Citations

Abstract Cholangiocarcinomas are rare but aggressive cancers, with an increasing incidence and a dismal 5-year survival rate of less than 5%. Mutations in the genes encoding isocitrate dehydrogenase, IDH1 and IDH2, have been reported in ∼70% of gliomas, ∼20% of myeloid leukemias, ∼56% of chondrosarcomas, and ∼10% of melanomas. We discovered IDH1 and IDH2 mutations in 29 of 305 (9%) intrahepatic cholangiocarcinomas. Tumors with mutations in IDH1 or IDH2 had lower 5-hydroxymethylcytosine and higher 5-methylcytosine levels, as well as increased dimethylation of histone H3K79. Mutations in IDH1 or IDH2 were independently associated with longer time to recurrence of cholangiocarcinoma in multivariate analysis (p = 0.046). We identified 2,267 genes that were significantly hypermethylated in tumors with mutations in IDH1 or IDH2. Hypermethylated CpG sites were significantly enriched in CpG shores and in the 1500 bp upstream of annotated transcription start sites, suggesting a global regulation of transcriptional potential. Gene expression profiling of 7 IDH1/2-mutant and 20 IDH1/2-wildtype tumors revealed increased expression of citric acid cycle and oxidative phosphorylation enzymes, as well as decreased expression of cytoskeleton organization genes. Integrated analyses of DNA methylation and gene expression identified interleukin-6 and several of its downstream targets as candidates for silencing by DNA methylation. Conclusions: Cholangiocarcinomas with mutations in IDH1 or IDH2 represent a molecular subclass with distinct signaling pathway alterations. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1058. doi:1538-7445.AM2012-1058

Abstract DNA double-strand breaks (DSBs) are highly cytotoxic lesions caused by genotoxin such as ionizing radiation (IR). Following DSB, cells activate the DNA-damage response pathway by activating protein kinases such as ATM, ATR and DNA-PK, which then trigger histone H2AX phosphorylation and the accumulation of proteins such as Mediator of DNA damage checkpoint protein 1 (MDC1), 53BP1, and BRCA1 into IR-induced foci. This process initiates the repair of DSB. Previously we have identified a novel biomarker for radiation response, Bora, by using a genome-wide association approach using data generated with 300 human lymphoblastoid cell liens. Bora is known as a cofactor of Aurora-A, which is involved in mitosis regulation. During G2, Aurora-A, in complex with Bora, phosphorylates Plk1 at Thr-210. Activated Plk1 phosphorylates Cdc25C and Wee1, which induces activation of cyclin B-cdk1 complexes and promotes mitotic entry. In this study, we want to determine the underlying mechanisms by which Bora regulates response to IR. We found that knockdown of Bora in human cancer cell lines including HupT3, MIAPaCa-2 and Hela (siBora) exhibit increased clonogenic survival rate in response to IR, an observation that is opposite from the effect of Plk1 knockdown, suggesting a different mechanism involved. Knockdown of Bora also desensitize cancer cells to chemotherapeutic agents including gemcitabine and oxiplatin. This enhanced resistance to genotoxin is primarily due to increased DNA DSB repair. More than 90% of DSBs were repaired in siBora cells compared with 60% in control cells 8 hours after cell exposure to 2 Gy IR. Upon IR, more cells with Bora knockdown retained in G2-M phase compared with control. Furthermore, Bora directly interacts with BRCT domain of MDC1 via its C terminus, and over expression of Bora can abolish MDC1 foci formation induced by IR. All of these observations suggested a role of Bora in DNA damage response pathway and in turn, in chemo-radio resistance. Indeed, overexpression of the full length or C-terminus of Bora sensitized cancer cells to IR treatment, while the N-terminal Bora did not have significant effect on IR response. In summary, we have identified a novel function of Bora involved in DNA damage and repair pathway, which indicates a broad role of Bora in both tumorgenesis and chemo-radio resistance. 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 2660. doi:10.1158/1538-7445.AM2011-2660

Abstract Purpose: Novel therapies are challenging current drug development standards. Agents with specific biologic targets, unknown dose-efficacy curves, limited toxicity profiles, and in combination therapy require novel statistical designs. We compared the operating characteristics of three model based designs incorporating both toxicity and a measure of efficacy to identify the optimal dose region for combination therapies. Methods: Three designs were considered: continuation ratio model with a trinary outcome, bivariate logistic model treating toxicity and efficacy as independent outcomes, and bivariate probit model allowing for dependent toxicity and efficacy outcomes. All designs utilized a model-based methodology to adaptively determine dose escalation/de-escalation, based on the data observed to date in the trial. The model parameters were estimated using Markov chain Monte Carlo approach in a Bayesian framework. The target threshold for toxicity was set at 33%; the minimum and maximum sample sizes were set at 30 and 45, respectively, for the simulated trials; and the cohort size was 3 with at least nine patients needed to be treated at the proposed combination dose level. The performance of the designs was evaluated in simulation studies under six clinically relevant scenarios. Results: As expected, the ability to correctly identify an optimal dose region was sensitive to the changes in the toxicity and/or efficacy across the dose level combinations. Considering 50% as a benchmark for the recommendation rate for the optimal dose or region (dose levels within 10% of the maximum efficacious dose level), at least one of the three models performed well in recommending the optimal dose region except when the dose-efficacy surface was non-monotone or the dose-toxicity surface was close to the target rate of 33%. All three models worked well in not recommending any dose combination when the starting dose level combination was too toxic. The median sample size across all scenarios ranged from 27–33. Conclusions: Despite favorable operating characteristics, the implementation of these new designs in practice is challenging for a variety of reasons. Adoption of novel designs require a multi-pronged approach that provides a) clinically obvious advantages, b) practical design framework with a transparent decision making process, c) timely access to both toxicity and preliminary efficacy data, and d) portable user-friendly software, or very attentive statisticians. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):C53.

Abstract Src transduces activated HER tyrosine kinase and phosphorylates HER to further increase its activity. Src also is involved in osteoclast differentiation. We hypothesized that combining a HER tyrosine kinase inhibitor with a Src inhibitor would result in increased therapeutic activity. To address this hypothesis we performed a phase I trial of D and L to: 1)determine the maximally tolerated dose (MTD) of D combined with L; 2)describe the toxicities associated with this combination; 3)assess the pharmacokinetic (PK) interaction of L and D; 4) assess the effect of the L and D combination on circulating tumor cells (CTC) and on osteoclast precursor activation; 5)study the association of toxicity and/or tumor response with PK, and/or pharmacodynamic parameters; and 6)describe the responses of this combination. Eligibility criteria included ≥ 18 years of age, incurable solid tumors not amenable to other therapies, ANC ≥ 1500/ L, PLT ≥ 100,000/ L, total bilirubin ≤ ULN, AST ≤ 3 × ULN or AST ≤5 × ULN if liver involvement, creatinine ≤ 1.5 × ULN, Hgb ≥ 9.0 g/dL, K+ and Mg++ WNL, life expectancy ≥ 12 weeks, ejection fraction > 50%, ECOG PS 0–2, and able to swallow pills whole. In addition to standard phase I exclusion criteria patients could not have received erlotinib, sunitinib, sorafenib, gefitinib, imatinib ≤ 4 weeks prior to registration. Each agent was administered once daily on a 28 day schedule. At the MTD patients were treated with D day 1, and day 9–28 and L day 2–28 to assess PK interaction. Dose levels (mg) were #1 D 70, L 1000, #2 D 100, L 1000, #3 D 140, L 1000. 12 patients were entered on the dose escalation portion of the trial and 15 were entered at the MTD. 5 patients entered at the MTD are too early to be fully evaluable. Characteristics of evaluable patients were: median age, 63; 46% female; PS 0 (64%) 1 (27%), 1 (9%); ≥ 3 prior chemotherapies (59%). DLT was seen in 2 patients at # 3 (1 patient, grade 3 hypermagnesemia, 1, grade 3 rash) and 1 patient at # 2 (grade 3 dyspnea). The MTD was determined to be # 2. No grade 4 or 5 events have been observed in this study. 6 patients had stable disease in the dose escalation cohort. 1 (RCC) was stable disease for 6 cycles, 2 (colorectal) were stable for 5 cycles, 1 (esophagus) was stable for 3 cycles, and 2 (GIST & leiomyosarcoma) were stable for 2 cycles. Analysis of drug levels, CTCs and circulating osteoclast precursors is ongoing. There was a consistent increase in the percentage of CD11b (monocyte/macrophage/osteoclast lineage marker) positive cells in circulation as treatment progressed. However, the late osteoclast lineage marker c-Fms was not similarly increased, suggesting that the elevated CD11b reflects an inflammatory response and not activation of osteoclastogenesis. D and L is a tolerable combination at nearly full doses of each drug. Funded by a grant from Glaxo Smith Kline and Bristol Myers Squibb. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):B56.

Abstract The 19p13.1 breast cancer susceptibility locus is a modifier of breast cancer risk in BRCA1 mutation carriers and is also associated with the risk of ovarian cancer. Here, we investigated 19p13.1 variation and risk of breast cancer subtypes, defined by estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor-2 (HER2) status, using 48,869 breast cancer cases and 49,787 controls from the Breast Cancer Association Consortium (BCAC). Variants from 19p13.1 were not associated with breast cancer overall or with ER-positive breast cancer but were significantly associated with ER-negative breast cancer risk [rs8170 OR, 1.10; 95% confidence interval (CI), 1.05–1.15; P = 3.49 × 10−5] and triple-negative (ER-, PR-, and HER2-negative) breast cancer (rs8170: OR, 1.22; 95% CI, 1.13–1.31; P = 2.22 × 10−7). However, rs8170 was no longer associated with ER-negative breast cancer risk when triple-negative cases were excluded (OR, 0.98; 95% CI, 0.89–1.07; P = 0.62). In addition, a combined analysis of triple-negative cases from BCAC and the Triple Negative Breast Cancer Consortium (TNBCC; N = 3,566) identified a genome-wide significant association between rs8170 and triple-negative breast cancer risk (OR, 1.25; 95% CI, 1.18–1.33; P = 3.31 × 10−13]. Thus, 19p13.1 is the first triple-negative–specific breast cancer risk locus and the first locus specific to a histologic subtype defined by ER, PR, and HER2 to be identified. These findings provide convincing evidence that genetic susceptibility to breast cancer varies by tumor subtype and that triple-negative tumors and other subtypes likely arise through distinct etiologic pathways. Cancer Res; 72(7); 1795–803. ©2012 AACR.

Abstract Background: The single-nucleotide polymorphism (SNP) 5p12-rs10941679 has been found to be associated with risk of breast cancer, particularly estrogen receptor (ER)-positive disease. We aimed to further explore this association overall, and by tumor histopathology, in the Breast Cancer Association Consortium. Methods: Data were combined from 37 studies, including 40,972 invasive cases, 1,398 cases of ductal carcinoma in situ (DCIS), and 46,334 controls, all of white European ancestry, as well as 3,007 invasive cases and 2,337 controls of Asian ancestry. Associations overall and by tumor invasiveness and histopathology were assessed using logistic regression. Results: For white Europeans, the per-allele OR associated with 5p12-rs10941679 was 1.11 (95% CI = 1.08–1.14, P = 7 × 10−18) for invasive breast cancer and 1.10 (95% CI = 1.01–1.21, P = 0.03) for DCIS. For Asian women, the estimated OR for invasive disease was similar (OR = 1.07, 95%CI = 0.99–1.15, P = 0.09). Further analyses suggested that the association in white Europeans was largely limited to progesterone receptor (PR)-positive disease (per-allele OR = 1.16, 95% CI = 1.12–1.20, P = 1 × 10−18 vs. OR = 1.03, 95% CI = 0.99–1.07, P = 0.2 for PR-negative disease; Pheterogeneity = 2 × 10−7); heterogeneity by ER status was not observed (P = 0.2) once PR status was accounted for. The association was also stronger for lower grade tumors [per-allele OR (95% CI) = 1.20 (1.14–1.25), 1.13 (1.09–1.16), and 1.04 (0.99–1.08) for grade 1, 2, and 3/4, respectively; Ptrend = 5 × 10−7]. Conclusion: 5p12 is a breast cancer susceptibility locus for PR-positive, lower grade breast cancer. Impact: Multicenter fine-mapping studies of this region are needed as a first step to identifying the causal variant or variants. Cancer Epidemiol Biomarkers Prev; 20(10); 2222–31. ©2011 AACR.

AbstractJAK-STAT signaling is involved in the regulation of cell survival, proliferation, and differentiation. JAK tyrosine kinases can be transiently activated by cytokines or growth factors in normal cells, whereas they become constitutively activated as a result of mutations that affect their function in tumors. Specifically, the JAK2V617F mutation is present in the majority of patients with myeloproliferative disorders (MPDs) and is implicated in the pathogenesis of these diseases. In the present study, we report that the kinase CK2 is a novel interaction partner of JAKs and is essential for JAK-STAT activation. We demonstrate that cytokine-induced activation of JAKs and STATs and the expression of suppressor of cytokine signaling 3 (SOCS-3), a downstream target, are inhibited by CK2 small interfering RNAs or pharmacologic inhibitors. Endogenous CK2 is associated with JAK2 and JAK1 and phosphorylates JAK2 in vitro. To extend these findings, we demonstrate that CK2 interacts with JAK2V617F and that CK2 inhibitors suppress JAK2V617F autophosphorylation and downstream signaling in HEL92.1.7 cells (HEL) and primary cells from polycythemia vera (PV) patients. Furthermore, CK2 inhibitors potently induce apoptosis of HEL cells and PV cells. Our data provide evidence for novel cross-talk between CK2 and JAK-STAT signaling, with implications for therapeutic intervention in JAK2V617F-positive MPDs.

Abstract SR13668, an orally active Akt pathway inhibitor, has demonstrated cancer chemopreventive potential in preclinical studies. To accelerate the clinical development of this promising agent, we designed and conducted the first-ever phase 0 chemoprevention trial to evaluate and compare the effects of food and formulation on SR13668 bioavailability. Healthy adult volunteers were randomly assigned to receive a single, 38-mg oral dose of SR13668 in one of five different formulations, with or without food. On the basis of existing animal data, SR13668 in a PEG400/Labrasol oral solution was defined as the reference formulation. Blood samples were obtained pre- and post-agent administration for pharmacokinetic analyses. Area under the plasma concentration–time curve (AUC0–∞) was defined as the primary endpoint. Data were analyzed and compared using established statistical methods for phase 0 trials with a limited sample size. Participants (n = 20) were rapidly accrued over a 5-month period. Complete pharmacokinetic data were available for 18 randomized participants. AUC0–∞ values were highest in the fed state (range = 122–439 ng/mL × hours) and were statistically significantly different across formulations (P = 0.007), with Solutol HS15 providing the highest bioavailability. SR13668 time to peak plasma concentration (3 hours; range, 2–6 hours) and half-life were (11.2 ± 3.1 hours) were not formulation-dependent. Using a novel, highly efficient study design, we rapidly identified a lead formulation of SR13668 for further clinical testing. Our findings support application of the phase 0 trial paradigm to accelerate chemoprevention agent development. Cancer Prev Res; 4(3); 347–53. ©2011 AACR.