Proteomics holds great promise for identifying potentially druggable effectors of common diseases, yet its application at population-scale across diverse ancestries, remains challenging. Here, we developed genetic imputation models for 2,594 plasma proteins using proteomic and genetic data from 54,219 UK Biobank participants, validating their performance across multiple ancestry groups and in an independent cohort. Plasma proteomes were then imputed for over 640,000 participants in the UK Biobank and the All of Us Research Program. To assess its aetiological value at population-scale, a further proteome-wide association study of cardiovascular diseases was performed across six genetic ancestries. We identified ~9000 protein-disease associations across 89 cardiovascular conditions (PheCodes), the majority of which show consistent effects across ancestries and biobanks, with many comprising known targets of drugs either approved or under development. The associations reveal both shared and distinct proteomic signatures across cardiovascular conditions and defined clusters of distinct pathophysiology with shared underlying molecular pathways. Integration of data on tissue specificity and single-cell transcriptomics prioritised liver-derived proteins in circulation as candidate effectors of coronary artery disease, highlighting inter-alpha-trypsin inhibitor heavy chain H4 (ITIH4) as a putative effector. Using a liver-targeted CRISPR gene-editing platform, we show that in vivo disruption of ITIH4 reduces plasma cholesterol and pro-atherogenic lipid species in a preclinical model, consistent with a causal role in cardiovascular disease. Our study enables study of large-scale proteomics in diverse populations, provides a systematic map of protein associations of cardiovascular diseases, and demonstrates the utility of genetically imputed proteomes for target discovery and experimental validation. To facilitate proteomic analyses for the research community, the resultant models and association results have been made freely available through the OmicsPred platform.
Yu Xu, Douglas P. Loesch, H. Taylor et al.· medRxiv· 0 citations
Background. Type 2 diabetes (T2D) and coronary artery disease (CAD) frequently co-occur, yet the biological pathways that jointly determine risk remain incompletely understood. Most genetic studies have examined shared risk from a single-disease perspective, limiting insight into the mechanisms that generate discordant risk between conditions. Methods. We applied PLACO to multi-ancestry GWAS data of T2D and CAD to identify shared loci, prioritising shared causal signals using colocalisation. Shared variants were clustered by their associations with 77 cardiometabolic traits, and cluster-specific genetic risk scores (GRS) were tested for association with 17 clinical biomarkers and 1,254 binary outcomes in 378,772 UK Biobank (UKB) participants. Two-sample Mendelian randomisation (MR) was used to test the causal role of liver fat. Results. We identified 149 loci shared between T2D and CAD; most novel loci had discordant effects (35 of 42), in contrast to the predominantly concordant signals reported previously. Clustering 187 independent shared variants revealed seven mechanistic clusters, three of them centred on liver fat and defined by discordant T2D?CAD effects. Enrichment analyses and cluster-GRS associations in UKB highlight associations between higher liver fat and T2D risk with a cardioprotective lipid profile and reduced CAD risk. Genetically higher liver fat increased T2D risk but lowered CAD risk in MR analyses; partitioning liver fat instruments by their effect on ApoB-containing lipoproteins indicates that the CAD effects are determined more by effects of circulating ApoB rather than liver fat itself. Conclusions. Liver fat largely sets the direction of T2D risk, whereas the fate of that lipid, retained in the liver with low circulating ApoB or exported as ApoB-containing lipoproteins, sets the direction of CAD risk. This liver-centric partitioning provides a mechanistic framework for the discordant cardiometabolic effects of hepatic lipid and lipid-lowering pathways, with implications for precision prevention.
X. Jiang, N. HirschmuÌller, H. Taylor et al.· medRxiv· 0 citations
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