Abstract 5182: Identifying differential gene expression and splicing events in chronic lymphocytic leukemia patients through whole transcriptome profiling
Authors: Shull Austin Y. , Luo Junfeng , Choi Jeong-Hyeon , Pei Lirong , Awan Farrukh T. , Lee Eun-Joon , Liu Jimei , Buckhaults Phillip J. , Yan Xiao-Jie , Chiorazzi Nicholas , Shi Huidong 
Published: May 2015

Chronic lymphocytic leukemia (CLL) is a cancer in which B-lymphocytes proliferate in an unchecked manner and escape normal apoptotic death. It is one of the most common leukemias in the Western world, and currently, there is no cure for CLL due to the heterogeneous ways in which it can proliferate. Due to the dynamics of how CLL can develop, it is very critical to investigate the oncogenic mechanisms that allow particular clinical CLL subtypes to expand, as well as discovering potential underlying mechanisms that are common among all CLL patients. With this comprehensive goal in mind, we investigated the gene expression landscape in CLL by performing whole transcriptome analysis via RNA sequencing in 47 CLL patients and 5 normal CD19+ B-cell donors to determine differential expression and isoform patterns in CLL. Between CLL and normal CD19+ B-cells, there were 725 differentially expressed genes (FDR p&lt;.01), with 217 of these genes being upregulated in CLL. Several of these upregulated genes include CTLA4, CD276, CLNK, and PDCD1, all of which are involved in T-cell interactions. We also discovered significant upregulation in the kinase suppressor of Ras 2 (KSR2) gene, an event previously not reported in CLL. We also see clear clinical separation of IGHV unmutated vs. IGHV mutated CLL patients based solely on the expression signature created by hierarchical clustering. Examples of prognostic genes that correspond to IGHV status include previously identified genes LPL, LDOC1, PTCH1, and CRY1, as well as potentially novel prognostic expression markers SPG20, ARSD, KLK2, and MTSS1. We also utilized the SpliceSeq algorithm software and investigated the differential isoform patterns that take place between CLL patients and normal B-cell donors. Based on the results, we discovered 300 alternative promoter, 135 alternative terminator, 287 exon skipping, and 30 premature stop events that differ between CLL and normal B-cells. From these results, we validated two isoform switching events that take place in the splicing machinery genes SF3B1 and SNRNP70. For SF3B1, a short transcript devoid of the critical protein domains is overexpressed in CLL compared to the normal B-cell counterpart. For SNRNP70, a particular transcript transcribed by an alternative promoter is overexpressed in CLL patients compared to normal CD19+ B-cells. This overexpressed SNRNP70 isoform does not contain the RNA recognition motif crucial for 5′ RNA binding and splicing initiation, thus theoretically rendering its canonical action nonfunctional. Overall, transcriptome profiling of CLL patients using RNA sequencing allowed for discovery of differential expression changes previously not reported in CLL, as well as discovering novel splicing events that provide insight into potentially new oncogenic mechanisms in CLL proliferation.

Citation Format: Austin Y. Shull, Junfeng Luo, Jeong-Hyeon Choi, Lirong Pei, Farrukh T. Awan, Eun-Joon Lee, Jimei Liu, Phillip J. Buckhaults, Xiao-Jie Yan, Nicholas Chiorazzi, Huidong Shi. Identifying differential gene expression and splicing events in chronic lymphocytic leukemia patients through whole transcriptome profiling. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5182. doi:10.1158/1538-7445.AM2014-5182