Lela Buckingham

PTEN, RASSF1 and DAPK site-specific hypermethylation and outcome in surgically treated stage I and II nonsmall cell lung cancer patients.

The primary objective of this study is to identify prognostic site‐specific epigenetic changes in surgically treated Stage I and II nonsmall cell lung cancer (NSCLC) patients by quantifying methylation levels at multiple CpG sites within each gene promoter. Paraffin‐embedded tumors from stage Ib, IIa and IIb in training and validation groups of 75 and 57 surgically treated NSCLC patients, respectively, were analyzed for p16, MGMT, RASSF1, RASSF5, CDH1, LET7, DAPK and PTEN promoter hypermethylation. Hypermethylation status was quantified individually at multiple CpG sites within each promoter by pyrosequencing. Molecular and clinical characteristics with time to recurrence (TTR) and overall survival (OS) were evaluated. Overall average promoter methylation levels of MGMT and RASSF1 were significantly higher in smokers than in nonsmokers (p = 0.006 and p = 0.029, respectively). Methylation levels of the p16 promoter were significantly higher in squamous cell carcinoma than in adenocarcinoma (p = 0.020). In univariate analysis, hypermethylation of RASSF1 at CpG sites −53 and −48 and PTEN at CpG site −1310 were the significantly associated with shorter TTR (p = 0.002 and p < 0.000, respectively). Hypermethylation of PTEN at −1310 and DAPK at −1482 were most significantly associated with outcome in multivariate analysis. These results show that methylation of specific promoter CpG sites in PTEN, RASSF1 and DAPK is associated with outcome in early stage surgically treated NSCLC.

Selecting Patients for Treatment with Epidermal Growth Factor Tyrosine Kinase Inhibitors

Identification of objective tumor regressions with epidermal growth factor receptor tyrosine kinases (EGFR TKI) in non–small cell lung cancer (NSCLC) patients has resulted in intense, worldwide clinical and basic research directed toward finding the optimal use of EGFR TKIs in NSCLC. EGFR TKI clinical trials have shown that higher response rates and longer survival are associated with specific patient characteristics and that using conventional chemotherapy simultaneously with EGFR TKIs in unselected patients does not increase survival. Molecular studies have revealed that EGFR-activating mutations and high EGFR gene copy number are frequently found in patients who have the best outcomes with EGFR TKIs. More recent studies suggest that KRAS mutations may identify the subset of patients who have the worst outcome with the EGFR TKI treatment. Currently, investigators are trying to determine the optimal approach to selecting patients for treatment with EGFR TKIs. Studies that have evaluated the potential predictive value of clinical features and/or molecular profiles in EGFR TKI-treated NSCLC patients are discussed in this review.

The Potential Predictive Value of Cyclooxygenase-2 Expression and Increased Risk of Gastrointestinal Hemorrhage in Advanced Non-Small Cell Lung Cancer Patients Treated with Erlotinib and Celecoxib

Purpose: Celecoxib, a cyclooxygenase-2 (COX-2) inhibitor, potentiates antitumor effects of erlotinib in preclinical studies, and COX-2 is frequently expressed in non–small cell lung cancer (NSCLC). With these observations, we designed a phase II trial to evaluate the efficacy and safety of erlotinib plus celecoxib in advanced NSCLC. Experimental Design: Previously treated stage IIIB/IV NSCLC patients were given celecoxib at 400 mg orally twice daily and erlotinib at 150 mg orally daily until disease progression. Planned accrual was 40 patients. Tissue was collected for epidermal growth factor receptor (EGFR) analysis and COX-2 immunohistochemistry. Results: Twenty-six patients were enrolled (17 men, 9 women; median age, 66 years). Eighteen and 21 patients had tissue available for EGFR analysis and COX-2 immunohistochemistry, respectively. The median progression-free survival (PFS) and overall survival were 2.0 and 9.2 months, respectively. Eleven of 21 patients tested had increased tumor COX-2 expression, which was strongly associated with prolonged PFS (P = 0.048). Four patients on anticoagulation or with a history of peptic ulcer disease had grade 3/grade 4 upper gastrointestinal bleeding (GIB), prompting early study closure. Three patients with GIB had endoscopy that found peptic ulcers. Conclusions: The combination of erlotinib and celecoxib does not seem superior to erlotinib alone in unselected patients. However, longer PFS with high-tumor COX-2 expression suggests that trials of EGFR and COX-2 inhibitors may be warranted in this patient subset. GIB observed in our trial supports excluding patients with a history of peptic ulcer disease or those requiring therapeutic anticoagulation from future EGFR and COX-2 inhibitor studies.

The prognostic value of chromosome 7 polysomy in non-small cell lung cancer patients treated with gefitinib.

Introduction: Specific subpopulations of non-small cell lung cancer (NSCLC) patients defined by clinical features and molecular profiles seem to derive greater benefit from epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors, but no general consensus on molecular testing to optimize treatment has emerged. The objective of this study was to evaluate chromosome 7 polysomy and other potential indicators of gefitinib efficacy in advanced NSCLC patients. Methods: Paraffin-embedded tumors from 82 patients treated with gefitinib were analyzed by immunohistochemistry for expression of EGFR and other markers, and by fluorescence in situ hybridization for EGFR gene or chromosome copy number. Mutational status was assessed by single-strand conformational polymorphism, sequence-specific polymerase chain reaction, and direct sequencing. Molecular and clinical characteristics were evaluated in relation to objective response (OR), progression-free survival (PFS), and overall survival (OS). Results: EGFR mutational status (p = 0.002), never smoking (p = 0.052), and chromosome 7 polysomy (p = 0.029) were significant indicators of OR. EGFR mutation, pAKT or PTEN expression, and chromosome 7 polysomy were associated with longer OS. There was a significant difference in OS between the chromosome 7 polysomy groups (p = 0.015) and the groups with both chromosome 7 polysomy and pAkt+ (p = 0.002) and both chromosome7 polysomy and PTEN+ (p = 0.04). In a stepwise proportional hazards analysis, chromosome 7 polysomy and PTEN+ expression were both significantly associated with longer OS (p = 0.004 and 0.017 respectively). Conclusion: These results suggest that further study of chromosome 7 polysomy and of pAKT and PTEN expression in patients treated with EGFR tyrosine kinase inhibitors is warranted in developing a clinical test for selecting patients for gefitinib therapy.

REVERSAL OF MULTI-DRUG RESISTANCE IN VITRO BY FATTY ACID-PEG-FATTY ACID DIESTERS

Fatty acid ester surfactants, e.g., Cremophor EL and Solutol HS 15, that modulate multi‐drug resistance (MDR) have been described; however, the drug potential of these preparations is unclear because of the molecular heterogeneity of these and other commercial surfactants. In previous experiments, an active but still polydisperse preparation, designated CRL 1337, was synthesized by reacting purified oleic acid with a 20‐fold molar excess of ethylene oxide. We have subjected this preparation to chromatographic separation, and infrared analysis of the active fractions revealed a significant component of diester structures (fatty acid‐PEG‐fatty acid). A new generation of diester compounds has now been synthesized. Preparations comprised of 99% diesters were significantly more potent than monoester preparations for MDR modification activity in vitro. As previously determined for ethylene oxide‐derived preparations similar to CRL 1337, the nature of the fatty acid domains proved to be important for activity, as was the relative length of the polyethylene glycol domain (which determines the hydrophile‐lipophile balance). The ester linkage appeared unimportant since homologous diethers and diamides had activity similar to that of diesters. Stearic acid diester was 1.5‐ to 7‐fold more potent than CRL 1337 when tested in cell proliferation inhibition assays. In light of these structural restrictions on drug potentiation, and since these surfactants are active at relatively low concentrations (below 1 μg/ml), investigations of their mechanism of action were initiated by exploring specific interactions with P‐glycoprotein. Both active and inactive diesters inhibited azidopine labeling of P‐glycoprotein, suggesting that fatty acid‐PEG diesters can interfere with P‐glycoprotein substrate binding. Other attributes of these preparations must contribute to their ability to reverse MDR.

Inhibition of cytarabine‐induced MDR1 (P‐glycoprotein) gene activation in human tumor cells by fatty acid‐polyethylene glycol‐fatty acid diesters, novel inhibitors of P‐glycoprotein function

Fatty acid ester surfactants Cremophor EL and Solutol HS 15 were described earlier as modulators of multidrug resistance mediated by MDR1 P‐glycoprotein (Pgp). We have shown that the most active components of these polydisperse surfactants are fatty acid‐polyethylene glycol‐fatty acid diesters (FA‐PEG‐FA). A new generation of Pgp‐surfactant inhibitors of defined structure was therefore synthesized. In the present study we show that these compounds are also able to inhibit up‐regulation of MDR1 gene expression caused by cytarabine (ARA‐C) and doxorubicin in human tumor cell lines H9 and KB 3‐1, which express minimal levels of MDR1 mRNA. The surfactant inhibitors, however, had no effect on the induction of MDR1 gene expression by protein kinase C agonists. Using a set of FA‐PEG‐FA diesters with various fatty acids and different lengths of the PEG domain, we demonstrated that the activity of diester preparations as inhibitors of drug‐induced MDR1 activation was in proportion to their activity as inhibitors of Pgp function. Oleic and stearic acid diesters with PEG 900 (20 ethylene oxide units) were the most potent. The poloxamer analogs of these diesters demonstrated similar effects. In contrast, the well‐known, structurally unrelated inhibitors of Pgp activity, verapamil, cyclosporin A and PSC 833, had no inhibitory effect on drug‐induced MDR1 activation. The ability of FA‐PEG‐FA diesters to inhibit both Pgp function and drug‐induced MDR1 activation suggests that these chemomodulators may be uniquely useful for the prophylaxis of Pgp‐mediated multidrug resistance in drug‐treated tumors.

PTEN and PIK3CA gene copy numbers and poor outcomes in non-small cell lung cancer patients with gefitinib therapy

Background:Preclinical studies in non-small cell lung cancer (NSCLC) suggest the interaction of PTEN and PI3K affects sensitivity to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs). We investigated outcomes in relation to PTEN, PIK3CA and EGFR gene copy number, and chromosome 7 (CEN7) polysomy in NSCLC patients treated with gefitinib.Methods:Fluorescent in situ hybridisation analyses of PTEN, PIK3CA, EGFR and CEN7 were performed on tumour specimens from patients treated on the expanded access gefitinib trial. Progression-free survival (PFS) and overall survival (OS) were correlated with outcomes in all patients and EGFR wild-type patients.Results:Progression-free survival (hazard ratio=2.54, P<0.001) and OS (hazard ratio=4.04, P<0.001) were significantly shorter in patients whose tumours had all of the following molecular patterns: CEN7 <4 copies per cell, PTEN loss (<2 copies in at least 20% of cells), and PIK3CA gain (>2 copies in at least 40% of cells) both in all and EGFR wild-type only patients.Conclusion:The combination of low CEN7 copy number, PTEN loss, and PI3KCA gain may be useful for identifying NSCLC patients unlikely to benefit from treatment with EGFR (TKIs), specifically in wild-type EGFR cases.

Gene expression in chronic lymphocytic leukemia B cells and changes during induction of apoptosis

Our studies in chronic lymphocytic leukemia (CLL) are directed at understanding which signals maintain viability in vivo and become lost upon removal of leukemic cells from the body, such that they immediately begin to undergo apoptosis ex vivo. In this report, we examine changes in gene expression observed between freshly isolated CLL B cells and after maintenance in vitro with and without Fludara. We compare these effects with an Epstein-Barr virus (EBV)-transformed cell line treated similarly. Kinetic effects of drug treatment on apoptosis and cell division were examined with DNA laddering, radioisotopic labeling, and flow cytometry using the fluorescent dye carboxyfluorescein diacetate succinimidyl ester. Reverse transcriptase polymerase chain reaction and hybridization blots of microarray cDNA analyses were performed to examine gene expression. We demonstrate that many genes, especially cyclin D1, were downregulated after culture of CLL cells. Anti-apoptotic genes BAG-1 and Akt2 were upregulated. The greatest positive effect with Fludara was the upregulation of JNK1. The EBV-transformed cell line was resistant to classic DNA laddering induced with Fludara. Although DNA synthesis was blocked, the EBV-transformed cell line had some ability to recover from treatment following drug washout. CLL cells express cell cycle regulatory genes that are specific for activated cells in the G(1)-S phase of the cell cycle. Growth regulatory signals are lost when the leukemic cells are isolated from the body. Fludara enhances kinetics of apoptosis and induces expression of a gene responsive to stress that regulates expression of a kinase involved in initiation of the apoptotic pathway.

CDKN2A (p16) promoter hypermethylation influences the outcome in young lung cancer patients.

Purpose:Non–small cell lung cancer (NSCLC) occurs most frequently in individuals older than 60 years of age. Currently, no biological indicators associated with NSCLC in younger patients (30 to 60 y) have been identified. To explore epigenetic influences, promoter methylation of selected tumor suppressor genes was analyzed in early-stage NSCLC patients ranging in age from 30 to 87 years at diagnosis. Experimental Design:The analysis was performed on formalin-fixed tumor tissue from 193 surgically treated NSCLC patients (127, older than 60 y; 66, 60 y and younger). Methylation was quantified in p16, MGMT, DAPK, RASSF1, CDH1, LET7-3-a, NORE1(RASSF5), and PTEN promoters by pyrosequencing. p16 protein expression was assessed by immunohistochemistry (IHC). Outcome, defined by time to recurrence and overall survival, was evaluated by Kaplan-Meier analysis. Results:Promoter methylation levels were generally higher in patients older than 60 years of age than in patients 60 years or younger at diagnosis. Of the genes tested, methylation levels of the p16 promoter showed age-related differences. Although p16 promoter methylation was significantly lower using cut-points of 50 years or younger and 40 years or younger (P=0.001 to 0.012, respectively), p16 protein expression increased with age. Patients 60 years or younger with p16 promoter hypermethylation had a significantly shortened time to recurrence (P=0.002) and a shortened survival time (P=0.011). No effect of p16 hypermethylation was seen in patients older than 60 years. Conclusions:p16 promoter hypermethylation was associated with a worse outcome in patients with age at diagnosis of 60 years or younger, but was not associated with the outcome in the older than 60-year age group. Overall, these data support methylation-dependent and methylation-independent age-related regulation of p16 expression with differential effects on the outcome after surgical resection for early-stage NSCLC.

The Sin3p PAH domains provide separate functions repressing meiotic gene transcription in Saccharomyces cerevisiae.

ABSTRACT Meiotic genes in budding yeast are repressed during vegetative growth but are transiently induced during specific stages of meiosis. Sin3p represses the early meiotic gene (EMG) by bridging the DNA binding protein Ume6p to the histone deacetylase Rpd3p. Sin3p contains four paired amphipathic helix (PAH) domains, one of which (PAH3) is required for repressing several genes expressed during mitotic cell division. This report examines the roles of the PAH domains in mediating EMG repression during mitotic cell division and following meiotic induction. PAH2 and PAH3 are required for mitotic EMG repression, while electrophoretic mobility shift assays indicate that only PAH2 is required for stable Ume6p-promoter interaction. Unlike mitotic repression, reestablishing EMG repression following transient meiotic induction requires PAH3 and PAH4. In addition, the role of Sin3p in reestablishing repression is expanded to include additional loci that it does not control during vegetative growth. These findings indicate that mitotic and postinduction EMG repressions are mediated by two separate systems that utilize different Sin3p domains.