Citations

Abstract Background: Breast tumors exhibit intratumor heterogeneity resulting in targeted therapy resistance and other challenges in disease management. To address the sources of heterogeneity, we performed a unique, in-depth analysis of clonal architecture in primary chemoradiation-naïve breast cancers. We combined DNA content-based flow cytometry and ploidy analysis with aCGH and next-generation sequencing (NGS) in multiple biopsies from the tumors and involved lymph nodes (LNs). Material and methods: We used DNA content-based flow sorting to isolate nuclei from distinct populations of diploid and aneuploid tumor cells in surgical tumor samples from two chemoradiation-naïve patients. Each sorted tumor cell population was interrogated with aCGH and exome NGS. In Patient #1, we used 12 fresh frozen sections morphologically mapped from within a HER2+, ER+, PR- primary invasive ductal carcinoma (IDC) of histological grade 3 with LN involvement and 2-3 sections from 2 out of 5 LNs. In Patient #2, 11 morphologically mapped fresh frozen sections were analyzed from a grade 2, ER+, PR+, HER2+, BRCA2 mutant LN- IDC. In parallel, matching samples were processed for IHC assays. Results: We identified multiple co-existing aneuploid populations within the biopsies. The 17 primary and LN biopsies from Patient #1 fell into 6 distinct ploidy groups albeit with aberrant but homogenous aCGH profiles, characterized by SARC amplification and homozygous deletions in ROBO1 and ROBO2. In contrast a dominant ploidy was identified throughout Patient #2 but with heterogeneous aCGH profiles. Mutation profiles obtained through exome sequencing further confirmed that ploidy was the main driver in Patient #1 whereas copy number aberrations played the key role in Patient #2 with the BRCA2 mutation (R3129X). A dendrogram based on exome variant calls of the aneuploid populations in Patient #1 strongly correlated with ploidy group and further revealed the specific clonal population characterized by a 5N ploidy and homozygous mutations in TP53 and PIK3CA as the progenitor to the ploidies present in the distant LNs. Strikngly, both patients had no HER2 amplification or mutation across their clonal populations, contradicting the initial IHC staining in a single core biopsy. Conclusions Rather than inferring the presence of distinct tumor cell populations, our novel flow-sorting based approach of first identifying the clonal populations and then interrogating their genomes, provides an objective method of exploring the sources and clinical significance of tumor heterogeneity. Our approach of clonal analysis has broad implications in the study of tumor heterogeneity and the identification of drivers in breast and other solid tumors that can advance more effective treatment and clinical management of patients with this disease. Citation Format: Princy Francis, Lucretia M Alvarez, Elizabeth Lenkiewicz, Mia Champion, Lisa Evers, Karen L Anderson, Ann E McCullough, Michael T Barrett, Barbara Pockaj. Deep clonal profiling identifies distinct mechanisms of heterogeneity and evolution in breast cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-03-07.

Abstract Targeted BRAF inhibition in melanoma yields frequent and dramatic responses, which are unfortunately followed by almost universal development of therapeutic resistance. In contrast to MAP kinase pathway activation, (e.g., differential BRAF splicing, MEK1 mutations), direct gatekeeper mutations, seen with other targeted therapies, have not yet been reported in association with resistance to targeted BRAF inhibition. Through a combination of genomic profiling of clonal diversity and molecular modeling, we documented a new molecular mechanism of vemurafenib resistance in a melanoma patient, occurring by selection of a pre-existing clonal subpopulation harboring a novel mutation in the vemurafenib-binding site of BRAF. We assessed melanoma clonal diversity using a novel approach for studying tumor heterogeneity in solid tumors, based on separating cellular subpopulations by nuclear flow sorting coupled to next generation sequencing. This approach identified distinct, coexisting melanoma subpopulations prior to initiation of vemurafenib. While vemurafenib treatment suppressed multiple clonal populations, a distinct population was noted at the time of relapse, harboring both the common activating V600E and a novel L567V mutation in the vemurafenib-binding site. Molecular modeling predicted that L567V would interfere with drug binding leading to decreased therapeutic response. Using a lentiviral expression system we assessed the functional effects of the L567V mutation both alone, and in combination with V600E. Assessment of the kinase activity in an in vitro kinase assay using MEK as a substrate indicates that the L567V mutant retains kinase activity. However, expression in a panel of melanoma cell lines demonstrates that while both the V600E single mutant and the L567V single mutant respond to BRAF inhibition by decreasing the levels of phospho-Erk, the double mutant actually responds to treatment by increasing phospho-Erk levels. This is also reflected in the increased viability of cells expressing double mutant in presence of increasing drug levels (PLX4720), compared to either of the single mutants. Taken together, the data suggest that the BRAF L567V/V600E double mutant confers insensitivity to vemurafenib, and that patients harboring both mutations may demonstrate clinically significant resistance to vemurafenib. Further, this data illustrates the role of clonal heterogeneity in mediating key clinical events including response to therapy and development of resistance, a major challenge of targeted BRAF therapies. Citation Format: Aleksandar Sekulic, Ashani T. Weeraratna, Jefferey L. MacKeigan, Amanpreet Kaur, Michael O'Connell, Megan L. Goodall, Michael Barrett, Elizabeth Lenkiewitz, Tara Holley, Victoria Zismann, Michael Gordon, Gideon Bollag, Chao Zhang, Jeffrey M. Trent. Discovery and molecular modeling of a novel mutation in the vemurafenib binding site of BRAF associated with therapeutic resistance in a patient with metastatic melanoma. [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 LB-213. doi:10.1158/1538-7445.AM2014-LB-213

Abstract Background: PARP inhibitors are thought to be effective therapy for cancers with homologous recombination (HR) deficiency, best shown to date in patients (pts) with a germline BRCA (gBRCA) mutation. The Cancer Genome Atlas (TCGA) estimated ∼ 50% of high-grade serous ovarian carcinoma (OC) pts have an HR defect (HRD) due to a BRCA mutation (germline or somatic), other HR gene mutation, or another mechanism, e.g., BRCA1 promoter methylation. A randomized maintenance trial of olaparib in recurrent OC demonstrated a clinical benefit in both gBRCA-mutated and gBRCA-wild-type pts. Currently, the best molecular predictors of PARPi response (other than a BRCA mutation) are not known. Platinum sensitivity, often used as a surrogate predictive indicator for PARPi response, is inadequate. A better technique, such as molecular analysis of tumor tissue, could be a superior method for selection of pts for PARPi therapy. Methods: The rucaparib development plan in OC employs a unique strategy of conducting the key trials in parallel, allowing the Phase 2 (ARIEL2) to complete first so that a molecular HRD signature, associated with sub-groups most likely to benefit, can be prospectively applied to the final analysis of the Phase 3 pivotal trial (ARIEL3). ARIEL2 is an ongoing, single-arm, open-label biomarker study designed to refine the molecular signature associated with a response to rucaparib. Eligible pts (n=180) have relapsed, platinum-sensitive, high-grade OC and measurable disease. All pts undergo a pre-dose biopsy and provide archival tumor tissue. Tumor tissue HR status is assessed using Foundation Medicine's next generation sequencing (NGS) platform and University of Washington's BROCA-HR panel, with the current HRD algorithm developed using in vitro/in vivo and TCGA (and similar) bioinformatic data. The key efficacy analyses to be correlated with tumor HR status are response by RECIST v1.1, GCIG-defined CA-125 response, and PFS. The number of gBRCA pts is limited to maximize non-gBRCA response predictors. Exploratory biomarkers include assessment of tissue NHEJ competency (candidate predictive biomarker) and circulating tumor DNA (candidate efficacy surrogate). The optimized algorithm will then be tested prospectively in ARIEL3 (n=540), an international, randomized (2:1), double-blind, placebo-controlled maintenance trial in platinum-sensitive OC in remission after platinum-based therapy. The primary endpoint of ARIEL3 is PFS in molecularly-defined HRD subgroups as determined by NGS analysis of archival tumor tissue using the optimized algorithm, refined (as required) through ARIEL2.Conclusion: This pair of clinical trials seeks to determine prospectively the appropriate population, among all women with platinum-sensitive OC, who derive a meaningful benefit from PARPi treatment in the maintenance setting. Citation Format: Elizabeth Swisher, Iain McNeish, Robert L. Coleman, James D. Brenton, Scott H. Kaufmann, Andrew Allen, Mitch Raponi, Heidi Giordano, Lara Maloney, Jeffrey Isaacson, Jonathan A. Ledermann. Prospective molecular identification of ovarian cancer patients benefiting from PARP inhibitor (PARPi, rucaparib) maintenance therapy - reaching beyond germline BRCA mutations. [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 CT339. doi:10.1158/1538-7445.AM2014-CT339

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

Abstract Background: Treatment options for women with ovarian cancer remain very limited and acquired resistance to current therapies is very common. Altered DNA repair capability in epithelial ovarian cancer (EOC) may underlie response to both standard therapy and novel treatments, such as PARP inhibitors. Molecular sub-classification of high-grade serous ovarian cancer (HG-SOC) may uncover potential drug targets and possible mechanisms of drug resistance. Understanding the contribution of DNA repair and other driver mutations to drug response and resistance requires the development of molecularly annotated preclinical models reflective of the clinic. Methods: A patient derived xenograft (PDX) cohort has been generated from consecutive, chemotherapy-naïve human HG-SOC and stratified according to in vivo response to standard chemotherapy, DNA repair capability and molecular characteristics, including next generation sequencing by Foundation Medicine. Resistance to therapy is driven by re-treating relapsed PDX in vivo providing invaluable “paired samples” (pre and post drug treatment), which are difficult to obtain from patients, to allow clonal evolution analysis of mechanisms of drug response and resistance. Results: The xenograft success rate was 83%. Of ten HG-SOC PDX, all exhibited mutations in TP53, five in BRCA1/2 (two of which were germline) and two were methylated for BRCA1. In vivo cisplatin response, determined as platinum sensitive (progression-free interval (PFI) ≥100 d, n=4), platinum resistant (PFI <100 d, n=3) or platinum refractory (n=3), was largely consistent with patient outcome. Three of four platinum sensitive HG-SOC PDX contained DNA repair gene mutations, and the fourth was methylated for BRCA1. In contrast, all three platinum refractory PDX overexpressed dominant oncogenes (CCNE1, LIN28B and/or BCL2). Molecular analysis of this cohort has revealed actionable targets for novel therapeutic strategies. In vivo studies, including with PARP inhibitors, are underway. Conclusion: PDX with histologic, molecular and therapeutic annotation, as well as clinical outcome data allow interrogation of molecular aberrations and drug resistance in vivo. This will inform targeting of novel therapies and the design of clinical trials for women. Citation Format: Monique D. Topp, Lynne Hartley, Michele Cook, Valerie Heong, Emma Boehm, Lauren McShane, Jan Pyman, Orla McNally, Sumi Ananda, Maria I. Harell, Dariush Etemadmoghadam, Laura Galletta, Kathryn Alsop, Gillian Mitchell, Stephen B. Fox, Jeff B. Kerr, Karla J. Hutt, Scott H. Kaufmann, Australian Ovarian Cancer Study (AOCS), Elizabeth M. Swisher, David D. Bowtell, Matthew M. Wakefield, Clare L. Scott. Using molecularly characterized patient-derived models to delineate underlying drivers and vulnerabilities of epithelial ovarian cancer. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Susceptibility and Cancer Susceptibility Syndromes; Jan 29-Feb 1, 2014; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(23 Suppl):Abstract nr 38. doi:10.1158/1538-7445.CANSUSC14-38

Objectives To assess whether HOUSES (HOUsing-based index of socioeconomic status (SES)) is associated with risk of and mortality after rheumatoid arthritis (RA). Design We conducted a population-based case–control study which enrolled population-based RA cases and their controls without RA. Setting The study was performed in Olmsted County, Minnesota. Participants Study participants were all residents of Olmsted County, Minnesota, with RA identified using the 1987 American College of Rheumatology criteria for RA from 1 January 1988, to 31 December 2007, using the auspices of the Rochester Epidemiology Project. For each patient with RA, one control was randomly selected from Olmsted County residents of similar age and gender without RA. Primary and secondary outcome measure The disease status was RA cases and their matched controls in relation to HOUSES as an exposure. As a secondary aim, post-RA mortality among only RA cases was an outcome event. The associations of SES measured by HOUSES with the study outcomes were assessed using logistic regression and Cox models. HOUSES, as a composite index, was formulated based on a summed z-score for housing value, square footage and number of bedrooms and bathrooms. Results Of the eligible 604 participants, 418 (69%) were female; the mean age was 56±15.6 years. Lower SES, as measured by HOUSES, was associated with the risk of developing RA (0.5±3.8 for controls vs −0.2±3.1 for RA cases, p=0.003), adjusting for age, gender, calendar year of RA index date, smoking status and BMI. The lowest quartile of HOUSES was significantly associated with increased post-RA mortality compared to higher quartiles of HOUSES (HR 1.74; 95% CI 1.10 to 2.74; p=0.017) in multivariate analysis. Conclusions Lower SES, as measured by HOUSES, is associated with increased risk of RA and mortality after RA. HOUSES may be a useful tool for health disparities research concerning rheumatological outcomes when conventional SES measures are unavailable.

The evolution of metabolic and cardiovascular disease (CVD) complications after liver transplantation (LT) is poorly characterized. We aim to illustrate the prevalence of obesity and metabolic syndrome (MS), define the cumulative incidence of CVD, and characterize risk factors associated with these comorbidities after LT. A retrospective review of 455 consecutive LT recipients from 1999 to 2004 with an 8‐ to 12‐year follow‐up was performed. Obesity increased from 23.8% (4 months) to 40.8% (3 years) after LT. Increase in body mass index predicted MS at 1 year after LT (odds ratio, 1.1; P < 0.001, per point). CVD developed in 10.6%, 20.7%, and 30.3% of recipients within 1, 5, and 8 years, respectively. Age, diabetes, hypertension, glomerular filtration rate < 60 mL/minute, prior CVD, ejection fraction < 60%, left ventricular hypertrophy, and serum troponin (TN) > 0.07 ng/mL were associated with CVD on univariate analysis. Age (hazard ratio [HR], 1.03; 95% confidence interval [CI], 1.01‐1.06; P = 0.019), diabetes (HR, 1.78; 95% CI, 1.09‐2.92; P = 0.022), prior history of CVD (HR, 2.46; 95% CI, 1.45‐4.16; P < 0.001), and serum TN > 0.07 ng/mL (HR, 1.98; 95% CI, 1.23‐3.18; P = 0.005) were independently associated with CVD in the long term. Smoking history (ever), sex, hyperlipidemia, and serum ferritin levels were not predictive of CVD. Tacrolimus use versus noncalcineurin‐based immunosuppression (HR, 0.26; 95% CI, 0.14‐0.49; P < 0.001) was associated with reduced risk of CVD but not versus cyclosporine (HR, 0.67; 95% CI, 0.30‐1.49; P = 0.322). CVD is common after LT. Independent of MS, more data are needed to identify nonconventional risk factors and biomarkers like serum TN. Curbing weight gain in the early months after transplant may impact MS and subsequent CVD in the long term. Liver Transpl 21:889‐896, 2015. © 2015 AASLD.

Background— Oxidative stress may contribute to heart failure (HF) progression. Inhibiting xanthine oxidase in hyperuricemic HF patients may improve outcomes. Methods and Results— We randomly assigned 253 patients with symptomatic HF, left ventricular ejection fraction ≤40%, and serum uric acid levels ≥9.5 mg/dL to receive allopurinol (target dose, 600 mg daily) or placebo in a double-blind, multicenter trial. The primary composite end point at 24 weeks was based on survival, worsening HF, and patient global assessment. Secondary end points included change in quality of life, submaximal exercise capacity, and left ventricular ejection fraction. Uric acid levels were significantly reduced with allopurinol in comparison with placebo (treatment difference, –4.2 [–4.9, –3.5] mg/dL and –3.5 [–4.2, –2.7] mg/dL at 12 and 24 weeks, respectively, both P <0.0001). At 24 weeks, there was no significant difference in clinical status between the allopurinol- and placebo-treated patients (worsened 45% versus 46%, unchanged 42% versus 34%, improved 13% versus 19%, respectively; P =0.68). At 12 and 24 weeks, there was no significant difference in change in Kansas City Cardiomyopathy Questionnaire scores or 6-minute walk distances between the 2 groups. At 24 weeks, left ventricular ejection fraction did not change in either group or between groups. Rash occurred more frequently with allopurinol (10% versus 2%, P =0.01), but there was no difference in serious adverse event rates between the groups (20% versus 15%, P =0.36). Conclusions— In high-risk HF patients with reduced ejection fraction and elevated uric acid levels, xanthine oxidase inhibition with allopurinol failed to improve clinical status, exercise capacity, quality of life, or left ventricular ejection fraction at 24 weeks. Clinical Trial Registration— URL: http://www.clinicaltrials.gov . Unique identifier: NCT00987415.

AbstractThe majority of kidney transplant recipients die from cardiovascular events. Physical activity may be a modifiable risk factor for cardiovascular disease following transplant. The goal of our study was to examine adherence to a physical activity intervention following kidney transplant and its impact on metabolic parameters. All patients who received a kidney transplant at our center between 12/2010 and 12/2011 received usual care (n = 162), while patients transplanted between 12/2011 and 1/2013 received a 90‐day pedometer‐based physical activity intervention (n = 145). Metabolic parameters were assessed at four and 12 months post‐transplant. Baseline demographics and clinical management were similar between cohorts. Adherence to the prescription was 36.5%. Patients in the physical activity cohort had lower systolic and diastolic blood pressure four months post‐transplant compared to the usual care cohort (122 ± 18 vs. 126 ± 16 mmHg, p = 0.049 and 73 ± 10 vs. 77 ± 9, p = 0.004) and less impaired fasting glucose (20.7% vs. 30.9%, p = 0.04). Twelve‐month outcomes were not different between cohorts. Over one‐third of our cohort adhered to a pedometer‐based physical activity intervention following kidney transplant, and the intervention was associated with improved metabolic parameters. Further study of post‐transplant exercise interventions and methods to optimize long‐term adherence are needed.