Analysis of Expression of RNA Helicases and Cofactors in Human Tissues and Cancer

Abstract

RNA helicases are ubiquitously expressed enzymes that function as key regulators of many different aspects of gene expression. They use their nucleoside triphosphate-dependent activity to drive the remodeling of various structured RNAs and RNA-protein complexes during their biogenesis and function. In the cellular environment, careful regulation of RNA helicases is critical and many RNA helicases associate with protein cofactors that either stimulate the catalytic activity of the helicase or direct its recruitment to it specific RNA substrates or both. The largest known family of RNA helicases are the so-called G-patch proteins, which are characterized by a glycine-rich domain. More than 20 human G-patch proteins are known, however, the roles of only some of these proteins have been analyzed so far. Due to their central roles in modulating gene expression, dysregulation of RNA helicases and their cofactors is often associated with disease, especially cancer. G-patch protein mRNA expression levels had been analyzed in high-throughput studies in particular cell types, but they had not been compared between different cell types or correlated with protein expression levels. The study aimed at exploring the expression levels on the mRNA and protein level of the human G-patch proteins and G-patch protein-interacting helicases in different cancer cell lines and in matched-pair tissue samples from patients with fibromyxosarcoma in limbs or squamous cell carcinoma in the oral cavity. This could provide a basis for studying the roles of differentially expressed proteins as well as differences in the regulation of RNA helicase functions in tumor cells and in the long term could highlight potential candidates for the development of novel therapeutic approaches. Multiple examples of specifically up- or downregulation of the expression of G-ptach proteins and RNA helicases analyzed could be observed. While many of the findings could be correlated with independent reports from other researchers, the study also highlights several significant changes in gene expression of G-patch proteins, which were not previously reported and can be further investigated in future studies. Since the beginning of the study presented here, the development of NGS technologies has allowed the generation of a large amount of sequencing data giving transcriptome-wide insights into mRNA expression levels in a range of different cell types and tissues. However, significant hits identified by NGS often still required to be confirmed using gene-specific qPCR. As a further outlook, it would be beneficial to conduct high-throughput sequencing analyses of various cancer samples in large sample sizes in comparison to matched-pair normal tissue to alleviate general differences in gene expression levels between individuals. The combination of whole-genome and exome sequencing as well as high-throughput mass spectrometry could provide comprehensive information on gene expression regulation in healthy tissues and in disease.