment of this important class of mutations across diagnostic laboratories.
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Affiliation(s)
- Michael A Iacocca
- Departments of Medicine and Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada.,Robarts Research Institute, Western University, London, Ontario, Canada
| | - Jian Wang
- Robarts Research Institute, Western University, London, Ontario, Canada
| | - Jacqueline S Dron
- Departments of Medicine and Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada.,Robarts Research Institute, Western University, London, Ontario, Canada
| | - John F Robinson
- Robarts Research Institute, Western University, London, Ontario, Canada
| | - Adam D McIntyre
- Robarts Research Institute, Western University, London, Ontario, Canada
| | - Henian Cao
- Robarts Research Institute, Western University, London, Ontario, Canada
| | - Robert A Hegele
- Departments of Medicine and Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada .,Robarts Research Institute, Western University, London, Ontario, Canada
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31
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Calandra S, Tarugi P, Bertolini S. Impact of rare variants in autosomal dominant hypercholesterolemia causing genes. Curr Opin Lipidol 2017; 28:267-272. [PMID: 28323660 DOI: 10.1097/mol.0000000000000414] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
PURPOSE OF REVIEW The systematic analysis of the major candidate genes in autosomal dominant hypercholesterolemia (ADH) and the use of next-generation sequencing (NGS) technology have made possible the discovery of several rare gene variants whose pathogenic effect in most cases remains poorly defined. RECENT FINDINGS One major advance in the field has been the adoption of a set of international guidelines for the assignment of pathogenicity to low-density lipoprotein receptor (LDLR) gene variants based on the use of softwares, complemented with data available from literature and public databases. The clinical impact of several novel rare variants in LDLR, APOB, PCSK9, APOE genes have been reported in large studies describing patients with ADH found to be homozygotes/compound heterozygotes, double heterozygotes, or simple heterozygotes. In-vitro functional studies have been conducted to clarify the effect of some rare ApoB variants on LDL binding to LDLR and the impact of a rare ApoE variant on the uptake of VLDL and LDL by hepatocytes. SUMMARY The update of the ADH gene variants database and the classification of variants in categories of pathogenicity is a major advance in the understanding the pathophysiology of ADH and in the management of this disorder. The studies of molecularly characterized patients with ADH have emphasized the impact of a specific variant and the variable clinical expression of different genotypes. The functional studies of some variants have increased our understanding of the molecular bases of some forms of ADH.
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Affiliation(s)
- Sebastiano Calandra
- aDepartment of Biomedical, Metabolic and Neural Sciences bDepartment of Life Sciences, University of Modena and Reggio Emilia, Modena cDepartment of Internal Medicine, University of Genova, Genova, Italy
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32
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Iacocca MA, Hegele RA. Recent advances in genetic testing for familial hypercholesterolemia. Expert Rev Mol Diagn 2017; 17:641-651. [DOI: 10.1080/14737159.2017.1332997] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Michael A. Iacocca
- Departments of Medicine and Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Robert A. Hegele
- Departments of Medicine and Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
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