Characterization of Alternative Spliceoforms and the RNA Splicing Machinery in Pancreatic Cancer

Objectives and Methods: Alternative splicing provides proteomic diversity that can have profound effects. The extent, pattern, and roles of alternative splicing in pancreatic cancer have not been systematically investigated. We have utilized a spliceoform-specific microarray and polymerase chain reaction to evaluate all known splice variants in human pancreatic cancer cell lines representing a spectrum of differentiation, from near-normal HPDE6 to Capan-1 and poorly differentiated MiaPaCa2 cells. Validation of altered spliceoforms was verified in primary cancer specimens and normal pancreatic ductal cells. In addition, expression of 92 spliceosomal genes was examined to better understand the mechanism for observed differences in mRNA splicing. Results: A statistically significant reduction in alternative splicing was found in the pancreatic cancer cell lines compared with HPDE6 cells. Many splice variants identified in Capan-1 and MiaPaCa2 cells were observed in grades 3 and 4 tumors. Analysis of genes encoding spliceosomal proteins revealed that 28 of 92 genes had significantly decreased expression in cancer compared with normal pancreas. Conclusions: Pancreatic cancer has reduced alternative splicing diversity compared with normal pancreas. This is demonstrated in both cell lines and primary tumors, with the loss in splicing diversity correlated with relative reduction in expression of spliceosomal genes.