Transcriptomics of PLAG1 VC and KD in K562 imatinib resistant cell using RNA-sequencing.
CML-CP Patients showing resistance to Imatinib, due to Bcr-Abl mechanisms of resistance  are treated with 2nd and 3rd generation TKIs but some non-responders shown Bcr-Abl independant mechanism of resistance. We hypothesize that this could be due to activation of novel pathway, or activation of downstream molecules of Bcr-Abl pathway. In this study we have performed Transcriptomics and epigenomics analysis of K562 and KU812 CML-BC cell sensitive and resistant to imatinib, ITGB3  showed high transcript levels, and was also  hypomethylated in K562/R cells as compared to sensitive counterparts and showed higher protein levels  in both K562 and KU812 resistant cell lines. Previous studies in the lab also showed  ITGB1 as a differentiator in proteomic analysis and further on-going studies indicate its role in resistance. ITGB1 was however not modulated at transcriptional level.  The protein levels of ITGB3 were significantly increased in resistant cells (K562; KU812: while those of ITGB1 were significantly decreased in resistant cells (K562; KU812. With the known switching of integrins, whether higher expression of ITGB3 had a role in modulating the levels of transcriptionally non-regulated ITGB1 was investigated in K562/S cells with ITGB1 knocked down (KD)  protein levels of ITGB3 were upregulated as compared to VC. Similarly,  knock down of ITGB3 in K562/R resulted in increased level of  ITGB1 protein. These striking results confirmed switching of integrins and explained reduced levels of ITGB1 despite no alteration at genomic or transcriptomic level in resistant cells. Overall design: RNA-Sequencing of PLAG1 VC and KD in K562 cells resistant to imatinib.