Natural antisense transcripts drive a regulatory cascade controlling c-MYC transcription

Cis-natural antisense transcripts (cis-NATs) are long noncoding RNAs transcribed from the opposite strand and overlapping coding and noncoding genes on the sense strand. cis-NATs are widely present in the human genome and can be involved in multiple mechanisms of gene regulation. Here, we describe the presence of cis-NATs in the 3′ distal region of the c-MYC locus and investigate their impact on transcriptional regulation of this key oncogene in human cancers. We found that cis-NATs are produced as consequence of the activation of cryptic transcription initiation sites in the 3′ distal region downstream of the c-MYC 3′UTR. The process is tightly regulated and leads to the formation of two main transcripts, NAT6531 and NAT6558, which differ in their ability to fold into stem-loop secondary structures. NAT6531 acts as a substrate for DICER and as a source of small RNAs capable of modulating c-MYC transcription. This complex system, based on the interplay between cis-NATs and NAT-derived small RNAs, may represent an important layer of epigenetic regulation of the expression of c-MYC and other genes in human cells.

Opposing effects of cancer-type-specific SPOP mutants on BET protein degradation and sensitivity to BET inhibitors

It is generally assumed that recurrent mutations within a given cancer driver gene elicit similar drug responses. Cancer genome studies have identified recurrent but divergent missense mutations in the substrate recognition domain of the ubiquitin ligase adaptor SPOP in endometrial and prostate cancer. Their therapeutic implications remain incompletely understood. Here, we analyzed changes in the ubiquitin landscape induced by endometrial cancer-associated SPOP mutations and identified BRD2, BRD3 and BRD4 proteins (BETs) as SPOP-CUL3 substrates that are preferentially degraded by endometrial SPOP mutants. The resulting reduction of BET protein levels sensitized cancer cells to BET inhibitors. Conversely, prostate cancer-specific SPOP mutants impaired degradation of BETs, promoting resistance against their pharmacologic inhibition. These results uncover an oncogenomics paradox, whereby mutations within the same domain evoke opposing drug susceptibilities. Specifically, we provide a molecular rationale for the use of BET inhibitors to treat endometrial but not prostate cancer patients with SPOP mutations.

Abstract 2900: Sigma-1 receptor control tumorigenic and stem cell-like phenotype in human cancers

Tumor-initiating stem-like cancer cells drive tumor progression, metastasis and treatment failure. Understanding the pathways driving self-renewal and expansion of cancer stem-like cells (CSCs) in human cancers may provide actionable therapeutic targets for developing novel treatment strategies. Metabolic reprogramming and mitochondrial homeostasis are emerging as key features of CSCs. The sigma-1 receptor (Sig-1R) is a ligand-activated chaperone protein localized at the ER-mitochondria membrane and involved in inter-organelle signaling, mitochondrial homeostasis and stress response. Sig-1R is up-regulated in many human cancers, although its role in tumorigenesis is unclear. Here, we examined the role of Sig-1R on survival and expansion of cancer cells with stem-like properties using genetic knockdown and selective pharmacological antagonists. Transient and stable depletion of Sig-1R using small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs), respectively, affected clonogenic and tumor-sphere forming capability of prostate cancer cell lines. Cell proliferation and viability under standard culture conditions were minimally affected. Selective high affinity Sig-1R antagonists also suppressed clonogenicity and tumor-sphere formation, reproducing the effects of genetic depletion. Notably, stable Sig-1R knockdown with shRNAs drastically reduced development of tumor xenografts in mice, indicating a reversal of tumorigenic and stem-like properties upon depletion of Sig-1R. Sig-1R knockdown impaired mitochondrial function with reduced mitochondrial membrane potential (flow cytometry JC-1 assay) and respiratory capacity (Seahorse Mito Stress assay). These effects were more evident under metabolic stress induced by glucose starvation and were associated with drastic changes in morphology and intracellular distribution of mitochondria. Similar metabolic effects were seen with selective Sig-1R antagonists. These findings indicate that Sig-1R sustains tumorigenic properties by enhancing mitochondrial homeostasis and metabolic adaptability of stem-like cancer cells ensuring their long-term survival and self-renewal capability. Targeting the Sig-1R with selective antagonists could be an innovative approach to cancer treatment capable of preventing survival and expansion of tumor-initiating stem-like cancer cells in human cancers.

Citation Format: Gianluca Civenni, Martina Marchetti, Shusil Pandit, Celeste De Monte, Federica Sereni, Jessica Merulla, Sabrina Zadic, Marco Losa, Sara Allegrini, Domenico Albino, Sarah Mapelli, Erik Laurini, Bernhard Wunsch, Sabrina Pricl, Giuseppina M. Carbone, Carlo V. Catapano. Sigma-1 receptor control tumorigenic and stem cell-like phenotype in human cancers [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 2900. doi:10.1158/1538-7445.AM2017-2900

A promoter-proximal transcript targeted by genetic polymorphism controls E-cadherin silencing in human cancers

Long noncoding RNAs are emerging players in the epigenetic machinery with key roles in development and diseases. Here we uncover a complex network comprising a promoter-associated noncoding RNA (paRNA), microRNA and epigenetic regulators that controls transcription of the tumour suppressor E-cadherin in epithelial cancers. E-cadherin silencing relies on the formation of a complex between the paRNA and microRNA-guided Argonaute 1 that, together, recruit SUV39H1 and induce repressive chromatin modifications in the gene promoter. A single nucleotide polymorphism (rs16260) linked to increased cancer risk alters the secondary structure of the paRNA, with the risk allele facilitating the assembly of the microRNA-guided Argonaute 1 complex and gene silencing. Collectively, these data demonstrate the role of a paRNA in E-cadherin regulation and the impact of a noncoding genetic variant on its function. Deregulation of paRNA-based epigenetic networks may contribute to cancer and other diseases making them promising targets for drug discovery.

The ETS factor ESE3/EHF represses IL-6 preventing STAT3 activation and expansion of the prostate cancer stem-like compartment

Metastatic prostate cancer represents a yet unsolved clinical problem due to the high frequency of relapse and treatment resistance. Understanding the pathways that lead to prostate cancer progression is an important task to prevent this deadly disease. The ETS transcription factor ESE3/EHF has an important role in differentiation of human prostate epithelial cells. Loss of ESE3/EHF in prostate epithelial cells determines transformation, epithelial-to-mesenchymal transition (EMT) and acquisition of stem-like properties. In this study we identify IL-6 as a direct target of ESE3/EHF that is activated in prostate epithelial cells upon loss of ESE3/EHF. ESE3/EHF and IL-6 were significantly inversely correlated in prostate tumors. Chromatin immunoprecipitation confirmed binding of ESE3/EHF to a novel ETS binding site in the IL-6 gene promoter. Inhibition of IL-6 reverted transformation and stem-like phenotype in tumorigenic ESE3/EHF knockdown prostate epithelial cell models. Conversely, IL-6 stimulation induced malignant phenotypes, stem-like behavior and STAT3 activation. Increased level of IL-6 was observed in prostatospheres compared with adherent bulk cancer cells and this was associated with stronger activation of STAT3. Human prostate tumors with IL-6 elevation and loss of ESE3/EHF were associated with STAT3 activation and displayed upregulation of genes related to cell adhesion, cancer stem-like and metastatic spread. Pharmacological inhibition of IL-6/STAT3 activation by a JAK inhibitor restrained cancer stem cell growth in vitro and inhibited self-renewal in vivo. This study identifies a novel connection between the transcription factor ESE3/EHF and the IL-6/JAK/STAT3 pathway and suggests that targeting this axis might be preferentially beneficial in tumors with loss of ESE3/EHF.

MicroRNA-424 impairs ubiquitination to activate STAT3 and promote prostate tumor progression

Mutations and deletions in components of ubiquitin ligase complexes that lead to alterations in protein turnover are important mechanisms in driving tumorigenesis. Here we describe an alternative mechanism involving upregulation of the microRNA miR-424 that leads to impaired ubiquitination and degradation of oncogenic transcription factors in prostate cancers. We found that miR-424 targets the E3 ubiquitin ligase COP1 and identified STAT3 as a key substrate of COP1 in promoting tumorigenic and cancer stem-like properties in prostate epithelial cells. Altered protein turnover due to impaired COP1 function led to accumulation and enhanced basal and cytokine-induced activity of STAT3. We further determined that loss of the ETS factor ESE3/EHF is the initial event that triggers the deregulation of the miR-424/COP1/STAT3 axis. COP1 silencing and STAT3 activation were effectively reverted by blocking of miR-424, suggesting a possible strategy to attack this key node of tumorigenesis in ESE3/EHF-deficient tumors. These results establish miR-424 as an oncogenic effector linked to noncanonical activation of STAT3 and as a potential therapeutic target.

A Small-Molecule Inhibitor of Lin28

New discoveries in RNA biology underscore a need for chemical tools to clarify their roles in pathophysiological mechanisms. In certain cancers, synthesis of the let-7 microRNA tumor suppressor is blocked by an RNA binding protein (RBP) Lin28, which docks onto a conserved sequence in let-7 precursor RNA molecules and prevents their maturation. Thus, the Lin28/let-7 interaction might be an attractive drug target, if not for the well-known difficulty in targeting RNA-protein interactions with drugs. Here, we describe a protein/RNA FRET assay using a GFP-Lin28 donor and a black-hole quencher (BHQ)-labeled let-7 acceptor, a fluorescent protein/quencher combination which is rarely used in screening despite favorable spectral properties. We tested 16 000 molecules and identified N-methyl-N-[3-(3-methyl[1,2,4]triazolo[4,3-b]pyridazin-6-yl)phenyl]acetamide, which blocked the Lin28/let-7 interaction, rescued let-7 processing and function in Lin28-expressing cancer cells, induced differentiation of mouse embryonic stem cells, and reduced tumor-sphere formation by 22Rv1 and Huh7 cells. A biotinylated derivative captured Lin28 from cell lysates consistent with an on-target mechanism in cells, though the compound also showed some activity against bromodomains in selectivity assays. The Lin28/let-7 axis is presently of high interest not only for its role as a bistable switch in stem-cell biology but also because of its prominent roles in numerous diseases. We anticipate that much can be learned from the use of this first reported small molecule antagonist of Lin28, including the potential of the Lin28/let-7 interaction as a new drug target for selected cancers. Furthermore, this approach to assay development may be used to identify antagonists of other RBP/RNA interactions suspected to be operative in pathophysiological mechanisms.

Aphanin, a triterpenoid from Amoora rohituka inhibits K-Ras mutant activity and STAT3 in pancreatic carcinoma cells

Mutations of the K-Ras gene occur in over 90 % of pancreatic carcinomas, and to date, no targeted therapies exist for this genetically defined subset of cancers. STAT3 plays a critical role in KRAS-driven pancreatic tumorigenesis, suggesting its potential as a therapeutic target in this cancer. Therefore, finding novel and potential drugs to inhibit oncogenic K-Ras is a major challenge in cancer therapy. In an attempt to develop novel anti-KRAS mutant chemotherapeutics, we isolated three novel triterpenoids from Amoora rohituka stem and their chemical structures were characterized by extensive 1H-NMR, 13C-NMR, Mass, IR spectroscopic studies and chemical transformations. Aphanin (3 alpha-angeloyloxyolean-12-en-28-oic acid) is one of the isolated novel triterpenoid compounds. We found aphanin exhibited antiproliferative effects, caused G0-G1 cell cycle arrest, inhibits K-Ras G12D mutant activity by decreased STAT3, p-STAT3, Akt, p-Akt, cyclin D1 and c-Myc expressions, and induced apoptosis in pancreatic cancer HPAF-II (ΔKRAS G12D ) cells. The apoptosis proceeded through depletion of GSH with a concomitant increase in the reactive oxygen species production. The results of our study have important implications for the development of aphanin as potential novel agent for the treatment of K-Ras mutant pancreatic cancer, and STAT3-cMyc-cyclinD1 axis may serve as an important predictive biomarker for the therapeutic efficacy.

Abstract 3343: Targeting the Lin28A/B axis reverts stem cell-like phenotype and tumor-initiating properties in prostate cancer

Cancer stem cells (CSCs) represent the most tumorigenic, metastatic and therapy resistant cell subpopulation within human tumors. Current therapies target bulk tumor cells while spare the most aggressive CSC subpopulation. Understanding the mechanisms responsible for the acquisition and maintenance of the CSC phenotype will help to identify new strategies to target CSCs. In this study, we describe a link between deregulated expression of the ETS transcription factor ESE3/EHF and upregulation of Lin28A and Lin28B in prostate CSC-enriched subpopulations. Furthermore, using various cell line models and in vitro/in vivo experimental systems we demonstrate the efficacy of targeting the Lin28A/B axis for selective elimination of cancer cells with tumor-initiating and stem-like properties. Mechanistically, we found that ESE3/EHF represses transcription of Lin28A and Lin28B in normal prostate epithelial cells. Downregulation of ESE3/EHF in prostate tumors led to upregulation of Lin28A and Lin28B and consequent reduction of microRNAs (miRNAs) of the let-7 family, which exert tumor suppressor functions. These events promoted cell transformation and expansion of the prostate CSC subpopulation. Conversely, targeting Lin28A/Lin28B with small interfering RNAs (siRNAs) in transformed prostate epithelial cells and prostate cancer cell lines restored the levels of let-7 miRNAs, decreased expression of several CSC marker genes, and restrained tumor-sphere formation and self-renewal properties in vitro and tumor-initiating capability in vivo. Notably, systemic treatment with a siRNA targeting Lin28B reduced growth of prostate tumor xenografts in mice. This was associated with a significant contraction of the CSC subpopulation in tumor xenografts, as demonstrated by the reduced content of ex vivo tumor-sphere forming cells, reduced expression of CSC marker genes, and upregulation of let-7 miRNAs. Furthermore, tumor cells derived from siLin28B-treated xenografts exhibited reduced in vivo tumor-initiating and self-renewal capability, in line with a persistent loss of CSC properties. Collectively, these data establish the Lin28/let-7 axis as a critical element in malignant transformation and acquisition of tumor-initiating and stem-like properties and identify a valid therapeutic strategy to antagonize CSCs in human prostate cancer.

Citation Format: Domenico Albino, Gianluca Civenni, Cecilia Dallavalle, Martina Roos, Hartmut Jahns, Jonathan Hall, Giuseppina M. Carbone, Carlo V. Catapano. Targeting the Lin28A/B axis reverts stem cell-like phenotype and tumor-initiating properties in prostate cancer. [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 3343.

Abstract 4545: The E3 ubiquitin ligase COP1 controls STAT3 turnover and its loss leads to increased STAT3 stabilization and activation in prostate cancer

The E3 ubiquitin ligase COP1 acts as a tumor suppressor and is deleted in a small percentage of prostate cancers. We reported that COP1 was repressed in prostate tumors through miRNA-mediated silencing, which represents an alternative and more frequent event than genetic deletion. COP1 controls ubiquitination and turnover of c-Jun and ETV1 and its loss has been associated with over-expression of these transcription factors. In this study, we identify STAT3 as a novel substrate of COP1 and report that concomitant deregulation of COP1 and STAT3 leads to prostate cancer progression. In a panel of prostate cancer cell lines, low expression of COP1 was associated with increased level of STAT3 protein and a more aggressive phenotype. Knockdown of COP1 in normal prostate epithelial RWPE-1 cells increased total (tSTAT3) and phosphorylated STAT3 (pSTAT3) and promoted tumorigenic properties. Conversely, over-expression of COP1 in DU145 cells, expressing low level of COP1, reversed the transformed phenotype and reduced tSTAT3 and pSTAT3 level and activation. COP1/STAT3 anti-correlation suggested that STAT3 was a substrate of COP1 for ubiquitination and degradation by the ubiquitin-proteasome system. Consistently, the proteasome inhibitor PS-341 prevented down-regulation of STAT3 in response to COP1 in DU145 cells. Furthermore, COP1 knockdown delayed significantly STAT3 protein turnover in RWPE-1 cells, indicating that COP1 regulated STAT3 degradation in these cells. Co-IP showed that COP1 and STAT3 directly interacted in RWPE-1 and DU145 cells. Interestingly, co-IP with the wild type and phosphorylation defective Y705F mutant STAT3 showed that the interaction with COP1 did not depend on STAT3 phosphorylation. Furthermore, the level of ubiquitinated STAT3 in RWPE1 cells was reduced after COP1 knockdown, whereas increased in DU145 cells after COP1 over-expression. These data provided evidence of COP1-dependent ubiquitination and degradation of STAT3 in normal prostate epithelial cells and, conversely, STAT3 accumulation and activation in prostate cancer cells with loss of COP1. To assess the clinical relevance of these findings, we examined the level of COP1, tSTAT3 and pSTAT3 by IHC in primary prostate tumors (n = 136) from patients with long-term clinical follow up. Low COP1 levels were significantly associated with high tSTAT3 expression (Fisher test p<0.001). Furthermore, pSTAT3 was prevalently observed in the group of COP1 negative/STAT3 high tumors indicative of STAT3 activation. The combination of low COP1 and high STAT3 expression was associated with significantly higher risk of disease recurrence after prostatectomy (p≤0.01) marking patients at risk of poor clinical outcome. Collectively, this study identifies STAT3 as a substrate of COP1 and provides evidence of a novel pathway leading to STAT3 activation in human tumors.

Citation Format: Cecilia Dallavalle, George Thalmann, Carlo V. Catapano, Giuseppina M. R. Carbone. The E3 ubiquitin ligase COP1 controls STAT3 turnover and its loss leads to increased STAT3 stabilization and activation in prostate cancer. [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 4545.

Activation of the Lin28/let-7 Axis by Loss of ESE3/EHF Promotes a Tumorigenic and Stem-like Phenotype in Prostate Cancer

Although cancer stem-like cells (CSC) are thought to be the most tumorigenic, metastatic, and therapy-resistant cell subpopulation within human tumors, current therapies target bulk tumor cells while tending to spare CSC. In seeking to understand mechanisms needed to acquire and maintain a CSC phenotype in prostate cancer, we investigated connections between the ETS transcription factor ESE3/EHF, the Lin28/let-7 microRNA axis, and the CSC subpopulation in this malignancy. In normal cells, we found that ESE3/EHF bound and repressed promoters for the Lin28A and Lin28B genes while activating transcription and maturation of the let-7 microRNAs. In cancer cells, reduced expression of ESE3/EHF upregulated Lin28A and Lin28B and downregulated the let-7 microRNAs. Notably, we found that deregulation of the Lin28/let-7 axis with reduced production of let-7 microRNAs was critical for cell transformation and expansion of prostate CSC. Moreover, targeting Lin28A/Lin28B in cell lines and tumor xenografts mimicked the effects of ESE3/EHF and restrained tumor-initiating and self-renewal properties of prostate CSC both in vitro and in vivo These results establish that tight control by ESE3/EHF over the Lin28/let-7 axis is a critical barrier to malignant transformation, and they also suggest new strategies to antagonize CSC in human prostate cancer for therapeutic purposes. Cancer Res; 76(12); 3629-43. ©2016 AACR.

EC-70124, a Novel Glycosylated Indolocarbazole Multikinase Inhibitor, Reverts Tumorigenic and Stem Cell Properties in Prostate Cancer by Inhibiting STAT3 and NF-κB

Cancer stem cells (CSC) contribute to disease progression and treatment failure in prostate cancer because of their intrinsic resistance to current therapies. The transcription factors NF-κB and STAT3 are frequently activated in advanced prostate cancer and sustain expansion of prostate CSCs. EC-70124 is a novel chimeric indolocarbazole compound generated by metabolic engineering of the biosynthetic pathways of glycosylated indolocarbazoles, such as staurosporine and rebeccamycin. In vitro kinome analyses revealed that EC-70124 acted as a multikinase inhibitor with potent activity against IKKβ and JAK2. In this study, we show that EC-70124 blocked concomitantly NF-κB and STAT3 in prostate cancer cells and particularly prostate CSCs, which exhibited overactivation of these transcription factors. Phosphorylation of IkB and STAT3 (Tyr705), the immediate targets of IKKβ and JAK2, respectively, was rapidly inhibited in vitro by EC-70124 at concentrations that were well below plasma levels in mice. Furthermore, the drug blocked activation of NF-κB and STAT3 reporters and suppressed transcription of their target genes. Treatment with EC-70124 impaired proliferation and colony formation in vitro and delayed development of prostate tumor xenografts. Notably, EC-70124 had profound effects on the prostate CSC subpopulation both in vitro and in vivo Thus, EC-70124 is a potent inhibitor of the NF-κB and STAT3 signaling pathways and blocked tumor growth and maintenance of prostate CSCs. EC-70124 may provide the basis for developing new therapeutic strategies that combine agents directed to the CSC component and the bulk tumor cell population for treatment of advanced prostate cancer. Mol Cancer Ther; 15(5); 806-18. ©2016 AACR.

Abstract B119: Blocking metabolic stress response with genetic knockdown and selective ligands of sigma-1 receptor in cancer cells

There is increasing interest in the biological pathways that determine the ability of cancer cells to adapt and survive to metabolic and micro-environmental stress and sustain tumor-initiating and metastatic properties. A better understanding of these pathways may lead to the identification of key nodes and targetable elements for development novel therapeutic strategies for cancer. The sigma-1 receptor (Sig1R) is a ubiquitously expressed membrane-bound protein that acts as ligand-activated molecular chaperone. Sig1R is localized preferentially at the endoplasmic reticulum (ER) and the mitochondria-associated ER membrane (MAM) domains and controls calcium signaling between ER and mitochondria in response to stress signals. Sig1R is often up-regulated in cancer cell lines and human tumors suggesting that it might have a role in tumorigenesis, although detailed functional studies are missing. In this study we examined whether Sig1R sustains proliferation, survival and tumorigenic properties of human cancer cells. Knockdown of Sig1R using small interfering RNA (siRNA) in human prostate and lung cancer cell lines had profound effect on proliferation, clonogenic capability and tumor-sphere formation, indicating reversal of the tumorigenic and stem-like phenotype in absence of Sig1R. Next, in the attempt to discover pharmacological agents that could phenocopy the effects of the genetic knockdown in cancer cells we tested a series of structurally diverse Sig1R ligands selected for high affinity and selectivity for the receptor. We identified various Sig1R ligands that behaved as antagonists of the receptor functions in cancer cells inhibiting clonogenicity and tumor-sphere formation. Effective concentrations of the ligands were in the micromolar range (1-10 μM). At these doses, Sig1R antagonistic ligands almost completely suppressed clonogenic and tumor sphere forming capability of cancer cells. Furthermore, whereas cell proliferation and viability under standard culture conditions were minimally affected by Sig1R ligands, their effects were more pronounced under glucose starvation, a condition that causes metabolic stress in cancer cells. Notably, both Sig1R knockdown and pharmacological antagonists led to impaired mitochondrial function, which was more evident under glucose starvation. Thus, the absence of functional Sig1R reduced mitochondrial activity and adaptability of cancer cells to metabolic stress. These results indicate that the presence of functional Sig1R sustains tumorigenic and stem-like properties by enhancing the metabolic flexibility of cancer cells through the control of ER-mitochondria functions. Highly selective Sig1R antagonists are promising leads for discovering innovative therapeutic strategies and represent effective candidates for pharmacological targeting of stem-like and tumor-initiating cells in human cancers.

Citation Format: Gianluca Civenni, Celeste De Monte, Federica Sereni, Sara Allegrini, Roberto Bosotti, Erik Laurini, Bernhard Wunsch, Sabrina Pricl, Giuseppina M. Carbone, Carlo V. Catapano. Blocking metabolic stress response with genetic knockdown and selective ligands of sigma-1 receptor in cancer cells. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B119.

Abstract 4968: microRNA-mediated silencing of COP1 and altered ubiquitination of key oncogenic transcription factors promote cancer stem cell (CSC) phenotype and prostate cancer progression

Mutations and deletions of ubiquitin ligase complex proteins are emerging as important mechanisms driving tumorigenesis. In this study we report an alternative mechanism, depending on microRNA-mediated post-transcriptional silencing, leading to altered ubiquitination of key oncogenic proteins and induction of tumorigenic and CSC properties in prostate epithelial cells (PrECs). We found that increased expression of miR-424 promotes malignant transformation of normal PrECs by targeting the E3 ubiquitin ligase COP1. miR-424 was upregulated in primary prostate cancers and prevalently in ERG negative tumors. Bioinformatics and functional analysis demonstrated that miR-424 targeted COP1 mRNA in PrECs drastically reducing its protein level. Moreover, miR-424 and COP1 expression were inversely correlated in prostate tumors and associated with enrichment of CSC features. Functionally, over-expression of miR-424 or knockdown of COP1 in PrECs increased anchorage-independent growth, cell migration and prostatosphere formation under CSC selective conditions. Consistently, inhibition of miR-424 or over-expression of COP1 prevented these phenotypic changes in normal PrECs and prostate cancer cell lines. Moreover, COP1 knockdown reproduced closely the effects of miR-424 upregulation in PrECs. Mechanistically, we found that silencing of COP1 by miR-424 resulted in reduced turnover and increased level of several oncogenic transcription factors, including known COP1 substrates like c-JUN and ETV1. Furthermore, we identified STAT3 as a novel substrate of the miR-424/COP1 axis. Consistently, miR-424 upregulation and COP1 silencing increased STAT3 protein level and enhanced basal and cytokine induced STAT3 activity in PrECs and prostate cancer cells. These effects were blocked by miR-424 inhibition and COP1 overexpression. These results establish the miR-424/COP1 axis as a relevant oncogenic pathway acting through deregulation of key transcription factors and with important prognostic and therapeutic implications.

Citation Format: Cecilia Dallavalle, Domenico Albino, Gianluca Civenni, Laura Curti, Paola Ostano, Maurizia Mello-Grand, Ramon Garcia-Escudero, Giovanna Chiorino, Carlo V. Catapano, Giuseppina M. R. Carbone. microRNA-mediated silencing of COP1 and altered ubiquitination of key oncogenic transcription factors promote cancer stem cell (CSC) phenotype and prostate cancer progression. [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 4968. doi:10.1158/1538-7445.AM2015-4968

Abstract 147: Epigenetic networks and promoter-associated long noncoding RNAs (paRNAs) in prostate cancer

Long noncoding RNAs (lncRNAs) are emerging as important players in epigenetic mechanisms and human diseases, including cancer. paRNAs represent a class of lncRNAs transcribed in promoter-proximal regions of genes. However, their function is still unknown. In this study we examined the functional relationship between paRNAs and expression of neighboring genes. By analyzing Global Run On sequencing (GRO-Seq) data from different cell lines and experimental conditions we identified large numbers of nascent transcripts with both sense (S) and antisense (AS) orientation in the 2 kb upstream region of many genes. Interestingly, many paRNAs were found to be shared across different cell lines, denoting a conserved function. Furthermore, many paRNAs were dynamically linked to their neighboring gene expression, exhibiting concomitant changes in transcription in different experimental conditions. Although the overall mechanisms and network of co-acting elements may be highly complex, we defined subgroups of genes whose paRNAs behaved consistently in similar ways. This genome-wide analysis suggested that specific patterns of S and AS paRNAs might be associated with either transcriptional activation or repression of neighboring genes. To provide support to this hypothesis, we focused on CDH1, the gene encoding E-cadherin, an important tumor suppressor silenced in many epithelial cancers. We uncovered a complex paRNA-based epigenetic network controlling CDH1 transcription in normal and cancer cells. In addition to S and AS paRNAs, the network included the RNA interference protein Argonaute 1 (AGO1) and the epigenetic effector SUV39H1. Silencing of CDH1 in prostate cancer cells relied on binding of AGO1 to the S paRNA, which in turn recruited SUV39H1 and induced repressive histone modifications (H3K9me) at the CDH1 promoter. Notably, this mechanism was shared by other genes that were similarly silenced by AGO1 and SUV39H1 and reactivated by AGO1 and SUV39H1 knockdown in prostate cancer cells. Integrating GRO-seq data and ChIP-seq data we found that many AGO1 and SUV39H1 co-regulated genes showed evidence of bidirectional paRNAs and AGO1 binding in their promoters. Furthermore, many co-regulated genes had putative tumor suppressor function, were downregulated in human tumors and were associated with metastasis and poor clinical outcome. This study reveals the presence of complex RNA-based epigenetic networks that rely on transcription of bidirectional paRNAs and interaction with AGO1 and epigenetic effectors. paRNA-based networks can coordinate epigenetic silencing of critical tumor suppressors, like CDH1, and promote tumor development and progression. These findings give also new perspectives and insights on epigenetic mechanisms and identify paRNAs as novel targetable elements in the epigenetic machinery.

Citation Format: Sara Napoli, Sarah Mapelli, Giuseppina Pisignano, Abhishek Mitra, Ramon Garcia-Escudero, Giuseppina M. R. Carbone, Carlo V. Catapano. Epigenetic networks and promoter-associated long noncoding RNAs (paRNAs) in prostate 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 147. doi:10.1158/1538-7445.AM2015-147

Abstract 2625: Targeting prostate cancer stem cells (CSCs) with the novel BET bromodomain (BRD) protein inhibitor OTX015

In human neoplasias small subpopulations of cancer cells with stem cell-like properties are thought to play a role in progression, metastasis, disease recurrence and treatment failure. Effective targeting of CSCs may thus provide the basis for a paradigm shift in cancer therapy. Epigenetic and transcriptional regulators such as BRD proteins (BRD2/3/4) may contribute to the CSC phenotype and as such represent druggable targets for CSC-directed therapies. No data are currently available on the anti-CSC activity of BRD protein inhibitors. OTX015 is an orally bioavailable small molecule BRD protein inhibitor. It demonstrates broad anticancer activity in vitro and is currently under clinical evaluation in hematologic malignancies and solid tumor patients, including castrate-resistant prostate cancer. We investigated the effects of OTX015 on the phenotypes of bulk tumor cells and CSCs in a panel of human prostate cancer cell lines, including the androgen receptor positive (LNCaP, VCaP and 22RV1) and negative (DU145 and PC3) prostate cell lines. Similar levels of BRD proteins were present in the cell lines independent of androgen receptor (AR) status and the presence of ETS gene fusions. OTX015 strongly inhibited proliferation in all cell lines tested (IC50, 200-800 nM) by MTT assays after 72h-exposure. Soft agar clonogenic capability of prostate cancer cells was also inhibited by OTX015 (IC50, 20-100 nM). OTX015 also potently inhibited the CSC component in prostato-sphere forming assays (IC50, 1-100 nM) after 10 days of treatment. Of note, the CSC-directed activity of OTX015 was independent of the AR and ETS translocation state. Effective inhibition of CSCs by OTX015 was consistently associated with downregulation of critical CSC genes, including c-Myc and Nanog mRNA. In vivo experiments in 5 human tumor xenografts models (LNCaP, VCaP, 22RV1, DU145 and PC3) in nude mice are ongoing to evaluate antitumor and anti-CSC activity of OTX015. To our knowledge, this is the first evidence implicating BRD proteins in the expansion and maintenance of prostate CSCs independently of the specific biologic and genetic features of the bulk tumor cell population. These results suggest that the BRD protein inhibitor OTX015 could be effective for eradicating the CSC component in prostate cancer, providing the basis for novel treatment approaches.

Citation Format: Gianluca Civenni, Silvia Pedrani, Sara Allegrini, Antonina Bruccoleri, Domenico Albino, Sandra Pinton, Ramon Garcia-Escudero, L'Houcine Ouafik, Esteban Cvitkovic, Giuseppina M. Carbone, Carlo V. Catapano. Targeting prostate cancer stem cells (CSCs) with the novel BET bromodomain (BRD) protein inhibitor OTX015. [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 2625. doi:10.1158/1538-7445.AM2015-2625

Hitting the right spot: Mechanism of action of OPB-31121, a novel and potent inhibitor of the Signal Transducer and Activator of Transcription 3 (STAT3)

STAT3 is a key element in many oncogenic pathways and, like other transcription factors, is an attractive target for development of novel anticancer drugs. However, interfering with STAT3 functions has been a difficult task and very few small molecule inhibitors have made their way to the clinic. OPB-31121, an anticancer compound currently in clinical trials, has been reported to affect STAT3 signaling, although its mechanism of action has not been unequivocally demonstrated. In this study, we used a combined computational and experimental approach to investigate the molecular target and the mode of interaction of OPB-31121 with STAT3. In parallel, similar studies were performed with known STAT3 inhibitors (STAT3i) to validate our approach. Computational docking and molecular dynamics simulation (MDS) showed that OPB-31121 interacted with high affinity with the SH2 domain of STAT3. Interestingly, there was no overlap of the OPB-31121 binding site with those of the other STAT3i. Computational predictions were confirmed by in vitro binding assays and competition experiments along with site-directed mutagenesis of critical residues in the STAT3 SH2 domain. Isothermal titration calorimetry experiments demonstrated the remarkably high affinity of OPB-31121 for STAT3 with Kd (10 nM) 2-3 orders lower than other STAT3i. Notably, a similar ranking of the potency of the compounds was observed in terms of inhibition of STAT3 phosphorylation, cancer cell proliferation and clonogenicity. These results suggest that the high affinity and efficacy of OPB-31121 might be related to the unique features and mode of interaction of OPB-31121 with STAT3. These unique characteristics make OPB-31121 a promising candidate for further development and an interesting lead for designing new, more effective STAT3i.

Short loop-targeting oligoribonucleotides antagonize Lin28 and enable pre-let-7 processing and suppression of cell growth in let-7-deficient cancer cells

MicroRNAs (miRNAs) originate from stem-loop-containing precursors (pre-miRNAs, pri-miRNAs) and mature by means of the Drosha and Dicer endonucleases and their associated factors. The let-7 miRNAs have prominent roles in developmental differentiation and in regulating cell proliferation. In cancer, the tumor suppressor function of let-7 is abrogated by overexpression of Lin28, one of several RNA-binding proteins that regulate let-7 biogenesis by interacting with conserved motifs in let-7 precursors close to the Dicer cleavage site. Using in vitro assays, we have identified a binding site for short modified oligoribonucleotides ('looptomirs') overlapping that of Lin28 in pre-let-7a-2. These looptomirs selectively antagonize the docking of Lin28, but still permit processing of pre-let-7a-2 by Dicer. Looptomirs restored synthesis of mature let-7 and inhibited growth and clonogenic potential in Lin28 overexpressing hepatocarcinoma cells, thereby demonstrating a promising new means to rescue defective miRNA biogenesis in Lin28-dependent cancers.

Abstract 1451: MicroRNAs regulated by ESE3/EHF control important mediators of epithelial cell differentiation and stemness in prostate tumors

Deregulated expression of ETS transcription factors has emerged as an important event in prostate cancer pathogenesis. We found that loss of the ETS factor ESE3/EHF induced a broad dedifferentiation program associated with epithelial-to-mesenchymal transition (EMT) and induction of metastatic and cancer stem-like cell properties. To understand the mechanism by which ESE3/EHF controls differentiation of prostate epithelial cells, we examined microRNA (miRNA) expression in a cohort of primary prostate tumors and prostate epithelial normal and cancer cells using miRNA gene arrays. A distinct set of miRNAs was specifically deregulated in cancer cells and tumors with low ESE3/EHF expression. Bioinformatic analysis indicated that the deregulated miRNAs controlled many genes involved in EMT and cell stemness. Interestingly, we found that miR-424 was at the top list of the miRNAs up-regulated in ESE3 low expressing tumors and cell lines. This finding was confirmed by qRT-PCR both in cells and human tumors. Functional assays showed that ESE3/EHF controlled directly miR-424 by binding to the pre-miRNA promoter and repressing its transcription. Inhibition of miR-424 using an antimiR reduced anchorage-independent growth and cell migration in cancer cells with low ESE3 expression and high miR-424 level. On the contrary, stable expression of pre-miR-424 in cells with low endogenous miR-424 level increased anchorage-independent growth and cell migration. Furthermore, modulation of miR-424 expression affected in vitro prostatosphere formation, a phenotype associated with cancer stem-like cell properties. Consistently, inhibition of miR-424 in DU145 prostate cancer cells reduced growth of tumor xenografts in immunodeficient mice. Integrating bioinformatic analyses of the predicted targets and gene profiling of cells with miR-424 overexpression we found that miRNA-424 controlled several factors involved in protein degradation. Collectively, these results show for the first time that ESE3/EHF controls a distinct network of miRNAs with both oncogenic and tumor suppressor functions. Loss of ESE3/EHF resulted specifically in increased expression of miR-424, which has oncogenic properties in prostate epithelial cells. This represents a novel mechanism by which deregulation of ESE3/EHF impact on prostate tumorigenesis. Thus, targeting miR-424 could be a novel therapeutic strategy for prostate cancer.

Citation Format: Cecilia Dallavalle, Domenico Albino, Gianluca Civenni, Paola Ostano, Davide Genini, Ramon Garcia-Escudero, Laura Curti, Sandra Pinton, Manuela Sarti, Giovanna Chiorino, Carlo V. Catapano, Giuseppina M. R. Carbone. MicroRNAs regulated by ESE3/EHF control important mediators of epithelial cell differentiation and stemness in prostate tumors. [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 1451. doi:10.1158/1538-7445.AM2014-1451

Abstract 2349: An RNA-based epigenetic network controls the expression of E-cadherin in epithelial normal and cancer cells

Epigenetic mechanisms play important roles in many human diseases. However, what drives epigenetic regulators to specific genomic locations is still an open question. Promoter-associated long non-coding RNAs (paRNAs) have been identified in many genes and have been proposed to act as docking elements for recruitment of epigenetic regulators to gene promoters, although the underlying mechanisms are still poorly characterized. In this study we investigated the role of paRNAs in transcriptional regulation of E-cadherin (CDH1), a trans-membrane glycoprotein and an important determinant of epithelial cell differentiation. Transcriptional silencing of E-cadherin is frequent in epithelial cancers and loss of E-cadherin expression triggers epithelial-to-mesenchymal transition (EMT) and acquisition of tumor-initiating properties. We found that bidirectional transcription occurred from independent initiation sites in the E-cadherin promoter and generated sense (S) and antisense (AS) paRNAs that coordinated the transcriptional activity of the gene. S and AS paRNAs had distinct expression patterns in normal and cancer cell lines and human prostate tumors. Both in cancer cell lines and human tumors the prevalence of S paRNAs and low AS/S paRNA ratio were associated with low E-cadherin expression. We found that the S paRNA bound Argonaute 1 (AGO1) and coordinated silencing of the gene by recruiting, along with AGO1, the histone methyltransferase SUV39H1 to the promoter. Consistently, knockdown of either S paRNA or AGO1 reduced SUV39H1 promoter occupancy and reactivated E-cadherin transcription in low expressing cells. Using promoter reporter and expression constructs we showed that the S paRNA and AGO1 acted in cis to control promoter activity and that the interaction with AGO1 required specific element of the S paRNA. Furthermore, recruitment of AGO1 to the S paRNA and CDH1 promoter depended on an isomiR derived through alternative processing and editing of pre-miR-4534. Accordingly, mutations that disrupted the isomiR binding sequence in the S paRNA reduced AGO1 binding and increased promoter activity, while depletion of the isomiR induced CDH1 expression. Notably, the novel isomiR was more abundant in transformed epithelial cells and cancer cell lines than normal prostate epithelial cells, accumulated preferentially in nuclei and was specifically associated with S paRNA and chromatin-bound AGO1 in low CDH1 expressing cancer cells. This study reveals a complex RNA-based epigenetic network that relies on sequence-specific interactions between a paRNA, a small RNA and AGO1 and coordinates transcriptional silencing of a critical gene involved in tumor development and progression. Our findings give also a new prospective and mechanistic insights on the interplay between epigenetic regulatory factors indentifying paRNAs as relevant elements in these processes and potential targets for gene modulation strategies.

Citation Format: Sara Napoli, Giuseppina Pisignano, Ramon Garcia-Escudero, Giuseppina Carbone, Carlo V. Catapano. An RNA-based epigenetic network controls the expression of E-cadherin in epithelial normal and cancer cells. [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 2349. doi:10.1158/1538-7445.AM2014-2349

Abstract 953: Novel inhibitors of signal transducer and activator of transcription 3 (STAT3) show potent activity in cell cultures and tumor xenografts

The transcription factor (TF) STAT3 is an attractive target for development of anticancer drugs. STAT3 is over-expressed and activated in many human malignancies and has an important role in multiple oncogenic signaling pathways affecting proliferation, survival and metabolic adaptation of cancer cells. It has been difficult, however, to develop effective inhibitors of STAT3. In this study, we performed an in-depth analysis of the mechanism of action of two compounds, OPB-31121 and OPB-51602, which are currently undergoing clinical testing. We combined computational docking (CD), molecular dynamic simulation (MDS) and in vitro binding assays to study the compounds interaction with STAT3. CD predicted that OPB-31121 and OPB-51602 could bind to a common pocket in the STAT3 SH2 domain, which was not shared with other STAT3 inhibitors. MDS and in silico mutational analysis allowed refinement of the binding site predictions and an estimate of the relative binding affinities. Isotermal titration calorimetry (ITC) studies confirmed that OPB-31121 and OPB-51602 bound with high affinity (Kd, 5-10 nM) to recombinant STAT3 SH2 domain. Binding of the two compounds was disrupted by mutations of aminoacid residues in the predicted binding pocket and was mutually exclusive in competition assays. In contrast, OPB-31121 and OPB-51602 did not compete for binding with other STAT3 inhibitors, confirming that they occupied distinct pockets in the SH2 domain. In cell culture assays, OPB-31121 and OPB-51602 interfered with both Tyr705 and Ser727 phosphorylation, which are required for full transcriptional activity of STAT3. Proliferation of cancer cells was strongly affected in vitro by OPB-51602 and OPB-31121 in anchorage-dependent growth and soft-agar assays. In these assays OPB-51602 and OPB-31121 were active at low nanomolar concentrations (IC50, 5-10 nM). Interestingly, the compounds were more effective in metabolic stress conditions (e.g., nutrient and glucose depletion), suggesting that STAT3 inhibition interfered with relevant metabolic functions in cancer cells. In vivo treatment with OPB-51602 (PO, 20-40 mg/kg, 3-5 days) reduced Tyr705 and Ser727 phosphorylation in tumor xenografts. Growth of DU145 prostate tumor xenografts was almost completely arrested by daily treatment with OPB-51602 (PO, 20-40 mg/kg, 2 weeks). Interestingly, tumor growth did not resume after discontinuation of the 2-weeks treatment, indicating a persistent impairment of tumor-initiating capability. Altogether, this study demonstrates that STAT3 is the relevant intracellular target of OPB-51602 and OPB-31121. The two compounds bound with high affinity to a distinct pocket in the SH2 domain of STAT3 and interfered with STAT3 functions both in cells and tumor xenografts. These features resulted in distinctive biological activity and pharmacological properties of these novel compounds.

Citation Format: Davide Genini, Lara Brambilla, Erik Laurini, Gianluca Civenni, Sandra Pinton, Manuela Sarti, Ramon Garcia-Escudero, Laurent Perez, Giuseppina M. Carbone, Sabrina Pricl, Carlo V. Catapano. Novel inhibitors of signal transducer and activator of transcription 3 (STAT3) show potent activity in cell cultures and tumor xenografts. [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 953. doi:10.1158/1538-7445.AM2014-953

Abstract 1936: The ETS factor ESE3/EHF controls Lin28A and Lin28B and acts as a barrier for stemness in prostate epithelial cells

Prostate cancer (PCa) is a leading cause of cancer death worldwide. Several studies have provided evidence for the presence of self-renewing cancer stem-like cells (CSCs) in many solid tumors, including prostate cancer. Understanding the molecular mechanism leading to induction of epithelial-to-mesenchymal transition (EMT) and stemness will help to find new therapies for metastatic PCa. We have reported that the ETS factor ESE3/EHF is a tumor suppressor involved in the maintenance of the differentiation state of normal prostate epithelial cells (PrECs). Prostate epithelial cells upon knockdown of ESE3/EHF (ESE3KD PrECs) undergo transformation involving EMT, enlargement of the stem cell compartment with broad reprogramming of the transcriptome. In the process to identify the genes responsible for the activation of stemness in ESE3KD PrECs, we found a significant increase of Lin28A and Lin28B compared to control PrECs. Consistent with their crucial role in stemness maintenance, higher level of Lin28A and Lin28B were detected in the cancer stem cell compartment compared to the bulk population of adherent growing cells and in xenografts derived from the cancer stem cell-enriched population. To relate these effects directly to ESE3/EHF we searched for ETS-binding sites (EBS) in the promoters of the Lin28A and Lin28B. Computational analysis revealed putative EBS in the promoter region of both genes and chromatin immunoprecipitation confirmed the binding of ESE3/EHF to the predicted sites in PrECs and LNCaP cells. Furthermore, ESE3/EHF repressed Lin28A and Lin28B promoter activity in luciferase reporters. Transcriptional repression of Lin28A and Lin28B by ESE3/EHF was confirmed by the enrichment of repressive markers H3K9me and H3K27me in their promoters in LNCAP cells. Knockdown of Lin28A and Lin28B in ESE3KD PrECs by siRNAs reversed anchorage independent growth and in vitro prostatosphere formation. Furthermore, inhibition of Lin28A and Lin28B significantly reduced tumor initiating properties of ESE3KD PrECs in vivo. In contrast, re-expression of Lin28A and Lin28B promoted anchorage-independent growth and increased prostatosphere formation and self renewal in PrECs and LNCaP cells. Together, these data indicate that ESE3/EHF maintains in a repressed state Lin28A and Lin28B and constitutes a barrier to dedifferentiation of prostate epithelial cells. These data indicate also a role of Lin28A and Lin28B in the expansion and maintenance of the stem cell compartment in prostate cancer and underscore their validity as potential therapeutic targets.

Citation Format: Domenico Albino, Gianluca Civenni, Mahnaz Nikpour, Carlo V. Catapano, Giuseppina M. R. Carbone. The ETS factor ESE3/EHF controls Lin28A and Lin28B and acts as a barrier for stemness in prostate epithelial cells. [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 1936. doi:10.1158/1538-7445.AM2014-1936