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Jawabri AA, John A, Ghattas MA, Mahgoub RE, Hamad MIK, Barakat MT, Shobi B, Daggag H, Ali BR. Cellular and functional evaluation of LDLR missense variants reported in hypercholesterolemic patients demonstrates their hypomorphic impacts on trafficking and LDL internalization. Front Cell Dev Biol 2024; 12:1412236. [PMID: 39114568 PMCID: PMC11303217 DOI: 10.3389/fcell.2024.1412236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/10/2024] [Indexed: 08/10/2024] Open
Abstract
Background Familial hypercholesterolemia (FH) is an autosomal dominant disorder characterized by increased LDL-cholesterol levels. About 85% of FH cases are caused by LDLR mutations encoding the low-density lipoprotein receptor (LDLR). LDLR is synthesized in the endoplasmic reticulum (ER) where it undergoes post-translational modifications and then transported through Golgi apparatus to the plasma membrane. Over 2900 LDLR variants have been reported in FH patients with limited information on the pathogenicity and functionality of many of them. This study aims to elucidate the cellular trafficking and functional implications of LDLR missense variants identified in suspected FH patients using biochemical and functional methods. Methods We used HeLa, HEK293T, and LDLR-deficient-CHO-ldlA7 cells to evaluate the subcellular localization and LDL internalization of ten LDLR missense variants (p.C167F, p.D178N, p.C243Y, p.E277K, p.G314R, p.H327Y, p.D477N, p.D622G, p.R744Q, and p.R814Q) reported in multiethnic suspected FH patients. We also analyzed the functional impact of three variants (p.D445E, p.D482H, and p.C677F), two of which previously shown to be retained in the ER. Results We show that p.D622G, p.D482H, and p.C667F are largely retained in the ER whereas p.R744Q is partially retained. The other variants were predominantly localized to the plasma membrane. LDL internalization assays in CHO-ldlA7 cells indicate that p.D482H, p.C243Y, p.D622G, and p.C667F have quantitatively lost their ability to internalize Dil-LDL with the others (p.C167F, p.D178N, p.G314R, p.H327Y, p.D445E, p.D477N, p.R744Q and p.R814Q) showing significant losses except for p.E277K which retained full activity. However, the LDL internalization assay is only to able evaluate the impact of the variants on LDL internalization and not the exact functional defects such as failure to bind LDL. The data represented illustrate the hypomorphism nature of variants causing FH which may explain some of the variable expressivity of FH. Conclusion Our combinatorial approach of in silico, cellular, and functional analysis is a powerful strategy to determine pathogenicity and FH disease mechanisms which may provide opportunitites for novel therapeutic strategies.
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Affiliation(s)
- Aseel A. Jawabri
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - Anne John
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | | | - Radwa E. Mahgoub
- College of Pharmacy, Al-Ain University, Abu Dhabi, United Arab Emirates
| | - Mohammad I. K. Hamad
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - Maha T. Barakat
- Research Institute, Imperial College London Diabetes Centre (ICLDC), Abu Dhabi, United Arab Emirates
| | - Bindu Shobi
- Research Institute, Imperial College London Diabetes Centre (ICLDC), Abu Dhabi, United Arab Emirates
| | - Hinda Daggag
- Research Institute, Imperial College London Diabetes Centre (ICLDC), Abu Dhabi, United Arab Emirates
| | - Bassam R. Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain, United Arab Emirates
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Athar M, Toonsi M, Abduljaleel Z, Bouazzaoui A, Bogari NM, Dannoun A, Al-Allaf FA. Novel LDLR Variant in Familial Hypercholesterolemia: NGS-Based Identification, In Silico Characterization, and Pharmacogenetic Insights. Life (Basel) 2023; 13:1542. [PMID: 37511917 PMCID: PMC10381584 DOI: 10.3390/life13071542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 06/25/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Familial Hypercholesterolemia (FH) is a hereditary condition that causes a rise in blood cholesterol throughout a person's life. FH can result in myocardial infarction and even sudden death if not treated. FH is thought to be caused mainly by variants in the gene for the low-density lipoprotein receptor (LDLR). This study aimed to investigate the genetic variants in FH patients, verify their pathogenicity, and comprehend the relationships between genotype and phenotype. Also, review studies assessed the relationship between the LDLR null variants and the reaction to lipid-lowering therapy. METHODS The study utilised high-throughput next-generation sequencing for genetic screening of FH-associated genes and capillary sequencing for cascade screening. Furthermore, bioinformatic analysis was employed to describe the pathogenic effects of the revealed novel variant on the structural features of the corresponding RNA molecule. RESULTS We studied the clinical signs of hypercholesterolemia in a Saudi family with three generations of FH. We discovered a novel frameshift variant (c.666_670dup, p.(Asp224Alafs*43) in the LDLR and a known single nucleotide variant (c.9835A > G, p.(Ser3279Gly) in the APOB gene. It is thought that the LDLR variant causes a protein to be prematurely truncated, likely through nonsense-mediated protein decay. The LDLR variant is strongly predicted to be pathogenic in accordance with ACMG guidelines and co-segregated with the FH clinical characteristics of the family. This LDLR variant exhibited severe clinical FH phenotypes and was restricted to the LDLR protein's ligand-binding domain. According to computational functional characterization, this LDLR variant was predicted to change the free energy dynamics of the RNA molecule, thereby affecting its stability. This frameshift variant is thought to eliminate important functional domains in LDLR that are required for receptor recycling and LDL particle binding. We provide insight into how FH patients with a null variant in the LDLR gene respond to lipid-lowering therapy. CONCLUSIONS The findings expand the range of FH variants and assist coronary artery disease preventive efforts by improving diagnosis, understanding the genotype-phenotype relationship, prognosis, and personalised therapy for patients with FH.
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Affiliation(s)
- Mohammad Athar
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
- Science and Technology Unit, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mawaddah Toonsi
- Department of Pediatrics, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Zainularifeen Abduljaleel
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
- Science and Technology Unit, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Abdellatif Bouazzaoui
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
- Science and Technology Unit, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Neda M Bogari
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Anas Dannoun
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Faisal A Al-Allaf
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
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Nasser KK, Shinawi T. Genotype-protein phenotype characterization of NOD2 and IL23R missense variants associated with inflammatory bowel disease: A paradigm from molecular modelling, dynamics, and docking simulations. Front Med (Lausanne) 2023; 9:1090120. [PMID: 36703890 PMCID: PMC9871552 DOI: 10.3389/fmed.2022.1090120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/21/2022] [Indexed: 01/12/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a gastrointestinal disease with an underlying contribution of genetic, microbial, environment, immunity factors. The coding region risk markers identified by IBD genome wide association studies have not been well characterized at protein phenotype level. Therefore, this study is conducted to characterize the role of NOD2 (Arg675Trp and Gly908Arg) and IL23R (Gly149Arg and Arg381Gln) missense variants on the structural and functional features of corresponding proteins. Thus, we used different variant pathogenicity assays, molecular modelling, secondary structure, stability, molecular dynamics, and molecular docking analysis methods. Our findings suggest that SIFT, Polyphen, GREP++, PhyloP, SiPhy and REVEL methods are very sensitive in determining pathogenicity of NOD2 and IL23R missense variants. We have also noticed that all the tested missense variants could potentially alter secondary (α-helices, β-strands, and coils) and tertiary (residue level deviations) structural features. Moreover, our molecular dynamics (MD) simulation findings have simulated that NOD2 (Arg675Trp and Gly908Arg) and IL23R (Gly149Arg and Arg381Gln) variants creates rigid local structures comprising the protein flexibility and conformations. These predictions are corroborated by molecular docking results, where we noticed that NOD2 and IL23R missense variants induce molecular interaction deformities with RIPK2 and JAK2 ligand molecules, respectively. These functional alterations could potentially alter the signal transduction pathway cascade involved in inflammation and autoimmunity. Drug library searches and findings from docking studies have identified the inhibitory effects of Tacrolimus and Celecoxib drugs on NOD2 and IL23R variant forms, underlining their potential to contribute to personalized medicine for IBD. The present study supports the utilization of computational methods as primary filters (pre-in vitro and in vivo) in studying the disease potential mutations in the context of genptype-protein phenotype characteristics.
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Affiliation(s)
- Khalidah Khalid Nasser
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia,Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia,Centre for Artificial Intelligence in Precision Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Thoraia Shinawi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia,*Correspondence: Thoraia Shinawi,
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Alnouri F, Al-Allaf FA, Athar M, Al-Rasadi K, Alammari D, Alanazi M, Abduljaleel Z, Awan Z, Bouazzaoui A, Dairi G, Elbjeirami WM, Karra H, Kinsara AJ, Taher MM. Identification of Novel and Known LDLR Variants Triggering Severe Familial Hypercholesterolemia in Saudi Families. Curr Vasc Pharmacol 2022; 20:361-369. [PMID: 35249492 DOI: 10.2174/1570161120666220304101606] [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: 07/27/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND Familial hypercholesterolemia (FH) is a common illness mainly caused by variants occurring in the low-density lipoprotein receptor (LDLR) gene. FH is a leading cause of coronary artery disease. OBJECTIVE This study aims to determine genetic defect(s) in homozygous and heterozygous FH index patients and their first-degree blood relatives and understand the genotype-phenotype correlation. METHODS This study employed the genetic screening of FH-related genes by next-generation sequencing and cascade screening by capillary sequencing. RESULTS We identified the presence of a novel frameshift variant [c.335_336insCGAG, p.(F114Rfs*17)] and three known missense variants [c.622G>A, p.(E208K)], [c.1474G>A, p.(D492N)], [c.1429G>A, p.(D477N)] in the LDLR gene of four unrelated Saudi families with FH. In proband 1, a nonsense variant c.1421C>G, p.(S474*) was also detected at exon 9 of the lipoprotein lipase gene. The segregation arrangement of the identified variants corresponded with the clinical characteristics. In this study, all the detected variants were confined in the ligand-binding domain and epidermal growth factor (EGF)-precursor homology domain of the LDLR protein, which portrayed severe clinical phenotypes of FH. Moreover, these LDLR variants were in a highly conserved residue of the proteins. CONCLUSION In addition to the finding of the novel variant in the LDLR gene that extends the spectrum of variants causing FH, the results of this study also support the need for diagnostic screening and cascade genetic testing of this high-risk condition and to understand the genotype-phenotype correlation, which could lead to better prevention of coronary artery disease.
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Affiliation(s)
- Fahad Alnouri
- Cardiovascular Prevention Unit, Department of Adult Cardiology, Prince Sultan Cardiac Centre, Riyadh, Saudi Arabia
| | - Faisal A Al-Allaf
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah Al Mukarramah, Saudi Arabia.,Science and Technology Unit, Umm Al-Qura University, Makkah Al Mukarramah, Saudi Arabia.,Molecular Diagnostics Unit, Department of Laboratory and Blood Bank, King Abdullah Medical City, Makkah Al Mukarramah, Saudi Arabia
| | - Mohammad Athar
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah Al Mukarramah, Saudi Arabia.,Science and Technology Unit, Umm Al-Qura University, Makkah Al Mukarramah, Saudi Arabia
| | - Khalid Al-Rasadi
- Director of Medical Research Center, Sultan Qaboos University, Muscat, Oman
| | - Dalal Alammari
- Department of Dermatology, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Menwar Alanazi
- Cardiovascular Prevention Unit, Department of Adult Cardiology, Prince Sultan Cardiac Centre, Riyadh, Saudi Arabia
| | - Zainularifeen Abduljaleel
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah Al Mukarramah, Saudi Arabia.,Science and Technology Unit, Umm Al-Qura University, Makkah Al Mukarramah, Saudi Arabia
| | - Zuhier Awan
- Department of Clinical Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdellatif Bouazzaoui
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah Al Mukarramah, Saudi Arabia.,Science and Technology Unit, Umm Al-Qura University, Makkah Al Mukarramah, Saudi Arabia
| | - Ghida Dairi
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah Al Mukarramah, Saudi Arabia
| | - Wafa M Elbjeirami
- Molecular Diagnostics Unit, Department of Laboratory and Blood Bank, King Abdullah Medical City, Makkah Al Mukarramah, Saudi Arabia
| | - Hussam Karra
- Cardiovascular Prevention Unit, Department of Adult Cardiology, Prince Sultan Cardiac Centre, Riyadh, Saudi Arabia
| | - Abdulhalim J Kinsara
- Ministry of National Guard-Health Affairs, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, COM-WR, Riyadh, Saudi Arabia
| | - Mohiuddin M Taher
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah Al Mukarramah, Saudi Arabia.,Science and Technology Unit, Umm Al-Qura University, Makkah Al Mukarramah, Saudi Arabia
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Structural and Molecular Interaction Studies on Familial Hypercholesterolemia Causative PCSK9 Functional Domain Mutations Reveals Binding Affinity Alterations with LDLR. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-020-10121-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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