Localized prostate cancers are genetically variable and frequently multifocal, comprising spatially distinct regions with multiple independently-evolving clones. To date there is no understanding of ...whether this variability can influence management decisions for patients with prostate tumors. Here, we present a single case from a clinical trial of neoadjuvant intense androgen deprivation therapy. A patient was diagnosed with a large semi-contiguous tumor by imaging, histologically composed of a large Gleason score 9 tumor with an adjacent Gleason score 7 nodule. DNA sequencing demonstrates these are two independent tumors, as only the Gleason 9 tumor harbors single-copy losses of PTEN and TP53. The PTEN/TP53-deficient tumor demonstrates treatment resistance, selecting for subclones with mutations to the remaining copies of PTEN and TP53, while the Gleason 7 PTEN-intact tumor is almost entirely ablated. These findings indicate that spatiogenetic variability is a major confounder for personalized treatment of patients with prostate cancer.
Localized prostate cancer develops very slowly in most men, with the androgen receptor (AR) and MYC transcription factors amongst the most well-characterized drivers of prostate tumorigenesis. ...Canonically, MYC up-regulation in luminal prostate cancer cells functions to oppose the terminally differentiating effects of AR. However, the effects of MYC up-regulation are pleiotropic and inconsistent with a poorly proliferative phenotype. Here we show that increased MYC expression and activity are associated with the down-regulation of MEIS1, a HOX-family transcription factor. Using RNA-seq to profile a series of human prostate cancer specimens laser capture microdissected on the basis of MYC immunohistochemistry, MYC activity, and MEIS1 expression were inversely correlated. Knockdown of MYC expression in prostate cancer cells increased the expression of MEIS1 and increased the occupancy of MYC at the MEIS1 locus. Finally, we show in laser capture microdissected human prostate cancer samples and the prostate TCGA cohort that MEIS1 expression is inversely proportional to AR activity as well as HOXB13, a known interacting protein of both AR and MEIS1. Collectively, our data demonstrate that elevated MYC in a subset of primary prostate cancers functions in a negative role in regulating MEIS1 expression, and that this down-regulation may contribute to MYC-driven development and progression.
e13727 Background: Cancers among adolescents and young adults (AYA, aged 15-39) are rising in incidence, yet formal guidelines for diagnosis, treatment, and management of AYA-specific cancers are not ...widely known or disseminated. Practice patterns vary widely, contributing to a lack of improvement in outcomes for this underserved population. Clinicians and health systems have reported a need for additional guidance in care delivery for AYAs. Methods: We conducted a comprehensive literature review to identify clinical practice guidelines for cancer care delivery specific to AYAs published in PubMed or MEDLINE since 2010. MeSH and other key words were applied, using a search strategy guided by a health science librarian (EM). 795 papers were identified, with 690 excluded based on title and abstract review. 105 papers underwent full text review, and 64 papers underwent complete data extraction. Using Covidence software, two team members independently reviewed articles at the data extraction phase, with disagreements resolved through discussion. Results: We identified 22 papers that met our inclusion criteria as clinical practice guidelines specific to AYA cancer care. Clinical focus included breast cancer (4), sarcoma (4), brain tumors (2), gynecologic malignancies (2), acute lymphoblastic leukemia (1), colorectal cancer (1), NUT carcinoma (1), and proton therapy (1). Six papers covered general principles of caring for AYAs, regardless of cancer diagnosis. Key themes across guidelines included the importance of fertility preservation and psychosocial support, multidisciplinary care provided at specialized centers, and consideration of long-term toxicities of treatment. Conclusions: Clinical practice guidelines exist to inform clinicians and health systems on best practices for caring for AYAs with cancer, a growing and underserved population. Further dissemination of these guidelines may assist with improving outcomes. Comprehensive summary of these and other AYA specific guidelines is forthcoming and may serve as a useful clinical reference. Table: see text
Patients diagnosed with high risk localized prostate cancer have variable outcomes following surgery. Trials of intense neoadjuvant androgen deprivation therapy (NADT) have shown lower rates of ...recurrence among patients with minimal residual disease after treatment. The molecular features that distinguish exceptional responders from poor responders are not known.
To identify genomic and histologic features associated with treatment resistance at baseline.
Targeted biopsies were obtained from 37 men with intermediate- to high-risk prostate cancer before receiving 6 mo of ADT plus enzalutamide. Biopsy tissues were used for whole-exome sequencing and immunohistochemistry (IHC).
We assessed the relationship of molecular features with final pathologic response using a cutpoint of 0.05 cm3 for residual cancer burden to compare exceptional responders to incomplete and nonresponders. We assessed intratumoral heterogeneity at the tissue and genomic level, and compared the volume of residual disease to the Shannon diversity index for each tumor. We generated multivariate models of resistance based on three molecular features and one histologic feature, with and without multiparametric magnetic resonance imaging estimates of baseline tumor volume.
Loss of chromosome 10q (containing PTEN) and alterations to TP53 were predictive of poor response, as were the expression of nuclear ERG on IHC and the presence of intraductal carcinoma of the prostate. Patients with incompletely and nonresponding tumors harbored greater tumor diversity as estimated via phylogenetic tree reconstruction from DNA sequencing and analysis of IHC staining. Our four-factor binary model (area under the receiver operating characteristic curve AUC 0.89) to predict poor response correlated with greater diversity in our cohort and a validation cohort of 57 Gleason score 8–10 prostate cancers from The Cancer Genome Atlas. When baseline tumor volume was added to the model, it distinguished poor response to NADT with an AUC of 0.98. Prospective use of this model requires further retrospective validation with biopsies from additional trials.
A subset of prostate cancers exhibit greater histologic and genomic diversity at the time of diagnosis, and these localized tumors have greater fitness to resist therapy.
Some prostate cancer tumors do not respond well to a hormonal treatment called androgen deprivation therapy (ADT). We used tumor volume and four other parameters to develop a model to identify tumors that will not respond well to ADT. Treatments other than ADT should be considered for these patients.
A subset of patients present with high-risk localized prostate cancer that exhibits greater histologic and genomic diversity. These patients are less likely to respond to intense neoadjuvant androgen deprivation therapy.
Abstract
Introduction: The single best predictor of prostate cancer (PCa) outcome is Gleason score (Gs); however, the molecular characteristics that underpin specific Gleason patterns (Gp) and the ...biology associated with the aggressiveness of higher grades remain understudied. In a series of Gs 7 cancers, we recently observed increased activation of MYC and increased MYC protein levels in Gp4 prostate foci as compared to adjacent Gp3. While MYC is often associated with proliferative potential in other cancer types, subsets of prostate cancers show dramatically elevated MYC levels despite no increase in proliferation. These data suggest that increased MYC activity may drive Gp3 progression to Gp4 in a subset of cancers. Thus, the objective of this study is to examine the genetic contribution of MYC to locally advanced PCa development.
Approach: To test the hypothesis that increased MYC activity drives the progression of Gp3 to Gp4 in a subset of cases, we screened a new series of Gs7 tumors in which the Gp3 and Gp4 components are adjacent and represent contributing elements of the index lesion. Guided by anti-MYC immunohistochemistry, tumor foci were collected by laser capture microdissection based on MYC staining, focusing in particular where MYC staining was markedly increased in Gp4 versus Gp3. We then copurified DNA and RNA; whole-exome sequencing and transcriptome profiling were performed. To further guide our bioinformatic analyses, we separately generated two prostate cell culture models with altered MYC levels: RWPE-1 cells to overexpress MYC and LNCAP cells to knockdown MYC. Total RNA was extracted and whole-transcriptome sequencing was used to assess differential gene expression.
Results: Preliminary results from our first case suggest distinct histology and biology based on MYC tumor status from whole-exome sequencing analyses. Using somatic mutations and somatic copy number alterations, we observed a clonal relationship between two MYC-positive foci: a region of intraductal carcinoma and MYC-positive Gp4 adenocarcinoma. These regions shared identical single copy arm-level losses in chromosomes 6q and 8p, single-copy arm-level gains of 8q, 9p, and 9q, and 14 high-confidence point mutations that were not observed in the MYC-negative Gp3 component, suggesting that MYC activation may have driven evolution of the Gp4 component. When we cross-referenced differentially expressed genes between the Gp3 and Gp4 foci with our engineered cell lines and performed gene set enrichment analysis, we found recurrent enrichment for a JAK2 gene set, correlating with MYC activity.
Conclusions: Our results demonstrate the feasibility of performing laser capture microdissection and integrated genomic analyses on tissue with differential MYC status. Although further cases are needed to determine the frequency at which JAK/STAT signaling drives MYC-driven prostate cancer, our improved understanding of its biology may lend itself to new strategies for managing newly diagnosed patients or delaying disease progression.
Citation Format: Nichelle C. Whitlock, Rayann Atway, Qi Yang, Huihui Ye, Adam Sowalsky. Genetic contribution of MYC to the development of primary prostate cancer 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 B058.
Abstract
Despite the predictive value of Gleason score (Gs), the molecular characteristics and associated biology that underpin specific Gleason patterns (Gp) remain understudied. Based on previous ...data showing increased MYC activity in higher-grade Gp4 versus lower-grade Gp3 tumor foci and addressing the paradox that prostate cancer is not hyper-proliferative, we sought to examine the genetic contribution of MYC to locally-advanced prostate cancer development. We screened a series of Gs7 cancers in which the Gp3 and Gp4 components were adjacent and represented contributing elements of the index lesion. Tumor foci were collected by laser capture microdissection based on MYC staining and purified for RNA; transcriptome profiling was performed. To further guide our bioinformatics analyses, we generated a LNCaP prostate cancer cell line harboring MYC knockdown. RNA-seq and ChIP-seq was performed to identify differentially bound regions of the cistrome that correlate with altered gene expression and elucidate potential mechanism(s) of action for MYC in primary prostate cancer. In contrast to other reports, MYC knockdown had the effect of increasing global transcription. Moreover, the publicly available Cancer Genome Atlas (TCGA) prostate cancer dataset was curated according to MYC status based on extreme case design using reverse phase protein assay data. Preliminary results show: (1) increased MYC protein levels, but not proliferation, in Gp4 tumor foci as compared to adjacent Gp3, (2) distinct histology and biology based on MYC tumor status, and (3) found recurrent enrichment for gene sets cross-referencing differentially expressed genes between TCGA, tissue, and our engineered cell line. Of note, we observed recurrent enrichment for the Acosta Proliferation Independent MYC Targets Up gene set, which correlated with MYC activity. When this gene set was cross-referenced between all three datasets, the gene NOLC1 was identified. Nucleolar and coiled-body phosphoprotein 1 (NOLC1) plays an important role in rRNA synthesis and ribosome biosynthesis; its role in tumorigenesis appears context dependent. NOLC1 was found to be positively correlated with MYC expression and may thus contribute to MYC-driven prostate cancer. Although further cases are needed to determine the frequency at which NOLC1 drives MYC-driven prostate cancer, our results suggest a novel role for MYC in mediating development of locally-advanced prostate cancer.
Citation Format: Nichelle C. Whitlock, Shana Trostel, Rayann Atway, Elizabeth Walton, Brian J. Capaldo, Huihui Ye, Adam G. Sowalsky. Genetic contribution of MYC to the development of primary 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 2606.
Abstract
Background: Genetic alterations in lethal, metastatic prostate cancer include the loss of PTEN, translocation of the TMPRSS2 and ERG genes, upregulation of the androgen receptor (AR), and ...disruption of the DNA homologous repair pathway driven by mutations to BRCA1, BRCA2, and ATM. Many of these mutations can be observed while the cancer is still localized in the prostate. Here, we seek to identify genetic features indicative of therapeutic response and novel drivers of cancer progression to inform clinical practice.
Methods: Using tissue from 33 patients in an intense neoadjuvant anti-androgen clinical trial at the NCI (NCT02430480), we examined genetic features that would predict exceptional or poor response to anti-androgen enzalutamide therapy. Each patient on trial presented with multiple tumor foci, allowing us to investigate the intratumoral heterogeneity across foci within individual patients, as well as investigating the tumor profiles across multiple patients. Several patients exhibited exceptional response with residual tumor burdens less than 0.5cc, while others had substantial treatment-resistant cancers. We developed a panel of 12 immunohistopathological stains and used this panel to guide laser capture microdissection on pre-treatment biopsies and spatially matched post-treatment radical prostatectomy specimens to isolate ultrapure tumor foci from each patient. DNA from these foci was used for whole exome sequencing, as somatic copy number alterations and mutations also confirm their evolutionary relationship. This enabled us to classify baseline specimens as responder or nonresponder, while examining variations in genetic features between the two cohorts.
Results: To date, focal PTEN loss was observed in all nonresponders, while focal ERG staining was absent in 100% of responders and present in 60% of nonresponders. Synaptophysin positivity was rare at baseline but predicted resistance to treatment with 100% sensitivity. Intriguingly, baseline copy number profiles highlight a 6q deletion in 100% of exceptional responders, but not in the non-responders. Together, these data suggest an immunostain panel to assess oncogene and tumor suppressor alterations can predict response to anti-androgen therapy, while also suggesting a novel role of 6q in resistance to anti-androgen hormone therapy. Current studies are examining the role of 6q in response to anti-androgen therapies, which remains an area of active interest in our laboratory.
Conclusions: These findings demonstrate the feasibility in identifying intratumoral heterogeneity based on prostate biomarker status both in pre-treatment and post-treatment specimens. Using these data, comprehensive molecular analysis of prostate cancer at diagnosis may better-enable physicians to predict response to anti-androgen therapy and provide tailored treatment based on gene expression status.
Citation Format: Scott Wilkinson, Huihui Ye, Nicole Carrabba, Rayann Atway, Shana Y. Trostel, Thomas Hennigan, Ross Lake, Stephanie Harmon, Guinevere Chun, Baris Turkbey, Peter A. Pinto, Peter L. Choyke, Fatima Karzai, David J. VanderWeele, Kathleen Kelly, William L. Dahut, Adam G. Sowalsky. Combining genetic and histopathologic features to predict response to anti-androgen therapy in aggressive 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 2510.
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Background: AR directed therapies are standard of care for metastatic prostate cancer, and their use for high-risk localized disease may improve survival. Previous trials showed that ...suppression of AR activity resulting in greater pathologic responses improved survival rates. However, the underlying biology and molecular features of exceptionally responding tumors remain unknown. Methods: Men with locally advanced prostate cancer (median Gleason score 8, median PSA 9.58 ng/dl) received mpMRI and MRI/US-fusion targeted biopsies at baseline. Patients received 6 months of ADT plus enzalutamide, then received a second mpMRI, and underwent radical prostatectomy. RP specimens were whole mounted in the same plane as MRI. The location of each tumor on biopsy was mapped to prostatectomy specimens using pathologic and imaging hallmarks. FFPE sections of baseline and post-treatment tumor were stained, laser capture microdissected, and analyzed using whole exome sequencing. Amongst nonresponding patients (residual tumor burden > 0.05 cc) comparison of pre- and post-treatment tumor specimens identified evolutionary phylogenies over space and time representing intrinsic or clonal selection of pre-existing cells. Amongst responding patients, clonal extinction was confirmed by sequencing and immunostaining of surgical specimens. Results: Gleason score at baseline did not differentiate responding and nonresponding patients. Focal ERG staining in biopsies was absent in 100% of responders and present in 60% of responders. Intraductal carcinoma architecture was also absent in all responding tumors. Focal PTEN loss was observed in all nonresponders at baseline. Responding tumor foci were enriched for deletion of chromosome 6q. Comparison of baseline mpMRI sequences indicated a trend towards lower variance on dynamic contract enhanced (DCE) MR and lower local texture heterogeneity metrics in responding lesions. Conclusions: Response to neoadjuvant intense ADT correlates with distinctive pathologic, molecular, and imaging features that can be observed prior to treatment. Selection of patients based on these parameters may improve overall responses to treatment in subsequent clinical trials. Clinical trial information: NCT02430480.
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Background: The differential aggressiveness of potentially independent prostate cancer clones remains largely unknown. Appropriate prostate cancer staging using mpMRI and biopsy ...tissue can be confounded by sampling error. To date, there has been no understanding of whether clonal variability influences management decisions for localized prostate tumors. We sought to identify the sensitivity and genomic profile of distinct localized tumors from a patient following systemic intense neoadjuvant androgen deprivation therapy (ADT). Methods: A 66-year-old man with high risk prostate cancer enrolled in a Phase 2 study of intense neoadjuvant ADT (goserelin + enzalutamide; inADT). Baseline mpMRI showed a single semi-contiguous lesion encompassing the right apical-mid PZ extending into the left distal apical PZ. MR/US-fusion targeted biopsy was performed before 6 months of inADT. A second mpMRI was performed before radical prostatectomy. Whole exome sequencing on microdissected tumor foci identified somatic mutations and copy number alterations, which were further used with immunohistochemistry to assess tumor clonal architecture and genomic/phenotypic evolution of treatment resistant tumor. Results: We found two clonally independent tumors exhibited intrinsic heterogeneity at baseline which correlated with response or resistance. Biopsies of distinct left- and right-sided tumors showed differing histologies. mpMRI and pathology showed near complete response of the left-sided tumor and substantial resistance of the right-sided tumor, which exhibited a large intraductal component. Histology and whole exome data highlighted a divergence in the status of PTEN and TP53, tumor suppressor genes implicated in prostate cancer progression. Conclusions: These data highlight that even nascent prostate cancer is heterogenous and neoadjuvant therapeutic strategies will need to consider this for clinical optimization. Evolutionary trajectories that resulted in tumor heterogeneity in this case likely contributed to our observation that two independent prostate tumor nodules with distinct genetic alterations responded differently to neoadjuvant intense ADT. Clinical trial information: NCT02430480.
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Background: AR directed therapies are standard of care for metastatic prostate cancer, and their use for high-risk localized disease may improve survival. Previous trials showed low ...rates of complete pathologic responses to neoadjuvant ADT. The underlying biology and molecular features of tumors that fail to respond remain unknown. Methods: Men with localized prostate cancer with high risk features received 6 months of GnRH agonist plus enzalutamide. mpMRI was performed at baseline and prior to RP. MRI-US fusion guided biopsies were performed at study enrollment. RP specimens were sectioned in the same plane as mpMRI. Imaging and anatomical landmarks on pre- and post-treatment mpMRI were used to match targeted biopsies to RPs. IHC stains including AR, GR, and SYP were performed to guide laser capture microdissection (LCM) and characterization of residual disease. DNA was extracted from LCM biopsy and RP tissues. Whole exome sequencing with somatic mutation calling and copy number analysis was performed. Results: Most patients showed incomplete pathologic responses despite reductions in tumor volume. Several patients harbored multiple tumor clones prior to treatment, distinguished by distinct copy number alterations and mutations in biopsies. Alignment of biopsies to pre- and post-treatment mpMRI correlated with imaging response and histopathology of matched RP sections. Minimal genomic divergence from untreated clones on biopsy suggested intrinsic resistance, while extensive divergence indicated selection for pre-existing subclones. Most residual tumor was AR- and GR-positive adenocarcinoma, with some regions of AR-negative Panneth cell-like differentiation positive for synaptophysin. AR-V7 was rare in residual tumor and < 1% cells were positive for KI-67. The most common alteration in all samples was single-copy loss of chromosome 16q overlapping with ZFHX3. Conclusions: Our approach of repeated sampling by matching targeted biopsies to mpMRI demonstrates feasibility in comparing mpMRI response, pathologic treatment response, and the underlying genomic features that drive tumor development versus treatment resistance. Clinical trial information: NCT02430480.
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