Hepatocellular carcinoma (HCC) typically develops from a background of cirrhosis resulting from chronic inflammation. This inflammation is frequently associated with chronic liver diseases (CLD). The advent of next generation sequencing has enabled extensive analyses of molecular aberrations in HCC. However, less attention has been directed to the chronically inflamed background of the liver, prior to HCC emergence and during recurrence following surgery. Hepatocytes within chronically inflamed liver tissues present highly activated inflammatory signaling pathways and accumulation of a complex mutational landscape. In this altered environment, cells may transform in a stepwise manner toward tumorigenesis. Similarly, the chronically inflamed environment which persists after resection may impact the timing of HCC recurrence. Advances in research are allowing an extensive epigenomic, transcriptomic and proteomic characterization of CLD which define the emergence of HCC or its recurrence. The amount of data generated will enable the understanding of oncogenic mechanisms in HCC from the CLD perspective and provide the possibility to identify robust biomarkers or novel therapeutic targets for the treatment of primary and recurrent HCC. Importantly, biomarkers defined by the analysis of CLD tissue may permit the early detection or prevention of HCC emergence and recurrence. In this review, we compile the current omics based evidence of the contribution of CLD tissues to the emergence and recurrence of HCC.

Introduction: Colorectal cancer is the second cause of cancer related deaths worldwide, with the poor survival outcomes attributable to the presence of metastases. To tackle this problem, (phospho)proteomics analysis enables valuable insights into changes of protein expression and signalling in cancer that can be perturbed by drugs. To study mechanisms driving metastasis and perform subsequent drug testing, patient derived organoids (PDOs) are in development as preclinical models. PDOs are obtained by 3D culture of tumour tissue ex-vivo, which enables them to retain the heterogeneity and architecture of the tumor source. To identify putative drug targets for colon cancer metastasis, we performed comparative (phospho)proteomics analysis of metastatic colon tissues and their matched PDOs. Methods: (Phospho)proteomics profiling was performed on PDOs generated from 10 patients with colon metastases to the liver, 10 matched tumour tissues and 4 normal colon mucosa. Unsupervised analysis of the (phospho)proteomic landscape was used to identify differentially expressed genes and pathways in colon metastases and their matched PDOs, compared to normal colon mucosa. We focused on phosphosites, proteins and pathways showing consistently altered expression in tumour tissues and PDOs. Kinase-substrate enrichment analysis was used to identify aberrantly activated kinases, based on the abundance of phosphorylation on the substrates. Putative drugs were selected using the consensus expression response to multiple small molecule drugs across cell lines and conditions from the Library of Integrated Network-Based Cellular Signatures (LINCS) database. Drug treatment of drug candidates was performed using the MTT Cell Proliferation Assay. Results: Using the approach described above we identified 103 differentially expressed proteins and 236 phosphosites between tumour tissues and normals, which were also detected in PDOs, with overall high correlation of t statistics (0.6 Spearman’s rho) between tumor tissues and PDOs. MYC-targets, G2M checkpoints and E2F-targets were amongst the top positively enriched pathways in common, and the LINCS analysis identified multi-kinase inhibitor Nintedanib and NFKB pathway-targeting KIN0-260 as putative drugs for upregulated proteins. The kinase CSNK2A1 was overactivated in both groups, pointing towards the use of CK2 inhibitors for drug testing. Treatment at 5 days with Nintedanib and KIN001-260 on the PDOs resulted in significant reduction of cell viability compared with 5-FU. Conclusion: Our study provides evidence that PDOs recapitulate relevant tumor features at the proteomic and phosphoproteomic levels, supporting the utility of this ex-vivo model as a tool for drug sensitivity testing for metastatic colon cancer. Citation Format: Gina Faye Boot, Federica Panebianco, John Gallon, Charlotte Kiu Yan Ng, Salvatore Piscuoglio. (Phospho)proteomics profiling of patient-derived colon cancer organoids for the discovery of putative drug targets [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3074.