Identifying proteomic risk factors for overall, aggressive, and early onset prostate cancer using Mendelian Randomisation and tumour spatial transcriptomics

Understanding the role of circulating proteins in prostate cancer risk can reveal key biological pathways and identify novel targets for cancer prevention. We investigated the association of 2002 genetically predicted circulating protein levels with risk of prostate cancer overall, and of aggressive and early onset disease, using cis-pQTL Mendelian randomisation (MR) and colocalisation. Findings for proteins with support from both MR, after correction for multiple-testing, and colocalisation were replicated using two independent cancer GWAS, one of European and one of African ancestry. Proteins with evidence of prostate-specific tissue expression were additionally investigated using spatial transcriptomic data in prostate tumour tissue to assess their role in tumour aggressiveness. Finally, we mapped risk proteins to drug and ongoing clinical trials targets. We identified 20 proteins genetically linked to prostate cancer risk (14 for overall 8 specific, 7 for aggressive 3 specific, and 8 for early onset disease 2 specific), of which the majority replicated where data were available. Among these were proteins associated with aggressive disease, such as PPA2 Odds Ratio (OR) per 1 SD increment = 2.13, 95% CI: 1.54-2.93, PYY OR = 1.87, 95% CI: 1.43-2.44 and PRSS3 OR = 0.80, 95% CI: 0.73-0.89, and those associated with early onset disease, including EHPB1 OR = 2.89, 95% CI: 1.99-4.21, POGLUT3 OR = 0.76, 95% CI: 0.67-0.86 and TPM3 OR = 0.47, 95% CI: 0.34-0.64. We confirmed an inverse association of MSMB with prostate cancer overall OR = 0.81, 95% CI: 0.80-0.82, and also found an inverse association with both aggressive OR = 0.84, 95% CI: 0.82-0.86 and early onset disease OR = 0.71, 95% CI: 0.68-0.74. Using spatial transcriptomics data, we identified MSMB as the genome-wide top-most predictive gene to distinguish benign regions from high grade cancer regions that comparatively had five-fold lower MSMB expression. Additionally, ten proteins that were associated with prostate cancer risk also mapped to existing therapeutic interventions. Our findings emphasise the importance of proteomics for improving our understanding of prostate cancer aetiology and of opportunities for novel therapeutic interventions. Additionally, we demonstrate the added benefit of in-depth functional analyses to triangulate the role of risk proteins in the clinical aggressiveness of prostate tumours. Using these integrated methods, we identify a subset of risk proteins associated with aggressive and early onset disease as priorities for investigation for the future prevention and treatment of prostate cancer. This work was supported by Cancer Research UK (grant no. C8221/A29017).