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Aggressive tumors of epithelial origin shed cells that intravasate and become circulating tumor cells (CTC). The CTCs that are able to survive the stresses encountered in the bloodstream can then seed metastases. We demonstrated previously that CTCs isolated from the blood of prostate cancer patients display specific nanomechanical phenotypes characteristic of cell endurance and invasiveness and patient sensitivity to androgen deprivation therapy. Here we report that patient-isolated CTCs are nanomechanically distinct from cells randomly shed from the tumor, with high adhesion as the most distinguishing biophysical marker. CTCs uniquely coisolated with macrophage-like cells bearing the markers of tumor-associated macrophages (TAM). The presence of these immune cells was indicative of a survival-promoting phenotype of “mechanical fitness” in CTCs based on high softness and high adhesion as determined by atomic force microscopy. Correlations between enumeration of macrophages and mechanical fitness of CTCs were strong in patients before the start of hormonal therapy. Single-cell proteomic analysis and nanomechanical phenotyping of tumor cell–macrophage cocultures revealed that macrophages promoted epithelial–mesenchymal plasticity in prostate cancer cells, manifesting in their mechanical fitness. The resulting softness and adhesiveness of the mechanically fit CTCs confer resistance to shear stress and enable protective cell clustering. These findings suggest that selected tumor cells are coached by TAMs and accompanied by them to acquire intermediate epithelial/mesenchymal status, thereby facilitating survival during the critical early stage leading to metastasis. Significance: The interaction between macrophages and circulating tumor cells increases the capacity of tumor cells to initiate metastasis and may constitute a new set of blood-based targets for pharmacologic intervention.

Emerging evidence indicates that adipose stromal cells (ASC) are recruited to enhance cancer development. In this study, we examined the role these adipocyte progenitors play relating to intercellular communication in obesity-associated endometrial cancer. This is particularly relevant given that gap junctions have been implicated in tumor suppression. Examining the effects of ASCs on the transcriptome of endometrial epithelial cells (EEC) in an in vitro coculture system revealed transcriptional repression of GJA1 (encoding the gap junction protein Cx43) and other genes related to intercellular communication. This repression was recapitulated in an obesity mouse model of endometrial cancer. Furthermore, inhibition of plasminogen activator inhibitor 1 (PAI-1), which was the most abundant ASC adipokine, led to reversal of cellular distribution associated with the GJA1 repression profile, suggesting that PAI-1 may mediate actions of ASC on transcriptional regulation in EEC. In an endometrial cancer cohort (n = 141), DNA hypermethylation of GJA1 and related loci TJP2 and PRKCA was observed in primary endometrial endometrioid tumors and was associated with obesity. Pharmacologic reversal of DNA methylation enhanced gap-junction intercellular communication and cell–cell interactions in vitro. Restoring Cx43 expression in endometrial cancer cells reduced cellular migration; conversely, depletion of Cx43 increased cell migration in immortalized normal EEC. Our data suggest that persistent repression by ASC adipokines leads to promoter hypermethylation of GJA1 and related genes in the endometrium, triggering long-term silencing of these loci in endometrial tumors of obese patients. Significance: Studies reveal that adipose-derived stem cells in endometrial cancer pathogenesis influence epigenetic repression of gap junction loci, which suggests targeting of gap junction activity as a preventive strategy for obesity-associated endometrial cancer.

Increasing evidence suggests the presence of minor cell subpopulations in prostate cancer that are androgen independent and poised for selection as dominant clones after androgen deprivation therapy. In this study, we investigated this phenomenon by stratifying cell subpopulations based on transcriptome profiling of 144 single LNCaP prostate cancer cells treated or untreated with androgen after cell-cycle synchronization. Model-based clustering of 397 differentially expressed genes identified eight potential subpopulations of LNCaP cells, revealing a previously unappreciable level of cellular heterogeneity to androgen stimulation. One subpopulation displayed stem-like features with a slower cell doubling rate, increased sphere formation capability, and resistance to G2–M arrest induced by a mitosis inhibitor. Advanced growth of this subpopulation was associated with enhanced expression of 10 cell-cycle–related genes (CCNB2, DLGAP5, CENPF, CENPE, MKI67, PTTG1, CDC20, PLK1, HMMR, and CCNB1) and decreased dependence upon androgen receptor signaling. In silico analysis of RNA-seq data from The Cancer Genome Atlas further demonstrated that concordant upregulation of these genes was linked to recurrent prostate cancers. Analysis of receiver operating characteristic curves implicates aberrant expression of these genes and could be useful for early identification of tumors that subsequently develop biochemical recurrence. Moreover, this single-cell approach provides a better understanding of how prostate cancer cells respond heterogeneously to androgen deprivation therapies and reveals characteristics of subpopulations resistant to this treatment. Significance: Illustrating the challenge in treating cancers with targeted drugs, which by selecting for drug resistance can drive metastatic progression, this study characterized the plasticity and heterogeneity of prostate cancer cells with regard to androgen dependence, defining the character or minor subpopulations of androgen-independent cells that are poised for clonal selection after androgen-deprivation therapy. Cancer Res; 78(4); 853–64. ©2017 AACR.

Emerging evidence indicates that adipose stromal cells (ASC) are recruited to enhance cancer development. In this study, we examined the role these adipocyte progenitors play relating to intercellular communication in obesity-associated endometrial cancer. This is particularly relevant given that gap junctions have been implicated in tumor suppression. Examining the effects of ASCs on the transcriptome of endometrial epithelial cells (EEC) in an in vitro co-culture system revealed transcriptional repression of GJA1 (encoding the gap junction protein Cx43) and other genes related to intercellular communication. This repression was recapitulated in an obesity mouse model of endometrial cancer. Furthermore, inhibition of plasminogen activator inhibitor 1 (PAI-1), which was the most abundant ASC adipokine, led to reversal of cellular distribution associated with the GJA1 repression profile, suggesting that PAI-1 may mediate actions of ASC on transcriptional regulation in EEC. In an endometrial cancer cohort (n=141), DNA hypermethylation of GJA1 and related loci TJP2 and PRKCA was observed in primary endometrial endometrioid tumors and was associated with obesity. Pharmacologic reversal of DNA methylation enhanced gap junction intercellular communication and cell-cell interactions in vitro. Restoring Cx43 expression in endometrial cancer cells reduced cellular migration; conversely, depletion of Cx43 increased cell migration in immortalized normal EEC. Our data suggest that persistent repression by ASC adipokines leads to promoter hypermethylation of GJA1 and related genes in the endometrium, triggering long-term silencing of these loci in endometrial tumors of obese patients.

Purpose: Little is known about adaptive selection of tumor cells transiting from in situ proliferation to distant colonization through blood circulation. This study used genomic, transcriptomic, and biophysical analyses at single-cell levels to explore biological and physical properties of circulating tumor cells (CTCs) undergoing hemodynamic stress. The aims are trying to understand how CTCs strive to survive in the bloodstream and to develop strategies for therapeutic intervention. Experimental Design: We compared genomic profiles of CTCs in blood and primary tumor cells shed in urine of prostate cancer patients to identify amplified regions preferentially retained in CTCs. Single-cell RNA-seq was used to confirm amplification-associated overexpression of genes in CTCs. Results: Among 261 recurrently amplified genomic regions in the analysis, 70 were found predominantly shown in CTCs relative to primary tumor cells. In line with the results at the genomic level, the transcriptomic data of CTCs demonstrate a great amount of cells showing high expression levels in the oxidative phosphorylation (OXPHOS) pathway compared to other hallmark gene sets. The finding suggests that tumor cells with these pre-existing genomic alterations were adaptively selected for transcription reprogramming during blood circulation. Specifically, amplified genes associated with OXPHOS were exploited by CTCs for alternative fuels. As to the upstream of this transcription event, we found the expression of MEN1, encoding menin known to form a transcription factor complex with the mixed-lineage leukemia protein (MLL) in prostate cancer cells, was positively correlated with 11 of the 14 OXPHOS loci in the Cancer Genomic Atlas prostate cancer cohort. In vitro assay showed that MEN1 knockdown by shRNA resulted in attenuation of both mRNA and protein expression of OXPHOS loci in PC-3 cells. Taken together pre-existing amplification of OXPHOS loci can be used as a transcription apparatus by menin for metabolic reprogramming of tumor cells in response to harsh microenvironments in the bloodstream. Conclusions: Single-cell profiling identified signaling pathways that are crucial for CTCs to survive in the bloodstream. The finding suggests that a metabolic shift from Warburg to OXPHOS metabolism can be associated with a hybrid mesenchymal-epithelial phenotype of CTCs. Moreover, the study demonstrates the feasibility of routinely conducting single-cell analysis of exfoliated tumor cells for minimally invasive monitoring of disease progression and treatment response in prostate cancer patients Citation Format: Chun-Lin Lin, Tan Xi, Chia-Nung Hung, Pawel A. Osmulski, Chih-Wei Chou, Meizhen Chen, Chiou-Miin Wang, Kohzoh Mitsuya, Nameer Kirma, Maria E. Gaczynska, Chun-Liang Chen, Tim H.-M. Huang. Amplification-associated upregulation of genes involved in oxidative phosphorylation for disseminated prostate cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2766.

Dysregulated dynamics and trafficking of receptor tyrosine kinases (RTK) have been linked to oncogenesis and metastasis. The mechanisms for disfunction of RTK dynamics are emerging and still not clear. Using single-particle tracking (SPT) techniques, we studied the dynamics and trafficking patterns of epidermal growth factor receptor (EGFR) and underlying mechanisms using prostate cancer cells (PCa) (LNCaP, DU145 and PC3) exhibiting variant metastatic capability. Through SPT and super-resolution imaging, it was revealed that cortical actin disorganization modulates increased dynamics of EGFRs, including high EGFR diffusivity, enlarged EGFR confinement size on the plasma membrane and faster EGFR internalization in advanced invasive cells. The elevated EGFR dynamics were associated with advanced aggressive behaviors, and highly upregulated EGFR, EPHB and SRC signaling as identified using single cell RNA-seq. Strong EGFR activation with relatively low EGFR expression in PC3 implicated some other mechanisms, likely biophysical, beyond EGFR quantity. Moreover, the upregulated EPHB and SRC pathways have been shown to regulate actin organization and metastasis and our in silico analysis indicated that genes in the two pathways predict poor prognosis for disease free and survival statuses in The Cancer Genome Atlas prostate cancer patient cohort. To interrogate the roles of EPHB and SRC pathways in actin organization and EGFR dynamics, a series of drug inhibitions and siRNA knockdown were applied to PCa cells followed by mRNA profiling, evaluations of EGFR dynamics, and cell behaviors. Functional knockdown of EPHB2 and SRC led to decreased EGFR dynamics, cell proliferation, migration and invasion. The loss-of-function effects were more profound in advanced invasive PCa. In this study, we discovered the roles of EPHB and SRC pathways in modulating actin organization and EGFR dynamics and leading to aggressive metastatic phenotypes. Additionally, EGFR dynamics were potential biophysical parameters to differentiate the highly-invasive from the non- and less-invasive PCa. Thus, we believe that the SPT-based EGFR dynamics can serve as a new biophysical assay to probe the metastatic malignancy of cancer cells and to monitor their response to anti-cancer drug treatment. Citation Format: Yen-Liang Liu, Aaron M. Horning, Che-Kuang Lin, Brandon Lieberman, Chia-Nung Hung, Chih-Wei Chou, Chiou-Miin Wang, Michael A. Liss, Mirae Kim, Rohan Vasisht, Evan P. Perillo, Katherine Blocher, Hannah Horng, Xi Tian, Chun-Lin Lin, Andrew K. Dunn, Tim H.-M. Huang, Hsin-Chih Yeh, Chun-Liang Chen. Upregulated EPHB2 and SRC pathways modulate spatial EGFR dynamics and malignant phenotypes and predict poor prognosis in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 173.

Background: Non-small cell lung cancer (NSCLC) is a molecularly heterogeneous disease with a high propensity for drug resistance and metastasis. AXL, a member of the Tyro3-AXL-Mer family of receptor tyrosine kinases, is a central regulator of epithelial-to-mesenchymal transition (EMT) and enables tumor cells to invade and acquire drug resistance. AXL is overexpressed in lung tumors, correlates positively with tumor invasion, drug resistance, and negatively predicts overall survival. We mechanistically interrogate the effects of AXL inhibitor TP-0903 on EMT in lung adenocarcinoma cells using transcriptomic and proteomic profiling. Methods: Atomic force microscopy, Western blot analysis, RNA sequencing and mass cytometry (CyTOF) were all used to scrutinize the biomechanical properties, phenotypic, transcriptomic and proteomic profiles of A549 cells treated with 40nM TP0903 or shAXL knockdown. Results: TP-0903 attenuates total AXL/AXL phosphorylation and blunts transcriptional responses to TGFβ-Hippo signaling by disrupting the transcriptional complexes formed by SMAD2/3, SMAD4, YAP1 and TAZ. AXL knockdown or TP-0903 reverses EMT phenotype and reduces migration potential in A549 and H2009 adenocarcinoma cell lines. CyTOF data also identified resistant clones that overexpress TGFβ receptor II, TAZ protein and display hybrid EMT phenotypes. Conclusions: We are the first to report the interplay between AXL and TGFβ-Hippo signaling axis. TP-0903 study agent has excellent therapeutic promise in NSCLC and we speculate that TP-0903 drug can target epithelial to mesenchymal transitional states in lung cancer cells possibly through the inhibition of the AXL-TGFβ-Hippo signaling axis. Citation Format: Josephine Amalia Taverna, Chia-Nung Hung, Chun-Lin Lin, Pawel Osmulski, Meizhen Chen, Chiou-Miin Wang, Nicholas L. L. Lucio, Nameer Kirma, Chih-Wei Chou, Maria E. Gaczynska, Alia Nazarullah, Mark Wade, Lars Mouritsen, Tim Huang. AXL inhibitor TP-0903 attenuates AXL-TGFbeta Hippo signaling axis in lung adenocarcinoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2193.

Endometrial cancer is the most common gynecologic cancer. It is divided into two major types, a less aggressive endometrioid type and a more aggressive serous type. Recent clinical observations underscore obesity as a major risk factor for endometrial cancer. In this study, we hypothesized that obesity can result in long term epigenetic modifications in the endometrial compartment, leading to the promotion of endometrial cancer. We examined the role of adipose-derived stem cells (ASCs), which are adipocyte progenitors, in the endometrial tumor microenvironment. By staining for ASCs in a tumor tissue microarray, we observed ASC infiltration that was specific to samples from obese patients, correlating with body mass index (R2=0.77, p Citation Format: Li-Ling Lin, Srikanth Polusani, Guangcun Huang, Chun-Lin Lin, Chiou-Miin Wang, Nicholas Lucio, Mikhail Kolonin, Alexes Daquinag, Pawel Osmulski, Bruce Nicholson, Edward Kost, Tim Huang, Nameer B. Kirma. Adipose-derived stem cell disruption of gap junction intercellular communication in obesity-associated endometrial cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5150.

Overexpression of epithelial cell adhesion molecule (EpCAM) has been implicated in advanced endometrial cancer, but its roles in this progression remain to be elucidated. In addition to its structural role in modulating cell-surface adhesion, here we demonstrate that EpCAM is a regulatory molecule in which its internalization into the nucleus turns on a transcription program. Activation of EGF/EGFR signal transduction triggered cell-surface cleavage of EpCAM, leading to nuclear internalization of its cytoplasmic domain EpICD. ChIP-seq analysis identified target genes that are coregulated by EpICD and its transcription partner, LEF-1. Network enrichment analysis further uncovered a group of 105 genes encoding functions for tight junction, adherent, and cell migration. Furthermore, nanomechanical analysis by atomic force microscopy revealed increased softness and decreased adhesiveness of EGF-stimulated cancer cells, implicating acquisition of an epithelial–mesenchymal transition (EMT) phenotype. Thus, genome editing of EpCAM could be associated with altering these nanomechanical properties towards a less aggressive phenotype. Using this integrative genomic–biophysical approach, we demonstrate for the first time an intricate relationship between EpCAM-regulated transcription and altered biophysical properties of cells that promote EMT in advanced endometrial cancer. Cancer Res; 76(21); 6171–82. ©2016 AACR.

Fatty acid synthase (FASN) is overexpressed in numerous tumor types, including breast carcinomas, and promotes changes in the genetic program controlling lipid biosynthesis. While inhibiting FASN appears to be an attractive therapeutic approach under development, the success of this approach may depend on the identification of tumor subtypes with specific metabolic requirements. Applying a comprehensive profile of circulating tumor cells (CTC) using canonical pathway gene sets, we identified a correlation of metabolic subtypes with breast tumor subtype. A lipogenic subtype is strongly associated with Luminal A subtype, whereas the glycolytic subtype associated with Luminal B tumors. The triple negative subtype was more heterogeneous and had the expression of both sets of gene. Such a difference in the metabolic profile may dictate differential sensitivity to inhibitors targeting de novo lipid synthesis, including FASN. This was supported by in vitro studies using selective FASN inhibitor, TVB-3166. Exposure to TVB-3166 over 14 days incubation in Advanced MEM with 1% charcoal-stripped FBS selectively inhibited growth and viability of Luminal A breast cancer cells, but had no effect on Luminal B subtype. This was further confirmed in short-term patient derived cultures. Mechanistic studies suggest that TVB-3166 quickly disrupts FA synthesis leading to the disruption of the lipid raft architecture and tumor cell death through an apoptotic mechanism. In conclusion, our findings highlight that success of targeting cancer metabolism directly may depend on identification of tumor subtypes with specific metabolic requirements. Citation Format: Gruslova AB, Chen C-L, Wang C-M, Elledge RM, Kaklamani VG, Lathrop K, Huang TH, Brenner A. FASN inhibition by TVB-3166 associates with breast cancer subtype [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-02-02.

Preclinical studies have shown that hypomethylating agents reverse platinum resistance in ovarian cancer. In this phase II clinical trial, based upon the results of our phase I dose defining study, we tested the clinical and biologic activity of low-dose decitabine administered before carboplatin in platinum-resistant ovarian cancer patients. Among 17 patients with heavily pretreated and platinum-resistant ovarian cancer, the regimen induced a 35% objective response rate (RR) and progression-free survival (PFS) of 10.2 months, with nine patients (53%) free of progression at 6 months. Global and gene-specific DNA demethylation was achieved in peripheral blood mononuclear cells and tumors. The number of demethylated genes was greater (P < 0.05) in tumor biopsies from patients with PFS more than 6 versus less than 6 months (311 vs. 244 genes). Pathways enriched at baseline in tumors from patients with PFS more than 6 months included cytokine–cytokine receptor interactions, drug transporters, and mitogen-activated protein kinase, toll-like receptor and Jak-STAT signaling pathways, whereas those enriched in demethylated genes after decitabine treatment included pathways involved in cancer, Wnt signaling, and apoptosis (P < 0.01). Demethylation of MLH1, RASSF1A, HOXA10, and HOXA11 in tumors positively correlated with PFS (P < 0.05). Together, the results of this study suggest that low-dose decitabine altered DNA methylation of genes and cancer pathways, restoring sensitivity to carboplatin in patients with heavily pretreated ovarian cancer and resulting in a high RR and prolonged PFS. Cancer Res; 72(9); 2197–205. ©2012 AACR.

Enhancer of zeste homolog 2 (EZH2) is the catalytic subunit of the Polycomb-repressive complex 2 (PRC2) that represses gene transcription through histone H3 lysine 27 trimethylation (H3K27me3). Although EZH2 is abundantly present in various cancers, the molecular consequences leading to oncogenesis remain unclear. Here, we show that EZH2 concordantly silences the Wnt pathway antagonists operating at several subcellular compartments, which in turn activate Wnt/β-catenin signaling in hepatocellular carcinomas (HCC). Chromatin immunoprecipitation promoter array and gene expression analyses in HCCs revealed EZH2 occupancy and reduced expression of Wnt antagonists, including the growth-suppressive AXIN2, NKD1, PPP2R2B, PRICKLE1, and SFRP5. Knockdown of EZH2 reduced the promoter occupancy of PRC2, histone deacetylase 1 (HDAC1), and H3K27me3, whereas the activating histone marks were increased, leading to the transcriptional upregulation of the Wnt antagonists. Combinatorial EZH2 and HDAC inhibition dramatically reduced the levels of nuclear β-catenin, T-cell factor–dependent transcriptional activity, and downstream pro-proliferative targets CCND1 and EGFR. Functional analysis revealed that downregulation of EZH2 reduced HCC cell growth, partially through the inhibition of β-catenin signaling. Conversely, ectopic overexpression of EZH2 in immortalized hepatocytes activated Wnt/β-catenin signaling to promote cellular proliferation. In human HCCs, concomitant overexpression of EZH2 and β-catenin was observed in one-third (61/179) of cases and significantly correlated with tumor progression. Our data indicate that EZH2-mediated epigenetic silencing contributes to constitutive activation of Wnt/β-catenin signaling and consequential proliferation of HCC cells, thus representing a novel therapeutic target for this highly malignant tumor. Cancer Res; 71(11); 4028–39. ©2011 AACR.

Trimethylation of histone 3 lysine 27 (H3K27me3) is a critical epigenetic mark for the maintenance of gene silencing. Additional accumulation of DNA methylation in target loci is thought to cooperatively support this epigenetic silencing during tumorigenesis. However, molecular mechanisms underlying the complex interplay between the two marks remain to be explored. Here we show that activation of PI3K/AKT signaling can be a trigger of this epigenetic processing at many downstream target genes. We also find that DNA methylation can be acquired at the same loci in cancer cells, thereby reinforcing permanent repression in those losing the H3K27me3 mark. Because of a link between PI3K/AKT signaling and epigenetic alterations, we conducted epigenetic therapies in conjunction with the signaling-targeted treatment. These combined treatments synergistically relieve gene silencing and suppress cancer cell growth in vitro and in xenografts. The new finding has important implications for improving targeted cancer therapies in the future. Cancer Res; 71(5); 1752–62. ©2011 AACR.

Fatal metastatic castration-resistant prostate cancer (mCRPC) remains without sensitive early detection biomarkers and effective therapeutic targets. Among 2.5 millions of prostate cancer patients, the majority will face a dilemma, to treat or not to treat, at a point as cancer progresses. Biomarkers for mRCPC at an early stage represent an unmet need. With early identification, clinicians could design new treatment strategies to reduce metastasis-related morbidity and to extend survival of patients. In this study, we deployed single-cell RNA-seq on prostate cancer cells (LNCaP, ABL and PC3) to determine the transcriptome in androgen independency and castration resistance of prostate cancer. We identified potential 336 androgen-independence specific genes and 2396 castration resistance specific genes in ABL and PC3 cells respectively, while only 136 genes were shared in both cells. These genes, mostly upregulated were enriched in 43 and 166 signaling pathways that implicated the complexity of the castration resistance transcriptomic systems and networks. The signaling pathways are involved in advanced and metastatic malignancies including WNT, TGFB, ITGA/B, STAT, EPH, focal adhesion, adherens junction, regulation of actin cytoskeleton, gap junction, tight junction and EMT. Malignant potencies of ~ 40 pathways were validated by in silico analysis of the RNA-seq data from the prostate cancer cohort of The Cancer Genomic Atlas (TCGA) using Kaplan-Meier disease free and survival curve analyses. The transcriptomic regulation of these genes was further validated and correlated with ATAC-seq data. In order to further verify the functions of those signaling pathways in castration resistance, 9 major signaling pathways were evaluated using small molecule inhibitors. Castration resistant prostate cancer cells showed significant defective cell proliferation, migration, invasion and sphere formation in the presence of inhibitors, whereas LNCaP and ABL cells displayed limited or non-significant changes. Interestingly, 4 small molecule inhibitors showed significant suppression on the growth of stem-like circulating tumor cells that were derived from clinical blood samples of prostate cancer patients. Our data suggest that those castration resistance specific genes and signaling pathways revealed by single-cell RNA-seq may serve as potential markers and therapeutic targets. Citation Format: Aaron M. Horning, Che-Kuang Lin, Yao Wang, Brandon Lieberman, Devalingam Mahalingam, Ming Gao, Pei Wang, Chiou-Miin Wang, Zhijie Liu, Jianhua Ruan, Michael A. Liss, Victor X. Jin, Tim H-M Huang, Chun-Liang Chen. Castration resistance transcriptome in prostate cancer revealed by single-cell RNA-seq [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3402.

Genetic amplification, mutation, and translocation are known to play a causal role in the upregulation of an oncogene in cancer cells. Here, we report an emerging role of microRNA, the epigenetic deregulation of which may also lead to this oncogenic activation. SOX4, an oncogene belonging to the SRY-related high mobility group box family, was found to be overexpressed (P < 0.005) in endometrial tumors (n = 74) compared with uninvolved controls (n = 20). This gene is computationally predicted to be the target of a microRNA, miR-129-2. When compared with the matched endometria, the expression of miR-129-2 was lost in 27 of 31 primary endometrial tumors that also showed a concomitant gain of SOX4 expression (P < 0.001). This inverse relationship is associated with hypermethylation of the miR-129-2 CpG island, which was observed in endometrial cancer cell lines (n = 6) and 68% of 117 endometrioid endometrial tumors analyzed. Reactivation of miR-129-2 in cancer cells by pharmacologic induction of histone acetylation and DNA demethylation resulted in decreased SOX4 expression. In addition, restoration of miR-129-2 by cell transfection led to decreased SOX4 expression and reduced proliferation of cancer cells. Further analysis found a significant correlation of hypermethylated miR-129-2 with microsatellite instability and MLH1 methylation status (P < 0.001) and poor overall survival (P < 0.039) in patients. Therefore, these results imply that the aberrant expression of SOX4 is, in part, caused by epigenetic repression of miR-129-2 in endometrial cancer. Unlike the notion that promoter hypomethylation may upregulate an oncogene, we present a new paradigm in which hypermethylation-mediated silencing of a microRNA derepresses its oncogenic target in cancer cells. [Cancer Res 2009;69(23):9038–46]

Early exposure to xenoestrogens may predispose to breast cancer risk later in adult life. It is likely that long-lived, self-regenerating epithelial progenitor cells are more susceptible to these exposure injuries over time and transmit the injured memory through epigenetic mechanisms to their differentiated progeny. Here, we used progenitor-containing mammospheres as an in vitro exposure model to study this epigenetic effect. Expression profiling identified that, relative to control cells, 9.1% of microRNAs (82 of 898 loci) were altered in epithelial progeny derived from mammospheres exposed to a synthetic estrogen, diethylstilbestrol. Repressive chromatin marks, trimethyl Lys27 of histone H3 (H3K27me3) and dimethyl Lys9 of histone H3 (H3K9me2), were found at a down-regulated locus, miR-9-3, in epithelial cells preexposed to diethylstilbestrol. This was accompanied by recruitment of DNA methyltransferase 1 that caused an aberrant increase in DNA methylation of its promoter CpG island in mammosphere-derived epithelial cells on diethylstilbestrol preexposure. Functional analyses suggest that miR-9-3 plays a role in the p53-related apoptotic pathway. Epigenetic silencing of this gene, therefore, reduces this cellular function and promotes the proliferation of breast cancer cells. Promoter hypermethylation of this microRNA may be a hallmark for early breast cancer development, and restoration of its expression by epigenetic and microRNA-based therapies is another viable option for future treatment of this disease. [Cancer Res 2009;69(14):5936–45]

Common sites of breast cancer metastasis include the lung, liver, and bone, and of these secondary metastatic sites, estrogen receptor α (ERα)–positive breast cancer often favors bone. Within secondary organs, cancer cells would predictably encounter tissue-specific fibroblasts or their soluble factors, yet our understanding of how tissue-specific fibroblasts directly affect cancer cell growth rates and survival remains largely unknown. Therefore, we tested the hypothesis that mesenchymal fibroblasts isolated from common sites of breast cancer metastasis provide a more favorable microenvironment with respect to tumor growth rates. We found a direct correlation between the ability of breast, lung, and bone fibroblasts to enhance ERα-positive breast cancer cell growth and the level of soluble interleukin-6 (IL-6) produced by each organ-specific fibroblast, and fibroblast-mediated growth enhancement was inhibited by the removal or inhibition of IL-6. Interestingly, mice coinjected with MCF-7 breast tumor cells and senescent skin fibroblasts, which secrete IL-6, developed tumors, whereas mice coinjected with presenescent skin fibroblasts that produce little to no IL-6 failed to form xenograft tumors. We subsequently determined that IL-6 promoted growth and invasion of breast cancer cells through signal transducer and activator of transcription 3–dependent up-regulation of Notch-3, Jagged-1, and carbonic anhydrase IX. These data suggest that tissue-specific fibroblasts and the factors they produce can promote breast cancer disease progression and may represent attractive targets for development of new therapeutics. [Cancer Res 2008;68(21):9087–95]

The objective of this study was to identify and characterize a self-renewing subpopulation of human ovarian tumor cells (ovarian cancer-initiating cells, OCICs) fully capable of serial propagation of their original tumor phenotype in animals. Ovarian serous adenocarcinomas were disaggregated and subjected to growth conditions selective for self-renewing, nonadherent spheroids previously shown to derive from tissue stem cells. To affirm the existence of OCICs, xenoengraftment of as few as 100 dissociated spheroid cells allowed full recapitulation of the original tumor (grade 2/grade 3 serous adenocarcinoma), whereas >105 unselected cells remained nontumorigenic. Stemness properties of OCICs (under stem cell–selective conditions) were further established by cell proliferation assays and reverse transcription–PCR, demonstrating enhanced chemoresistance to the ovarian cancer chemotherapeutics cisplatin or paclitaxel and up-regulation of stem cell markers (Bmi-1, stem cell factor, Notch-1, Nanog, nestin, ABCG2, and Oct-4) compared with parental tumor cells or OCICs under differentiating conditions. To identify an OCIC cell surface phenotype, spheroid immunostaining showed significant up-regulation of the hyaluronate receptor CD44 and stem cell factor receptor CD117 (c-kit), a tyrosine kinase oncoprotein. Similar to sphere-forming OCICs, injection of only 100 CD44+CD117+ cells could also serially propagate their original tumors, whereas 105 CD44−CD117− cells remained nontumorigenic. Based on these findings, we assert that epithelial ovarian cancers derive from a subpopulation of CD44+CD117+ cells, thus representing a possible therapeutic target for this devastating disease. [Cancer Res 2008;68(11):4311–20]

Estrogen imprinting is used to describe a phenomenon in which early developmental exposure to endocrine disruptors increases breast cancer risk later in adult life. We propose that long-lived, self-regenerating stem and progenitor cells are more susceptible to the exposure injury than terminally differentiated epithelial cells in the breast duct. Mammospheres, containing enriched breast progenitors, were used as an exposure system to simulate this imprinting phenomenon in vitro. Using MeDIP-chip, a methylation microarray screening method, we found that 0.5% (120 loci) of human CpG islands were hypermethylated in epithelial cells derived from estrogen-exposed progenitors compared with the non–estrogen-exposed control cells. This epigenetic event may lead to progressive silencing of tumor suppressor genes, including RUNX3, in these epithelial cells, which also occurred in primary breast tumors. Furthermore, normal tissue in close proximity to the tumor site also displayed RUNX3 hypermethylation, suggesting that this aberrant event occurs in early breast carcinogenesis. The high prevalence of estrogen-induced epigenetic changes in primary tumors and the surrounding histologically normal tissues provides the first empirical link between estrogen injury of breast stem/progenitor cells and carcinogenesis. This finding also offers a mechanistic explanation as to why a tumor suppressor gene, such as RUNX3, can be heritably silenced by epigenetic mechanisms in breast cancer. [Cancer Res 2008;68(6):1786–96]

Histone modifications and DNA methylation are epigenetic phenomena that play a critical role in many neoplastic processes, including silencing of tumor suppressor genes. One such histone modification, particularly at H3 and H4, is methylation at specific lysine (K) residues. Whereas histone methylation of H3-K9 has been linked to DNA methylation and aberrant gene silencing in cancer cells, no such studies of H3-K27 have been reported. Here, we generated a stable cell line overexpressing a dominant-negative point mutant, H3-K27R, to examine the role of that specific lysine in ovarian cancer. Expression of this construct resulted in loss of methylation at H3-K27, global reduction of DNA methylation, and increased expression of tumor suppressor genes. One of the affected genes, RASSF1, was shown to be a direct target of H3-K27 methylation–mediated silencing. By increasing DNA-platinum adduct formation, indicating increased access of the drug to target DNA sequences, removal of H3-K27 methylation resensitized drug-resistant ovarian cancer cells to the chemotherapeutic agent cisplatin. This increased platinum-DNA access was likely due to relaxation of condensed chromatin. Our results show that overexpression of mutant H3-K27 in mammalian cells represents a novel tool for studying epigenetic mechanisms and the Histone Code Hypothesis in human cancer. Such findings show the significance of H3-K27 methylation as a promising target for epigenetic-based cancer therapies. (Cancer Res 2006; 66(11): 5582-91)

Alterations in histones, chromatin-related proteins, and DNA methylation contribute to transcriptional silencing in cancer, but the sequence of these molecular events is not well understood. Here we demonstrate that on disruption of estrogen receptor (ER) α signaling by small interfering RNA, polycomb repressors and histone deacetylases are recruited to initiate stable repression of the progesterone receptor (PR) gene, a known ERα target, in breast cancer cells. The event is accompanied by acquired DNA methylation of the PR promoter, leaving a stable mark that can be inherited by cancer cell progeny. Reestablishing ERα signaling alone was not sufficient to reactivate the PR gene; reactivation of the PR gene also requires DNA demethylation. Methylation microarray analysis further showed that progressive DNA methylation occurs in multiple ERα targets in breast cancer genomes. The results imply, for the first time, the significance of epigenetic regulation on ERα target genes, providing new direction for research in this classical signaling pathway.

Total osteopontin (OPN) is overexpressed in endometrium carcinoma (EC) and modifications at TP53 and PTEN genes correspond to major genetic alterations in these tumors. Althought total OPN expression has been correlated to p53 and PTEN expression, no data is available regarding OPN splice variants and their association to p53 and PTEN isoforms expression. OPN has three splicing isoforms (OPN-SI), named OPNa, OPNb and OPNc, while p53 has at least 12 variants, such as p53 (full lenght), p53β, p53γ, Δ40p53, Δ133p53 and Δ160p53. Moreover, PTEN splicing isoforms (PTEN-SI) are named vs-fl (full lenght variant), vs-3a-3c, vs-5a-5d, and vs-D6. We aimed to evaluate the expression profile of OPN, p53 and PTEN isoforms as a first approach to establish their presumptive associations and functional interactions in endometrial tumoral and non tumoral cells. Total RNA has been extracted from endometrial non-tumoral (E6/E7 and EM42) and tumoral (Ishikawa, RL95-2, AN3CA and KLE) cell lines, followed by cDNA synthesis. Transcriptional and protein expression patterns have been evaluated for OPN, p53 or PTEN isoforms, using quantitative real time PCR, immunoblot or immunofluorescence. OPNa is overexpressed in tumoral and non-tumoral cell lines in relation to OPNb and OPNc. Regarding p53, the full lengh isoform is overexpressed, followed by Δ40p53, in relation to other variants in EC cells. Conversely, Δ40p53 it is the major expressed transcript in both EM42 and E6/E7 non-tumoral cells. Otherwise, in EC and endometrial non-tumoral cells, PTEN vs-fl isoform is overexpressed in relation to the other splice variants. Specifically in E6/E7 cells, all PTEN-SI, except vs-3b e vs-D6, are overexpressed in relation to EC cell lines. At the protein level, both p53 and PTEN isoforms are overexpressed in E6/E7 cells, when compared to EC cells. Of note, distinct isoforms for most of these variant transcripts have not been detected at the protein level. Our data demonstrate that full lenght OPN, p53 and PTEN are the major expressed variants in EC tumor cell lines. However, most of these transcript variants display differential expression between endometrial tumor and non-tumoral cells and also among distinct EC cell lines. These data provide early evidence that these variants can differently modulate the expression and functional roles of their full length couterparts. Further work should investigate the impact of OPNa overerexpression on p53 and PTEN isoforms and their putative cellular and molecular roles on modulating p53 and PTEN tumor supressive roles. Citation Format: Vanessa F. Franco, Nataly dos Santos Melo, Iaci N. Soares, Ya-Ting Hsu, Ya-Ting, Tim H. Huang, Wallace M. Araujo, José A. Morgado-Diaz, Jerson L. Silva, Etel Rodrigues Pereira Gimba. Osteopontin, p53 and PTEN isoforms expression patterns in endometrium carcinoma cell lines [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 4482. doi:10.1158/1538-7445.AM2017-4482

We would like to thank Dr. Gires for the letter concerning our article ([1][1]). We are very glad that Dr. Gires considers our data on how EGFR activation affects endometrial cancer cell invasiveness via EpCAM activity novel and interesting. The study highlights not only the function of EpCAM as a

The growing epidemic of obesity, which causes nonalcoholic fatty liver disease (NAFLD) and the more severe phenotype nonalcoholic steatohepatitis (NASH), has paralleled the increasing incidence of hepatocellular carcinoma (HCC). Accumulating evidence demonstrates that overnutrition and metabolic pathways can trigger modifications of DNA and histones via deregulation of chromatin modifiers, resulting in aberrant transcriptional activity. However, the epigenetic regulation of HCC development in NAFLD remains obscure. Here, we uncover key epigenetic regulators using both dietary and genetic obesity-promoted HCC models through quantitative expression profiling and characterize the oncogenic activities of histone deacetylase HDAC8 in NAFLD-associated hepatocarcinogenesis. HDAC8 is directly upregulated by the lipogenic transcription factor SREBP-1 where they are coexpressed in dietary obesity models of NASH and HCC. Lentiviral-mediated HDAC8 attenuation in vivo reversed insulin resistance and reduced NAFLD-associated tumorigenicity. HDAC8 modulation by genetic and pharmacologic approaches inhibited p53/p21-mediated apoptosis and G2–M phase cell-cycle arrest and stimulated β-catenin–dependent cell proliferation. Mechanistically, HDAC8 physically interacted with the chromatin modifier EZH2 to concordantly repress Wnt antagonists via histone H4 deacetylation and H3 lysine 27 trimethylation. In human NAFLD-associated HCC, levels of SREBP-1, HDAC8, EZH2, H4 deacetylation, H3K27me3, and active β-catenin were all correlated positively in tumors compared with nontumor tissues. Overall, our findings show how HDAC8 drives NAFLD-associated hepatocarcinogenesis, offering a novel epigenetic target to prevent or treat HCC in obese patients. Cancer Res; 75(22); 4803–16. ©2015 AACR.

Epidemiological studies reveal that maternal exposure to estrogenic chemicals during pregnancy results in higher risk of breast cancer in offspring. One of possible causal mechanisms is epigenetic reprogramming, but how estrogen/ERα signaling contributes to tumorigenesis through epigenetic machinery remains unclear. In this study, we demonstrate that the epigenetic modulation mediated by estrogen-driven amplification of distant-acting regulatory elements, or enhancers, may be an explanation addressing to this question. Enhancers contain transcription factor binding sites known to remotely regulate transcription through chromatin looping or transvection. Using our in vitro model to mimic maternal estrogen exposure and a "Seq-to-Seek" strategy integrating three next-generation sequencing approaches, we comprehensively mapped distant estrogen response elements (DEREs) that remotely control transcription of target genes through chromatin proximity. Surprisingly, a densely mapped DERE region located on chromosome 20q13 frequently amplifies in ERα-positive breast cancer with poor prognosis. Progressive accumulation of DERE copies was observed in normal breast progenitor and cancer cells chronically exposed to estrogen. Upon estrogen stimulation, these aberrantly amplified DEREs are clustered as a potential transcriptional depot for suppressing target gene expression through altering chromatin interactions, leading to accumulation of repressive histone marks (e.g. trimethylated H3K27 and H3K9), polycomb repressive complex 2, the presence of heterochromatin protein 1 (HP1) and DNA methylation, following prevention of RNA polymerase II and active histone mark- H3K4me3 binding. Furthermore, neutralization of HP1 function can significantly attenuate estrogen-driven DERE clustering and DERE-mediated repressive chromatin interactions, resulting in inhibition of cell proliferation. Deletion of the interested DERE regions using CRISPR/Cas9 genomic editing system further demonstrated that DERE-driven remote transcriptional control play a crucial role in tumor cell growth. Our data support a model in which amplified DEREs preferentially induce repressive epigenetic modulation of target genes. These findings indicate that 20q13 DERE region is a potential transcriptionally repressive domain whose aberrant amplification can result in suppressing expression of tumor suppressor genes, leading to tumorigenesis. In summary, our findings suggest that amplification of DNA regulatory elements can profoundly alter target transcriptome during tumorigenesis and amplified DEREs can be used as potential prognostic markers for endocrine resistance and predicative for progeny at risk of breast cancer. Citation Format: Pei-Yin Hsu, Hang-Kai Hsu, Yi-dong Chen, Victor X Jin, Zelton D Sharp, Tim H-M Huang. Amplified DERE-mediated epigenetic repression in ERα-mediated breast tumorigenesis [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P6-07-02.

Epithelial cell adhesion molecule (EpCAM), a membrane protein known to modulate cell-cell adhesion, is also a regulatory molecule internalized into the nucleus for transcriptional control of gene expression. Here we demonstrate that activated EGF/EGFR is a signaling factor to drive the cleavage of the extracellular fragment EpEX culminating in removal of cell-surface EpCAM as monitored with recognition atomic force microscopy (AFM). As a result, internalization of the cytoplasmic domain EpICD leads to formation of transcription factor complexes with LEF1 that regulate gene transcription for enhancing mobility functions of cancer cells. Comprehensive probing with AFM further reveals increased elasticity and decreased adhesiveness of these cells, implicating acquisition of an epithelial-mesenchymal transition phenotype. While EpCAM cleavage contributes to the loss of cell-surface adhesiveness, its internalized EpICD additionally regulates targets for promoting cell migration. Thus, this EGF/EGFR-modulated action on structural EpCAM and regulatory EpICD can enhance invasion potential of transformed cells. Citation Format: Ya-Ting Hsu, Pawel A. Osmulski, Yao Wang, Yi-Wen Huang, Lu Liu, Jianhua Ruan, Victor X. Jin, Nameer B. Kirma, Maria E. Gaczynska, Tim H.M. Huang. Dual role of EpCAM cleavage in adhesion attenuation and transcription enhancement for cell migration. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2871.

The enhancer pioneer transcription factor FoxA1 is a global mediator of steroid receptor (SR) action in hormone-dependent cancers. In castration-resistant prostate cancer (CRPC), FoxA1 acts as an androgen receptor cofactor to drive G2 to M-phase cell-cycle transit. Here, we describe a mechanistically distinct SR-independent role for FoxA1 in driving G1 to S-phase cell-cycle transit in CRPC. By comparing FoxA1 binding sites in prostate cancer cell genomes, we defined a codependent set of FoxA1-MYBL2 and FoxA1-CREB1 binding sites within the regulatory regions of the Cyclin E2 and E2F1 genes that are critical for CRPC growth. Binding at these sites upregulate the Cyclin E2 and Cyclin A2 genes in CRPC but not in earlier stage androgen-dependent prostate cancer, establishing a stage-specific role for this pathway in CRPC growth. Mechanistic investigations indicated that FoxA1, MYBL2, or CREB1 induction of histone H3 acetylation facilitated nucleosome disruption as the basis for codependent transcriptional activation and G1 to S-phase cell-cycle transit. Our findings establish FoxA1 as a pivotal driver of the cell-cycle in CRPC which promotes G1 to S-phase transit as well as G2 to M-phase transit through two distinct mechanisms. Cancer Res; 71(21); 6738–48. ©2011 AACR.

The interplay between histone modifications and promoter hypermethylation provides a causative explanation for epigenetic gene silencing in cancer. Less is known about the upstream initiators that direct this process. Here, we report that the Cystatin M (CST6) tumor suppressor gene is concurrently down-regulated with other loci in breast epithelial cells cocultured with cancer-associated fibroblasts (CAF). Promoter hypermethylation of CST6 is associated with aberrant AKT1 activation in epithelial cells, as well as the disabled INNP4B regulator resulting from the suppression by CAFs. Repressive chromatin, marked by trimethyl-H3K27 and dimethyl-H3K9, and de novo DNA methylation is established at the promoter. The findings suggest that microenvironmental stimuli are triggers in this epigenetic cascade, leading to the long-term silencing of CST6 in breast tumors. Our present findings implicate a causal mechanism defining how tumor stromal fibroblasts support neoplastic progression by manipulating the epigenome of mammary epithelial cells. The result also highlights the importance of direct cell-cell contact between epithelial cells and the surrounding fibroblasts that confer this epigenetic perturbation. Because this two-way interaction is anticipated, the described coculture system can be used to determine the effect of epithelial factors on fibroblasts in future studies. [Cancer Res 2008;68(24):10257–66]

Epigenetic alterations of the genome such as DNA promoter methylation and chromatin remodeling play an important role in tumorigenesis. These modifications take place throughout development with subsequent events occurring later in adulthood. Recent studies, however, suggest that some epigenetic alterations that influence cancer risk are inherited through the germline from parent to child and are observed in multiple generations. Epigenetic changes may be inherited as Mendelian, non-Mendelian, or environmentally induced traits. Here, we will discuss Mendelian, non-Mendelian, and environmentally induced patterns of multigenerational epigenetic alterations as well as some possible mechanisms for how these events may be occurring. [Cancer Res 2008;68(22):9116–21]

Indoleamine 2, 3-dioxygenase 1, encoded by IDO1, is a key immunosuppressive enzyme that catabolizes essential amino acid tryptophan to kynurenine in the tumor microenvironment. Severe depletion of tryptophan by IDO1 affects proliferation of T cells and tryptophan metabolites cause T-cell anergy and induce apoptosis. In this study, we investigated the epigenetic regulation of IDO1 expression by DNA methylation in breast cancer cells. Bisulfite pyrosequencing analysis of IDO1 promoter methylation performed on a panel of 10 breast cancer cell lines revealed that triple negative breast cancer (TNBC) cell lines (i.e. MDA-MB-231, Hs578t, SUM159) are hypomethylated compared to estrogen receptor positive (ER+) cell lines (i.e. MCF7, BT474, T47D). The same analysis was extended to 30 primary breast tumor and normal control samples and the results demonstrated that TNBC tumors had lower IDO1 promoter methylation compared to ER+ tumors. RT-PCR analysis showed that IDO1 mRNA expression is higher in TNBC cell lines than ER+ cell lines. This inverse correlation between IDO1 promoter methylation and mRNA expression can also be observed in TCGA 450K methylation and RNA-seq data sets in which promoter is hypomethylated and mRNA is up-regulated in basal-like molecular subtypes as compared to other breast cancer subtypes. IDO1 promoter is relatively CpG poor with most CpG sites concentrated near interferon γ (IFNg) responsive GAS and ISRE transcription factor binding sites. To investigate the role of CpG methylation in regulating IDO1 induction by IFNg, we cloned either methylated or unmethylated IDO1 promoter DNA into a luciferase reporter plasmid. Methylated promoter reporter exhibited significantly lower luciferase activity at basal or with IFNg stimulation compared to unmethylated reporter plasmid when transfected into MCF-7 or MDA-MB-231 cell lines. Treatment with a demethylating agent, 5-aza-deoxycytidine, synergistically up-regulated IDO1 mRNA expression with IFNg in MCF7 cells which have hypermethylated IDO1 promoter further supporting the influence of CpG methylation on IDO1 expression. IFNg stimulation or co-culture with activated T-cells significantly induced IDO1 protein expression in MDA-MB-231 cells, but not in MCF7 cells. We found no difference in IDO1 mRNA stability and IFNg induced JAK/STAT signaling pathway between MDA-MB-231 and MCF7 cell lines except promoter methylation. Furthermore, RNA-seq analysis of MDA-MB-231 and MCF7 cell lines co-cultured with activated T-cells revealed an active immune signaling mediated through JAK/STAT pathway shared by both cell lines, but also differential induction of IDO1 transcription between these two cell lines. These findings indicate IDO1 promoter methylation status as an important factor that regulates anti-immune responses by tumor cells towards tumor infiltrating lymphocytes and it could be used as a useful biomarker for IDO inhibitor based immunotherapy. Citation Format: Satish Kumar Reddy Noonepalle, Eun Joon Lee, Maria Ouzounova, Jaejik Kim, Jeong-Hyeon Choi, Austin Shull, Lirong Pei, Ravindra Kolhe, Pei-Yin Hsu, Nagireddy Putluri, Tim Hui-Ming Huang, Arun Sreekumar, Hasan Korkaya, David Munn, Huidong Shi. Promoter methylation regulates interferon-γ induced indoleamine 2,3-dioxygenase expression in breast cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4060. doi:10.1158/1538-7445.AM2015-4060

Recruitment of transcriptional machinery to target promoters for aberrant gene expression has been well studied, but underlying control directed by distant-acting enhancers remains unclear in cancer development. Our previous study demonstrated that distant estrogen response elements (DEREs) located on chromosome 20q13 were frequently amplified (50∼60 copies) and translocated to other chromosomes in ERα-positive breast cancer cells. In this study, we used three-dimensional interphase fluorescence in situ hybridization to decipher spatiotemporal gathering of multiple DEREs in the nucleus. Upon estrogen stimulation, the majority of 20q13 DEREs were mobilized to form regulatory depots for synchronized regulation of target loci. A chromosome conformation capture assay coupled with chromatin immunoprecipitation further uncovered that ERα-bound regulatory depots are tethered to heterochromatin protein 1 (HP1) for coordinated chromatin movement and subsequent facilitation of histone modifications of target loci, resulting in transcription repression. Neutralizing HP1 function dissembled these regulatory depots and reversed this transcription inactivation of candidate tumor-suppressor genes. Deletion of amplified DEREs using the CRISPR/Cas9 genomic-editing system profoundly altered transcriptional profiles of JAK/STAT signaling networks, leading to proliferation inhibition of cancer cells with beneficial outcome of breast cancers. These findings reveal a formerly uncharacterized feature of oncogenic amplicons that multiple copies of the amplicon congregate as transcriptional unions in the nucleus for synchronous regulation of function-related loci in tumorigenesis. Disruption of their assembly can be a new strategy for treating breast cancers and other malignancies. Citation Format: Pei-Yin Hsu, Hang-Kai Hsu, Victor X. Jin, Zelton D. Sharp, Tim H.-M. Huang. HP1-mediated spatiotemporal control of estrogen-responsive transcription in breast cancer cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4778. doi:10.1158/1538-7445.AM2015-4778

The development of targeted therapies for antiestrogen-resistant breast cancer requires a detailed understanding of its molecular characteristics. To further elucidate the molecular events underlying acquired resistance to the antiestrogens tamoxifen and fulvestrant, we established drug-resistant sublines from a single colony of hormone-dependent breast cancer MCF7 cells. These model systems allowed us to examine the cellular and molecular changes induced by antiestrogens in the context of a uniform clonal background. Global changes in both basal and estrogen-induced gene expression profiles were determined in hormone-sensitive and hormonal-resistant sublines using Affymetrix Human Genome U133 Plus 2.0 Arrays. Changes in DNA methylation were assessed by differential methylation hybridization, a high-throughput promoter CpG island microarray analysis. By comparative studies, we found distinct gene expression and promoter DNA methylation profiles associated with acquired resistance to fulvestrant versus tamoxifen. Fulvestrant resistance was characterized by pronounced up-regulation of multiple growth-stimulatory pathways, resulting in estrogen receptor α (ERα)–independent, autocrine-regulated proliferation. Conversely, acquired resistance to tamoxifen correlated with maintenance of the ERα-positive phenotype, although receptor-mediated gene regulation was altered. Activation of growth-promoting genes, due to promoter hypomethylation, was more frequently observed in antiestrogen-resistant cells compared with gene inactivation by promoter hypermethylation, revealing an unexpected insight into the molecular changes associated with endocrine resistance. In summary, this study provides an in-depth understanding of the molecular changes specific to acquired resistance to clinically important antiestrogens. Such knowledge of resistance-associated mechanisms could allow for identification of therapy targets and strategies for resensitization to these well-established antihormonal agents. (Cancer Res 2006; 66(24): 11954–66)

In the post-genome era, attention has focused on the functions of genome sequences and how they are regulated. The emerging epigenomic changes and the interactions between cis-acting elements and protein factors may play a central role in gene regulation. To understand the crosstalk between DNA and protein on a genome-wide scale, one emerging technique, called ChIP-chip, takes the strategy of combining chromatin immunoprecipitation with microarray. This new high-throughput strategy helps screen the targets of critical transcription factors and profile the genome-wide distribution of histone modifications, which will enable the feasibility of conducting a large-scale study, such as the Human Epigenome Project. (Cancer Res 2006; 66(14): 6899-902)

The endometrium is the major target of oncogenesis in the uterus. Endometrial tissue undergoes several cycles of disintegration and repair during women's reproductive years. The involvement of repair mechanisms that include transforming growth factor beta (TGF-beta) pathway may entail epithelial msenchymal transition (EMT) known to be involved in tissue repair. This suggests that the EMT program is inherent in endometrial epithelial cells and may be subverted during the development of invasive disease, whether benign such as endometriosis or malignant such as endometroid endometrial carcinoma. We therefore examined candidate mechanistic modulators of EMT in normal and malignant endometrial epithelial cells as well as endometrial carcinoma samples using cell signaling, gene expression and epigenetic regulation methodologies. Our evidence strikingly show that although both TGF-beta and epidermal growth factor (EGF) stimulated primary normal endometrial epithelial cell invasiveness, EGF was the main inducer of EMT in these cells. EGF also strongly induced EMT in endometrial cancer cells. In normal and malignant cells, Raf-1/MAPK mediated EGF actions. Interestingly, EGF stimulated epithelial adhesion molecule (EpCAM) cleavage and internalization of its intracellular domain EpICD into the nucleus to activate EMT-related genes such as mesenchymal cadherins. This was associated with loss of the epithelial marker E-cadherin and upregulation of its negative regulator Snail1. The involvement of EMT in aggressive endometrial malignancy was further confirmed in a permissive transcriptional epigenetic profile of mesenchymal cadherins in endometrial cancers with poor survival compared to a silenced epigenetic signature in less aggressive tumors. This epigenetic regulation including DNA methylation and histone modification was mediated by EpCAM, as shown in EpCAM-knockdown endometrial cancer cells, suggesting that EpCAM binding to target promoters maintains an open transcriptional conformation. Combined, our data suggest that while plasticity is required for endometrial regeneration during the menstrual cycles, committed epigenetic signatures may alter the path of normal tissue repair to aberrant growth associated with benign tumors or malignant growth. In concert, activation by cell signaling such as EGF/EpCAM may determine the extent of invasiveness and disease progression. Citation Format: Ya-Ting Hsu, Joseph Liu, Peter A. Binkley, Robert S. Schenken, Rajshwar R. Tekmal, Tim H.-M. Huang, Nameer B. Kirma. Parallel EMT pathways mediated by epidermal growth factor, EpCAM and mesenchymal cadherins in benign endometriotic lesions and endometrial cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3326. doi:10.1158/1538-7445.AM2014-3326

Since the first amplified gene, MYCN, was identified in neuroblastomas, considerable effort has been directed toward discovery of oncogenes in amplified genomic regions. However, there is no significant correlation between copy number gains and increased expression of corresponding genes within amplicons. We demonstrate that amplification of distant-acting regulatory elements, or enhancers, may be an alternative mechanism contributing to an oncogenic event. Enhancers comprise transcription factor binding sites known to remotely regulate transcription through chromatin looping or transvection. Using a “Seq-to-Seek” strategy integrating three next-generation sequencing approaches, we comprehensively mapped distant estrogen response elements (DEREs) that remotely control transcription of target genes through chromatin proximity. Surprisingly, a densely mapped DERE region located on chromosome 20q13 frequently amplifies in ERα-positive breast cancer with poor prognosis. Progressive accumulation of DERE copies was observed in normal breast progenitor and cancer cells chronically exposed to estrogen or estrogenic chemicals. Pharmacological studies with either an ERα antagonist or an ataxia telangiectasia mutated (ATM) kinase inhibitor further showed that ATM-dependent DNA repair pathway participates in ERα-driven increase of 20q13 DERE copies, suggesting involvement of breakage-fusion-bridge mechanism in DERE amplification. Furthermore, these aberrantly amplified DEREs altered chromatin interactions, leading to transcriptional repression of genes that are associated with tumor-suppressor and apoptosis pathways and potentially linked to cancer development and tamoxifen resistance. Correlation analyses of copy-number variation, occupancy of the repressive histone mark, H3K27me3, and methylation profiling of 20q13 DEREs in ERα-positive cancer cells support a model in which amplified DEREs preferentially induce repressive epigenetic modulation of target genes. In addition, interphase fluorescence in situ hybridization coupled with immunofluorescence analyses revealed that estrogen stimulation leads to DERE clustering in a transcriptional hub nearby in a heterochromatic region. These findings indicate that the 20q13 DERE region is a potential transcriptionally repressive domain whose aberrant amplification can result in suppressing expression of tumor suppressor genes. To determine the precise role of amplified DEREs in epigenetic transcription and their biological significance, our ongoing studies use CRISPR/Cas genomic editing system to delete candidate DEREs at 20q13. In summary, our findings suggest that amplification of DNA regulatory elements can profoundly alter target transcriptome during tumorigenesis and amplified DEREs can be used as potential prognostic markers for endocrine resistance. Citation Format: PEI-YIN HSU, HANG-KAI HSU, Victor X. Jin, Zelton D. Sharp, Tim H.-M. Huang. Amplification of distant estrogen response elements epigenetically deregulates target genes in ERα-mediated breast tumorigenesis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4783. doi:10.1158/1538-7445.AM2014-4783

Endometrial cancer (EC) is the most common gynecologic malignancy, with approximately 20% of EC patients developing advanced stage recurrent tumors and frequent metastasis. Our goal was to investigate whether DNA methylation signatures associated with low promoter methylation (hypomethylation) and specific oncogenic signaling delineate predictive markers of endometrial cancer recurrence. Global screening by Methyl-CpG-capture sequencing revealed aberrant DNA methylation in our endometrial cancer cohort and identified a subset of bone morphogenetic protein family (BMP1, 2, 3, 4, and 7) exhibiting frequent hypomethylation in primary tumors with subsequent recurrence compared with non-recurrent tumors. This epigenetic signature correlated with poor survival and was validated in The Cancer Genome Atlas endometrial cancer cohort. Our functional studies also implicated epidermal growth factor receptor (EGFR) pathway in the transcriptional activation of these BMPs and inducing epithelial-mesenchymal transition (EMT). In addition to AKT and MAPK, the epithelial cell adhesion molecule (EpCAM) mediated these actions by EGFR. EpCAM involvement in cancer progression includes nuclear co-translocation of its intracellular domain EpICD with Lef-1 complexes and targeting oncogene promoter activation. In this study, EGF stimulated EpICD-Lef-1 binding on BMP genes accompanied with histone active modification marks. EpICD knockdown resulted in increased repressive histone marks and DNA methylation at these loci, suggesting that EpICD occupancy is involved in their epigenetic modification to an open transcriptional conformation. Knockdown of candidate BMPs led to decreased endometrial cancer cell invasiveness, implicating them in aggressive growth. Extending our studies, we performed ChIP-Seq analysis to identify global regulation by the EpICD-Lef-1 complexes in endometrial cancer. Interestingly, under basal levels only about 28% of loci targeted by either EpICD or Lef-1 were commonly targeted by EpICD-Lef-1, with common targets increasing to about 50% in 24 hrs and 73% in 48 hrs post EGF treatment. This indicates that EGFR signaling stimulates a time-course dependent enrichment of EpICD-Lef-1 convergence on target loci. Our initial studies of these EpICD target pathways included genes with cell adhesion functions. Future studies on the regulation of the EpICD-Lef-1 regulated genes and their mechanisms of action in aggressive endometrial cancer will provide a better understanding of this gene network in endometrial cancer. Hypomethylation signatures of candidate loci in this regulatory network may present putative predictive markers of poor survival and which may be used to tailor individualized therapy. Citation Format: Ya-Ting Hsu, Fei Gu, Yi-Wen Huang, Joseph Liu, Jianhua Ruan, Rui-Lan Huang, Chiou-Miin Wang, Chun-Liang Chen, Rohit R. Jadhav, Yao Wang, Victor X. Jin, Hung-Cheng Lai, David G. Mutch, Paul J. Goodfellow, Ian M. Thompson, Nameer B. Kirma, Tim H.M. Huang. EpCAM-mediated hypomethylation of BMP and cell adhesion genes is associated with advanced endometrial cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1376. doi:10.1158/1538-7445.AM2014-1376

Recently, we have described that the breast of parous postmenopausal women exhibits a specific gene expression profile induced by full term pregnancy (FTP) [Belitskaya-Levy, I. et al. 2011 and Peri, S. et al. 2012], which is centered on chromatin remodeling [Russo, J. 2012]. In order to better understand the molecular mechanism of gene regulation induced by FTP, we have investigated the DNA methylation profile in breast core needle biopsies of five nulliparous (NP) and five parous (P) postmenopausal women between the ages of 50 and 69. DNA was extracted from core needle biopsies and highly methylated fragments of the DNA were separated from the un-methylated DNA using MBD-Capture. The hypermethylated DNA was then sequenced using the Illumina system. Image analysis and base calling were performed with the standard Illumina pipeline, and the reads were aligned to human reference genome (hg18). Differentially methylated regions (DMR) were identified by comparing the differences of averaged methylation values between P and NP samples using Student's t-test (P Citation Format: Julia Santucci-Pereira, Colleen O'Malley, Ricardo López de Cicco, Nameer B. Kirma, Tim H. Huang, Joseph Liu, Eric A. Ross, Michael Slifker, Suraj Peri, Irma H. Russo, Pal Bordas, Per Lenner, Göran Hallmans, Paolo Toniolo, Jose Russo. Pregnancy changes the DNA methylation profile of the breast in postmenopausal women. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2294. doi:10.1158/1538-7445.AM2014-2294

The TGF-β signaling regulates numerous cellular processes, including cell proliferation, cell differentiation, apoptosis, migration and cell fate. It was also demonstrated that TGF-β functions as a tumor suppressor in normal ovarian surface epithelium (OSE) cells but promotes tumor proliferation and epithelial-mesenchymal transition (EMT) during ovarian cancer progression. Nevertheless, the molecular mechanisms leading to this divert role of TGF-β signaling in ovarian cancer remains to be elucidated. Our previous studies demonstrated that several TGF-β/SMAD4 regulated targeted are epigenetically silenced by DNA methylation and histone modification including H3K27me3. We therefore hypothesized that the histone-lysine N-methyltransferase, EZH2 may act as an epigenetic switch to facilitate the TGF-β mediated EMT in ovarian cancer. In this study, we utilized our previously identified TGF-β responsive targets using combined ChIP-chip and expression arrays in an immortalized ovarian surface epithelial (IOSE) cell which showed TGF-β growth inhibition. Bioinformatics analysis using ENCODE ChiP-Seq data identified that several of these TGF-β targets are marked by EZH2. To investigate the effect of TGF-β signaling on the methylome of ovarian cancer, we performed MBDcap-Seq in SMAD4 knockdown CP70 cells. Our result showed that there are 99 and 73 TGF-β targets showing hyper- or hypo-methylation respectively after SMAD4 knockdown. Analysis of the gene functions on DAVID has uncovered that some of these hypermethylated genes are associated with EMT process and the TGF-β signaling pathway. On the other hand, the hypomethylated genes are associated with transcription repressor activity. We selected one of the hypermethylated target, LTBP2 which was previously found to be a tumor suppressor for further experiment. This gene was expressed in IOSE but down regulated in a panel of ovarian cancer cells showing overexpression of EZH2. Except for IOSE, promoter hypermethylation of LTBP2 was found in ovarian cancer cells as revealed by bisulphite pyrosequencing. In consistent with deep sequencing result, knock-down of SMAD4 further increased the promoter methylation in CP70 cells. Treatment of demethylation agent, 5azaDC partially restored its expression in these cancer cells. Interestingly, synergistic treatment of 5azaDC and EZH2 inhibitor, GSK343 resulted in a dramatic increase of LTBP2 expression in MCP3 and CP70 cells. Taken together, our result suggested that EZH2 may be involved in the epigenetic silencing of TGF-β/SMAD4-regulated tumor suppressors in ovarian cancer. The differential occupancy of EZH2 into these SMAD4 loci may act as an epigenetic switch to turn the function of TGF-β from a tumor suppressor into an EMT regulator. The therapeutic potential of targeting EZH2 in the inhibition of EMT in ovarian cancer deserves further investigation. Citation Format: Jora Meng-Ju Lin, Jacqueline Shay, Jian-Liang Chou, Pearlly S. Yan, Tim H.-M. Huang, Hung Cheng Lai, Michael W.y. Chan. The role of EZH2 as an epigenetic switch of the TGF-β/SMAD4 targets in regulating EMT in ovarian cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2318. doi:10.1158/1538-7445.AM2014-2318

Gene expression profiles of microdissected tissue are frequently used to stratify cancer subtypes and to predict patients' clinical outcome. This type of analysis usually operates under the assumption that uniform gene expression is present in a cancer cell population. However, high fluctuation of gene expression in single cells stemming from intra-clonal heterogeneity within a cancer cell population can lead to misinterpretation of the data. An important challenge then lies in developing approaches to decipher this expression chaos for cancer diagnostic and/or prognostic strategies. We have developed a novel digitizing approach to analyze single-cell gene expression in exfoliated prostate cells isolated from urine sediment. In analyzing 1220 single cells, we observed a panel of genes with dichotomous expression patterns (DEP) and further digitized their expression levels to either 1 for high or 0 for low expression. Of 35 androgen-responsive genes examined, 6 genes exhibited DEP characteristics. When aligning the dichotomous numbers of these genes in the order of CXCL6-TGFBR2-GSK3B-CDKN1C-GATA3-EIF4EBP1, we identified 64 (26) types of code; e.g., 1-0-1-0-1-0. With the conversion from original expression levels to a series of dichotomous numbers, these new codes not only reduced the complexity associated with single cell expression, they also enabled us to decipher expression heterogeneity in the samples by considering multiple gene expression codes simultaneously. Importantly, these digitized codes identified distinct clonal prostate cell populations in the urine samples. At the single-cell level, high volumes of cells with the same code (common codes) in a collection of cells suggested the presence of a large clonal cell population. By examining the types of code and the size of clonal populations, we found that increasing clonal size of cells carrying common codes was associated with high-grade cancers. Certain common codes were also found in cells from patients diagnosed with benign prostate hyperplasia and prostatic intraepithelial neoplasia. On the other hand, digitized code types appeared to be highly diverse in normal cell populations. Our data suggest that digitizing single-cell expression can stratify benign, low grade and high grade prostate cancer. This analysis pipeline has a wider application for disease diagnosis/prognosis using cancer cells isolated by non-invasive means from biological fluids or washes from biopsy needles and surgical blades. Citation Format: Chun-Lin Lin, Chun-Liang Chen, Chiou-Miin Wang, Joseph Liu, Susan Huang, Tim Huang. Digitizing single-cell expression patterns in urine for prostate cancer detection. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4569. doi:10.1158/1538-7445.AM2014-4569

Nasopharyngeal carcinoma (NPC) is a prevalent cancer in southern China and south east Asian countries. A variety of tumor suppressor (TS) genes including p16, RASSF1A, EDNRB, DAP-Kinase, RIZ1, E-Cadherin were found to be hypermethylated in NPC. This, however, could only be the tip of an iceberg. We made use of the high throughput differential methylation hybridization (DMH) technique in screening for methylated DNA markers in 244K CpG island DNA chip in three NPC xenografts (C15, C17, 99-186), a NPC tumor cell line (C666) versus an immortalized NP non-cancer cell line (NP69). This DMH screening discovered 100, 213, 372 and 977 genes respectively in 99-186, C17, C15 and C666 with ≥ 5 CpG sites in their gene promotors being methylated. Among these genes, 28 of them were found to have DNA methylation in all the 4 NPC xenografts/ tumor cell line. Bisulphite sequencing was performed in 17 pairs of tumor and normal biopsy samples from 17 NPC patients. This confirmed tumor specific methylation in the promotor regions of 8 gene markers, namely, NRP3, PCDH10, PENK, ADHFE1, IRX4, GSC, PFN2 & GFI1 with positive methylation ratios (+ve MR) in tumor biopsies of 86.7%, 85.7%, 80%, 72.7%, 54.5%, 50%, 41.7% &23.1% respectively and +ve MR of 18.2%, 0%, 0%, 0%, 0%, 37.5%, 12.5% & 0% respectively in normal biopsies. Methylation of CpG sites appears to occur either all or none with 15 to 45 consecutive CpG sites in these genes either all methylated or non-methylated in tumor biopsies probably indicating the need of methylation of a full cluster of CpG sites in order to affect the gene transcription of the discovered genes. Functions of the DMH identified genes includes cell adhesion (PCDH10), signal transduction (PENK), chloride ion binding (NPR3), regulation of DNA dependent transcription (IRX4) and xenobiotic metabolism (ADHFE1). In fact, PCDH10, PENK and GFI1 genes have been reported to be closely associated with NPC/esophageal carcinoma, pancreatic adenocarinoma and T-cell lymphoma respectively. Further analyses in these methylated markers could be useful in the diagnosis and study of etiology of NPC. Citation Format: Wai Wai Cheng, Roger K.C. Ngan, Dora L.W. Kwong, Tim H.M. Huang, Victor W.S. Ma, Stephen C.K. Law, Loretta Tse, Pierre Busson, George S.W. Tsao, Maria Li Lung, Timothy T.C. Yip. Methylated gene markers discovered in nasopharyngeal carcinoma by differential methylation hybridization (DMH) in high density CpG island DNA chips. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2298. doi:10.1158/1538-7445.AM2014-2298

Approximately 30% of prostate cancer (PCa) patients who receive androgen-deprivation therapy experience disease progression, including bone metastasis, in 18-36 months. Clinical diagnosis of this castration resistance is primarily based on a continuous rise in serum PSA levels during therapy. However, the underlying disease progression predates the clinical onset of castration resistance by many months. The clinical challenge is to distinguish indolent vs aggressive cancer for better disease management. During the prostate cancer progression, malignant circulating tumor cells (CTC) shed from the primary site into the bloodstream through epigenetic modifications and an epithelial-to-mesenchymal transition (EMT). Evidence suggests that increased CTCs are present in the blood of castration-resistant PCa patients and can be obtained through routine phlebotomy. EMT changes of CTCs present a great potential for disease prognosis, treatment stratification and subsequent disease monitoring. We have recently established the combined microfiltration-micromanipulation system (CM2S) to enrich prostate CTCs from blood as published in The Prostate. Our preliminary studies based on a relatively small sample size show that CTCs isolated from advanced PCa patients often lose the typical features of prostate epithelial cells and display incremental EMT-related gene expression signatures, higher elasticity and smoother membrane features. Furthermore, incremental expression of these genes and particular nanomechanical features in CTCs are associated with castration-resistant and metastatic PCa. In this study, we would like expand the sample size to clinically develop this methodology. CTCs were isolated from patients' blood (∼15 ml) using microfiltration system (ScreenCell). We analyzed castration-sensitive (CS) and castration-resistant (CR) PCa cells and CTCs using high throughput microfluidic single-cell RT-PCR. The data were subject to hierarchical clustering, violin plot and Ingenuity Pathway Analysis (IPA). Increased expression of EMT genes was found in CR PCa cells and CTCs as compared to CS counterparts. IPA indicated that these EMT genes are closely related to AKT, β-catenin, Myc and NFκB pathways. Some of CTCs isolated from patients were subject to nanomechanical and nanochemical analysis using PeakForce QNM Catalyst atomic force microscopy (AFM) (Bruker). CTCs of CR patients are about 3 fold more elastic and 7 fold more adherent than CTCs of CS patients. Additionally, CTCs of CR patients are about 3 fold more deformable than CTCs of CS patients. In conclusion, we confirmed our previous study with a larger patient sample size. The increased expression of EMT-related genes and nanomechanical and nanochemical phenotypes in CTCs are potential biomarkers for detection of the castration-resistant PCa, treatment stratification and subsequent disease monitoring. Citation Format: Chun-Liang Chen, Pawel Osmulski, Devalingam Mahalingam, Aaron M. Horning, Rohit R. Jadhav, Anna D. Louie, Chiou-Miin Wang, Tim H.-M. Huang. Epithelial-to-mesenchymal markers of circulating tumor cells for detection of castration-resistant prostate cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5588. doi:10.1158/1538-7445.AM2014-5588

The phosphatidylinositol 3-kinase (PI3K)/AKT pathway is a critical survival cascade in tumor progression. Our previous study demonstrated that combinational treatment of a potent PI3K inhibitor, LY294002 (LY), and DNA methyltransferase inhibitor, 5’-Aza-deoxycytidine (DAC), compounds effectively reduce tumor formation in the immunodeficiency mouse model, suggesting that PI3K/AKT signaling suppresses tumorigenesis through the epigenetic modulation. While tumor size of the LY-treated xenografts is dramatically decreased compared to the control group, the tumor growth cannot be completely attenuated by either LY or LY/DAC treatment, indicating that there is an alternative route for tumor survival. Here, we performed a microarray analysis to identify LY-mediated expression profiling on an ERα-positive breast cancer cell line, T-47D, the cell line applied in the previous xenograft experiments. A subset of 24 LY-activated genes associated with better clinical outcome are found to be not only direct targets of PI3K/AKT but involved in estrogen (E2)/ERα signaling by ingenuity pathway analysis, suggesting the involvement of ERα signaling in PI3K/AKT-mediated tumor growth. To clarify their relationship, pharmacological experiments using an ERα antagonist, ICI 182, 780 (ICI) and LY coupled with E2 was conducted. We observed that E2 stimulation induces both AKT and ERα activation in a time-dependent manner. Either ICI or LY treatment cannot repress the activation levels of AKT or ERα, respectively. Though, either single or combined inhibitor treatment can effectively restore E2-suppressed gene expression. These findings indicate that cross-talk between PI3K/AKT and ERα signaling cascades may cooperatively regulate cell growth and associated gene expression. In addition, transcription factor motif analysis showed that signal transducer and activator of transcription 3 and 6 (STAT3/6) binding motifs are enriched with highest prediction score on the promoter regions of the examined AKT-directed targets. Inhibitors prohibit E2-mediated assembly of STAT3/6 with ERα and STAT3/6 recruitment onto the promoter regions of target loci using co-immunoprecipitation (co-IP) and chromatin IP-qPCR. Moreover, repressive histone marks, H3K27me3 and H3K9me3, are found to occupy on the same regions as STAT3/6 upon E2 treatment. DAC treatment can effectively restore E2-induced suppression of AKT-directed target genes. Further association studies are ongoing to interrogate whether STAT3/6 is part of repressive transcription complex with H3K27me3 and H3K9me3. In summary, we propose that cross-talk of ERα with PI3K/AKT signaling represents the potential function switch of ERα from genomic binding to no-genomic binding. Combined treatment of PI3K/AKT inhibitors with hormone therapy may shed a light of therapeutic strategy to patients with aggressive or metastatic breast tumors. Citation Format: Hang-Kai Hsu, Pei-Yin Hsu, Yao Wang, Zelton D. Sharp, Tim H.-M. Huang, Victor X. Jin. Cross-talk between PI3K/AKT and ERα signaling leads to STAT3/6-modulated epigenetic transcription in aggressive breast cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3341. doi:10.1158/1538-7445.AM2014-3341

While cancer as a complex disease is known to arise from a series of aberrant genetic and epigenetic profiles, its growth and disease-specific outcome can often be characterized by status of one oncogene, such as Estrogen Receptor (ER) of breast cancer. Positive ER appears in around 70% of human breast cancer cases and recent studies dissected the Estrogen-mediated gene regulation through specific DNA methylation patterns by comparison between ER+ and ER- tumor samples. However, this simple approach did not take into consideration the influence of other confounding regulation factors due to the heterogeneity of breast cancer and may be limited in uncovering complex underlying mechanism. To address this problem, we first hypothesize that DNA methylation status and its inter-gene similarity are modulated by multiple factors including ER. The disruption of ER will disrupt association of methylation patterns between two genes which are correlated otherwise. The epigenetic signaling cascade maintained by specific ER status can be further interpreted from the “co-methylation” relationship among genes. Here we proposed a novel algorithm to identify the modulated gene methylation based on the “modulator of regulation” concept. Setting ER as the modulator, an ER modulated gene pair (ER-GP) was defined as pair of genes with differential correlation between ER+ and ER- samples. Fisher transformation on Pearson correlation coefficients was adopted for statistical power adjustment on sample sizes and the differences of absolute correlation coefficients were tested for statistical significance in the Fisher transform domain. By applying the algorithm to the MBDCap-Seq data of 76 breast tumors (47 ER+ and 29 ER-), we identified 5,673 putative ER-GPs of co-methylation (co-methyl. ER-GPs) involving 1,657 unique genes. In order to delineate a comprehensive and systematic view of interaction between identified ER-GPs, the co-methyl. ER-GPs were combined to construct the ER modulated gene methylation network. With an overall connectivity (average number of first-order neighbors of each gene in a network) of 6.85, genes in the methylation network were highly linked to each other and formed a branched signaling cascade. The nucleosome assembly protein 1-like 5 NAP1L5, previously reported as regulated by both estradiol and tamoxifen treatment, was identified as the top hub gene, indicating that it may serve as an important regulator in the ER modulation. Further Gene Ontology analysis revealed that NAP1L5 and its co-methylated genes were involved in nucleotide biosynthetic process, chromosome organization, and cell proliferation. In the present study, we proposed a novel algorithm to identify the ER modulated methylation regulatory network. The findings provided biological insights into the underlying mechanism of epigenetic signaling governed by ER and may contribute to improvement of breast cancer treatment. Citation Format: Yu-Chiao Chiu, Tzu-Hung Hsiao, Fei Gu, Yidong Chen, Tim H-M Huang, Eric Y. Chuang. Identification of estrogen receptor modulated gene methylation network in breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2889. doi:10.1158/1538-7445.AM2013-2889 Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.

Casp8AP2 is a FLASH protein that is critical for the formation of death complex and the relay of death signal into the cells. Genetic defect of Casp8AP2 was found in diseases like acute lymphoblastic leukemia, implying that the miss-expression of Casp8AP2 might cause disease. On the other hand, the promoter of Casp8AP2 is enriched with CpG islands and we observed differential methylation changes within Casp8AP2 promoter during mesenchymal stem cell (MSCs) differentiation. Aberrant DNA methylation was also identified within the Casp8AP2 promoter in vivo like in liver cancers. It was then hypothesized that the abnormal DNA methylation within the Casp8AP2 promoter might contribute to the enhanced survival or drug resistance in cancer development. We determined the epigenetic states within the Casp8AP2 promoter in different cells and confirmed that there are methylation differences between the normal and tumoral samples within the Casp8AP2 promoter. Differential methylation was also observed between the drug resistant cancer cells and primary cancer cells. Global demethylation in drug resistant cell lines reversed the Casp8AP2 methylation, which was correlated with the reversed resistance phenotype. We then target-methylated the Casp8AP2 promoter in normal somatic stem cells and cancer cells like MDA-MB-231 and found increased drug resistance in these cells. These data point out that methylation within the death complex like Casp8AP2 might be able to serve as biomarker and treatment target for drug resistance in cancer cells. (Supported in part by NSC100-2320-B-194-001) Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 603. doi:1538-7445.AM2012-603

We previously reported in a Phase I clinical trial that black raspberry (BRB) powder is well tolerated by humans when administered in a slurry of water at 45g/day for 7 days. We then undertook a study to determine if BRB might regress rectal polyps in familial adenomatous polyposis (FAP) patients. Fourteen FAP patients who had undergone a colectomy were treated with BRB daily for a period of nine months. Seven patients received BRB powder (20g/3x/day) orally in water plus two suppositories (each composed of 700 mg BRB) that patients inserted into the rectum one hour before bedtime. The other seven patients were randomized to receive an oral placebo plus the two rectal suppositories. Rectal polyp counts were taken at time zero and after nine months of BRB treatment. The number of rectal polyps was reduced by a median of 43% at nine months overall including a median reduction of 59% in patients treated by both routes and 36% in patients treated with the suppositories only. Polyps and aberrant crypt foci, both were histopathologically identified as tubular adenomas, and adjacent normal tissues were collected both before and after berry treatment. Promoter methylation of CDKN2A, also known as p16, in collected specimens was measured using MassARRAY. Global methylation LINE-1 was determined by Pyrosequencing. MBDCap-seq genome-wide methylation analysis was used to discover other genes demethylated by berries. Further, the specimens were evaluated for p16, Ki-67, TUNEL, DNMT1 and DNMT3B expression by semi-quantitative immunohistochemistry. Our results showed that treatment with BRB powder, both orally and in the form of a BRB suppository, significantly reduced cell proliferation in the tubular adenomas. The suppository alone was sufficient to decrease promoter methylation of p16 leading to an increase in p16 protein expression in adjacent normal rectum and in tubular adenomas. This was associated with decreased protein expression of DNMT1 and DNMT3B. Based on MBDCap-seq data, BRBs significantly demethylated promoter CpGs of 44 genes in tubular adenomas. These genes are involved in the regulation of important cellular functions; e.g., cell proliferation, Wnt signaling and Notch pathway, etc. Lastly, berry treatment did not induce changes in global methylation LINE-1. In conclusion, our data provide evidence that one of the mechanisms for BRB-induced rectal polyp regression in FAP patients is through the demethylation and reactivation of tumor suppressor genes.(Supported by NCI grants CA148818 and CA103180, and USDA grant 38903-03560). Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1009. doi:1538-7445.AM2012-1009

Previously, based on well-known stem cell phenotypes (sphere formation, potent tumorigenicity, embryonic gene expression, and chemoresistance), we used patient tumors to isolate high-grade serous (HGS) ovarian cancer-initiating cells (OCICs) that express the cell surface markers CD44 (a hyaluronate receptor) and CD117 (c-kit) (Zhang et al., 2008, Cancer Res 68:4311). Here, to identify biological pathways that underlie HGS ovarian tumorigenesis, including the specific role of OCICs in that process, we performed integrated analyses of global gene expression, DNA copy number, and DNA methylation patterns. To that end, OCICs and “bulk” (i.e., disaggregated but unsorted) tumor cells were compared to primary human normal ovarian surface epithelial (nOSE) cells that, along with fallopian tube epithelial (FTE) cells, represent hypothesized cells-of-origin for HGS pelvic cancers. Principle components analysis and unsupervised hierarchical clustering revealed distinct DNA methylation and gene expression profiles for replicate (n=3) samples of each cell type (i.e., OCIC, bulk tumor, and nOSE). Gene ontology and additional unsupervised analyses of “gene expression signatures” corresponding to the epithelial-to-mesenchymal transition (82 of 159 signature genes), TGF-beta (47 of 86 genes), and Wnt (75 of 151 genes) pathways demonstrated well-defined segregation of the three cell types, with mesenchymal and Wnt signaling hierarchies being nOSE > OCIC > bulk tumor cells. To examine early events in HGS ovarian tumorigenesis, previously published (Tone et al., 2008, Clin Cancer Res 14:4067) gene expression datasets were employed to show that nOSE, OCIC, and bulk ovarian tumor cell transcriptomes distinctly segregate from normal (FTE) and malignant fallopian epithelial transcriptomes. Interestingly, the largest divergence was between the nOSE and FTE gene expression profiles. Finally, DNA methylation and gene expression patterns were integrated, implicating specific networks/circuits in ovarian carcinogenesis. Taken together, these results support a mesenchymal-to-epithelial transition during ovarian tumorigenesis, reveal legitimate therapeutic targets (at the pathway level), and raise uncertainty that surface epithelial cells of the fallopian tube and ovary are reciprocal cells-of-origin for HGS pelvic carcinomas. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5206. doi:1538-7445.AM2012-5206

Breast cancer is the most common type of cancer among women in the US and the second leading cause of death associated to cancer. microRNA (miRNA) are short ribonucleic acids with important regulatory functions and with an increasingly acknowledged role in cancer. We recently found that progestins modulate miRNA expression in a progestin-dependent murine breast cancer model. In particular, miR-16 was found to be downregulated by progestins. We here demonstrate that the treatment of T47D and BT-474 human breast cancer cells with the synthetic progestin medroxyprogesterone acetate (MPA) results in a significant miR-16 decrease and a concomitant cell proliferation augment. Interestingly, MPA treatment of T47D-Y cells, a variant of T47D lacking progesterone receptor (PR) expression, did not modify miR-16 levels. Furthermore, transfection of T47D-Y with PR-mPRO, a mutant PR which lacks the ability to activate nongenomic signaling pathways (but retains the transcriptional activity of PR), or with PR-C587A, a variant with the capacity to activate nongenomic pathways but uncapable of binding to DNA, did not recover the ability of progestins to downregulate miR-16, suggesting that both PR actions are necessary for miR-16 dowregulation by progestins. In addition, MPA induced a potent increase in the levels of the oncogenic transcription factor c-Myc, a previously reported suppressor of miR-16. Silencing of the signal transducer and activator of transcription 3 (Stat3) by siRNA, abrogated MPA capacity to induce c-Myc expression. Cyclin E, a cell cycle promoter with a major role in breast cancer progression, has been shown to be a miR-16 target. In this study, we not only demonstrate that MPA induces Cyclin E upregulation (both at the mRNA and protein level), but also that this can be prevented by the inhibition of Stat3 and/or c-Myc. We then wondered whether this regulation would occur in vivo. Thus, we injected 2 x 107 BT-474 cells in nude mice carrying a 17α-Estradiol (E2) pellet, in the absence of matrigel. As previously reported, the tumors first grew but started to regress soon afterwards. At that time point (7 days post-injection), half of the animals were administered MPA. The tumors in the group treated with MPA started to grow at a higher rate than the group supplied with E2 alone. Seven days after MPA supply, we excised some of the tumors and measured miR-16 levels, which showed that the treatment with MPA in vivo, produced a profound downregulation of miR-16. Furthermore, these tumors exhibited a higher level of cyclin E by western blot, validating cyclin E as a target of miR-16 in vivo. Our results are the first ones to identify miR-16 as a tumor suppressor modulated by progestins in human breast cancer cells, demonstrating as well that this regulation is relevant for the proliferative biological effect of progestins. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2305. doi:1538-7445.AM2012-2305

MicroRNAs (miRNAs), a class of small non-coding RNAs, play important roles in cancer development by perturbing the expression of target genes. DNA methylation, a well-studied epigenetic event, also influences gene expression and aberrant methylation is frequently observed in cancer. We previously reported a new paradigm in which hypermethylation-mediated silencing of a miRNA de-repressed its oncogenic target in cancer cells. SOX4, an oncogene, was found to be overexpressed in endometrial cancer, partly because of hypermethylation of miR-129-2. Herein, thirteen additional miRNAs targeting on the 3′-end of untranslated regions of SOX4, and encompassing CpG islands, were identified using computational analysis. Hypermethylation of eight of the thirteen miRNAs was detected in at least two of seven endometrial cancer cell lines. miR-203 was selected for further analysis because this locus was predominantly hypermethylated in endometrial cancer cell lines, but not in normal endometrium. miR-203 expression can be reactivated by pharmacologic induction of DNA demethylation and histone acetylation, indicating that the loss of miR-203 expression is associated with promoter hypermethylation in endometrial cancer. Restoration of miR-203 by cell transfection decreased SOX4 expression and reduced proliferation of endometrial cancer cells. To confirm these in vitro findings in primary endometrial tumors, specimens from two cohorts were analyzed for miR-203 methylation by quantitative pyrosequencing or MassARRAY. In one cohort, miR-203 was significantly hypermethylated in endometrial tumors (n=31), but not in adjacent or un-related normal (n=18) specimens. Methylation of this locus is related to lymphatic and vascular invasion. In the other cohort, increased methylation was observed in primary tumors (n=114), but not in normal controls (n=22). Hypermethylation of miR-203 was positively associated with MLH1 methylation and MSI status. In conclusion, we present an emerging phenomenon that epigenetic silencing of multiple miRNAs could lead to overexpression of a single oncogene in endometrial cancer. This work is supported, in part, by NIH grants U54 CA113001 (THH) and P50 CA134254 (PJG, THH). Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4040. doi:1538-7445.AM2012-4040

Women with advanced stage ovarian cancer have a five-year survival rate of less than 25%. Although most patients respond to platinum-based chemotherapy, relapses are common, leading to platinum-resistant ovarian cancer, which is uniformly fatal. Similar to other malignancies, ovarian cancer progression is associated with transcriptional deregulation and such changes contribute to ovarian cancer progression and development of resistance to chemotherapy. In an effort to better understand the causes of acquired platinum resistance in ovarian cancer, we performed whole transcriptome analysis of platinum sensitive and resistant ovarian cancer cell lines. We used RNA-sequencing to identify candidate genes and pathways that contribute to platinum-resistant ovarian cancer. We detected altered mRNA expression of transcription factors (DMRT3, DMRT1, GATA1, EMX2, LHX1, SRY, SOX9, FOXL2, LHX9) and signaling pathway genes (RXFP2, AR, WT1, FGF9, RSPO1, TUSC3, NROB1, WNT4). Additionally, significant up regulation (>20 fold increase) of the long non-coding RNAs (lncRNAs) HOTAIR and HOTTIP, which direct polycomb group and trithorax complexes to HOX promoters, was detected. We observed elevated HoxA gene expression (> 100 fold in some cases) associated with increased HOTTIP lncRNA expression in the platinum resistant cells. Altered expression of genes associated with DNA methylation (DNMT1, DNMT3A, DNMT3B, DNMT3L MECP2, MBD3L1, MBD6, MBD2, MBD3L2, MBD5, MBD1, MBD3, MBD4) was also observed. Furthermore, the splicing patterns of BRCA1 and BRCA2 genes in platinum resistant cells were altered, resulting in splice variants lacking functional coding regions. Altered BRCA1 and BRCA2 splicing patterns were correlated with reduced expression levels for numerous splicing factors (A2BP1, PTBP1, RBM9, SFRS3, ARID3A, ARID3B, SF1). DNA methylation analysis indicated epigenetic derepression consistent with increased expression for gonad developmental genes (HOTAIR, HOTTIP, HOXA genes). Our data suggest that genes associated ovarian development and differentiation contribute to the development of platinum resistant ovarian cancer. We are currently conducting integrated data and bioinformatics analyses to further investigate changes found in platinum resistance. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4188. doi:1538-7445.AM2012-4188

Caveolin-1 (Cav1), a multifunctional membrane protein, regulates caveolae-dependent lipid trafficking, vesicular transport and signal transduction. Cav1 expression is decreased in breast carcinomas compared to normal tissue, and loss of Cav1 expression promotes mammary tumorigenesis. However, recent reports indicate that Cav1 is overexpressed in a subset of basal-like breast carcinomas and consider it as a basal marker. To investigate the mechanism that results in differential Cav1 expression in breast cancer, we performed genome-wide profiling of DNA methylation using affinity purification and subsequent next-generation sequencing of eluted DNA (MethylCap-seq) on 30 breast cancer cell lines. In breast cancer cell lines displaying low Cav1 expression (“Cav1-low;” n=15, mostly luminal subtype), Cav1 promoter CpG island (CGI) hypermethylation was observed in only four cell lines. In the remaining Cav1-low lines, dense methylation at “CGI shores” (methylation at regions outside of CGI) was seen, while Cav1 promoter CGI methylation was strikingly low or absent. In “Cav1-high” cell lines (n=15 of basal-like subtype), hypomethylation of both promoter CGI and CGI shores was observed. By integrating the methylome data with Cav1 mRNA expression profiles, we found a significant negative correlation between Cav1 CGI shore methylation and Cav1 gene expression. A similar DNA methylation pattern was observed in a panel of antiestrogen-sensitive and -resistant cell lines previously generated by our lab, with hypermethylation at CGI shores for a Cav1-low, tamoxifen-resistant line, and CGI shore hypomethylation in Cav1-high, fulvestrant-resistant lines (basal-like). Treatment of Cav1-low cells with the DNA methyltransferase inhibitor 5-aza-deoxycytidine resulted in demethylation of CGI shores and Cav1 re-expression, further confirming the regulation of Cav1 expression by CGI shore methylation. ChIP-seq results of Cav1-low cells indicated that the Cav1 CGI hypomethylation was due to H3K4me2 occupancy. SiRNA-mediated Cav1 knockdown resulted in a significant inhibition of cell growth and invasion, indicating an important role of Cav1 in supporting breast cancer cell progression. Furthermore, by using an on-line survival analysis tool (Kaplan Meier Plotter), we determined a significant negative correlation between Cav1 levels and overall survival for patients with ERα-negative breast tumors. The results of this study demonstrate that DNA methylation at Cav1 CGI shores is associated with tumor progression, displaying hypomethylation in normal breast epithelial cells, hypermethylation in luminal breast cancer cells, and hypomethylation in basal-like breast cancer cells. In addition, Cav1 CGI shore methylation may represent a novel prognostic factor for ERα-negative, fulvestrant-resistant breast cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5013. doi:1538-7445.AM2012-5013