Collins, Irene

Abstract Pancreatic ductal adenocarcinoma (PDAC), as with all cancer, is driven by dysregulation of genetic programs due to accumulation of somatic mutations, epigenetic modifications and changes in the micro-environment. Holistic views of perturbations in gene expression networks could illuminate key regulators and pathways for this highly lethal cancer. Toward this end, we performed massively-parallel mRNA-sequencing in normal (n = 10) and tumor (n = 8) derived pancreatic tissue samples as well as pancreatic cancer cell lines (n = 9), and determined differential gene expression (DE) patterns. Sub-network enrichment analyses of all expressed genes based on magnitude of DE identified HNF1A as the regulator of the most significantly and consistently dysregulated expression sub-network in our pancreatic tumor samples (median P = 7.56 x 10-7, median rank = 1, range = 1-25). To explore the effect of HNF1A expression in pancreatic tumor-derived cells we generated stable HNF1A-inducible clones in two pancreatic cancer cell lines. Induction of HNF1A overexpression caused severe growth inhibition (5.3-fold, P = 4.5x10-5 for MIA PaCa-2 clones; 7.2-fold, P = 2.2x10-5 for PANC-1 clones), and G0/G1 cell cycle arrest. This was accompanied by down-regulation of 49 out of 84 assayed cell cycle genes, while only 1 displayed increased expression. These data, combined with HNF1A’s direct regulation of pancreatic development and homeostasis genes (i.e. PDX1, PTF1A and NR5A2), suggest it may be an important tumor suppressor in pancreatic cells. Citation Format: Jason W. Hoskins, Marta Flandez, Jinping Jia, Hemang Parikh, Irene Collins, Mickey Emmanuel, Abdisamad Ibrahim, Wenming Xiao, John Powell, Nuria Malats, Gloria M. Petersen, Fransisco X. Real, Laufey T. Amundadottir. Transcriptome analysis in pancreatic cancer reveals a tumor suppressor function for HNF1A. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Innovations in Research and Treatment; May 18-21, 2014; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2015;75(13 Suppl):Abstract nr B112.

Abstract A genome-wide association study (GWAS) of pancreatic cancer conducted within the NCI Cohort Consortium (PanScan I and II) identified pancreatic cancer susceptibility loci on chromosomes 1q32.1/NR5A2, 5p15.33/CLPTM1L/TERT, 9q34.2/ABO, and 13q22.1. The most significant single-nucleotide polymorphism (SNP) identified on 13q22.1, rs9543325, lies in a 600 kb gene desert; the nearest genes are KLF5, KLF12, PIBF1, DIS3, and BORA (265–586 kb). Imputation using the 1000 Genomes and DCEG reference datasets did not improve the GWAS signal, but produced a set of highly correlated SNPs for functional follow-up. We performed eQTL analysis to test for association between the genotypes of these functional candidate variants and expression of nearby genes. Among 100 normal derived pancreatic tissue samples, DIS3 expression showed the strongest association with a novel 30 bp indel variant in the risk locus (P = 4.0 × 104), indicating risk alleles associate with reduced DIS3 expression. Mutations in DIS3 have previously been identified in acute myeloid leukemia and multiple myeloma, and its expression has been correlated with metastatic potential in colorectal cancer, suggesting DIS3 is relevant to cancer biology. Chromosome conformation capture identified a physical interaction between the indel-containing locus and a region near the DIS3 promoter. Luciferase assay for regulatory function of this indel-containing locus revealed allele-specific silencer activity for the insertion allele. Supershift electromobility shift assay (EMSA) demonstrated binding of LEF1 specifically to the insertion allele of the indel, which contains two in silico predicted LEF1 binding elements. Finally, through immunohistochemical analysis, high DIS3 protein levels associated with better survival for pancreatic cancer patients (hazard ratio = 2.87, 95% CI = 1.49–5.53, P = 0.001). Our results suggest that at least one target gene for the pancreatic cancer risk variants on chr13q22.1 may be DIS3, and that the underlying biology may be mediated by the novel indel through a long-range repressive effect on DIS3 expression. Citation Format: Jason W. Hoskins, Abdisamad Ibrahim, Mickey Emmanuel, Hemang Parikh, Jinping Jia, Irene Collins, Kris Ylaya, Sean F. Altekruse, Stephen M. Hewitt, Gloria M. Petersen, Laufey T. Amundadottir. Functional analysis of the chr13q22.1 pancreatic cancer risk locus suggests allele-specific effects on DIS3 expression with prognostic implications. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Innovations in Research and Treatment; May 18-21, 2014; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2015;75(13 Suppl):Abstract nr B111.

Abstract Pancreatic cancer is the 10th most common cancer and 4th most common cause of cancer mortality in the United States. A genome wide association study has revealed pancreatic cancer susceptibility loci on chromosomes 13q22.1, 1q32.1 and 5p15.33. The chr13q22.1 region contains the most significant of all risk SNPs, rs9543325, (P= 3.27 x 10−11) which is located in a gene desert. The nearest genes are KLF5, KLF12, PIBF1, DIS3 and BORA, which range in distance from 265kb to 586kb, respectively, from the most significant variants. Given the high linkage disequilibrium across this risk locus, there are many candidate functional variants to consider. Imputation in the region did not improve the signal but gave a set of highly correlated SNPs which likely includes the functional variant(s). In an effort to identify the functional variant(s) we performed eQTL analyses to test the association between the genotypes of these candidate SNPs and expression of nearby genes. Among 100 normal pancreatic tissue samples, DIS3 showed the strongest association with SNPs in our risk locus (P-values as low as 0.0004). Mutations in DIS3 have been identified in acute myeloid leukemia and multiple myeloma, and its expression has been correlated with metastatic potential in colorectal cancer, suggesting this gene could be important in pancreatic cancer biology. Chromosome Conformation Capture (3C) was performed to test for physical interactions between the risk locus and nearby genes. This assay confirmed the three dimensional proximity of the risk locus and DIS3 promoter. Sub-regions of the risk locus were then cloned upstream of a minimal promoter controlling luciferase expression to assay for potential allele specific enhancer/silencer activity. This assay revealed a sub-region downstream of rs9543325 that causes allele-specific silencing. These results suggest that a sub-region of the chr13q22.1 risk locus has allele-specific effects on DIS3 expression, which may have implications in the susceptibility to pancreatic cancer. Citation Format: Jason Hoskins, Abdisamad Ibrahim, Jinping Jia, Irene Collins, Hemang Parikh, Gloria M. Petersen, Laufey Amundadottir. Functional analysis of the chr13q22.1 pancreatic cancer risk locus suggests allele-specific effects on DIS3 expression. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3137. doi:10.1158/1538-7445.AM2013-3137

Abstract Genome-wide association studies (GWAS) of 10 different cancers have identified pleiotropic cancer predisposition loci across a region of chromosome 5p15.33 that includes the TERT and CLPTM1L genes. Of these, susceptibility alleles for pancreatic cancer have mapped to the CLPTM1L gene, thus prompting an investigation of the function of CLPTM1L in the pancreas. Immunofluorescence analysis indicated that CLPTM1L localized to the endoplasmic reticulum where it is likely embedded in the membrane, in accord with multiple predicted transmembrane domains. Overexpression of CLPTM1L enhanced growth of pancreatic cancer cells in vitro (1.3–1.5–fold; PDAY7 < 0.003) and in vivo (3.46-fold; PDAY68 = 0.039), suggesting a role in tumor growth; this effect was abrogated by deletion of two hydrophilic domains. Affinity purification followed by mass spectrometry identified an interaction between CLPTM1L and non-muscle myosin II (NMM-II), a protein involved in maintaining cell shape, migration, and cytokinesis. The two proteins colocalized in the cytoplasm and, after treatment with a DNA-damaging agent, at the centrosomes. Overexpression of CLPTM1L and depletion of NMM-II induced aneuploidy, indicating that CLPTM1L may interfere with normal NMM-II function in regulating cytokinesis. Immunohistochemical analysis revealed enhanced staining of CLPTM1L in human pancreatic ductal adenocarcinoma (n = 378) as compared with normal pancreatic tissue samples (n = 17; P = 1.7 × 10−4). Our results suggest that CLPTM1L functions as a growth-promoting gene in the pancreas and that overexpression may lead to an abrogation of normal cytokinesis, indicating that it should be considered as a plausible candidate gene that could explain the effect of pancreatic cancer susceptibility alleles on chr5p15.33. Cancer Res; 74(10); 2785–95. ©2014 AACR.

Abstract Pancreatic cancer is highly lethal with an estimated 5-year relative survival rate of less than 5%. A genome wide association study (GWAS) of pancreatic cancer (PanScan) conducted within the NCI Cohort Consortium and the Pancreatic Cancer Case-Control Consortium (PANC4) recently identified four common susceptibility loci for pancreatic cancer on chromosomes 1q32.1, 5p15.33, 9q34.2 and 13q22.1. To investigate how these germline variants influence pancreatic cancer risk, we are employing both genome wide and targeted approaches. For the former, we are characterizing the epigenome and transcriptome of pancreatic cell lines and tissue samples for genomic annotation and prioritization of methods to use in targeted approaches with the aim of directly linking pancreatic cancer risk variants to molecular phenotypes and mechanisms that underlie the association signals. As an example of our approach we will present results in a pancreatic cancer susceptibility locus on chromosome 1q32.2 marked by SNP (single nucleotide polymorphism) rs3790844. This SNP is located in the first intron of the NR5A2 gene that encodes a nuclear receptor of the Ftz-F1 family known to be involved in pancreatic development, cholesterol and bile acid homeostasis, steroidogenesis and cell proliferation. In ChIP-sequencing and MeDIP-chip experiments, we observed repressive histone modification marks (H3K27me3) and regions of DNA methylation in the NR5A2 gene locus in pancreatic cell lines whereas only a few weak positive histone modification marks were observed (H3K4me1 and H3K4me3). This pattern of epigenetic marks correlates well with low expression of NR5A2 in the same cell lines. Expression of the NR5A2 gene at the RNA level is high in normal pancreatic tissue samples as compared to stage I-III pancreatic adenocarcinoma, most islet cell and neuroendocrine tumors. Using immunohistochemistry, nuclear NR5A2 was detected in normal acinar cells and – at lower levels – in normal ductal cells. The protein was also expressed in low and high grade PanINs and in the majority of PDAC analyzed. Our analysis of the tissue specific expression of NR5A2 shows that it is mainly expressed in normal pancreas, colon, small intestine, liver and breast but detected at low levels or not at all in most other tissue types and cancer cell lines. Furthermore we have identified a novel NR5A2 transcript by rapid amplification of cDNA ends (RACE) and mapped a promoter in front of this transcript in the genomic region corresponding to first intron of the two annotated Refseq transcripts. Establishing a comprehensive catalog of epigenetic patterns coupled with targeted analysis to correlate risk variants to molecular phenotypes could provide functional plausibility for known pancreatic cancer association signals discovered by GWAS findings. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4965. doi:10.1158/1538-7445.AM2011-4965