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de Freitas RCC, Bortolin RH, Borges JB, de Oliveira VF, Dagli-Hernandez C, Marçal EDSR, Bastos GM, Gonçalves RM, Faludi AA, Silbiger VN, Luchessi AD, Hirata RDC, Hirata MH. LDLR and PCSK9 3´UTR variants and their putative effects on microRNA molecular interactions in familial hypercholesterolemia: a computational approach. Mol Biol Rep 2023; 50:9165-9177. [PMID: 37776414 DOI: 10.1007/s11033-023-08784-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 08/25/2023] [Indexed: 10/02/2023]
Abstract
BACKGROUND Familial hypercholesterolemia (FH) is caused by pathogenic variants in low-density lipoprotein (LDL) receptor (LDLR) or its associated genes, including apolipoprotein B (APOB), proprotein convertase subtilisin/kexin type 9 (PCSK9), and LDLR adaptor protein 1 (LDLRAP1). However, approximately 40% of the FH patients clinically diagnosed (based on FH phenotypes) may not carry a causal variant in a FH-related gene. Variants located at 3' untranslated region (UTR) of FH-related genes could elucidate mechanisms involved in FH pathogenesis. This study used a computational approach to assess the effects of 3'UTR variants in FH-related genes on miRNAs molecular interactions and to explore the association of these variants with molecular diagnosis of FH. METHODS AND RESULTS Exons and regulatory regions of FH-related genes were sequenced in 83 FH patients using an exon-target gene sequencing strategy. In silico prediction tools were used to study the effects of 3´UTR variants on interactions between miRNAs and target mRNAs. Pathogenic variants in FH-related genes (molecular diagnosis) were detected in 44.6% FH patients. Among 59 3'UTR variants identified, LDLR rs5742911 and PCSK9 rs17111557 were associated with molecular diagnosis of FH, whereas LDLR rs7258146 and rs7254521 and LDLRAP1 rs397860393 had an opposite effect (p < 0.05). 3´UTR variants in LDLR (rs5742911, rs7258146, rs7254521) and PCSK9 (rs17111557) disrupt interactions with several miRNAs, and more stable bindings were found with LDLR (miR-4435, miR-509-3 and miR-502) and PCSK9 (miR-4796). CONCLUSION LDLR and PCSK9 3´UTR variants disturb miRNA:mRNA interactions that could affect gene expression and are potentially associated with molecular diagnosis of FH.
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Affiliation(s)
- Renata Caroline Costa de Freitas
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580. São Paulo, Sao Paulo, 05508-000, Brazil
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Raul Hernandes Bortolin
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580. São Paulo, Sao Paulo, 05508-000, Brazil
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Jessica Bassani Borges
- Department of Research, Hospital Beneficiencia 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, Av. Prof. Lineu Prestes, 580. São Paulo, Sao Paulo, 05508-000, Brazil
| | - Carolina Dagli-Hernandez
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580. São Paulo, Sao Paulo, 05508-000, Brazil
| | - Elisangela da Silva Rodrigues Marçal
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580. São Paulo, Sao Paulo, 05508-000, Brazil
- Laboratory of Molecular Research in Cardiology, Institute of Cardiology Dante Pazzanese, Sao Paulo, 04012-909, Brazil
| | - Gisele Medeiros Bastos
- Department of Research, Hospital Beneficiencia Portuguesa de Sao Paulo, Sao Paulo, 01323-001, Brazil
| | | | - Andre Arpad Faludi
- Medical Division, Institute of Cardiology Dante Pazzanese, Sao Paulo, 04012-909, Brazil
| | - Vivian Nogueira Silbiger
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, Federal University of Rio Grande do Norte, Natal, 59012-570, Brazil
- Northeast Biotechnology Network (RENORBIO), Graduate Program in Biotechnology, Federal University of Rio Grande do Norte, Natal, 59078-900, Brazil
| | - André Ducati Luchessi
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, Federal University of Rio Grande do Norte, Natal, 59012-570, Brazil
- Northeast Biotechnology Network (RENORBIO), Graduate Program in Biotechnology, Federal University of Rio Grande do Norte, Natal, 59078-900, Brazil
| | - Rosario Dominguez Crespo Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580. São Paulo, Sao Paulo, 05508-000, Brazil
| | - Mario Hiroyuki Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580. São Paulo, Sao Paulo, 05508-000, Brazil.
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PCSK9 pathway-noncoding RNAs crosstalk: Emerging opportunities for novel therapeutic approaches in inflammatory atherosclerosis. Int Immunopharmacol 2022; 113:109318. [DOI: 10.1016/j.intimp.2022.109318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022]
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APOE Molecular Spectrum in a French Cohort with Primary Dyslipidemia. Int J Mol Sci 2022; 23:ijms23105792. [PMID: 35628605 PMCID: PMC9145810 DOI: 10.3390/ijms23105792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/17/2022] Open
Abstract
Primary hypercholesterolemia is characterized by elevated LDL-cholesterol (LDL-C) levels isolated in autosomal dominant hypercholesterolemia (ADH) or associated with elevated triglyceride levels in familial combined hyperlipidemia (FCHL). Rare APOE variants are known in ADH and FCHL. We explored the APOE molecular spectrum in a French ADH/FCHL cohort of 5743 unrelated probands. The sequencing of LDLR, PCSK9, APOB, and APOE revealed 76 carriers of a rare APOE variant, with no mutation in LDLR, PCSK9, or APOB. Among the 31 APOE variants identified here, 15 are described in ADH, 10 in FCHL, and 6 in both probands. Five were previously reported with dyslipidemia and 26 are novel, including 12 missense, 5 synonymous, 2 intronic, and 7 variants in regulatory regions. Sixteen variants were predicted as pathogenic or likely pathogenic, and their carriers had significantly lower polygenic risk scores (wPRS) than carriers of predicted benign variants. We observed no correlation between LDL-C levels and wPRS, suggesting a major effect of APOE variants. Carriers of p.Leu167del were associated with a severe phenotype. The analysis of 11 probands suggests that carriers of an APOE variant respond better to statins than carriers of a LDLR mutation. Altogether, we show that the APOE variants account for a significant contribution to ADH and FCHL.
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Xia XD, Peng ZS, Gu HM, Wang M, Wang GQ, Zhang DW. Regulation of PCSK9 Expression and Function: Mechanisms and Therapeutic Implications. Front Cardiovasc Med 2021; 8:764038. [PMID: 34782856 PMCID: PMC8589637 DOI: 10.3389/fcvm.2021.764038] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 09/16/2021] [Indexed: 12/25/2022] Open
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9) promotes degradation of low-density lipoprotein receptor (LDLR) and plays a central role in regulating plasma levels of LDL cholesterol levels, lipoprotein(a) and triglyceride-rich lipoproteins, increasing the risk of cardiovascular disease. Additionally, PCSK9 promotes degradation of major histocompatibility protein class I and reduces intratumoral infiltration of cytotoxic T cells. Inhibition of PCSK9 increases expression of LDLR, thereby reducing plasma levels of lipoproteins and the risk of cardiovascular disease. PCSK9 inhibition also increases cell surface levels of major histocompatibility protein class I in cancer cells and suppresses tumor growth. Therefore, PCSK9 plays a vital role in the pathogenesis of cardiovascular disease and cancer, the top two causes of morbidity and mortality worldwide. Monoclonal anti-PCSK9 antibody-based therapy is currently the only available treatment that can effectively reduce plasma LDL-C levels and suppress tumor growth. However, high expenses limit their widespread use. PCSK9 promotes lysosomal degradation of its substrates, but the detailed molecular mechanism by which PCSK9 promotes degradation of its substrates is not completely understood, impeding the development of more cost-effective alternative strategies to inhibit PCSK9. Here, we review our current understanding of PCSK9 and focus on the regulation of its expression and functions.
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Affiliation(s)
- Xiao-Dan Xia
- Department of Orthopedics, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Zhong-Sheng Peng
- School of Economics, Management and Law, University of South China, Hengyang, China
| | - Hong-Mei Gu
- Group on the Molecular and Cell Biology of Lipids, Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Maggie Wang
- Group on the Molecular and Cell Biology of Lipids, Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Gui-Qing Wang
- Department of Orthopedics, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Da-Wei Zhang
- Group on the Molecular and Cell Biology of Lipids, Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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Warren T, McAllister R, Morgan A, Rai TS, McGilligan V, Ennis M, Page C, Kelly C, Peace A, Corfe BM, Mc Auley M, Watterson S. The Interdependency and Co-Regulation of the Vitamin D and Cholesterol Metabolism. Cells 2021; 10:2007. [PMID: 34440777 PMCID: PMC8392689 DOI: 10.3390/cells10082007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 12/30/2022] Open
Abstract
Vitamin D and cholesterol metabolism overlap significantly in the pathways that contribute to their biosynthesis. However, our understanding of their independent and co-regulation is limited. Cardiovascular disease is the leading cause of death globally and atherosclerosis, the pathology associated with elevated cholesterol, is the leading cause of cardiovascular disease. It is therefore important to understand vitamin D metabolism as a contributory factor. From the literature, we compile evidence of how these systems interact, relating the understanding of the molecular mechanisms involved to the results from observational studies. We also present the first systems biology pathway map of the joint cholesterol and vitamin D metabolisms made available using the Systems Biology Graphical Notation (SBGN) Markup Language (SBGNML). It is shown that the relationship between vitamin D supplementation, total cholesterol, and LDL-C status, and between latitude, vitamin D, and cholesterol status are consistent with our knowledge of molecular mechanisms. We also highlight the results that cannot be explained with our current knowledge of molecular mechanisms: (i) vitamin D supplementation mitigates the side-effects of statin therapy; (ii) statin therapy does not impact upon vitamin D status; and critically (iii) vitamin D supplementation does not improve cardiovascular outcomes, despite improving cardiovascular risk factors. For (iii), we present a hypothesis, based on observations in the literature, that describes how vitamin D regulates the balance between cellular and plasma cholesterol. Answering these questions will create significant opportunities for advancement in our understanding of cardiovascular health.
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Affiliation(s)
- Tara Warren
- Northern Ireland Centre for Stratified Medicine, C-TRIC, Altnagelvin Hospital Campus, School of Biomedical Sciences, Ulster University, Derry BT47 6SB, UK; (T.W.); (R.M.); (T.S.R.); (V.M.); (M.E.); (C.P.); (C.K.)
| | - Roisin McAllister
- Northern Ireland Centre for Stratified Medicine, C-TRIC, Altnagelvin Hospital Campus, School of Biomedical Sciences, Ulster University, Derry BT47 6SB, UK; (T.W.); (R.M.); (T.S.R.); (V.M.); (M.E.); (C.P.); (C.K.)
| | - Amy Morgan
- Department of Chemical Engineering, Faculty of Science & Engineering, University of Chester, Parkgate Road, Chester CH1 4BJ, UK; (A.M.); (M.M.A.)
| | - Taranjit Singh Rai
- Northern Ireland Centre for Stratified Medicine, C-TRIC, Altnagelvin Hospital Campus, School of Biomedical Sciences, Ulster University, Derry BT47 6SB, UK; (T.W.); (R.M.); (T.S.R.); (V.M.); (M.E.); (C.P.); (C.K.)
| | - Victoria McGilligan
- Northern Ireland Centre for Stratified Medicine, C-TRIC, Altnagelvin Hospital Campus, School of Biomedical Sciences, Ulster University, Derry BT47 6SB, UK; (T.W.); (R.M.); (T.S.R.); (V.M.); (M.E.); (C.P.); (C.K.)
| | - Matthew Ennis
- Northern Ireland Centre for Stratified Medicine, C-TRIC, Altnagelvin Hospital Campus, School of Biomedical Sciences, Ulster University, Derry BT47 6SB, UK; (T.W.); (R.M.); (T.S.R.); (V.M.); (M.E.); (C.P.); (C.K.)
| | - Christopher Page
- Northern Ireland Centre for Stratified Medicine, C-TRIC, Altnagelvin Hospital Campus, School of Biomedical Sciences, Ulster University, Derry BT47 6SB, UK; (T.W.); (R.M.); (T.S.R.); (V.M.); (M.E.); (C.P.); (C.K.)
| | - Catriona Kelly
- Northern Ireland Centre for Stratified Medicine, C-TRIC, Altnagelvin Hospital Campus, School of Biomedical Sciences, Ulster University, Derry BT47 6SB, UK; (T.W.); (R.M.); (T.S.R.); (V.M.); (M.E.); (C.P.); (C.K.)
| | - Aaron Peace
- Cardiology Unit, Western Health and Social Care Trust, Altnagelvin Regional Hospital, Derry BT47 6SB, UK;
| | - Bernard M. Corfe
- Human Nutrition Research Centre, Institute of Cellular Medicine, William Leech Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK;
| | - Mark Mc Auley
- Department of Chemical Engineering, Faculty of Science & Engineering, University of Chester, Parkgate Road, Chester CH1 4BJ, UK; (A.M.); (M.M.A.)
| | - Steven Watterson
- Northern Ireland Centre for Stratified Medicine, C-TRIC, Altnagelvin Hospital Campus, School of Biomedical Sciences, Ulster University, Derry BT47 6SB, UK; (T.W.); (R.M.); (T.S.R.); (V.M.); (M.E.); (C.P.); (C.K.)
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Los B, Borges JB, Oliveira VF, Freitas RC, Dagli-Hernandez C, Bortolin RH, Gonçalves RM, Faludi AA, Rodrigues AC, Bastos GM, Jannes CE, Pereira AC, Hirata RD, Hirata MH. Functional analysis of PCSK9 3'UTR variants and mRNA-miRNA interactions in patients with familial hypercholesterolemia. Epigenomics 2021; 13:779-791. [PMID: 33899508 DOI: 10.2217/epi-2020-0462] [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] [Indexed: 12/16/2022] Open
Abstract
Aim: Functional analysis of PCSK9 3'UTR variants and mRNA-miRNA interactions were explored in patients with familial hypercholesterolemia (FH). Materials & methods: PCSK9 3'UTR variants were identified by exon-targeted gene sequencing. Functional effects of 3'UTR variants and mRNA-miRNA interactions were analyzed using in silico and in vitro studies in HEK293FT and HepG2 cells. Results: Twelve PCSK9 3'UTR variants were detected in 88 FH patients. c.*75C >T and c.*345C >T disrupted interactions with miR-6875, miR-4721 and miR-564. Transient transfection of the c.*345C >T decreased luciferase activity in HEK293FT cells. miR-4721 and miR-564 mimics reduced PCSK9 expression in HepG2 cells. Conclusion: PCSK9 c.*345C >T has a possible role as loss-of-function variant. miR-4721 and miR-564 downregulate PCSK9 and may be useful to improve lipid profile in FH patients.
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Affiliation(s)
- Bruna Los
- Department of Clinical & Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Jéssica B Borges
- Department of Clinical & 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 F Oliveira
- Department of Clinical & Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Renata Cc Freitas
- Department of Clinical & Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Carolina Dagli-Hernandez
- Department of Clinical & Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Raul H Bortolin
- Department of Clinical & Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Rodrigo M Gonçalves
- Medical Clinic Division, Institute Dante Pazzanese of Cardiology, Sao Paulo 04012-909, Brazil
| | - André A Faludi
- Medical Clinic Division, Institute Dante Pazzanese of Cardiology, Sao Paulo 04012-909, Brazil
| | - Alice C Rodrigues
- Department of Pharmacology, University of Sao Paulo Institute of Biomedical Sciences, Sao Paulo 05508-000, Brazil
| | - Gisele M 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
| | - Cinthia E Jannes
- Laboratory of Genetics and Molecular Cardiology,HeartInstitute, University of Sao Paulo, Sao Paulo 05403-900 , Brazil
| | - Alexandre C Pereira
- Laboratory of Genetics and Molecular Cardiology,HeartInstitute, University of Sao Paulo, Sao Paulo 05403-900 , Brazil
| | - Rosario Dc Hirata
- Department of Clinical & Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Mario H Hirata
- Department of Clinical & Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
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