Non-linear Genetic Regulation of the Blood Plasma Proteome

Although thousands of genetic variants are linked to human traits and diseases, the underlying mechanisms influencing these traits remain largely unexplored. One important aspect is to understand how proteins are regulated by the genome by identifying protein quantitative trait loci (pQTLs). Beyond this, there is a need to understand the role of complex genetics effects such as dominance and epistasis that regulate plasma proteins and protein biomarkers. Therefore, we developed EIR-auto-GP, a deep learning-based approach, to identify such effects. Our results complement the additive genetic regulation identified in previous pQTLs screens by adding a nuanced view of the complex genetic regulation of plasma proteins. Applying this method to the UK Biobank proteomics cohort of 48,594 individuals, we identified 138 proteins that were regulated by non-linear effects, including non-linear covariates (123) as well as genetic dominance and epistasis (15). We uncovered a novel epistatic interaction between the ABO and FUT3 loci, and demonstrated dominance effects of the ABO locus on plasma levels of pathogen recognition receptors CD209 and CLEC4M. Furthermore, we replicated these findings and the methodology across Olink and mass spectrometry-based cohorts and concluded that large sample sizes are needed to discover more complex genetic effects. Our approach presents a systematic, large-scale attempt to identify complex effects of plasma protein levels and can be applied to study other tissues or molecular QTLs. ### Competing Interest Statement S.R. is the founder and owner of BioAI. The remaining authors declare no competing interests. ### Funding Statement S.R. and M.M. were supported by the Novo Nordisk Foundation (NNF14CC0001). S.R., J.F.G., R.L. and T.H. were supported by the Novo Nordisk Foundation (NNF23SA0084103). S.R., R.L. and B.M.N. were supported by the Novo Nordisk Foundation (NNF21SA0072102). J.F.G. was supported by a research grant from the Danish Cardiovascular Academy, which is funded by the Novo Nordisk Foundation, grant number NNF20SA0067242 and The Danish Heart Foundation. The FinnGen project is funded by two grants from Business Finland (HUS 4685/31/2016 and UH 4386/31/2016) and the following industry partners: AbbVie Inc., AstraZeneca UK Ltd, Biogen MA Inc., Bristol Myers Squibb (and Celgene Corporation & Celgene International II Sàrl), Genentech Inc., Merck Sharp & Dohme LCC, Pfizer Inc., GlaxoSmithKline Intellectual Property Development Ltd., Sanofi US Services Inc., Maze Therapeutics Inc., Janssen Biotech Inc, Novartis AG, and Boehringer Ingelheim International GmbH. ### 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: The present analyses were conducted under UK Biobank data application number 1251. The UK Biobank received ethical approval from the North West - Haydock Research Ethics Committee (21/NW/0157). Study subjects in FinnGen provided informed consent for biobank research, based on the Finnish Biobank Act. Alternatively, separate research cohorts, collected prior the Finnish Biobank Act came into effect (in September 2013) and start of FinnGen (August 2017), were collected based on study-specific consents and later transferred to the Finnish biobanks after approval by Fimea (Finnish Medicines Agency), the National Supervisory Authority for Welfare and Health. Recruitment protocols followed the biobank protocols approved by Fimea. The Coordinating Ethics Committee of the Hospital District of Helsinki and Uusimaa (HUS) statement number for the FinnGen study is Nr HUS/990/2017. The FinnGen study is approved by Finnish Institute for Health and Welfare (permit numbers: THL/2031/6.02.00/2017, THL/1101/5.05.00/2017, THL/341/6.02.00/2018, THL/2222/6.02.00/2018, THL/283/6.02.00/2019, THL/1721/5.05.00/2019 and THL/1524/5.05.00/2020), Digital and population data service agency (permit numbers: VRK43431/2017-3, VRK/6909/2018-3, VRK/4415/2019-3), the Social Insurance Institution (permit numbers: KELA 58/522/2017, KELA 131/522/2018, KELA 70/522/2019, KELA 98/522/2019, KELA 134/522/2019, KELA 138/522/2019, KELA 2/522/2020, KELA 16/522/2020), Findata permit numbers THL/2364/14.02/2020, THL/4055/14.06.00/2020, THL/3433/14.06.00/2020, THL/4432/14.06/2020, THL/5189/14.06/2020, THL/5894/14.06.00/2020, THL/6619/14.06.00/2020, THL/209/14.06.00/2021, THL/688/14.06.00/2021, THL/1284/14.06.00/2021, THL/1965/14.06.00/2021, THL/5546/14.02.00/2020, THL/2658/14.06.00/2021, THL/4235/14.06.00/2021, Statistics Finland (permit numbers: TK-53-1041-17 and TK/143/07.03.00/2020 (earlier TK-53-90-20) TK/1735/07.03.00/2021, TK/3112/07.03.00/2021) and Finnish Registry for Kidney Diseases permission/extract from the meeting minutes on 4th July 2019. 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 UK Biobank genotype, proteomics and covariate data is available to approved researchers through the UK Biobank (https://www.ukbiobank.ac.uk/enable-your-research/apply-for-access). All analyses using UK Biobank data were performed at the Research Analysis Platform at DNAnexus (https://ukbiobank.dnanexus.com/). Combined summary statistics of the per-protein GWAS performed in this study (Supplementary Data) are available through Zenodo (https://doi.org/10.5281/zenodo.12654966). Individual-level genotypes and register data from FinnGen participants can be accessed by approved researchers via the Fingenious portal (https://site.fingenious.fi/en/) hosted by the Finnish Biobank Cooperative FinBB (https://finbb.fi/en/). Data release to FinBB is timed to the biannual public release of FinnGen summary results, which occurs 12 months after FinnGen consortium members can start working with the data. Data from The HOLBAEK Study is not publicly available due to the need to maintain privacy of study participants but is available on reasonable request. Searchable results are available online at proteomevariation.org.