Genomic Alterations In Prostate Cancer Research Articles

Genomic alterations related to HPV infection status in a cohort of Chinese prostate cancer patients

BackgroundHuman papillomavirus (HPV) has been proposed as a potential pathogenetic organism involved in prostate cancer (PCa), but the association between HPV infection and relevant genomic changes in PCa is poorly understood.MethodsTo evaluate the relationship between HPV genotypes and genomic alterations in PCa, HPV capture sequencing of DNA isolated from 59 Han Chinese PCa patients was performed using an Illumina HiSeq2500. Additionally, whole-exome sequencing of DNA from these 59 PCa tissue samples and matched normal tissues was carried out using the BGI DNBSEQ platform. HPV infection status and genotyping were determined, and the genetic disparities between HPV-positive and HPV-negative PCa were evaluated.ResultsThe presence of the high-risk HPV genome was identified in 16.9% of our cohort, and HPV16 was the most frequent genotype detected. The overall mutational burden in HPV-positive and HPV-negative PCa was similar, with an average of 2.68/Mb versus 2.58/Mb, respectively, in the targeted whole-exome region. HPV-negative tumors showed a mutational spectrum concordant with published PCa analyses with enrichment for mutations in SPOP, FOXA1, and MED12. HPV-positive tumors showed more mutations in KMT2C, KMT2D and ERCC2. Copy number alterations per sample were comparable between the two groups. However, the significantly amplified or deleted regions of the two groups only partially overlapped. We identified amplifications in oncogenes, including FCGR2B and CCND1, and deletions of tumor suppressors, such as CCNC and RB1, only in HPV-negative tumors. HPV-positive tumors showed unique deletions of tumor suppressors such as NTRK1 and JAK1.ConclusionsThe genomic mutational landscape of PCa differs based on HPV infection status. This work adds evidence for the direct involvement of HPV in PCa etiology. Different genomic features render HPV-positive PCa a unique subpopulation that might benefit from virus-targeted therapy.

Predicting Prostate Cancer Molecular Subtype With Deep Learning on Histopathologic Images

Microscopic examination of prostate cancer has failed to reveal a reproducible association between molecular and morphologic features. However, deep-learning algorithms trained on hematoxylin and eosin (H&E)-stained whole slide images (WSI) may outperform the human eye and help to screen for clinically-relevant genomic alterations. We created deep-learning algorithms to identify prostate tumors with underlying ETS-related gene (ERG) fusions or PTEN deletions using the following 4 stages: (1) automated tumor identification, (2) feature representation learning, (3) classification, and (4) explainability map generation. A novel transformer-based hierarchical architecture was trained on a single representative WSI of the dominant tumor nodule from a radical prostatectomy (RP) cohort with known ERG/PTEN status (n = 224 and n = 205, respectively). Two distinct vision transformer-based networks were used for feature extraction, and a distinct transformer-based model was used for classification. The ERG algorithm performance was validated across 3 RP cohorts, including 64 WSI from the pretraining cohort (AUC, 0.91) and 248 and 375 WSI from 2 independent RP cohorts (AUC, 0.86 and 0.89, respectively). In addition, we tested the ERG algorithm performance in 2 needle biopsy cohorts comprised of 179 and 148 WSI (AUC, 0.78 and 0.80, respectively). Focusing on cases with homogeneous (clonal) PTEN status, PTEN algorithm performance was assessed using 50 WSI reserved from the pretraining cohort (AUC, 0.81), 201 and 337 WSI from 2 independent RP cohorts (AUC, 0.72 and 0.80, respectively), and 151 WSI from a needle biopsy cohort (AUC, 0.75). For explainability, the PTEN algorithm was also applied to 19 WSI with heterogeneous (subclonal) PTEN loss, where the percentage tumor area with predicted PTEN loss correlated with that based on immunohistochemistry (r = 0.58, P = .0097). These deep-learning algorithms to predict ERG/PTEN status prove that H&E images can be used to screen for underlying genomic alterations in prostate cancer.

Abstract A049: Immunohistochemical detection of ERG, ETV1, ETV4, and PTEN in prostate tumor specimens reveals the heterogeneity of multi-focal prostate cancer

Abstract Introduction: ETS gene rearrangements involving ERG, ETV1 and ETV4, as well as PTEN deletions are among the most common genomic alterations in prostate cancer. Although these events are found to be mutually exclusive, the multifocality of prostate cancer suggests that they may co-occur in some tumors. The immunohistochemistry (IHC) detection of both ERG overexpression and PTEN protein loss are reliable substitutes for fluorescence in situ hybridization (FISH) assay to probe genomic alterations. The lack of specific antibodies that can discriminate between multiple ETS factors, however, has limited the evaluation for the co-occurrence of these genomic alterations in prostate cancer. Improving our ability to identify the multifocality or inter-focal heterogeneity of tumors can enhance our understanding of biological mechanisms of tumor initiation and progression, and help stratify patients for treatment. Methods: Using monoclonal antibodies (mAbs) that we developed against ETV1 and ETV4, we examined their expression in relation to ERG and PTEN expression by IHC using two TMAs constructed from primary prostate cancer specimens of independent patient cohorts: one was constructed from multiple 1 mm cores representing distinct tumor focus from multifocal tumors from 50 African American (AA) and 50 Caucasian American (CA) men; the other, from a single 2 mm core of individual tumors from a cohort of 152 AA and 304 CA men. Positive expression for each ETS factor and PTEN were evaluated for association with race and clinico-pathologic features that include PSA at diagnosis, Gleason score, pathologic T stage, biochemical recurrence, and metastasis. Univariate analysis of BCR free survival as a function of ERG, ETV1 and ETV4 and PTEN expression was performed for both patient cohorts. Results: ERG(+) expression alone or in combination with PTEN loss were significantly higher in CA men in both patient cohorts. When expression of ETS factors were evaluated together with PTEN status, positive expression of ETS factors and PTEN loss were significantly more prevalent among CA men in both patient cohorts ETV1 and ETV4 expression were detected at 5% or less in both patient cohorts. Cases harboring tumor foci that were positive for more than one marker evaluated frequently showed either intra-tumor or inter-tumor heterogeneity. Univariate analysis of PTEN-ETS protein expression status and BCR free survival showed that patients with loss of PTEN expression trends towards poorer BCR free survival regardless of ETS expression status. Conclusion: We showed that the IHC detection of multiple aberrantly expressed proteins such as ERG, ETV1, ETV4 and PTEN in prostate tumor specimens using highly specific mAbs can reveal the heterogeneity and multi-focality in prostate cancer, which could be used to enhance the stratification of patients for novel treatment strategies. Citation Format: Shyh-Han Tan, Cara Schafer, Denise Young, Jiji Jiang, Yingjie Song, Albert Dobi, Gyorgy Petrovics, Bettina F. Drake, Gregory T. Chesnut, Isabell A. Sesterhenn. Immunohistochemical detection of ERG, ETV1, ETV4, and PTEN in prostate tumor specimens reveals the heterogeneity of multi-focal prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A049.

Actionable Genomic Alterations in Prostate Cancer Among Black and White United States Veterans.

Black Veterans have higher a incidence of localized and metastatic prostate cancer compared to White Veterans yet are underrepresented in reports of frequencies of somatic and germline alterations. This retrospective analysis of somatic and putative germline alterations was conducted in a large cohort of Veterans with prostate cancer (N = 835 Black, 1613 White) who underwent next generation sequencing through the VA Precision Oncology Program, which facilitates molecular testing for Veterans with metastatic cancer. No differences were observed in gene alterations for FDA approved targetable therapies (13.5% in Black Veterans vs. 15.5% in White Veterans, P = .21), nor in any potentially actionable alterations (25.5% vs. 28.7%, P =.1). Black Veterans had higher rates of BRAF (5.5% vs. 2.6%, P < .001) alterations, White Veterans TMPRSS2 fusions (27.2% vs. 11.7%, P < .0001). Putative germline alteration rates were higher in White Veterans (12.0% vs. 6.1%, P < .0001). Racial disparities in outcome are unlikely attributable to acquired somatic alterations in actionable pathways.

Role of Olaparib in the Management of Metastatic Castration-Resistant Prostate Cancer: A Japanese Clinician's Perspective.

Several studies have identified various targetable genomic alterations in prostate cancer, which accumulate during carcinogenesis and cancer progression. Genomic alterations in genes involved in DNA damage repair by homologous recombination repair may predict increased sensitivity to poly-ADP ribose polymerase (PARP) inhibitors. The Phase 3 PROfound trial has shown that treatment with the PARP inhibitor olaparib was associated with an improved radiographic progression-free survival and overall survival among patients with homologous recombination repair-deficient metastatic castration-resistant prostate cancer (mCRPC) after the treatment with androgen receptor targeting therapy, especially in men with BRCA1 or BRCA2 mutation. In Japan, olaparib was approved in December 2020 for the treatment of mCRPC with BRCA1 or BRCA2 mutation. In addition, genetic tests to detect BRCA1 or BRCA2 mutation to select patients who are likely to benefit from olaparib were also approved. This review summarizes the status of olaparib treatment for mCRPC, focusing on the situation in Japan.

The Genetic Complexity of Prostate Cancer.

Prostate cancer (PCa) is a major concern in public health, with many genetically distinct subsets. Genomic alterations in PCa are extraordinarily complex, and both germline and somatic mutations are of great importance in the development of this tumor. The aim of this review is to provide an overview of genetic changes that can occur in the development of PCa and their role in potential therapeutic approaches. Various pathways and mechanisms proposed to play major roles in PCa are described in detail to provide an overview of current knowledge.

Cyclin pathway genomic alterations across 5,356 prostate cancers.

179 Background: The cyclin pathway is comprised of possible targetable alterations as well as resistant alterations that affect treatment, including hormonal agents. We describe the landscape of cyclin genomic alterations in prostate cancer. Methods: Consecutive samples were analyzed in a CLIA-certified laboratory using comprehensive genomic profiling (CGP) performed by next-generation sequencing (315 genes, &gt;500X coverage). We describe alterations in activating genes (Table) and co-alterations in resistant genes ( RB1 and CCNE1) (related to cyclin inhibition) and androgen receptor ( AR). Results: Alterations in any cyclin pathway genes were found in 9.7% of the 5,356 tumors analyzed. Frequent alterations included CCND1 amplification (4.2%) and CDKN2A and B loss (2.4% each). Frequencies were substantially different according to prostate cancer histology (Table). The majority of alterations were copy number changes. Alterations in possible resistance genes, RB1 and CCNE1 were detected in 9.7% (up to 54.6% in neuroendocrine) and 1.2% of cases, respectively, while AR alterations were seen in 20.9% (up to 27.3% in anaplastic). Co-occurrence analysis demonstrated a lower likelihood of concomitant vs. isolated alterations in cyclin activating and resistance pathway (odds ratio (OR), 0.44, p&lt;0.001). Conversely, we detected a higher likelihood of co-occurrence between AR and cyclin alterations (OR 1.79, p&lt;0.001). Conclusions: Cyclin pathway genomic abnormalities were observed in about 10% of prostate cancer tumors, and are more frequently associated with concomitant AR alterations and absence of co-alterations associated with resistance to cyclin inhibition.[Table: see text]

The Genomic and Molecular Pathology of Prostate Cancer: Clinical Implications for Diagnosis, Prognosis, and Therapy.

Prostate cancer (PCa) is the most common noncutaneous malignancy affecting American men and the second most common cause of cancer death. The traditional risk classification schemes for PCa are limited due to the vast clinical and molecular heterogeneity of the disease. Fortunately, recent advancements in sequencing technologies have provided us with valuable insight into the genomics of PCa. To date, a wide array of recurrent genomic alterations in PCa have been identified. Incorporating these distinct molecular subtypes of PCa into prediction models provides opportunities for improved risk stratification and ultimately better patient outcomes. In this review, we summarize the key molecular subtypes of PCa and focus on those genomic alterations that have clinical implications for diagnosis, prognosis, and therapeutic response.

Abstract A018: Distinct genomic alterations in prostate cancer of African American men

Abstract Background: In recent years remarkable ethnic/racial differences in the frequency of prostate cancer (CaP) driver gene alterations have emerged. Along the lines of ethnic differences in CaP genomes, oncogenic activation of ERG proto-oncogene and deletion of the PTEN tumor suppressor gene are most widely studied. These findings underscore distinct biology of prostate cancer in different ethnicities and races. We have reported the cumulative analyses of 435 patients (whole genome sequencing (WGS): 14, FISH evaluations: 101, SNP array: 320) comparing CaP genomes of African American (AA) and Caucasian American (CA) patients. An AA CaP genome-associated deletion was identified and mapped to the Limbic System-Associated Membrane Protein (LSAMP) gene locus. Further examination of the data indicated the AA CaP-genome associated deletion of the Chromodomain Helicase DNA Binding Protein 1(CHD1) gene. The goal of the current study is the comparative assessment of frequencies and prognostic associations of CaP genome alterations in the context of racial/ethnic differences. Methods: A prostate tumor tissue microarray (TMA) of benign and tumor foci (500+ cores) was generated by sampling 2-3 cores representing the range of cell morphology in matched cohort of 42 AA and 59 CA patients with up to 20 years of follow-up. Comparative evaluation of frequencies and prognostic associations of ERG oncoprotein by immunohistochemistry and the deletion of LSAMP, CHD1, and PTEN genes by FISH was performed. ERG frequencies were further assessed in index tumors of Chinese CaPs (N=100) and were compared to ERG frequencies in index tumors of patients from the United States equal-access military health-care system (N=336 AA and N=594 CA). Results: Higher frequencies of recurrent deletions of CHD1 (29% AA vs. 10% CA p=0.017) and LSAMP (26% AA vs. 7% CA, p=0.006) were identified in AA CaP compared to CA CaPs. These deletions were associated with significantly higher risk of rapid biochemical recurrence. In contrast, PTEN deletions (15% AA vs. 63% CA) and the frequency of ERG positive CaPs (26% AA vs. 64% CA) were more frequent among CA CaPs. Comparative evaluation of ERG frequencies in CaPs (N=1,292) underscores highest ERG frequency among CA patients (49.3%) followed by AA (23.2%) and Chinese (22%) men. Conclusions: In light of distinct biology of CaPs in ethnically/racially diverse CaP patient populations, there is a need for developing broadly applicable diagnostic, prognostic marker panels and therapeutic approaches. Higher frequency of CHD1 deletion in CaPs of AA patients may provide new therapeutic opportunities due to the sensitivity of CHD1 deletion harboring tumors to PARP inhibitors and platinum agents. Acknowledgments: This research was supported by the CPDR-USU program HU0001-10-2-0002, the National Cancer Institute R01CA162383 grant, the EDRN/NCI ACN12011-001-0 grant, the Snyder Medical Foundation, the Otto Mønsteds Foundation, the Mazzone Foundation, the Breast Cancer Research Foundation, the Novo Nordisk Foundation, and grants by MTA-TKI643/2012, KTIA_NAP_13-2014-0021. Citation Format: Albert Dobi, Gyorgy Petrovics, Hua Li, Denise Young, Shyh-Han Tan, Yongmei Chen, Qingyu Xiao, Yidi Sun, Hong Li, Yixue Li, Yuan Ji, Jun Hou, Wendy Wang, Jacob Kagan, Guo-Ping Zhao, Sudhir Srivastava, Reinhard Ebner, Inger L. Rosner, Jennifer Cullen, Matthew Freedman, Isabell Sesterhenn, Zoltan Szallasi, Shiv Srivastava. Distinct genomic alterations in prostate cancer of African American men [abstract]. In: Proceedings of the AACR Special Conference: Prostate Cancer: Advances in Basic, Translational, and Clinical Research; 2017 Dec 2-5; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(16 Suppl):Abstract nr A018.

Abstract B57: Distinct genomic alterations in prostate cancer of African American men

Abstract This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section (PR01) of the Conference Proceedings. Note: This abstract was not presented at the conference. Citation Format: Albert Dobi, Gyorgy Petrovics, Hua Li, Denise Young, Yongmei Chen, Jacob Kagan, Sudhir Srivastava, Reinhard Ebner, Inger L. Rosner, Jennifer Cullen, Matthew L. Freedman, Isabell A. Sesterhenn, Zoltan Szallasi, Shiv Srivastava. Distinct genomic alterations in prostate cancer of African American men [abstract]. In: Proceedings of the Tenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2017 Sep 25-28; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2018;27(7 Suppl):Abstract nr B57.

Abstract PR01: Distinct genomic alterations in prostate cancer of African American men

Abstract Background: Emerging observations highlight distinct biology of prostate cancer (CaP) among men of different ethnicities and races. Studies including reports from our institute have demonstrated remarkable ethnic/racial differences in the frequency of ERG oncogenic activation, one of the most common and widely studied CaP driver genes. Similarly, deletion of the PTEN tumor suppressor gene, an established cancer driver gene alteration, was shown to be more prevalent among men of European ancestry. We have reported the cumulative analyses of 435 patients (whole-genome sequencing [WGS]: 14, FISH evaluations: 101, SNP array: 320) comparing CaP genomes of African American and Caucasian American patients. An AA CaP genome associated minimum deletion site on 3q13.31 was identified by WGS and mapped to the Limbic System-Associated Membrane Protein (LSAMP) gene locus using the TCGA SNP array data of 44 AA and 260 CA tumors. Further, we also noted the AA CaP genome association of the Chromodomain Helicase DNA Binding Protein 1(CHD1) gene deletion. Methods: The frequency and prognostic associations of LSAMP, CHD1, and PTEN deletions was evaluated by FISH analyses in prostate tumor tissue microarray (TMA) with up to 20 years of follow-up. The TMA represented normal and tumor foci (1000+ cores) sampled by 2-3 cores including the spectrum of cell morphology and tumor pathology in matched cohort of 42 AA and 59 CA patients. ERG was evaluated in the same TMA by immunohistochemistry. Evaluation of ERG was extended to the assessment of whole mounted prostate sections of 336 AA and 594 CA patients from the equal-access military health care system, in which disparities in socioeconomic status, health awareness, and physical activity are minimized. Results: AA CaP genome-associated recurrent deletions of LSAMP (26% AA vs. 7% CA, p=0.006) and CHD1 (29% AA vs. 10% CA p=0.017) genes were identified. AA CaP patients harboring these genomic deletions in their CaP showed significantly higher risk of rapid disease progression as measured by biochemical recurrence. Consistent with previous reports, we noted significantly lower frequency of PTEN deletions (15% AA vs. 63% CA) and ERG expression (26% AA vs. 64%) in prostate cancers among AA men. In-depth evaluation of ERG frequencies in the context of multifocal disease provided definitive evidence for the difference in the frequency of ERG between AA (23%) and CA (49%) patients from the equal-access military health care system. Conclusions: Our study underscores that the biology of CaP has to be taken into consideration when new diagnostic and prognostic markers and therapeutic approaches are being developed in order to realize the true potential of precision medicine for all cancer patients. Note: This abstract was not presented at the conference. Citation Format: Albert Dobi, Gyorgy Petrovics, Hua Li, Denise Young, Yongmei Chen, Jacob Kagan, Sudhir Srivastava, Reinhard Ebner, Inger L. Rosner, Jennifer Cullen, Matthew L. Freedman, Isabell A. Sesterhenn, Zoltan Szallasi, Shiv Srivastava. Distinct genomic alterations in prostate cancer of African American men [abstract]. In: Proceedings of the Tenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2017 Sep 25-28; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2018;27(7 Suppl):Abstract nr PR01.

Abstract 5420: Nuclear PTEN directly regulates androgen receptor activity in prostate cancer

Abstract The deletion of PTEN, a negative regulator of the PI3K pathway, is among the most frequent genomic alterations in prostate cancer. Attempts to target this alteration using PI3K pathway inhibitors, however, have yielded little clinical benefit for patients, and the function of PTEN loss in prostate cancer progression is not fully understood. Prostate cancers lacking PTEN are less responsive to therapy targeting the Androgen Receptor (AR), a dominant driver of prostate cancer growth, but how PTEN function interacts with AR activity is not clear. We used immunoblotting, immunoprecipitation, proximity ligation assay, chromatin immunoprecipitation, and transcriptome sequencing in cells with endogenous PTEN or PTEN knocked down to evaluate the interactions between these major factors in prostate cancer progression. We demonstrate that PTEN interacts with the Androgen Receptor in the nucleus, and PTEN can bind chromatin at known Androgen Response Elements. Stimulation of cells with androgen and other media components leads to accumulation of phosphorylated (inactive) PTEN, loss of nuclear PTEN, and decreased PTEN-AR interaction. Transcriptome analysis of cells with PTEN knocked down demonstrates increased expression of AR pathway genes, even in the absence of androgen stimulation. These results suggest nuclear PTEN may play a direct role in negative regulation of the Androgen Receptor, with implications for management of PTEN-negative prostate cancers. Citation Format: Yen T. Nguyen, Jose A. Rodriguez-Nieves, Qi Yang, David VanderWeele. Nuclear PTEN directly regulates androgen receptor activity in prostate cancer [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 5420.

Abstract 4332: Meta-analysis of molecular features associated with aggressive prostate cancer

Abstract The TMPRSS2:ERG fusion is the most common genomic alteration in prostate cancer, occurring in 40-50% of primary tumors. The frequency of the ERG fusion remains between 40-50% in metastatic tumors, supporting previous findings that the fusion can drive tumor development, but is not sufficient to drive aggressive, lethal disease. Large -omic datasets collected over thousands of patient tumors, such as The Cancer Genome Atlas (TCGA), paired with outcomes present the raw data needed to associate genetic aberrations with markers of aggressive disease. Accordingly, we performed a meta-analysis of over 2,000 patient samples to identify combinations of -omic features associated with aggressive ERG fusion-positive and ERG fusion-negative prostate cancer. The data were collected from 8 independent, publicly available prostate cancer cohorts and cover range of disease phenotypes (e.g., neuroendocrine, castration resistance). Our analysis consisted of training univariate Cox regression models separately for single genomic or pairs of genomic features within each independent dataset. Based on the availability, we explored gene expression, mutation, and copy number alterations, all used to build separate models. We then combined models for a genomic feature across all datasets by weighting individual coefficients by the inverse of their squared error in a fixed effects model; final results are reported as corrected p-values. We compared and contrasted results from combined models within data type (i.e., only gene expression) to models integrating multiple data types. Interestingly, we find that the genomic features associated with aggressive disease differed based on ERG status. We report genomic loci that are altered in all patients, but associate with aggressive disease only in patients with an ERG fusion. We also report loci that co-occur or are mutually exclusive of the ERG fusion and associated with aggressiveness. For example, SPOP mutations are known to be mutually exclusive of ERG fusions. We report a finer stratification of patients with SPOP mutations based on biochemical relapse. Our results present a compressive meta-analysis of molecular features in prostate cancer and identify novel molecular subtypes associated with aggressive disease. Citation Format: James C. Costello, Rani Powers, Andrew Goodspeed, Scott D. Cramer. Meta-analysis of molecular features associated with aggressive prostate cancer [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 4332.

Abstract 3392: Genomic analysis of prostate cancer in Korean men

Abstract Prostate cancer currently has the fifth highest incidence rate in Korean males, and is the most common cancer in western males. Prostate cancer is the second most common malignancy in men worldwide, and is responsible for approximately 250,000 cancer-related deaths annually. The search for accurate biomarkers and characterization of prostate cancer is critical for evolution of accurate management of prostate cancer. Previous studies have identified that several genomic alterations in prostate cancer including TMPRSS2-ERG fusion, PTEN deletion and SPOP single nucleotide variants (SNVs), the majority of which are from western population. In order to investigate the somatic mutations of Korean prostate cancers, we performed whole exome sequencing on 51 prostate cancer patient’s tumor tissues, and matched normal tissue. For the accurate detections of structural variations, we additionally performed whole genome sequencing on 9 matched pairs (tumor, normal). A total of 738 somatic non-silent variants affecting 692 distinct genes were identified. In addition to already known genes such as SPOP, FOXA1, TP53 and PTEN, we also found previously uncharacterized genes such as GRIN2A, LRP1, FNDC1 and LRP1B. Of the 40 mutated genes across multiple cases, missense SNVs of SPOP (10/60 cases, 16.7%) were the most frequent, followed by missense and splice-site SNVs of GRIN2A (5/60 cases, 8.3%). Mutations in low-density lipoprotein-related protein encoded by LRP1 and LRP1B affected considerable portion of all cases (7/60, 11.7%), describe the probable relation between lipid metabolism and prostate cancer. We found TMPRSS2-ERG fusion in 4 of 9 whole genome samples. Moreover, 5 samples had 8p whole arm deletion, which is found frequent in western prostate cancers. As a result, we describe the genomic patterns of genetic variations and structural variations involved in prostate cancer of Korean population. Citation Format: Se Song Jang, Min Jung Kim, Dong Wan Hong, Jae Young Joung, Sung Han Kim, Kang Hyun Lee, Weon Seo Park, Jong-Il Kim. Genomic analysis of prostate cancer in Korean men [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3392. doi:10.1158/1538-7445.AM2017-3392

Abstract 2702: Mutations of SPOP, FOXA1 and IDH1 are associated with prostate cancer metastasis and biochemical outcomes

Abstract Recent genomic studies have shed light on cataloging genomic alterations in prostate cancer. Mechanistic studies allow the use of this information to subclassify the heterogeneous prostate tumors for optimized treatment planning. Speckle-Type POZ Protein (SPOP), Forkhead Box Protein A1 (FOXA1) and Isocitrate Dehydrogenase 1 (IDH1) are among the genes that show frequent point mutations in primary prostate cancers. However, the clinical significance of these gene mutations in cancer patients is less clear. To determine the whether SPOP, FOXA1 and IDH1 mutations are associated with clinical outcomes in prostate cancer, we pyro-sequenced the three genes in prostate cancer patients and evaluated the clinical and prognostic significance. 198 patients from the first hospital of Xi’An Jiaotong University (China) were analyzed. All patients were newly diagnosed with prostate cancer from January 2010 to December 2015. No patient was lost to follow-up. The average follow-up time after the primary diagnosis was 27 months. The Fisher’s exact tests were used to compare categorical data. The risk of metastasis among patients with SPOP, FOXA1 and IDH1 mutations was evaluated using univariate and multivariate logistic regression models. The prognostic significance of clinical and gene mutations was determined using multivariate Cox regression analysis. SPOP mutations were found in 16 patients (8.1%), with all of the mutations clustered in the substrate-binding MATH domain. FOXA1 mutationswere found in nine patients (4.5%), and were clustered in the Forkhead domain. IDH1 mutations were detected in three patients (1.5%). Mutation frequencies of SPOP, FOXA1 and IDH1 were associated with prostate-specific antigen (PSA), a biochemical marker of prostate tumor presence/risk which is decided by Gleason Score, T stage and PSA level, along with prostate cancer PSA failure and metastasis. Among patients with SPOP mutation, 56.3% showed metastasis at the time of diagnosis of primary cancer, compared to only 11.5% of patients with wild-type SPOP. Similarly, the probabilities of FOXA1 and IDH1 mutations with metastasis were approximately 44.4% and 66.7% versus 13.8% and 14.4%, respectively, comparing to their wild-type counterparts. The metastasis risk for patients with SPOP mutation was 1.27 times of the SPOP wild-type patients (P = 0.003). We also found that patients with SPOP (P &amp;lt; 0.0001) and FOXA1 (P = 0.0403) mutations showed higher risk of PSA failure compared with wild-type. The PSA failure risk for patients with SPOP mutation was 35.49 times of the SPOP wild-type patients. In contrast, IDH1 mutation was not associated with PSA failure (P = 0.054). Multivariate analyses demonstrate that SPOP mutation is an independent factor that is associated with prostate cancer metastasis and PSA failure recurrence. These findings underscore the clinical significance for profiling SPOP, FOXA1 and IDH1. Note: This abstract was not presented at the meeting. Citation Format: Jinlu Ma, Suxia Han, Xin Sui, Wenyan Lu, Yonghe Li, Bo Xu. Mutations of SPOP, FOXA1 and IDH1 are associated with prostate cancer metastasis and biochemical outcomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2702. doi:10.1158/1538-7445.AM2017-2702

Abstract 4435: Exosomal miR-3622a as prognostic marker in prostate cancer

Abstract Loss of chromosome (chr) 8p21 is a frequent genomic alteration in prostate cancer (PCa). Genomic deletions of this region increase significantly with tumor grade and are associated with tumor progression and poor prognosis. A common region of loss of heterozygosity (LOH) has been mapped to the chr8p21 locus that primarily harbors prostate-specific NKX3.1 homeobox gene. We recently demonstrated that this frequently deleted locus is associated with a cluster of microRNA genes- miR-3622a/b- that are lost in prostate cancer and play an important mechanistic role in PCa progression and metastasis. MicroRNA expression profiling in microdissected human PCa clinical tissues showed that miR-3622a/b expression is widely downregulated and is correlated with poor survival outcome in prostate cancer. Our analyses suggested that miR-3622a has potential as a prognostic and diagnostic marker for prostate cancer. Extending these findings, we explored the prognostic potential of serum miR-3622a in prostate cancer patients. Since exosomes provide an important source of non-invasive, circulating biomarkers and represent an enriched source of microRNAs for biomarker profiling, we profiled the microRNA content of exosomes derived from sera of prostate cancer patients. In a pilot study, we profiled exosomal miRNAs from a training cohort of individuals with benign prostate hyperplasia (BPH), an indolent form of PCa or aggressive metastatic PCa. Exosomes were isolated from sera of prostate cancer patients and integrity of exosomal preparations was confirmed by nanoparticle tracking analysis and Western blot analyses for exosomal markers. Expression analyses of exosomal miR-3622a expression showed that this miRNA is enriched in exosomes. Higher levels of miR-3622a were significantly associated with tumor stage and lymph node metastasis in a cohort of prostate cancer clinical specimens. Further, ROC (Receiver Operating Characteristic) analyses showed that exosomal miR-3622a expression can be a single significant parameter to discriminate between BPH and prostate cancer. Overall, our data suggests that exosomal miR-3622a is a promising prognostic biomarker for prostate cancer. patients. Citation Format: Thao Yang, Divya Bhagirath, Kirandeep Sekhon, Nathan Bucay, Shahana Majid, Varahram Shahryari, Marisa Shiina, Yutaka Hashimoto, Priyanka Kulkarni, Pritha Dasgupta, Mitsuho Imai-Sumida, Soichiro Yamamura, Z Laura Tabatabai, Kirsten Greene, Yuichiro Tanaka, Rajvir Dahiya, Guoren Deng, Sharanjot Saini. Exosomal miR-3622a as prognostic marker in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4435. doi:10.1158/1538-7445.AM2017-4435

Predicting Prostate Cancer Progression as a Function of ETS-related Gene Status, Race, and Obesity in a Longitudinal Patient Cohort

BackgroundETS-related gene (ERG) oncogenic activation is the most common genomic alteration in prostate cancer (CaP) although it occurs less frequently in African American (AA) versus Caucasian (CA) patients, and the potential role of ERG as a prognostic marker has not been confirmed. ObjectiveThis study was conducted to confirm strong racial variation in the prevalence of ERG oncoprotein expression and to examine ERG oncoprotein expression, race, and body mass index as independent and joint predictors of CaP biochemical recurrence (BCR) following radical prostatectomy (RP). Design, setting, and participantsA retrospective cohort study of CA and AA CaP patients enrolled at Walter Reed National Military Medical Center, who donated clinically annotated, whole-mounted, prostatectomy specimens between 1994 and 2014 following RP, was conducted. Outcome measurements and statistical analysisKaplan–Meier (KM) estimation curves and multivariable Cox proportional hazards models were used to examine time to BCR as a function of ERG status, patient race, and obesity. Results and limitationsAmong 930 eligible patients (36.1% AA and 63.9% CA), with 155 (16.7%) BCR events and a median follow-up time of 5.1 yr, ERG oncoprotein expression was significantly less prevalent in index tumors of AA versus CA patients (23.2% vs 49.3%; p<0.0001). KM curves showed significantly poorer BCR-free survival for CA patients with ERG-negative index tumors but not for AA patients. Race-stratified multivariable analyses revealed a significant association between ERG-negative index tumors and poorer BCR-free survival among CA patients (hazards ratio=1.67, confidence interval=1.07, 2.61; p=0.024). Less heterogeneity in ERG expression among AA patients may reduce the ability to show its association with BCR. ConclusionsStriking racial variation in ERG oncoprotein expression was confirmed. A novel observation was the importance of index tumor ERG-negative status in predicting CaP progression for CA patients. Patient summaryETS-related gene (ERG) typing of tumors may be useful in prognosticating prostate cancer aggressiveness.

MicroRNA-383 located in frequently deleted chromosomal locus 8p22 regulates CD44 in prostate cancer.

A major genomic alteration in prostate cancer (PCa) is frequent loss of chromosome (chr) 8p with a common region of loss of heterozygosity (LOH) at chr8p22 locus. Genomic studies implicate this locus in the initiation of clinically significant PCa and with progression to metastatic disease. However, the genes within this region have not been fully characterized to date. Here we demonstrate for the first time that a microRNA component of this region –miR-383- is frequently downregulated in prostate cancer, plays a critical role in determining tumor initiating potential and is involved in prostate cancer metastasis via direct regulation of CD44, a ubiquitous marker of PCa tumor initiating cells (TICs)/ stem cells. Expression analyses of miR-383 in PCa clinical tissues established that low miR-383 expression is associated with poor prognosis. Functional data suggests that miR-383 regulates PCa tumor initiating/ stem-like cells via CD44 regulation. Ectopic expression of miR-383 inhibited tumor initiating capacity of CD44+ PCa cells. Also, ‘anti-metastatic’ effects of ectopic miR-383 expression were observed in a PCa experimental metastasis model. In view of our results, we propose that frequent loss of miR-383 at chr8p22 region leads to tumor initiation and prostate cancer metastasis. Thus, we have identified a novel finding that associates a long observed genomic alteration to PCa stemness and metastasis. Our data suggests that restoration of miR-383 expression may be an effective therapeutic modality against PCa. Importantly, we identified miR-383 as a novel PCa tissue diagnostic biomarker with a potential that outperforms that of serum PSA.

Non-immunosuppressive triazole-based small molecule induces anticancer activity against human hormone-refractory prostate cancers: the role in inhibition of PI3K/AKT/mTOR and c-Myc signaling pathways.

A series of triazole-based small molecules that mimic FTY720-mediated anticancer activity but minimize its immunosuppressive effect have been produced. SPS-7 is the most effective derivative displaying higher activity than FTY720 in anti-proliferation against human hormone-refractory prostate cancer (HRPC). It induced G1 arrest of cell cycle and subsequent apoptosis in thymidine block-mediated synchronization model. The data were supported by a decrease of cyclin D1 expression, a dramatic increase of p21 expression and an associated decrease in RB phosphorylation. c-Myc overexpression replenished protein levels of cyclin D1 indicating that c-Myc was responsible for cell cycle regulation. PI3K/Akt/mTOR signaling pathways through p70S6K- and 4EBP1-mediated translational regulation are critical to cell proliferation and survival. SPS-7 significantly inhibited this translational pathway. Overexpression of Myr-Akt (constitutively active Akt) completely abolished SPS-7-induced inhibitory effect on mTOR/p70S6K/4EBP1 signaling and c-Myc protein expression, suggesting that PI3K/Akt serves as a key upstream regulator. SPS-7 also demonstrated substantial anti-tumor efficacy in an in vivo xenograft study using PC-3 mouse model. Notably, FTY720 but not SPS-7 induced a significant immunosuppressive effect as evidenced by depletion of marginal zone B cells, down-regulation of sphingosine-1-phosphate receptors and a decrease in peripheral blood lymphocytes. In conclusion, the data suggest that SPS-7 is not an immunosuppressant while induces anticancer effect against HRPC through inhibition of Akt/mTOR/p70S6K pathwaysthat down-regulate protein levels of both c-Myc and cyclin D1, leading to G1 arrest of cell cycle and subsequent apoptosis. The data also indicate the potential of SPS-7 since PI3K/Akt signalingis responsive for the genomic alterations in prostate cancer.

Abstract 1934: MicroRNA-383 located in frequently deleted chromosomal locus 8p22 regulates prostate cancer stem cell marker CD44

Abstract A major genomic alteration in prostate cancer (PCa) is frequent loss of chromosome (chr) 8p with a common region of loss of heterozygosity (LOH) at chr8p22 locus. Genomic studies implicate this locus in the initiation of clinically significant PCa and with progression to metastatic disease. However, the genes within this region have not been fully characterized to date. Here we demonstrate for the first time that a microRNA component of this region -miR-383- is frequently downregulated in prostate cancer, plays a critical role in determining tumor initiating potential and is involved in prostate cancer metastasis via direct regulation of CD44, a ubiquitous marker of PCa tumor initiating cells (TICs)/ stem cells. Expression analyses of miR-383 in PCa clinical tissues established that low miR-383 expression is associated with poor prognosis. Functional data suggests that miR-383 regulates PCa tumor initiating/ stem-like cells via CD44 regulation. Ectopic expression of miR-383 inhibited tumor initiating capacity of CD44+ PCa cells. Also, ‘anti-metastatic’ effects of ectopic miR-383 expression were observed in a PCa experimental metastasis model. In view of our results, we propose that frequent loss of miR-383 at chr8p22 region leads to tumor initiation and prostate cancer metastasis. Thus, we have identified a novel finding that associates a long observed genomic alteration to PCa stemness and metastasis. Our data suggests that restoration of miR-383 expression may be an effective therapeutic modality against PCa relapse and metastasis. Importantly, we identified miR-383 as a novel PCa diagnostic biomarker with potential that outperforms that of serum PSA. Citation Format: Nathan Bucay, Kiran Sekhon, Varahram Shahryari, Yozo Mitsui, Guoren Deng, Z. Laura Tabatabai, Shahana Majid, Soichiro Yamamura, Rajvir Dahiya, Yuichiro Tanaka, Sharanjot Saini. MicroRNA-383 located in frequently deleted chromosomal locus 8p22 regulates prostate cancer stem cell marker CD44. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1934.