Comprehensive kinome NGS targeted expression profiling by KING-REX

• Main Authors: Giovanni Carapezza, Carlo Cusi, Ettore Rizzo, Laura Raddrizzani, Sebastiano Di Bella, Alessio Somaschini, Antonella Leone, Rosita Lupi, Margherita Mutarelli, Vincenzo Nigro, Diego di Bernardo, Paolo Magni, Antonella Isacchi, Roberta Bosotti
• Format: Article
• Language: English
• Published: BMC 2019-04-01
• Series: BMC Genomics
• Subjects: Kinome gene expression; NGS RNA targeted panel
• Online Access: http://link.springer.com/article/10.1186/s12864-019-5676-3

Abstract Background 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. Results 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. Conclusions 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.