Development and validation of a clinical decision support system based on PSA, microRNAs, and MRI for the detection of prostate cancer

OBJECTIVES

The aims of this study are to develop and validate a clinical decision support system based on demographics, prostate-specific antigen (PSA), microRNA (miRNA), and MRI for the detection of prostate cancer (PCa) and clinical significant (cs) PCa, and to assess if this system performs better compared to MRI alone.

METHODS

This retrospective, multicenter, observational study included 222 patients (mean age 66, range 46-75 years) who underwent prostate MRI, miRNA (let-7a-5p and miR-103a-3p) assessment, and biopsy. Monoparametric and multiparametric models including age, PSA, miRNA, and MRI outcome were trained on 65% of the data and then validated on the remaining 35% to predict both PCa (any Gleason grade [GG]) and csPCa (GG ≥ 2 vs GG = 1/negative). Accuracy, sensitivity, specificity, positive and negative predictive value (NPV), and area under the receiver operating characteristic curve were calculated.

RESULTS

MRI outcome was the best predictor in the monoparametric model for both detection of PCa, with sensitivity of 90% (95%CI 73-98%) and NPV of 93% (95%CI 82-98%), and for csPCa identification, with sensitivity of 91% (95%CI 72-99%) and NPV of 95% (95%CI 84-99%). Sensitivity and NPV of PSA + miRNA for the detection of csPCa were not statistically different from the other models including MRI alone.

CONCLUSION

MRI stand-alone yielded the best prediction models for both PCa and csPCa detection in biopsy-naïve patients. The use of miRNAs let-7a-5p and miR-103a-3p did not improve classification performances compared to MRI stand-alone results.

CLINICAL RELEVANCE STATEMENT

The use of miRNA (let-7a-5p and miR-103a-3p), PSA, and MRI in a clinical decision support system (CDSS) does not improve MRI stand-alone performance in the detection of PCa and csPCa.

KEY POINTS

• Clinical decision support systems including MRI improve the detection of both prostate cancer and clinically significant prostate cancer with respect to PSA test and/or microRNA. • The use of miRNAs let-7a-5p and miR-103a-3p did not significantly improve MRI stand-alone performance. • Results of this study were in line with previous works on MRI and microRNA.

Plasma microRNA ratios associated with breast cancer detection in a nested case-control study from a mammography screening cohort

Mammographic breast cancer screening is effective in reducing breast cancer mortality. Nevertheless, several limitations are known. Therefore, developing an alternative or complementary non-invasive tool capable of increasing the accuracy of the screening process is highly desirable. The objective of this study was to identify circulating microRNA (miRs) ratios associated with BC in women attending mammography screening. A nested case-control study was conducted within the ANDROMEDA cohort (women of age 46-67 attending BC screening). Pre-diagnostic plasma samples, information on life-styles and common BC risk factors were collected. Small-RNA sequencing was carried out on plasma samples from 65 cases and 66 controls. miR ratios associated with BC were selected by two-sample Wilcoxon test and lasso logistic regression. Subsequent assessment by RT-qPCR of the miRs contained in the selected miR ratios was carried out as a platform validation. To identify the most promising biomarkers, penalised logistic regression was further applied to candidate miR ratios alone, or in combination with non-molecular factors. Small-RNA sequencing yielded 20 candidate miR ratios associated with BC, which were further assessed by RT-qPCR. In the resulting model, penalised logistic regression selected seven miR ratios (miR-199a-3p_let-7a-5p, miR-26b-5p_miR-142-5p, let-7b-5p_miR-19b-3p, miR-101-3p_miR-19b-3p, miR-93-5p_miR-19b-3p, let-7a-5p_miR-22-3p and miR-21-5p_miR-23a-3p), together with body mass index (BMI), menopausal status (MS), the interaction term BMI * MS, life-style score and breast density. The ROC AUC of the model was 0.79 with a sensitivity and specificity of 71.9% and 76.6%, respectively. We identified biomarkers potentially useful for BC screening measured through a widespread and low-cost technique. This is the first study reporting circulating miRs for BC detection in a screening setting. Validation in a wider sample is warranted.Trial registration: The Andromeda prospective cohort study protocol was retrospectively registered on 27-11-2015 (NCT02618538).

Identification of a minimum number of genes to predict triple-negative breast cancer subgroups from gene expression profiles

BACKGROUND

Triple-negative breast cancer (TNBC) is a very heterogeneous disease. Several gene expression and mutation profiling approaches were used to classify it, and all converged to the identification of distinct molecular subtypes, with some overlapping across different approaches. However, a standardised tool to routinely classify TNBC in the clinics and guide personalised treatment is lacking. We aimed at defining a specific gene signature for each of the six TNBC subtypes proposed by Lehman et al. in 2011 (basal-like 1 (BL1); basal-like 2 (BL2); mesenchymal (M); immunomodulatory (IM); mesenchymal stem-like (MSL); and luminal androgen receptor (LAR)), to be able to accurately predict them.

METHODS

Lehman's TNBCtype subtyping tool was applied to RNA-sequencing data from 482 TNBC (GSE164458), and a minimal subtype-specific gene signature was defined by combining two class comparison techniques with seven attribute selection methods. Several machine learning algorithms for subtype prediction were used, and the best classifier was applied on microarray data from 72 Italian TNBC and on the TNBC subset of the BRCA-TCGA data set.

RESULTS

We identified two signatures with the 120 and 81 top up- and downregulated genes that define the six TNBC subtypes, with prediction accuracy ranging from 88.6 to 89.4%, and even improving after removal of the least important genes. Network analysis was used to identify highly interconnected genes within each subgroup. Two druggable matrix metalloproteinases were found in the BL1 and BL2 subsets, and several druggable targets were complementary to androgen receptor or aromatase in the LAR subset. Several secondary drug-target interactions were found among the upregulated genes in the M, IM and MSL subsets.

CONCLUSIONS

Our study took full advantage of available TNBC data sets to stratify samples and genes into distinct subtypes, according to gene expression profiles. The development of a data mining approach to acquire a large amount of information from several data sets has allowed us to identify a well-determined minimal number of genes that may help in the recognition of TNBC subtypes. These genes, most of which have been previously found to be associated with breast cancer, have the potential to become novel diagnostic markers and/or therapeutic targets for specific TNBC subsets.

Two Novel Ceramide-Like Molecules and miR-5100 Levels as Biomarkers Improve Prediction of Prostate Cancer in Gray-Zone PSA

Reliable liquid biopsy-based tools able to accurately discriminate prostate cancer (PCa) from benign prostatic hyperplasia (BPH), when PSA is within the “gray zone” (PSA 4–10), are still urgent. We analyzed plasma samples from a cohort of 102 consecutively recruited patients with PSA levels between 4 and 16 ng/ml, using the SANIST-Cloud Ion Mobility Metabolomic Mass Spectrometry platform, combined with the analysis of a panel of circulating microRNAs (miR). By coupling CIMS ion mobility technology with SANIST, we were able to reveal three new structures among the most differentially expressed metabolites in PCa vs. BPH. In particular, two were classified as polyunsaturated ceramide ester-like and one as polysaturated glycerol ester-like. Penalized logistic regression was applied to build a model to predict PCa, using six circulating miR, seven circulating metabolites, and demographic/clinical variables, as covariates. Four circulating metabolites, miR-5100, and age were selected by the model, and the corresponding prediction score gave an AUC of 0.76 (C.I. = 0.66–0.85). At a specified cut-off, no high-risk tumor was misclassified, and 22 out of 53 BPH were correctly identified, reducing by 40% the false positives of PSA. We developed and applied a novel, minimally invasive, liquid biopsy-based powerful tool to characterize novel metabolites and identified new potential non-invasive biomarkers to better predict PCa, when PSA is uninformative as a tool for precision medicine in genitourinary cancers.

Castration-Induced Downregulation of SPARC in Stromal Cells Drives Neuroendocrine Differentiation of Prostate Cancer

Fatal neuroendocrine differentiation (NED) of castration-resistant prostate cancer is a recurrent mechanism of resistance to androgen deprivation therapies (ADT) and antiandrogen receptor pathway inhibitors (ARPI) in patients. The design of effective therapies for neuroendocrine prostate cancer (NEPC) is complicated by limited knowledge of the molecular mechanisms governing NED. The paucity of acquired genomic alterations and the deregulation of epigenetic and transcription factors suggest a potential contribution from the microenvironment. In this context, whether ADT/ARPI induces stromal cells to release NED-promoting molecules and the underlying molecular networks are unestablished. Here, we utilized transgenic and transplantable mouse models and coculture experiments to unveil a novel tumor-stroma cross-talk that is able to induce NED under the pressure of androgen deprivation. Castration induced upregulation of GRP78 in tumor cells, which triggers miR29-b-mediated downregulation of the matricellular protein SPARC in the nearby stroma. SPARC downregulation enabled stromal cells to release IL6, a known inducer of NED. A drug that targets GRP78 blocked NED in castrated mice. A public, human NEPC gene expression dataset showed that Hspa5 (encoding for GRP78) positively correlates with hallmarks of NED. Finally, prostate cancer specimens from patients developing local NED after ADT showed GRP78 upregulation in tumor cells and SPARC downregulation in the stroma. These results point to GRP78 as a potential therapeutic target and to SPARC downregulation in stromal cells as a potential early biomarker of tumors undergoing NED. SIGNIFICANCE: Tumor-stroma cross-talk promotes neuroendocrine differentiation in prostate cancer in response to hormone therapy via a GRP78/SPARC/IL6 axis, providing potential therapeutic targets and biomarkers for neuroendocrine prostate cancer.

GJB5 association with BRAF mutation and survival in cutaneous malignant melanoma

BACKGROUND

Gap junctional intercellular communication is crucial for epidermal cellular homeostasis. Inability to establish melanocyte-keratinocytes contacts and loss of intercellular junction's integrity may contribute to melanoma development. Connexins, laminins and desmocollins have been implicated in the control of melanoma growth, where their reduced expression has been reported in metastatic lesions.

OBJECTIVES

The aim of this study was to investigate Connexin 31.1 (GJB5) expression and identify any association with BRAF mutational status, melanoma patient prognosis and MAPK inhibitors (MAPKi) treatment.

MATERIAL AND METHODS

GJB5 expression was measured at RNA and protein level in melanoma clinical samples and established cell lines treated or not with BRAF and MEK inhibitors, as well as in cell lines which developed MAPK inhibitors resistance. Findings were further validated and confirmed by analysis of independent datasets.

RESULTS

Our analysis reveals significant downregulation of GJB5 expression in metastatic melanoma lesions compared to primary ones and in BRAF mutated versus BRAF wild-type melanomas. Likewise, GJB5 expression is significantly lower in BRAF^V600E compared with BRAF^WT cell lines and increases upon MAPKi treatment. MAPKi-resistant melanoma cells display a similar expression pattern compared to BRAF^WT cells, with increased GJB5 expression associated with morphological changes. Enhancement of BRAF^V600E expression in BRAF^WT melanoma cells significantly upregulates miR-335-5p expression with consequent downregulation of GJB5, one of its targets. Furthermore, overexpression of miR-335-5p in two BRAF^WT cell lines confirms specific GJB5 protein downregulation. RT-qPCR analysis also revealed upregulation of miR-335 in BRAF^V600E melanoma cells, which is significantly downregulated in cells resistant to MEK inhibitors. Our data were further validated using the TCGA-SKCM dataset, where BRAF mutations associate with increased miR-335 expression and inversely correlate with GJB5 expression. In clinical samples, GJB5 underexpression is also associated with patient overall worse survival, especially at early stages.

CONCLUSION

We identified a significant association between metastases / BRAF mutation and low GJB5 expression in melanoma. Our results identify a novel mechanism of Gap-junctional protein regulation, suggesting a prognostic role for GJB5 in cutaneous melanoma.

AKR1C3 is a biomarker and druggable target for oropharyngeal tumors

PURPOSE

Oropharynx squamous cell carcinoma (OPSCC) is a subtype of head and neck squamous cell carcinoma (HNSCC) arising from the base of the tongue, lingual tonsils, tonsils, oropharynx or pharynx. The majority of HPV-positive OPSCCs has a good prognosis, but a fraction of them has a poor prognosis, similar to HPV-negative OPSCCs. An in-depth understanding of the molecular mechanisms underlying OPSCC is mandatory for the identification of novel prognostic biomarkers and/or novel therapeutic targets.

METHODS

14 HPV-positive and 15 HPV-negative OPSCCs with 5-year follow-up information were subjected to gene expression profiling and, subsequently, compared to three extensive published OPSCC cohorts to define robust biomarkers for HPV-negative lesions. Validation of Aldo-keto-reductases 1C3 (AKR1C3) by qRT-PCR was carried out on an independent cohort (n = 111) of OPSCC cases. In addition, OPSCC cell lines Fadu and Cal-27 were treated with Cisplatin and/or specific AKR1C3 inhibitors to assess their (combined) therapeutic effects.

RESULTS

Gene set enrichment analysis (GSEA) on the four datasets revealed that the genes down-regulated in HPV-negative samples were mainly involved in immune system, whereas those up-regulated mainly in glutathione derivative biosynthetic and xenobiotic metabolic processes. A panel of 30 robust HPV-associated transcripts was identified, with AKR1C3 as top-overexpressed transcript in HPV-negative samples. AKR1C3 expression in 111 independent OPSCC cases positively correlated with a worse survival, both in the entire cohort and in HPV-positive samples. Pretreatment with a selective AKR1C3 inhibitor potentiated the effect of Cisplatin in OPSCC cells exhibiting higher basal AKR1C3 expression levels.

CONCLUSIONS

We identified AKR1C3 as a potential prognostic biomarker in OPSCC and as a potential drug target whose inhibition can potentiate the effect of Cisplatin.

Gene Expression Signature Predictive of Neuroendocrine Transformation in Prostate Adenocarcinoma

Neuroendocrine prostate cancer (NEPC) can arise de novo, but much more commonly occurs as a consequence of a selective pressure from androgen deprivation therapy or androgen receptor antagonists used for prostate cancer (PCa) treatment. The process is known as neuroendocrine transdifferentiation. There is little molecular characterization of NEPCs and consequently there is no standard treatment for this kind of tumors, characterized by highly metastases rates and poor survival. For this purpose, we profiled 54 PCa samples with more than 10-years follow-up for gene and miRNA expression. We divided samples into two groups (NE-like vs. AdenoPCa), according to their clinical and molecular features. NE-like tumors were characterized by a neuroendocrine fingerprint made of known neuroendocrine markers and novel molecules, including long non-coding RNAs and components of the estrogen receptor signaling. A gene expression signature able to predict NEPC was built and tested on independently published datasets. This study identified molecular features (protein-coding, long non-coding, and microRNAs), at the time of surgery, that may anticipate the NE transformation process of prostate adenocarcinoma. Our results may contribute to improving the diagnosis and treatment of this subgroup of tumors for which traditional therapy regimens do not show beneficial effects.

A Novel Prostate Cell Type-Specific Gene Signature to Interrogate Prostate Tumor Differentiation Status and Monitor Therapeutic Response (Running Title: Phenotypic Classification of Prostate Tumors)

In this study, we extracted prostate cell-specific gene sets (metagenes) to define the epithelial differentiation status of prostate cancers and, using a deconvolution-based strategy, interrogated thousands of primary and metastatic tumors in public gene profiling datasets. We identified a subgroup of primary prostate tumors with low luminal epithelial enrichment (LumE^low). LumE^low tumors were associated with higher Gleason score and mutational burden, reduced relapse-free and overall survival, and were more likely to progress to castration-resistant prostate cancer (CRPC). Using discriminant function analysis, we generate a predictive 10-gene classifier for clinical implementation. This mini-classifier predicted with high accuracy the luminal status in both primary tumors and CRPCs. Immunohistochemistry for COL4A1, a low-luminal marker, sustained the association of attenuated luminal phenotype with metastatic disease. We found also an association of LumE score with tumor phenotype in genetically engineered mouse models (GEMMs) of prostate cancer. Notably, the metagene approach led to the discovery of drugs that could revert the low luminal status in prostate cell lines and mouse models. This study describes a novel tool to dissect the intrinsic heterogeneity of prostate tumors and provide predictive information on clinical outcome and treatment response in experimental and clinical samples.

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.

lncRNAs as Novel Indicators of Patients' Prognosis in Stage I Epithelial Ovarian Cancer: A Retrospective and Multicentric Study

Purpose: Stage I epithelial ovarian cancer (EOC) represents about 10% of all EOCs and is characterized by good prognosis with fewer than 20% of patients relapsing. As it occurs less frequently than advanced-stage EOC, its molecular features have not been thoroughly investigated. We have demonstrated that in stage I EOC miR-200c-3p can predict patients' outcome. In the present study, we analyzed the expression of long non-coding RNAs (lncRNA) to enable potential definition of a non-coding transcriptional signature with prognostic relevance for stage I EOC.Experimental Design: 202 snap-frozen stage I EOC tumor biopsies, 47 of which relapsed, were gathered together from three independent tumor tissue collections and subdivided into a training set (n = 73) and a validation set (n = 129). Median follow up was 9 years. LncRNAs' expression profiles were correlated in univariate and multivariate analysis with overall survival (OS) and progression-free survival (PFS).Results: The expression of lnc-SERTAD2-3, lnc-SOX4-1, lnc-HRCT1-1, and PVT1 was associated in univariate and multivariate analyses with relapse and poor outcome in both training and validation sets (P < 0.001). Using the expression profiles of PVT1, lnc-SERTAD2-3, and miR-200c-3p simultaneously, it was possible to stratify patients into high and low risk. The OS for high- and low-risk individuals are 36 and 123 months, respectively (OR, 15.55; 95% confidence interval, 3.81-63.36).Conclusions: We have identified a non-coding transcriptional signature predictor of survival and biomarker of relapse for stage I EOC. Clin Cancer Res; 23(9); 2356-66. ©2016 AACR.

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.

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

Identification of two regions in the p140Cap adaptor protein that retain the ability to suppress tumor cell properties

p140Cap is an adaptor protein that negatively controls tumor cell properties, by inhibiting in vivo tumor growth and metastasis formation. Our previous data demonstrated that p140Cap interferes with tumor growth and impairs invasive properties of cancer cells inactivating signaling pathways, such as the tyrosine kinase Src or E-cadherin/EGFR cross-talk. In breast cancer p140Cap expression inversely correlates with tumor malignancy. p140Cap is composed of several conserved domains that mediate association with specific partners. Here we focus our attention on two domains of p140Cap, the TER (Tyrosine Enriched Region) which includes several tyrosine residues, and the CT (Carboxy Terminal) which contains a proline rich sequence, involved in binding to SH2 and SH3 domains, respectively. By generating stable cell lines expressing these two proteins, we demonstrate that both TER and CT domains maintain the ability to associate the C-terminal Src kinase (Csk) and Src, to inhibit Src activation and Focal adhesion kinase (Fak) phosphorylation, and to impair in vitro and in vivo tumor cell features. In particular expression of TER and CT proteins in cancer cells inhibits in vitro and in vivo growth and directional migration at a similar extent of the full length p140Cap protein. Moreover, by selective point mutations and deletion we show that the ability of the modules to act as negative regulators of cell migration and proliferation mainly resides on the two tyrosines (Y) inserted in the EPLYA and EGLYA sequences in the TER module and in the second proline-rich stretch contained in the CT protein. Gene signature of cells expressing p140Cap, TER or CT lead to the identification of a common pattern of 105 down-regulated and 128 up-regulated genes, suggesting that the three proteins can act through shared pathways. Overall, this work highlights that the TER and CT regions of p140Cap can efficiently suppress tumor cell properties, opening the perspective that short, defined p140Cap regions can have therapeutic effects.

ETS transcription factor ESE1/ELF3 orchestrates a positive feedback loop that constitutively activates NF-κB and drives prostate cancer progression

Chromosomal translocations leading to deregulated expression of ETS transcription factors are frequent in prostate tumors. Here, we report a novel mechanism leading to oncogenic activation of the ETS factor ESE1/ELF3 in prostate tumors. ESE1/ELF3 was overexpressed in human primary and metastatic tumors. It mediated transforming phenotypes in vitro and in vivo and induced an inflammatory transcriptome with changes in relevant oncogenic pathways. ESE1/ELF3 was induced by interleukin (IL)-1β through NF-κB and was a crucial mediator of the phenotypic and transcriptional changes induced by IL-1β in prostate cancer cells. This linkage was mediated by interaction of ESE1/ELF3 with the NF-κB subunits p65 and p50, acting by enhancing their nuclear translocation and transcriptional activity and by inducing p50 transcription. Supporting these findings, gene expression profiling revealed an enrichment of NF-κB effector functions in prostate cancer cells or tumors expressing high levels of ESE1/ELF3. We observed concordant upregulation of ESE1/ELF3 and NF-κB in human prostate tumors that was associated with adverse prognosis. Collectively, our results define an important new mechanistic link between inflammatory signaling and the progression of prostate cancer.

Abstract 3118: ESE1/ELF3 and constitutive activation of NF-kB in human prostate cancer: prognostic relevance and rationale for context-dependent therapeutic strategies

Activation of inflammatory circuits occurs frequently in human cancers. Here, we show that ESE1/ELF3 exerts oncogenic functions and is an important link between inflammatory signaling and prostate cancer progression. We found that ESE1/ELF3 is overexpressed in human primary and metastatic prostate tumors, mediates key transforming phenotypes in prostate cancer cells and induces transcriptional changes in relevant oncogenic pathways. Moreover, ESE1/ELF3 contributes to IL-1beta induced and constitutive activation of NF-kB by multiple transcriptional and post-transcriptional mechanisms. ESE1/ELF3 interacts with p65/RELA and p50/NFKB1, enhances nuclear localization and transcriptional activity of the NF-kB complex, and induces transcription of p50/NFKB1by binding to the gene promoter. This positive feedback loop leading to ESE1/ELF3 upregulation and NF-kB activation is also active in human prostate tumors. Bioinformatic analyses revealed that the ESE1/ELF3 transcriptional program converged with NF-kB and IL-1beta target genes in experimental models and human tumors. Furthermore, human prostate tumors with high ESE1/ELF3 expression were enriched of ESE1/ELF3 and NF-kB target genes. Evaluation of tumor tissue microarrays by immunohistochemistry and of multiple gene expression datasets revealed that combined upregulation of ESE1/ELF3 and p65/p50 was associated with significantly reduced overall survival and increased disease recurrence. Furthermore, we speculated that the positive feedback loop between ESE1/ELF3 and NF-kB could be selectively disrupted by NF-kB inhibitors. To test this hypothesis, we used BAY-117085, a known inhibitor of NF-kB, and a second compound, EC-70124, which was recently reported to potently inhibit NF-kB. Both compounds inhibited NF-kB reporter activity in prostate cancer cells and reduced phosphorylation of IkBα. Moreover, expression of genes induced by ESE1/ELF3, cell migration and proliferation were significantly reduced by NF-kB inhibitors selectively in ESE1/ELF3 expressing cells. Collectively, this study provides a mechanistic link between inflammation and prostate cancer progression and suggests new tools for patient stratification and design of context-dependent strategies for a subset of prostate cancer patients with clinically aggressive and high risk tumors marked by ESE1/ELF3 and NF-kB activation.

Citation Format: Nicole Longoni, Domenico Albino, Gianluca Civenni, Sandra Pinton, Maurizia Mello-Grand, Paola Ostano, Gioacchino D’ Ambrosio, Fausto Sessa, George N. Thalmann, Manuela Sarti, Ramon Garcia-Escudero, Francisco Morris, Giovanna Chiorino, Carlo V. Catapano, Giuseppina M. Carbone. ESE1/ELF3 and constitutive activation of NF-kB in human prostate cancer: prognostic relevance and rationale for context-dependent therapeutic strategies. [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 3118. doi:10.1158/1538-7445.AM2013-3118

Regulation of aromatase expression in breast cancer treated with anastrozole neoadjuvant therapy

Aromatase inhibitors (AIs), such as anastrozole, are established in the treatment of hormone-dependent breast cancer. However, ∼20% of patients with hormone receptor-positive breast tumors treated with anastrozole do not respond and it remains impossible to accurately predict sensitivity. Since polymorphisms in the aromatase gene may influence the response to inhibitory drugs, we evaluated the presence of rs6493497 and rs7176005 polymorphisms (mapping in the 5′-flanking region of the CYP19A1 gene coding for the aromatase protein) in a cohort of 37 patients with postmenopausal breast cancer who received three-month neoadjuvant treatment with anastrozole. We then investigated any association of the polymorphisms with changes in aromatase mRNA expression change and/or response to treatment. We also analyzed five miRNAs computationally predicted to target aromatase, to observe any association between their expression and sensitivity to anastrozole. Three samples carried the two polymorphisms and the remaining samples were wild-type for both, however, no association with response or with aromatase mRNA basal expression level or expression difference after therapy was observed. Polymorphic samples that were resistant to anastrozole showed no change or decrease in aromatase expression following AI treatment, whereas an increase in expression was observed for the polymorphic responsive samples. No statistically significant correlation was observed between miRNA and aromatase mRNA expression, or with response to anastrozole neoadjuvant treatment. These data indicate that the polymorphisms analyzed are not involved in aromatase activity and that other epigenetic mechanisms may regulate aromatase protein expression.

ESE3/EHF controls epithelial cell differentiation and its loss leads to prostate tumors with mesenchymal and stem-like features

Cancer stem cells (CSC) play a significant role in tumor progression, disease recurrence, and treatment failure. Here, we show that the endogenously expressed ETS transcription factor ESE3/EHF controls prostate epithelial cell differentiation and stem-like potential. We found that loss of ESE3/EHF induced epithelial-to-mesenchymal transition (EMT), stem-like features, and tumor-initiating and metastatic properties in prostate epithelial cells, and reexpression of ESE3/EHF inhibited the stem-like properties and tumorigenic potential of prostate cancer cells. Mechanistically, ESE3/EHF repressed the expression of key EMT and CSC genes, including TWIST1, ZEB2, BMI1, and POU5F1. Analysis of human tissue microarrays showed that reduced ESE3/EHF expression is an early event in tumorigenesis, frequently occurring independently of other ETS gene alterations. Additional analyses linked loss of ESE3/EHF expression to a distinct group of prostate tumors with distinctive molecular and biologic characteristics, including increased expression of EMT and CSC genes. Low ESE3/EHF expression was also associated with increased biochemical recurrence of prostate cancer and reduced overall survival after prostatectomy. Collectively, our findings define a key role for ESE3/EHF in the development of a subset of prostate tumors and highlight the clinical importance of identifying molecularly defined tumor subgroups.

Abstract B24: Loss of expression of the endogenous ETS factor ESE3/EHF is associated with a distinct tumor subtype with stem-like and basal cell features

Gene fusions leading to ectopic expression of ETS transcription factors are frequent in prostate tumors. However, the impact of endogenously expressed ETS factors on prostate tumorigenesis has not been deeply investigated. A comprehensive analysis of the ETS transcriptional network in normal and prostate tumor samples revealed frequent deregulation of multiple ETS factors, including endogenously expressed ETS like ESE3/EHF. We found that ETS gene expression patterns could be used to classify prostate tumors in subgroups characterized by partially distinct transcriptional and biological features. To further explore this concept we analyzed in greater details the properties of the group of ETS fusion negative tumors characterized by exclusive loss of ESE3/EHF expression without other ETS gene alterations (ESE3low tumors). ESE3low tumors represented approximately 25% of all tumors in multiple patient cohorts. Loss of ESE3/EHF expression determined by IHC on tissue microarray (TMAs) was an early event occurring at the level of HGPINs and tumors. Furthermore, reduced or absent ESE3/EHF stain in TMAs was associated with significantly increased biochemical relapse and reduced 10-year survival following prostatectomy for primary prostate cancer, independently of ERG status. Consistent with a role in tumor initiation and progression, ESE3/EHF knockdown in immortalized prostate epithelial cells induced epithelial-to-mesenchymal transition (EMT), in vitro stem-like properties and in vivo tumour-initiating and metastatic capability. Conversely, re-expression of ESE3/EHF in prostate cancer cells reduced stem-like potential and tumorigenicity. Analysis of gene expression profiling (GEP) data from three independent studies showed that the ESE3low tumours shared unique characteristics and displayed transcriptional features strikingly similar to transformed ESE3/EHF-knockdown prostate epithelial cells. Functional annotation and gene set enrichment analysis (GSEA) showed that ESE3low tumors were enriched of EMT and stem cell features. Furthermore, GSEA and unsupervised clustering indicated that ESE3low tumors retained prevalently expression of basal cell markers over luminal markers and displayed significant attenuation of androgen-induced genes compared to all other tumors. Interestingly, most of the ERG expressing tumors displayed opposite characteristics with expression of luminal markers. MicroRNA and lincRNA expression profiling also showed distinctive patterns between ESE3low tumors and the other tumors, while confirming the similarity with ESE3/EHF-knockdown cells. Collectively, these findings support a direct role of loss of ESE3/EHF expression in the pathogenesis of a subset of prostate tumors. Moreover, these data imply that distinct tumor subtypes can be indentified based on the expression of specific molecular marker that could reflect intrinsic differences in tumour biology and clinical evolution.

Citation Format: Maurizia Mello-Grand, Manuela Sarti, Gioacchino D'Ambrosio, Fausto Sessa, George Thalmann, Giovanna Chiorino, Carlo V. Catapano, Giuseppina MR Carbone, Domenico Albino, Vijay Kumar Singh, Gianluca Civenni, Nicole Longoni, Chiara Ghimenti, Paola Ostano, Sandra Pinton. Loss of expression of the endogenous ETS factor ESE3/EHF is associated with a distinct tumor subtype with stem-like and basal cell features [abstract]. In: Proceedings of the AACR Special Conference on Advances in Prostate Cancer Research; 2012 Feb 6-9; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(4 Suppl):Abstract nr B24.

Abstract B25: The ETS transcription factor ESE1 promotes activation of the NFKB pathway in prostate tumors

ETS transcription factors are important elements in the pathogenesis of prostate cancer. Here, we report that the ETS factor ESE1, which is expressed in normal prostate epithelial cells, is frequently upregulated in prostate tumors and functionally linked to activation of the NFkB pathway and inflammation. Immunohistochemistry and QRT-PCR in normal prostate and primary prostate tumor samples showed increased expression of ESE1 in about 35% of tumors. Over-expression of ESE1 was observed both in the presence and absence of ERG over-expression, indicating that activation of ESE1 could have an independent role in a subset of prostate tumors. Furthermore, elevated levels of ESE1 were significantly associated with higher rates of biochemical relapses in patients with primary tumors treated with radical prostatectomy (Log Rank (Mantel-Cox)=0.018). Overexpression of ESE1 in prostate cancer cells, like LNCaP and 22RV1, promoted a more aggressive phenotype with increased growth in soft-agar, resistance to anoikis and cell migration. When injected in nude mice, ESE1 over-expressing prostate cancer cells exhibited greater ability to form lung metastasis compared to control cells. ESE1 affected transcription of many genes and ChIP showed binding of ESE1 to ETS binding sites in the promoter of key genes involved in cell adhesion, metastasis and inflammation. Relevantly, we observed that mRNA and protein level of the NFkB subunit NFKB1 (p50) was increased in stable ESE1 expressing cells. Analysis of NFKB1 promoter revealed the presence of a previously unknown ETS binding site and ChIP demonstrated binding of ESE1 to this site, consistent with transcriptional activation of the gene by ESE1. Immunofluorescence microscopy showed a marked intranuclear localization of the NFkB p50/p65 complex, indicating that ESE1 promoted also NFkB activation. Consistently, the activity of the NFkB-responsive luciferase reporter was increased in ESE1 expressing cells compared to control cells. Furthermore, we found that the pro-inflammatory cytokine IL-1beta increased ESE1 mRNA and protein level in LNCaP cells while promoting intranuclear localization of the NFkB complex. This was associated with the induction of anoikis resistance and cell migration. All these effects were rescued by siRNA mediated knockdown of ESE1 indicating that ESE1 had a key role in mediating the effects of IL-1beta in these cells. We propose that the production of pro-inflammatory cytokines like IL-1beta within the tumor microenvironment results in the upregulation of ESE1 and establishment of a feed-forward loop leading to the constitutive activation of the NFkB linked to the ability of ESE1 to induce p50 transcription and NFkB nuclear translocation. These data show an important oncogenic role of ESE1 in prostate tumors and reveal a previously unidentified link between this ETS factor and the NFkB pathway.

Citation Format: Nicole Longoni, Maurizia Mello-Grand, Manuela Sarti, Sandra Pinton, Cecilia Dallavalle, Giovanna Chiorino, Carlo V. Catapano, Giuseppina M. Carbone. The ETS transcription factor ESE1 promotes activation of the NFKB pathway in prostate tumors [abstract]. In: Proceedings of the AACR Special Conference on Advances in Prostate Cancer Research; 2012 Feb 6-9; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(4 Suppl):Abstract nr B25.

Abstract C21: LincRNA expression data analysis identifies prostate tumor subtypes with distinct biological processes

Prostate cancer (PCa) shows tremendous heterogeneity which makes it difficult to identify patients with an increased risk of disease recurrence. A better understanding of the biological mechanism of prostate cancer formation and progression is crucial for the discovery of new markers for this disease. In recent years it has become apparent that different non-coding RNAs are also implicated in prostate cancer. Several microRNAs are now associated with progression and classification of prostate cancer and other malignancies. The role played in progression and differentiation of distinct PCa subtypes by a recently discovered class of non-coding RNAs, called large intergenic non-coding RNAs (lincRNAs), has remained unexplored. LincRNAs are believed to have major consequences on gene expression patterns through epigenetic mechanisms. Thousands of lincRNAs have been identified in human tissues, but only few have been functionally characterized. To assess the role of lincRNAs in PCa, we analysed the expression pattern of nearly 28000 Entrez genes and 7500 unique lincRNAs in 56 primary PCas and 5 normal prostate tissues, using Agilent 8x60k arrays. Unsupervised clustering over 1610 lincRNAs, selected after filtering out non informative probes, classified 61 samples into 5 distinct classes. Anova analysis was done to identify genes specifically over or under expressed in each cluster and was followed by functional annotation analysis. Normal samples were separated into a cluster characterized by the down regulation of genes involved in chemotaxis and intracellular signaling cascade. The four tumor clusters showed up regulation of distinct biological processes, like cell cycle, chromatin organization and immune response, together with deregulation of MAP-kinase signaling through EGFR and members of the RAS family oncogene. These results show that sample classification based on lincRNA profiling is able to separate tumors into subgroups with distinct biological processes.

Citation Format: Maurizia Mello-Grand, Vijay K. Singh, Chiara Ghimenti, Maria Scatolini, Nicole Longoni, Laura Curti, Andrea Zitella, Paolo Gontero, Carlo V. Catapano, Giuseppina M. Carbone, Giovanna Chiorino. LincRNA expression data analysis identifies prostate tumor subtypes with distinct biological processes [abstract]. In: Proceedings of the AACR Special Conference on Advances in Prostate Cancer Research; 2012 Feb 6-9; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(4 Suppl):Abstract nr C21.

Epidermal Growth Factor Receptor (EGFR) mutation analysis, gene expression profiling and EGFR protein expression in primary prostate cancer

BACKGROUND

Activating mutations of the epidermal growth factor receptor (EGFR) confer sensitivity to the tyrosine kinase inhibitors (TKi), gefitinib and erlotinib. We analysed EGFR expression, EGFR mutation status and gene expression profiles of prostate cancer (PC) to supply a rationale for EGFR targeted therapies in this disease.

METHODS

Mutational analysis of EGFR TK domain (exons from 18 to 21) and immunohistochemistry for EGFR were performed on tumour tissues derived from radical prostatectomy from 100 PC patients. Gene expression profiling using oligo-microarrays was also carried out in 51 of the PC samples.

RESULTS

EGFR protein overexpression (EGFRhigh) was found in 36% of the tumour samples, and mutations were found in 13% of samples. Patients with EGFRhigh tumours experienced a significantly increased risk of biochemical relapse (hazard ratio-HR 2.52, p=0.02) compared with patients with tumours expressing low levels of EGFR (EGFRlow). Microarray analysis did not reveal any differences in gene expression between EGFRhigh and EGFRlow tumours. Conversely, in EGFRhigh tumours, we were able to identify a 79 gene signature distinguishing mutated from non-mutated tumours. Additionally, 29 genes were found to be differentially expressed between mutated/EGFRhigh (n=3) and mutated/EGFRlow tumours (n=5). Four of the down-regulated genes, U19/EAF2, ABCC4, KLK3 and ANXA3 and one of the up-regulated genes, FOXC1, are involved in PC progression.

CONCLUSIONS

Based on our findings, we hypothesize that accurate definition of the EGFR status could improve prognostic stratification and we suggest a possible role for EGFR-directed therapies in PC patients. Having been generated in a relatively small sample of patients, our results warrant confirmation in larger series.

Absence of the K303R estrogen receptor α mutation in breast cancer patients exhibiting different responses to aromatase inhibitor anastrozole neoadjuvant treatment

Aromatase inhibitors, such as anastrozole, are established in the treatment of hormone-dependent breast cancer. However, approximately 20% of patients treated with anastrozole do not respond, and it remains impossible to accurately predict sensitivity. Thus, novel markers to predict response are required. The K303R estrogen receptor (ER)α mutation confers resistance to tamoxifen treatment. Moreover, K303R-expressing MCF-7 cells, transfected with an aromatase expression vector and stimulated with androstenedione (an aromatase substrate), were found to be resistant to the inhibitory effect of anastrozole. The aim of this study was to verify whether the presence of the K303R ERα mutation is associated with response to 3-month neoadjuvant treatment with anastrozole (Arimidex) in a cohort of post-menopausal breast cancer patients. Of 37 patients with ER(+) tumors, 19 showed a clinical response to anastrozole and 18 were resistant. Biopsies were obtained from tumors responding to the therapy or from non-responding tumors. None carried the K303R ERα mutation. To our knowledge, this is the first study to search for K303R ERα mutations in tumors clinically responsive or resistant to an aromatase inhibitor. Lack of the mutation leads us to believe that this mutation has in vivo biological significance in only a subset of breast cancers.

ETS transcription factors control transcription of EZH2 and epigenetic silencing of the tumor suppressor gene Nkx3.1 in prostate cancer

Background

ETS transcription factors regulate important signaling pathways involved in cell differentiation and development in many tissues and have emerged as important players in prostate cancer. However, the biological impact of ETS factors in prostate tumorigenesis is still debated.

Methodology/Principal Findings

We performed an analysis of the ETS gene family using microarray data and real-time PCR in normal and tumor tissues along with functional studies in normal and cancer cell lines to understand the impact in prostate tumorigenesis and identify key targets of these transcription factors. We found frequent dysregulation of ETS genes with oncogenic (i.e., ERG and ESE1) and tumor suppressor (i.e., ESE3) properties in prostate tumors compared to normal prostate. Tumor subgroups (i.e., ERG^high, ESE1^high, ESE3^low and NoETS tumors) were identified on the basis of their ETS expression status and showed distinct transcriptional and biological features. ERG^high and ESE3^low tumors had the most robust gene signatures with both distinct and overlapping features. Integrating genomic data with functional studies in multiple cell lines, we demonstrated that ERG and ESE3 controlled in opposite direction transcription of the Polycomb Group protein EZH2, a key gene in development, differentiation, stem cell biology and tumorigenesis. We further demonstrated that the prostate-specific tumor suppressor gene Nkx3.1 was controlled by ERG and ESE3 both directly and through induction of EZH2.

Conclusions/Significance

These findings provide new insights into the role of the ETS transcriptional network in prostate tumorigenesis and uncover previously unrecognized links between aberrant expression of ETS factors, deregulation of epigenetic effectors and silencing of tumor suppressor genes. The link between aberrant ETS activity and epigenetic gene silencing may be relevant for the clinical management of prostate cancer and design of new therapeutic strategies.