Transcriptome characterization of chronic myeloid leukemia by RNA sequencing

To determine differentially expressed and spliced transcripts in chronic myeloid leukemia, a high throughput RNA-sequencing (RNA-seq) analysis of ten CML specimens and five normal peripheral blood samples was performed. Thousands of differentially expressed genes between CML and normal control were detected, including genes involved in ribosome and signaling pathway. Splicing alterations analysis performed by an independently developed algorithm reveals that intron retention was the most frequent alternative splicing (AS) events in all the samples. Functional groups of differentially spliced genes most highly correlated with disease phase was (blast crisis relative to chronic phase) included spliceosome and nucleotide excision repair (NER), suggesting that genes involved in these processes may have a major contribution to CML progression by affecting splicing factors and DNA damage and repair as a consequence of mis-splicing. Overall design: mRNA profiles of peripheral blood mononuclear cells from five patients in chronic phase(CP), five in blast crisis(BC) of chronic myeloid leukemia and five healthy volunteers were generated by deep sequencing using Illumina NextSeq 500.