Background The molecular evolution of colorectal cancer (CRC) from normal colon (N), hyperplastic polyp (P), adenomas (A) to carcinoma (C) remains largely unclear, preventing effective diagnosis and drug target discovery. Here we aim to profile the proteomic dynamics of CRC evolution using primary tissue samples and discover novel drug targets.
Methods We procured 180 FFPE tissue samples from 90 patients (two biological replicates), including 20 normal (N), 18 polys (P), 22 adenoma (A), 15 tubular adenocarcinoma and 15 mucinous adenocarcinoma (C). The samples were processed using pressure cycling technology (PCT) followed by data independent acquisition (DIA) mass spectrometry. Selected proteins were further verified using parallel reaction monitoring (PRM). PLOD2 was further investigated for potential as drug targets in CRC cell lines and mouse model.
Results We quantified 4858 SwissProt proteotypic proteins from 180 samples with high technical reproducibility (r =0.97), and identified 155 proteins consistently up- or down-regulated along the CRC evolution process, as well as 491 up-regulated proteins in the early carcinogenesis (adjusted p value < 0.05, fold change > 2), most of which are involved in inflammation. The transition from A to C is accompanied by up-regulation of 63 proteins mainly involved in metabolism. Then we further verified the expression of 31 dysregulated proteins using PRM, and focused on a microenvironmental protein lysyl hydroxylase 2 (PLOD2) as a novel drug target. PLOD2 knocked-out HCT116 and HT-29 were created using Crispr-Cas9, exhibting low proliferation and migration. Finally we observed the effectiveness of administration of an FDA approved PLOD2 inhibitor Minoxidil in 3 CRC patient-derived tumor xenograft.
Conclusion We demonstrated the effectiveness and practicality of PCT-DIA in studying the proteome evolution of CRC samples based on FFPE biopsy tissue samples, and identified microenvironmental regulation, driven by PLOD2, as a critical contributor that can be exploited as novel therapeutics for CRC.