McWilliams, Robert R.

Abstract Background: Whole genome/exome/RNA sequencing has revolutionized the ability to assess the genomic landscape of cancer and is increasingly being utilized for clinical decision-making. Initial clinical applications have been constrained by specimen quantity, analyte quality and the time from sample acquisition to results report. Methods: Patients with advanced cancers underwent surgical resection, excisional/core biopsies, or bone marrow biopsy. Samples were analyzed by whole genome or exome sequencing in addition to RNA sequencing, bioinformatics analysis, and therapeutic target prioritization by a multi-disciplinary Clinical Genomics Board. All prioritized targets were CLIA validated using Sanger sequencing, RT-qPCR, FISH, or IHC as appropriate. Treatment was delivered using off-label FDA approved drugs, clinical trials, or single patient INDs. Results: We have enrolled 40 patients for whom sequencing data is available on 33. The initial 6 patients were evaluated in a non-CLIA pilot phase and 27 in a CLIA-enabled phase. Tumor types in the CLIA-enabled phase with the highest enrollment were pancreatic cancer (n=8) and cholangiocarcinoma (n=8). We sought to quantify the targets identified along with clinical benefit, defining these as the “Actionable Index” (AI) (proportion of patients with ≥ 1 putative drug target) and “Utility Index” (UI) (proportion of patients who derive clinical benefit). Putative therapeutic targets were identified in 7/8 (AI=0.88) cholangiocarcinoma (CC) patients and in 5/8 (AI=0.63) pancreatic cancer (PC) patients. All 3 CC patients who received target directed treatment achieved a partial response (UI=0.38). In contrast, none of the 4 PC patients who received target directed therapy had treatment response (UI=0.0). Interestingly no actionable targets were identified in 1 CC and in 2 PCs. One CC with an identified target was unable to access the drug and subsequently died. A CC patient and a PC patient, each with identified targets, expired prior to the initiation of therapy. Conclusions: While whole genome/exome/RNA sequencing is providing unparalleled detail of tumor genomes, the application to the clinic must be carefully considered. Actionability of targets will eventually need to be defined in close relation to eventual clinical utility and appropriate refinements to disease-gene-drug databases implemented. Preliminary observations in pancreatic cancer and cholangiocarcinoma demonstrate disparity in correlation between utility indices and actionable indices. Application of these tools in larger cohorts and types of tumors will need to be conducted to ascertain more precise estimates. Additional measures that are organ-site agnostic but pertain to specific targets (e.g. BRAF) will also need to be developed in order to facilitate more judicious application of sequencing in the clinical setting. Citation Format: Jan B. Egan, Alan H. Bryce, Mia D. Champion, Winnie S. Liang, Rafael Fonseca, Ann E. McCullough, Michael T. Barrett, Katherine Hunt, Rachel M. Condjella, Robert R. McWilliams, Stephen D. Mastrian, Janine LoBello, Daniel Von Hoff, David W. Craig, A. Keith Stewart, John D. Carpten, Mitesh J. Borad. Indices of actionability and clinical utility in a CLIA-enabled study of whole genome/exome/RNA sequencing in 33 cancer patients: Actionable vs. utility. [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 4694. doi:10.1158/1538-7445.AM2014-4694

Abstract Introduction Pancreatic cancer is a highly lethal malignancy due to late diagnosis and aggressiveness of the tumor. Characterization of high-risk populations for monitoring, intervention and early detection remains challenging. Obesity and diabetes are potentially modifiable contributors to pancreatic cancer. Genetic factors modifying the risk of obesity- and diabetes-induced pancreatic cancer have previously not been fully investigated at the genome-wide level. Hypothesis There are potential genetic factors modifying the associations between obesity/diabetes and pancreatic cancer. Methods Integrating genotype with risk factor data from a GWAS for the Pancreatic Cancer Case Control Consortium, we performed a genome-wide gene-environment interaction (G x E) scan for 457,688 SNPs in a discovery study of 2,028 cases and 2,109 controls using state-of-the-art methods including case-only (CO), case-control (CC), Empirical Hierarchical Bayes (EHB), Empirical-Bayes test (EB) and three 2-step approaches (DG2, EG2, DGEG2). Results We detected a genome-wide significant (P < 1.09 x 10-7 ) interaction of diabetes with rs13061928 (in CNTN4) in CO (P = 8.8 x 10-8 ), which was independent of diabetes in control group (P = 0.08). The minor allele was in a synergism with diabetes on the cancer risk: diabetics carrying GA/AA genotype had a 3.39-fold (95% CI: 2.47-4.65) increased disease risk compared with non-diabetics carrying GG genotype. Consistently, the SNP-diabetes interaction had a high ranking statistic in EHB (No.1) and high p-value ranks for EG2 and DGEG2 methods (No.1, P= 5.44 x 10-5). Conclusions These observations, once validated/confirmed, may help define at-risk subpopulation and initiate targeted intervention and prevention of pancreatic cancer. Genome-wide G x E analysis requires larger sample size than genetic main effects scan; combining the CO method with alternative methods may be the optimal scheme for genome-wide G x E analysis. Citation Format: Hongwei Tang, Eric J. Duell, Harvey A. Risch Risch, Sara H. Olson, H. Bas Bueno-de-Mesquita, Steven Gallinger, Elizabeth A. Holly, Gloria M. Petersen, Paige M. Bracci, Robert R. McWilliams, Mazda Jenab, Elio Riboli, Anne Tjønneland, Marie Christine Boutron-Ruault, Rudolf Kaaks, Dimitrios Trichopoulos, Salvatore Panico, Malin Sund, Petra H. M Peeters, Kay-Tee Khaw, Christopher I Amos, Donghui Li, Peng Wei. Genome-wide gene-diabetes and gene-obesity interaction scan in the pancreatic cancer case control consortium. [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 2214. doi:10.1158/1538-7445.AM2014-2214

The authors conclude that single-item measures of pain, fatigue, and QOL can be incorporated into oncology clinical practice with positive implications for patients and physicians without increasing duration of visits or work burden.

Abstract Purpose: To explore the effects of single-nucleotide polymorphisms (SNP) on pancreatic cancer risk and overall survival (OS). Experimental Design: The germ line DNA of 531 pancreatic cancer cases and 305 healthy controls from a hospital-based study was genotyped at SNPs previously reported to be associated with pancreatic cancer risk or clinical outcome. We analyzed putative risk SNPs for replication of their reported effects on risk and tested for novel effects on OS. Similarly, we analyzed putative survival-associated SNPs for replication of their reported effects on OS and tested for novel effects on risk. Finally, we conducted a genome-wide association study (GWAS) of OS using a subset of 252 cases, with two subsequent validation sets of 261 and 572 patients, respectively. Results: Among seven risk SNPs analyzed, two (rs505922 and rs9543325) were associated with risk (P < 0.05). Among 24 survival-associated SNPs analyzed, one (rs9350) was associated with OS (P < 0.05). No putative risk SNPs or putative survival-associated SNPs were found to be associated with OS or risk, respectively. Furthermore, our GWAS identified a novel SNP [rs1482426, combined stage I and II, P = 1.7 × 10−6, per-allele HR, 1.74; 95% confidence interval (CI), 1.38–2.18] to be putatively associated with OS. Conclusions: The effects of SNPs on pancreatic cancer risk and OS were replicated in our study, although further work is necessary to understand the functional mechanisms underlying these effects. More importantly, the putative association with OS identified by GWAS suggests that GWAS may be useful in identifying SNPs associated with clinical outcome in pancreatic cancer. Clin Cancer Res; 18(14); 3942–51. ©2012 AACR.

Abstract The Hedgehog (HH) pathway has been identified as an important deregulated signal transduction pathway in pancreatic ductal adenocarcinoma (PDAC), a cancer type characterized by a highly metastatic phenotype. In PDAC, the canonical HH pathway activity is restricted to the stromal compartment while HH signaling in the tumor cells is reduced as a consequence of constitutive KRAS activation. Here, we report that in the tumor compartment of PDAC the HH pathway effector transcription factor GLI1 regulates epithelial differentiation. RNAi-mediated knockdown of GLI1 abolished characteristics of epithelial differentiation, increased cell motility, and synergized with TGFβ to induce an epithelial-to-mesenchymal transition (EMT). Notably, EMT conversion in PDAC cells occurred in the absence of induction of SNAIL or SLUG, two canonical inducers of EMT in many other settings. Further mechanistic analysis revealed that GLI1 directly regulated the transcription of E-cadherin, a key determinant of epithelial tissue organization. Collectively, our findings identify GLI1 as an important positive regulator of epithelial differentiation, and they offer an explanation for how decreased levels of GLI1 are likely to contribute to the highly metastatic phenotype of PDAC. Cancer Res; 72(1); 88–99. ©2011 AACR.

Abstract We have demonstrated that crosstalk between the Hedgehog-GLI-GLI and EGFR signaling pathway exists and contribute to pancreatic tumorigenesis. This interaction can be abrogated by targeting both pathways simultaneously and results in a synergistic antitumor effect in vitro and in vivo in pancreatic tumor models. Based on these results we have undertaken a phase I trial of GDC-0449 (an orally administered Hedgehog pathway inhibitor) and erlotinib (EGFR tyrosine kinase inhibitor to: 1) determine the maximally tolerated dose (MTD) of GDC-0449 combined with erlotinib in unresectable solid tumors; 2) describe the adverse events associated with this treatment combination; 3) describe the responses of this treatment combination; and 4) to assess the effect of the erlotinib and GDC-0449 combination on selected biomarkers in circulating tumor cells (CTCs), tumor biopsies, and FDG-PET in a cohort of patients with metastatic pancreatic cancer patients treated at the MTD. During the dose escalation portion of the trial, eligible patients receive GDC-0449 150 mg p.o. daily and erlotinib 50, 75, 100, or 150 mg daily p.o. at dose levels 1, 2, 3, and 4 respectively. Eligibility criteria include: histologic proof of solid tumors that are unresectable, not amenable to any other standard therapies, or patient refused standard therapy,; ANC ≥> 1500/μL; PLT ≥> 100,000/ μL; Total bilirubin ≤< upper limit of normal (ULN); AST ≤< 3 x ULN; Creatinine ≤< 1.5 x ULN; Hemoglobin ≥> 9.0 g/dL; INR within normal limits (Cohort II [MTD Cohort] only); ECOG performance status (PS) 0, 1 or ≤ 2. For the MTD cohort, only patients with metastatic adenocarcinoma of the pancreas without prior systemic therapy for metastatic disease and tumor amenable to biopsies are eligible. Toxicity assessment is performed at each 28-day treatment cycles and response assessment every second treatment 28 day cycle. 12 patients have been entered-pancreas (3), colorectal (3), neuroendocrine (2), scc anus (2), gallbladder (1), thymoma (1). No dose-limiting toxicity (DLT) was reported at dose level 4. At the MTD, up to 20 patients with previously untreated metastatic pancreatic cancer will be entered to assess the biologic effect of GDC-0449+erlotinib. Pre- and post- treatment biopsies of metastases and FDG-PET will be performed. Weekly collection of CTCs will be undertaken and immunofluorescence microscopy of total & phosphoMAPK, EGFR, AKT, PATCHED1, GLI1, BCL-2, and quantitative PCR (Q-PCR) of PATCHED1, GLI1, and its target genes (BCL-2, BFL-1/A1, 4-1BB) will be performed. In addtion, total & phosphoMAPK, EGFR, and AKT, as well as PATCHED1, GLI1, BCL-2 by immunohistochemistry and Q-PCR of PATCHED1, GLI1, BCL-2, BFL-1/A1, 4-1BB will be analyzed in tumor biopsies. Supported by CA69912, CA136526 and CA102701. 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 1807.

Without adequate safety measures, oral chemotherapy can lead to undetected dosing errors. The Mayo Clinic launched a project to ensure that all capecitabine and temozolomide prescriptions receive an independent double check.

Abstract Background: Mitosis is a highly regulated process that serves to ensure the fidelity of cell division. The disruption of mitotic regulators leading to aneuploidy and polyploidy is commonly observed in cancer cells. Single nucleotide polymorphisms (SNP) in regulators of mitosis may promote chromosome missegregation and influence pancreatic cancer and/or survival. Methods: Thirty-four SNPs, previously associated with breast cancer risk, from 33 genes involved in the regulation of mitosis, were investigated for associations with pancreatic cancer risk in 1,143 Caucasian patients with pancreatic adenocarcinoma and 1,097 unaffected controls from the Mayo Clinic. Associations with survival from pancreatic cancer were also assessed using 1,030 pancreatic cancer cases with known outcome. Results: Two SNPs in the APC (rs2431238) and NIN (rs10145182) loci, of 34 examined, were significantly associated with pancreatic cancer risk (P = 0.035 and P = 0.038, respectively). Further analyses of individuals categorized by smoking and body mass index identified several SNPs displaying significant associations (P < 0.05) with pancreatic cancer risk, including APC rs2431238 in individuals with high body mass index (≥30; P = 0.031) and NIN rs10145182 in ever smokers (P = 0.01). In addition, survival analyses detected significant associations between SNPs in EIF3S10 and overall survival (P = 0.009), SNPs from five genes and survival in resected cancer cases (P < 0.05), and SNPs from two other genes (P < 0.05) and survival of locally advanced cancer cases. Conclusion: Common variation in genes encoding regulators of mitosis may independently influence pancreatic cancer susceptibility and survival. Cancer Epidemiol Biomarkers Prev; 19(1); 251–7

AbstractBackground: A number of susceptibility genes are common to breast and pancreatic cancer. Recently, several breast cancer susceptibility loci have been identified through genome-wide association studies. Here we evaluated possible associations between these single nucleotide polymorphisms (SNP) and pancreatic cancer risk.Methods: Ten SNPs from FGFR2, TOX3, MAP3K1, H19, LSP1, chromosome 8q24, CASP8, and LUM were investigated for associations with pancreatic cancer risk following genotyping in 1,143 Caucasian individuals with pancreatic adenocarcinoma and 1,097 unaffected controls from a clinic-based pancreatic cancer case-control study.Results: CASP8 rs1045485 [odds ratio (OR), 0.78; 95% confidence interval (95% CI), 0.65-0.9; P = 0.005] and MAP3K1 rs889312 (OR, 0.85; 95% CI, 0.74-0.97; P = 0.017) showed evidence of association with risk of pancreatic cancer. The CASP8 rs1045485 association was evident in ever smokers (P = 0.002), but not in nonsmokers (P = 0.55), and the effect was strongest in heavy smokers (OR, 0.52; 95% CI, 0.29-0.93; P = 0.03). In contrast the MAP3K1 rs889312 association was only evident in nonsmokers (OR, 0.78; 95% CI, 0.64-0.95; P = 0.01). In addition, evaluation of the influence of the 10 SNPs on survival detected significant associations between outcome for locally advanced pancreatic cancer cases and both 8q rs6983561 (P = 0.045) and LUM rs2268578 (P = 0.02).Conclusion: Association studies in a large pancreatic case-control study indicate that SNPs associated with breast cancer may also be associated with pancreatic cancer susceptibility and survival. (Cancer Epidemiol Biomarkers Prev 2009;18(11):3044–8)