Abstract: Objective To investigate aberrant alternative splicing and splicing factor-mediated regulation in chronic lymphocytic leukemia (CLL). Methods High-throughput transcriptome sequencing was performed on peripheral blood mononuclear cells from 3 healthy controls (HC), and public data from 2 CLL patients and 6 patients treated with voruciclib (PT) were included. The rMATS software was used to quantify alternative splicing events (ASEs) and identify differential alternative splicing events (DASEs). The expression changes and self-splicing alterations of splicing factors (SFs)were analyzed. Results A total of 12 933, 32 908, and 32 862 ASEs were identified in HC, CLL, and PT samples, respectively, with skipped exons being the predominant type. 4 134 DASEs were detected in CLL vs. HC, among which 69.5% corresponded to decrease in percent spliced-in (PSI). Complex interactions were observed between PSI changes and gene expression alterations. Splicing factors exhibited alterations at both expression and PSI levels in CLL. In total, 330 DASEs displayed opposite ΔPSI trends between disease progression and treatment response including 276 events with a “PSI decrease in disease-PSI increase after treatment” pattern enriched in the cell cycle and DNA repair processes, and 54 events with a “PSI increase in disease-PSI decrease after treatment” pattern enriched in autophagy and phosphorylation pathways. Conclusions Aberrant ASEs exist in CLL, and the altered expression and splicing levels of SFs may contribute to this dysregulation.

Key words: alternative splicing, chronic lymphocytic leukemia, splicing factors, transcriptome sequencing