Hijacking of stress response machinery by oncogenes in acute leukaemia [RNA-seq]

Our data demonstrate binding of NOTCH1 on the promoters of HSF1 and HSF1 targets. We performed RNA-seq upon control conditions, inhibition of the NOTCH1 pathway by gSI, HSF1 knockdown and combination of HSF1 knockdown and gSI treatment. Our results show that NOTCH1 regulates the expression of heat shock response genes. Moreover, combination of HSF1 downregulation and gSI treatment further decreased the expression of heat shock response genes compared to single treatments. Whole RNA was extracted from 1 million CUTLL1 cells treated as described below using the RNAeasy kit (Qiagen) according to the manufacturer’s protocol. Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) or Ribominus RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina HiSeq 2000 using 50bp single-read method. Differential gene expression analysis was performed between shRenilla_DMSO vs shRenilla_gSI, shRenilla vs shHSF1 and shHSF1_DMSO vs shHSF1_GSI.