Citations

Abstract Lung adenocarcinoma is the most common type of primary lung cancer. Previous studies have shown that gene expression signatures may predict clinical outcome. In this study, we used a systems biology approach, weighted gene co-expression network analysis (WGCNA), to identify survival related networks and gene signatures. We first analyzed whole genome gene expression profiles in 82 lung adenocarcinoma tumor tissues from never smokers (smoked <100 cigarettes lifetime) and found a significant correlation of an expression module with tumor grade of differentiation (r=0.38, p=4×10−4) and overall survival (OS, p =0.027, HR, 1.71; 95% CI, 1.06-2.74) after adjusting for potential confounders (age and tumor grade). When this module signature was incorporated and compared to the conventional model consisting of clinical variables only, the survival prediction accuracy was increased from 0.70 to 0.75. Gene Ontology (GO) enrichment analysis indicated this module was significantly enriched in biological process GO term “cell cycle” (p = 2.1×10−53). To explore the effect of this network module at germline level, we performed the WGCNA on normal lung tissues derived from 78 of the 82 patients and observed significant association of an expression module with OS (adjusted p=3×10−4, HR=1.98; 95% CI, 1.36-2.87). Interestingly, this module was also significantly enriched in cell cycle-related genes (p=4.1×10−41). To further validate this result, we analyzed an independent microarray gene expression dataset including 442 lung adenocarcinoma patients from NCI Director's Challenge Consortium. We found the same association: the cell cycle-enriched module was correlated with tumor grade of cell differentiation (r=0.55, p-value=5×10−37) and OS (adjusted p=7.4×10−3; HR, 1.20; 95% CI, 1.05-1.37). We further identified 30 genes in the OS-related module that overlapped between the discovery and validation data sets. Furthermore, all these 30 genes were found to be up-regulated in adenocarcinoma compared to adjacent normal lung tissues in the discovery data set. Of the 30 genes, three key genes, UBE2C, TPX2 and MELK, were identified with highest connectivity in cell cycle-enriched module; their expression levels were significantly associated with OS in both discovery and validation sets. UBE2C and TPX2 have been reported as gene signatures for human lung cancer prognosis in vitro lung carcinogenesis system; MELK was identified as a key regulator of the proliferation of malignant brain tumors and malignant grade in human astrocytomas, and was also associated with breast cancer prognosis. Our results suggest that genes involved in cell-cycle are likely related with tumor aggressiveness and therefore can predict survival in lung adenocarcinoma. Further studies are needed to validate the key genes that could improve survival prediction and provide potential new targets to intervene progression of lung adenocarcinoma. 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 5060. doi:10.1158/1538-7445.AM2011-5060

Abstract Background: ABT-888 is an inhibitor of poly(ADP-ribose) polymerase1 (PARP1) and PARP2, two highly conserved enzymes implicated in DNA repair, maintenance of genomic stability, and regulation of transcription. Topotecan (TPT) is a water soluble camptothecin derivative with antitumor activity against ovarian tumors. The combination of ABT-888 with TPT is under investigation in phase I trials because PARP inhibition sensitizes tumors cells to TPT in vitro and in vivo. In those trials, the pharmacokinetics of TPT and ABT-888 are being studied to determine if ABT-888 levels are sufficient to modulate PARP activity and to investigate the potential interaction between TPT and ABT-888. Methods: Advanced cancer patients with ECOG performance scores 0-2, adequate hematological, renal and hepatic function were treated with ABT-888 on days 1-3, 8-10, and 15-17 every 28 days. Topotecan was administered on days 2, 9 and 16 every 28 days. DLTs were defined as grade 4 neutropenia, grade 4 thrombocytopenia, grade 4 anemia or ≥ grade 3 non-hematologic toxicities despite maximal supportive care. ABT-888 and Toptoecan pharmacokinetics were characterized in all patients. Analysis of urinary recovery is ongoing. Results: In this ongoing Phase I trial, 13 female patients with ovarian (n=12) or breast (n=1) cancer have been enrolled to date and pharmacokinetic data is available for 12 of those patients. ABT-888/TPT dose levels are: Level 1- 10 mg/ 2 mg/m2, Level 2- 20 mg/2 mg/m2, Level 3- 10 mg/3 mg/m2, and Level 4- 20 mg/3 mg/m2. The combination of ABT-888 with topotecan has been tolerable, with no dose limiting toxicity, and dose escalation continues at dose level 5. Topotecan t1/2 and clearance values were 3.0 ± 0.5 hrs and 9.50 ± 1.51 L/hr/m2 when administered alone, and were not affected by administration with ABT-888. When administered alone, ABT-888 t1/2, Cmax, AUC0-∞ values after the 10 mg dose were 8.2 ± 2.4 hrs, 432 ± 217 nM, and 2568 ± 1300 nM*hr, respectively. ABT-888 t1/2, Cmax, AUC values after the 20 mg dose were 5.7 ± 3.1 hrs, 600 ± 165 nM, and 3870± 934 respectively. When administered with TPT, ABT-888 t1/2, Cmax, AUC values after the 10 mg dose were 7.2 ± 2.1 hrs, 412 ± 283 nM, and 2705± 1089 nM*hr are: nM*hr respectively. ABT-888 t1/2, Cmax and AUC values after the 20 mg dose combined with TPT were 5.8 ± 2.2 hrs, 664 ± 97.6 nM, and 4283± 936 nM*hr respectively. Conclusions: Plasma clearance of TPT and ABT-888 does not appear to be altered when they are administered together. The effect of co-administration of these agents on renal clearance is presently under investigation and those results will be presented. This work was supported by NIH grants R25 GM75148-04, U01CA069912-16S and MM01-RR00585. 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 1301. doi:10.1158/1538-7445.AM2011-1301

Abstract Purpose: miRNA plays an important role in human disease and cancer. We seek to investigate the expression status, clinical relevance, and functional role of miRNA in non–small cell lung cancer. Experimental Design: We conducted miRNA expression profiling in matched lung adenocarcinoma and uninvolved lung using 56 pairs of fresh-frozen (FF) and 47 pairs of formalin-fixed, paraffin-embedded (FFPE) samples from never smokers. The most differentially expressed miRNA genes were evaluated by Cox analysis and log-rank test. Among the best candidate, miR-708 was further examined for differential expression in two independent cohorts. Functional significance of miR-708 expression in lung cancer was examined by identifying its candidate mRNA target and through manipulating its expression levels in cultured cells. Results: Among the 20 miRNAs most differentially expressed between tested tumor and normal samples, high expression level of miR-708 in the tumors was most strongly associated with an increased risk of death after adjustments for all clinically significant factors including age, sex, and tumor stage (FF cohort: HR, 1.90; 95% CI, 1.08–3.35; P = 0.025 and FFPE cohort: HR, 1.93; 95% CI, 1.02–3.63; P = 0.042). The transcript for TMEM88 gene has a miR-708 binding site in its 3′ UTR and was significantly reduced in tumors high of miR-708. Forced miR-708 expression reduced TMEM88 transcript levels and increased the rate of cell proliferation, invasion, and migration in culture. Conclusions: miRNA-708 acts as an oncogene contributing to tumor growth and disease progression by directly downregulating TMEM88, a negative regulator of the Wnt signaling pathway in lung cancer. Clin Cancer Res; 18(13); 3658–67. ©2012 AACR.

Purpose The trial objectives were to identify the maximum-tolerated dose (MTD) of first-line gemcitabine plus nab-paclitaxel in metastatic pancreatic adenocarcinoma and to provide efficacy and safety data. Additional objectives were to evaluate positron emission tomography (PET) scan response, secreted protein acidic and rich in cysteine (SPARC), and CA19-9 levels in relation to efficacy. Subsequent preclinical studies investigated the changes involving the pancreatic stroma and drug uptake. Patients and Methods Patients with previously untreated advanced pancreatic cancer were treated with 100, 125, or 150 mg/m 2 nab-paclitaxel followed by gemcitabine 1,000 mg/m 2 on days 1, 8, and 15 every 28 days. In the preclinical study, mice were implanted with human pancreatic cancers and treated with study agents. Results A total of 20, 44, and three patients received nab-paclitaxel at 100, 125, and 150 mg/m 2 , respectively. The MTD was 1,000 mg/m 2 of gemcitabine plus 125 mg/m 2 of nab-paclitaxel once a week for 3 weeks, every 28 days. Dose-limiting toxicities were sepsis and neutropenia. At the MTD, the response rate was 48%, with 12.2 median months of overall survival (OS) and 48% 1-year survival. Improved OS was observed in patients who had a complete metabolic response on [ 18 F]fluorodeoxyglucose PET. Decreases in CA19-9 levels were correlated with increased response rate, progression-free survival, and OS. SPARC in the stroma, but not in the tumor, was correlated with improved survival. In mice with human pancreatic cancer xenografts, nab-paclitaxel alone and in combination with gemcitabine depleted the desmoplastic stroma. The intratumoral concentration of gemcitabine was increased by 2.8-fold in mice receiving nab-paclitaxel plus gemcitabine versus those receiving gemcitabine alone. Conclusion The regimen of nab-paclitaxel plus gemcitabine has tolerable adverse effects with substantial antitumor activity, warranting phase III evaluation.

X chromosome inactivation (XCI) is the most dramatic example of epigenetic silencing in eukaryotes. Once established, the inactivated X chromosome (Xi) remains silenced throughout subsequent cell divisions. Though the initiation of XCI has been studied extensively, the protein factors involved in Xi silencing and maintenance are largely unknown. Here we report the discovery of a diverse set of 32 proteins involved in maintenance of Xi silencing through a genome-wide RNAi screen. In addition, we describe the mechanistic roles of two proteins—origin recognition complex 2 (Orc2) and heterochromatin protein 1 (HP1α)—in Xi silencing. Immunofluorescence studies indicate that Orc2 and HP1α localize on Xi in mouse cells. Depletion of Orc2 by shRNA leads to the loss of both Orc2 and HP1α localization on Xi. Furthermore, the silencing of genes on Xi is disrupted in both Orc2- and HP1α-depleted cells. Finally, we show, using ChIP assay, that the localization of HP1α and Orc2 to the promoter regions of Xi-silenced genes is interdependent. These findings reveal a diverse set of proteins involved in Xi silencing, show how Orc2 and HP1α impact Xi silencing, and provide a basis for future studies on the maintenance of Xi silencing.

Abstract Background: Single nucleotide polymorphisms (SNP) in microRNA-related genes have been associated with epithelial ovarian cancer (EOC) risk in two reports, yet associated alleles may be inconsistent across studies. Methods: We conducted a pooled analysis of previously identified SNPs by combining genotype data from 3,973 invasive EOC cases and 3,276 controls from the Ovarian Cancer Association Consortium. We also conducted imputation to obtain dense coverage of genes and comparable genotype data for all studies. In total, 226 SNPs within 15 kb of 4 miRNA biogenesis genes (DDX20, DROSHA, GEMIN4, and XPO5) and 23 SNPs located within putative miRNA binding sites of 6 genes (CAV1, COL18A1, E2F2, IL1R1, KRAS, and UGT2A3) were genotyped or imputed and analyzed in the entire dataset. Results: After adjustment for European ancestry, no overall association was observed between any of the analyzed SNPs and EOC risk. Conclusions: Common variants in these evaluated genes do not seem to be strongly associated with EOC risk. Impact: This analysis suggests earlier associations between EOC risk and SNPs in these genes may have been chance findings, possibly confounded by population admixture. To more adequately evaluate the relationship between genetic variants and cancer risk, large sample sizes are needed, adjustment for population stratification should be carried out, and use of imputed SNP data should be considered. Cancer Epidemiol Biomarkers Prev; 20(8); 1793–7. ©2011 AACR.