Abstract

BackgroundProtein 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.ResultsIn 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.ConclusionsThese 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.

Highlights

  • Protein kinases are enzymes controlling different cellular functions

  • We describe the development of KINGREX (KINase Gene RNA EXpression), a kinome RNA targeted custom panel based on the TruSeq Targeted RNA expression Illumina kit (TREx, [18]) and coupled with a custom dedicated bioinformatics pipeline

  • For 514 unique genes, clearly annotated as protein kinases, we retrieved genomic coordinates for 2230 kinase isoforms from the UCSC database, providing an acceptable confidence level for transcript annotation [24]

Read more

Summary

Introduction

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. Carapezza et al BMC Genomics (2019) 20:307 effects of highly promiscuous kinase inhibitors [11] Based on these considerations, the quest for novel kinase targets effective in oncogene-defined tumor types [5] is strongly encouraged to investigate tumor biology and to identify new candidate targets in specific disease contexts, through the continuous generation of molecular data and the development of novel methods for kinome screening. A number of commercial and custom approaches have been developed targeting small kinase panels (Illumina TruSight RNA Pan-Cancer panel [12], Illumina TruSight RNA Fusion Panel [13], Archer® FusionPlex® NGS assays [14,15,16,17]), allowing the detection of specific kinase gene and isoform expression, mutation and gene fusion events. To our knowledge, none of the reported NGS targeted RNA applications allow a comprehensive whole kinome expression analysis

Methods
Results
Discussion
Conclusion
Full Text
Published version (Free)

Talk to us

Join us for a 30 min session where you can share your feedback and ask us any queries you have

Schedule a call