PHF6 and JAK3 mutations cooperate to drive T-cell acute lymphoblastic leukemia progression

Purpose: For RNA-Seq analysis of isogenic Phf6 WT and KO mouse T-ALL cells Methods: Phf6 WT and KO mouse T-ALL cells were analyzed by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Results: Using an optimized data analysis workflow, we identified 2377 genes up-regulated and 3751 genes down-regulated (P < 0.05) in the BM cells from Phf6 WT and KO mice. Altered expression of 16 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes may contribute to analyze PHF6 function. Conclusions: Our study represents the first detailed analysis of T-ALL cell transcriptomes with PHF6 deficiency and JAK3 mutation. Our results suggested that Phf6 loss promoted JAK3M511I induced T-ALL progression by accelerating cell cycle and impairing T cell differentiation. Overall design: BM cells from Phf6 WT and KO mice in the context of JAK3M511I