Novel in-vitro models and correlative experiments with primary tumor/normal tissue specimens have been utilized to identify epigenomic alterations which contribute to initiation and progression of tobacco -associated thoracic malignancies. Our recent experiments have identified several micro-RNAs that are either up-regulated or silenced in normal respiratory epithelia and lung cancer cells by cigarette smoke. For example, we observed that CSC mediated a 4-7 fold up-regulation of the long non-coding RNA (Lnc-RNA) BC070487, with a 4-8 fold down-regulation of ZNFX1 in cultured normal or immortalized human respiratory epithelial cells, as well as Calu-6 and H841 lung cancer cells. BC070487 expression correlated inversely with expression of ZNFX1 in primary lung cancers relative to adjacent normal lung parenchyma. Overexpression or depletion of BC070487 inhibited or enhanced expression of ZNFX1, respectively in normal respiratory epithelia and lung cancer cells. CSC as well as BC070487-mediated repression of ZNFX1 coincided with increased occupancy of EZH2, SUZ12, BMI1, and increased levels of H3K27Me3, with decreased H3K4Me3 within the ZNFX1 promoter region. CSC as well as BC070487 overexpression enhanced binding of BC070487 with EZH2, SUZ12 and BMI1 proteins in SAEC and Calu-6 cells. CSC exposure significantly increased DNA methylation in one of three CpG islands spanning the regulatory elements of ZNFX1. In addition, CSC enhanced binding of BC070487 with DNMT3A and DNMT3B with site-specific de novo DNA methylation of ZNFX1 in SAEC and Calu-6 cells. FAIRE assays identified an 800 bp regulatory sequence for BC070487; CSC-mediated activation of BC070487 coincided with increased levels of H3K4Me3, H3K27Ac, H3K36Me3, Sp1, and Ago proteins, with decreased levels of H3K27Me3 and H3K9Me3 within this regulatory region. miR-31, which we have previously shown to be an oncomiR upregulated by CSC in respiratory epithelia, modulated the transcriptional activity of BC070487 in association with modification of histone marks within the regulatory region of BC070487. Overexpression or depletion of BC070487 increased or inhibited proliferation and invasion of lung cancer cells, and similarly modulated growth of SAEC and HBEC cells. In contrast, ZNFX1 overexpression or depletion decreased or enhanced growth of normal respiratory epithelial cells and lung cancer cells. BC070487 overexpression enhanced growth of lung cancer cells xenografts in athymic nude mice, while forced expression of ZNFX1 arrested growth of these xenografts. Collectively, these data suggest that CSC-mediated up-regulation of BC070487 represses ZNFX1 to promote pulmonary carcinogenesis. Results of these studies were presented in oral format at the World Lung Cancer Conference in September 2015, and a manuscript pertaining to these experiments will be submitted for publication in the near future. In additional experiments, array and qRT-PCR techniques were used to examine miR expression in immortalized esophageal epithelia (IEE) and esophageal adenocarcinoma (EAC) cells cultured in normal media (NM) with or without CSC. Under relevant exposure conditions, CSC significantly decreased miR-217 expression in these cells. Endogenous levels of miR-217 expression in EAC cells (EACC)/ primary EACs were significantly lower than those observed in IEE/ paired normal esophageal tissues. Subsequent experiments demonstrated direct interaction of miR-217 with kallikrein 7 (KLK7), encoding a putative oncogene not previously implicated in EAC. Repression of miR-217 correlated with increased levels of KLK7 in primary EACs, particularly those from smokers. Additional experiments demonstrated that CSC-mediated repression of miR-217 coincided with DNMT3b-dependent hypermethylation and decreased occupancy of nuclear factor 1 (NF-1) within the miR-217 genomic locus. Deoxyazacytidine induced miR-217 expression, and down-regulated KLK7 in EACC; deoxyazacytidine also attenuated CSC-mediated miR-217 repression and up-regulation of KLK7 in IEE and EACC. Over-expression of miR-217 significantly decreased, whereas over-expression of KLK7 increased proliferation, invasion and tumorigenicity of EACC. Collectively, these data demonstrate that epigenetic repression of miR-217 contributes to the pathogenesis of EAC via up-regulation of KLK7, and suggest that restoration of miR-217 expression may be a novel treatment strategy for these malignancies. A manuscript summarizing these experiments has been published in Oncogene. Previously we have demonstrated that approximately 80% of sporadic MPM exhibit over-expression of EZH2 [the core catalytic component of polycomb repressive complex-2 (PRC-2)] and a global increase in the PRC-2 mediated repressive histone mark, H3K27Me3. EZH2 over-expression correlated with decreased survival in MPM patients undergoing potentially curative surgery. Because the available EZH2 inhibitors are only active against cancer cells such as lymphomas with gain of function EZH2 mutations, we have sought to develop additional strategies to target PRC-2 expression/activity in MPM since such mutations are uncommon in these neoplasms. Software guided analysis of the EZH2 promoter demonstrated multiple potential recognition elements for Specificity Protein 1 (SP1). Promoter-reporter, qRT-PCR and immunoblot experiments demonstrated that SP1 directly modulates EZH2. qRT-PCR and immunoblot experiments demonstrated markedly higher SP1 expression in MPM cell lines and pleural mesotheliomas relative to cultured normal mesothelial cells or normal pleura. IHC experiments using commercial tissue arrays demonstrated significantly increased SP1 expression in MPMs compared to normal mesothelia. Knock-down of SP1 significantly diminished proliferation, migration, soft agar clonogenicity, and tumorigenicity of MPM cells. Mithramycin (MM), an antineoplastic agent that inhibits binding of SP1 to DNA significantly inhibited proliferation, invasion and soft agar clonogenicity, and tumorigenicity of MPM cells, in part via depletion of SP1 and activation of p53. These studies, which were the first to demonstrate that SP1 is a novel, druggable target in MPM were published in Clinical Cancer Research. In more recent experiments, we have sought to develop clinically relevant strategies to enhance the potential efficacy of MM using inhibitors of HDM2. When combined with MM, RITA and RG7388 exhibited additive to supra-additive pro-apoptotic effects in MPM cells in-vitro and in-vivo, allowing for a 66% reduction in MM dose. A manuscript pertaining to these experiments is in the final phase of preparation for peer review.
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