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Background: An exhaled microRNA-based lung cancer case-control discriminant biomarker strategy is reported.Methods: A microRNA-seq discovery effort compared paired tumor to non-tumor tissue, was reconciled with analogous TCGA and published literature-based tissue-discriminant microRNA data, yielding a candidate panel of 24 microRNAs that are upregulated in either adenocarcinomas and/or squamous cell carcinomas. The technical feasibility of microRNA-PCR assays in exhaled breath condensate (EBC) was tested. The airway origin of exhaled microRNAs was then topographically “fingerprinted”, using paired EBC and bronchoscopic samples. For initial EBC testing, a clinic-based case-control set of 351 individuals (166 NSCLC cases, 185 non-cancer controls) was interrogated with the 24-candidate microRNA panel by qualitative RT-PCR, and curated by melt curve analysis. Data were analyzed by both logistic regression (LR), and by random-forest (RF) models, validated by iterative resampling.Results: Both feasibility of exhaled microRNA detection, and its origins in part from lower airway sources, were confirmed. LR models adjusted for age, sex, smoking status, pack years, quit-years, and underlying lung disease identified exhaled miR-21, 33b, 212 (p.adj,=0.019, 0.018, 0.033, resp.) as case-control discriminant. For the RF analysis, the combined clinical + microRNA models showed modest added discrimination capacity (1.1–2.5%) beyond the clinical models alone: by subgroup, all subjects 1.1% (p = 8.7e-04)); former smokers 2.5% (p = 3.6e-05); early stage 1.2% (p = 9.0e-03). Sensitivity, specificity, positive- and negative-predictive values of the clinical + microRNA models for the entire cohort were 71%-76%.Conclusion: This work suggests that exhaled microRNAs are measurable qualitatively; reflect in part lower airway signatures; and if improved/refined, can potentially help distinguish lung cancer cases from controls.

Background Aerosolized Azacitidine has been shown to inhibit orthotopic lung cancer growth and induce re-expression of methylated tumor suppressor genes in murine models. We hypothesized that inhaled Azacitidine is safe and effective in reversing epigenetic changes in the bronchial epithelium secondary to chronic smoking. Patients and Methods We report the first in human study of inhaled Azacitidine. Azacitidine in aqueous solution was used to generate an aerosol suspension of 0.25–5 μm particle size. Main inclusion criteria: Stage IV or recurrent NSCLC with predominantly lung involvement, ≥1 prior systemic therapy, ECOG PS 0–1, and adequate pulmonary function. Patients received inhaled Azacitidine daily on days 1–5 and 15–19 of 28-day cycles, at 3 escalating doses (15, 30 and 45 mg/m2 daily). The primary objective was to determine the feasibility and tolerability of this new therapeutic modality. The key secondary objectives included pharmacokinetics, methylation profiles and efficacy. Results From 3/2015 to 2/2018, eight patients received a median number of 2 (IQR = 1) cycles of inhaled Azacitidine. No clinically significant adverse events were observed, except one patient treated at the highest dose developed an asymptomatic grade 2 decreased DLCO which resolved spontaneously. One patient receiving 12 cycles of therapy had an objective and durable partial response, and two patients had stable disease. Plasma Azacitidine was only briefly detectable in patients treated at the higher doses. Moreover, in 2 of 3 participants who agreed and underwent pre- and post-treatment bronchoscopy, the global DNA methylation in the bronchial epithelium decreased by 24 % and 79 % post-therapy, respectively. The interval between last inhaled treatment and bronchoscopy was 3 days. Conclusions Inhaled Azacitidine resulted in negligible plasma levels compared to the previously reported subcutaneous administration and was well-tolerated. The results justify the continued development of inhaled Azacitidine at non-cytotoxic doses for patients with lung-confined malignant and/or premalignant lesions.

Background Sarcoidosis is believed to represent a genetically primed, abnormal immune response to an antigen exposure or inflammatory trigger, with both genetic and environmental factors playing a role in disease onset and phenotypic expression. In a population of firefighters with post-World Trade Center (WTC) 9/11/2001 (9/11) sarcoidosis, we have a unique opportunity to describe the clinical course of incident sarcoidosis during the 15 years postexposure and, on average, 8 years following diagnosis. Methods Among the WTC-exposed cohort, 74 firefighters with post-9/11 sarcoidosis were identified through medical records review. A total of 59 were enrolled in follow-up studies. For each participant, the World Association of Sarcoidosis and Other Granulomatous Diseases organ assessment tool was used to categorize the sarcoidosis involvement of each organ system at time of diagnosis and at follow-up. Results The incidence of sarcoidosis post-9/11 was 25 per 100,000. Radiographic resolution of intrathoracic involvement occurred in 24 (45%) subjects. Lung function for nearly all subjects was within normal limits. Extrathoracic involvement increased, most prominently joints (15%) and cardiac (16%) involvement. There was no evidence of calcium dysmetabolism. Few subjects had ocular (5%) or skin (2%) involvement, and none had beryllium sensitization. Most (76%) subjects did not receive any treatment. Conclusions Extrathoracic disease was more prevalent in WTC-related sarcoidosis than reported for patients with sarcoidosis without WTC exposure or for other exposure-related granulomatous diseases (beryllium disease and hypersensitivity pneumonitis). Cardiac involvement would have been missed if evaluation stopped after ECG, 48-h recordings, and echocardiogram. Our results also support the need for advanced cardiac screening in asymptomatic patients with strenuous, stressful, public safety occupations, given the potential fatality of a missed diagnosis.

BACKGROUND: Nasal polyps influence the burden of aspirin exacerbated respiratory disease (AERD) by contributing to eicosanoid production. AERD is diagnosed through graded aspirin challenges. It is not known how sinus surgery affects aspirin challenge outcomes. OBJECTIVE: To investigate the effects of endoscopic sinus surgery (ESS) on aspirin-induced reaction severity and on the levels of eicosanoids associated with these reactions. METHODS: Twenty-eight AERD patients were challenged with aspirin before and 3-4 weeks after ESS. Respiratory parameters and plasma and urine levels of eicosanoids were compared before and after challenges. RESULTS: Before ESS, AERD diagnosis was confirmed in all study patients by aspirin challenges that resulted in hypersensitivity reactions. After ESS, reactions to aspirin were less severe in all patients and twelve out of twenty-eight patients (43%, p

Gene regulatory analysis of highly diverse human tissues in vivo is essentially constrained by the challenge of performing genome-wide, integrated epigenetic and transcriptomic analysis in small selected groups of specific cell types. Here we performed genome-wide bisulfite sequencing and RNA-seq from the same small groups of bronchial and alveolar cells isolated by laser capture microdissection from flash-frozen lung tissue of 12 donors and their peripheral blood T cells. Methylation and transcriptome patterns differed between alveolar and bronchial cells, while each of these epithelia showed more differences from mesodermally-derived T cells. Differentially methylated regions (DMRs) between alveolar and bronchial cells tended to locate at regulatory regions affecting promoters of 4,350 genes. A large number of pathways enriched for these DMRs including GTPase signal transduction, cell death, and skeletal muscle. Similar patterns of transcriptome differences were observed: 4,108 differentially expressed genes (DEGs) enriched in GTPase signal transduction, inflammation, cilium assembly, and others. Prioritizing using DMR-DEG regulatory network, we highlighted genes, e.g., ETS1, PPARG, and RXRG, at prominent alveolar vs. bronchial cell discriminant nodes. Our results show that multi-omic analysis of small, highly specific cells is feasible and yields unique physiologic loci distinguishing human lung cell types in situ.

Asthma prevalence is reportedly higher among U.S.-born relative to foreign-born Hispanics/Latinos. Little is known about rates of asthma onset before and after relocation to the U.S. in Latinos. Asthma rates were examined by U.S. residence and country/territory of origin.In 2015-2016, age at first onset of asthma symptoms was analyzed, defined retrospectively from a cross-sectional survey in 2008-2011, in relation to birthplace and U.S. residence among 15,573 U.S.-dwelling participants (aged 18-76 years) in the Hispanic Community Health Study/Study of Latinos.Cumulative incidence of asthma through age 30 years ranged from 7.9% among Mexican background individuals to 29.4% among those of Puerto Rican background. Among those born outside the U.S. mainland, the adjusted hazard for asthma was 1.52-fold higher (95% CI=1.25, 1.85) after relocation versus before relocation to the U.S. mainland, with heterogeneity in this association by Hispanic/Latino background (p-interaction0.0001). Among foreign-born Dominicans and Mexicans, rates of asthma were greater after relocation versus before relocation (adjusted hazard ratio [AHR] for after versus before relocation, 2.42, 95% CI=1.44, 4.05 among Dominicans; AHR=2.90, 95% CI=2.02, 4.16 among Mexicans). Puerto Ricans had modestly increased asthma onset associated with U.S. mainland residence (AHR=1.52, 95% CI=1.06, 2.17). No similar increase associated with U.S. residence was observed among Central/South American immigrants (AHR=0.94, 95% CI=0.53, 1.67). Asthma rates among Cuban immigrants were lower after relocation (AHR=0.45, 95% CI=0.24, 0.82).The effect of relocation to the U.S. on asthma risk among Hispanics is not uniform across Hispanic/Latino groups.

The identification of specific microRNAs (miRNAs) that target a given messenger RNA (mRNA) is essential for studies in gene regulation, but the available bioinformatic software programs are often unreliable. We have developed a unique experimental miRNA affinity assay whereby a 3'UTR RNA is end-labeled with biotin, immobilized, and then used as a bait sequence for affinity pull-down of miRNAs. After washes and release, cloning and sequencing identify the miRNAs. Binding affinity is quantitated by quantitative polymerase chain reaction (qPCR), comparing released and original input concentrations. As an initial demonstration, the TCF8/ZEB1 mRNA affinity pull-down yielded miR-200 family member miRs in the majority of clones, and binding affinity was approximately 100%; virtually all copies of miR-200c bound the immobilized mRNA transcript. For validation in cells, miR-200c strongly inhibited expression of a TCF8 luciferase reporter, native TCF8 mRNA, and protein levels, which contrasted with other recovered miRNAs with lower binding affinities. For Smad4 mRNA, miR-150 (and others) displayed a binding affinity of 39% (or less) yet did not inhibit a Smad4 reporter, native Smad4 mRNA, or protein levels. These results were not predicted by available software. This work demonstrates this miRNA binding affinity assay to be a novel yet facile experimental means of identification of miRNAs targeting a given mRNA.

Methods to experimentally alter and functionally evaluate cytosine methylation in a site-specific manner have proven elusive. We describe a site-specific DNA methylation method, using synthetically methylated primers and high fidelity PCR coupled with ligation of reporter constructs. We applied this method to introduce methylated cytosines into fragments of the respective DAPK and RASSF1A promoters that had been cloned into luciferase reporters. We found that methylation of 3-7 residue CpG clusters that were 5' adjacent to the transcription start site (TSS) of the DAPK gene produced up to a 54% decrease in promoter activity (p0.01). Similarly, for RASSF1A promoter reporter constructs, the methylation of either of two clusters of four CpGs each, but not an intervening cluster, produced a 63% decrease in promoter activity (p0.01), suggesting that precise mCpG position is crucial, and factors other than simple proximity to the TSS are at play. Chromatin immunoprecipitation analysis of these reporter constructs demonstrated that transcription factor Oct-1 and Sp1 preferentially bound the unmethylated vs. methylated DAPK or RASSF1A promoter reporter constructs at the functional CpG sites. Histone H1, hnRNP1, and MeCP2 showed preferential binding to methylated sequence at functional sites in these reporter constructs, as well as highly preferential (8-80-fold) binding to native methylated vs. unmethylated chromatin. These results suggest that: (1) site-specific, precision DNA methylation of a reporter construct can be used for functional analysis of commonly observed gene promoter methylation patterns; (2) the reporter system contains key elements of the endogenous chromatin machinery.

Aspirin-exacerbated respiratory disease (AERD) is diagnosed through graded aspirin challenges that induce hypersensitivity reactions and eicosanoid level changes. It is not known whether diagnostically useful changes also occur after low-dose aspirin challenges that do not induce hypersensitivity reactions.To investigate the utility of low-dose oral aspirin challenges for diagnosing AERD by measuring different clinical parameters and eicosanoid changes.Sixteen patients with AERD and 13 patients with aspirin-tolerant asthma underwent oral challenges with low-dose (20 or 40 mg) aspirin and diagnostic oral graded aspirin challenges (up to 325 mg of aspirin). Forced expiratory volume in 1 second, nasal peak flow, the fraction of exhaled nitric oxide (FeNO), and eicosanoid levels in plasma and urine were analyzed.In patients with AERD but not in those with aspirin-tolerant asthma, 40-mg aspirin challenges induced a significant mean (SEM) decrease from baseline in FeNO (19% [5.1%]; P = .001) without causing any hypersensitivity reaction. The FeNO decrease also occurred after higher-dose aspirin challenges (27.8% [4.9%]; P.001). The sensitivity and specificity of 40-mg aspirin-induced FeNO changes for identifying AERD were 90% and 100% with an area under the curve of 0.98 (95% CI, 0.92-1.00). The low-dose challenge also induced a significant leukotriene E4 urine increase in patients with AERD (from 6.32 [0.08] to 6.91 [0.15] log-pg/mg creatinine; P.001), but the sensitivity and specificity of these changes were less than for the FeNO changes.The low-dose aspirin-induced decrease in FeNO in patients with AERD may be useful for the diagnosis of aspirin allergy without inducing a hypersensitivity reaction.clinicaltrials.gov Identifier: NCT01320072.

Many phytochemicals possess antioxidant and cancer-preventive properties, some putatively through antioxidant response element-mediated phase II metabolism, entailing mutagen/oxidant quenching. In our recent studies, however, most candidate phytochemical agents were not potent in inducing phase II genes in normal human lung cells. In this study, we applied a messenger RNA (mRNA)-specific gene expression-based high throughput in vitro screening approach to discover new, potent plant-derived phase II inducing chemopreventive agents. Primary normal human bronchial epithelial (NHBE) cells and immortalized human bronchial epithelial cells (HBECs) were exposed to 800 individual compounds in the MicroSource Natural Products Library. At a level achievable in humans by diet (1.0 μM), 2,3-dihydroxy-4-methoxy-4'-ethoxybenzophenone (DMEBP), triacetylresveratrol (TRES), ivermectin, sanguinarine sulfate, and daunorubicin induced reduced nicotinamide adenine dinucleotide phosphate:quinone oxidoreductase 1 (NQO1) mRNA and protein expression in NHBE cells. DMEBP and TRES were the most attractive agents as coupling potency and low toxicity for induction of NQO1 (mRNA level, ≥3- to 10.8-fold that of control; protein level, ≥ two- to fourfold that of control). Induction of glutathione S-transferase pi mRNA expression was modest, and none was apparent for glutathione S-transferase pi protein expression. Measurements of reactive oxygen species and glutathione/oxidized glutathione ratio showed an antioxidant effect for DMEBP, but no definite effect was found for TRES in NHBE cells. Exposure of NHBE cells to H(2)O(2) induced nuclear translocation of nuclear factor erythroid 2-related factor 2, but this translocation was not significantly inhibited by TRES and DMEBP. These studies show that potency and low toxicity may align for two potential NQO1-inducing agents, DMEBP and TRES.

The number of predicted human microRNAs in Sanger miRBase currently stands at over a thousand, with each of these in turn predicted to target numerous mRNAs. However, those microRNAs for which mRNA targets have been evaluated, verified and reported in the literature are still in the minority and the bulk of microRNA/mRNA interactions are yet to be confirmed. Confirmation of microRNA interaction with predicted mRNA targets represents a considerable undertaking, made more complex by potential synergistic effects of multiple microRNAs and the three possible outcomes (translational repression, degradation or a mixture of both). In addition, contrasting results obtained when either stably expressing or transiently transfecting members of the miR-200 family illustrate limitations in the verification methods currently in use. In this article we suggest that instead of allowing computational predictions to drive investigation, it would be desirable, when possible, to systematically evaluate microRNA targets using inducible, stable, ectopic expression. The advantage of stable lines ectopically expressing microRNA(s) is that they allow an analysis of changes to both the proteome and the transcriptome. This would allow verification of targets, improve the design of prediction algorithms and greatly increase our understanding of the outcome of microRNA/mRNA interaction.

Many phytochemicals possess cancer-preventive properties, some putatively through phase II metabolism-mediated mutagen/oxidant quenching. We applied human lung cells in vitro to investigate the effects of several candidate phytopreventive agents, including green tea extracts (GTE), broccoli sprout extracts (BSE), epigallocatechin gallate (EGCG), sulforaphane (SFN), phenethyl isothiocyanate (PEITC), and benzyl isothiocyanate (BITC), on inducing phase II enzymes glutathione S-transferase P1 (GSTP1) and NAD(P)H:quinone oxidoreductase 1 (NQO1) at mRNA and protein levels. Primary normal human bronchial epithelial cells (NHBE), immortalized human bronchial epithelial cells (HBEC), and lung adenocarcinoma cells (A549) were exposed to diet-achievable levels of GTE and BSE (0.5, 1.0, 2.0 mg/L), or individual index components EGCG, SFN, PEITC, BITC (0.5, 1.0, 2.0 μmol/L) for 24 h, 48 h, and 6 d, respectively. mRNA assays employed RNA-specific quantitative RT-PCR and protein assays employed Western blotting. We found that in NHBE cells, while GSTP1 mRNA levels were slightly but significantly increased after exposure to GTE or BSE, NQO1 mRNA increased to 2- to 4-fold that of control when exposed to GTE, BSE, or SFN. Effects on NQO1 mRNA expression in HBEC cells were similar. NQO1 protein expression increased up to 11.8-fold in SFN-treated NHBE cells. Both GSTP1 and NQO1 protein expression in A549 cells were constitutively high but not induced under any condition. Our results suggest that NQO1 is more responsive to the studied chemopreventive agents than GSTP1 in human lung cells and there is discordance between single agent and complex mixture effects. We conclude that modulation of lung cell phase II metabolism by chemopreventive agents requires cell- and agent-specific discovery and testing.

DNA adducts of carcinogens derived from tobacco smoke and cooked meat were identified by liquid chromatography-electrospray ionization/multistage tandem mass spectrometry (LC-ESI/MS/MS(n)) in saliva samples from 37 human volunteers on unrestricted diets. The N-(deoxyguanosin-8-yl) (dG-C8) adducts of the heterocyclic aromatic amines 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), 2-amino-9H-pyrido[2,3-b]indole (AalphaC), 2-amino-3,8-dimethylmidazo[4,5-f]quinoxaline (MeIQx), and the aromatic amine, 4-aminobiphenyl (4-ABP), were characterized and quantified by LC-ESI/MS/MS(n), employing consecutive reaction monitoring at the MS(3) scan stage mode with a linear quadrupole ion trap (LIT) mass spectrometer (MS). DNA adducts of PhIP were found most frequently: dG-C8-PhIP was detected in saliva samples from 13 of 29 ever-smokers and in saliva samples from 2 of 8 never-smokers. dG-C8-AalphaC and dG-C8-MeIQx were identified solely in saliva samples of three current smokers, and dG-C8-4-ABP was detected in saliva from two current smokers. The levels of these different adducts ranged from 1 to 9 adducts per 10(8) DNA bases. These findings demonstrate that PhIP is a significant DNA-damaging agent in humans. Saliva appears to be a promising biological fluid in which to assay DNA adducts of tobacco and dietary carcinogens by selective LIT MS techniques.

Purpose: The origins of expression microarray and reverse transcription-PCR (RT-PCR) signals in human saliva were evaluated. Experimental Design: The “RNA” extracts from human saliva samples were treated with vehicle, DNase, or RNase. Two-step amplification and hybridization to Affymetrix 133A cDNA microarrays were then done. Confirmatory RT-PCR experiments used conventionally designed PCR primer pairs for the reference housekeeper transcripts encoding 36B4, β-actin, and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA sequences, which are known to be homologous to genomic DNA pseudogene sequences. Negative controls included the omission of reverse transcriptase (“no-RT”) to detect any DNA-derived signal. Finally, an RNA-specific RT-PCR strategy eliminated confounding signals from contaminating genomic DNA. Results: Microarray experiments revealed that untreated, DNase-treated, and RNase-treated “RNA” extracts from saliva all yielded negligible overall signals. Specific microarray signals for 36B4, β-actin, and GAPDH were low, and were unaffected by RNase. Real-time quantitative RT-PCR reactions using conventional, non–RNA-specific primers on saliva samples yielded PCR products for 36B4, β-actin, and GAPDH; DNase-treated saliva samples did not yield a PCR product, and the “no-RT” and “+RT” conditions yielded similar amounts of PCR product. The RNA-specific RT-PCR strategy, across all conditions, yielded no PCR product from saliva. Conclusions: The combination of (a) a minimal microarray signal, which was unaffected by RNase treatment, (b) the presence of a conventional RT-PCR housekeeper product in both RNase-treated and no-RT saliva samples, (c) the absence of a conventional RT-PCR housekeeper product in DNase-treated conditions, and (d) the absence of a RNA-specific RT-PCR product shows that any microarray or RT-PCR signal in the saliva must arise from genomic DNA, not RNA. Thus, saliva extracts do not support mRNA expression studies.

Exfoliated cytologic specimens from mouth (buccal) epithelium may contain viable cells, permitting assay of gene expression for direct and noninvasive measurement of gene-environment interactions, such as for inhalation (e.g., tobacco smoke) exposures. We determined specific mRNA levels in exfoliated buccal cells collected by cytologic brush, using a recently developed RNA-specific real-time quantitative reverse transcription-PCR strategy. In a pilot study, metabolic activity of exfoliated buccal cells was verified by 3-[4,5-dimethylthiazol-2-yl]-2,5- diphenyltetrazolium assay in vitro. Transcriptional activity was observed, after timed in vivo exposure to mainstream tobacco smoke resulted in induction of CYP1B1 in serially collected buccal samples from the one subject examined. For a set of 11 subjects, mRNA expression of nine genes encoding carcinogen- and oxidant-metabolizing enzymes qualitatively detected in buccal cells was then shown to correlate with that in laser-microdissected lung from the same individuals (χ2 = 52.91, P < 0.001). Finally, quantitative real-time reverse transcription-PCR assays for seven target gene (AhR, CYP1A1, CYP1B1, GSTM1, GSTM3, GSTP1, and GSTT1) and three reference gene [glyceraldehyde-3-phosphate dehydrogenase (GAPDH), β-actin, and 36B4] transcripts were performed on buccal specimens from 42 subjects. In multivariate analyses, gender, tobacco smoke exposure, and other factors were associated with the level of expression of CYP1B1, GSTP1, and other transcripts on a gene-specific basis, but substantial interindividual variability in mRNA expression remained unexplained. Within the power limits of this pilot study, gene expression signature was not clearly predictive of lung cancer case or control status. This noninvasive and quantitative method may be incorporated into high-throughput human applications for probing gene-environment interactions associated with cancer.

Background Aspirin desensitization followed by daily aspirin provides therapeutic benefits to patients with aspirin-exacerbated respiratory disease (AERD). It is not well understood how eicosanoid levels change during aspirin treatment. Objective To investigate associations between clinical outcomes of aspirin treatment and plasma eicosanoid levels in patients with AERD. Methods Thirty-nine patients with AERD were offered aspirin treatment (650 mg twice daily) for 4 weeks. Respiratory parameters and plasma levels of multiple eicosanoids were recorded at baseline and after 4 weeks of aspirin therapy using the Asthma Control Test and Rhinoconjunctivitis Quality of Life Questionnaire. Respiratory function was evaluated using the FEV 1 and nasal inspiratory peak flow. Results After aspirin treatment, respiratory symptoms improved in 16 patients, worsened in 12 patients, and did not change in 4 patients. Seven patients were unable to complete the desensitization protocol. Patients with symptom improvement had higher baseline plasma 15-hydroxyeicosatetraenoic acid (15-HETE) levels than did patients with symptom worsening: 7006 pg/mL (interquartile range, 6056-8688 pg/mL) versus 4800 pg/mL (interquartile range, 4238-5575 pg/mL), P = .0005. Baseline 15-HETE plasma levels positively correlated with the change in Asthma Control Test score ( r = 0.61; P = .001) and in FEV 1 after 4 weeks of aspirin treatment ( r = 0.49; P = .01). It inversely correlated with Rhinoconjunctivitis Quality of Life Questionnaire score ( r = −0.58; P = .002). Black and Latino patients were more likely to have symptom worsening on aspirin or fail to complete the initial desensitization than white, non-Latino patients ( P = .02). Conclusions In patients with AERD, low baseline 15-HETE plasma levels and black or Latino ethnicity are associated with worsening of respiratory symptoms during aspirin treatment.

Background: There is a need for non-invasive airway-based biomarkers in lung carcinogenesis for both risk assessment of the ex-smoker, and earlier diagnosis. Recent studies have revealed that microRNAs play important regulatory roles in carcinogenesis. Exhaled breath condensate (EBC) contains airway lining fluid molecules, including nucleic acids, presumably in part from epithelial cellular origins. Here we further develop and begin validation of the detection of microRNAs in EBC from lung cancer patients and controls. Methods: Exhaled breath condensate (EBC) was collected non-invasively, using a handheld device in ambulatory subjects. MicroRNA expression profiling using RNA-specific RT-qPCR was performed in EBC in an initial batch (E) of 88 individuals (41 lung cancer cases, 47 controls), and a second batch D of 88 individuals (41, cases and 47 controls). We generated a 39 miR panel based on literature-derived microRNAs, combined with a lung tissue-based discovery effort we have performed using microRNA-seq on lung tumors and surrounding non-tumor tissue. The qPCR primers were designed using our previously published RNA-specific realtime RT-PCR technique. All samples were run twice with positive and negative controls. Results: Qualitative analyses of the first donor batch E was performed on 39 microRNAs measured in 41 cases and 47 controls. Chi-square analysis (univariate) within the training set (batch E) revealed that exhaled miR-31, 33, 105, 200b, 944, 1269a were significantly different between the initial set of cases and controls; their absence marked the cases. In the validation batch (D) preliminary analysis, exhaled miRs 200b (this time present in cases, p=0.044) and 944 (again absent in cases, p=0.052) were case-control discriminant. In addition, test set batch D showed case-control discrimination for additional miRs 130b-3p (present in cases, p=0.035), 212 (absent in cases, p=0.009), 1910a (absent in cases, p=0.006) and other microRNAs that were not seen in the qualitative training set (batch E). Importantly, multi-miR discriminant signatures, quantitative analysis, and risk ROC/modelling analyses are pending as of this AACR abstract deadline. Conclusion: This new exhaled biomarker platform can yield case-control discriminant microRNA sets, including a subset of miRs that can validate in test sets. Once further distilled and validated, our goal is to apply this non-invasive biomarker approach to prospective cohorts for non-invasive lung cancer risk assessment, in order to better select higher risk individuals who should undergo CT screening. Note: This abstract was not presented at the meeting. Citation Format: Simon D. Spivack. An exhaled microRNA panel interrogation and validation as risk biomarkers for lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4429. doi:10.1158/1538-7445.AM2017-4429

Background: Developing technologies for precise manipulation of individual DNA methylation loci is an attractive challenge in cancer and lung biology, because aberrant expression via hyper- or hypo-methylation is so common. Projects such as ENCODE and the Roadmap Epigenetics Project, have identified thousands of epigenetic marks from human genome. However, the functional evaluation of these marks has been largely limited to determining their associations with gene expression. Technologies for targeting manipulation of epigenetic marks would allow direct experimental testing of the impact of DNA methylation at specific residues, mechanisms of gene regulation, and potential use as interventions, for example to silence constitutively active oncogenes. Methods: Here, we developed a CRISPR Cas9-based tool for specific DNA methylation in which the catalytic domain of DNMT3a (DNMT3a-CD) is fused to the carboxy-terminus of Cas9 D10A-H840A mutant (dCas9). Both construct promoter strength and transfection strategies were optimized. Results: We demonstrated targeted and consistent CpG methylation in 30~100bp regions downstream of the PAM (binding) site of the gRNA guided fusion protein in HEK293 cells. The multiple guide RNAs could target the dCas9-DNMT3A to multiple sites consistently. DNA methylation activity was specific for the targeted region and was heritable across cell divisions. We also found directed promoter DNA methylation of DAL1, GATA5 and C-MYC could decrease the corresponding mRNA expression by up to 80%; different DNA methylation positions had consequently different effects on gene expression. We have now performed C-MYC methylation-mediated knockdown in A549 lung cancer cells and are evaluating resulting cell cycle and apoptosis phenotypes. Conclusion: We believe this new targeted epigenetic technology can be directed to cancer cells for the purpose of reprogramming lung cancer, and unregulated stromal and microenvironment cells, for preventive and therapeutic uses. Note: This abstract was not presented at the meeting. Citation Format: Simon D. Spivack. Inactivation of endogenous genes in cancer cells using targeted promoter DNA methylation via CRISPR-DNMT3a fusion protein [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5380. doi:10.1158/1538-7445.AM2017-5380

We evaluated the importance of tumor cell selection for generating gene signatures in non–small cell lung cancer. Tumor and nontumor tissue from macroscopically dissected (Macro) surgical specimens (31 pairs from 32 subjects) was homogenized, extracted, amplified, and hybridized to microarrays. Adjacent scout sections were histologically mapped; sets of approximately 1000 tumor cells and nontumor cells (alveolar or bronchial) were procured by laser capture microdissection (LCM). Within histological strata, LCM and Macro specimens exhibited approximately 67% to 80% nonoverlap in differentially expressed (DE) genes. In a representative subset, LCM uniquely identified 300 DE genes in tumor versus nontumor specimens, largely attributable to cell selection; 382 DE genes were common to Macro, Macro with preamplification, and LCM platforms. RT-qPCR validation in a 33-gene subset was confirmatory (ρ = 0.789 to 0.964, P = 0.0013 to 0.0028). Pathway analysis of LCM data suggested alterations in known cancer pathways (cell growth, death, movement, cycle, and signaling components), among others (eg, immune, inflammatory). A unique nine-gene LCM signature had higher tumor–nontumor discriminatory accuracy (100%) than the corresponding Macro signature (87%). Comparison with Cancer Genome Atlas data sets (based on homogenized Macro tissue) revealed both substantial overlap and important differences from LCM specimen results. Thus, cell selection via LCM enhances expression profiling precision, and confirms both known and under-appreciated lung cancer genes and pathways.

Ever since a lung cancer epidemic emerged in the mid-1900 s, the epidemiology of lung cancer has been intensively investigated to characterize its causes and patterns of occurrence. This report summarizes the key findings of this research.A detailed literature search provided the basis for a narrative review, identifying and summarizing key reports on population patterns and factors that affect lung cancer risk.Established environmental risk factors for lung cancer include smoking cigarettes and other tobacco products and exposure to secondhand tobacco smoke, occupational lung carcinogens, radiation, and indoor and outdoor air pollution. Cigarette smoking is the predominant cause of lung cancer and the leading worldwide cause of cancer death. Smoking prevalence in developing nations has increased, starting new lung cancer epidemics in these nations. A positive family history and acquired lung disease are examples of host factors that are clinically useful risk indicators. Risk prediction models based on lung cancer risk factors have been developed, but further refinement is needed to provide clinically useful risk stratification. Promising biomarkers of lung cancer risk and early detection have been identified, but none are ready for broad clinical application.Almost all lung cancer deaths are caused by cigarette smoking, underscoring the need for ongoing efforts at tobacco control throughout the world. Further research is needed into the reasons underlying lung cancer disparities, the causes of lung cancer in never smokers, the potential role of HIV in lung carcinogenesis, and the development of biomarkers.

The aryl hydrocarbon receptor (AhR), a ligand-activated transcription factor, contributes to carcinogenesis through its role in the regulation of cytochrome P450 1 (CYP1)-catalyzed metabolism of carcinogens. Here, we investigated genetic and epigenetic mechanisms that affect AhR expression. Analyses of the human AHR proximal promoter in MCF-7 human breast cancer cells using luciferase assays and electrophoretic mobility shift assays revealed multiple specificity protein (Sp) 1 binding sequences that are transcriptional activators in vitro. The regulation of AhR expression was evaluated in long-term estrogen exposed (LTEE) MCF-7 cells, which showed increased AhR expression, enhanced CYP1 inducibility, and increased capacity to form DNA adducts when exposed to the dietary carcinogen, 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine. The increased AhR expression in LTEE cells was found not to result from increased mRNA stability, differential RNA processing, or decreased DNA methylation. Analysis of the AHR proximal promoter region using chromatin immunoprecipitation confirmed that enhanced expression of AhR in LTEE cells involves changes in histone modifications, notably decreased trimethylation of histone 3, lysine 27. Upon further examination of the GC-rich Sp1-binding region, we confirmed that it contains a polymorphic (GGGGC)(n) repeat. In a population of newborns from New York State, the allele frequency of (GGGGC)(n) was n = 4 > 5 ≫ 6, 2. Circular dichroism spectroscopy revealed the ability of sequences of this GC-rich region to form guanine-quadruplex structures in vitro. These studies revealed multiple levels at which AhR expression may be controlled, and offer additional insights into mechanisms regulating AhR expression that can ultimately impact carcinogenesis.

Aberrant cytosine 5-methylation underlies many deregulated elements of cancer. Among paired non-small cell lung cancers (NSCLC), we sought to profile DNA 5-methyl-cytosine features which may underlie genome-wide deregulation. In one of the more dense interrogations of the methylome, we sampled 1.2 million CpG sites from twenty-four NSCLC tumor (T)–non-tumor (NT) pairs using a methylation-sensitive restriction enzyme- based HELP-microarray assay. We found 225,350 differentially methylated (DM) sites in adenocarcinomas versus adjacent non-tumor tissue that vary in frequency across genomic compartment, particularly notable in gene bodies (GB; p

Purpose: Interindividual differences in quantitative expression could underlie a propensity for lung cancer. To determine precise individual gene expression signatures on a lung compartment–specific basis, we investigated the expression of carcinogen metabolism genes encoding cytochromes P450 (CYP) 1B1, 2A13, GSTP1, and a tumor suppressor gene p16 in laser capture–microdissected samples of human alveolar compartment (AC) and bronchial epithelial compartment (BEC) lung tissue from 62 smokers and nonsmokers. Experimental Design: Tobacco exposure was determined by plasma nicotine, cotinine, and smoking history. Precise mRNA expression was determined using our RNA-specific qRT-PCR strategy, and correlated with detailed demographic and clinical characteristics. Results: Several correlations of mRNA expression included (a) CYP1B1 in AC (positively with plasma nicotine level, P = 0.008; plasma cotinine level, P = 0.001), (b) GSTP1 in AC (positively with plasma cotinine level, P = 0.003), and (c) GSTP1 in BEC (negatively with smoke dose, P = 0.043; occupational risk, P = 0.019). CYP2A13 was rarely expressed in AC and not expressed in BEC. p16 expression was not correlated with any measured factor. For each gene, subjects showed expression that was individually concordant between these compartments. No clear association of mRNA expression with lung cancer risk was observed in this pilot analysis. Conclusions: The association between lung mRNA expression and tobacco exposure implies that gene-tobacco interaction is a measurable quantitative trait, albeit with wide interindividual variation. Gene expression tends to be concordant for alveolar and bronchial compartments for these genes in an individual, controlling for proximate tobacco exposure. (Clin Cancer Res 2009;15(24):7562–70)

International audience; A two-dimensional linear quadrupole ion trap mass spectrometer (LIT/MS) was employed to simultaneously screen for DNA adducts of environmental, dietary, and endogenous genotoxicants, by data-dependent constant neutral loss scanning followed by triple-stage mass spectrometry (CNL-MS3). The loss of the deoxyribose (dR) from the protonated DNA adducts ([M + H - 116]+) in the MS/MS scan mode triggered the acquisition of MS3 product ion spectra of the aglycone adducts [BH2]+. Five DNA adducts of the tobacco carcinogen 4-aminobiphenyl (4-ABP) were detected in human hepatocytes treated with 4-ABP, and three DNA adducts of the cooked-meat carcinogen 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx) were identified in the livers of rats exposed to MeIQx, by the CNL-MS3 scan mode. Buccal cell DNA from tobacco smokers was screened for DNA adducts of various classes of carcinogens in tobacco smoke including 4-ABP, 2-amino-9H-pyrido[2,3-b]indole (AalphaC), and benzo[a]pyrene (BaP); the cooked-meat carcinogens MeIQx, AalphaC, and 2-amino-1-methyl-6-phenylmidazo[4,5-b]pyridine (PhIP); and the lipid peroxidation products acrolein (AC) and trans-4-hydroxynonenal (HNE). The CNL-MS3 scanning technique can be used to simultaneously screen for multiple DNA adducts derived from different classes of carcinogens, at levels of adduct modification approaching 1 adduct per 108 unmodified DNA bases, when 10 microg of DNA is employed for the assay.

Background : Glutathione S-transferase (GST) P1 is a major phase II xenobiotic-metabolizing enzyme in the human lung. Our laboratory had previously identified nine single nucleotide polymorphisms (SNPs) in the GSTP1 gene promoter, which were then grouped into three main haplotypes (Hap1, Hap2, and Hap3) based on statistical inference. Hap3 was found to display a high expression phenotype. The main objective of the current study was to test the association between GSTP1 promoter haplotypes with the risk of lung cancer after determining the promoter haplotypes experimentally through cloning and sequencing. Methods : We conducted a case–control analysis of 150 subjects with lung cancer and 329 controls with no personal history of the disease. The three statistically inferred GSTP1 promoter haplotypes were confirmed experimentally through cloning and sequencing. Haplotype-tagging SNPs were selected and GSTP1 haplotypes were tested for genetic association to lung cancer using unconditional logistic regression after adjusting for confounders. Statistical interaction between GSTP1 promoter haplotypes with either cigarette smoking or dietary fruit and vegetable intake were tested using the likelihood ratio test. Results : We did not find protective effects of Hap3 against lung cancer, despite an adequately powered design for this main effect. Homozygous variants of tagSNPs −1738 T>A and −354 G>T, which tag Hap2, showed an increased (but statistically non-significant) risk of lung cancer among all subjects as well as among individuals with low fruit and vegetable intake, compared to homozygous wildtypes for these SNPs. We did not find significant interactions between Hap2 and dietary intake of fruits and vegetables. Conclusions : Our results do not support significant main and modifying effects for GSTP1 promoter haplotypes on susceptibility to lung cancer in this population, but reinforce the protective effects of dietary intake of fruits and vegetables.

MicroRNAs are ∼22-nucleotide sequences thought to interact with multiple mRNAs resulting in either translational repression or degradation. We previously reported that several microRNAs had variable expression in mammalian cell lines, and we examined one, miR-200c, in more detail. A combination of bioinformatics and quantitative reverse transcription-PCR was used to identify potential targets and revealed that the zinc finger transcription factor transcription factor 8 (TCF8; also termed ZEB1, δEF1, Nil-2-α) had inversely proportional expression levels to miR-200c. Knockout experiments using anti-microRNA oligonucleotides increased TCF8 levels but with nonspecific effects. Therefore, to investigate target predictions, we overexpressed miR-200c in select cells lines. Ordinarily, the expression level of miR-200c in non–small-cell lung cancer A549 cells is low in contrast to normal human bronchial epithelial cells. Stable overexpression of miR-200c in A549 cells results in a loss of TCF8, an increase in expression of its regulatory target, E-cadherin, and altered cell morphology. In MCF7 (estrogen receptor–positive breast cancer) cells, there is endogenous expression of miR-200c and E-cadherin but TCF8 is absent. Conversely, MDA-MB-231 (estrogen receptor–negative) cells lack detectable miR-200c and E-cadherin (the latter reportedly due to promoter region methylation) but express TCF8. The ectopic expression of miR-200c in this cell line also reduced levels of TCF8, restored E-cadherin expression, and altered cell morphology. Because the down-regulation of E-cadherin is a crucial event in epithelial-to-mesenchymal transition, loss of miR-200c expression could play a significant role in the initiation of an invasive phenotype, and, equally, miR-200c overexpression holds potential for its reversal. [Cancer Res 2007;67(17):7972–6]

Phase II detoxification of carcinogens is reported to mediate some of the anticarcinogenesis effects of candidate chemopreventive agents. We explored the interaction between sequence variation in the GSTP1 gene promoter and candidate chemopreventive exposure in regulating human GSTP1 expression. Polymorphisms along 1.8 kb of the GSTP1 promoter were identified in leukocytes [peripheral blood mononuclear cells (PBMC)] from 40 Caucasian subjects. Ten promoter polymorphisms (9 previously unreported) displayed strong linkage disequilibrium, yielding identification of three frequently observed haplotypes [HAP1 (43%), HAP2 (36%), and HAP3 (8%)]. Each haplotype was cloned into luciferase reporter constructs and transfected into normal human bronchial epithelial cells. Basal HAP3 reporter activity was significantly elevated (1.8-fold) but decreased to the same levels as HAP2 and HAP1 with increasing concentrations of sulforaphane, benzyl isothiocyanate (BITC), and epigallocatechin gallate (EGCG). To confirm native HAP3 functionality, we quantitated mRNA expression in uncultured PBMCs and in laser microdissected normal lung epithelial cells (MNLEC) from the same patients. Basal mRNA expression was higher in HAP3 individuals [1.8-fold (PBMC) and 4-fold (MNLEC) for HAP3 heterozygotes and 2.3-fold (PBMC), and 15-fold (MNLEC) for the HAP3 homozygote] than in the other genotypes. PBMC GSTP1 mRNA expression correlated to MNLEC expression (R2 = 0.77). After culture and in vitro exposure to sulforaphane, BITC, or EGCG, the elevated GSTP1 mRNA expression of PBMCs from HAP3 individuals decreased to common expression levels. Elevated HAP3 function was confirmed at the protein level in PBMCs (5-fold higher for HAP3 heterozygotes and 7.6-fold for the HAP3 homozygote). These data suggest a potentially protective GSTP1 promoter haplotype and unpredicted inhibitory chemopreventive agent-haplotype interactions. (Cancer Res 2006; 66(12): 6439-48)

The regulation of carcinogen metabolism machinery may involve proximate tobacco smoke exposure, hormonal and other endogenous coregulatory factors, and an individual's underlying genetic responsiveness. The mRNA and protein expression patterns of known carcinogen metabolism genes encoding the aromatic hydrocarbon receptor Ahr; the cytochromes P450 CYP1A1 and CYP1B1; glutathione S-transferases GSTM1, GSTM3, GSTP1, and GSTT1; and NADPH quinone oxidoreductase NQO1 were examined.Paired tumor and nontumor lung tissue from 45 subjects was subject to a recently devised RNA-specific qualitative reverse transcription-PCR strategy, as well as Western immunoblotting. Tobacco exposure measured by plasma biomarkers nicotine and cotinine, plasma estradiol levels, alpha and beta estrogen receptor (ER) expression in the lung, gender, age, and histological diagnosis were then analyzed using multivariate regression models.In nontumor lung tissue, multivariate models identified several correlates of mRNA expression: (a) CYP1B1 in females (positively: smoke status, P=0.024; ER-beta expression, P=0.024); (b) GSTT1 in females (positively: cotinine, P=0.007; negatively: age, P=0.001; ER-beta expression, P=0.005) and in males (positively: plasma estradiol, P=0.015; ER-beta expression, P=0.025); and (c) NQO1 in females (positively: smoke status, P=0.002) and in males (positively: ER-beta expression, P=0.001). CYP1A1 (mRNA, 9.1%) and GSTM1 (mRNA, 17.5%) are uncommonly expressed in human lung. Confirmation by Western immunoassayed protein is described. The results in nontumor tissue differed from that in tumor tissue.Regulation of carcinogen metabolism genes expressed in human lung seems impacted by hormonal and gender factors, as well as ongoing tobacco exposure. Expression differences between tumor and nontumor tissue in this pathway have both susceptibility and therapeutic implications.

Background Ever since a lung cancer epidemic emerged in the mid-1900s, the epidemiology of lung cancer has been intensively investigated to characterize its causes and patterns of occurrence. This report summarizes the key findings of this research. Methods A detailed literature search provided the basis for a narrative review, identifying and summarizing key reports on population patterns and factors that affect lung cancer risk. Results Established environmental risk factors for lung cancer include smoking cigarettes and other tobacco products and exposure to secondhand tobacco smoke, occupational lung carcinogens, radiation, and indoor and outdoor air pollution. Cigarette smoking is the predominant cause of lung cancer and the leading worldwide cause of cancer death. Smoking prevalence in developing nations has increased, starting new lung cancer epidemics in these nations. A positive family history and acquired lung disease are examples of host factors that are clinically useful risk indicators. Risk prediction models based on lung cancer risk factors have been developed, but further refinement is needed to provide clinically useful risk stratification. Promising biomarkers of lung cancer risk and early detection have been identified, but none are ready for broad clinical application. Conclusions Almost all lung cancer deaths are caused by cigarette smoking, underscoring the need for ongoing efforts at tobacco control throughout the world. Further research is needed into the reasons underlying lung cancer disparities, the causes of lung cancer in never smokers, the potential role of HIV in lung carcinogenesis, and the development of biomarkers.

Background: Recent studies have revealed that microRNAs play important regulatory roles in carcinogenesis. Some key miRNAs may regulate lung carcinogenesis and be useful for lung cancer early detection. For discovery, we used high-throughput next-gen sequencing technology to investigate miRNA expression profiles in a study of 25 lung adeno- and squamous cell carcinomas, paired with far-adjacent noncancerous lung tissues from the same donors. Method: Total RNA was isolated by Trizol from 14 pairs of lung adenocarcinomas, 11 squamous cell cancers, and paired noncancerous lung tissues, from the same patients. Small RNA library of each total RNA was constructed with Illumina's Small RNA Sample Prep Kit, followed by high-throughput sequencing using the Illumina IIa platform. In parallel, transcriptome microarrays (Affymetrix GA 1.0) were run on these same paired samples. Statistical differences in microRNA expression between groups were analyzed by GenePattern software, logistic regression, and other methods. Results: For adeno, 128 micros were differentially expressed and 63 were two-fold differentially expressed between the tumors and non-tumor tissue; for squamous, the numbers of altered microRNAs were 42 overall, and 25 >two-fold. Among adenocarcinoma, the top 10 upregulated were miRs-147b, 577, 877, 556, 449c, and others; and downregulated were miRs 516b, 1251, 486, 139, 516a, and others. Among squamous cell carcinomas, the top up-regulated miRs were 708, 1259, 494, 200a, 216b, and others; and down-regulated miRs were 184, 1251, 144, 516a, 584, and others. MiRs 1259, 135b, 200a, 21, 494, 708 were upregulated in both tumor histologies. When the highest expressed microRNAs were correlated with the most altered mRNA transcripts, putative mRNA targets were more often anti-correlated to the individual microRNAs (Chi Square, p = 4.6 × 10-6), and this anticorrelation generally held true for the top differentially expressed microRNAs and their putative mRNA targets, and within histology strata. Conclusion: The lung cancer microRNA complement differs from non-tumor tissue, adeno- differs from squamous, and many of the most dysregulated miRs appear to be anticorrelated with putative mRNA targets. Which of the putative mRNA targets are actual biological targets awaits experimental functional work. Once constructed, the combined microRNA:mRNA signature of lung cancer is likely to be more informative for biologic potential than either signature alone. [Funding source: NCI 1RC1 CA145422-01; 1K24-CA139054-01]

Background: Hypermethylation in specific candidate gene promoters has been found during progressive lung carcinogenesis. To explore common methylation events on a genome-wide scale in lung cancer, we analyzed the methylation profiles of paired NSCLC tumor and far adjacent non-tumor samples using the HELP-microarray assay, which yields information on 1.2 million fragments throughout the genome. Methods: The HELP (HpaII tiny fragment Enriched by Ligation mediated PCR) assay is based on the generation of restriction enzyme libraries generated by methylation sensitive (HpaII) and methylation insensitive (MspI) isoschizomers, in its second generation as a microarray platform. The assay lends itself to low starting amounts of DNA (3 ug) and robust assessment of methylation status by comparing ratios of HpaII- generated-fragments to MspI- generated fragments co-hybridized to a Nimbelgen custom high-density microarrays. The CCGG sites were weighted if neighboring CCGGs were methylated in same direction. Here, 24 pairs of tumor and adjacent non-tumor samples were analyzed using the HELP assay. Summary of results: At p = 5E-6, we identified 26,138 differentially methylated fragments (corresponding to 2 CpG sites each) in tumor versus non-tumor. The overall trend was consistent with genome-wide hypomethylation and locus specific hypermethylation (localized to CG-island containing promoters). We could identify both known and novel regions of the genome as well as specific gene-promoters that are hypermethylated in tumor versus non-tumor. Region # loci # signif loci T Hypomethyl T Hypermethyl Promoter 151,568 576 69% 31% Gene Body 551,628 9,817 62% 38% Intergenic 540,473 15,745 97% 3% Conclusion: An interrogation of methylation status of 1.2 million loci throughout the genome in paired lung tumor/non-tumor specimens reveals many more differential methylation events in gene bodies and intergenic regions than in promoters. That said, many previously unreported differentially-methylated gene promoters were identified. We are able to discover individual methylation events common across different clinical specimens. Based on a set of priors, we have narrowed down promoter-specific hypermethylation events for further validation using tagged Bisulfite Genomic Sequencing. We are also working on the integration of methylome date with other genome-wide epigenetic and expression data from the same clinical samples. [Funding source: NCI 1RC1 CA145422-01; 1K24-CA139054-01]

Introduction: Gene silencing by promoter methylation is common in carcinogenesis. In lung cancer, hypermethylation of specific gene promoters has been found to occur during the earliest histologic stages of the cancer. Thus far surveys of methylation in lung tumors have focused on specific gene panels (5 – 10 genes). A few large scale studies have reported selection of longer gene lists or focused on larger sets of CpG islands. Methods: We have adapted an approach to survey genome-wide methylation events in tumor and adjacent non-tumor tissue from clinical lung resection samples using the HELP (HpaII tiny fragment Enrichment by Ligation mediated PCR) assay. This assay, based on the generation of restriction enzyme libraries generated by methylation sensitive (HpaII) and methylation insensitive (MspI) isoschizomers yields information on 1.2 million HpaII fragments throughout the genome. Each HpaII fragment corresponds to two CpG sites. The assay lends itself to low starting amounts of DNA (3 ug) and robust assessment of methylation status by comparing ratios of HpaII- generated- fragments to MspI- generated fragments co-hybridized to a Nimbelgen custom high-density microarray. Summary of results: In a pilot set of three paired tumor and non-tumor tissue samples, we identified 1504 fragments (corresponding to two CpG sites each) that were hypermethylated in tumor versus non-tumor in all three pairs. Of these, 165 fragments were located within gene promoters. In the opposite direction, 2907 fragments were found to be hypermethylated in non-tumor versus tumor. Of these, 81 were located within gene promoters. We could identify both known and novel regions of the genome as well as specific gene-promoters that are hypermethylated in tumor versus non-tumor. We will discuss selected methylation events in further detail. Conclusion: The HELP assay is a powerful approach to interrogate methylation status of individual HpaII fragments across the whole genome, offering a large sample size of 1.2 million HpaII fragments. We are able to discover individual methylation events common across different clinical specimens and are currently expanding our sample set, and planning correlations with transcriptome-wide studies. 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 4820. doi:10.1158/1538-7445.AM2011-4820

Introduction: There is a need for non-invasive airway-based biomarkers in lung carcinogenesis for both diagnosis, and risk assessment. MicroRNAs are small, stable, noncoding RNAs that function in gene regulation. Recent studies have revealed that microRNAs play important regulatory roles in carcinogenesis. Exhaled breath condensate (EBC) contains airway lining fluid molecules, including nucleic acids, as we've previously reported for DNA methylation. We previously developed an RNA-specific microRNA-PCR, whereby PCR artifact can be detected. Here we pilot the detection of microRNAs in EBC of lung cancer patients and controls. Methods: MicroRNA expression profiling using RNA-specific RT-qPCR was performed in EBC from 28 subjects, choosing literature-derived microRNAs that segregate tumors and non-tumor tissue, and an ongoing discovery effort we have commenced using microRNA-seq for tumor versus non-tumor comparison. As of abstract deadline, the top 12 significantly different microRNAs between lung tumor and non-tumor were chosen and their qPCR primers were designed. Results: So far, we have detected several microRNAs in EBC including 21, 34a, 153, 193b, 200c, 221; case-control comparisons are pending. Topographic validation studies are pending. Conclusion: By comparing the differences of microRNA expression between EBC from lung cancer cases and EBC from non-cancer controls, potential exhaled microRNA biomarkers might be found and used in early detection of lung cancer. This work was supported by National Institutes of Health grants1RC1 CA145422-01, 1K24-CA139054-01. 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 3863. doi:10.1158/1538-7445.AM2011-3863

One strategy for lung cancer chemoprevention focuses on the use of agents to modulate the metabolism and disposition of tobacco, environmental and endogenous carcinogens through up-regulation of detoxifying phase II enzymes. However, in studies to date, most candidate agents are not active in human lung cells. Therefore we previously applied a gene expression-based high-throughput screening approach to investigate n=800 plant-derived polyphenolic- and flavenoid- predominant compounds in the MicroSource Natural Products Library as to their effect on inducing the phase II metabolic enzymes glutathione S-transferases (GSTP1) and NAD(P)H:quinone oxidoreductase 1 (NQO1) in primary normal human bronchial epithelial (NHBE) cells and immortalized human bronchial epithelial cells (HBEC). We had identified 2, 3-dihydroxy-4-methoxy-4’-ethoxybenzophenone (DMEBP, putative source arctic sponge) and triacetylresveratrol (TRES, putative source plant myrtle) as new inducers for NQO1 mRNA expression. In the current study, in order to confirm our results, NHBE and HBEC cells in culture were exposed to diet-achievable levels of TRES and DMEBP (0.5, 1.0, 2.0 µM), as well as a panel of conventionally-recognized phytopreventive agents [epigallocatechin gallate (EGCG), resveratrol (RES) and sulforaphane (SFN)] for 24 h, 48 h, and 6 d, respectively. Quantitative RNA-specific RT-PCR showed an up-regulation of NQO1 mRNA expression of up to 10.8 fold in DMEBP-treated NHBE cells and an up-regulation of up to 4.6 fold in TRES-treated NHBE cells. NQO1 protein expression increased up to 3.4 fold in DMEBP-treated and up to 1.8 fold in TRES-treated NHBE cells. HBEC cells showed similar results for mRNA expression — an up-regulation of NQO1 mRNA expression of up to 9.7 fold in DMEBP-treated HBEC cells and an up-regulation of up to 3.1 fold in TRES-treated HBEC cells — whereas none of the tested compounds had an effect on protein expression in HBEC cells. DMEBP had a narrow therapeutic window, and was notably toxic to lung cells at 1-2 µM. We then measured accumulation of reactive oxygen species (ROS) in NHBE cell using DFA, and total GSH assays. Our ROS data so far show a slight anti-oxidant effect for DMEBP, but no effect yet found for TRES. Our data show two new agents have some effect on the up-regulation of the detoxifying enzyme NQO1 at mRNA and protein levels, but the effect was modest, and none was observed for GSTP1. Among the newly discovered agents, TRES is the most plausible candidate resulting from this search, and compares favorably, to conventional plant-derived polyphenolics/flavenoids tested. Citation Information: Cancer Prev Res 2010;3(12 Suppl):A49.

Introduction: MicroRNAs (miRNAs) are small noncoding RNAs functioning in gene regulation. In animal cells, miRNAs bind to target sites in the 3’ UTR of mRNAs, causing posttranscriptional repression or degradation of mRNAs. The identification of specific miRNAs to target a 3′UTR of a given gene is essential for studies in gene regulation. However, the sequence software programs conventionally used to predict binding of individual microRNAs to a given mRNA transcript are notoriously unreliable, and specific microRNA-mRNA binding is very difficult to directly affirm using currently available techniques. We have developed a microRNA affinity assay that addresses this need. Methods: We chose a candidate gene that had been extensively studied experimentally for microRNA regulation; it is known that miR-200c and miR-200b can bind to 3′UTR RNA of TCF8 [Hurteau 2007]. Here, a 500bp fragment of the 3′UTR RNA of TCF8 was generated by IVT, and used as a bait sequence to identify miRNAs that bind a mixture of known miRNA composition, and alternately a naturally produced cellular miRNA pool. After separation, miRNA qPCR was used to check recovery rate of miRNA, and cloning and sequencing was used to identify miRNAs. Results: Specific miRNAs from a synthetic mixture miRNAs, miRNA qPCR results displayed excellent recovery rates (151.57% with pipetting error, for miR-200c), 88.88% for the closely related miR-200b, 0.31% for the sequence-unrelated miR-9, 0.67% (miR-10a), 0.1% (miR-20a), 8.78% (miR-34a with some 3′UTR homology), 0.11% (miR-100), 0.16% (miR-140-5p), 0.98% (miR-144), 0.33% (miR-802) and 1.58% (miR-1234). After cloning the captured miRNAs, there were 10 sequences from miR-200c, 7 sequences from miR-200b, and one other sequence in 18 sequenced clones. When separating specific miRNAs from naturally produced NHBE cell miRNA pool, miRNA qPCR results show that their recovery rates are 88.88% (miR-200c), 80% (miR-200b), 0.07% (miR-20a), less than 0.006% (miR-34a) and 0.01% (miR-100). Conclusions: For both simple known and complex unknown microRNA pools, this pull-down strategy is effective in determining microRNA-mRNA binding. In future work, we will use other 3′UTR RNA sequences of candidate genes as bait sequence, for microRNA-related discovery and confirmation. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2021.

Cigarette smoke (CS) contains 1,000-10,000 fold more acrolein (Acr) and crotonaldehyde (Crot) than polycyclic aromatic hydrocarbons (PAHs). These aldehydes can induce propanoldeoxyguanosine (propanol-dG) DNA adducts formation in cultured normal human lung epithelial cells. Previously, we have found that the distribution of Acr-dG in the p53 gene coincides with the lung cancer p53 mutational spectrum of cigarette smokers, and that Acr-dG induces similar level of G to T transversion and G to A transition mutations as in lung cancer of cigarette smokers. Hence, we have proposed that Acr is a major etiological agent of CS related lung cancer. We developed a 32P-postlabelling method in combination with 2D TLC/HPLC method to quantify propanol-dG formation in human lung tissue. To date we have determined Acr-dG and Crot-dG in the lung tissue of cigarette smokers (n=27) and nonsmokers (n=25) with lung cancer. We found that 1) both α- and γ-Acr-dG are formed in lung tissues of smokers and nonsmokers, and the level of these two types of adduct in lung tissue varies from 10-4,510, and 0-1,900 fmole/μmole, respectively; and 2) smokers appear to have a higher level of γ-Acr-dG than nonsmokers although the differences have not reached statistical significance (p=0.1854); 3) the level of Crot-dG in smokers is significant higher than that in nonsmokers (p=0.0279). These results indicate a substantial amount of Acr-dG and Crot-dG formed in lung tissue of lung cancer. Key words: α, β-unsaturated aldehydes, cigarette smoking, DNA adducts, lung cancer. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4700.

Many phytochemicals possess anti-oxidant and cancer-preventive properties, some putatively through phase II metabolism-mediated mutagen/oxidant quenching. However, in studies to date, most candidate agents are not active in human lung cells. In vitro and in vivo screening studies for discovery are clearly needed for new, more potent chemopreventive agents for lung cancer. Here we applied an mRNA-specific gene expression-based high-throughout screening approach to identify phytochemical inducers of phase II metabolism enzymes GSTP1 and NQO1 in primary normal human bronchial epithelial (NHBE) cells and immortalized human bronchial epithelial cells (HBEC). We have screened 800 compounds in the MicroSource Natural Products Library for inducers of GSTP1 and NQO1 expression, and identified 2, 3-dihydroxy-4-methoxy-4′-ethoxybenzophenone, triacetylresveratrol, ivermectin, sanguinarine sulfate, and daunorubicin as new inducers for GSTP1 and NQO1 mRNA expression. Consistent with this effect, the induction of NQO1 protein expression by immunoblot was found for all these agents in both HBEC and NHBE cells at the same concentration that induced NQO1 mRNA expression. However, GSTP1 protein expression did not significantly change with any selected agents. Proliferation/viability assays showed that HBEC and NHBE were significantly inhibited by ivermectin, sanguinarine sulfate, and daunorubicin. These data demonstrate the feasibility of high-throughput screening for inducers of NQO1. Moreover, the data identify 2, 3-dihydroxy-4-methoxy-4′-ethoxybenzophenone and triacetylresveratrol as the most potent and low toxicity inducers [≥3-6-fold, at the protein level], implying they are potential new agents for further in vitro and preclinical in vivo testing for prevention of oxidant-related disease. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5706.

Many phytochemicals possess cancer-preventive properties, some putatively through phase II metabolism-mediated mutagen/oxidant quenching. However, in studies to date, most candidate agents are not active in human lung cells. In vitro and in vivo screening studies for discovery are clearly needed for new, more potent chemopreventive agents for lung cancer. Here we applied a gene expression-based high-throughput screening approach to identify phytochemical inducers of phase II metabolism enzymes GSTP1 and NQO1 in primary normal human bronchial epithelial (NHBE) cells and immortalized human bronchial epithelial cells (HBEC). We have screened 800 compounds in the MicroSource Natural Products Library for inducers of GSTP1 and NQO1 expression, and identified 2, 3-dihydroxy-4-methoxy-4′-ethoxybenzophenone, triacetylresveratrol, ivermectin, sanguinarine sulfate, and daunorubicin as new inducers for GSTP1 and NQO1 mRNA expression. Consistent with this effect, the induction of NQO1 protein expression by immunoblot was found for all these agents in both HBEC and NHBE cells at the same concentration (1.0 µM, final concentration) that induced NQO1 mRNA expression. However, GSTP1 protein expression did not significantly change with any selected agents. Proliferation/viability assays showed that HBEC and NHBE were significantly inhibited by ivermectin, sanguinarine sulfate, and daunorubicin. These data demonstrate the feasibility of high-throughput screening for inducers of NQO1. Moreover, the data identify 2, 3-dihydroxy-4-methoxy-4′-ethoxybenzophenone and triacetylresveratrol as most potent and low toxicity inducers [12-fold, and 10-fold, respectively, at the protein level], implying they are potential new agents for further in vitro and preclinical in vivo testing for prevention of tobacco-related lung cancer. Citation Information: Cancer Prev Res 2010;3(1 Suppl):A69.

Background There is a need for new, noninvasive risk assessment tools for use in lung cancer population screening and prevention programs. Methods To investigate the technical feasibility of determining DNA methylation in exhaled breath condensate, we applied our previously-developed method for tag-adapted bisulfite genomic DNA sequencing (tBGS) for mapping of DNA methylation, and adapted it to exhaled breath condensate (EBC) from lung cancer cases and non-cancer controls. Promoter methylation patterns were analyzed in DAPK, RASSF1A and PAX5β promoters in EBC samples from 54 individuals, comprised of 37 controls [current- (n = 19), former- (n = 10), and never-smokers (n = 8)] and 17 lung cancer cases [current- (n = 5), former- (n = 11), and never-smokers (n = 1)]. Results We found: (1) Wide inter-individual variability in methylation density and spatial distribution for DAPK, PAX5β and RASSF1A. (2) Methylation patterns from paired exhaled breath condensate and mouth rinse specimens were completely divergent. (3) For smoking status, the methylation density of RASSF1A was statistically different (p = 0.0285); pair-wise comparisons showed that the former smokers had higher methylation density versus never smokers and current smokers (p = 0.019 and p = 0.031). For DAPK and PAX5β, there was no such significant smoking-related difference. Underlying lung disease did not impact on methylation density for this geneset. (4) In case-control comparisons, CpG at -63 of DAPK promoter and +52 of PAX5β promoter were significantly associated with lung cancer status (p = 0.0042 and 0.0093, respectively). After adjusting for multiple testing, both loci were of borderline significance (padj = 0.054 and 0.031). (5) The DAPK gene had a regional methylation pattern with two blocks (1)~-215~-113 and (2) -84 ~+26); while similar in block 1, there was a significant case-control difference in methylation density in block 2 (p = 0.045); (6)Tumor stage and histology did not impact on the methylation density among the cases. (7) The results of qMSP applied to EBC correlated with the corresponding tBGS sequencing map loci. Conclusion Our results show that DNA methylation in exhaled breath condensate is detectable and is likely of lung origin. Suggestive correlations with smoking and lung cancer case-control status depend on individual gene and CpG site examined.