[Show abstract][Hide abstract] ABSTRACT: Prophylactic cranial irradiation (PCI) has become a standard option for patients with extensive-stage small cell lung cancer (ES-SCLC). The Cancer and Leukemia Group B 30504 trial was a randomized phase II study of the effect of sunitinib versus placebo in ES-SCLC patients responding to platinum-based systemic therapy. The study required preenrollment brain imaging. PCI was provided at the discretion of treating physicians. We performed a secondary analysis of the Cancer and Leukemia Group B trial to determine the impact of PCI on patients with ES-SCLC.
Preview · Article · Dec 2015 · Journal of thoracic oncology: official publication of the International Association for the Study of Lung Cancer
[Show abstract][Hide abstract] ABSTRACT: In drug development, when the drug class has a relatively well defined path to regulatory approval and the enrollment is slow with certain patient populations, one may want to consider combining studies of different phases. This paper considers combining a proof of concept (POC) study and a dose finding (DF) study with a control treatment. Conventional DF study designs sometimes are not efficient, or do not have a high probability to find the optimal dose(s) for phase III trials. This paper seeks more efficient DF strategies that allow economical testing of more doses. Hypothetical examples are simulated to compare the proposed adaptive design versus the conventional design based on different models of the overall quantitative representation of efficacy, safety and tolerability. The results show that the proposed adaptive design tests more active doses with higher power and comparable or smaller sample size in a shorter overall study duration for POC and DF, compared to a conventional design.
No preview · Article · Sep 2015 · Journal of Biopharmaceutical Statistics
[Show abstract][Hide abstract] ABSTRACT: High-throughput expression profiling techniques bring novel tools and also statistical challenges to genetic research. In addition to detecting differentially expressed genes, testing the significance of gene sets or pathway analysis has been recognized as an equally important problem. Owing to the "large p small n" paradigm, the traditional Hotelling's T2 test suffers from the singularity problem and therefore is not valid in this setting. In this paper, we propose a shrinkage-based diagonal Hotelling's test for both one-sample and two-sample cases. We also suggest several different ways to derive the approximate null distribution under different scenarios of p and n for our proposed shrinkage-based test. Simulation studies show that the proposed method performs comparably to existing competitors when n is moderate or large, but it is better when n is small. In addition, we analyze four gene expression data sets and they demonstrate the advantage of our proposed shrinkage-based diagonal Hotelling's test.
No preview · Article · Sep 2015 · Journal of Multivariate Analysis
[Show abstract][Hide abstract] ABSTRACT: Inhibition of tumor angiogenesis is an effective mechanism to limit tumor growth; dual inhibition may result in additional benefit. Bevacizumab is a monoclonal antibody directed against vascular endothelial growth factor (VEGF), and intetumumab is a fully humanized monoclonal antibody that blocks αv integrins when complexed with β integrins. We evaluated the safety, tolerability, and efficacy of the combination of bevacizumab plus intetumumab in patients with refractory solid tumors. We also explored the effects of these agents on plasma-based biomarkers and wound angiogenesis.
Patients with refractory solid tumors, Karnofsky performance status ≥70 %, and adequate organ function were eligible. Plasma samples and wound biopsies were obtained at baseline and on-treatment.
Twelve patients were enrolled and received study drug. No tumor responses were noted. Observed toxicities included three cases of transient uveitis likely related to intetumumab and one case of reversible posterior leukoencephalopathy syndrome likely related to bevacizumab. Biomarker analysis revealed changes in soluble endoglin, soluble E-cadherin, and soluble E-selectin as well as PlGF and VEGF-D while on treatment. There was no observed impact of bevacizumab plus intetumumab on the phosphorylated or total levels of paxillin in wound tissue; however, an increase in the ratio of phospho/total paxillin levels was noted.
Bevacizumab and intetumumab can be administered safely in combination. Bevacizumab plus intetumumab treatment resulted in changes in the plasma levels of several extracellular matrix interacting proteins and angiogenic factors.
No preview · Article · Dec 2014 · Cancer Chemotherapy and Pharmacology
[Show abstract][Hide abstract] ABSTRACT: Cancer biomarker discovery can facilitate drug development, improve staging of patients, and predict patient prognosis. Because cancer is the result of many interacting genes, analysis based on a set of genes with related biological functions or pathways may be more informative than single gene-based analysis for cancer biomarker discovery. The relevant pathways thus identified may help characterize different aspects of molecular phenotypes related to the tumor. Although it is well known that cancer patients may respond to the same treatment differently because of clinical variables and variation of molecular phenotypes, this patient heterogeneity has not been explicitly considered in pathway analysis in the literature. We hypothesize that combining pathway and patient clinical information can more effectively identify relevant pathways pertinent to specific patient subgroups, leading to better diagnosis and treatment. In this article, we propose to perform stratified pathway analysis based on clinical information from patients. In contrast to analysis using all the patients, this more focused analysis has the potential to reveal subgroup-specific pathways that may lead to more biological insights into disease etiology and treatment response. As an illustration, the power of our approach is demonstrated through its application to a breast cancer dataset in which the patients are stratified according to their oral contraceptive use.
[Show abstract][Hide abstract] ABSTRACT: Thyroid hormone (TH) is important for tissue repair because it regulates cellular differentiation. Intrahepatic TH activity is controlled by both serum TH levels and hepatic deiodinases. TH substrate (thyroxine, T4) is converted into active hormone (triidothyronine, T3) by deiodinase 1 (D1), but into inactive hormone (reverse T3, rT3) by deiodinase 3 (D3). Although the relative expressions of D1 and D3 are known to change during liver injury, the cell types and signaling mechanisms involved are unclear. We evaluated the hypothesis that changes in hepatic deiodinases result from repairrelated activation of the Hedgehog pathway in stromal cells. We localized deiodinase expression, assessed changes during injury, and determined how targeted manipulation of Hedgehog signaling in stromal cells impacted hepatic deiodinase expression, TH content, and TH action in rodents. Humans with chronic liver disease were also studied. In healthy liver, hepatocytes strongly expressed D1 and stromal cells weakly expressed D3. During injury, hepatocyte expression of D1 decreased, while stromal expression of D3 increased, particularly in myofibroblasts. Conditionally disrupting Hedgehog signaling in myofibroblasts normalized deiodinase expression. Repairrelated changes in deiodinases were accompanied by reduced hepatic TH content and TH-regulated gene expression. In patients, this was reflected by increased serum rT3. Moreover, decreases in fT3/rT3 and fT4/rT3 distinguished advanced from mild fibrosis, even in individuals with similar serum levels of TSH and fT4. Conclusion: Hedgehog-dependent changes in liver stromal cells drive repair-related changes in hepatic deiodinase expression that promote intrahepatic hypothyroidism, thereby limiting exposure to T3, an important factor for cellular differentiation.
[Show abstract][Hide abstract] ABSTRACT: Recent method development has included multi-dimensional genomic data algorithms because such methods have more accurately predicted clinical phenotypes related to disease. This study is the first to conduct an integrative genomic pathway-based analysis with a graph-based learning algorithm. The methodology of this analysis, graph-based semi-supervised learning, detects pathways that improve prediction of a dichotomous variable, which in this study is cancer stage. This analysis integrates genome-level gene expression, methylation, and single nucleotide polymorphism (SNP) data in serous cystadenocarcinoma (OV) and colon adenocarcinoma (COAD). The top 10 ranked predictive pathways in COAD and OV were biologically relevant to their respective cancer stages and significantly enhanced prediction accuracy and area under the ROC curve (AUC) when compared to single data-type analyses. This method is an effective way to simultaneously predict binary clinical phenotypes and discover their biological mechanisms.
Full-text · Article · Jul 2014 · Cancer informatics
[Show abstract][Hide abstract] ABSTRACT: TRC105 is an endoglin-targeting drug that possesses anti-angiogenic and antitumor potential. Analysis of the initial phase I trial of TRC105 demonstrated good tolerability and efficacy in cancer patients. In this report, we analyzed multiple circulating biomarkers at baseline, cycle 2 day 1 (C2D1), and end of study (EOS) for each patient. The baseline level and the fold change from baseline to both C2D1 and EOS for each marker were statistically analyzed. At C2D1, seven markers were significantly downregulated (angiopoietin-2 [Ang-2], insulin-like growth factor-binding protein-3 [IGFBP-3], plasminogen activator inhibitor-1 [PAI-1] total, platelet-derived growth factor [PDGF]-AA, PDGF-BB, thrombospondin-1 [TSP-1], and vascular endothelial growth factor [VEGF]-D). Meanwhile, seven markers were upregulated by C2D1 (E-Cadherin, soluble Endoglin [sEnd], E-Selectin, interleukin-6 [IL-6], osteopontin [OPN], TSP-2, and von Willebrand factor [vWF]). At EOS, seven markers were upregulated including Ang-2, C-reactive protein (CRP), intercellular adhesion molecule-1 (ICAM-1), IGFBP-1, IL-6, TSP-2, and vascular cell adhesion molecule-1 (VCAM-1). A statistical trend was also seen for increases of VEGF-A and placenta growth factor (PlGF) at EOS. Throughout treatment, sEnd levels significantly increased, an observation that was recapitulated in cultured endothelial cells. This is the first report of plasma-based biomarkers in patients receiving TRC105. TRC105 treatment by C2D1 was associated with decreases in several angiogenic factors, including Ang-2, PDGF isoforms, and VEGF isoforms, offering insight into the mechanisms underlying TRC105's anti-angiogenic, antitumor function. Increases in sEnd were the most significant of all observed biomarker changes and may reflect direct drug effects. Additionally, biomarker changes in response to TRC105 are distinct from those seen in patients treated with VEGF-targeting drugs, suggesting the possible utility of combining these two classes of angiogenesis inhibitors in patients.
[Show abstract][Hide abstract] ABSTRACT: Purpose:
To define maximum tolerated dose (MTD), toxicities, and pharmacodynamics of capecitabine, oxaliplatin, bevacizumab, and everolimus in advanced solid tumor patients.
This was a standard "3 + 3" dose-escalation trial. All subjects received bevacizumab 7.5 mg/kg on day 1 of each cycle. Doses for capecitabine, oxaliplatin and everolimus were modified per dose limiting toxicity (DLT). Baseline and on-treatment plasma biomarkers were analyzed. Archived tumor mRNA levels were evaluated for NRP1, NRP2 and VEGF-A isoforms.
Twenty-nine patients were evaluable for toxicity and 30 for efficacy. Two DLTs were observed in cohort 1 and one DLT each was observed in cohort -1 and -1b. Grade ≥3 toxicities included neutropenia, hypertension, perforation/fistula/hemorrhage, hypertriglyceridemia, diarrhea, and thromboembolism. Twelve subjects experienced partial response (PR); 12 had stable disease as best response. Three of seven chemorefractory metastatic colorectal cancer (mCRC) subjects experienced PR; 8 of 15 chemonaive mCRC subjects experienced PR. Plasma TβRIII and IL-6 increased on treatment but without correlation to outcome. Increased VEGF165 levels significantly correlated with longer progression free survival.
Everolimus with full dose capecitabine, oxaliplatin, and bevacizumab had unacceptable toxicity. MTD was: everolimus 5 mg daily; capecitabine 680 mg/m(2) BID days 1-14; oxaliplatin 100 mg/m(2) and bevacizumab 7.5 mg/kg, day 1. Activity was noted in mCRC.
No preview · Article · Apr 2014 · Investigational New Drugs
[Show abstract][Hide abstract] ABSTRACT: Unlabelled:
Estrogens inhibit stellate cell activation and fibrogenesis. Thus, gender and reproductive states may influence the degree of fibrosis in patients with nonalcoholic steatohepatitis (NASH). To investigate the association between gender, menopause, and the severity of liver fibrosis in patients with NASH, we analyzed 541 adult patients enrolled from our Duke Liver Clinics (n = 338) and the Duke Metabolic and Weight Loss Surgery Program (n = 203) who had a histologic diagnosis of NASH. Multiple ordinal logistic regression models were used to assess the association between gender, menopause, and severity of liver fibrosis. Overall, men, premenopausal, and postmenopausal women composed 35.1%, 28.4%, and 36.5% of the population, respectively. The mean age was 48 years and 22% had advanced fibrosis. After adjusting for covariates (enrolling site, grades of portal inflammation, and hepatocyte ballooning) and potential confounders (race, body mass index, diabetes/prediabetes, hypertension), adjusted cumulative odd ratio (ACOR) and 95% confidence interval (CI) for greater fibrosis severity was 1.4 (0.9, 2.1) (P = 0.17) for postmenopausal women and 1.6 (1.0, 2.5) (P = 0.03) for men, having premenopausal women as a reference. There was borderline interaction between gender and age group divided by age 50, the average age at menopause in the U.S. (P = 0.08): ACOR and 95% CI of having greater fibrosis severity in men compared to women was 1.8 (1.1, 2.9) for patients with age <50 years (P = 0.02) and 1.2 (0.7, 2.1) for patients with age ≥50 years (P = 0.59).
Men are at a higher risk of having more severe fibrosis compared to women before menopause, while postmenopausal women have a similar severity of liver fibrosis compared to men. These findings may be explained by the protective effects of estrogen against fibrogenesis.
[Show abstract][Hide abstract] ABSTRACT: Unlabelled:
Clinicians rely upon the severity of liver fibrosis to segregate patients with well-compensated nonalcoholic fatty liver disease (NAFLD) into subpopulations at high- versus low-risk for eventual liver-related morbidity and mortality. We compared hepatic gene expression profiles in high- and low-risk NAFLD patients to identify processes that distinguish the two groups and hence might be novel biomarkers or treatment targets. Microarray analysis was used to characterize gene expression in percutaneous liver biopsies from low-risk, "mild" NAFLD patients (fibrosis stage 0-1; n = 40) and high-risk, "severe" NAFLD patients (fibrosis stage 3-4; n = 32). Findings were validated in a second, independent cohort and confirmed by real-time polymerase chain reaction and immunohistochemistry (IHC). As a group, patients at risk for bad NAFLD outcomes had significantly worse liver injury and more advanced fibrosis (severe NAFLD) than clinically indistinguishable NAFLD patients with a good prognosis (mild NAFLD). A 64-gene profile reproducibly differentiated severe NAFLD from mild NAFLD, and a 20-gene subset within this profile correlated with NAFLD severity, independent of other factors known to influence NAFLD progression. Multiple genes involved with tissue repair/regeneration and certain metabolism-related genes were induced in severe NAFLD. Ingenuity Pathway Analysis and IHC confirmed deregulation of metabolic and regenerative pathways in severe NAFLD and revealed overlap among the gene expression patterns of severe NAFLD, cardiovascular disease, and cancer.
By demonstrating specific metabolic and repair pathways that are differentially activated in livers with severe NAFLD, gene profiling identified novel targets that can be exploited to improve diagnosis and treatment of patients who are at greatest risk for NAFLD-related morbidity and mortality.
[Show abstract][Hide abstract] ABSTRACT: Close to three percent of the world’s population suffer from diabetes. Despite the range of treatment options available for diabetes patients, not all patients benefit from them. Investigating how different pathways correlate with phenotype of interest may help unravel novel drug targets and discover a possible cure. Many pathway-based methods have been developed to incorporate biological knowledge into the study of microarray data. Most of these methods can only analyze individual pathways but cannot deal with two or more pathways in a model based framework. This represents a serious limitation because, like genes, individual pathways do not work in isolation, and joint modeling may enable researchers to uncover patterns not seen in individual pathway-based analysis. In this paper, we propose a random effects model to analyze two or more pathways. We also derive score test statistics for significance of pathway effects. We apply our method to a microarray study of Type II diabetes. Our method may eludicate how pathways crosstalk with each other and facilitate the investigation of pathway crosstalks. Further hypothesis on the biological mechanisms underlying the disease and traits of interest may be generated and tested based on this method.
No preview · Article · Jan 2014 · Statistics in Biosciences
[Show abstract][Hide abstract] ABSTRACT: Standard therapy for limited stage small cell lung cancer (L-SCLC) is concurrent chemotherapy and radiotherapy followed by prophylactic cranial radiotherapy. Predictors of post chemoradiotherapy pulmonary toxicity in limited stage (LS) small cell lung cancer (SCLC) patients are not well defined. Current guidelines are derived from non-small cell lung cancer regimens, and do not account for the unique biology of this disease. Therefore, we analyzed patients on three consecutive CALGB LS-SCLC trials treated with concurrent chemotherapy and daily high dose radiotherapy (70 Gy) to determine patient and treatment related factors predicting for post-treatment pulmonary toxicity.
Patients treated on CALGB protocols 39808, 30002, 30206 investigating two cycles of chemotherapy followed by concurrent chemotherapy and 70 Gy daily thoracic radiation therapy were pooled. Patient, tumor, and treatment related factors were evaluated to determine predictors of grade 3–5 pulmonary toxicities after concurrent chemoradiotherapy.
100 patients were included. No patient experienced grade 4–5 post-treatment pulmonary toxicity. Patients who experienced post-treatment pulmonary toxicity were more likely to be older (median age 69 vs 60, p = 0.09) and have smaller total lung volumes (2565 cc vs 3530 cc, p = 0.05).). Furthermore,exposure of larger volumes of lung to lower (median V5 = 70%, p = 0.09, median V10 = 63%, p = 0.07), inter-mediate (median V20 = 50, p = 0.04) and high (median V60 = 25%, p = 0.01) doses of radiation were all associated with post-treatment grade 3 pulmonary toxicity, as was a larger mean lung radiation dose(median 31 Gy) p = 0.019.
Post-treatment pulmonary toxicity following the completion of 2 cycles of chemotherapy followed by concurrent chemotherapy and high dose daily radiation therapy was uncommon. Care should be taken to minimize mean lung radiation exposure, as well as volumes of low, intermediate and high doses of radiation.
Full-text · Article · Dec 2013 · Lung cancer (Amsterdam, Netherlands)