Abstract A57: Platinum induces IL-6-signaling mediated activation of ALDH1A1 and enriches the cancer stem cell population in ovarian cancer

Purpose: While chemotherapy may succeed initially at decreasing the number of ovarian cancer (OC) cells, it leaves behind tumors enriched in ovarian cancer stem cells (OCSCs), which most likely drive chemoresistance and tumor relapse. An emerging model indicates that non-OCSCs may dedifferentiate and acquire stem cell properties under certain circumstances. Recent studies in OC implicate a critical role for aberrant cytokine interleukin-6 (IL-6) secretion and the IL-6 signaling pathway may play a critical role in converting non-CSCs to CSC. In the current study, we investigated the mechanism contributing to OCSC enrichment after platinum treatment in vivo. We hypothesize that platinum-induced IL-6 secretion activates STAT3 signaling-mediated expression of the cancer stem cell marker ALDH1A1, resulting in CSC enrichment. In addition, based on our previous study in OCSCs (Wang et al., 2014, Cancer Res.), we sought to examine the mechanism by which guadecitabine (SGI-110), a second generation hypomethylating agent HMA, inhibits OCSCs in OC xenograft residuals after platinum treatment.

Methods: OC cells (OVCAR4 and A2780) were cultured alone or co-cultured with normal omental fibroblasts (NOFs) or guadecitabine (100nM, 3days)-treated NOFs in the starving condition for 24h and then treated with 3h cisplatin (CDDP; respective IC50 doses of 27.4 and 14.7μM), guadecitabine, IL-6 (100ng/ml), neutralizing antibody (Nab) against IL-6 (IL-6-Nab, 200ng/mL) or IL-6+IL-6-Nab. IL-6 secretion levels were measured by ELISA. FACS was used to analyze OCSC population marked as aldehyde dehydrogenase (ALDH)+ cells, and western blot was used to examine ALDH1A1 and pSTAT3 levels in cells treated as described above. An ALDH1A1 promoter-luciferase reporter (pGL3-ALDH1A1-Luc; -1 to -1031) assay was used to determine whether IL-6 transactivates ALDH1A1 expression in OC cells. OC cell migration under the described conditions was determined by transwell migration assays.

Results: We found that CDDP induced (P<0.05) IL-6 secretion by OCs up to 48h post-treatment and up to 96h by NOFs or by co-cultured cells, suggesting a role of the tumor microenvironment in platinum-induced IL-6 secretion. Guadecitabine inhibited (P<0.05) CDDP-induced IL-6 secretion by NOFs alone or in co-culture with OVCAR4, suggesting an inhibitory role of the HMA on IL-6 signaling. By assaying FACS sorted ALDH+/- cells, we determined that ALDH+ cells express increased (P<0.05) levels of the IL-6 receptor and secrete higher (P<0.05) levels of IL-6 in the conditioned media compared to ALDH- cells. Treatment of OC cells with IL-6 enriched the percentage of ALDH+, which was inhibited by IL-6-Nab. Luciferase assay results revealed that IL-6 transactivated (p<0.05) ALDH1A1 reporter gene expression in ALDH- cells, which was blocked by IL-6-Nab. Further, we observed that IL-6- or CDDP-treated OC cells increased (P<0.05) ALDH1A1 and pSTAT3 protein expression, and guadecitabine treatment inhibited (P<0.05) expression of ALDH1A1 and pSTAT3 in OCs. ALDH+ cells showed greater migration potential than ALDH- cells, and guadecitabine inhibited (P<0.05) migration of both ALDH+ and ALDH- cells. Guadecitabine, alone or combination with IL-6-Nab, inhibited (P<0.05) CDDP-induced OVCAR4 migration in co-culture with NOFs.

Conclusion: Our data indicate that IL-6 is a potent regulator of ALDH1A1 expression and the OCSC phenotype and further suggest an inhibitory effect of guadecitabine on the conversion of non-OCSCs to OCSCs. The data support a role for IL-6 in OCSC enrichment after platinum treatment and suggest that a combination approach of IL-6 neutralizing antibody with guadecitabine could represent a novel maintenance strategy after chemotherapy for eradicating OCSCs and preventing tumor recurrence.

Citation Format: Yinu Wang, Anirban Kumar Mitra, Kenneth P. Nephew. Platinum induces IL-6-signaling mediated activation of ALDH1A1 and enriches the cancer stem cell population in ovarian cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr A57.

Identification of novel immunomodulatory tumor biology through comprehensive characterization of a metastases-specific epigenome in patients with metachronous primary and metastatic urothelial carcinoma (UC) tumor pairs

452

Background: The Cancer Genome Atlas project identified a distinct cluster of hypermethylated muscle-invasive UC tumors in one third of patients. It is unknown if this epigenetic biology persists or changes in UC metastases. The present study aimed to identify uniquely hypermethylated regions in UC metastases compared to their matched primary tumors. Methods: UC patients with paired formalin fixed paraffin embedded tissue samples ( > 75% tumor) from primary and metachronous metastatic tumors were identified. DNA methylation was analyzed on the Illumina HiSeq platform by double-enzyme reduced representation bisulfite sequencing (dRRBS). Results were analyzed by BS-seq within BSmooth open source software. Alignment and methylation estimation was done using Bismark open source software. CpG regions with coverage < 2 in more than 66% of samples were removed to reduce false positive results. Differentially methylated regions (DMRs) in metastases compared to primary tumors were determined by paired t-test. Gene set enrichment analysis (GSEA) of the top 5% DMRs was performed utilizing multiple gene set collections including c7IMMUNO. A false discovery rate of < 10% defined significant DMRs. Results: 15 UC primary/metachronous metastases pairs were analyzed. After filtering for low coverage, 1,781,762 loci remained for analysis. After merging loci within 2500 bp of each other, the top 5% DMRs resulted in 18,452 DMRs. GSEA including the c7IMMUNO gene set identified multiple previously undescribed hypermethylated genes modulating immune function through TGF-beta and Treg signaling including: TGFBR2, TGFBR3, SMAD1, SMAD3, SMAD4, BACH1, BACH2, and VDR all q < 0.05. Conclusions: We identified numerous genes with immunomodulatory functions significantly hypermethylated in UC metastases compared to their matched primary tumors. Our findings provide rationale to examine epigenetic approaches as a means to improve clinical outcomes of UC patients treated with immunotherapy. Our small sample size limits definitive conclusions and warrants validation in independent data sets.

Abstract B2-09: A systems biology approach to understanding estrogen responsiveness in breast cancer cells using the MCF7 model

Estrogen receptor alpha (ER) is expressed in 70% of breast cancers and is critical for breast cancer cell proliferation, differentiation, and apoptosis. ER functions primarily as a nuclear transcription factor that dimerizes upon binding of the natural ligand, 17beta estradiol (E2). ER is a potent regulator of gene expression, altering the transcriptome, and ultimately both the proteome and metabolome. In the clinic, ER+ tumors are often treated with antiestrogens or aromatase inhibitors. However, resistance to these endocrine therapies is common, and there is an urgent need to understand how estrogen signaling contributes to the malignancy of breast cancer cells. The MCF7 ER+ breast cancer cell line is a commonly used cell model to study estrogen responsiveness in ER+ breast cancers. However, the field lacks a clear and detailed description of all the changes that occur in response to E2 by time and dose in MCF7 cells. Additionally, there is a great need to obtain a consistent view of the estrogen-regulated gene set, resolve the disconnections among epigenetics regulation of estrogen signaling and protein phosphoproteomics, and provide reliable metabolomics data sets for MCF7 cells. In this multi-institutional project, we have generated multi-omics data and cell cycle profile for MCF7 cells treated with 1 pM and 1 nM of E2 for 26-time points, 0 to 72 h. MCF7 cell line was obtained from American Type Culture Collection (ATCC), fingerprinted and confirmed for E2 and Tamoxifen sensitivity prior to omics studies. Moreover, ER expression (basal and with E2 stimulation) was determined using Western blotting and qPCR. Omics data generated include: RNA-seq (coding and non-coding), reverse phase protein array (RPPA; proteins and phospho-proteins), methylome analysis, cell cycle analysis and metabolomics (metabolites). Using our data sets, comprehensive responses to physiologically relevant E2 concentrations, including both rapid and long-term E2 responses, can be determined. Our data were processed using current best practices and the time trends for the 1 pM and 1 nM doses of E2 were assessed via linear models separately for the various omics features. Global differences between samples were further assessed via principal components analysis. The features which showed the most significant differences in time trends between the two dose groups were visualized as heatmaps. The objective of this study is to provide our data and discoveries as a common resource for the systems biology centers and the broader research community. A multi-dimensional dataset such as our will enable the development of dynamic network model(s) to interrogate estrogen signaling, from nucleic acids to proteins, with changes in the MCF7 metabolome.

Citation Format: Ayesha N. Shajahan-Haq, Lang Li, Yunlong Liu, Lu Jin, David F. Miller, Jay Pilrose, Amrita K. Cheema, Simina M. Boca, Krithika Bhuvaneshwar, Subha Madhavan, Robert Clarke, Kenneth P. Nephew. A systems biology approach to understanding estrogen responsiveness in breast cancer cells using the MCF7 model. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B2-09.

Rethinking ovarian cancer II: reducing mortality from high-grade serous ovarian cancer

High-grade serous ovarian cancer (HGSOC) accounts for 70-80% of ovarian cancer deaths, and overall survival has not changed significantly for several decades. In this Opinion article, we outline a set of research priorities that we believe will reduce incidence and improve outcomes for women with this disease. This 'roadmap' for HGSOC was determined after extensive discussions at an Ovarian Cancer Action meeting in January 2015.

Rethinking ovarian cancer II: reducing mortality from high-grade serous ovarian cancer

High-grade serous ovarian cancer (HGSOC) accounts for 70-80% of ovarian cancer deaths, and overall survival has not changed significantly for several decades. In this Opinion article, we outline a set of research priorities that we believe will reduce incidence and improve outcomes for women with this disease. This 'roadmap' for HGSOC was determined after extensive discussions at an Ovarian Cancer Action meeting in January 2015.

Carboplatin with Decitabine Therapy, in Recurrent Platinum Resistant Ovarian Cancer, Alters Circulating miRNAs Concentrations: A Pilot Study

Objective

Plasma miRNAs represent potential minimally invasive biomarkers to monitor and predict outcomes from chemotherapy. The primary goal of the current study—consisting of patients with recurrent, platinum-resistant ovarian cancer—was to identify the changes in circulating miRNA concentrations associated with decitabine followed by carboplatin chemotherapy treatment. A secondary goal was to associate clinical response with changes in circulating miRNA concentration.

Methods

We measured miRNA concentrations in plasma samples from 14 patients with platinum-resistant, recurrent ovarian cancer enrolled in a phase II clinical trial that were treated with a low dose of the hypomethylating agent (HMA) decitabine for 5 days followed by carboplatin on day 8. The primary endpoint was to determine chemotherapy-associated changes in plasma miRNA concentrations. The secondary endpoint was to correlate miRNA changes with clinical response as measured by progression free survival (PFS).

Results

Seventy-eight miRNA plasma concentrations were measured at baseline (before treatment) and at the end of the first cycle of treatment (day 29). Of these, 10 miRNAs (miR-193a-5p, miR-375, miR-339-3p, miR-340-5p, miR-532-3p, miR-133a-3p, miR-25-3p, miR-10a-5p, miR-616-5p, and miR-148b-5p) displayed fold changes in concentration ranging from -2.9 to 4 (p<0.05), in recurrent platinum resistant ovarian cancer patients, that were associated with response to decitabine followed by carboplatin chemotherapy. Furthermore, lower concentrations of miR-148b-5p after this chemotherapy regimen were associated (P<0.05) with the PFS.

Conclusions

This is the first report demonstrating altered circulating miRNA concentrations following a combination platinum plus HMA chemotherapy regiment. In addition, circulating miR-148b-5p concentrations were associated with PFS and may represent a novel biomarker of therapeutic response, with this chemotherapy regimen, in women with recurrent, drug-resistant ovarian cancer.

Regulation of triple-negative breast cancer cell metastasis by the tumor-suppressor liver kinase B1

Liver kinase B1 (LKB1), also known as serine/threonine kinase 11 (STK11), has been identified as a tumor suppressor in many cancers including breast. Low LKB1 expression has been associated with poor prognosis of breast cancer patients, and we report here a significant association between loss of LKB1 expression and reduced patient survival specifically in the basal subtype of breast cancer. Owing to the aggressive nature of the basal subtype as evidenced by high incidences of metastasis, the purpose of this study was to determine if LKB1 expression could regulate the invasive and metastatic properties of this specific breast cancer subtype. Induction of LKB1 expression in basal-like breast cancer (BLBC)/triple-negative breast cancer cell lines, MDA-MB-231 and BT-549, inhibited invasiveness in vitro and lung metastatic burden in an orthotopic xenograft model. Further analysis of BLBC cells overexpressing LKB1 by unbiased whole transcriptomics (RNA-sequencing) revealed striking regulation of metastasis-associated pathways, including cell adhesion, extracellular matrix remodeling, and epithelial-to-mesenchymal transition (EMT). In addition, LKB1 overexpression inhibited EMT-associated genes (CDH2, Vimentin, Twist) and induced the epithelial cell marker CDH1, indicating reversal of the EMT phenotype in the MDA-MB-231 cells. We further demonstrated marked inhibition of matrix metalloproteinase 1 expression and activity via regulation of c-Jun through inhibition of p38 signaling in LKB1-expressing cells. Taken together, these data support future development of LKB1 inducing therapeutics for the suppression of invasion and metastasis of BLBC.

MiR-373 targeting of the Rab22a oncogene suppresses tumor invasion and metastasis in ovarian cancer

Metastasis is major cause of mortality in patients with ovarian cancer. MiR-373 has been shown to play pivotal roles in tumorigenesis and metastasis; however, a role for miR-373 in ovarian cancer has not been investigated. In this study, we show that the miR-373 expression is down-regulated in human epithelial ovarian cancer (EOC) and inversely correlated with clinical stage and histological grade. Ectopic overexpression of miR-373 in human EOC cells suppressed cell invasion in vitro and metastasis in vivo, and the epithelial–mesenchymal transition process. Silencing the expression of miR-373 resulted in an increased migration and invasion of EOC cells. Using integrated bioinformatics analysis, gene expression arrays, and luciferase assay, we identified Rab22a as a direct and functional target of miR-373 in EOC cells. Expression levels of miR-373 were inversely correlated with Rab22a protein levels in human EOC tissues. Rab22a knockdown inhibited invasion and migration of EOC cells, increased E-cadherin expression, and suppressed the expression of N-cadherin. Moreover, overexpression of Rab22a abrogated miR-373-induced invasion and migration of EOC cells. Taken together, these results demonstrate that miR-373 suppresses EOC invasion and metastasis by directly targeting Rab22a gene, a new potential therapeutic target in EOC.

Abstract POSTER-BIOL-1306: DNA methylation changes during epithelial-to-mesenchymal transition in ovarian cancer cells

Epithelial-to-mesenchymal transition (EMT) is an important step in the process of metastasis and has been linked to cancer cell stemness. We hypothesize that aside from defined genetic changes associated with EMT, epigenetic mechanisms are involved and have not been fully elucidated. We determined DNA methylation in SKOV3 ovarian cancer (OC) cells during EMT induced by TGF-ß using the Infinium HumanMethylation450 array. Methylation levels of CpG sites were expressed as ß-values ranging from 0 (totally unmethylated) to 1 (totally methylated). Methylation of 468 and 390 sites changed (P&lt;.01, ANOVA and FDR&lt;0.05) after 48h and 120h of TGF-ß stimulation. The majority of changes (81%) reflected TGF-ß-induced increase in methylation. Methylation of 160 sites changed similarly at 48 and 120 h indicating that 34% of initial changes were sustained. The number of methylation changes decreased significantly after TGF-ß removal from the cell cultures, demonstrating that removal of TGF-ß stimulation reversed the methylation changes at most sites and restituted the baseline methylome. These results were consistent with those of the principal component and hierarchical clustering analyses. TGF-ß increased overall (average of all CpG sites) DNA methylation, total DNA methyltransferase activity, and amounts of DNMT1 protein and mRNA. The average methylation of CpG islands located in or near promoters increased in 193 genes at 24h and 494 at 120h, while no changes were observed after TGF-ß removal. Pathway analysis identified methylation changes in genes belonging to functional networks relevant to EMT and cancer progression, including: cellular movement, cell cycle, organ morphology, cellular development, and cell death and survival. Treatment of OC cells with the DNA methylation inhibitor SGI-110 prevented TGF-ß-induced EMT in association with an inhibition of the TGF-ß-induced downregulation of E-Cadherin. Results demonstrate that DNA methylation is a dynamic process involved in regulation of genes implicated in EMT and metastasis.

Citation Format: Horacio Cardenas, Edyta Vieth, Jiyoon Lee, Yunlong Liu, Kenneth P. Nephew, Daniela Matei. DNA methylation changes during epithelial-to-mesenchymal transition in ovarian cancer cells [abstract]. In: Proceedings of the 10th Biennial Ovarian Cancer Research Symposium; Sep 8-9, 2014; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(16 Suppl):Abstract nr POSTER-BIOL-1306.

Abstract POSTER-THER-1421: Epigenetic targeting of ovarian cancer stem cells

In ovarian and other cancers, emerging data indicate that cancer stem cells contribute to chemoresistance and that their persistence alters clinical outcome. As epigenetic regulators play a major role in the control of normal stem cell differentiation, epigenetics may play a critical role in targeting this subpopulation. Epigenetic aberrations, especially DNA methylation, result in silencing of tumor suppressor and differentiation-associated genes and regulate ovarian cancer stem cell (OCSCs) survival. To test the hypothesis that DNA hypomethylating agents “reset” OCSCs towards differentiation, we investigated the effect of the new DNA methytransferase inhibitor SGI-110 on OCSCs, defined as aldehyde dehydrogenase 1 (ALDH)(+) cells. We demonstrated that ALDH(+) OC cells possess multiple stem cell characteristics, were highly chemoresistant, and were enriched in xenografts residual after platinum therapy. Low dose SGI-110 reduced the stemness properties of ALDH(+) cells, including their tumor initiating capacity, resensitized these OCSCs to platinum, and induced re-expression of differentiation-associated genes. Maintenance treatment with SGI-110 after carboplatin inhibited OCSCs, caused profound global tumor hypomethylation, and delayed tumor progression, supporting epigenomic targeting as a novel strategy after platinum-based therapy in OC. Collectively, our data suggest that a strategy targeting DNA methylation in OC exerts potent anti-tumor activity by allowing elimination of OCSCs enriched in residual, platinum resistant tumors. Our study provides the first evidence that epigenome targeting strategies delay tumor progression by targeting and reprogramming residual cancer stem cells, suggesting that SGI-110 in combination with platinum has the potential to prevent recurrent and chemoresistant OC.

Citation Format: Yinu Wang, Horacio Cardenas, Fang Fang, Salvatore Condello, Pietro Taverna, Matthew Segar, Yunlong Liu, Daniela Matei, Kenneth P. Nephew. Epigenetic targeting of ovarian cancer stem cells [abstract]. In: Proceedings of the 10th Biennial Ovarian Cancer Research Symposium; Sep 8-9, 2014; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(16 Suppl):Abstract nr POSTER-THER-1421.

In vivo tumor growth of high-grade serous ovarian cancer cell lines

OBJECTIVE

Genomic studies of ovarian cancer (OC) cell lines frequently used in research revealed that these cells do not fully represent high-grade serous ovarian cancer (HGSOC), the most common OC histologic type. However, OC lines that appear to genomically resemble HGSOC have not been extensively used and their growth characteristics in murine xenografts are essentially unknown.

METHODS

To better understand growth patterns and characteristics of HGSOC cell lines in vivo, CAOV3, COV362, KURAMOCHI, NIH-OVCAR3, OVCAR4, OVCAR5, OVCAR8, OVSAHO, OVKATE, SNU119 and UWB1.289 cells were assessed for tumor formation in nude mice. Cells were injected intraperitoneally (i.p.) or subcutaneously (s.c.) in female athymic nude mice and allowed to grow (maximum of 90 days) and tumor formation was analyzed. All tumors were sectioned and assessed using H&E staining and immunohistochemistry for p53, PAX8 and WT1 expression.

RESULTS

Six lines (OVCAR3, OVCAR4, OVCAR5, OVCAR8, CAOV3, and OVSAHO) formed i.p xenografts with HGSOC histology. OVKATE and COV362 formed s.c. tumors only. Rapid tumor formation was observed for OVCAR3, OVCAR5 and OVCAR8, but only OVCAR8 reliably formed ascites. Tumors derived from OVCAR3, OVCAR4, and OVKATE displayed papillary features. Of the 11 lines examined, three (Kuramochi, SNU119 and UWB1.289) were non-tumorigenic.

CONCLUSIONS

Our findings help further define which HGSOC cell models reliably generate tumors and/or ascites, critical information for preclinical drug development, validating in vitro findings, imaging and prevention studies by the OC research community.

Stranded Whole Transcriptome RNA-Seq for All RNA Types

Stranded whole transcriptome RNA-Seq described in this unit captures quantitative expression data for all types of RNA including, but not limited to, miRNA (microRNA), piRNA (Piwi-interacting RNA), snoRNA (small nucleolar RNA), lincRNA (large non-coding intergenic RNA), SRP RNA (signal recognition particle RNA), tRNA (transfer RNA), mtRNA (mitochondrial RNA), and mRNA (messenger RNA). The size and nature of these types of RNA are irrelevant to the approach described here. Barcoded libraries for multiplexing on the Illumina platform are generated with this approach but it can be applied to other platforms with a few modifications.

Hypermethylation of the TGF-β target, ABCA1 is associated with poor prognosis in ovarian cancer patients

Background

The dysregulation of transforming growth factor-β (TGF-β) signaling plays a crucial role in ovarian carcinogenesis and in maintaining cancer stem cell properties. Classified as a member of the ATP-binding cassette (ABC) family, ABCA1 was previously identified by methylated DNA immunoprecipitation microarray (mDIP-Chip) to be methylated in ovarian cancer cell lines, A2780 and CP70. By microarray, it was also found to be upregulated in immortalized ovarian surface epithelial (IOSE) cells following TGF-β treatment. Thus, we hypothesized that ABCA1 may be involved in ovarian cancer and its initiation.

Results

We first compared the expression level of ABCA1 in IOSE cells and a panel of ovarian cancer cell lines and found that ABCA1 was expressed in HeyC2, SKOV3, MCP3, and MCP2 ovarian cancer cell lines but downregulated in A2780 and CP70 ovarian cancer cell lines. The reduced expression of ABCA1 in A2780 and CP70 cells was associated with promoter hypermethylation, as demonstrated by bisulfite pyro-sequencing. We also found that knockdown of ABCA1 increased the cholesterol level and promoted cell growth in vitro and in vivo. Further analysis of ABCA1 methylation in 76 ovarian cancer patient samples demonstrated that patients with higher ABCA1 methylation are associated with high stage (P = 0.0131) and grade (P = 0.0137). Kaplan-Meier analysis also found that patients with higher levels of methylation of ABCA1 have shorter overall survival (P = 0.019). Furthermore, tissue microarray using 55 ovarian cancer patient samples revealed that patients with a lower level of ABCA1 expression are associated with shorter progress-free survival (P = 0.038).

Conclusions

ABCA1 may be a tumor suppressor and is hypermethylated in a subset of ovarian cancer patients. Hypermethylation of ABCA1 is associated with poor prognosis in these patients.

Electronic supplementary material

The online version of this article (doi:10.1186/s13148-014-0036-2) contains supplementary material, which is available to authorized users.

Effects of the endocrine-disrupting chemical DDT on self-renewal and differentiation of human mesenchymal stem cells

BACKGROUND

Although the global use of the endocrine-disrupting chemical DDT has decreased, its persistence in the environment has resulted in continued human exposure. Accumulating evidence suggests that DDT exposure has long-term adverse effects on development, yet the impact on growth and differentiation of adult stem cells remains unclear.

OBJECTIVES

Human mesenchymal stem cells (MSCs) exposed to DDT were used to evaluate the impact on stem cell biology.

METHODS

We assessed DDT-treated MSCs for self-renewal, proliferation, and differentiation potential. Whole genome RNA sequencing was performed to assess gene expression in DDT-treated MSCs.

RESULTS

MSCs exposed to DDT formed fewer colonies, suggesting a reduction in self-renewal potential. DDT enhanced both adipogenic and osteogenic differentiation, which was confirmed by increased mRNA expression of glucose transporter type 4 (GLUT4), lipoprotein lipase (LpL), peroxisome proliferator-activated receptor gamma (PPARγ), leptin, osteonectin, core binding factor 1 (CBFA1), and FBJ murine osteosarcoma viral oncogene homolog (c-Fos). Expression of factors in DDT-treated cells was similar to that in estrogen-treated MSCs, suggesting that DDT may function via the estrogen receptor (ER)-mediated pathway. The coadministration of ICI 182,780 blocked the effects of DDT. RNA sequencing revealed 121 genes and noncoding RNAs to be differentially expressed in DDT-treated MSCs compared with controls cells.

CONCLUSION

Human MSCs provide a powerful biological system to investigate and identify the molecular mechanisms underlying the effects of environmental agents on stem cells and human health. MSCs exposed to DDT demonstrated profound alterations in self-renewal, proliferation, differentiation, and gene expression, which may partially explain the homeostatic imbalance and increased cancer incidence among those exposed to long-term EDCs.

A mathematical model of bimodal epigenetic control of miR-193a in ovarian cancer stem cells

Accumulating data indicate that cancer stem cells contribute to tumor chemoresistance and their persistence alters clinical outcome. Our previous study has shown that ovarian cancer may be initiated by ovarian cancer initiating cells (OCIC) characterized by surface antigen CD44 and c-KIT (CD117). It has been experimentally demonstrated that a microRNA, namely miR-193a, targets c-KIT mRNA for degradation and could play a crucial role in ovarian cancer development. How miR-193a is regulated is poorly understood and the emerging picture is complex. To unravel this complexity, we propose a mathematical model to explore how estrogen-mediated up-regulation of another target of miR-193a, namely E2F6, can attenuate the function of miR-193a in two ways, one through a competition of E2F6 and c-KIT transcripts for miR-193a, and second by binding of E2F6 protein, in association with a polycomb complex, to the promoter of miR-193a to down-regulate its transcription. Our model predicts that this bimodal control increases the expression of c-KIT and that the second mode of epigenetic regulation is required to generate a switching behavior in c-KIT and E2F6 expressions. Additional analysis of the TCGA ovarian cancer dataset demonstrates that ovarian cancer patients with low expression of EZH2, a polycomb-group family protein, show positive correlation between E2F6 and c-KIT. We conjecture that a simultaneous EZH2 inhibition and anti-estrogen therapy can constitute an effective combined therapeutic strategy against ovarian cancer.

Agonist and antagonist switch DNA motifs recognized by human androgen receptor in prostate cancer

Human transcription factors recognize specific DNA sequence motifs to regulate transcription. It is unknown whether a single transcription factor is able to bind to distinctly different motifs on chromatin, and if so, what determines the usage of specific motifs. By using a motif-resolution chromatin immunoprecipitation-exonuclease (ChIP-exo) approach, we find that agonist-liganded human androgen receptor (AR) and antagonist-liganded AR bind to two distinctly different motifs, leading to distinct transcriptional outcomes in prostate cancer cells. Further analysis on clinical prostate tissues reveals that the binding of AR to these two distinct motifs is involved in prostate carcinogenesis. Together, these results suggest that unique ligands may switch DNA motifs recognized by ligand-dependent transcription factors in vivo. Our findings also provide a broad mechanistic foundation for understanding ligand-specific induction of gene expression profiles.

TGF-β induces global changes in DNA methylation during the epithelial-to-mesenchymal transition in ovarian cancer cells

A key step in the process of metastasis is the epithelial-to-mesenchymal transition (EMT). We hypothesized that epigenetic mechanisms play a key role in EMT and to test this hypothesis we analyzed global and gene-specific changes in DNA methylation during TGF-β-induced EMT in ovarian cancer cells. Epigenetic profiling using the Infinium HumanMethylation450 BeadChip (HM450) revealed extensive (P < 0.01) methylation changes after TGF-β stimulation (468 and 390 CpG sites altered at 48 and 120 h post cytokine treatment, respectively). The majority of gene-specific TGF-β-induced methylation changes occurred in CpG islands located in or near promoters (193 and 494 genes hypermethylated at 48 and 120 h after TGF-β stimulation, respectively). Furthermore, methylation changes were sustained for the duration of TGF-β treatment and reversible after the cytokine removal. Pathway analysis of the hypermethylated loci identified functional networks strongly associated with EMT and cancer progression, including cellular movement, cell cycle, organ morphology, cellular development, and cell death and survival. Altered methylation and corresponding expression of specific genes during TGF-β-induced EMT included CDH1 (E-cadherin) and COL1A1 (collagen 1A1). Furthermore, TGF-β induced both expression and activity of DNA methyltransferases (DNMT) -1, -3A, and -3B, and treatment with the DNMT inhibitor SGI-110 prevented TGF-β-induced EMT. These results demonstrate that dynamic changes in the DNA methylome are implicated in TGF-β-induced EMT and metastasis. We suggest that targeting DNMTs may inhibit this process by reversing the EMT genes silenced by DNA methylation in cancer.

Elevated expression of long intergenic non-coding RNA HOTAIR in a basal-like variant of MCF-7 breast cancer cells

Epigenetic regulation of gene expression is critical to phenotypic maintenance and transition of human breast cancer cells. HOX antisense intergenic RNA (HOTAIR) is a long intergenic non-coding RNA that epigenetically represses gene expression via recruitment of enhancer of zeste homolog 2 (EZH2), a histone methyltransferase. Elevated expression of HOTAIR promotes progression of breast cancer. In the current study we examined the expression and function of HOTAIR in MCF-7-TNR cells, a derivative of the luminal-like breast cancer cell line MCF-7 that acquired resistance to TNF-α-induced cell death. The expression of HOTAIR, markers of the luminal-like and basal-like subtypes, and growth were compared between MCF-7 and MCF-7-TNR cells. These variables were further assessed upon inhibition of HOTAIR, EZH2, p38 MAPK, and SRC kinase in MCF-7-TNR cells. When compared with MCF-7 cells, MCF-7-TNR cells exhibited an increase in the expression of HOTAIR, which correlated with characteristics of a luminal-like to basal-like transition as evidenced by dysregulated gene expression and accelerated growth. MCF-7-TNR cells exhibited reduced suppressive histone H3 lysine27 trimethylation on the HOTAIR promoter. Inhibition of HOTAIR and EZH2 attenuated the luminal-like to basal-like transition in terms of gene expression and growth in MCF-7-TNR cells. Inhibition of p38 and SRC diminished HOTAIR expression and the basal-like phenotype in MCF-7-TNR cells. HOTAIR was robustly expressed in the native basal-like breast cancer cells and inhibition of HOTAIR reduced the basal-like gene expression and growth. Our findings suggest HOTAIR-mediated regulation of gene expression and growth associated with the basal-like phenotype of breast cancer cells.

Mg2+ effect on argonaute and RNA duplex by molecular dynamics and bioinformatics implications

RNA interference (RNAi), mediated by small non-coding RNAs (e.g., miRNAs, siRNAs), influences diverse cellular functions. Highly complementary miRNA-target RNA (or siRNA-target RNA) duplexes are recognized by an Argonaute family protein (Ago2), and recent observations indicate that the concentration of Mg²⁺ ions influences miRNA targeting of specific mRNAs, thereby modulating miRNA-mRNA networks. In the present report, we studied the thermodynamic effects of differential [Mg²⁺] on slicing (RNA silencing cycle) through molecular dynamics simulation analysis, and its subsequent statistical analysis. Those analyses revealed different structural conformations of the RNA duplex in Ago2, depending on Mg²⁺ concentration. We also demonstrate that cation effects on Ago2 structural flexibility are critical to its catalytic/functional activity, with low [Mg²⁺] favoring greater Ago2 flexibility (e.g., greater entropy) and less miRNA/mRNA duplex stability, thus favoring slicing. The latter finding was supported by a negative correlation between expression of an Mg²⁺ influx channel, TRPM7, and one miRNA’s (miR-378) ability to downregulate its mRNA target, TMEM245. These results imply that thermodynamics could be applied to siRNA-based therapeutic strategies, using highly complementary binding targets, because Ago2 is also involved in RNAi slicing by exogenous siRNAs. However, the efficacy of a siRNA-based approach will differ, to some extent, based on the Mg²⁺ concentration even within the same disease type; therefore, different siRNA-based approaches might be considered for patient-to-patient needs.

The novel, small-molecule DNA methylation inhibitor SGI-110 as an ovarian cancer chemosensitizer

PURPOSE

To investigate SGI-110 as a "chemosensitizer" in ovarian cancer and to assess its effects on tumor suppressor genes (TSG) and chemoresponsiveness-associated genes silenced by DNA methylation in ovarian cancer.

EXPERIMENTAL DESIGN

Several ovarian cancer cell lines were used for in vitro and in vivo platinum resensitization studies. Changes in DNA methylation and expression levels of TSG and other cancer-related genes in response to SGI-110 were measured by pyrosequencing and RT-PCR.

RESULTS

We demonstrate in vitro that SGI-110 resensitized a range of platinum-resistant ovarian cancer cells to cisplatin (CDDP) and induced significant demethylation and reexpression of TSG, differentiation-associated genes, and putative drivers of ovarian cancer cisplatin resistance. In vivo, SGI-110 alone or in combination with CDDP was well tolerated and induced antitumor effects in ovarian cancer xenografts. Pyrosequencing analyses confirmed that SGI-110 caused both global (LINE1) and gene-specific hypomethylation in vivo, including TSGs (RASSF1A), proposed drivers of ovarian cancer cisplatin resistance (MLH1 and ZIC1), differentiation-associated genes (HOXA10 and HOXA11), and transcription factors (STAT5B). Furthermore, DNA damage induced by CDDP in ovarian cancer cells was increased by SGI-110, as measured by inductively coupled plasma-mass spectrometry analysis of DNA adduct formation and repair of cisplatin-induced DNA damage.

CONCLUSIONS

These results strongly support further investigation of hypomethylating strategies in platinum-resistant ovarian cancer. Specifically, SGI-110 in combination with conventional and/or targeted therapeutics warrants further development in this setting.