Department of Chemistry, University of Massachusetts Lowell, Lowell, MA 01854-2874, USA.
Department of Natural Compound, Nutrition, and Health, MIGAL Galilee Research Institute, Kiryat Shmona 1101600, Israel.
Molecules. 2023 May 31;28(11):4452. doi: 10.3390/molecules28114452.
The vulnerabilities of cancer cells constitute a promising strategy for drug therapeutics. This paper integrates proteomics, bioinformatics, and cell genotype together with in vitro cell proliferation assays to identify key biological processes and potential novel kinases that could account, at least in part, for the clinical differences observed in colorectal cancer (CRC) patients. This study started by focusing on CRC cell lines stratified by their microsatellite () state and p53 genotype. It shows that cell-cycle checkpoint, metabolism of proteins and RNA, signal transduction, and WNT signaling processes are significantly more active in MSI-High p53-WT cell lines. Conversely, MSI-High cell lines with a mutant (Mut) p53 gene showed hyperactivation of cell signaling, DNA repair, and immune-system processes. Several kinases were linked to these phenotypes, from which RIOK1 was selected for additional exploration. We also included the KRAS genotype in our analysis. Our results showed that RIOK1's inhibition in CRC MSI-High cell lines was dependent on both the p53 and KRAS genotypes. Explicitly, Nintedanib showed relatively low cytotoxicity in MSI-High with both mutant p53 and KRAS (HCT-15) but no inhibition in p53 and KRAS WT (SW48) MSI-High cells. This trend was flipped in CRC MSI-High bearing opposite p53-KRAS genotypes (e.g., p53-Mut KRAS-WT or p53-WT KRAS-Mut), where observed cytotoxicity was more extensive compared to the p53-KRAS WT-WT or Mut-Mut cells, with HCT 116 (KRAS-Mut and p53-WT) being the most sensitive to RIOK1 inhibition. These results highlight the potential of our in silico computational approach to identify novel kinases in CRC sub-MSI-High populations as well as the importance of clinical genomics in determining drug potency.
癌细胞的脆弱性为药物治疗提供了一个有前景的策略。本文将蛋白质组学、生物信息学和细胞基因型与体外细胞增殖测定相结合，以鉴定关键的生物过程和潜在的新激酶，这些激酶至少部分解释了在结直肠癌（CRC）患者中观察到的临床差异。本研究首先关注的是根据微卫星（）状态和 p53 基因型分层的 CRC 细胞系。结果表明，细胞周期检查点、蛋白质和 RNA 的代谢、信号转导和 WNT 信号通路在 MSI-High p53-WT 细胞系中更为活跃。相反，具有突变（Mut）p53 基因的 MSI-High 细胞系表现出细胞信号、DNA 修复和免疫系统过程的过度激活。有几个激酶与这些表型相关，其中 RIOK1 被选中进行进一步探索。我们还将 KRAS 基因型纳入我们的分析中。结果表明，在 CRC MSI-High 细胞系中 RIOK1 的抑制取决于 p53 和 KRAS 基因型。具体来说，Nintedanib 在同时具有 Mut p53 和 KRAS（HCT-15）的 MSI-High 中显示出相对较低的细胞毒性，但在 p53 和 KRAS WT（SW48）MSI-High 细胞中没有抑制作用。这种趋势在具有相反 p53-KRAS 基因型的 CRC MSI-High 中发生了反转（例如，p53-Mut KRAS-WT 或 p53-WT KRAS-Mut），与 p53-KRAS WT-WT 或 Mut-Mut 细胞相比，观察到的细胞毒性更为广泛，其中 HCT 116（KRAS-Mut 和 p53-WT）对 RIOK1 抑制最为敏感。这些结果强调了我们的计算方法在识别 CRC 亚 MSI-High 群体中的新型激酶方面的潜力，以及临床基因组学在确定药物效力方面的重要性。
