Abstract 5017: Identification and characterization of tumor suppressor genes located within chromosomal regions frequently deleted in pancreatic cancer

Genome-wide transcript profiling has been frequently used to aid prognostication in cancers that exhibit extensive heterogeneity in their clinical presentation. For cancers that are consistently associated with a high mortality rate such as pancreatic cancer, it is more relevant to design efficient therapeutic strategies. DNA copy number alterations are expected to harbor deregulated oncogenes and tumor suppressor genes (TSGs) important for maintaining the tumor phenotype, which in turn may yield novel therapeutic targets. We earlier carried out array-based comparative genomic hybridization on a panel of pancreatic cancer cell lines and xenografts and identified GATA6 as a novel lineage specific deregulated oncogene. In the current study, we have characterized two recurrent deletions; one located at 6q25.3 and the other at 18q23. Careful analysis of genes located within the 6q25.3 deletion revealed only two genes, one of which, ARID1B, is a component of the human SWI/SNF complex. The gene was cloned in pCDNA3.1His vector and transiently transfected into the pancreatic cancer cell line MiaPaCa2 harboring a homozygous deletion of ARID1B. FACS analysis revealed no significant change in S-phase fraction of cells when compared to results obtained with the vector alone. A stable ARID1B expression clone was generated in MiaPaCa2; gene expression was confirmed using reverse transcription (RT) PCR. Colony forming assay revealed a significant reduction in the size and number of colonies formed by the ARID1B stable clone as compared to the vector stable clone indicating that expression of ARID1B could alleviate tumor-related phenotype in pancreatic cancer cell lines. Azacytidine treatment in SW1990, a pancreatic cancer cell line harboring a single copy loss of ARID1B and exhibiting low expression, appeared to alleviate transcriptional repression indicating that the gene may be regulated through promoter hypermethylation in pancreatic cancer cells. RT-PCR analysis has revealed the authentic transcript isoform of ARID1B in pancreatic cancer. Analysis of another recurrent deletion located at 18q23 revealed the PARD6G gene as the possible TSG in this locus. PARD6G is a component of the cell polarity complex and is expected to regulate cell motility. Analysis of DNA copy number and transcript levels of PARD6G in various pancreatic cell lines and xenografts revealed a strong concordance. The gene exhibited a single copy loss in several pancreatic cancer cell lines; Bisulphite sequencing analysis revealed strong hypermethylation of CpG islands spanning the first intron in the remaining allele. Further studies are underway to determine the role played by ARID1B and PARD6G in pancreatic cancer progression. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5017.