Causal Inference and Annotation of Phosphoproteomics Data in Multi-omics Cancer Studies

Protein phosphorylation plays a crucial role in regulating diverse biological processes. Perturbations in protein phosphorylation are closely associated with downstream pathway dysfunctions, while alterations in protein expression could serve as sensitive indicators of pathological status. However, there are currently few methods that can accurately identify the regulatory links between protein phosphorylation and expression, given issues like reverse causation and confounders. Here, we present Phoslink, a causal inference model to infer causal effects between protein phosphorylation and expression, integrating prior evidence and multi-omics data. We demonstrated the feasibility and advantages of our method under various simulation scenarios. Phoslink exhibited more robust estimates and lower FDR than commonly used Pearson and Spearman correlations, with better performance than canonical IV selection methods for Mendelian randomization. Applying this approach, we identified 345 causal links involving 109 phosphosites and 310 proteins in 79 lung adenocarcinoma (LUAD) samples. Based on these links, we constructed a causal regulatory network and identified 26 key regulatory phosphosites as regulators strongly associated with LUAD. Notably, 16 of these regulators were exclusively identified through phosphosite-protein causal regulatory relationships, highlighting the significance of causal inference. We explored potentially druggable phosphoproteins and provided critical clues for drug repurposing in LUAD. We also identified significant mediation between protein phosphorylation and LUAD through protein expression. In summary, our study introduces a new approach for causal inference in phosphoproteomics studies. Phoslink demonstrates its utility in potential drug target identification thereby accelerating the clinical translation of cancer proteomics and phosphoproteomic data.