Differential gene expression analysis by RNA-seq reveals the importance of actin cytoskeletal proteins in leukemia cells

Development of drug resistance limits the effectiveness of anticancer treatments. Understanding the molecular mechanisms triggering this event in tumor cells may lead to improved therapeutic strategies. Here we used RNA-seq to compare the transcriptomes of an erythroleukemia progenitor cell line (MEL-DS19) and a derived cell line with induced resistance to differentiation (MEL-R). RNA-seq analysis identified a total of 596 genes that were differentially expressed by more than two-fold, of which 486 genes were up-regulated in MEL-DS19 cells and 110 up-regulated in MEL-R cells. These observations revealed that the number of genes expressed in the parental cell line decreased as the cells acquired the resistant phenotype. Clustering analysis of a group of genes showing the highest differential expression allowed identification of a sub-group among genes up-regulated in MEL cells. These genes are related with the organization of the actin cytoskeleton network. Moreover, the majority of these genes are preferentially expressed in the hematopoietic lineage and at least three of them, Was (Wiskott Aldrich syndrome), Btk (Bruton tyrosine kinase) and Rac2, when mutated in humans, give rise to severe hematopoietic deficiencies. Among the group of genes that were up-regulated in MEL-R cells, a significant percentage (16%) corresponded to genes coding for histone proteins, both canonical and variants. A potential implication of these results on the blockade of differentiation in resistant cells is discussed.