1
|
Mori AA, Malaquias VB, Bonjour K, Ferreira GM, Bortolin RH, Borges JB, Oliveira VFD, Gonçalves RM, Faludi AA, Bastos GM, Thurow H, Sampaio MF, Ciconelli RM, Cury AN, Fajardo CM, Hirata RDC, Hirata MH. Effects of LDLR variants rs5928, rs750518671 and rs879254797 on protein structure and functional activity in HepG2 cells transfected with CRISPR/Cas9 constructs. Gene 2024; 890:147821. [PMID: 37739193 DOI: 10.1016/j.gene.2023.147821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/24/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
Familial Hypercholesterolemia (FH) is a genetic disorder associated with premature atherosclerosis and increased risk of cardiovascular diseases. LDLR deleterious mutations are associated with FH, however the role of some missense variants in FH pathogenicity remains to be elucidated. This study explored the predictive impact of LDLR missense variants on protein structure and investigated their functional effects on LDLR expression in HepG2 cells transfected with CRISPR/Cas9 constructs. FH (n = 287) and non-FH patients (n = 45) were selected, and lipid profile was obtained from medical records. LDLR variants were identified using an exon-targeted gene sequencing strategy, considering its cost-effective to increase accuracy in the identification step of the most likely FH-related variants in a less laborious process. LDLR variants were selected based on conflicting pathogenicity results found in Clinvar, in silico prediction tools, affected LDLR domains, and less common variants considering minor allele frequency < 0.05. Molecular modeling studies were used to predict the effects of LDLR missense variants on protein structure. Recombinant LDLR variants were constructed using CRISPR/Cas9 system and were used to transfect HepG2 cells. Functional assays in transfected cells were performed to assess LDLR expression using flow cytometry and western blotting, and LDLR activity using flow cytometry and confocal microscopy. The variants rs121908039 (c.551G>A, p.C184Y), rs879254797 (c.1118G>A, p.G373D), rs28941776 (c.1646G>A, p.G549D), rs750518671 (c.2389G>C, p.V797L), rs5928 (c.2441G>A, p.R814Q) and rs137853964 (c.2479G>A, p.V827I) were selected for molecular docking analysis. The p.C184Y exhibited a favorable energy change for protein stability due to its interaction with EGF-A/EGF-B regions; p.G373D and p.G549D displayed intermediate energy changes; and p.R814Q and p.V827I showed smaller energy changes. The results of functional assays showed that p.G373D, p.V797L and p.R814Q reduced LDLR expression and activity (p < 0.05). Microscopic analysis of the p.V797L and p.G373D variants revealed altered lipid localization and accumulation in transfected HepG2 cells. Carriers of p.G549D, p.V797L and p.R814Q had higher LDL cholesterol levels than non-FH group, and (p < 0.05). p.G373D and p.G549D were associated with clinical manifestations of FH. In conclusion, the p.C184Y, p.G373D, p.G549D and p.R814Q variants alter protein stability and intramolecular interactions, while p.V797L has a minimal impact on protein stability, and p.V827I has no significant intramolecular interactions. p.G373D, p.V767L and p.R814Q are associated with impaired LDLR expression and activity.
Collapse
Affiliation(s)
- Augusto Akira Mori
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Vanessa Barbosa Malaquias
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Kennedy Bonjour
- Laboratory of Molecular and Morphological Pathology, Department of Pathology, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo 05508-000, Brazil; Laboratory Membrane Biochemistry and Transport, Department of Cell Biology and Infection, Institut Pasteur, Paris 75724 Paris Cedex 15, France
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | | | - Jéssica Bassani Borges
- Laboratory of Molecular Research in Cardiology, Institute of Cardiology Dante Pazzanese, Sao Paulo 04012-909, Brazil; Department of Research, Hospital Beneficência Portuguesa de Sao Paulo, Sao Paulo 01323-001, Brazil
| | - Victor Fernandes de Oliveira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil; Laboratory of Physiological Genomics of Mental Health, Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo 05508-000, Brazil
| | | | - Andre Arpad Faludi
- Medical Clinic Division, Institute of Cardiology Dante Pazzanese, Sao Paulo 04012-909, Brazil
| | - Gisele Monteiro Bastos
- Department of Research, Hospital Beneficência Portuguesa de Sao Paulo, Sao Paulo 01323-001, Brazil
| | - Helena Thurow
- Department of Research, Hospital Beneficência Portuguesa de Sao Paulo, Sao Paulo 01323-001, Brazil
| | - Marcelo Ferraz Sampaio
- Department of Cardiology, Hospital Beneficência Portuguesa de São Paulo, Sao Paulo 01323-001, Brazil
| | | | - Adriano Namo Cury
- Department of Endocrinology, Hospital Beneficência Portuguesa de Sao Paulo, Sao Paulo 01323-001, Brazil
| | - Cristina Moreno Fajardo
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Rosario Dominguez Crespo Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Mario Hiroyuki Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil.
| |
Collapse
|
2
|
Barbosa TKA, Hirata RDC, Ferreira GM, Borges JB, Oliveira VFD, Gorjão R, Marçal ERDS, Gonçalves RM, Faludi AA, Freitas RCCD, Dagli-Hernandez C, Bortolin RH, Bastos GM, Pithon-Curi TC, Nader HB, Hirata MH. LDLR missense variants disturb structural conformation and LDLR activity in T-lymphocytes of Familial hypercholesterolemia patients. Gene X 2023; 853:147084. [PMID: 36464169 DOI: 10.1016/j.gene.2022.147084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/16/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
Familial hypercholesterolemia (FH) is caused by deleterious mutations in the LDLR that increase markedly low-density lipoprotein (LDL) cholesterol and cause premature atherosclerotic cardiovascular disease. Functional effects of pathogenic LDLR variants identified in Brazilian FH patients were assessed using in vitro and in silico studies. Variants in LDLR and other FH-related genes were detected by exon-target gene sequencing. T-lymphocytes were isolated from 26 FH patients, and 3 healthy controls and LDLR expression and activity were assessed by flow cytometry and confocal microscopy. The impact of LDLR missense variants on protein structure was assessed by molecular modeling analysis. Ten pathogenic or likely pathogenic LDLR variants (six missense, two stop-gain, one frameshift, and one in splicing region) and six non-pathogenic variants were identified. Carriers of pathogenic and non-pathogenic variants had lower LDL binding and uptake in activated T-lymphocytes compared to controls (p < 0.05), but these variants did not influence LDLR expression on cell surface. Reduced LDL binding and uptake was also observed in carriers of LDLR null and defective variants. Modeling analysis showed that p.(Ala431Thr), p.(Gly549Asp) and p.(Gly592Glu) disturb intramolecular interactions of LDLR, and p.(Gly373Asp) and p.(Ile488Thr) reduce the stability of the LDLR protein. Docking and molecular interactions analyses showed that p.(Cys184Tyr) and p.(Gly373Asp) alter interaction of LDLR with Apolipoprotein B (ApoB). In conclusion, LDLR null and defective variants reduce LDL binding capacity and uptake in activated T-lymphocytes of FH patients and LDLR missense variants affect LDLR conformational stability and dissociation of the LDLR-ApoB complex, having a potential role in FH pathogenesis.
Collapse
Affiliation(s)
- Thais Kristini Almendros Barbosa
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Rosario Dominguez Crespo Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil; Laboratory of Molecular Research in Cardiology, Institute Dante Pazzanese of Cardiology, Sao Paulo 04012-909, Brazil
| | - Jéssica Bassani Borges
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil; Laboratory of Molecular Research in Cardiology, Institute Dante Pazzanese of Cardiology, Sao Paulo 04012-909, Brazil
| | - Victor Fernandes de Oliveira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Renata Gorjão
- Interdisciplinary Post-graduate Program in Health Sciences, Cruzeiro do Sul University, Sao Paulo 01506-000, Brazil
| | - Elisangela Rodrigues da Silva Marçal
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil; Laboratory of Molecular Research in Cardiology, Institute Dante Pazzanese of Cardiology, Sao Paulo 04012-909, Brazil
| | | | - André Arpad Faludi
- Medical Clinic Division, Institute Dante Pazzanese of Cardiology, Sao Paulo 04012-909, Brazil
| | - Renata Caroline Costa de Freitas
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil; Department of Cardiac Surgery, Boston Children's Hospital, Boston, MA 02115, United States
| | - Carolina Dagli-Hernandez
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Raul Hernandes Bortolin
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil; Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, United States
| | - Gisele Medeiros Bastos
- Laboratory of Molecular Research in Cardiology, Institute Dante Pazzanese of Cardiology, Sao Paulo 04012-909, Brazil; Department of Teaching and Research, Real e Benemerita Associaçao Portuguesa de Beneficiencia, Sao Paulo 01323-001, Brazil
| | - Tania Cristina Pithon-Curi
- Interdisciplinary Post-graduate Program in Health Sciences, Cruzeiro do Sul University, Sao Paulo 01506-000, Brazil
| | - Helena Bonciani Nader
- Department of Biochemistry, School of Medicine, Federal University of Sao Paulo, Sao Paulo 04044-020, Brazil
| | - Mario Hiroyuki Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil.
| |
Collapse
|
3
|
Bhunia SS, Saxena AK. Efficiency of Homology Modeling Assisted Molecular Docking in G-protein Coupled Receptors. Curr Top Med Chem 2021; 21:269-294. [PMID: 32901584 DOI: 10.2174/1568026620666200908165250] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/20/2020] [Accepted: 09/01/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Molecular docking is in regular practice to assess ligand affinity on a target protein crystal structure. In the absence of protein crystal structure, the homology modeling or comparative modeling is the best alternative to elucidate the relationship details between a ligand and protein at the molecular level. The development of accurate homology modeling (HM) and its integration with molecular docking (MD) is essential for successful, rational drug discovery. OBJECTIVE The G-protein coupled receptors (GPCRs) are attractive therapeutic targets due to their immense role in human pharmacology. The GPCRs are membrane-bound proteins with the complex constitution, and the understanding of their activation and inactivation mechanisms is quite challenging. Over the past decade, there has been a rapid expansion in the number of solved G-protein-coupled receptor (GPCR) crystal structures; however, the majority of the GPCR structures remain unsolved. In this context, HM guided MD has been widely used for structure-based drug design (SBDD) of GPCRs. METHODS The focus of this review is on the recent (i) developments on HM supported GPCR drug discovery in the absence of GPCR crystal structures and (ii) application of HM in understanding the ligand interactions at the binding site, virtual screening, determining receptor subtype selectivity and receptor behaviour in comparison with GPCR crystal structures. RESULTS The HM in GPCRs has been extremely challenging due to the scarcity in template structures. In such a scenario, it is difficult to get accurate HM that can facilitate understanding of the ligand-receptor interactions. This problem has been alleviated to some extent by developing refined HM based on incorporating active /inactive ligand information and inducing protein flexibility. In some cases, HM proteins were found to outscore crystal structures. CONCLUSION The developments in HM have been highly operative to gain insights about the ligand interaction at the binding site and receptor functioning at the molecular level. Thus, HM guided molecular docking may be useful for rational drug discovery for the GPCRs mediated diseases.
Collapse
Affiliation(s)
- Shome S Bhunia
- Global Institute of Pharmaceutical Education and Research, Kashipur, Uttarakhand, India
| | - Anil K Saxena
- Division of Medicinal and Process Chemistry, CSIR-CDRI, Lucknow 226031, India
| |
Collapse
|
4
|
Sánchez A, Bustos P, Honorato P, Burgos CF, Barriga N, Jannes CE, Sáez K, Alonso R, Asenjo S, Radojkovic C. Phenotypic characterization and predictive analysis of p.Asp47Asn LDL receptor mutation associated with Familial Hypercholesterolemia in a Chilean population. J Clin Lipidol 2021; 15:366-374.e1. [PMID: 33547002 DOI: 10.1016/j.jacl.2021.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/22/2020] [Accepted: 01/11/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Familial hypercholesterolemia (FH) is an inherited disorder mainly caused by mutations in the LDL receptor (LDL-R) and characterized by elevation of low-density lipoprotein cholesterol (LDL-C) levels and premature cardiovascular disease. OBJECTIVE In this study, we evaluated the clinical phenotype of the p.Asp47Asn, described as an uncertain pathogenic variant, and its effect on the structure of LDL-R and ligand interactions with apolipoproteins. METHODS 27 children and adolescents with suspected FH diagnosis were recruited from a pediatric endocrinology outpatient clinic. Blood samples were collected after 12 h fasting for lipid profile analysis. DNA sequencing was performed for six FH-related genes by Ion Torrent PGM platform and copy number variation by MLPA. For index cases, a familial cascade screening was done restricted to the same mutation found in the index case. In silico analysis were developed to evaluate the binding capacity of LDL-R to apolipoproteins B100 and E. RESULTS Lipid profile in children and adolescents demonstrated higher LDL-C levels in p.Asp47Asn carriers compared to the wild type genotype. In silico analysis predicted a reduction in the binding capacity of the ligand-binding modules LA1-2 of p.Asp47Asn LDL-R for ApoB100 and ApoE, which was not produced by local structural changes or folding defects but as a consequence of a decreased apparent affinity for both apolipoproteins. CONCLUSION The clinical phenotype and the structural effects of p.Asp47Asn LDL-R mutation suggest that this variant associates to FH.
Collapse
Affiliation(s)
- Andrea Sánchez
- Departamento de Bioquímica Clínica e Inmunología, Facultad de Farmacia, Universidad de Concepción, Concepción, Chile
| | - Paulina Bustos
- Departamento de Bioquímica Clínica e Inmunología, Facultad de Farmacia, Universidad de Concepción, Concepción, Chile
| | - Paula Honorato
- Departamento de Bioquímica Clínica e Inmunología, Facultad de Farmacia, Universidad de Concepción, Concepción, Chile
| | - Carlos F Burgos
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Natalia Barriga
- Departamento de Bioquímica Clínica e Inmunología, Facultad de Farmacia, Universidad de Concepción, Concepción, Chile
| | - Cinthia E Jannes
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of São Paulo Medical School Hospital, São Paulo, Brazil
| | - Katia Sáez
- Departamento de Estadística, Facultad de Ciencias Físicas y Matemáticas, Universidad de Concepción, Concepción, Chile
| | - Rodrigo Alonso
- Center for Advanced Metabolic Medicine and Nutrition, Santiago de Chile. Fundación Hipercolesterolemia Familiar, Madrid, Spain
| | - Sylvia Asenjo
- Departamento de Pediatría, Facultad de Medicina, Universidad de Concepción, Concepción, Chile
| | - Claudia Radojkovic
- Departamento de Bioquímica Clínica e Inmunología, Facultad de Farmacia, Universidad de Concepción, Concepción, Chile.
| |
Collapse
|
5
|
de Paiva Silvino JP, Jannes CE, Tada MT, Lima IR, Silva IDFO, Pereira AC, Gomes KB. Cascade screening and genetic diagnosis of familial hypercholesterolemia in clusters of the Southeastern region from Brazil. Mol Biol Rep 2020; 47:9279-9288. [PMID: 33231818 DOI: 10.1007/s11033-020-06014-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/16/2020] [Indexed: 01/04/2023]
Abstract
Familial hypercholesterolemia (FH) is an autosomal dominant genetic disease characterized by high levels of low-density lipoprotein-cholesterol (LDLc), associated to premature cardiovascular disease. The detection of the variants related to FH is important to improve the early diagnosis in probands / index-cases (ICs) and their relatives. We included ICs with FH and their relatives, living in a small region of Minas Gerais state-Brazil, which were classified according to Dutch Lipid Clinic Network Criteria (DLCNC) and submitted to sequencing of genes related to FH (LDLR, APOB, PCSK9, LDLRAP1, LIPA, STAP1, APOE, ABCG5 e ABCG8). In a total of 143 subjects (32 ICs and 111 relatives), eight variants were identified in 91 individuals. From these variants, five were in LDLR [p.(Asp224Asn), p.(Ser854Gly), p.(Cys34Arg), p.(Asp601His), deletion of exon15 in LDLR)], one in APOB [p.(Met499Val)], one in PCSK9 [p.(Arg237Trp)] and one in APOE [p.(Pro28Leu)] genes. The variants were detected in 100% of those subjects classified as definitive, 87% as probable and 69% as possible FH cases based on DLCNC. The LDLc level was higher in individuals with corneal arch and xanthomas or xanthelasmas, as well as in pathogenic or probably pathogenic variants carriers. This study showed higher frequency of LDLR gene variants compared to other genes related to LDL metabolism in individuals with FH in Minas Gerais - Brazil and the presence of FH in relatives without previous diagnosis. Our data reinforce the importance of molecular and clinical evaluation of FH relatives in order to early diagnosis the FH, as well as cardiovascular diseases prevention.
Collapse
Affiliation(s)
| | - Cinthia Elim Jannes
- Laboratório de Genética e Cardiologia Molecular do Instituto do Coração de São Paulo (INCOR), Hospital das Clínicas da Universidade de São Paulo, São Paulo, Brazil
| | - Mauricio Teruo Tada
- Laboratório de Genética e Cardiologia Molecular do Instituto do Coração de São Paulo (INCOR), Hospital das Clínicas da Universidade de São Paulo, São Paulo, Brazil
| | - Isabella Ramos Lima
- Laboratório de Genética e Cardiologia Molecular do Instituto do Coração de São Paulo (INCOR), Hospital das Clínicas da Universidade de São Paulo, São Paulo, Brazil
| | - Iêda de Fátima Oliveira Silva
- Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Alexandre Costa Pereira
- Laboratório de Genética e Cardiologia Molecular do Instituto do Coração de São Paulo (INCOR), Hospital das Clínicas da Universidade de São Paulo, São Paulo, Brazil
| | - Karina Braga Gomes
- Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerias, Brazil. .,Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, Minas Gerais, Brazil.
| |
Collapse
|