Mechanisms and Targeting of RIPK2 in Cancer Metastasis and Drug Resistance
Currently, there is a paucity of clinically actionable targets whose pharmacological inhibition can potently suppress cancer metastasis. Via an integrated analysis of multiple clinical omics databases, the Yang Laboratory discovered that RIPK2 is a top candidate druggable driver of prostate cancer metastasis. Phenotypically, CRISPR/Cas9 knockout of RIPK2 substantially reduced prostate cancer progression in vitro and metastasis in vivo. Mechanistically, multilevel proteomics analysis unveiled a novel noncanonical RIPK2 signaling pathway, where RIPK2 stabilizes and activates c-Myc via activating MKK7/JNK/c-Myc and MKK7/c-Myc phosphorylation cascades. Importantly, pharmacological inhibition of RIPK2 blocked the signaling pathways and impaired prostate cancer metastasis. Of clinical relevance, RIPK2 and MYC are frequently co-amplified in prostate cancer and several other cancer types, and their activity scores are highly correlated in clinical tissue specimens of many cancers. Collectively, targeting RIPK2 in preselected patients, either alone or in combination with standard or emerging therapies, holds great potential for improving the survival time and quality of life of cancer patients.
Proteome-Scale Analysis of Protein Palmitoylation (S-Acylation)
Protein palmitoylation, more accurately termed S-acylation, is a pervasive post-translational modification that plays critical roles in regulating protein localization, activity, stability and complex formation. However, it was technically challenging to analyze palmitoyl-proteins on a large scale, due to their low abundance and high hydrophobicity. To address this challenge, the Yang Lab developed powerful palmitoyl-proteomics approaches such as PalmPISC (Palmitoyl-protein Identification and Site Characterization) and LB-ABE (Low-Background Acyl-Biotinyl Exchange). Using these methods, we comprehensively mapped the palmitoyl-proteomes in cancer cells, extracellular vesicles, platelets and patient plasma. We also uncovered substrates of cancer-relevant palmitoylation enzymes, as well as palmitoyl-proteins associated with cisplatin resistance.
Complexome (Interactome) Profiling of Clinical Tissue Specimens
Protein complexes are highly specialized molecular machines, carrying out essentially all major biological processes in cells. Mass spectrometry-based proteomics is the workhorse for global profiling of protein complexes. However, the studies are time-consuming and require a large amount of protein. Therefore, it remains very challenging to analyze protein complexes in clinical tissue specimens on a large scale. To address this issue, we developed a novel approach by integrating tandem mass tag-based accurate proteome quantification and differential expression and co-regulation analyses. Using this approach, we identified many protein complexes that are deregulated along with prostate cancer progression.