NMS Oncology, Nerviano Medical Sciences Srl, Nerviano, MI, Italy.
Department of Electrical, Computer, and Biomedical Engineering, University of Pavia, Pavia, Italy.
BMC Genomics. 2019 Apr 23;20(1):307. doi: 10.1186/s12864-019-5676-3.
Protein kinases are enzymes controlling different cellular functions. Genetic alterations often result in kinase dysregulation, making kinases a very attractive class of druggable targets in several human diseases. Existing approved drugs still target a very limited portion of the human 'kinome', demanding a broader functional knowledge of individual and co-expressed kinase patterns in physiologic and pathologic settings. The development of novel rapid and cost-effective methods for kinome screening is therefore highly desirable, potentially leading to the identification of novel kinase drug targets.
In this work, we describe the development of KING-REX (KINase Gene RNA EXpression), a comprehensive kinome RNA targeted custom assay-based panel designed for Next Generation Sequencing analysis, coupled with a dedicated data analysis pipeline. We have conceived KING-REX for the gene expression analysis of 512 human kinases; for 319 kinases, paired assays and custom analysis pipeline features allow the evaluation of 3'- and 5'-end transcript imbalances as readout for the prediction of gene rearrangements. Validation tests on cell line models harboring known gene fusions demonstrated a comparable accuracy of KING-REX gene expression assessment as in whole transcriptome analyses, together with a robust detection of transcript portion imbalances in rearranged kinases, even in complex RNA mixtures or in degraded RNA.
These results support the use of KING-REX as a rapid and cost effective kinome investigation tool in the field of kinase target identification for applications in cancer biology and other human diseases.
蛋白激酶是控制不同细胞功能的酶。遗传改变通常导致激酶失调，使激酶成为人类多种疾病中非常有吸引力的一类可药物治疗靶点。现有的批准药物仍然针对人类“激酶组”中非常有限的一部分，这就要求在生理和病理环境中对单个和共表达的激酶模式有更广泛的功能了解。因此，开发新的快速且具有成本效益的激酶组筛选方法是非常需要的，这可能会导致新的激酶药物靶点的发现。
在这项工作中，我们描述了 KING-REX（KINase Gene RNA EXpression）的开发，这是一种基于高通量测序分析的综合激酶 RNA 靶向定制检测试剂盒面板，与专用数据分析管道相结合。我们设计 KING-REX 用于 512 个人类激酶的基因表达分析；对于 319 个激酶，配对检测和定制分析管道功能允许评估 3' 和 5' 端转录物失衡作为预测基因重排的指标。在携带已知基因融合的细胞系模型上的验证测试表明，KING-REX 基因表达评估的准确性与全转录组分析相当，同时在重排激酶中稳健地检测到转录部分失衡，即使在复杂的 RNA 混合物或降解的 RNA 中也是如此。
这些结果支持将 KING-REX 用作激酶靶标鉴定领域的快速且具有成本效益的激酶组研究工具，可应用于癌症生物学和其他人类疾病。
