PTEN Alterations Research Articles

Abstract 95: Somatic mutations and copy number variations in cancer-associated genes in 695 ovarian cancer patients

Abstract Background: Recent genomic studies have improved molecular understanding of ovarian cancer but have had limited impact on therapeutic improvements. We sought to review somatic mutations and copy-number variations (CNVs) in cancer-associated genes in the tumors of 695 patients with ovarian, peritoneal, or fallopian tube cancer (ovarian cancer) at Dana-Farber Cancer Institute, with associated pathologic and clinical data. Methods: Testing was performed on formalin-fixed tumor tissue without germline analysis, with IRB approval and patient consent. 310 patients underwent genotyping for 471 mutations in 41 cancer-related genes (OncoMap test). 388 patients underwent next-generation sequencing (NGS) of 300 cancer-associated genes (OncoPanel test). Most samples were primary tumors, with a small subset recurrent. The majority of tumors were adenocarcinoma/carcinoma histology. Results: Of 310 patients tested by OncoMap, 102 had at least one variant. Among tumors with adenocarcinoma/carcinoma histology, mutations were most frequent in TP53, KRAS, PIK3CA, JAK3, MET, and CTNNB1. Gene alterations varied by subtype and supported previously reported associations including BRAF in borderline, KRAS in mucinous, PIK3CA in clear cell, and PIK3CA/CTNNB1/AKT1 in endometrioid tumors. From 388 patients tested by OncoPanel, 3903 single nucleotide variants were detected. Variants were classified by clinical pathologists according to evidence-based potential clinical relevance. 27 variants were “Tier 1” (evidence confirming clinical utility in ovarian cancer) and 127 variants were “Tier 2” (possible clinical utility in specific contexts). Tier 1 variants were most frequent in BRCA1 and BRCA2. Common Tier 2 variants included alterations in TP53, PIK3CA, KRAS, PTEN, BRCA1, BRCA2, ARID1A, and BRAF. Several alterations may be considered “actionable” in terms of eligibility for clinical trials. Finally, 227 patients tested by OncoPanel had CNV data for the panel of cancer-associated genes. CNVs were numerous with 12368 CNVs reported. CNVs were classified as 1-copy deletion (n = 6033), 2-copy deletion (n = 108), high amplification (n = 114), and low amplification (n = 6103). Among adenocarcinoma/carcinoma tumors, 2-copy deletions were frequent in RB1, PTEN, CDKN2A, and MAP2K4, and common highly amplified genes were CCNE1, KRAS, AKT2, ERBB2, and MECOM. Conclusions: Genotyping and/or NGS of cancer-associated genes in formalin-fixed tissue from ovarian tumors is feasible and can identify potentially clinically actionable alterations. Preliminary correlations with survival and treatment response are being explored. Citation Format: Elizabeth H. Stover, Brooke Howitt, Neal I. Lindeman, Levi A. Garraway, Ursula A. Matulonis. Somatic mutations and copy number variations in cancer-associated genes in 695 ovarian cancer patients. [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 95.

Abstract 4504: Developing a PTEN-ETS signature to improve molecular risk stratification in prostate cancer

Abstract Prostate cancer (PCa) is a heterogeneous disease and the development of a molecular classification is critical to distinguish lethal from indolent tumors and reduce overtreatment. Genomic alterations of the PTEN and ETS genes (e.g., ERG) are among the most common in PCa and there is a huge interest in exploiting these alterations for risk assessment. We have found that PTEN loss is associated with PCa death most strongly in patients whose tumors do not carry an ERG rearrangement, contradicting findings from mouse models. Despite technological advances have enabled extraordinary insight into PCa molecular alterations, our understanding of the interaction between PTEN and ETS genes during PCa progression remains very limited. Hence, we have analyzed a large collection of multi-omics datasets to characterize the molecular underpinnings of PTEN loss in the context of ETS-negative versus ETS-positive tumors and further investigate their role in driving PCa prognosis. First we have developed a classification approach for PCa stratification based on dichotomized gene expression of PTEN and ETS family members. We have then validated this approach using TCGA DNA copy number variation and rearrangement status information. Our results confirmed that transcriptome analysis can be used for detecting PTEN and ETS alterations, and that in the absence of ERG rearrangements, tumors with PTEN loss frequently overexpress alternative ETS genes. Next, we examined whether somatic mutation profiles might differ by PTEN/ETS status, providing an potential explanation for the lethal behavior of ERG-negative/PTEN-negative tumors. As expected SPOP mutation was found to be mutually exclusive with ERG expression, but it did not vary significantly by PTEN status. Most interestingly, TP53 mutation - the most frequently altered gene in lethal metastatic PCa - was significantly enriched among PTEN-negative tumors irrespective to ERG- status. Collectively these findings suggest that known prognosis-driving somatic mutations do not explain the aggressive behavior of ERG-negative/PTEN-negative tumors. Finally, we analyzed differential gene expression associated with PTEN loss in the presence or absence of ERG gene expression and identified the associated biological processes and signaling pathways. This analysis failed to confirm the correlation between ERG/ETV1 expression and higher androgen signaling output previously reported in murine models. Furthermore, our findings revealed that MYC targets and the genes involved in cell cycle progression are the most up-regulated by PTEN loss in ETS-negative tumors, while genes involved in cell differentiation, response to DNA damage, and TNF signaling are the most induced by PTEN loss in ERG-positive tumors. Overall, our analysis clarified some important aspects of the role of PTEN/ETS network in PCa progression, suggesting a number of promising targets for the development of novel therapeutic interventions. Citation Format: Luigi Marchionni, Tamara L. Lotan. Developing a PTEN-ETS signature to improve molecular risk stratification in prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4504.

Abstract 140: LSAMP gene deletion is associated with rapid disease progression in prostate cancer of African American men

Abstract INTRODUCTION: Disproportionately higher rates of prostate cancer (CaP) incidence and mortality have been reported among African American (AA) men. Although oncogenic TMPRSS2-ERG gene fusion and deletion of the PTEN tumor suppressor gene are established cancer driver gene alterations in CaP, they are known to be more prevalent among men of European ancestry. By utilizing carefully annotated specimens, this study focused on the discovery of recurrent genomic alterations in CaP of AA men in comparison to Caucasian Americans (CA). METHODS: Genomic DNA from clinically localized primary prostate tumors (Gleason 6 or 7 with primary pattern 3) and matched peripheral blood lymphocytes of seven AA and seven CA patients, were analyzed by paired-end sequencing on Illumina Genome Analyzer IIx to a depth of 30x. Following alignment to reference genome, somatic alterations on tumor DNA that include single nucleotide variants (SNVs), insertion and deletions (Indels), structural variations, copy number variations, and inter- and intra-chromosomal translocations of tumor DNA sequence were identified. To confirm prevalent genomic deletions we performed FISH analysis on a tissue microarray constructed from 42 AA and 59 CA tumor and normal samples of an independent cohort. Frequently deleted loci were further validated by analysis of TCGA CaP SNP array data from 41 AA and 279 CA prostate tumors. RESULTS: A comparative evaluation of whole genome sequences of AA and CA CaP revealed a prevalent deletion of the LSAMP locus of chromosome 3q13.31 in AA CaP. These observations were confirmed by SNP array and FISH assays in independent cohorts of specimens. AA CaP patients with LSAMP deletion showed rapid disease progression. In contrast to higher frequency of LSAMP deletion, significantly lower frequencies of PTEN and ERG alterations were noted in CaP of AA men. Furthermore, CaP genomes of AA men displayed a higher rate of inter-chromosomal rearrangements than those from CA men. CONCLUSIONS: We highlight distinct features of AA and CA CaP genomes including common CaP driver genes (TMPRSS2- ERG, PTEN) and define a novel recurrent deletion of the LSAMP locus. This study underscores the need for careful evaluations of cancer genomes in underrepresented populations in the global context with implications for precision medicine strategies. Citation Format: Albert Dobi, Gyorgy Petrovics, Hua Li, Shyh-Han Tan, Tanja Stümpel, Denise Young, Shilpa Katta, Qiyuan Li, Kai Ying, Bernward Klocke, Lakshmi Ravindranath, Indu Kohaar, Yongmei Chen, Dezső Ribli, Korbinian Grote, Hau Zou, Joseph Cheng, Clifton L. Dalgard, Shimin Zhang, István Csabai, Jacob Kagan, David Takeda, Massimo Loda, Sudhir Srivastava, Matthias Scherf, Martin Seifert, Timo Gaiser, David G. McLeod, Zoltan Szallasi, Reinhard Ebner, Thomas Werner, Isabell A. Sesterhenn, Matthew Freedman, Shiv Srivastava. LSAMP gene deletion is associated with rapid disease progression in prostate cancer of African American men. [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 140.

Abstract 3538: Effects of oral chloroquine administration on a preclinical mouse model of PTEN/p53-deficient prostate cancer

Abstract Autophagy is cellular process that can promote tumor survival during periods of metabolic and therapeutic stress. Inhibition of autophagy can promote senescence resulting in decreased tumor growth. Genetic alterations of PTEN and p53 are frequently present in advanced human prostate cancer and are associated with poor prognosis. In mouse models, the inactivation of PTEN leads to the development of prostate tumors that progress slowly, in part due to the induction of PTEN-(loss)-induced cellular senescence. Concomitant inactivation of both PTEN and P53 in prostate leads to the development of an aggressive cancer phenotype that can overcome PTEN-(loss)-induced cellular senescence and is characterized with accelerated growth, metastatic development and decreased survival. Published findings show that in some cancer models, the effects of autophagy inhibition are dependent on p53 status. In this study we assessed the effects of pharmacological inhibition of autophagy with chloroquine (CQ) on the growth and progression of mouse prostate tumors driven by the concomitant inactivation of PTEN and p53. CQ is a lysosomotropic agent that has widely used to impede autophagy and inhibit the growth of human tumor cells in vitro and in vivo. Genetically engineered mice with the conditional inactivation of PTEN and p53 were used to evaluate the antitumor effects and therapeutic benefit of CQ in a drug intervention model of prostate cancer. Twenty-seven-week-old PTEN/p53 double knockout mice bearing prostate tumors were randomized to control and oral CQ (100 mg/kg in drinking water) treatment groups. Progression-free survival was 145 days versus 161 days (P = 0.703) for control and CQ treated mice, respectively. Median overall survival was 170 days versus 147 days (P = 0.523) for control and CQ treated mice, respectively. Tumor burden assed by the median genitourinary tract weight was 2.42 grams versus 2.19 grams (P = 0.645) for control and CQ treated mice, respectively. Our molecular assays revealed that CQ failed to consistently inhibit autophagy in tumors at the present dose. Overall, our findings show that CQ alone did not provide treatment benefit in mouse prostate cancer with loss of p53. Citation Format: Marco A. De Velasco, Koichi Sugimoto, Yurie Kura, Yuji Hatanaka, Yutaka Yamamoto, Takashi Oki, Kazuhiro Yoshimura, Masahiro Nozawa, Kazuhiro Yoshikawa, Kazuto Nishio, Hirotsugu Uemura. Effects of oral chloroquine administration on a preclinical mouse model of PTEN/p53-deficient prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3538.

Clinicopathogenomic analysis of mismatch repair proficient colorectal adenocarcinoma uncovers novel prognostic subgroups with differing patterns of genetic evolution.

Cancer somatic genetic evolution is a direct contributor to heterogeneity at the clonal and molecular level in colorectal adenocarcinoma (COAD). We sought to determine the extent to which genetic evolution may be detected in COAD in routinely obtained single clinical specimens and establish clinical significance with regard to clinicopathologic and outcome data. One hundred and twenty three cases of routinely collected mismatch repair proficient COAD were sequenced on the Illumina Truseq Amplicon assay. Measures of intratumoral heterogeneity and the preferential timing of mutational events were assessed and compared to clinicopathologic data. Survival subanalysis was performed on 55 patients. Patient age (p = 0.013) and specimen percent tumor (p = 0.033) was associated with clonal diversity, and biopsy (p = 0.044) and metastasis (p = 0.044) returned fewer mutations per case. APC and TP53 mutations preferentially occurred early while alterations in FBXW7, FLT3, SMAD4, GNAS and PTEN preferentially occurred as late events. Temporal heterogeneity was evident in KRAS and PIK3CA mutations. Hierarchical clustering revealed a TP53 mutant subtype and a MAPK-PIK3CA subtype with differing patterns of late mutational events. Survival subanalysis showed a decreased median progression free survival for the MAPK-PIK3CA subtype (8 months vs. 13 months; univariate logrank p = 0.0380, cox model p= 0.018). Neoadjuvant therapy associated mutations were found for ERBB2 (p = 0.0481) and FBXW7 (p = 0.015). Our data indicate novel molecular subtypes of mismatch repair proficient COAD display differing patterns of genetic evolution which correlate with clinical outcomes. Furthermore, we report treatment acquired and/or selected mutations in ERBB2 and FBXW7.

Confirmatory analysis to determine associations between platinum-sensitivity, molecular signature of combined tumor suppressor defects and aggressive variant prostate carcinomas (AVPC).

5020Background: Clinically defined AVPC is associated with platinum-sensitivity and a molecular profile of combined (≥2) alterations in PTEN, Tp53 and/or RB1 (Aparicio et al. Clin Cancer Res 2013;1...

Multiplexed immunofluorescence delineates proteomic cancer cell states associated with metabolism.

The phenotypic diversity of cancer results from genetic and nongenetic factors. Most studies of cancer heterogeneity have focused on DNA alterations, as technologies for proteomic measurements in clinical specimen are currently less advanced. Here, we used a multiplexed immunofluorescence staining platform to measure the expression of 27 proteins at the single-cell level in formalin-fixed and paraffin-embedded samples from treatment-naive stage II/III human breast cancer. Unsupervised clustering of protein expression data from 638,577 tumor cells in 26 breast cancers identified 8 clusters of protein coexpression. In about one-third of breast cancers, over 95% of all neoplastic cells expressed a single protein coexpression cluster. The remaining tumors harbored tumor cells representing multiple protein coexpression clusters, either in a regional distribution or intermingled throughout the tumor. Tumor uptake of the radiotracer 18F-fluorodeoxyglucose was associated with protein expression clusters characterized by hormone receptor loss, PTEN alteration, and HER2 gene amplification. Our study demonstrates an approach to generate cellular heterogeneity metrics in routinely collected solid tumor specimens and integrate them with in vivo cancer phenotypes.

Phosphatase and Tensin Homolog Is a Potential Target for Ovarian Cancer Sensitization to Cytotoxic Agents.

The phosphatase and tensin homolog (PTEN) tumor suppressor protein has been found to be inactivated or mutated in various human malignancies and to play a role in cisplatin and poly(ADP-ribose) polymerase inhibitor sensitivity. In this study, we assessed the association of PTEN loss with homologous recombination (HR) deficiency and increased chemosensitivity. The PTEN knockdown models were created using MISSION shRNA lentiviral transduction particles in cell lines derived from normal ovarian surface epithelium and a mixed endometrioid/clear-cell carcinoma. Sensitivity to common therapeutics was assessed using sulforhodamine B assay. Twenty-eight unselected primary epithelial ovarian cancer cultures derived from ascitic fluid collected at the time of surgery and matched genomic DNA were assessed for PTEN mutations using polymerase chain reaction amplification and Sanger sequencing and for mRNA expression using quantitative reverse transcription-polymerase chain reaction; HR was determined using γH2AX/RAD51 assay. The Cancer Genome Atlas data were analyzed using cBioPortal. In the carcinoma cell line, the PTEN knockdown enhanced sensitivity to cisplatin, rucaparib, doxorubicin, camptothecin, paclitaxel, and irradiation. In the primary ovarian cancer cultures, 2 point mutations were found (1105T>TG, 25L>L in 6 cultures and 1508G>GA, 159R>R in 4 cultures). The PTEN mRNA expression varied over 40-fold between the cultures, but did not correlate with HR status or in vitro sensitivity to cisplatin or rucaparib. The Cancer Genome Atlas data showed a rate of 8% alteration in PTEN and a trend toward improved survival in PTEN-mutated cases. These data indicate that although PTEN mutations in ovarian cancer are rare, PTEN inhibition results in therapeutic sensitization. Therefore, PTEN may be an important therapeutic target, in at least some cancers.

A comprehensive system of congenic mouse melanoma models for evaluation of immune therapies

Abstract There has been longstanding interest in the relationship between the immune system and malignant melanoma, the deadliest form of skin cancer. Melanoma has been the tumor of choice for the evaluation of a wide variety of therapeutic approaches that rely on stimulation of the immune system to combat cancer. The striking responses to immune checkpoint inhibitors noted in some melanoma patients have now been observed in several other malignancies, including renal cell carcinoma, lung cancer, and prostate cancer. These findings are very encouraging, however the specific mechanisms of response and reasons why only a subset of patients respond to therapy are not known. The extraordinary potential of immune therapies in cancer suggests that human-relevant mouse models of cancer are required to understand mechanisms of response and to optimize therapy so that a larger proportion of patients respond. We have generated and evaluated a series of genetically engineered mouse models driven by alterations in Braf, Pten, Cdkn2a, beta catenin, p53, and Nras that reflect the genetic diversity of the vast majority of human melanoma. We have backcrossed 7 of these models to C57Bl/6, generated tumors, and isolated a series of over 30 congenic mouse melanoma cell lines. Several independent lines have been isolated for each melanoma genotype generated. We are in the process of characterizing the tumor microenvironment in each of the models using flow cytometry and a novel quantitative imaging approach of histological sections. This series of congenic lines represents an ideal set of models for the study of cancer immunology and responses to immune therapies.

MP84-10 ERG INDUCES ENDOPLASMIC RETICULUM STRESS (ER) AND UNFOLDED PROTEIN RESPONSE (UPR) TO INITIATE PROSTATE CANCER CARCINOGENESIS

You have accessJournal of UrologyProstate Cancer: Basic Research & Pathophysiology III1 Apr 2016MP84-10 ERG INDUCES ENDOPLASMIC RETICULUM STRESS (ER) AND UNFOLDED PROTEIN RESPONSE (UPR) TO INITIATE PROSTATE CANCER CARCINOGENESIS Taduru L. Sreenath, Shiela S. Macalindong, Natallia Mikhalkevich, Shashwat Sharad, Parameet Kumar, Denise Young, Rishita Gupta, Shilpa Katta, Ahmed Mohamed, Shyh-Han Tan, Albert Dobi, Gyorgy Petrovics, Isabell A. Sesterhenn, Charles J. Bieberich, Peter Nelson, David G. McLeod, Valeri Vasioukhin, and Shiv Srivastava Taduru L. SreenathTaduru L. Sreenath More articles by this author , Shiela S. MacalindongShiela S. Macalindong More articles by this author , Natallia MikhalkevichNatallia Mikhalkevich More articles by this author , Shashwat SharadShashwat Sharad More articles by this author , Parameet KumarParameet Kumar More articles by this author , Denise YoungDenise Young More articles by this author , Rishita GuptaRishita Gupta More articles by this author , Shilpa KattaShilpa Katta More articles by this author , Ahmed MohamedAhmed Mohamed More articles by this author , Shyh-Han TanShyh-Han Tan More articles by this author , Albert DobiAlbert Dobi More articles by this author , Gyorgy PetrovicsGyorgy Petrovics More articles by this author , Isabell A. SesterhennIsabell A. Sesterhenn More articles by this author , Charles J. BieberichCharles J. Bieberich More articles by this author , Peter NelsonPeter Nelson More articles by this author , David G. McLeodDavid G. McLeod More articles by this author , Valeri VasioukhinValeri Vasioukhin More articles by this author , and Shiv SrivastavaShiv Srivastava More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2016.02.2234AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES High levels of the ERG expression due to gene fusions (predominantly TMPRSS2-ERG) is frequently detected in prostate cancer (CaP) in Western countries. Better understanding of the roles of the ERG oncogenic functions in CaP initiation and/or progression will enhance its utility as the therapeutic target. Transgenic mice generated to understand ERG’s role in the development of prostate adenocarcinoma have shown focal proliferative and dysplastic PIN lesions and later developed adenocarcinoma in older mice. Mice with ERG and PTEN alterations exhibit more accelerated malignant progression in prostate. The present study was aimed towards understanding the biological functions of ERG in early stages oncogenic transformation of prostate epithelium. METHODS Morphological analyses of mouse prostate glands were analyzed by H&E staining and by electron microscopy. Luminal cell surface markers were analyzed by FACS analysis. Luminal cells were analyzed for their potential to proliferate and form spheres by prostate sphere formation assay. ER stress and UPR marker proteins were analyzed by Western blot analysis. Analysis of representative ER stress pathway in ERG-positive human prostate cancer was analyzed in CPDR-80 gene-chip array data set representing well- and poor differentiated tumors. RESULTS Histological examination of ERG-Tg mouse prostates revealed increased luminal cell death due to apoptosis. Subsequently, TEM analysis revealed significant morphological differences such as increased numbers of lysosomes, autophagosomes, concentric membrane bodies with ribosomes, and lipid droplets in the cytoplasm of transgenic secretory luminal epithelial cells. Epithelial cells of ERG-Tg mouse prostates showed ~70% increase in CD49f (low) and Sca-1 (med) population with increased sphere formation capability and resistance to induced cell death. Western blots of ERG-Tg mouse and LNCaP-ERG transfectants showed increased expression of ER stress sensors and UPR proteins. A strong positive correlation was also observed between ERG and P4HB/PDI, one of the ER stress response proteins in human prostate tumors. CONCLUSIONS Cumulative data from experimental models of ERG and human CaP suggests that ERG mediates ER stress resulting into the activation of UPR, cell death with eventual biological selection for cell survival. Taken together these data indicate a critical biological function for ERG in prostate cancer initiation. © 2016FiguresReferencesRelatedDetails Volume 195Issue 4SApril 2016Page: e1093 Advertisement Copyright & Permissions© 2016MetricsAuthor Information Taduru L. Sreenath More articles by this author Shiela S. Macalindong More articles by this author Natallia Mikhalkevich More articles by this author Shashwat Sharad More articles by this author Parameet Kumar More articles by this author Denise Young More articles by this author Rishita Gupta More articles by this author Shilpa Katta More articles by this author Ahmed Mohamed More articles by this author Shyh-Han Tan More articles by this author Albert Dobi More articles by this author Gyorgy Petrovics More articles by this author Isabell A. Sesterhenn More articles by this author Charles J. Bieberich More articles by this author Peter Nelson More articles by this author David G. McLeod More articles by this author Valeri Vasioukhin More articles by this author Shiv Srivastava More articles by this author Expand All Advertisement Advertisement PDF downloadLoading ...

Combined Tumor Suppressor Defects Characterize Clinically Defined Aggressive Variant Prostate Cancers.

Morphologically heterogeneous prostate cancers that behave clinically like small-cell prostate cancers (SCPC) share their chemotherapy responsiveness. We asked whether these clinically defined, morphologically diverse, "aggressive variant prostate cancer (AVPC)" also share molecular features with SCPC. Fifty-nine prostate cancer samples from 40 clinical trial participants meeting AVPC criteria, and 8 patient-tumor derived xenografts (PDX) from 6 of them, were stained for markers aberrantly expressed in SCPC. DNA from 36 and 8 PDX was analyzed by Oncoscan for copy number gains (CNG) and losses (CNL). We used the AVPC PDX to expand observations and referenced publicly available datasets to arrive at a candidate molecular signature for the AVPC. Irrespective of morphology, Ki67 and Tp53 stained ≥10% cells in 80% and 41% of samples, respectively. RB1 stained <10% cells in 61% of samples and AR in 36%. MYC (surrogate for 8q) CNG and RB1 CNL showed in 54% of 44 samples each and PTEN CNL in 48%. All but 1 of 8 PDX bore Tp53 missense mutations. RB1 CNL was the strongest discriminator between unselected castration-resistant prostate cancer (CRPC) and the AVPC. Combined alterations in RB1, Tp53, and/or PTEN were more frequent in the AVPC than in unselected CRPC and in The Cancer Genome Atlas samples. Clinically defined AVPC share molecular features with SCPC and are characterized by combined alterations in RB1, Tp53, and/or PTEN.

Alterations in PTEN, MDM2, TP53 and AR protein and gene expression are associated with canine prostate carcinogenesis

The PTEN, AR, MDM2 and p53 protein network plays a central role in the development of many human cancers, thus eliciting the development of targeted cancer therapeutics. Dogs spontaneously develop tumours, and they are considered a good model for comparative oncology initiatives. Due to the limited information on these proteins in canine tumours, this study aimed to investigate gene and protein alterations in PTEN, AR, MDM2 and p53 in canine prostate cancer (PC). Protein expression was evaluated by immunohistochemistry (15 normal, 22 proliferative inflammatory atrophy (PIA) and 19 PC samples) and Western blotting (2 normal prostate tissue, 2 BPH, 2 PIA samples and 2 PC samples) and gene expression by RT-qPCR (10 normal, 10 PIA and 15 PC samples) of formalin-fixed tissue. We identified nuclear and cytoplasmic expression of PTEN and p53 in all samples, with only nuclear staining found for MDM2 and AR. Our results revealed high expression of MDM2 in PC and PIA samples compared to normal samples, whereas PTEN, P53 and AR expression was down-regulated in PC compared to normal tissue. All tumour samples (n=19) showed loss of nuclear PTEN expression, and all cancer mimickers showed positive nuclear staining. Therefore, nuclear PTEN staining could be a good diagnostic marker for differentiating between malignant lesions and mimickers. Canine prostate carcinogenesis involves increased expression of MDM2 in association with decreased expression of PTEN, p53 and AR, such as occurs in hormone refractory PC in men. Thus, dogs may be an important model for studying advanced stage PC.

Abstract P4-08-04: Navigating genomic landscape to find a PI3K-signaling algorithm for a rational combinatin in precision medicine

Abstract Background: Treatment of BC is conventionally based on the presence/absence of ER/PR or HER2 status of the primary tumor. We have enriched this approach by including major genetic and proteomic changes in tumors of individual patients in order to develop a better treatment-rationale based on an alteration driven signaling algorithm. Methods: Genomic and proteomic data from 75 BC patients seen in our center were retrospectively analyzed. Patients were re-biopsied after consultation and samples were characterized (IHC for ER, PR, and HER2; FFPE samples for genomic [Foundation Medicine] and proteomic analyses [Theranostics]). In vivo studies were conducted using xenograft models. Results: Although alterations of PIK3CA, PIK3R1, AKT, PTEN, MDM2, MDM4, TSC1, mTOR and RICTOR are most frequently observed in our patients, there is a distinct pattern of alteration(s) of the PI3K pathway genes in different subtypes of BC. A total of 76 genes were altered in 48 ER+BC patients. In 79% of ER+BC patients the above mentioned PI3K pathway genes were altered. Analyzing the set of alterations of genes in individual patients, we observed that within these 48 patients 25% exhibited alterations in more than one node of the pathway; the most common combination (alterations) being the amplification/mutation of PIK3CA with the amplification of MDM2/4 genes. The percentage of patients belonging to HER2+ &amp; TNBC exhibiting similar alterations in the PI3K pathway genes were significantly lower (∼40%). Our previous in vivo studies demonstrated that GDC-0980 and BEZ235 enhanced the antitumor activity of ABT888 plus carboplatin in TNBC or trastuzumab in HER2+ BC respectively and blocked the growth of established xenograft tumors by 80% to 90% with a concomitant decrease in tumor Ki67, pS6RP and CD31. Mechanistically the action of the PI3K-mTOR pathway targeted drug(s) was tested using cell line based models of BC subtypes pertaining to their respective genomic alterations. A combination of a pan-PI3K pathway inhibitor, GDC-0941 or isoform-specific inhibitors along with AI, trastuzumab, or HRD inhibitors (PARP) blocked proliferative signals and enhanced apoptosis (cleaved caspase3) in ER+/PIK3CA mutated, HER2+/PIK3CA mutated or PTEN-null TNBC cells respectively as demonstrated by WB, flow cytometry, cell proliferation, viability and cytotoxicity assays. A recent study demonstrated that exposure to chemotherapy induced a phenotypic shift or cell state transition towards a transient CD44Hi/CD24Hi chemotherapy-tolerant state, leading to the activation of downstream non-receptor tyrosine kinase signaling towards an emerging adaptive resistance (Goldman et al., Nature Comm. 2015). Hence drug combination(s) are being tested for their effect on CD44/CD24 expression levels, results of which will be presented in the meeting. Conclusion: Plotting the genetic alterations from the patient on the signaling landscape will be useful in cracking the code leading to improved treatment options. Patient specific in-depth plotting of genetic alterations of the PI3K-mTOR pathway and the relevance of these alterations in the context of (1) mechanisms of PI3K-mTOR pathway targeted drugs and (2) cell signaling are critical in determining choice of drugs in BC subtypes. Citation Format: Carlson JH, Krie A, Williams C, Sun Y, Lin X, Williams K, Klein J, Friedman L, De P, Dey N, Leyland-Jones B. Navigating genomic landscape to find a PI3K-signaling algorithm for a rational combinatin in precision medicine. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P4-08-04.

Integrated analysis of the genomic instability of PTEN in clinically insignificant and significant prostate cancer

Patients with clinically insignificant prostate cancer remain a major over-treated population. PTEN loss is one of the most recurrent alterations in prostate cancer associated with an aggressive phenotype, however, the occurrence of PTEN loss in insignificant prostate cancer has not been reported and its role in the separation of insignificant from significant prostate cancer is unclear. An integrated analysis of PTEN loss was, therefore, performed for structural variations, point mutations and protein expression in clinically insignificant (48 cases) and significant (76 cases) prostate cancers treated by radical prostatectomy. Whole-genome mate pair sequencing was performed on tumor cells isolated by laser capture microdissection to characterize PTEN structural alterations. Fluorescence in situ hybridization probes were constructed from the sequencing data to detect the spectrum of these PTEN alterations. PTEN loss by mate pair sequencing and fluorescence in situ hybridization occurred in 2% of insignificant, 13% of large volume Gleason score 6, and 46% of Gleason score 7 and higher cancers. In Gleason score 7 cancers with PTEN loss, PTEN alterations were detected in both Gleason pattern 3 and 4 in 57% of cases by mate pair sequencing, 75% by in situ hybridization and 86% by immunohistochemistry. PTEN loss by sequencing was strongly associated with TMPRSS2-ERG fusion, biochemical recurrence, PTEN loss by in situ hybridization and protein loss by immunohistochemistry. The complex nature of PTEN rearrangements was unveiled by sequencing, detailing the heterogeneous events leading to homozygous loss of PTEN. PTEN point mutation was present in 5% of clinically significant tumors and not in insignificant cancer or high-grade prostatic intraepithelial neoplasia. PTEN loss is infrequent in clinically insignificant prostate cancer, and is associated with higher grade tumors. Detection of PTEN loss in Gleason score 6 cancer in a needle biopsy specimen indicates a higher likelihood of clinically significant prostate cancer.

Pilot study of clinical targeted next generation sequencing for prostate cancer: Consequences for treatment and genetic counseling.

251 Background: Targeted next generation sequencing (NGS) panels for identification of actionable mutations are increasingly used in oncology for therapeutic decision-making, but have yet to be widely used for prostate cancer.To determine the utility of applying a targeted next generation sequencing to prostate cancer management, we conducted a pilot study using the clinical molecular diagnostic assay, UW-OncoPlex, on primary and metastatic tumors from patients with prostate cancer. Methods: Patients receiving treatment for prostate cancer by a medical oncologist were eligible. After providing informed consent, tumor DNA was extracted from formalin-fixed, paraffin-embedded (FFPE)primary tumors and/or metastatic biopsies. Extracted DNA was analyzed using UW-OncoPlex, a targeted NGS panel designed to assess genomic alterations in 234 cancer-associated genes (PMID: 24189654). Results were discussed at a monthly multidisciplinary precision tumor board prior to communicating results to patients. Results: Forty patients consented to the study and 31 (78%) had reportable results. Findings included frequently observed prostate cancer genomic aberrations, including: TMPRSS2-ERG fusions and copy-number alterations of PTEN, TP53, FOXA1, AR, and SPOP. We also observed potentially actionable alterations in BRAF, MAP2K1 (MEK1), PIK3R1, MET, FGFR1, and FGFR3, which inform future treatment and clinical trial considerations. Notably, 8/31 (25%) patients had suspected high penetrance germline mutations, including in BRCA2 (N = 3), TP53 (N = 2), ATM (N = 1), and CHEK2 (N = 2). These 8 individuals were referred to medical genetics and 7 of 8 mutations were confirmed to be germline. One patient was found to have a hypermutated phenotype associated with bi-allelic MSH6 mutation and microsatellite instability. Conclusions: Targeted NGS panel testing may be useful in informing future treatment approaches and clinical trial selection for patients with prostate cancer. In addition, we observed a high proportion of cases with suspected high-penetrance germline mutations and immediate actionability through referral to medical genetics.

Retained PTEN Expression Preferentially Identifies Mismatch Repair-Proficient Breast Cancers

Introduction/ Background Loss of phosphatase and tensin homolog (PTEN) expression and alterations in mismatch repair (MMR) genes are regarded as early oncogenic events in breast cancer. It has recently been hypothesized that the polyadenosine tract in PTEN might be a target for mutation in MMR-deficient endometrial tumors. However, the frequency and significance of MMR alterations in breast cancer is debated, and their relationship with PTEN status has not been investigated in the breast. Aims In this study, we sought to explore the relationships between PTEN expression and MMR alterations and to define whether PTEN immunohistochemistry is a predictor of MMR status in breast cancer. Methods 309 cases, including 261 invasive ductal carcinomas, no special type, 32 invasive lobular carcinomas, and 16 invasive ductal carcinomas, mixed types, carefully characterized from clinical and pathological standpoints, were reviewed and used to construct 11 tissue microarrays (TMAs). For each case, a mean of 4.5 tumor tissue cores (range 3 to 6 cores) was sampled, incorporating distinct topographic areas of the tumor, as well as matched non-neoplastic breast tissue, and, when present, associated in situ carcinoma. Taken together, 1381 spots were generated. Each TMA was subjected to immunohistochemical analysis of PTEN and the DNA MMR proteins MLH1, MSH2, MSH6 and PMS2. In order to allow a quick navigation within each TMA, and to minimize human-related biases, each stained slide was digitalized and blindly analyzed by two pathologists using a dedicated software able to segment TMA cores. The pattern of expression was therefore annotated manually on a digital database using a specific add-on module. Results According to clinicopathologic surrogate definition of intrinsic subtypes, PTEN protein loss was more frequent in luminal A-like and triple negative groups compared to luminal B-like carcinomas, as recently observed in other studies. MMR status in Luminal B-like tumors did not differ significantly between PTEN-retained and PTEN-loss groups, regardless HER2 amplification. In particular, retained PTEN expression was a predictor of MMR proficiency in approximately 35% of cases for this group. However, in luminal A-like and triple negative breast cancer groups, retained positive expression of MMR proteins was observed in 100% of cases showing PTEN wild-type immunohistochemical expression. Discussion: The present study is the first to investigate PTEN protein loss in a large set of breast carcinomas based on DNA MMR status by immunohistochemistry. Our findings broaden the understanding of the biology underpinning breast cancer, suggesting that MMR alterations are likely to be independent of PTEN status in the majority of luminal B-like breast cancers and that, in a way akin to endometrial carcinoma, MMR deficiency could play a part in the development of PTEN alterations in luminal A-like and triple negative breast cancers. The integration of traditional pathology with cutting-edge digital tools allowed a rapid quantification of immunohistochemistry and effective data organization in this wide cohort multi-variable study. Conclusion: PTEN immunohistochemistry is a useful adjunct in the clinical evaluation of breast cancer patients, being able to capture all MMR-proficient luminal A-like and triple negative tumors.

The PTEN tumor suppressor gene and its role in lymphoma pathogenesis.

The phosphatase and tensin homolog gene PTEN is one of the most frequently mutated tumor suppressor genes in human cancer. Loss of PTEN function occurs in a variety of human cancers via its mutation, deletion, transcriptional silencing, or protein instability. PTEN deficiency in cancer has been associated with advanced disease, chemotherapy resistance, and poor survival. Impaired PTEN function, which antagonizes phosphoinositide 3-kinase (PI3K) signaling, causes the accumulation of phosphatidylinositol (3,4,5)-triphosphate and thereby the suppression of downstream components of the PI3K pathway, including the protein kinase B and mammalian target of rapamycin kinases. In addition to having lipid phosphorylation activity, PTEN has critical roles in the regulation of genomic instability, DNA repair, stem cell self-renewal, cellular senescence, and cell migration. Although PTEN deficiency in solid tumors has been studied extensively, rare studies have investigated PTEN alteration in lymphoid malignancies. However, genomic or epigenomic aberrations of PTEN and dysregulated signaling are likely critical in lymphoma pathogenesis and progression. This review provides updated summary on the role of PTEN deficiency in human cancers, specifically in lymphoid malignancies; the molecular mechanisms of PTEN regulation; and the distinct functions of nuclear PTEN. Therapeutic strategies for rescuing PTEN deficiency in human cancers are proposed.

P27(KIP1) and PTEN cooperate in myeloproliferative neoplasm tumor suppression in mice.

PTEN acts as a phosphatase for PIP3 and negatively regulates the PI3K/AKT pathway, and p27KIP1 is a cyclin-dependent kinase inhibitor that regulates the G1 to S-phase transition by binding to and regulating the activity of cyclin-dependent kinases. Genetic alterations of PTEN or CDKN1B (p27KIP1) are common in hematological malignancies. To better understand how mutations in these two genes might cooperate in leukemogenesis, we inactivated both genes in the hematological compartment in mice. Here, we show that the combined inactivation of Pten and Cdkn1b results in a more severe myeloproliferative neoplasm phenotype associated with lower hemoglobin, enlarged spleen and liver, and shorter lifespan compared to inactivation of Pten alone. More severe anemia and increased myeloid infiltration and destruction of the spleen contributed to the earlier death of these mice, and elevated p-AKT, cyclin D1, and cyclin D3 might contribute to the development of this phenotype. In conclusion, PTEN and p27KIP1 cooperate in tumor suppression in the hematological compartment.

ATPS-46PRECLINICAL THERAPEUTIC EFFICACY OF A NOVEL BLOOD-BRAIN BARRIER-PENETRANT DUAL PI3K/MTOR INHIBITOR WITH PREFERENTIAL RESPONSE IN PI3K/PTEN MUTANT GLIOMA

Glioblastoma (GBM) is an ideal candidate disease for signal transduction targeted therapy because the majority of these tumors harbor genetic alterations that result in aberrant activation of growth factor signaling pathways. Loss of heterozygosity of chromosome 10, mutations in the tumor suppressor gene PTEN, and PI3K mutations are molecular hallmarks of GBM and indicate poor prognostic outcomes in many cancers. Consequently, inhibiting the PI3K pathway may provide therapeutic benefit in these cancers. PI3K inhibitors generally block proliferation rather than induce apoptosis. To restore the sensitivity of GBM to apoptosis induction, targeted agents have been combined with conventional therapy. However, the molecular heterogeneity and infiltrative nature of GBM make it resistant to traditional single agent therapy. Our objectives were to test a dual PI3K/mTOR inhibitor that may cross the blood-brain barrier (BBB) and provide the rationale for using this inhibitor in combination regimens to chemotherapy-induced synergism in GBM. Here we report the preclinical potential of a novel, orally bioavailable PI3K/mTOR dual inhibitor, DS7423 (hereafter DS), in in-vitro and in-vivo studies. DS was tested in mice, and DS plasma and brain concentrations were determined. DS crossed the BBB and led to potent suppression of PI3K pathway biomarkers in the brain. The physiologically relevant concentration of DS was tested in 9 glioma cell lines and 22 glioma-initiating cell (GIC) lines. DS inhibited the growth of glioma tumor cell lines and GICs at mean 50% inhibitory concentration values of less than 250 nmol/L. We found that PI3K mutations and PTEN alterations were associated with cellular response to DS treatment; with preferential inhibition of cell growth in PI3KCA-mutant and PTEN altered cell lines. DS showed efficacy and survival benefit in the U87 and GSC11 orthotopic models of GBM. Furthermore, administration of DS enhanced the antitumor efficacy of temozolomide against GBM in U87 glioma models, which shows that PI3K/mTOR inhibitors may enhance alkylating agent-mediated cytotoxicity, providing a novel regimen for the treatment of GBM. Our present findings establish that DS can specifically be used in patients who have PI3K pathway activation and/or loss of PTEN function. Further studies are warranted to determine the potential of DS for glioma treatment.

A novel genomic alteration of LSAMP associates with aggressive prostate cancer in African American men

Evaluation of cancer genomes in global context is of great interest in light of changing ethnic distribution of the world population. We focused our study on men of African ancestry because of their disproportionately higher rate of prostate cancer (CaP) incidence and mortality. We present a systematic whole genome analyses, revealing alterations that differentiate African American (AA) and Caucasian American (CA) CaP genomes. We discovered a recurrent deletion on chromosome 3q13.31 centering on the LSAMP locus that was prevalent in tumors from AA men (cumulative analyses of 435 patients: whole genome sequence, 14; FISH evaluations, 101; and SNP array, 320 patients). Notably, carriers of this deletion experienced more rapid disease progression. In contrast, PTEN and ERG common driver alterations in CaP were significantly lower in AA prostate tumors compared to prostate tumors from CA. Moreover, the frequency of inter-chromosomal rearrangements was significantly higher in AA than CA tumors. These findings reveal differentially distributed somatic mutations in CaP across ancestral groups, which have implications for precision medicine strategies.