Post-translational regulation of the exon skipping machinery controls aberrant splicing in T cell leukemia [Patients II]

In this study, we show that pediatric T-cell acute lymphoblastic leukemia (T-ALL) has an alternative mechanism for aberrant splicing that involves post-translational regulation of the splicing machinery via deubiquitination. Overall design: Whole RNA was extracted from 1-5 million T-ALL (lines) cells or primary cells using the Total RNA Mini Kit (Bio-Rad) according to the manufacturer's protocol. Poly-A+ (magnetic oligodT-containing beads (Illumina)) or Ribominus RNA was used for library preparation. cDNA preparation and unstranded library construction was performed using the TruSeq RNA Sample Preparation Kit. Libraries were sequenced on the NextSeq 500/HiSeq 2500 using 76bp or 50bp paired-end read method. Differential gene expression analysis was performed for primary T cells vs T-ALL patients samples, or each matched treatment vs control pairs, separately in each biological or technical replicate in each of two cell lines (CUTLL1, Jurkat). Seven types of comparisons were tested: (a) T-Cells vs T-ALL, (b) Non high risk T-ALL vs high risk T-ALL, (c) Control vs H3B-8800 treated Jurkat cells, (d) Control vs H3B-8800 treated CUTLL1 cells, (e) Control vs P5091 treated Jurkat cells, (f) Control vs P5091 treated CUTLL1 cells, (g) Control vs SRSF6 knockdown Jurkat cells. Analysis was performed using edgeR package.