Phosphoproteomics profiling of sorafenib-resistant HCC patient-derived xenografts reveals potential therapeutic strategies

Hepatocellular carcinoma (HCC) is the most common form of primary liver cancer with poor prognosis. However, effective treatment options for advanced HCC are limited. Sorafenib, a first-line treatment for advanced HCC, has shown limited clinical benefits due to the onset of drug resistance. Thus, it is imperative to comprehend the mechanisms underlying sorafenib resistance and explore novel strategies to overcome or delay it. Here, we established HCC patient-derived xenograft (PDX) models with acquired resistance to sorafenib and performed comprehensive proteomic and phosphoproteomic analyses on these models. This investigation led to the identification of 9,366 proteins and 20,127 unique phosphosites. The active cell cycle pathway, along with the active cyclin-dependent kinase CDK1 and DNA-dependent protein kinase PRKDC, was identified through KEGG pathway enrichment and kinase substrate enrichment analyses. Upon investigating the potential of combining sorafenib with putative kinase inhibitors, we found that the combination displays synergistic anti-proliferative effects in both the sorafenib-resistant liver cancer cell line and PDX models, thus providing a proof-of-concept for phosphoproteomic-guided design of precision medicine.

肝细胞癌（Hepatocellular carcinoma, HCC）是最常见的原发性肝癌类型，预后不良。然而，晚期HCC的有效治疗方案仍十分有限。索拉非尼（Sorafenib）作为晚期HCC的一线治疗药物，因耐药性的出现而临床获益有限。因此，阐明索拉非尼耐药的潜在机制，并探索克服或延缓耐药的新策略迫在眉睫。在此，我们建立了对索拉非尼获得性耐药的HCC患者来源异种移植（patient-derived xenograft, PDX）模型，并对这些模型进行了全面的蛋白质组学（proteomic）和磷酸化蛋白质组学（phosphoproteomic）分析。本研究共鉴定出9366种蛋白质和20127个独特的磷酸化位点（phosphosites）。通过KEGG通路富集分析（Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis）和激酶底物富集分析，我们发现了活跃的细胞周期通路，以及活化的细胞周期蛋白依赖性激酶（cyclin-dependent kinase, CDK1）和DNA依赖性蛋白激酶（DNA-dependent protein kinase, PRKDC）。在研究索拉非尼与潜在激酶抑制剂联合使用的潜力时，我们发现该联合方案在索拉非尼耐药肝癌细胞系和PDX模型中均表现出协同抗增殖效应，为磷酸化蛋白质组学指导的精准医学（precision medicine）设计提供了概念验证（proof-of-concept）。