Increased MYBL2 expression in aggressive hormone-sensitive prostate cancer

Loss of the histone demethylase KDM5D (lysine-specific demethylase 5D) leads to in vitro resistance of prostate cancer cells to androgen deprivation therapy (ADT) with and without docetaxel. We aimed to define downstream drivers of the KDM5D effect. Using chromatin immunoprecipitation sequencing (ChIP-seq) of the LNCaP cell line (androgen-sensitive human prostate adenocarcinoma) with and without silenced KDM5D, MYBL2-binding sites were analyzed. Associations between MYBL2 mRNA expression and clinical outcomes were assessed in cohorts of men with localized and metastatic hormone-sensitive prostate cancer. In vitro assays with silencing and overexpression of MYBL2 and KDM5D in androgen receptor (AR)-positive hormone-sensitive prostate cancer cell lines, LNCaP and LAPC4, were used to assess their influence on cellular proliferation, apoptosis, and cell cycle distribution, as well as sensitivity to androgen deprivation, docetaxel, and cabazitaxel. We found that silencing KDM5D increased histone H3 lysine K4 (H3K4) trimethylation and increased MYBL2 expression. KDM5D and MYBL2 were negatively correlated with some but not all clinical samples. Higher MYBL2 expression was associated with a higher rate of relapse in localized disease and poorer overall survival in men with metastatic disease in the CHAARTED trial. Lower MYBL2 levels enhanced LNCaP and LAPC4 sensitivity to androgen deprivation and taxanes. In vitro, modifications of KDM5D and MYBL2 altered cell cycle distribution and apoptosis in a cell line-specific manner. These results show that the transcription factor MYBL2 impacts in vitro hormone-sensitive prostate cancer sensitivity to androgen deprivation and taxanes, and lower levels are associated with better clinical outcomes in men with hormone-sensitive prostate cancer.

The Impact of PIK3R1 Mutations and Insulin-PI3K-Glycolytic Pathway Regulation in Prostate Cancer

PURPOSE

Oncogenic alterations of the PI3K/AKT pathway occur in >40% of patients with metastatic castration-resistant prostate cancer, predominantly via PTEN loss. The significance of other PI3K pathway components in prostate cancer is largely unknown.

EXPERIMENTAL DESIGN

Patients in this study underwent tumor sequencing using the MSK-IMPACT clinical assay to capture single-nucleotide variants, insertions, and deletions; copy-number alterations; and structural rearrangements, or were profiled through The Cancer Genome Atlas. The association between PIK3R1 alteration/expression and survival was evaluated using univariable and multivariable Cox proportional-hazards regression models. We used the siRNA-based knockdown of PIK3R1 for functional studies. FDG-PET/CT examinations were performed with a hybrid positron emission tomography (PET)/CT scanner for some prostate cancer patients in the MSK-IMPACT cohort.

RESULTS

Analyzing 1,417 human prostate cancers, we found a significant enrichment of PIK3R1 alterations in metastatic cancers compared with primary cancers. PIK3R1 alterations or reduced mRNA expression tended to be associated with worse clinical outcomes in prostate cancer, particularly in primary disease, as well as in breast, gastric, and several other cancers. In prostate cancer cell lines, PIK3R1 knockdown resulted in increased cell proliferation and AKT activity, including insulin-stimulated AKT activity. In cell lines and organoids, PIK3R1 loss/mutation was associated with increased sensitivity to AKT inhibitors. PIK3R1-altered patient prostate tumors had increased uptake of the glucose analogue 18F-fluorodeoxyglucose in PET imaging, suggesting increased glycolysis.

CONCLUSIONS

Our findings describe a novel genomic feature in metastatic prostate cancer and suggest that PIK3R1 alteration may be a key event for insulin-PI3K-glycolytic pathway regulation in prostate cancer.

Prognostic and therapeutic significance of COP9 signalosome subunit CSN5 in prostate cancer

Chromosome 8q gain is associated with poor clinical outcomes in prostate cancer, but the underlying biological mechanisms remain to be clarified. CSN5, a putative androgen receptor (AR) partner that is located on chromosome 8q, is the key subunit of the COP9 signalosome, which deactivates ubiquitin ligases. Deregulation of CSN5 could affect diverse cellular functions that contribute to tumor development, but there has been no comprehensive study of its function in prostate cancer. The clinical significance of CSN5 amplification/overexpression was evaluated in 16 prostate cancer clinical cohorts. Its oncogenic activity was assessed by genetic and pharmacologic perturbations of CSN5 activity in prostate cancer cell lines. The molecular mechanisms of CSN5 function were assessed, as was the efficacy of the CSN5 inhibitor CSN5i-3 in vitro and in vivo. Finally, the transcription cofactor activity of CSN5 in prostate cancer cells was determined. The prognostic significance of CSN5 amplification and overexpression in prostate cancer was independent of MYC amplification. Inhibition of CSN5 inhibited its oncogenic function by targeting AR signaling, DNA repair, multiple oncogenic pathways, and spliceosome regulation. Furthermore, inhibition of CSN5 repressed metabolic pathways, including oxidative phosphorylation and glycolysis in AR-negative prostate cancer cells. Targeting CSN5 with CSN5i-3 showed potent antitumor activity in vitro and in vivo. Importantly, CSN5i-3 synergizes with PARP inhibitors to inhibit prostate cancer cell growth. CSN5 functions as a transcription cofactor to cooperate with multiple transcription factors in prostate cancer. Inhibiting CSN5 strongly attenuates prostate cancer progression and could enhance PARP inhibition efficacy in the treatment of prostate cancer.

Dynamic expression of SNAI2 in prostate cancer predicts tumor progression and drug sensitivity

Prostate cancer is a highly heterogeneous disease, understanding the crosstalk between complex genomic and epigenomic alterations will aid in developing targeted therapeutics. We demonstrate that, even though snail family transcriptional repressor 2 (SNAI2) is frequently amplified in prostate cancer, it is epigenetically silenced in this disease, with dynamic changes in SNAI2 levels showing distinct clinical relevance. Integrative clinical data from 18 prostate cancer cohorts and experimental evidence showed that gene fusion between transmembrane serine protease 2 (TMPRSS2) and ETS transcription factor ERG (ERG) (TMPRSS2–ERG fusion) is involved in the silencing of SNAI2. We created a silencer score to evaluate epigenetic repression of SNAI2, which can be reversed by treatment with DNA methyltransferase inhibitors and histone deacetylase inhibitors. Silencing of SNAI2 facilitated tumor cell proliferation and luminal differentiation. Furthermore, SNAI2 has a major influence on the tumor microenvironment by reactivating tumor stroma and creating an immunosuppressive microenvironment in prostate cancer. Importantly, SNAI2 expression levels in part determine sensitivity to the cancer drugs dasatinib and panobinostat. For the first time, we defined the distinct clinical relevance of SNAI2 expression at different disease stages. We elucidated how epigenetic silencing of SNAI2 controls the dynamic changes of SNAI2 expression that are essential for tumor initiation and progression and discovered that restoring SNAI2 expression by treatment with panobinostat enhances dasatinib sensitivity, indicating a new therapeutic strategy for prostate cancer.

Abstract 2498: Identification and characterization of the PIK3R1-mutant subtype in PI3K-addicted prostate cancer

Metastatic castration-resistant metastatic prostate cancer (mCRPC) is incurable. Recent comprehensive genomic characterization of localized and metastatic prostate cancer has identified a long tail of oncogenic driver mutations and demonstrated recurrent alteration of genes involved in phosphoinositide 3-kinase (PI3K) signaling in ~40% mCRPC cases. Alterations in the PI3K-signaling pathway in cancer have led to a surge in the development of PI3K/Akt inhibitors and many of these targeted therapies are currently in clinical trials and show great promise for the treatment of PI3K-addicted tumors. Therefore, in precision oncology, the identification of advanced prostate cancers with high PI3K activity is critical for treatment selection and eligibility into clinical trials of PI3K/Akt inhibitors.

We analyzed panel sequencing data from 2965 prostate cancer patients (1770 localized and 1195 mCRPC cases) from the Memorial Sloan Kettering Cancer Center clinical sequencing cohort (MSK-IMPACT). The MSK-IMPACT panel sequencing includes all protein-coding mutations, copy number alterations, selected promoter mutations and structural rearrangements of 341, 410 and 468 cancer-associated genes (all panels included). Among the PI3K-AKT-mTOR pathway components (19 genes in MSK-IMPACT panel) we identified a significant enrichment of PIK3R1 (regulatory subunit that codes for p85α protein and modulates the catalytic activity of PI3K-pathway) alterations in mCRPC patients compared to localized prostate cancer (5% mCRPC vs 2% localized cases; p<0.0001). Copy number analysis identified more frequent deletion of the PIK3R1 chromosomal region in mCRPC compared to localized disease (Chromosome 5q13.1; 25% vs 15% p< 0.0001). We also observed that loss of PIK3R1 mRNA is associated with shorter biochemical recurrence-free survival of patients in primary prostate cancer cohorts (low vs high quartile; TCGA; HR: 2.8 and Taylor et al, HR: 2.6) indicating that PIK3R1 inactivation may act as a driver of aggressive prostate cancer. Experimentally we showed that RNAi mediated knockdown of PIK3R1 was sufficient to induce Akt-activation and increase cell growth in human prostate cancer cell line (LAPC4 and 22RV1) models. Most importantly we showed that Akt-inhibitors ipatasertib and MS2206 strongly reduced the viability of prostate cancer cells (LAPC4 and 22RV1) with PIK3R1 knockdown or PIK3R1 mutated mCRPC derived organoid (MSKPCa3) compared to PIK3R1 wild type cells irrespective of their PTEN status.

In summary, our study identified an association between PIK3R1 alterations and lethal prostate cancer and demonstrated that men with mCRPC who harbor defective PIK3R1 may benefit from Akt inhibitors. Further in-depth studies are warranted to uncover the biological and phenotypic characterization of PIK3R1-altered prostate cancer.

Citation Format: Goutam Chakraborty, Subhiksha Nandakumar, Rahim Hirani, Sai Harisha Rajanala, Bastien Nguyen, Romina Ghale, Ying Z. Mazzu, Lina E. Jehane, Gwo-Shu Mary Lee, Lorelei A. Mucci, Nikolaus Schultz, Philip W. Kantoff. Identification and characterization of the PIK3R1-mutant subtype in PI3K-addicted prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2498.

Attenuation of SRC Kinase Activity Augments PARP Inhibitor-mediated Synthetic Lethality in BRCA2-altered Prostate Tumors

PURPOSE

Alterations in DNA damage repair (DDR) pathway genes occur in 20%-25% of men with metastatic castration-resistant prostate cancer (mCRPC). Although PARP inhibitors (PARPis) have been shown to benefit men with mCRPC harboring DDR defects due to mutations in BRCA1/2 and ATM, additional treatments are necessary because the effects are not durable.

EXPERIMENTAL DESIGN

We performed transcriptomic analysis of publicly available mCRPC cases, comparing BRCA2 null with BRCA2 wild-type. We generated BRCA2-null prostate cancer cells using CRISPR/Cas9 and treated these cells with PARPis and SRC inhibitors. We also assessed the antiproliferative effects of combination treatment in 3D prostate cancer organoids.

RESULTS

We observed significant enrichment of the SRC signaling pathway in BRCA2-altered mCRPC. BRCA2-null prostate cancer cell lines had increased SRC phosphorylation and higher sensitivity to SRC inhibitors (e.g., dasatinib, bosutinib, and saracatinib) relative to wild-type cells. Combination treatment with PARPis and SRC inhibitors was antiproliferative and had a synergistic effect in BRCA2-null prostate cancer cells, mCRPC organoids, and Trp53/Rb1-null prostate cancer cells. Inhibition of SRC signaling by dasatinib augmented DNA damage in BRCA2-null prostate cancer cells. Moreover, SRC knockdown increased PARPi sensitivity in BRCA2-null prostate cancer cells.

CONCLUSIONS

This work suggests that SRC activation may be a potential mechanism of PARPi resistance and that treatment with SRC inhibitors may overcome this resistance. Our preclinical study demonstrates that combining PARPis and SRC inhibitors may be a promising therapeutic strategy for patients with BRCA2-null mCRPC.

Abstract 6219: Combined inhibition of androgen signaling and apoptosis pathways in hormone sensitive prostate cancer

In the United States, where prostate cancer (PC) screening is common, over 90% of patients present initially with localized or locally advanced disease. Over the past decade, research has confirmed that PC tumor cells' response to the presence of androgen (testosterone) is a principal driver of PC. Men with PC who recur after surgery or radiation frequently undergo androgen deprivation therapy (ADT), wherein androgen exposure is chemically diminished. However, it is frequently followed by resistance, androgen-independent growth, and eventually the development of metastatic castration-resistant prostate cancer (mCRPC), the most lethal form of the disease. For those cancers that become mCRPC, many respond to other forms of ADT or chemotherapy. Therefore, it is vital to investigate additional therapeutic strategy to delay or prevent the transition of hormone sensitive cancer to mCRPC.

In response to stress signals from anti-cancer therapies, malignant cells may express pro-apoptotic activator proteins, such as the expression of the Bcl2 family of proteins. The block in apoptosis (Bcl2 family) that keeps cancer cells alive in response to anti-cancer agents is therefore an attractive candidate for targeted therapies. Previous studies have documented that overexpression of Bcl2 family proteins are associated with therapeutic resistance of PC, disease recurrence and shortened survival in CRPC. However, association between androgen signaling pathways and Bcl2 family proteins is not clearly understood. In our current study we observed that treatment with androgen inhibits the expression of Bcl2 family proteins (Bcl2, Bcl-w, Bcl-xL) in hormone sensitive human PC LNCaP cell lines. Importantly, we also observed that treatment with the androgen receptor (AR) inhibitor enzalutamide restores their (Bcl2, Bcl-w, Bcl-xL) expression even when treated with a very low concentration. This data indicates that there is direct negative-regulation of the Bcl2 family of proteins by the AR-signaling pathway. We also observed that there is synergistic effect of enzalutamide and the Bcl2-inhibitor venetoclax on growth inhibition of LNCaP cells. Our current study develops a rationale for combining enzalutamide or other androgen signaling agent inhibitors with Bcl2 targeted therapies for hormone sensitive prostate cancer. We believe this combinatorial therapeutic approach will show great potential for future clinical trials of high-risk hormone sensitive PC patients and may block the ADT-induced shift of hormone sensitive PC to mCRPC.

Citation Format: Goutam Chakraborty, Rahim Hirani, Lina E. Jehane, Ying Z. Mazzu, Yuki Yoshikawa, Sai Harisha Rajanala, Gwo-Shu M. Lee, Philip W. Kantoff. Combined inhibition of androgen signaling and apoptosis pathways in hormone sensitive prostate cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6219.

Ribonucleotide reductase small subunit M2 is a master driver of aggressive prostate cancer

Although there are molecularly distinct subtypes of prostate cancer, no molecular classification system is used clinically. The ribonucleotide reductase small subunit M2 (RRM2) gene plays an oncogenic role in many cancers. Our previous study elucidated comprehensive molecular mechanisms of RRM2 in prostate cancer (PC). Given the potent functions of RRM2, we set out to determine whether the RRM2 signature can be used to identify aggressive subtypes of PC. We applied gene ontology and pathway analysis in RNA‐seq datasets from PC cells overexpressing RRM2. We refined the RRM2 signature by integrating it with two molecular classification systems (PCS and PAM50 subtypes) that define aggressive PC subtypes (PCS1 and luminal B) and correlated signatures with clinical outcomes in six published cohorts comprising 4000 cases of PC. Increased expression of genes in the RRM2 signature was significantly correlated with recurrence, high Gleason score, and lethality of PC. Patients with high RRM2 levels showed higher PCS1 score, suggesting the aggressive PC feature. Consistently, RRM2‐regulated genes were highly enriched in the PCS1 signature from multiple PC cohorts. A simplified RRM2 signature (12 genes) was identified by intersecting the RRM2 signature, PCS1 signature, and the PAM50 classifier. Intriguingly, inhibition of RRM2 specifically targets PCS1 and luminal B genes. Furthermore, 11 genes in the RRM2 signature were correlated with enzalutamide resistance by using a single‐cell RNA‐seq dataset from PC circulating tumor cells. Finally, high expression of RRM2 was associated with an immunosuppressive tumor‐immune microenvironment in both primary prostate cancer and metastatic prostate cancer using CIBERSORT analysis and LM22, a validated leukocyte gene signature matrix. These data demonstrate that RRM2 is a driver of aggressive prostate cancer subtypes and contributes to immune escape, suggesting that RRM2 inhibition may be of clinical benefit for patients with PC.

Specific adsorption of tetracycline from milk by using biocompatible magnetic molecular imprinting material and evaluation by ECD

Biocompatible magnetic molecularly imprinted polymers (BMMIPs) were prepared with Zein for the first time, and were used to enrich tetracycline compounds selectively. Innovative combination of BMMIPs and electrochemistry to obtain lower detection line to satisfy industrial detection demands. Using Zein as the crosslinking agent, the polymers were synthesized on the surface of Fe₃O₄ particles. The scanning electron microscope, transmission electron microscope and X-ray diffraction technologies were used to characterize BMMIPs. Through optimization, BMMIPs attained large adsorption capacity (236.40 mg/g) with fast kinetics (40 min) and followed the Langmuir isotherm and pseudo-second-order kinetic models. BMMIPs had good recognition ability, the selective factors of oxytetracycline, chlortetracycline, doxycycline were 4.78, 4.23, and 3.39, respectively. Excellent linearity was attained in the range of 0.025-500 μg/mL, with low detection limits and low quantitation limits of 0.025 and 0.083 μg/mL. According to our exploring, BMMIPs was ideal materials for enrichment of tetracycline in complex biological samples.

Significance of BRCA2 and RB1 Co-loss in Aggressive Prostate Cancer Progression

PURPOSE

Previous sequencing studies revealed that alterations of genes associated with DNA damage response (DDR) are enriched in men with metastatic castration-resistant prostate cancer (mCRPC). BRCA2, a DDR and cancer susceptibility gene, is frequently deleted (homozygous and heterozygous) in men with aggressive prostate cancer. Here we show that patients with prostate cancer who have lost a copy of BRCA2 frequently lose a copy of tumor suppressor gene RB1; importantly, for the first time, we demonstrate that co-loss of both genes in early prostate cancer is sufficient to induce a distinct biology that is likely associated with worse prognosis.

EXPERIMENTAL DESIGN

We prospectively investigated underlying molecular mechanisms and genomic consequences of co-loss of BRCA2 and RB1 in prostate cancer. We used CRISPR-Cas9 and RNAi-based methods to eliminate these two genes in prostate cancer cell lines and subjected them to in vitro studies and transcriptomic analyses. We developed a 3-color FISH assay to detect genomic deletions of BRCA2 and RB1 in prostate cancer cells and patient-derived mCRPC organoids.

RESULTS

In human prostate cancer cell lines (LNCaP and LAPC4), loss of BRCA2 leads to the castration-resistant phenotype. Co-loss of BRCA2-RB1 in human prostate cancer cells induces an epithelial-to-mesenchymal transition, which is associated with invasiveness and a more aggressive disease phenotype. Importantly, PARP inhibitors attenuate cell growth in human mCRPC-derived organoids and human CRPC cells harboring single-copy loss of both genes.

CONCLUSIONS

Our findings suggest that early identification of this aggressive form of prostate cancer offers potential for improved outcomes with early introduction of PARP inhibitor-based therapy.See related commentary by Mandigo and Knudsen, p. 1784.

Methylation-associated miR-193b silencing activates master drivers of aggressive prostate cancer

Epigenetic silencing of miRNA is a primary mechanism of aberrant miRNA expression in cancer, and hypermethylation of miRNA promoters has been reported to contribute to prostate cancer initiation and progression. Recent data have shown that the miR‐193b promoter is hypermethylated in prostate cancer compared with normal tissue, but studies assessing its functional significance have not been performed. We aimed to elucidate the function of miR‐193b and identify its critical targets in prostate cancer. We observed an inverse correlation between miR‐193b level and methylation of its promoter in The Cancer Genome Atlas (TCGA) cohort. Overexpression of miR‐193b in prostate cancer cell lines inhibited invasion and induced apoptosis. We found that a majority of the top 150 genes downregulated when miR‐193b was overexpressed in liposarcoma are overexpressed in metastatic prostate cancer and that 41 miR‐193b target genes overlapped with the 86 genes in the aggressive prostate cancer subtype 1 (PCS1) signature. Overexpression of miR‐193b led to the inhibition of the majority of the 41 genes in prostate cancer cell lines. High expression of the 41 genes was correlated with recurrence of prostate cancer. Knockdown of miR‐193b targets FOXM1 and RRM2 in prostate cancer cells phenocopied overexpression of miR‐193b. Dual treatment with DNA methyltransferase (DNMT) and histone deacetylase (HDAC) inhibitors decreased miR‐193b promoter methylation and restored inhibition of FOXM1 and RRM2. Our data suggest that silencing of miR‐193b through promoter methylation may release the inhibition of PCS1 genes, contributing to prostate cancer progression and suggesting a possible therapeutic strategy for aggressive prostate cancer.

Abstract 4327: Hypermethylation of miR193b reactivates master drivers of the poor prognosis prostate cancer

Epigenetic silencing of miRNAs is one of the major mechanisms of aberrant miRNA expression in cancer. Several studies showed that hypermethylation of miRNAs contributes to prostate cancer (PC) initiation and progression. Recent screening for epigenetically regulated miRNAs in PC revealed hypermethylation of the miR-193b in tumor, but no related functional studies of miR-193b have been pursued. miR-193b functions as a tumor suppressor in various cancer by targeting multiple oncogenic pathways. Methylation regulated miR-193b silencing has been observed in multiple cancer types. In this study, we aimed to elucidate the function of miR-193b and related molecular mechanisms in PC. In TCGA cohort, we observed a significant correlation between methylation of the miR-193b and its expression level. We further confirmed that some of PC cell lines recapitulate the methylation of miR-193b seen in clinical samples. The phenotypes induced by exogenous miR-193b in PC cell lines showed the tumor suppressive property of miR-193b. Since some of miRNA-target interactions are conserved across organisms, we selected the top 150-downregulated genes by miR-193b in liposarcoma from public available datasets and unraveled the correlation between these genes with PC progression. We further applied the 150 genes to the PC subtype (PCS) signatures. There were 41 genes overlapping with the aggressive PCS1 among 150 genes, indicating miR-193b may affect these key 41 genes that regulate PC progression. The inhibition of the 41 genes by miR-193b was validated in multiple PC cell lines. Furthermore, high expression of these genes was highly correlated with recurrence of PC. The GSEA analysis of 41 genes revealed high enrichment in the FOXM1 target network. We further identified FOXM1 as a direct target of miR-193b and overexpression of FOXM1 is highly correlated with clinical outcomes including metastasis and lethality. Besides FOXM1, we also identified RRM2 as another important target of miR-193b, which is part of the PCS1 signature. Knockdown of RRM2 phenocopied miR-193b in PC cells. Its overexpression is highly correlated clinical outcomes. To explore the therapeutic potential of regulating miR-193b levels, we restored miR-193b expression by using combination treatment with DNMT and HDAC inhibitors (5-azacytidine and mocetinostat), resulting in the inhibition of FOXM1 and RRM2 expression. Interestingly, FOXM1 and RRM2 expression are highly correlated in multiple PC cohorts. All together, we revealed the tumor suppressive function of miR-193b in PC. A 41-gene set was identified and validated as the targets of miR-193b in PC cells, and showed a high correlation with PC progression in multiple PC cohorts. FOXM1 and RRM2 may be the key targets of miR-193b in PC. Our findings suggest that hypermethylation of miR-193b in PC may release the inhibition of some key oncogenes that contribute PC progression.

Citation Format: Ying Z. Mazzu, Yuki Yoshikawa, Subhiksha Nandakumar, Joshua Armenia, Lina Jehane, Gwo-Shu Lee, Goutam Chakraborty, Philp Kantoff. Hypermethylation of miR193b reactivates master drivers of the poor prognosis prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4327.

Abstract 283: Combination treatment of PARP and SRC inhibitors in BRCA2 mutated prostate cancer

Background: Recently, poly (adenosine diphosphate [ADP]-ribose) polymerase inhibitors (PARPi) have shown promise in metastatic castration resistant prostate cancers (mCRPC) patients harboring DNA repair defects due to mutations of BRCA1/2 and ATM. Despite responses, resistance is common and treatment modalities for PARPi-resistant patients are limited. We hypothesized that combining PARPi with other agents in BRCA2 altered tumors would create synergy and greater response rate and durability.

Methods: We established a transcriptomic profile associated with genomic deletion of BRCA2 (homozygous and heterozygous) using publicly available datasets from mCRPC patient tumors. To identify the significantly unregulated oncogenic signaling pathways associated with BRCA2 loss, we used gene-set enrichment analysis (GSEA). We also analyzed this transcriptomic profile by Toppgene suite to identify potential drug targets for BRCA2 deleted tumors. We used experimental human prostate cancer cell lines to validate our current observations from human clinical datasets and pathway analysis.

Results: Our GSEA analysis showed significant enrichment of the SRC signaling pathway in BRCA2-altered tumors, and based on the Toppgene suite, we also identified dasatinib (pharmacological inhibitor of SRC) as a potential agent for BRCA2-deleted tumors. Similarly, we observed significant up regulation of SRC phosphorylation in human prostate cancer cells (LNCaP-abl and PC3M) that harbor genomic deletion of BRCA2. We performed cell growth assays in these BRCA2 deleted cells treated with PARPi (olaparib, talazoparib), and dasatinib alone or in combination and calculated drug synergy based on the Chou-Talay Method. PC3M and LNCaP-abl prostate cancer cell lines showed different sensitivities to olaparib and talazoparib. We used olaparib for PC3M and talazoparib for LNCaP-abl cells. Co-administration of the PARPi and SRCi showed significant synergy in both cell lines compared to either inhibitors alone. We will develop the rationale for combining PARPi and SRCi in CRPC patients who harbor defects of BRCA2 after completion of our study in xenograft models.

Conclusion: Our study reveals the synergistic effect of PARPi and SRCi in prostate cancer cell lines. We believe this shows great potential for future clinical trials in patients with mCRPC harboring BRCA2 deletions.

Citation Format: Nabeela Khan, Goutam Chakraborty, Subhiksha Nandakumar, Ying Z. Mazzu, Mohammad Atiq, Yuki Yoshikawa, Gwo-Shu Mary Lee, Philip Kantoff. Combination treatment of PARP and SRC inhibitors in BRCA2 mutated prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 283.

Abstract 2534: A comparative analysis of fraction genome altered vs tumor mutational count in prostate cancer

Prostate cancer is the second leading cause of cancer related death among men in the United States. Although 5 new life-prolonging agents have been FDA-approved for castration resistant prostate cancer in the past 8 years, drug resistance limits the durability of responses to these agents for most patients. We hypothesized that biomarkers of genomic alterations, defined as fraction genome altered (% of copy number altered chromosome regions out of measured regions) and mutational count (number of mutational events per cases), were prognostic biomarkers which might provide insights into resistance mechanisms. We used The Cancer Genome Atlas (TCGA; n= 490 primary prostate cancer) dataset to analyze fraction of genome altered and tumor mutational count in prostate tumors. Patients whose primary prostate cancer harbored a high frequency of fraction genome altered exhibited significant disease progression in TCGA cohort . In contrast, we did not observe a significant association between high tumor mutational count and disease progression. Fraction genome altered was more significantly associated with Gleason grade compare to tumor mutation count. Interestingly, our preliminary observation showed that primary prostate cancer patients who harbor high fraction genome altered (>6%), but low tumor mutational count (<30/cases) exhibited shorter disease-free survival, indicating that those primary prostate cancer patients who harbor high fraction genome altered but low mutational count may have more aggressive prostate cancer. We have also developed a transcriptional signature which is associated with high fraction genome altered. . A detailed understanding of these molecular features will help us to design appropriate therapeutic approaches for different subsets of the disease. We hypothesize that cases with a high fraction of genome altered are associated with aggressive disease and those with lower mutational count may be associated with a diminished immunoresponsiveness.

Tumor mutational count and fraction genome alteration in various stages TCGA prostate cancerDisease Status (Gleason unadjusted)p valueGleasonp value (trend)Disease FreeRecurred/ Progressed6 (n=45)7 (n=244)>=8 (n=198)Fraction Genome Altered (Mean + SEM)0.08248 ± 0.00490.1254 ± 0.01120.00030.02504 ±0.00370.05985 ± 0.00390.1425 ± 0.0087< 2.2e-16Mutational Count (Mean + SEM)35.05 ± 1.35439.88 ± 2.6550.394429.42 ± 1.749,34.69 ± 0.9089,38.58 ± 1.272,=9.971e-05 (7 vs >=8; p value 0.0445)

Citation Format: Goutam Chakraborty, Mohammad Atiq, Subhiksha Nandakumar, Ying Z. Mazzu, Joshua Armenia, Yuki Yoshikawa, Nabeela Khan, Gwo-Shu M. Lee, Lorelei Mucci, Philip W. Kantoff. A comparative analysis of fraction genome altered vs tumor mutational count in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2534.

Abstract 339: Mechanisms of resistance to poly (ADP-ribose) polymerase inhibitors in prostate cancer

Background: Poly (ADP-ribose) polymerase inhibitors (PARPi) have demonstrated promise in treating cancers with DNA damage repair (DDR) gene abnormalities. As a result, olaparib and more recently, rucaparib have been given Breakthrough Therapy designation by the FDA for use in metastatic castration resistant prostate cancer (mCRPC) with BRCA1/2 and ATM mutations. One of the problems encountered with PARPi is drug resistance which generally limits drug efficacy. Mechanistic studies on PARPi resistance have shown one of the main mechanisms of acquired resistance to be a reversion mutation of BRCA1/2. However, this is likely more applicable to cancers in which impaired BRCA1/2 function is due to a mutation rather than in prostate cancer (PC) where BRCA2 tends to be frequently deleted. Therefore, we hypothesize that mechanisms of resistance to PARPi in PC may involve alternative molecular mechanisms rather than a reversion mutation.

Methods: We used human castration-resistant PC cell lines that harbor genomic deletions of BRCA2, PC-3 and LnCaP-Abl, and performed cell viability (MTT) assays to determine the inhibitory growth (IG) concentrations of these cell lines with talazoparib and olaparib. We cultured parental PC-3 cells in sublethal concentrations (IG 50% and IG 90%) of talazoparib-supplemented media to develop talazoparib-resistant cells. RNA sequencing followed by gene-set enrichment analysis (GSEA) of hallmark gene sets was performed on the talazoparib-resistant PC-3 cells to understand the underlying molecular mechanisms.

Results: We observed that the talazoparib-resistant PC-3 cells exhibited significantly enhanced cell growth compared to parental cells when cultured in the IG 90% concentration of olaparib. However, interestingly, the talazoparib-resistant cells grew much slower in 2D compared to parental PC-3 cells when cultured in the PARPi-free media. Our transcriptomic analysis showed significant enrichment of various inflammatory response pathways, including TNF-α and IFNα/γ signaling pathways, in the talazoparib-resistant cells and even in the parental PC-3 cells transiently treated with talazoparib.

Conclusion: We hypothesize that resistance to PARPi in PC may be related to upregulation of inflammatory signaling. Therefore, further exploration of TNF-α and IFNα/γ and their role in PARPi resistance mechanisms may lead to the identification of targets that allow for overcoming PARPi resistance in PC.

Citation Format: Mohammad Atiq, Goutam Chakraborty, Subhiksha Nandakumar, Ying Z. Mazzu, Konrad Stopsack, Yuki Yoshikawa, Nabeela Khan, Gwo-Shu Mary Lee, Philip W. Kantoff. Mechanisms of resistance to poly (ADP-ribose) polymerase inhibitors in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 339.

A Novel Mechanism Driving Poor-Prognosis Prostate Cancer: Overexpression of the DNA Repair Gene, Ribonucleotide Reductase Small Subunit M2 (RRM2)

PURPOSE

Defects in genes in the DNA repair pathways significantly contribute to prostate cancer progression. We hypothesize that overexpression of DNA repair genes may also drive poorer outcomes in prostate cancer. The ribonucleotide reductase small subunit M2 (RRM2) is essential for DNA synthesis and DNA repair by producing dNTPs. It is frequently overexpressed in cancers, but very little is known about its function in prostate cancer.

EXPERIMENTAL DESIGN

The oncogenic activity of RRM2 in prostate cancer cells was assessed by inhibiting or overexpressing RRM2. The molecular mechanisms of RRM2 function were determined. The clinical significance of RRM2 overexpression was evaluated in 11 prostate cancer clinical cohorts. The efficacy of an RRM2 inhibitor (COH29) was assessed in vitro and in vivo. Finally, the mechanism underlying the transcriptional activation of RRM2 in prostate cancer tissue and cells was determined.

RESULTS

Knockdown of RRM2 inhibited its oncogenic function, whereas overexpression of RRM2 promoted epithelial mesenchymal transition in prostate cancer cells. The prognostic value of RRM2 RNA levels in prostate cancer was confirmed in 11 clinical cohorts. Integrating the transcriptomic and phosphoproteomic changes induced by RRM2 unraveled multiple oncogenic pathways downstream of RRM2. Targeting RRM2 with COH29 showed excellent efficacy. Thirteen putative RRM2-targeting transcription factors were bioinformatically identified, and FOXM1 was validated to transcriptionally activate RRM2 in prostate cancer.

CONCLUSIONS

We propose that increased expression of RRM2 is a mechanism driving poor patient outcomes in prostate cancer and that its inhibition may be of significant therapeutic value.

miR-193b regulates tumorigenesis in liposarcoma cells via PDGFR, TGFβ, and Wnt signaling

Liposarcoma is the most common soft tissue sarcoma. Molecularly targeted therapeutics have had limited efficacy in liposarcomas, in part because of inadequate knowledge of the complex molecular alterations in these tumors. Our recent study revealed the tumor suppressive function of miR-193b in liposarcoma. Considering the biological and clinical heterogeneity of liposarcoma, here, we confirmed the under-expression of miR-193b in additional patient liposarcoma samples and cell lines. Based on STRING analysis of protein-protein interactions among the reported putative miR-193b targets, we validated three: PDGFRβ, SMAD4, and YAP1, belonging to strongly interacting pathways (focal adhesion, TGFβ, and Hippo, respectively). We show that all three are directly targeted by miR-193b in liposarcoma. Inhibition of PDGFRβ reduces liposarcoma cell viability and increases adipogenesis. Knockdown of SMAD4 promotes adipogenic differentiation. miR-193b targeting of the Hippo signaling effector YAP1 indirectly inhibits Wnt/β-catenin signaling. Both a PDGFR inhibitor (CP-673451) and a Wnt/ β-catenin inhibitor (ICG-001) had potent inhibitory effects on liposarcoma cells, suggesting their potential application in liposarcoma treatment. In summary, we demonstrate that miR-193b controls cell growth and differentiation in liposarcoma by targeting multiple key components (PDGFRβ, SMAD4, and YAP1) in several oncogenic signaling pathways.

Low Expression of the Androgen-Induced Tumor Suppressor Gene PLZF and Lethal Prostate Cancer

BACKGROUND

4%-9% of prostate cancers harbor homozygous deletions of the androgen-induced tumor suppressor gene, promyelocytic leukemia zinc finger (PLZF, ZBTB16). PLZF loss induces an in vitro phenotype of castration resistance and enzalutamide resistance. The association of low expression of PLZF and clinical outcomes is unclear.

METHODS

We assessed PLZF mRNA expression in patients diagnosed with primary prostate cancer during prospective follow-up of the Health Professionals Follow-up Study (HPFS; n = 254) and the Physicians' Health Study (PHS; n = 150), as well as in The Cancer Genome Atlas (n = 333). We measured PTEN status (using copy numbers and IHC) and transcriptional activation of the MAPK pathway. Patients from HPFS and PHS were followed for metastases and prostate cancer-specific mortality (median, 15.3 years; 113 lethal events).

RESULTS

PLZF mRNA expression was lower in tumors with PLZF deletions. There was a strong, positive association between intratumoral androgen receptor (AR) signaling and PLZF expression. PLZF expression was also lower in tumors with PTEN loss. Low PLZF expression was associated with higher MAPK signaling. Patients in the lowest quartile of PLZF expression compared with those in the highest quartile were more likely to develop lethal prostate cancer, independent of clinicopathologic features, Gleason score, and AR signaling (odds ratio, 3.17; 95% confidence interval, 1.32-7.60).

CONCLUSIONS

Low expression of the tumor suppressor gene PLZF is associated with a worse prognosis in primary prostate cancer.

IMPACT

Suppression of PLZF as a consequence of androgen deprivation may be undesirable. PLZF should be tested as a predictive marker for resistance to androgen deprivation therapy.

Abstract LB-275: Targeting poor-prognosis subtypes of prostate cancer by inhibition of DNA repair gene ribonucleotide reductase small subunit M2

Studies reveal defective DNA repair contribute to prostate cancer (PC) progression. We hypothesize that overexpression of DNA repair genes could also contribute to poorer outcomes in PC. The nucleotide metabolism enzyme ribonucleotide reductase (RNR) is essential for DNA synthesis and DNA repair by producing dNTPs. The small subunit M2 (RRM2), as the rate-limiting RNR subunit, is frequently up-regulated in cancers. Clinically, targeting of RRM2 with small molecules is being tested in multiple cancers, but there is little knowledge of RRM2 function in PC. The analysis of multiple PC clinical cohorts (total include 1602 cases) revealed that high RRM2 level was associated with poor clinical outcomes, including a higher likelihood of metastasis (p<0.001), biochemical recurrence (p<0.001), and lethality (p<0.0001). In PC cells, knockdown of RRM2 inhibited dNTP production and induced DNA damage, which led to significant cell growth inhibition, major S phase arrest, and apoptosis. Overexpression of RRM2 promoted epithelial-mesenchymal transition (EMT) by increasing the expression of multiple EMT markers. Furthermore, the small molecule RRM2 inhibitor (COH29) induced a similar phenotype as knocking down RRM2 in PC cells. RNA-Seq analysis in siRRM2 or COH29 treated PC cells provided a global assessment of RRM2-regulated transcriptome changes. GSEA analysis revealed that inhibition of RRM2 could activate biological processes including cell cycle checkpoint, DNA damage response, and apoptotic signaling. COH29 treatment could target genes highly enriched in PC. We further applied an RRM2-regulated gene signature (from RNA-Seq datasets) to TCGA and Taylor cohorts. Intriguingly, the RRM2 signature was highly correlated with metastasis and disease free survival (p<0.001). Furthermore, inhibition of RRM2 specifically targets poor prognostic luminal subtypes (PCS1 subtype; Lum B in PAM50 classifier) recently reported. Besides transcriptome changes, protein kinase arrays showed that AKT/mTOR and SFK-STAT signaling were repressed by inhibition of RRM2. These oncogenic signaling pathways are crucial for EMT program. Amplification of RRM2 is rare in PC and transcriptional activation of RRM2 may play a major role in overexpression of RRM2. H3K27ac ChIP-Seq from tissues revealed more activated RRM2 promoter in PC than in normal prostate. 13 potential RRM2-targeting transcription factors (TFs) were identified by integrating clinical cohorts and a TF database. They showed a positive correlation with RRM2 expression in PC cohorts. Among these TFs, FOXM1 was reported to be the master driver of the aggressive luminal subtype of PC. We revealed that FOXM1 expression was associated with clinical outcomes. The ChIP-PCR and luciferase reporter assays provided evidence of physical binding of FOXM1 to the RRM2 promoter in PC cells. Knockdown of FOXM1 significantly repressed RRM2 mRNA and protein levels. Altogether, FOXM1-regulated transcriptional activation contributes to overexpression of RRM2. Intriguingly, COH29 can also repress FOXM1 expression, which leads to transcription repression of RRM2. Altogether, our study elucidated the molecular mechanisms underlying RRM2 oncogenic functions and the transcriptional regulation of RRM2 in PC cells. We suggest that RRM2 can be a novel therapeutic target for PC treatment.

Citation Format: Ying Z. Mazzu, Joshua Armenia, Goutam Chakraborty, Yuki Yoshikawa, Travis A. Gerke, Si Ana A. Coggins, Xintao Qiu, Mohammad Atiq, Konrad H. Stopsack, Gwo-Shu Mary Lee, Henry W. Long, Baek Kim, Matthew L. Freedman, Mark M. Pomerantz, Lorelei A. Mucci, Philip W. Kantoff. Targeting poor-prognosis subtypes of prostate cancer by inhibition of DNA repair gene ribonucleotide reductase small subunit M2 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-275.

ATR inhibition controls aggressive prostate tumors deficient in Y-linked histone demethylase KDM5D

Epigenetic modifications control cancer development and clonal evolution in various cancer types. Here, we show that loss of the male-specific histone demethylase lysine-specific demethylase 5D (KDM5D) encoded on the Y chromosome epigenetically modifies histone methylation marks and alters gene expression, resulting in aggressive prostate cancer. Fluorescent in situ hybridization demonstrated that segmental or total deletion of the Y chromosome in prostate cancer cells is one of the causes of decreased KDM5D mRNA expression. The result of ChIP-sequencing analysis revealed that KDM5D preferably binds to promoter regions with coenrichment of the motifs of crucial transcription factors that regulate the cell cycle. Loss of KDM5D expression with dysregulated H3K4me3 transcriptional marks was associated with acceleration of the cell cycle and mitotic entry, leading to increased DNA-replication stress. Analysis of multiple clinical data sets reproducibly showed that loss of expression of KDM5D confers a poorer prognosis. Notably, we also found stress-induced DNA damage on the serine/threonine protein kinase ATR with loss of KDM5D. In KDM5D-deficient cells, blocking ATR activity with an ATR inhibitor enhanced DNA damage, which led to subsequent apoptosis. These data start to elucidate the biological characteristics resulting from loss of KDM5D and also provide clues for a potential novel therapeutic approach for this subset of aggressive prostate cancer.

miR-193b-Regulated Signaling Networks Serve as Tumor Suppressors in Liposarcoma and Promote Adipogenesis in Adipose-Derived Stem Cells

Well-differentiated and dedifferentiated liposarcomas (WDLS/DDLS) account for approximately 13% of all soft tissue sarcoma in adults and cause substantial morbidity or mortality in the majority of patients. In this study, we evaluated the functions of miRNA (miR-193b) in liposarcoma in vitro and in vivo Deep RNA sequencing on 93 WDLS, 145 DDLS, and 12 normal fat samples demonstrated that miR-193b was significantly underexpressed in DDLS compared with normal fat. Reintroduction of miR-193b induced apoptosis in liposarcoma cells and promoted adipogenesis in human adipose-derived stem cells (ASC). Integrative transcriptomic and proteomic analysis of miR-193b-target networks identified novel direct targets, including CRK-like proto-oncogene (CRKL) and focal adhesion kinase (FAK). miR-193b was found to regulate FAK-SRC-CRKL signaling through CRKL and FAK. miR-193b also stimulated reactive oxygen species signaling by targeting the antioxidant methionine sulfoxide reductase A to modulate liposarcoma cell survival and ASC differentiation state. Expression of miR-193b in liposarcoma cells was downregulated by promoter methylation, resulting at least in part from increased expression of the DNA methyltransferase DNMT1 in WDLS/DDLS. In vivo, miR-193b mimetics and FAK inhibitor (PF-562271) each inhibited liposarcoma xenograft growth. In summary, miR-193b not only functions as a tumor suppressor in liposarcoma but also promotes adipogenesis in ASC. Furthermore, this study reveals key tyrosine kinase and DNA methylation pathways in liposarcoma, some with immediate implications for therapeutic exploration. Cancer Res; 77(21); 5728-40. ©2017 AACR.

Epigallocatechin-3-gallate Prevents Triptolide-Induced Hepatic Injury by Restoring the Th17/Treg Balance in Mice

Drug-induced liver injury (DILI) is the most common cause of acute liver failure. Disruption of the Th17/Treg balance can lead to hepatic inflammation, which causes the main symptoms of DILI. Here we investigate the protective mechanisms of (-)-Epigallocatechin-3-gallate (EGCG) on triptolide (TP)-induced DILI that shows the Th17/Treg imbalance. Pretreatment with EGCG (5[Formula: see text]mg/kg) for 10 days before TP (0.5[Formula: see text]mg/kg) administration in mice significantly reduced the increased alanine aminotransferase (ALT) level ([Formula: see text]) induced by TP treatment. The hepatic histology analysis further proved that EGCG protected mice from TP-induced liver injury. The imbalance of Th17/Treg was induced by TP treatment, as shown by the upregulation of TLR4 and downregulation of Tim3 expression. EGCG pretreatment can maintain the expression of TLR4 and Tim3 at normal levels to restore the Th17/Treg imbalance. In addition, EGCG can block the TP-induced expression of the downstream targets of TLR4, including MyD88, NF[Formula: see text]B, and retinoid related orphan receptor (ROR-[Formula: see text]t), while EGCG can restore the TP inhibition of forkhead/winged-helix family transcriptional repressor p3 (FoxP3) that is the downstream target of Tim3. Consequently, EGCG pretreatment can effectively inhibit the Th17-related pro-inflammatory cytokine (e.g. IL-17 and IL-6) upregulation induced by TP treatment. However, TP inhibition of Treg-related anti-inflammatory cytokine IL-10 production was restored by EGCG pretreatment. Taken together, these results suggest that EGCG possesses significant protective properties against TP-induced hepatic inflammatory injury, and that these properties are carried out via the restoration of the Th17/Treg imbalance by the inhibition of the TLR4 signaling pathway and the enhanced activation of the Tim3 signaling pathway.