Miao Shi

Candidate Dietary Phytochemicals Modulate Expression of Phase II Enzymes GSTP1 and NQO1 in Human Lung Cells

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 micromol/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.

Site-specific methylated reporter constructs for functional analysis of DNA methylation

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 (p < 0.01). 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 (p < 0.01), 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.

Global, integrated analysis of methylomes and transcriptomes from laser capture microdissected bronchial and alveolar cells in human lung

ABSTRACT 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.

Abstract 4820: Whole methylome explorations of paired tumor and non-tumor clinical samples using HELP

Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL 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

Abstract 3863: Exhaled microRNAs as potential biomarkers in lung cancer

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 we9ve 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

Abstract 2021: MicroRNA affinity assay

Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC 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.

Abstract 5706: High-throughout library screening identifies phytochemical inducers of phase II metabolism enzymes GSTP1 and NQO1 in human lung cells

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.

Abstract A69: High‐throughput library screening identifies phytochemical inducers of phase II metabolism enzymes GSTP1 and NQO1 in human lung cells

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.

Abstract A37: Modulation of GSTP1 and NQO1 by plant-derived chemopreventive agents in human lung normal, immortalized, and malignant bronchial cells

A37 Modulation of GSTP1 and NQO1 by plant-derived chemopreventive agents in human lung normal, immortalized, and malignant bronchial cells Xiang-Lin Tan 1, 2 Shengli Xiong1, 2 Miao Shi1, Weiguo Han1, 2 Simon D. Spivack 1, 2, 3, 4, 5 1 Division of Pulmonary Medicine, Albert Einstein College of Medicine, Bronx, NY, 2 Laboratory of Human Toxicology and Molecular Epidemiology, Wadsworth Center, New York State Department of Health, Albany, NY 3 Environmental Health Sciences, School of Public Health, University at Albany, Albany, NY 4 Department of Epidemiology, Albert Einstein College of Medicine, Bronx, NY, 5 Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, Many phytochemicals possess putative cancer-preventive properties. However, none have yet demonstrated clear benefit for lung cancer prevention in clinical trials. In this study, we applied an in vitro system of assay to systematically investigate the influence of putative anti-mutagen, phase II metabolism inducing naturally-occurring mixtures and single compounds, including green tea extracts (GTE), broccoli sprout ITC extracts (ITCs), epigallocatechin gallate (EGCG), sulforaphane (SFN), phenethyl isothiocyanate (PEITC) and benzyl isothiocyanate (BITC), for phase II enzymes GSTP1 and NQO1 in the mRNA and protein level. Primary normal human bronchial epithelial cells (NHBE), immortalized human bronchial epithelial cells (HBEC), and overtly malignant lung adenocarcinoma cells (A549) were incubated with 0.5, 1.0, 5.0 µg/ml mixture or 0.5, 1.0, 2.0 µM single index compounds for 24h, 48h and 7 days, respectively. The proliferation of normal and malignant cells determined by MTT assay was significantly reduced by all studied agents, with relative activities of BITC > PEITC > ITCs > SFN > EGCG > GTE. We then determined the mRNA expression by RNA-specific quantitative RT-PCR previously developed in the laboratory, and the protein expression by conventional Western blot. Overall, the mixtures GTE and ITC increased GSTP1 and NQO1 mRNA levels up to two-fold (1ug/ml) to four-fold (5 ug/ml) increased. However, these mRNA levels were decreased by single compounds PEITC and BITC, in a time and dose dependent manner. EGCG and SFN did not show a consistent effect on the mRNA expression of both GSTP1 and NQO1 genes, although SFN showed two- to four-fold induction activity for NQO1 mRNA expression at 0.5-1.0 uM, uniquely for NHBE. The results were largely confirmed at the protein level, although there was some mRNA-protein discordance. Our results suggest that further in vitro and in vivo screening studies are needed to discover new, more potent phase II-inducing chemopreventive agents for lung cancer, along with mechanistic studies of gene regulation for these key upstream anti-carcinogenesis genes. Such studies are in process in the laboratory. 1 Citation Information: Cancer Prev Res 2008;1(7 Suppl):A37.