Dual site proteomic analyses reveal potential drug targets for cardiovascular disease

Background: While genome-wide association studies (GWAS) hold great promise for unravelling disease pathophysiology, the translation of disease-associated genetic loci into clinically actionable information remains a challenge. Mendelian randomisation (MR), using expressed proteins as exposures and disease as an outcome, stands as a powerful analytical approach for leveraging GWAS data to identify potential drug-targets--at scale--in a data-driven manner. Cardiovascular disease (CVD) is a major health burden worldwide, and therefore is an important outcome for which to establish and prioritise potential therapeutic targets. Methods: In this study, we utilised generalised summary-data-based MR (GSMR) with novel mass-spectrometry-based isoform-specific protein groups measured from peripheral-blood mononuclear cell (PBMC) obtained from Generation Scotland and antibody-based plasma protein measures from UK Biobank as exposures, and two CVD and three CVD-related risk-factors from UK Biobank as outcomes. Further, we used colocalisation to assess support for a shared causal variant between the proteins and the disease outcomes providing further evidence supporting a causal link. Results: We evaluate expression of 5,114 isoform-specific protein groups in PBMCs from 862 individuals. GSMR analysis, using this data, found 16 putative causal proteins across three of the CVD/CVD-related risk-factors with seven supported by colocalisation analysis. Within the plasma GSMR analysis, 761 putative causal proteins were identified, of which 145 were supported by colocalisation. In addition, we go on to examine enrichment amongst the results and find enrichment of pathways which relate to cholesterol metabolism and platelet function. There was an overlap of three proteins between significant GSMR results in PBMCs and plasma, with two proteins (COMT and SWAP70) identifying opposite directions of effect of the relevant outcome, and one identifying a concordant direction of effect (HLA-DRA). Discussion: This study identifies a number of proteins and pathways that may be involved in CVD pathogenesis. It also demonstrates the importance of the location of protein measurement and the methods by which it is quantified. Our research contributes to ongoing efforts to bridge the gap between genotype and phenotype. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement CAO was supported by the EPSRC Centre for Doctoral Training in Mathematical Modelling, Analysis and Computation (MAC-MIGS) funded by the UK Engineering and Physical Sciences Research Council (grant EP/S023291/1), Heriot-Watt University and The University of Edinburgh. TR would like to acknowledge strategic funding grant BBSRC Institute Strategic Programme grants (BBS/E/D/20002172 and BBS/E/D/20002174). SCH would like to acknowledge the BBSRC Strategic Programme Grant to the Roslin Institute (BB/P013732/1, BB/P013759/1). JKB gratefully acknowledges funding support from a Wellcome Trust Senior Research Fellowship (223164/Z/21/Z), UKRI grants (MR/Y030877/1, MC\_PC\_20004, MC\_PC\_19025, MC\_PC\_1905, MRNO2995X/1, and MC\_PC\_20029), Sepsis Research (Fiona Elizabeth Agnew Trust), a BBSRC Institute Strategic Programme Grant to the Roslin Institute (BB/P013732/1, BB/P013759/1) and support of Baillie Gifford and the Baillie Gifford Science Pandemic Hub at the University of Edinburgh. AK is supported by a Langmuir Talent Development Fellowship from the Institute of Genetics and Cancer, and a philanthropic donation from Hugh and Josseline Langmuir. ADB would like to acknowledge funding from the Wellcome PhD training fellowship for clinicians (204979/Z/16/Z), the Edinburgh Clinical Academic Track (ECAT) programme. CH and AR would like to acknowledge the MRC University Unit Programme Grant to the Human Genetics Unit (MC\_UU\_00007/10). Mass-spectrometry proteomics was funded by the Wellcome Trust (204979/Z/16/Z), with supplemental funding from the MRC University Unit Programme Grant to the Human Genetics Unit (MC\_UU\_00007/10). Generation Scotland received core support from the Chief Scientist Office of the Scottish Government Health Directorates [CZD/16/6] and the Scottish Funding Council [HR03006]. Genotyping of the GS:SFHS samples was carried out by the Genetics Core Laboratory at the Wellcome Trust Clinical Research Facility, Edinburgh, Scotland and was funded by the Medical Research Council UK and the Wellcome Trust (Wellcome Trust Strategic Award 'STratifying Resilience and Depression Longitudinally' (STRADL) Reference 104036/Z/14/Z). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Generation Scotland was granted Research Tissue Bank status by the East of Scotland Research Ethics Service committee (REC reference 15/ES/0040). This project was approved by Generation Scotland as reference GS18318. Generation Scotland participants provided written informed consent. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Summary statistics for the significant (p-value 5x10^{-8}/5114; Bonferroni correction) results from the isoform-specific SwissProt protein group GWAS are available in Supplementary Table 4, and those with a p-value 5x10^{-8} in the cis region (within 1Mb) of the gene to which protein group was mapped are available in Supplementary Table 5. Full GWAS summary statistics of the isoform-specific SwissProt protein groups and modification-specific peptides are available via Generation Scotland, and individual level data are available to bona fide researchers, subject to approval by the Generation Scotland data access committee: https://genscot.ed.ac.uk/for-researchers/access. GWAS summary files for all 2,941 proteins were downloaded from the Synapse data storage platform (https://doi.org/10.7303/syn51364943). These files were used in the GSMR procedure. Summary-level data, from Gene Atlas, was used for outcome GWAS data (http://geneatlas.roslin.ed.ac.uk).