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LDLR and PCSK9 3´UTR variants and their putative effects on microRNA molecular interactions in familial hypercholesterolemia: a computational approach

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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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Data availability

All relevant data of this study are available within the article and its Supplementary Information. The raw DNA sequence reads (BioProject accession number PRJNA662090) are available for download at https://www.ncbi.nlm.nih.gov/sra/PRJNA662090. Source data are provided with this paper.

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Acknowledgements

The authors thank Adriana Garofalo, Cristina Moreno Fajardo and other colleagues at Laboratory of Molecular Research in Cardiology and Dyslipidemia Division of the Institute of Cardiology Dante Pazzanese for technical support and assistance in patient selection and data collection. RCCF, RHB, CDH and VFO, are grateful to Sao Paulo Research Foundation (FAPESP) Research Fellowship Program, Brazil. ESRM, ADL, RDCH and MHH are grateful to National Council for Scientific and Technological Development (CNPq) Research Fellowship Program, Brazil.

Funding

This study is funded by Sao Paulo Research Foundation (FAPESP, # 2016/12899-6), National Council for Scientific and Technological Development (CNPq, # 447120/2014-0), and Coordination of Superior Level Staff Improvement (CAPES, # code001), Brazil.

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Author notes

  1. Renata Caroline Costa de Freitas and Raul Hernandes Bortolin contributed equally to this work.

Authors and Affiliations

  1. 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

    Renata Caroline Costa de Freitas, Raul Hernandes Bortolin, Victor Fernandes de Oliveira, Carolina Dagli-Hernandez, Elisangela da Silva Rodrigues Marçal, Rosario Dominguez Crespo Hirata & Mario Hiroyuki Hirata

  2. Department of Cardiac Surgery, Boston Children’s Hospital, Boston, MA, 02115, USA

    Renata Caroline Costa de Freitas

  3. Department of Cardiology, Boston Children’s Hospital, Boston, MA, 02115, USA

    Raul Hernandes Bortolin

  4. Department of Research, Hospital Beneficiencia Portuguesa de Sao Paulo, Sao Paulo, 01323-001, Brazil

    Jessica Bassani Borges & Gisele Medeiros Bastos

  5. Laboratory of Molecular Research in Cardiology, Institute of Cardiology Dante Pazzanese, Sao Paulo, 04012-909, Brazil

    Elisangela da Silva Rodrigues Marçal

  6. Medical Division, Institute of Cardiology Dante Pazzanese, Sao Paulo, 04012-909, Brazil

    Rodrigo Marques Gonçalves & Andre Arpad Faludi

  7. Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, Federal University of Rio Grande do Norte, Natal, 59012-570, Brazil

    Vivian Nogueira Silbiger & André Ducati Luchessi

  8. Northeast Biotechnology Network (RENORBIO), Graduate Program in Biotechnology, Federal University of Rio Grande do Norte, Natal, 59078-900, Brazil

    Vivian Nogueira Silbiger & André Ducati Luchessi

Authors
  1. Renata Caroline Costa de Freitas
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  2. Raul Hernandes Bortolin
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Contributions

MHH, RCCF, RHB and RDCH conceived and designed the study. RMG and AAF conducted the selection, clinical evaluation and follow-up of FH patients. RCCF, CDH, ESRM, GMB and VNS acquired and analyzed clinical data. JBB and VFO performed DNA sequencing and bioinformatics data analysis. RCCF performed in silico studies and data analysis and interpretation. RCCF, RHB and ADL performed the statistical analysis. RCCF and RHB drafted the manuscript. MHH, RDCH, ADL and VNS critically reviewed the manuscript. All authors reviewed and approved the final version of the manuscript.

Corresponding author

Correspondence to Mario Hiroyuki Hirata.

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Competing interests

The authors have no relevant financial and non-financial interests to disclose.

Ethics approval

The study protocol was approved by Local Ethics Committees (CAAE 24618713.0.0000.5462, 24618713.0.1001.5462, 24618713.0.3001.0067 and 24618713.0.2001.5292) and conducted according to good clinical practices and the Declaration of Helsinki guidelines (as revised in 2013).

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Informed consent was collected from all subjects who participated in the study.

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de Freitas, R.C.C., Bortolin, R.H., Borges, J.B. et al. LDLR and PCSK9 3´UTR variants and their putative effects on microRNA molecular interactions in familial hypercholesterolemia: a computational approach. Mol Biol Rep 50, 9165–9177 (2023). https://doi.org/10.1007/s11033-023-08784-9

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