Bio

Clinical Focus


  • Prostate Cancer - Urologic Oncology
  • Male Cancers - Prostate
  • Cancer > Urologic Oncology
  • Urology
  • Urologic Cancers - Urologic Oncology
  • Prostate Cancer
  • Urologic Cancers
  • Nerve-sparing radical prostatectomy

Academic Appointments


Administrative Appointments


  • Associate Dean, Academic Affairs, Stanford University School of Medicine (2013 - Present)
  • Chief, Urologic Oncology, Department of Urology (2012 - Present)
  • Acting Chair, Department of Urology (2012 - 2012)
  • Associate Chair, Prostate Cancer Working Group EDRN (2010 - Present)
  • Editor-in-Chief, The Open Prostate Cancer Journal (2008 - Present)
  • Editorial Board, Andrology (2011 - Present)
  • Editorial Board, Prostate Cancer (2010 - Present)
  • Editorial Board, The Prostate (2000 - Present)
  • Membership Committee, Society for Basic Urologic Research (2004 - 2008)

Honors & Awards


  • Keith and Jan Hurlbut Professor, Stanford University (2012)
  • Listing in Guide to America's Top Surgeons, Consumers' Research Council (2010)
  • Best Doctors in America, Best Doctors Inc. (2004-2013)
  • Leutje-Stubbs Faculty Scholar, Stanford University School of Medicine (2002-2003)
  • Eugene P. Schonfeld Medical Research Award, Kidney Cancer Association (2000-2002)
  • Clinician Scientist Award, Doris Duke Foundation (1998-2002)
  • Dornier Research Scholar, American Foundation for Urologic Disease (1995-1997)

Professional Education


  • Fellowship:Johns Hopkins University (1997) MD
  • Residency:Johns Hopkins University (1994) MD
  • Residency:Johns Hopkins University (1990) MD
  • Board Recertification, Urology, American Board of Urology (2009)
  • Board Certification: Urology, American Board of Urology (2000)
  • Internship:Johns Hopkins University (1989) MD
  • Medical Education:Stanford University School of Medicine (1988) CA
  • A. B., University of Chicago, Biology (1982)

Research & Scholarship

Current Research and Scholarly Interests


Our interest is in developing diagnostic and prognostic markers for urological diseases. We have approached this question broadly. We are active in biomarker discovery using genomic approaches. While our primary focus has been in prostate cancer, we have also worked in kidney bladder and testicular cancer. We are also actively seeking markers that reflect renal damage in patients with urinary obstruction. We are also interested in developing platforms for translating biomarkers discovered in the laboratory into clinical practice. For instance, we have active collaborations in developing novel molecular imaging strategies for prostate cancer. We also participate in several large clinical trials for development, validation and implementation of clinical biomarkers in prostate cancer.

Clinical Trials


  • Hypofractionated Radiotherapy for Localized Prostate Cancer (With CyberKnife or With IMRT) Not Recruiting

    To demonstrate that a hypo-fractionated course of radiotherapy (ie. an accelerated radiotherapy course where fewer but larger doses of radiotherapy are given) is both safe and effective in the treatment of low-risk localized prostate cancer.

    Stanford is currently not accepting patients for this trial. For more information, please contact Gillian McFarlane, (650) 721 - 2034.

    View full details

  • Prostate Active Surveillance Study Not Recruiting

    The Prostate Active Surveillance Study (PASS) is a research study for men who have chosen active surveillance as a management plan for their prostate cancer. Active surveillance is defined as close monitoring of prostate cancer with the offer of treatment if there are changes in test results. This study seeks to discover markers that will identify cancers that are more aggressive from those tumors that grow slowly.

    Stanford is currently not accepting patients for this trial. For more information, please contact Michelle Ferrari, (650) 725 - 5543.

    View full details

  • Quality of Life Following Radical Prostatectomy Recruiting

    This study will utilize the Expanded Prostate Cancer Index Composite questionnaire to learn what impact the surgery has upon the participant's sense of health, sexual and urinary quality of life.

    View full details

  • Imaging During Surgery in Diagnosing Patients With Prostate, Bladder, or Kidney Cancer Not Recruiting

    This pilot clinical trial studies imaging during surgery in diagnosing patients with prostate, bladder, or kidney cancer. New diagnostic imaging procedures, may find prostate, bladder, or kidney cancer

    Stanford is currently not accepting patients for this trial. For more information, please contact Mark Gonzalgo, 650-725-5544.

    View full details

  • Photoacoustic Imaging (PAI) of the Prostate: A Clinical Feasibility Study Recruiting

    PRIMARY OBJECTIVE(S): The primary objective of this pilot study is to assess PAI-performance in a clinical setting to understand limitations of our current PAI instrumentation and to help improve the next-generation design. SECONDARY OBJECTIVE(S): To do preliminary evaluations of oxygen saturation in lesions based on PAI-measurements in order to distinguish malignant from benign prostatic tissue as a basis for future studies.

    View full details

  • Microarray Analysis of Gene Expression in Prostate Tissues Not Recruiting

    The purpose of this study is to investigate gene expression profiles and biologic features of prostate tissue and how they relate to prostate cancer development and growth.

    Stanford is currently not accepting patients for this trial. For more information, please contact Cancer Clinical Trials Office, 650-498-7061.

    View full details

Teaching

2013-14 Courses


Postdoctoral Advisees


Graduate and Fellowship Programs


Publications

Journal Articles


  • Evaluation of SF-1 Expression in Testicular Germ Cell Tumors: A Tissue Microarray Study of 127 Cases. Applied immunohistochemistry & molecular morphology Sangoi, A. R., McKenney, J. K., Brooks, J. D., Higgins, J. P. 2013; 21 (4): 318-321

    Abstract

    Differentiating testicular germ cell tumors from sex-cord stromal tumors can be difficult in certain cases because of overlapping morphologic features and/or an absence of clinically apparent hormonal symptoms. Immunohistochemistry may be needed as an ancillary diagnostic tool in this differential diagnostic setting. Steroidogenic factor-1 (SF-1) is a nuclear transcription factor controlling steroidogenesis and is expressed in developing Sertoli and Leydig cells. Although 1 recent study has reported SF-1 nuclear immunoreactivity in testicular sex-cord stromal tumors, the specificity for this marker in germ cell tumors has not been evaluated. After encountering several problematic cases (including some on testicular biopsy), we sought to determine the diagnostic specificity of SF-1 in a large series of germ cell tumors. Nuclear immunohistochemical expression of SF-1 was evaluated in 127 germ cell tumors using tissue microarray technology with 23 non-germ cell tumor tissues as positive internal controls. No nuclear SF-1 expression was identified in any of the 127 germ cell tumors [including choriocarcinoma (3), embryonal carcinoma (25), epidermal inclusion cyst (1), intratubular germ cell neoplasia unclassified (4), seminoma (72), spermatocytic seminoma (2), teratoma (8), and yolk sac tumor (12)]. All 23 non-germ cell tumor tissues showed strong nuclear SF-1 expression in Sertoli and/or Leydig cells [including testicular atrophy (10), cryptorchidism (2), normal testis (4), hypospermatogenesis (1), immature testis (1), intratubular large cell calcifying Sertoli cell tumor (1), Leydig cell tumor (3), and Sertoli only (1)]. This study documents the absence of SF-1 expression in testicular germ cell tumors and supports its specificity for sex-cord stromal lesions in this diagnostic context.

    View details for DOI 10.1097/PAI.0b013e318277cf5a

    View details for PubMedID 23165333

  • Epigenetic changes in histologically normal prostate tissues. journal of urology Brooks, J. D. 2013; 189 (6): 2020-2021

    View details for DOI 10.1016/j.juro.2013.02.3193

    View details for PubMedID 23465550

  • Comprehensive gene expression changes associated with mouse postnatal kidney development. journal of urology Wu, B., Sahoo, D., Brooks, J. D. 2013; 189 (6): 2385-2390

    Abstract

    To provide a portrait of the molecular alterations in renal growth that occur in mice postnatally, we performed gene expression profiling at discrete time points during the first 5 weeks of life.Kidneys were harvested from C57BL/6 mice at embryonic day 19.5, and postnatal days 1, 3, 5, 7, 10, 14, 21, 28 and 35. Total RNA was extracted and gene expression profiling was done using microarrays (Agilent Technologies, Santa Clara, California). Transcripts whose expression levels changed during the study course were identified using StepMiner software (http://chicory.stanford.edu/sahoo/public/StepMiner/). Biological functions of the modulated genes were identified using IPA® software.Postnatal kidney growth and development are associated with widespread changes in gene expression with 6,949 transcripts significantly up-regulated and 6,696 down-regulated during the first 5 weeks of life. Pathway analysis showed progressive down-regulation of pathways associated with cell growth and embryonic development (postnatal days 5 to 7). This was followed by increased expression of transcripts associated with lipid/energy metabolism and molecular transport (postnatal days 10 to 14), and down-regulation of genes related to DNA replication, cell cycle, tissue development, protein trafficking and cell morphology (postnatal days 14 to 21).To our knowledge we report the most comprehensive temporal survey of postnatal kidney development to date. This data set provides a framework for interpreting nephropathy, such as that induced by congenital obstruction.

    View details for DOI 10.1016/j.juro.2012.12.002

    View details for PubMedID 23220383

  • Increased expression of NuSAP in recurrent prostate cancer is mediated by E2F1 ONCOGENE Gulzar, Z. G., McKenney, J. K., Brooks, J. D. 2013; 32 (1): 70-77

    Abstract

    Increasing evidence suggests that prostate cancer is overdiagnosed and overtreated, and prognostic biomarkers would aid in treatment selection. To define prognostic biomarkers for aggressive prostate cancer, we carried out gene-expression profiling of 98 prostate tumors and 52 benign adjacent prostate tissue samples with detailed clinical annotation. We identified 28 transcripts significantly associated with recurrence after radical prostatectomy including NuSAP, a protein that binds DNA to the mitotic spindle. Elevated NuSAP transcript levels were associated with poor outcome in two independent prostate cancer gene-expression datasets. To characterize the role and regulation of NuSAP in prostate cancer, we studied the expression of NuSAP in the LNCaP and PC3 human prostate cancer cell lines. Posttranscriptional silencing of the NuSAP gene severely hampered the ability of PC3 to invade and proliferate in vitro. The promoter region of the NuSAP gene contains two CCAAT boxes and binding sites for E2F. Transient transfection of an E2F1 cDNA and 431?bp of the NuSAP promoter demonstrated E2F1 as an important regulator of expression. Deletion of the E2F-binding site at nucleotide -246 negated the effects of E2F1 on NuSAP expression. Electrophoretic mobility shift assays demonstrated that nuclear extracts of cells overexpressing E2F1 bound directly to the E2F-binding site in the NuSAP promoter region. Finally, immunohistochemistry showed a strong correlation between E2F1 and NuSAP expression in human prostate cancer samples. NuSAP is a novel biomarker for prostate cancer recurrence after surgery and its overexpression appears to be driven in part by E2F1 activation.

    View details for DOI 10.1038/onc.2012.27

    View details for Web of Science ID 000313029500007

    View details for PubMedID 22349817

  • Treatment and mortality in men with localized prostate cancer: a population-based study in California. The Open Prostate Cancer Journal Sieh W, Lichtensztajn DY, Nelson DO, Brooks JD, Chang ET 2013; 6: 1-9
  • Urinary TMPRSS2:ERG and PCA3 in an active surveillance cohort: results from a baseline analysis in the Canary Prostate Active Surveillance Study. Clinical cancer research : an official journal of the American Association for Cancer Research Lin, D. W., Newcomb, L. F., Brown, E. C., Brooks, J. D., Carroll, P. R., Feng, Z., Gleave, M. E., Lance, R. S., Sanda, M. G., Thompson, I. M., Wei, J. T., Nelson, P. S. 2013; 19 (9): 2442-50

    Abstract

    Active surveillance is used to manage low-risk prostate cancer. Both PCA3 and TMPRSS2:ERG are promising biomarkers that may be associated with aggressive disease. This study examines the correlation of these biomarkers with higher cancer volume and grade determined at the time of biopsy in an active surveillance cohort.Urine was collected after digital rectal examination prospectively as part of the multi-institutional Canary Prostate Active Surveillance Study (PASS). PCA3 and TMPRSS2:ERG levels were analyzed in urine collected at study entry. Biomarker scores were correlated to clinical and pathologic variables.In 387 men, both PCA3 and TMPRSS2:ERG scores were significantly associated with higher volume disease. For a negative repeat biopsy, and 1% to 10%, 11% to 33%, 34% or more positive cores, median PCA3, and TMPRSS2:ERG scores increased incrementally (P < 0.005). Both PCA3 and TMPRSS2:ERG scores were also significantly associated with the presence of high-grade disease. For a negative repeat biopsy, Gleason 6 and Gleason ?7 cancers, the median PCA3, and TMPRSS2:ERG scores also increased incrementally (P = 0.02 and P = 0.001, respectively). Using the marker scores as continuous variables, the ORs for a biopsy in which cancer was detected versus a negative repeat biopsy (ref) on modeling was 1.41 (95% CI: 1.07-1.85), P = 0.01 for PCA3 and 1.28 (95% CI: 1.10-1.49), P = 0.001 for TMPRSS2:ERG.For men on active surveillance, both PCA3 and TMPRSS2:ERG seem to stratify the risk of having aggressive cancer as defined by tumor volume or Gleason score.

    View details for PubMedID 23515404

  • Identification and Characterization of 2 Testicular Germ Cell Markers, Glut3 and CyclinA2. Applied immunohistochemistry & molecular morphology : AIMM / official publication of the Society for Applied Immunohistochemistry Howitt, B. E., Brooks, J. D., Jones, S., Higgins, J. P. 2013

    Abstract

    Testicular germ cell tumors (TGCT) are the most common type of testicular tumor and encompass different histologic types that greatly influence treatment and prognosis. Immunohistochemical studies may be required for accurate classification, particularly when these tumors present at extragonadal sites, and to aid in distinguishing histologic types. Traditional markers for identifying and distinguishing TGCT include PLAP, CD117, AFP, and CD30. More recently, the addition of OCT3/4 and SALL4 has increased sensitivity for immunohistochemical detection of germ cell tumors. We examined gene expression data from a previously published microarray study that compared normal testis mRNA expression to various TGCT. We also performed a search of the literature to identify less well-characterized markers. Glut3 and cyclinA2 showed promise as TGCT markers. Therefore, we evaluated expression of glut3 and cyclinA2 by immunohistochemistry using tissue microarrays (TMAs). Of 66 seminomas included in the TMA, 64 (97%) showed positive nuclear staining for cyclinA2 and 58 (88%) were strongly positive. Strong positive staining for cyclinA2 was also seen in the spermatocytic seminoma. All 20 of the embryonal carcinomas stained positively with cyclinA2, and 19 (95%) displayed strong nuclear staining for cyclinA2. Twenty of the 20 embryonal carcinomas stained for glut3 in a strong membranous pattern. Of 8 yolk sac tumors, 100% stained with glut3. We also evaluated glut3 and cyclinA2 staining on a general TMA containing 486 samples representing 156 different tumors. CyclinA2 stained a number of other tumor types, but the majority of these were weak or focal staining. Glut3 was rarely positive in other tumors; interestingly, most of these were of ovarian origin. We conclude that glut3 is a sensitive (96%) and specific (92%) marker for embryonal carcinomas and yolk sac tumors. Although cyclinA2 is a sensitive marker of seminomas and embryonal carcinomas (98%), its specificity is lower if focal and weak staining of nongerm cell tumors is considered positive. The sensitivity and specificity of glut3 are comparable with that seen for SALL4.

    View details for PubMedID 23343953

  • A Model for the Design and Construction of a Resource for the Validation of Prognostic Prostate Cancer Biomarkers: The Canary Prostate Cancer Tissue Microarray ADVANCES IN ANATOMIC PATHOLOGY Hawley, S., Fazli, L., McKenney, J. K., Simko, J., Troyer, D., Nicolas, M., Newcomb, L. F., Cowan, J. E., Crouch, L., Ferrari, M., Hernandez, J., Hurtado-Coll, A., Kuchinsky, K., Liew, J., Mendez-Meza, R., Smith, E., Tenggara, I., Zhang, X., Carroll, P. R., Chan, J. M., Gleave, M., Lance, R., Lin, D. W., Nelson, P. S., Thompson, I. M., Feng, Z., True, L. D., Brooks, J. D. 2013; 20 (1): 39-44

    Abstract

    Tissue microarrays (TMAs) provide unique resources for rapid evaluation and validation of tissue biomarkers. The Canary Foundation Retrospective Prostate Tissue Microarray Resource used a rigorous statistical design, quota sampling, a variation of the case-cohort study, to select patients for inclusion in a multicenter, retrospective prostate cancer TMA cohort. The study is designed to definitively validate tissue biomarkers of prostate cancer recurrence after radical prostatectomy. Tissue samples from over 1000 participants treated for prostate cancer with radical prostatectomy between 1995 and 2004 were selected at 6 participating institutions in the United States and Canada. This design captured the heterogeneity of screening and clinical practices in the contemporary North American population. Standardized clinical data were collected in a centralized database. The project has been informative in several respects. The scale and complexity of assembling TMAs with over 200 cases at each of 6 sites involved unanticipated levels of effort and time. Our statistical design promises to provide a model for outcome-based studies where tissue localization methods are applied to high-density TMAs.

    View details for DOI 10.1097/PAP.0b013e31827b665b

    View details for Web of Science ID 000312346800005

    View details for PubMedID 23232570

  • Managing localized prostate cancer in the era of prostate-specific antigen screening. Cancer Brooks, J. D. 2013

    View details for DOI 10.1002/cncr.28301

    View details for PubMedID 24006273

  • Utilization of cytoreductive nephrectomy and patient survival in the targeted therapy era. International journal of cancer. Journal international du cancer Conti, S. L., Thomas, I. C., Hagedorn, J. C., Chung, B. I., Chertow, G. M., Wagner, T. H., Brooks, J. D., Srinivas, S., Leppert, J. T. 2013

    Abstract

    We sought to analyze utilization and survival outcomes of cytoreductive nephrectomy in patients with metastatic renal cell carcinoma (RCC) before and after introduction of targeted therapy. We identified patients with metastatic RCC between 1993 and 2010 in the SEER registry and examined temporal trends in utilization. We performed a joinpoint regression to determine when changes in utilization of cytoreductive nephrectomy occurred. We fitted multivariable proportional hazard models in full and propensity score-matched cohorts. We performed a difference-in-difference analysis to compare survival outcomes before and after introduction of targeted therapy. The proportion of patients undergoing cytoreductive nephrectomy increased from 1993 to 2004, from 29% to 39%. We identified a primary joinpoint of 2004, just prior to the introduction of targeted therapy. Beginning in 2005, there was a modest decrease in utilization of cytoreductive nephrectomy. Cytoreductive nephrectomy was associated with a lower adjusted relative hazard (0.41, 95% confidence interval 0.34 to 0.43). Median survival among patients receiving cytoreductive nephrectomy increased in the targeted therapy era (19 versus 13 months), while median survival among patients not receiving cytoreductive nephrectomy increased only slightly (4 versus 3 months). Difference-in-difference analysis showed a significant decrease in hazard of death among patients who received cytoreductive nephrectomy in the targeted therapy era. Despite decreased utilization in the targeted therapy era, cytoreductive nephrectomy remains associated with improved survival. Prospective randomized trials are needed to confirm the benefit of cytoreductive nephrectomy among patients with metastatic RCC treated with novel targeted therapies. © 2013 Wiley Periodicals, Inc.

    View details for DOI 10.1002/ijc.28553

    View details for PubMedID 24135850

  • Higher rates of upgrading and upstaging in older patients undergoing radical prostatectomy and qualifying for active surveillance. BJU international Busch, J., Magheli, A., Leva, N., Ferrari, M., Kramer, J., Klopf, C., Kempkensteffen, C., Miller, K., Brooks, J. D., Gonzalgo, M. L. 2013

    Abstract

    Active surveillance (AS) for low-risk prostate cancer represents an acceptable management strategy especially for older patients. We determined pathologic and oncologic outcomes of patients diagnosed with low-risk prostate cancer in two age cohorts who underwent radical prostatectomy (RP) and qualified for AS according to Prostate Cancer Research International: Active Surveillance (PRIAS) criteria.A total of 320 patients ≥ 65 years of age who underwent RP and were eligible for AS according to PRIAS criteria were propensity score matched 1:1 to patients < 65 years of age. Patient characteristics were compared with chi-square, Kruskal-Wallis, and one-way ANOVA tests. Predictors of RP pathologic upgrading or upstaging were analyzed using logistic regression. Recurrence-free survival (RFS) and overall survival (OS) were calculated with the Kaplan-Meier method. Predictors of RFS were analyzed within Cox regression models.Pathologic upgrading and upstaging were significantly higher among older (≥ 65 yrs) versus younger (< 65 yrs) patients (53.1% vs. 44.1% and 12.2% vs. 7.2%, respectively). Higher PSA and increasing age were independent predictors of upgrading among patients < 65 years. There were no differences in RFS or OS between the two age groups. Positive surgical margin status was the only independent predictor of shorter RFS.Patients ≥ 65 years of age who are eligible for AS by PRIAS criteria have a higher risk of being upgraded and upstaged at the time of RP compared to patients < 65 years of age. These findings should be taken into consideration when discussing treatment options for patients diagnosed with prostate cancer.

    View details for DOI 10.1111/bju.12466

    View details for PubMedID 24112652

  • Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape. Genome biology Day, K., Waite, L. L., Thalacker-Mercer, A., West, A., Bamman, M. M., Brooks, J. D., Myers, R. M., Absher, D. 2013; 14 (9): R102

    Abstract

    DNA methylation is an epigenetic modification that changes with age in human tissues, although the mechanisms and specificity of this process are still poorly understood. We compared CpG methylation changes with age across 283 human blood, brain, kidney, and skeletal muscle samples using methylation arrays to identify tissue-specific age effects.We found age-associated CpGs (ageCGs) that are both tissue-specific and common across tissues. Tissue-specific ageCGs are frequently located outside CpG islands with decreased methylation, and common ageCGs show the opposite trend. AgeCGs are significantly associated with poorly expressed genes, but those with decreasing methylation are linked with higher tissue-specific expression levels compared with increasing methylation. Therefore, tissue-specific gene expression may protect against common age-dependent methylation. Distinguished from other tissues, skeletal muscle ageCGs are more associated with expression, enriched near genes related to myofiber contraction, and closer to muscle-specific CTCF binding sites. Kidney-specific ageCGs are more increasingly methylated compared to other tissues as measured by affiliation with kidney-specific expressed genes. Underlying chromatin features also mark common and tissue-specific age effects reflective of poised and active chromatin states, respectively. In contrast with decreasingly methylated ageCGs, increasingly methylated ageCGs are also generally further from CTCF binding sites and enriched within lamina associated domains.Our data identified common and tissue-specific DNA methylation changes with age that are reflective of CpG landscape and suggests both common and unique alterations within human tissues. Our findings also indicate that a simple epigenetic drift model is insufficient to explain all age-related changes in DNA methylation.

    View details for DOI 10.1186/gb-2013-14-9-r102

    View details for PubMedID 24034465

  • mRNA-Seq of Single Prostate Cancer Circulating Tumor Cells Reveals Recapitulation of Gene Expression and Pathways Found in Prostate Cancer PLOS ONE Cann, G. M., Gulzar, Z. G., Cooper, S., Li, R., Luo, S., Tat, M., Stuart, S., Schroth, G., Srinivas, S., Ronaghi, M., Brooks, J. D., Talasaz, A. H. 2012; 7 (11)

    Abstract

    Circulating tumor cells (CTC) mediate metastatic spread of many solid tumors and enumeration of CTCs is currently used as a prognostic indicator of survival in metastatic prostate cancer patients. Some evidence suggests that it is possible to derive additional information about tumors from expression analysis of CTCs, but the technical difficulty of isolating and analyzing individual CTCs has limited progress in this area. To assess the ability of a new generation of MagSweeper to isolate intact CTCs for downstream analysis, we performed mRNA-Seq on single CTCs isolated from the blood of patients with metastatic prostate cancer and on single prostate cancer cell line LNCaP cells spiked into the blood of healthy donors. We found that the MagSweeper effectively isolated CTCs with a capture efficiency that matched the CellSearch platform. However, unlike CellSearch, the MagSweeper facilitates isolation of individual live CTCs without contaminating leukocytes. Importantly, mRNA-Seq analysis showed that the MagSweeper isolation process did not have a discernible impact on the transcriptional profile of single LNCaPs isolated from spiked human blood, suggesting that any perturbations caused by the MagSweeper process on the transcriptional signature of isolated cells are modest. Although the RNA from patient CTCs showed signs of significant degradation, consistent with reports of short half-lives and apoptosis amongst CTCs, transcriptional signatures of prostate tissue and of cancer were readily detectable with single CTC mRNA-Seq. These results demonstrate that the MagSweeper provides access to intact CTCs and that these CTCs can potentially supply clinically relevant information.

    View details for DOI 10.1371/journal.pone.0049144

    View details for Web of Science ID 000311935800219

    View details for PubMedID 23145101

  • Evaluation of Putative Renal Cell Carcinoma Markers PAX-2, PAX-8, and hKIM-1 in Germ Cell Tumors: A Tissue Microarray Study of 100 Cases APPLIED IMMUNOHISTOCHEMISTRY & MOLECULAR MORPHOLOGY Sangoi, A. R., McKenney, J. K., Brooks, J. D., Bonventre, J. V., Higgins, J. P. 2012; 20 (5): 451-453

    Abstract

    In a subset of cases, metastatic renal cell carcinoma can demonstrate significant morphologic overlap with germ cell neoplasms, making accurate diagnosis challenging. In such cases, immunohistochemistry is often used as an adjunct diagnostic tool. Expression of the putative renal cell carcinoma markers PAX-2, PAX-8, and hKIM-1 has been reported in a small series of certain germ cell tumors, raising doubt about their specificity for renal cell carcinoma. To further characterize these markers, we evaluated PAX-2, PAX-8, and hKIM-1 staining in 100 germ cell tumors using tissue microarrays. PAX-2 and PAX-8 staining was identified in 50% and 25% of yolk sac tumors (respectively), with hKIM-1 staining identified in 48% of embryonal carcinomas and 50% of yolk sac tumors. All other germ tumor cells (notably including 62 seminomas) were negative for all 3 markers, in contrast to prior reports of PAX-8 reactivity in seminoma. This study indicates that PAX-2, PAX-8, and hKIM-1 should be used cautiously in distinguishing renal cell carcinoma from nonseminomatous germ cell neoplasia and also adds to the growing list of nonrenal tumors that express these 3 markers.

    View details for DOI 10.1097/PAI.0b013e31824bb404

    View details for Web of Science ID 000309551700003

    View details for PubMedID 22495365

  • Gene Expression Changes Induced by Unilateral Ureteral Obstruction in Mice JOURNAL OF UROLOGY Wu, B., Brooks, J. D. 2012; 188 (3): 1033-1041

    Abstract

    Loss of renal function is often the impetus for operative intervention in renal obstruction cases. Obstructive nephropathy is characterized by discrete morphological and physiological changes, including tubular dilatation, apoptosis and atrophy as well as interstitial cellular infiltration and progressive interstitial fibrosis. We hypothesized that gene expression alterations correlate with obstructive nephropathy and could serve as biomarkers for early intervention.C57BL/6 mice were subjected to unilateral ureteral obstruction or sham surgery at postnatal day 21. Kidneys were harvested 1, 2, 5 and 9 days postoperatively. RNA was extracted from kidneys and comprehensive gene expression profiling was performed with microarrays. IPA® pathway analysis software was used to analyze the biological function and gene networks of gene expression data.Microarray analysis revealed more than 1,800 transcripts that were up-regulated or down-regulated during days 1 through 9 after obstruction, including many previously reported transcripts (FOS, CD44, CLU, SPP1 and EGF). Pathway analysis showed significant enrichment of transcripts in cell activation/differentiation, immune/inflammatory responses, cell cycle, metabolic process and transport. Network analysis using IPA showed that transcriptional regulatory pathways involving CEBPB and HNF4A are involved in obstructive nephropathy.This data set provides a foundation for development of biomarkers for obstructive nephropathy.

    View details for DOI 10.1016/j.juro.2012.05.004

    View details for Web of Science ID 000307551200115

    View details for PubMedID 22819101

  • Recurrent deletion of CHD1 in prostate cancer with relevance to cell invasiveness ONCOGENE Huang, S., Gulzar, Z. G., Salari, K., Lapointe, J., Brooks, J. D., Pollack, J. R. 2012; 31 (37): 4164-4170

    Abstract

    Though prostate cancer is often indolent, it is nonetheless a leading cause of cancer death. Defining the underlying molecular genetic alterations may lead to new strategies for prevention or treatment. Towards this goal, we performed array-based comparative genomic hybridization (CGH) on 86 primary prostate tumors. Among the most frequent alterations not associated with a known cancer gene, we identified focal deletions within 5q21 in 15 out of 86 (17%) cases. By high-resolution tiling array CGH, the smallest common deletion targeted just one gene, the chromatin remodeler chromodomain helicase DNA-binding protein 1 (CHD1). Expression of CHD1 was significantly reduced in tumors with deletion (P=0.03), and compared with normal prostate (P=0.04). Exon sequencing analysis also uncovered nonsynonymous mutations in 1 out of 7 (14%) cell lines (LAPC4) and in 1 out of 24 (4%) prostate tumors surveyed. RNA interference-mediated knockdown of CHD1 in two nontumorigenic prostate epithelial cell lines, OPCN2 and RWPE-1, did not alter cell growth, but promoted cell invasiveness, and in OPCN2-enhanced cell clonogenicity. Taken together, our findings suggest that CHD1 deletion may underlie cell invasiveness in a subset of prostate cancers, and indicate a possible novel role of altered chromatin remodeling in prostate tumorigenesis.

    View details for DOI 10.1038/onc.2011.590

    View details for Web of Science ID 000308688900008

    View details for PubMedID 22179824

  • Methods for registration of magnetic resonance images of ex vivo prostate specimens with histology JOURNAL OF MAGNETIC RESONANCE IMAGING Kimm, S. Y., Tarin, T. V., Lee, J. H., Hu, B., Jensen, K., Nishimura, D., Brooks, J. D. 2012; 36 (1): 206-212

    Abstract

    To evaluate two methods of scanning and tissue processing to achieve accurate magnetic resonance (MR)-histologic correlation in human prostate specimens.Two prostates had acrylic paint markers injected to define the plane of imaging and serve as internal fiducials. Each was placed on a polycarbonate plane-finder device (PFD), which was adjusted to align the imaging and cutting planes. Three prostates were aligned by use of a plane finder key (PFK), a polycarbonate plate that locks the specimen in a cylindrical carrier. Markers were injected for registration analysis. Prostates were imaged, then sectioned. Imaging software was used to create registration maps of the MR and histology images. Measurements between control points were made and compared.Accurate correlation was achieved between MR and histologic images. The mean displacement (MD) between the corresponding registration points using the PFD technique ranged from 1.11-1.38 mm for each section. The MD for all sections was 1.24 mm. The MD using the PFK technique ranged from 0.79-1.01 mm for each section, and the MD across all sections for the PFK was 0.92 mm.We describe two methods that can achieve accurate, reproducible correlation between MR imaging and histologic sections in human prostatectomy specimens.

    View details for DOI 10.1002/jmri.23614

    View details for Web of Science ID 000305185700021

    View details for PubMedID 22359365

  • Even-skipped homeobox 1 is frequently hypermethylated in prostate cancer and predicts PSA recurrence BRITISH JOURNAL OF CANCER Truong, M., Yang, B., Wagner, J., Kobayashi, Y., Rajamanickam, V., Brooks, J., Jarrard, D. F. 2012; 107 (1): 100-107

    Abstract

    DNA methylation is an important epigenetic mechanism in prostate cancer (PCa) progression. Given the role of even-skipped homeobox 1 (EVX1) in the regulation of multiple genes during embryogenesis, we postulated that EVX1 methylation is altered in PCa progression.Bisulphite sequencing and quantitative MethyLight were used to assess methylation in human prostate epithelial cells, four PCa cell lines, liver, lung, spleen, kidney, 35 paired tumour and tumour-associated benign tissues, and 11 normal prostate tissues. Prostate cancer cell lines were treated with 5-azacytidine (AzaC) or trichostatin A (TSA), and expression of EVX1 transcript and variants was assessed by qPCR. Hypermethylation was compared with clinicopathological features in a validation set of 58 patients using microarray.Even-skipped homeobox 1 hypermethylation was observed in all four PCa cell lines and 57% of tumours. High-grade tumours exhibited increased methylation compared with intermediate-grade tumours. Even-skipped homeobox 1 expression was induced in PCa cell lines after treatment with AzaC or TSA. In the validation set, 83% of tumours were hypermethylated and hypermethylation was associated with worse recurrence-free survival.In this first evaluation of EVX1 methylation in human cancer, EVX1 is one of the most commonly hypermethylated genes observed in PCa and predicted treatment failure in moderate risk patients.

    View details for DOI 10.1038/bjc.2012.216

    View details for Web of Science ID 000305888400015

    View details for PubMedID 22596233

  • Performance Characteristics of Prostate-specific Antigen in Patients Undergoing Radical Prostatectomy UROLOGY Liu, J., Ferrari, M., Nolley, R., Brooks, J. D., Presti, J. C. 2012; 79 (6): 1336-1339

    Abstract

    To assess the performance characteristics of prostate-specific antigen (PSA) for predicting the volume of total or high-grade cancer in men undergoing radical prostatectomy. It is known that the performance characteristics of PSA are improved for predicting the presence of high-grade prostate cancer.We identified 1459 patients from the Stanford Radical Prostatectomy Database with clinical Stage T1c (n = 783) and T2 (n = 676) disease who underwent surgery from 1988 to 2003 with detailed morphometric mapping. We generated receiver operating characteristic curves for PSA levels according to the total and high-grade (Gleason score 4 or 5) cancer volume and compared the areas under the curve (AUC) for the various total and high-grade cancer volumes.For patients with Stage T1c disease, the AUC for the PSA ROC curve increased in a stepwise fashion as both the total cancer volume and the high-grade cancer volume increased. Significant differences between the AUCs for low and high volumes of total and high-grade disease were observed. For T2 disease, the AUCs for predicting high-grade cancer volume were generally greater than the corresponding AUCs for T1c disease, although no incremental increase was observed.In patients with Stage T1c disease, in whom the PSA level was the driving force for biopsy, the PSA performance improved in a stepwise fashion with greater total and high-grade cancer volumes as evidenced by improved ROC. Previous studies have shown that PSA performs better for detecting the presence of high-grade disease. We have shown that PSA performs better in predicting greater volumes of high-grade disease in radical prostatectomy specimens.

    View details for DOI 10.1016/j.urology.2012.02.036

    View details for Web of Science ID 000304720600046

    View details for PubMedID 22516358

  • Deficiency in Mammalian Histone H2B Ubiquitin Ligase Bre1 (Rnf20/Rnf40) Leads to Replication Stress and Chromosomal Instability CANCER RESEARCH Chernikova, S. B., Razorenova, O. V., Higgins, J. P., Sishc, B. J., Nicolau, M., Dorth, J. A., Chernikova, D. A., Kwok, S., Brooks, J. D., Bailey, S. M., Game, J. C., Brown, J. M. 2012; 72 (8): 2111-2119

    Abstract

    Mammalian Bre1 complexes (BRE1A/B (RNF20/40) in humans and Bre1a/b (Rnf20/40) in mice) function similarly to their yeast homolog Bre1 as ubiquitin ligases in monoubiquitination of histone H2B. This ubiquitination facilitates methylation of histone H3 at K4 and K79, and accounts for the roles of Bre1 and its homologs in transcriptional regulation. Recent studies by others suggested that Bre1 acts as a tumor suppressor, augmenting expression of select tumor suppressor genes and suppressing select oncogenes. In this study, we present an additional mechanism of tumor suppression by Bre1 through maintenance of genomic stability. We track the evolution of genomic instability in Bre1-deficient cells from replication-associated double-strand breaks (DSB) to specific genomic rearrangements that explain a rapid increase in DNA content and trigger breakage-fusion-bridge cycles. We show that aberrant RNA-DNA structures (R-loops) constitute a significant source of DSBs in Bre1-deficient cells. Combined with a previously reported defect in homologous recombination, generation of R-loops is a likely initiator of replication stress and genomic instability in Bre1-deficient cells. We propose that genomic instability triggered by Bre1 deficiency may be an important early step that precedes acquisition of an invasive phenotype, as we find decreased levels of BRE1A/B and dimethylated H3K79 in testicular seminoma and in the premalignant lesion in situ carcinoma.

    View details for DOI 10.1158/0008-5472.CAN-11-2209

    View details for Web of Science ID 000302905700022

    View details for PubMedID 22354749

  • Translational genomics: The challenge of developing cancer biomarkers GENOME RESEARCH Brooks, J. D. 2012; 22 (2): 183-187

    Abstract

    Early detection and definitive treatment of cancer have been shown to decrease death and suffering in epidemiologic and intervention studies. Application of genomic approaches to many malignancies has produced thousands of candidate biomarkers for detection and prognostication, yet very few have become established in clinical practice. Fundamental issues related to tumor heterogeneity, cancer progression, natural history, and biomarker performance have provided challenges to biomarker development. Technical issues in biomarker assay detection limits, specificity, clinical deployment, and regulation have also slowed progress. The recent emergence of biomarkers and molecular imaging strategies for treatment selection and monitoring demonstrates the promise of cancer biomarkers. Organized efforts by interdisciplinary teams will spur progress in cancer diagnostics.

    View details for DOI 10.1101/gr.124347.111

    View details for Web of Science ID 000299606400002

    View details for PubMedID 22301132

  • PIVOT and the challenges of localized prostate cancer care Translational Andrology and Urology Weinberg, A. E., Brooks, J. D. 2012
  • The Potential Impact of Reproducibility of Gleason Grading in Men With Early Stage Prostate Cancer Managed by Active Surveillance: A Multi-Institutional Study JOURNAL OF UROLOGY McKenney, J. K., Simko, J., Bonham, M., True, L. D., Troyer, D., Hawley, S., Newcomb, L. F., Fazli, L., Kunju, L. P., Nicolas, M. M., Vakar-Lopez, F., Zhang, X., Carroll, P. R., Brooks, J. D. 2011; 186 (2): 465-469

    Abstract

    We evaluated the reproducibility of Gleason grading as relevant to the clinical treatment of men on active surveillance.Three sets of digital images of prostatic adenocarcinoma in biopsies were reviewed and assigned Gleason scores by a total of 11 pathologists from 7 institutions. Interobserver and intra-observer reproducibility were assessed for assignment of the highest Gleason pattern (3 vs 4 or higher). We also identified 97 consecutive patients on active surveillance. Prostate biopsy glass slides from 82 of the patients were available for re-review and the frequency of carcinoma requiring the distinction of tangentially sectioned Gleason pattern 3 from 4 was determined.Interobserver reproducibility for classic Gleason patterns was substantial (Light's ? 0.76). Interobserver reproducibility for the histological distinction of tangentially sectioned Gleason pattern 3 from Gleason pattern 4 was only fair (Light's ? 0.27). Intra-observer reproducibility ranged from 65% to 100% (mean 81.5%). Of the 82 patients on active surveillance 61 had carcinoma and 15 (24.5%) had a set of biopsies with at least 1 focus in which the distinction between tangentially sectioned Gleason pattern 3 and poorly formed pattern 4 glands had to be considered.The reproducibility of grading classic Gleason patterns is high. However, variability in grading occurred when distinguishing between tangentially sectioned pattern 3 glands and the poorly formed gland subset of pattern 4. Developing universally accepted histological and/or molecular criteria to distinguish these patterns and subsequently characterizing their natural history would be useful when treating patients on active surveillance.

    View details for DOI 10.1016/j.juro.2011.03.115

    View details for Web of Science ID 000292545100030

    View details for PubMedID 21679996

  • DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer GENOME RESEARCH Kobayashi, Y., Absher, D. M., Gulzar, Z. G., Young, S. R., McKenney, J. K., Peehl, D. M., Brooks, J. D., Myers, R. M., Sherlock, G. 2011; 21 (7): 1017-1027

    Abstract

    Candidate gene-based studies have identified a handful of aberrant CpG DNA methylation events in prostate cancer. However, DNA methylation profiles have not been compared on a large scale between prostate tumor and normal prostate, and the mechanisms behind these alterations are unknown. In this study, we quantitatively profiled 95 primary prostate tumors and 86 benign adjacent prostate tissue samples for their DNA methylation levels at 26,333 CpGs representing 14,104 gene promoters by using the Illumina HumanMethylation27 platform. A 2-class Significance Analysis of this data set revealed 5912 CpG sites with increased DNA methylation and 2151 CpG sites with decreased DNA methylation in tumors (FDR < 0.8%). Prediction Analysis of this data set identified 87 CpGs that are the most predictive diagnostic methylation biomarkers of prostate cancer. By integrating available clinical follow-up data, we also identified 69 prognostic DNA methylation alterations that correlate with biochemical recurrence of the tumor. To identify the mechanisms responsible for these genome-wide DNA methylation alterations, we measured the gene expression levels of several DNA methyltransferases (DNMTs) and their interacting proteins by TaqMan qPCR and observed increased expression of DNMT3A2, DNMT3B, and EZH2 in tumors. Subsequent transient transfection assays in cultured primary prostate cells revealed that DNMT3B1 and DNMT3B2 overexpression resulted in increased methylation of a substantial subset of CpG sites that showed tumor-specific increased methylation.

    View details for DOI 10.1101/gr.119487.110

    View details for Web of Science ID 000292298000003

    View details for PubMedID 21521786

  • Integrated genomic analyses of ovarian carcinoma NATURE Bell, D., Berchuck, A., Birrer, M., Chien, J., Cramer, D. W., Dao, F., Dhir, R., Disaia, P., Gabra, H., Glenn, P., Godwin, A. K., GROSS, J., Hartmann, L., Huang, M., Huntsman, D. G., Iacocca, M., Imielinski, M., Kalloger, S., Karlan, B. Y., Levine, D. A., Mills, G. B., Morrison, C., Mutch, D., Olvera, N., Orsulic, S., Park, K., Petrelli, N., Rabeno, B., Rader, J. S., Sikic, B. I., Smith-McCune, K., Sood, A. K., Bowtell, D., PENNY, R., Testa, J. R., Chang, K., Dinh, H. H., Drummond, J. A., Fowler, G., Gunaratne, P., Hawes, A. C., Kovar, C. L., Lewis, L. R., Morgan, M. B., Newsham, I. F., Santibanez, J., Reid, J. G., Trevino, L. R., Wu, Y., Wang, M., Muzny, D. M., Wheeler, D. A., Gibbs, R. A., Getz, G., Lawrence, M. S., Cibulskis, K., Sivachenko, A. Y., Sougnez, C., VOET, D., Wilkinson, J., Bloom, T., Ardlie, K., Fennell, T., Baldwin, J., Gabriel, S., Lander, E. S., Ding, L., Fulton, R. S., Koboldt, D. C., McLellan, M. D., Wylie, T., Walker, J., O'Laughlin, M., Dooling, D. J., Fulton, L., Abbott, R., Dees, N. D., Zhang, Q., Kandoth, C., Wendl, M., Schierding, W., Shen, D., Harris, C. C., Schmidt, H., Kalicki, J., Delehaunty, K. D., Fronick, C. C., Demeter, R., Cook, L., Wallis, J. W., Lin, L., Magrini, V. J., Hodges, J. S., ELDRED, J. M., Smith, S. M., Pohl, C. S., Vandin, F., Raphael, B. J., Weinstock, G. M., Mardis, R., Wilson, R. K., Meyerson, M., Winckler, W., Getz, G., Verhaak, R. G., Carter, S. L., Mermel, C. H., Saksena, G., Nguyen, H., Onofrio, R. C., Lawrence, M. S., Hubbard, D., Gupta, S., Crenshaw, A., RAMOS, A. H., Ardlie, K., Chin, L., Protopopov, A., Zhang, J., Kim, T. M., Perna, I., Xiao, Y., Zhang, H., Ren, G., Sathiamoorthy, N., Park, R. W., Lee, E., Park, P. J., Kucherlapati, R., Absher, D. M., Waite, L., Sherlock, G., Brooks, J. D., Li, J. Z., Xu, J., Myers, R. M., Laird, P. W., Cope, L., Herman, J. G., Shen, H., Weisenberger, D. J., Noushmehr, H., Pan, F., Triche, T., Berman, B. P., Van den Berg, D. J., Buckley, J., BAYLIN, S. B., Spellman, P. T., Purdom, E., Neuvial, P., Bengtsson, H., Jakkula, L. R., Durinck, S., Han, J., Dorton, S., Marr, H., Choi, Y. G., Wang, V., Wang, N. J., Ngai, J., Conboy, J. G., Parvin, B., Feiler, H. S., Speed, T. P., Gray, J. W., Levine, D. A., Socci, N. D., Liang, Y., Taylor, B. S., Schultz, N., Borsu, L., Lash, A. E., Brennan, C., Viale, A., Sander, C., Ladanyi, M., Hoadley, K. A., Meng, S., Du, Y., Shi, Y., Li, L., Turman, Y. J., Zang, D., Helms, E. B., Balu, S., Zhou, X., Wu, J., Topal, M. D., Hayes, D. N., Perou, C. M., Getz, G., VOET, D., Saksena, G., Zhang, J., Zhang, H., Wu, C. J., Shukla, S., Cibulskis, K., Lawrence, M. S., Sivachenko, A., Jing, R., Park, R. W., Liu, Y., Park, P. J., Noble, M., Chin, L., Carter, H., Kim, D., Karchin, R., Spellman, P. T., Purdom, E., Neuvial, P., Bengtsson, H., Durinck, S., Han, J., Korkola, J. E., Heiser, L. M., Cho, R. J., Hu, Z., Parvin, B., Speed, T. P., Gray, J. W., Schultz, N., Cerami, E., Taylor, B. S., Olshen, A., Reva, B., Antipin, Y., Shen, R., Mankoo, P., Sheridan, R., Ciriello, G., Chang, W. K., Bernanke, J. A., Borsu, L., Levine, D. A., Ladanyi, M., Sander, C., Haussler, D., Benz, C. C., Stuart, J. M., Benz, S. C., Sanborn, J. Z., Vaske, C. J., Zhu, J., Szeto, C., Scott, G. K., Yau, C., Hoadley, K. A., Du, Y., Balu, S., Hayes, D. N., Perou, C. M., Wilkerson, M. D., Zhang, N., Akbani, R., Baggerly, K. A., YUNG, W. K., Mills, G. B., Weinstein, J. N., PENNY, R., Shelton, T., Grimm, D., Hatfield, M., Morris, S., Yena, P., Rhodes, P., Sherman, M., Paulauskis, J., Millis, S., Kahn, A., Greene, J. M., Sfeir, R., Jensen, M. A., Chen, J., Whitmore, J., Alonso, S., Jordan, J., Chu, A., Zhang, J., Barker, A., Compton, C., Eley, G., Ferguson, M., Fielding, P., Gerhard, D. S., Myles, R., Schaefer, C., Shaw, K. R., Vaught, J., Vockley, J. B., Good, P. J., Guyer, M. S., Ozenberger, B., Peterson, J., Thomson, E. 2011; 474 (7353): 609-615

    Abstract

    A catalogue of molecular aberrations that cause ovarian cancer is critical for developing and deploying therapies that will improve patients' lives. The Cancer Genome Atlas project has analysed messenger RNA expression, microRNA expression, promoter methylation and DNA copy number in 489 high-grade serous ovarian adenocarcinomas and the DNA sequences of exons from coding genes in 316 of these tumours. Here we report that high-grade serous ovarian cancer is characterized by TP53 mutations in almost all tumours (96%); low prevalence but statistically recurrent somatic mutations in nine further genes including NF1, BRCA1, BRCA2, RB1 and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes. Analyses delineated four ovarian cancer transcriptional subtypes, three microRNA subtypes, four promoter methylation subtypes and a transcriptional signature associated with survival duration, and shed new light on the impact that tumours with BRCA1/2 (BRCA1 or BRCA2) and CCNE1 aberrations have on survival. Pathway analyses suggested that homologous recombination is defective in about half of the tumours analysed, and that NOTCH and FOXM1 signalling are involved in serous ovarian cancer pathophysiology.

    View details for DOI 10.1038/nature10166

    View details for Web of Science ID 000292204300032

    View details for PubMedID 21720365

  • Small Prostate Size and High Grade Disease-Biology or Artifact? JOURNAL OF UROLOGY Liu, J., Brooks, J. D., Ferrari, M., Nolley, R., Presti, J. C. 2011; 185 (6): 2108-2111

    Abstract

    Prior radical prostatectomy series have shown an inverse association between prostate size and high grade cancer. It has been suggested that smaller size prostates arise in a low androgen environment, enabling development of more aggressive cancer. We propose that this observation is the result of ascertainment bias driven by prostate specific antigen performance.We identified 1,404 patients from the Stanford Radical Prostatectomy Database with clinical stage T1c (723) and T2 (681) disease who underwent surgery between 1988 and 2002, and underwent detailed morphometric mapping by a single pathologist. Multivariate linear regression was performed to assess for the effects of age, prostate weight and prostate specific antigen on total and high grade (Gleason grade 4/5) cancer volume and percentage of high grade disease.In patients who underwent biopsy due to abnormal prostate specific antigen (stage T1c), prostate weight was negatively associated (p = 0.0002) with total cancer volume, volume of high grade disease and percentage of high grade disease. For patients who underwent biopsy based on abnormal digital rectal examination (stage T2) these associations were not observed.Improved prostate specific antigen performance for high grade disease results in ascertainment bias in patients with T1c disease. Thus, the association between prostate size and high grade disease may be a consequence of grade dependent performance of prostate specific antigen rather than true tumor biology.

    View details for DOI 10.1016/j.juro.2011.02.053

    View details for Web of Science ID 000290389600027

    View details for PubMedID 21496855

  • A Tri-Marker Proliferation Index Predicts Biochemical Recurrence after Surgery for Prostate Cancer PLOS ONE Malhotra, S., Lapointe, J., Salari, K., Higgins, J. P., Ferrari, M., Montgomery, K., van de Rijn, M., Brooks, J. D., Pollack, J. R. 2011; 6 (5)

    Abstract

    Prostate cancer exhibits tremendous variability in clinical behavior, ranging from indolent to lethal disease. Better prognostic markers are needed to stratify patients for appropriately aggressive therapy. By expression profiling, we can identify a proliferation signature variably expressed in prostate cancers. Here, we asked whether one or more tissue biomarkers might capture that information, and provide prognostic utility. We assayed three proliferation signature genes: MKI67 (Ki-67; also a classic proliferation biomarker), TOP2A (DNA topoisomerase II, alpha), and E2F1 (E2F transcription factor 1). Immunohistochemical staining was evaluable on 139 radical prostatectomy cases (in tissue microarray format), with a median clinical follow-up of eight years. Each of the three proliferation markers was by itself prognostic. Notably, combining the three markers together as a "proliferation index" (0 or 1, vs. 2 or 3 positive markers) provided superior prognostic performance (hazard ratio = 2.6 (95% CI: 1.4-4.9); P = 0.001). In a multivariate analysis that included preoperative serum prostate specific antigen (PSA) levels, Gleason grade and pathologic tumor stage, the composite proliferation index remained a significant predictor (P = 0.005). Analysis of receiver-operating characteristic (ROC) curves confirmed the improved prognostication afforded by incorporating the proliferation index (compared to the clinicopathologic data alone). Our findings highlight the potential value of a multi-gene signature-based diagnostic, and define a tri-marker proliferation index with possible utility for improved prognostication and treatment stratification in prostate cancer.

    View details for DOI 10.1371/journal.pone.0020293

    View details for Web of Science ID 000291005200049

    View details for PubMedID 21629784

  • Comparison of prostate cancer tumor volume and percent cancer in prediction of biochemical recurrence and cancer specific survival UROLOGIC ONCOLOGY-SEMINARS AND ORIGINAL INVESTIGATIONS Chung, B. I., Tarin, T. V., Ferrari, M., Brooks, J. D. 2011; 29 (3): 314-318

    Abstract

    Tumor volume and percent cancer (ratio of tumor volume/prostate volume) have been proposed as predictors of biochemical recurrence and cancer specific survival after radical prostatectomy. However, their relative merits as prognosticators have not been tested. We therefore evaluated and compared tumor volume and percent cancer as independent predictors of biochemical recurrence and prostate cancer specific death after radical prostatectomy.A retrospective review of 739 patients who underwent radical prostatectomy for prostate cancer between 1984 and 2004 was conducted. Median follow-up was 91.7 months, and 22 patients died of prostate cancer. Univariate and multivariate analysis evaluated the following factors in predicting biochemical recurrence and prostate cancer specific death: tumor volume, prostate volume, percent cancer, Gleason score, percentage of Gleason grade 4/5, margin status, capsular invasion status, seminal vesicle invasion status, preoperative PSA, and lymph node status.In univariate analysis, both tumor volume (P<0.001) and percent cancer (P<0.001) significantly correlated with biochemical recurrence. Since they are highly correlated, they did not predict outcome independently when included in the same model; however, both were highly predictive for biochemical recurrence in separate multivariate models (P=0.01 for both). Both also correlated with cancer specific survival as single variables; however, in separate multivariate models, only tumor volume (P=0.03) predicted death, while percent cancer did not (P=0.09).Tumor volume and percent cancer are independent predictors of recurrence after radical prostatectomy. However, in our series, tumor volume predicted cancer specific death better than percent cancer. Therefore, accurate determination of tumor volume, along with other accepted pathologic indices, is sufficient and preferred over percent cancer for prognostication after radical prostatectomy.

    View details for DOI 10.1016/j.urolonc.2009.06.017

    View details for Web of Science ID 000290779400016

    View details for PubMedID 19837617

  • Specificity of brachyury in the distinction of chordoma from clear cell renal cell carcinoma and germ cell tumors: a study of 305 cases MODERN PATHOLOGY Sangoi, A. R., Karamchandani, J., Lane, B., Higgins, J. P., Rouse, R. V., Brooks, J. D., McKenney, J. K. 2011; 24 (3): 425-429

    Abstract

    Brachyury is recognized as a specific marker for notochord-derived tissues and neoplasms, and has become a defining immunohistochemical feature of chordoma. The main differential diagnostic consideration for chordoma is chondrosarcoma, which is known to lack brachyury expression. However, within the spectrum of genitourinary neoplasia, metastatic germ cell tumors and clear cell renal cell carcinoma may also be close morphological mimics of chordoma, particularly given the increasing prevalence of small tissue samples from image-guided biopsies. Although immunoreactivity for brachyury has been reported in a few germ cell tumors, a thorough characterization of staining by specific subtype has not been performed in a large series. Additionally, brachyury expression in clear cell renal cell carcinoma has not been well studied. In this study, immunohistochemical expression with the brachyury antibody was evaluated in 111 germ cell tumors, 30 non-neoplastic and neoplastic (non-germ cell) testicular tissues, and 184 metastatic clear cell renal cell carcinomas using tissue microarray technology. In addition, immunoreactivity for PAX-8 and SALL-4 was evaluated in 12 chordomas on whole section. No nuclear brachyury expression was identified in any of the 101 germ cell tumors within the tissue microarray (including choriocarcinoma (1), embryonal carcinoma (20), intratubular germ cell neoplasia unclassified (2), seminoma (64), spermatocytic seminoma (1), teratoma (5) and yolk sac tumor (8)), in any of the 30 non-neoplastic and neoplastic (non-germ cell) testicular tissues, or in any of the 10 whole-section seminomas. All 184 metastatic clear cell renal cell carcinomas were also non-reactive for brachyury. All 12 chordomas showed strong nuclear immunoreactivity for brachyury, but no expression of SALL-4. In all, 1 of 12 chordoma cases showed patchy, 1+ nuclear immunoreactivity for PAX-8. This study confirms the specificity of brachyury for chordoma in the differential diagnostic distinction from the potential genitourinary mimics, germ cell tumors and metastatic clear cell renal cell carcinoma.

    View details for DOI 10.1038/modpathol.2010.196

    View details for Web of Science ID 000287986600010

    View details for PubMedID 21102418

  • Length of site-specific positive surgical margins as a risk factor for biochemical recurrence following radical prostatectomy. International journal of urology : official journal of the Japanese Urological Association Hsu, M., Chang, S. L., Ferrari, M., Nolley, R., Presti Jr, J. C., Brooks, J. D. 2011

    Abstract

    Objectives:? Positive surgical margins (PSM) have been associated with biochemical recurrence (BCR) after radical prostatectomy, but the significance of PSM length and location are debated. We assessed the impact of PSM lengths at specific locations for BCR in an open radical prostatectomy series. Methods:? Detailed clinical and pathological data were collected from 117 post-prostatectomy patients with PSM from 1984 to 2004 at our institution. PSM locations were classified as apex, mid-gland, base, bladder neck, and anterior fibromuscular region with lengths measured at each site. Aggregate PSM length was obtained by summing lengths of all PSM areas in contact with the inked surface. BCR was defined as serum prostate specific antigen level 0.2?ng/mL or greater. Cox proportional hazards regression analyses of PSM lengths were conducted either as a continuous or categorical variable relative to location as a predictor of BCR. Results:? Multivariate analyses demonstrated that as a continuous variable, PSM length at the anterior fibromuscular region (Hazard ratio [HR]?=?1.17; P?=?0.027) and bladder neck (HR?=?1.29; P?=?0.046) were significant predictors for BCR. As a categorical variable, PSM length???2?mm at the anterior fibromuscular area was significant for BCR (HR?=?3.02; P?=?0.036). Increasing Gleason grade and positive lymph node status were also found to be significant independent predictors for BCR. Conclusion:? PSM length at the anterior fibromuscular region (continuous and categorical) and the bladder neck (continuous) was significantly associated with BCR. Site-specific PSM length, along with Gleason grade and lymph node status, can be predictive of BCR and assist in risk stratification of patients with PSM following radical prostatectomy.

    View details for PubMedID 21342296

  • Smoking and adverse outcomes at radical prostatectomy. Urologic oncology Ngo, T. C., Lee, J. J., Brooks, J. D., Nolley, R., Ferrari, M., Presti Jr, J. C. 2011

    Abstract

    BACKGROUND: Multiple large epidemiologic studies have examined the relationship between smoking and prostate cancer incidence and mortality only to arrive at contradictory results. In this series, we studied the effect of smoking on pathologic outcomes and biochemical recurrence in a cohort of men undergoing radical prostatectomy. METHODS: We identified 630 men who underwent radical prostatectomy between 1989 and 2005 who had detailed smoking histories. There were 321 smokers and 309 nonsmokers. Pathologic outcomes included prostate weight, volume of cancer, volume of high grade cancer, margin status, seminal vesicle involvement, extraprostatic extension, perineural invasion, angiolymphatic invasion, and the presence of nodal metastasis. Biochemical recurrence was defined as a postoperative PSA ? 0.1 ng/ml. Univariate analysis and multivariate linear and Cox regression were used to study the impact of smoking on these outcomes. RESULTS: The volume of cancer (2.54 vs. 2.16 ml, P = 0.016) and the volume of high grade cancer (0.58 vs. 0.28 ml, P = 0.004) were greater in smokers compared with nonsmokers. Smoking independently predicted greater volumes of cancer and high grade cancer in multivariate analysis. Heavy smokers (?20 pack-year history) had a greater risk of biochemical recurrence on univariate survival analysis. Smoking also predicted a greater risk of biochemical recurrence on Cox regression, the magnitude of which was approximately 1% per pack-year smoked. CONCLUSIONS: Smoking is associated with adverse pathologic features and a higher risk of biochemical recurrence in men undergoing radical prostatectomy. If confirmed by additional studies, smoking history may need to be included into risk assessment models.

    View details for PubMedID 21824793

  • The distribution of PAX-2 immunoreactivity in the prostate gland, seminal vesicle, and ejaculatory duct: comparison with prostatic adenocarcinoma and discussion of prostatic zonal embryogenesis HUMAN PATHOLOGY Quick, C. M., Gokden, N., Sangoi, A. R., Brooks, J. D., McKenney, J. K. 2010; 41 (8): 1145-1149

    Abstract

    PAX-2 is a homeogene strongly expressed during development of the genitourinary tract, including the kidney and both wolffian- and müllerian-derived tissues. Expression of PAX-2 by immunohistochemistry has been studied mainly in renal epithelial neoplasms with little attention to the lower male genitourinary tract. We studied PAX-2 expression in epithelium of normal seminal vesicle, normal ejaculatory duct, normal prostatic secretory epithelium, and prostatic adenocarcinoma to define its immunoreactivity pattern throughout the prostate gland and to evaluate its potential diagnostic role in the discrimination of seminal vesicle/ejaculatory duct epithelium from prostatic adenocarcinoma. In addition, given that PAX-2 is highly expressed in tissues of wolffian duct embryologic origin, we also sought to confirm the divergent embryogenesis of the central zone, seminal vesicle, and ejaculatory duct from other regions of the prostate. Prostatectomy specimens from 12 patients were reviewed to identify blocks containing seminal vesicle, ejaculatory duct, periurethral glands, benign prostatic glands, and prostatic acinar adenocarcinoma. A total of 35 blocks from the 12 patients were evaluated. In addition, 2 tissue microarrays representing 15 additional seminal vesicles and 45 prostatic adenocarcinomas, 7 whole sections from prostatic adenocarcinomas of the central zone, and 5 core needle biopsies of seminal vesicle were also evaluated with anti-PAX-2 antibody. In the 12 radical prostatectomy whole sections, nuclear reactivity for PAX-2 was identified in 12 (100%) of 12 of the seminal vesicle epithelium, 9 (90%) of 10 of the ejaculatory duct epithelium, 0 of 12 of the prostatic adenocarcinoma, and 0 of 6 of the high-grade prostatic intraepithelial neoplasia. All 20 total additional seminal vesicles were positive for PAX-2 in the tissue microarray and biopsies; and all 52 additional prostatic adenocarcinomas were negative, including 7 of central zone origin. The staining intensity and percentage of immunoreactive cells in seminal vesicle were both 3+ in all cases. Although the ejaculatory ducts also showed diffuse staining, their staining intensity was less (2+) than that in the seminal vesicles, particularly in the ejaculatory ducts in the periurethral area (1-2+intensity). The smaller glands surrounding the main seminal vesicle duct also showed less intense staining than the luminal cells of the main duct. Of the 19 total cases with evaluable central zone glands, 2 (10.5%) had focal nuclear reactivity in normal, benign prostatic secretory cells. All other benign prostatic secretory epithelia from the peripheral and transition zones were negative for PAX-2. In conclusion, nuclear PAX-2 immunoreactivity is typical in epithelium of the seminal vesicle and ejaculatory duct; but the intensity of staining is less in the ejaculatory duct. No reactivity for PAX-2 was seen in prostatic adenocarcinoma or high-grade prostatic intraepithelial neoplasia. PAX-2 has diagnostic utility as a positive immunohistochemical marker of seminal vesicle and ejaculatory duct epithelium. In addition, these data add further support to the proposed embryogenesis of the prostatic central zone, seminal vesicle, and ejaculatory ducts from the wolffian system.

    View details for DOI 10.1016/j.humpath.2010.01.010

    View details for Web of Science ID 000280128300011

    View details for PubMedID 20413145

  • Canary Prostate Active Surveillance Study: Design of a Multi-institutional Active Surveillance Cohort and Biorepository UROLOGY Newcomb, L. F., Brooks, J. D., Carroll, P. R., Feng, Z., Gleave, M. E., Nelson, P. S., Thompson, I. M., Lin, D. W. 2010; 75 (2): 407-413

    Abstract

    Active surveillance is a management plan for localized prostate cancer that offers selective delayed intervention on indication of disease progression, allowing patients to delay or avoid treatment and associated side-effects. Outcomes from centers that promote active surveillance are favorable, with high rates of disease-specific survival. However, there remains a need for prognostic variables or biomarkers that distinguish with high specificity the aggressive cancers that progress on surveillance from the indolent cancers. The Canary Prostate Active Surveillance Study is a multicenter study and a biorepository that will discover and confirm biomarkers of aggressive disease as defined by histologic, prostate-specific antigen, or clinical criteria.

    View details for DOI 10.1016/j.urology.2009.05.050

    View details for Web of Science ID 000274393300051

    View details for PubMedID 19758683

  • Molecular Stratification of Clear Cell Renal Cell Carcinoma by Consensus Clustering Reveals Distinct Subtypes and Survival Patterns. Genes & cancer Brannon, A. R., Reddy, A., Seiler, M., Arreola, A., Moore, D. T., Pruthi, R. S., Wallen, E. M., Nielsen, M. E., Liu, H., Nathanson, K. L., Ljungberg, B., Zhao, H., Brooks, J. D., Ganesan, S., Bhanot, G., Rathmell, W. K. 2010; 1 (2): 152-163

    Abstract

    Clear cell renal cell carcinoma (ccRCC) is the predominant RCC subtype, but even within this classification, the natural history is heterogeneous and difficult to predict. A sophisticated understanding of the molecular features most discriminatory for the underlying tumor heterogeneity should be predicated on identifiable and biologically meaningful patterns of gene expression. Gene expression microarray data were analyzed using software that implements iterative unsupervised consensus clustering algorithms to identify the optimal molecular subclasses, without clinical or other classifying information. ConsensusCluster analysis identified two distinct subtypes of ccRCC within the training set, designated clear cell type A (ccA) and B (ccB). Based on the core tumors, or most well-defined arrays, in each subtype, logical analysis of data (LAD) defined a small, highly predictive gene set that could then be used to classify additional tumors individually. The subclasses were corroborated in a validation data set of 177 tumors and analyzed for clinical outcome. Based on individual tumor assignment, tumors designated ccA have markedly improved disease-specific survival compared to ccB (median survival of 8.6 vs 2.0 years, P = 0.002). Analyzed by both univariate and multivariate analysis, the classification schema was independently associated with survival. Using patterns of gene expression based on a defined gene set, ccRCC was classified into two robust subclasses based on inherent molecular features that ultimately correspond to marked differences in clinical outcome. This classification schema thus provides a molecular stratification applicable to individual tumors that has implications to influence treatment decisions, define biological mechanisms involved in ccRCC tumor progression, and direct future drug discovery.

    View details for PubMedID 20871783

  • Gene expression changes induced by genistein in the prostate cancer cell line LNCaP The Open Prostate Cancer Journal Bhamre S, Sahoo D, Tibshirani R, Dill DL, Brooks JD 2010; 3: 86-98
  • Adjuvant docetaxel and abbreviated androgen deprivation therapy in patients with high risk prostate cancer The Open Prostate Cancer Journal Bazan JG, King CR, Brooks JD, Srinivas S 2010; 3: 99-104
  • Prognostic significance of prostate cancer originating from the transition zone UROLOGIC ONCOLOGY-SEMINARS AND ORIGINAL INVESTIGATIONS King, C. R., Ferrari, M., Brooks, J. D. 2009; 27 (6): 592-597

    Abstract

    Transition zone (TZ) cancers are reported to have better biochemical relapse-free survival (bRFS) after radical prostatectomy (RP) than cancers from the peripheral zone (PZ). To understand the influence of tumor location, we compared bRFS for TZ and PZ cancers stratified for risk using known clinical and pathological prognostic factors.The surgical pathology and outcomes of 494 patients were reviewed. Cancers originating from the TZ and PZ were identified from step sectioning of surgical specimens and tumor mapping. Univariate and multivariate analyses of bRFS after RP were compared.TZ cancers were present in 89 (18%) patients. On univariate analysis, most factors predicted bRFS, although cancer location did not: 5-year bRFS was 85% for TZ vs. 77% for PZ (P = 0.12). However, on multivariate analysis, all factors except SV involvement were significant, including TZ cancer location (P = 0.04, HR = 1.88 [1.02-3.47]). Interestingly, TZ location was correlated with improved 5-year bRFS for cancers > 2 cc (81% for TZ vs. 65% for PZ, P = 0.017), for preop PSA >10 (80% for TZ vs. 59% for PZ, P = 0.027), and for PSAV > 2 (85% for TZ vs. 66% for PZ, P = 0.08). However, TZ cancers showed no difference in outcome for small volumes, low preop PSA, low PSAV, or high Gleason grade.TZ cancers that are large, with high preop PSA, low Gleason scores, and high PSAV show better outcomes than their PZ counterparts. However, high-grade cancer tumor location had no apparent influence on outcome. Tumor location could be considered in subsets for optimal prognostication.

    View details for DOI 10.1016/j.urolonc.2008.05.009

    View details for Web of Science ID 000271801200003

    View details for PubMedID 18799332

  • Disorders of sex development expose transcriptional autonomy of genetic sex and androgen-programmed hormonal sex in human blood leukocytes BMC GENOMICS Holterhus, P., Bebermeier, J., Werner, R., Demeter, J., Richter-Unruh, A., Cario, G., Appari, M., Siebert, R., Riepe, F., Brooks, J. D., Hiort, O. 2009; 10

    Abstract

    Gender appears to be determined by independent programs controlled by the sex-chromosomes and by androgen-dependent programming during embryonic development. To enable experimental dissection of these components in the human, we performed genome-wide profiling of the transcriptomes of peripheral blood mononuclear cells (PBMC) in patients with rare defined "disorders of sex development" (DSD, e.g., 46, XY-females due to defective androgen biosynthesis) compared to normal 46, XY-males and 46, XX-females.A discrete set of transcripts was directly correlated with XY or XX genotypes in all individuals independent of male or female phenotype of the external genitalia. However, a significantly larger gene set in the PBMC only reflected the degree of external genital masculinization independent of the sex chromosomes and independent of concurrent post-natal sex steroid hormone levels. Consequently, the architecture of the transcriptional PBMC-"sexes" was either male, female or even "intersex" with a discordant alignment of the DSD individuals' genetic and hormonal sex signatures.A significant fraction of gene expression differences between males and females in the human appears to have its roots in early embryogenesis and is not only caused by sex chromosomes but also by long-term sex-specific hormonal programming due to presence or absence of androgen during the time of external genital masculinization. Genetic sex and the androgen milieu during embryonic development might therefore independently modulate functional traits, phenotype and diseases associated with male or female gender as well as with DSD conditions.

    View details for DOI 10.1186/1471-2164-10-292

    View details for Web of Science ID 000268754800001

    View details for PubMedID 19570224

  • Alteration of Gene Expression Signatures of Cortical Differentiation and Wound Response in Lethal Clear Cell Renal Cell Carcinomas PLOS ONE Zhao, H., Ma, Z., Tibshirani, R., Higgins, J. P., Ljungberg, B., Brooks, J. D. 2009; 4 (6)

    Abstract

    Clear cell renal cell carcinoma (ccRCC) is the most common malignancy of the adult kidney and displays heterogeneity in clinical outcomes. Through comprehensive gene expression profiling, we have identified previously a set of transcripts that predict survival following nephrectomy independent of tumor stage, grade, and performance status. These transcripts, designated as the SPC (supervised principal components) gene set, show no apparent biological or genetic features that provide insight into renal carcinogenesis or tumor progression. We explored the relationship of this gene list to a set of genes expressed in different anatomical segments of the normal kidney including the cortex (cortex gene set) and the glomerulus (glomerulus gene set), and a gene set expressed after serum stimulation of quiescent fibroblasts (the core serum response or CSR gene set). Interestingly, the normal cortex, glomerulus (part of the normal renal cortex), and CSR gene sets captured more than 1/5 of the genes in the highly prognostic SPC gene set. Based on gene expression patterns alone, the SPC gene set could be used to sort samples from normal adult kidneys by the anatomical regions from which they were dissected. Tumors whose gene expression profiles most resembled the normal renal cortex or glomerulus showed better survival than those that did not, and those with expression features more similar to CSR showed poorer survival. While the cortex, glomerulus, and CSR signatures predicted survival independent of traditional clinical parameters, they were not independent of the SPC gene list. Our findings suggest that critical biological features of lethal ccRCC include loss of normal cortical differentiation and activation of programs associated with wound healing.

    View details for DOI 10.1371/journal.pone.0006039

    View details for Web of Science ID 000267356900003

    View details for PubMedID 19557179

  • Apolipoprotein D (APOD) is a putative biomarker of androgen receptor function in androgen insensitivity syndrome JOURNAL OF MOLECULAR MEDICINE-JMM Appari, M., Werner, R., Wuensch, L., Cario, G., Demeter, J., Hiort, O., Riepe, F., Brooks, J. D., Holterhus, P. 2009; 87 (6): 623-632

    Abstract

    Androgen insensitivity syndrome (AIS) is the most common cause of disorders of sex development usually caused by mutations in the androgen receptor (AR) gene. AIS is characterized by a poor genotype-phenotype correlation, and many patients with clinically presumed AIS do not seem to have mutations in the AR gene. We therefore aimed at identifying a biomarker enabling the assessment of the cellular function of the AR as a transcriptional activator. In the first step, we used complementary DNA (cDNA) microarrays for a genome-wide screen for androgen-regulated genes in two normal male primary scrotal skin fibroblast strains compared to two labia majora fibroblast strains from 46,XY females with complete AIS (CAIS). Apolipoprotein D (APOD) and two further transcripts were significantly upregulated by dihydrotestosterone (DHT) in scrotum fibroblasts, while CAIS labia majora cells were unresponsive. Microarray data were well correlated with quantitative real-time polymerase chain reaction (qRT-PCR; R = 0.93). Subsequently, we used qRT-PCR in independent new cell cultures and confirmed the significant DHT-dependent upregulation of APOD in five normal scrotum strains [13.5 +/- 8.2 (SD)-fold] compared with three CAIS strains (1.2 +/- 0.7-fold, p = 0.028; t test) and six partial androgen insensitivity syndrome strains (2 +/- 1.3-fold, p = 0.034; t test). Moreover, two different 17ss-hydroxysteroid dehydrogenase III deficiency labia majora strains showed APOD induction in the range of normal scrotum (9.96 +/- 1.4-fold), supporting AR specificity. Therefore, qRT-PCR of APOD messenger RNA transcription in primary cultures of labioscrotal skin fibroblasts is a promising tool for assessing AR function, potentially allowing a function-based diagnostic evaluation of AIS in the future.

    View details for DOI 10.1007/s00109-009-0462-3

    View details for Web of Science ID 000266475800009

    View details for PubMedID 19330472

  • Prostatic Soy Isoflavone Concentrations Exceed Serum Levels After Dietary Supplementation PROSTATE Gardner, C. D., Oelrich, B., Liu, J. P., Feldman, D., Franke, A. A., Brooks, J. D. 2009; 69 (7): 719-726

    Abstract

    The effects of soy isoflavones on prostate cancer may be concentration-dependent. The impact of soy supplementation on isoflavone concentrations in prostate tissues and serum remain unclear.To assess and compare concentrations of soy isoflavones in prostate tissue and serum among 19 men with prostate cancer who had elected to undergo radical prostatectomy.Participants were randomized to receive either daily soy supplements (82 mg/day aglycone equivalents) or placebos for 2 weeks (14 days) prior to surgery. Serum samples were obtained at the time of the surgery. Isoflavone concentrations were measured by HPLC/ESI-MS-MS.The median (25th, 75th percentile) total isoflavone concentration in the isoflavone-supplemented group was 2.3 micromol/L (1.2, 6.9) in the prostate tissue and 0.7 micromol/L (0.2, 1.2) in the serum. Total isoflavone concentrations in this group were an average of approximately 6-fold higher in prostate tissue compared to serum; the tissue versus serum ratio was significantly lower for genistein than daidzein, 4-fold versus 10-fold, P = 0.003. Tissue and serum levels of isoflavones among the placebo group were negligible with a few exceptions.The findings from the present study suggest that prostate tissue may have the ability to concentrate dietary soy isoflavones to potentially anti-carcinogenic levels.

    View details for DOI 10.1002/pros.20922

    View details for Web of Science ID 000265727700004

    View details for PubMedID 19180569

  • Recommendations for the Reporting of Surgically Resected Specimens of Renal Cell Carcinoma AMERICAN JOURNAL OF CLINICAL PATHOLOGY Higgins, J. P., McKenney, J. K., Brooks, J. D., Argani, P., Epstein, J. I. 2009; 131 (5): 623-?

    View details for DOI 10.1309/AJCP84ESGXKXYNRA

    View details for Web of Science ID 000265264200003

    View details for PubMedID 19369620

  • Inhibition of prostaglandin synthesis and actions by genistein in human prostate cancer cells and by soy isoflavones in prostate cancer patients INTERNATIONAL JOURNAL OF CANCER Swami, S., Krishnan, A. V., Moreno, J., Bhattacharya, R. S., Gardner, C., Brooks, J. D., Peehl, D. M., Feldman, D. 2009; 124 (9): 2050-2059

    Abstract

    Soy and its constituent isoflavone genistein inhibit the development and progression of prostate cancer (PCa). Our study in both cultured cells and PCa patients reveals a novel pathway for the actions of genistein, namely the inhibition of the synthesis and biological actions of prostaglandins (PGs), known stimulators of PCa growth. In the cell culture experiments, genistein decreased cyclooxygenase-2 (COX-2) mRNA and protein expression in both human PCa cell lines (LNCaP and PC-3) and primary prostate epithelial cells and increased 15-hydroxyprostaglandin dehydrogenase (15-PGDH) mRNA levels in primary prostate cells. As a result genistein significantly reduced the secretion of PGE(2) by these cells. EP4 and FP PG receptor mRNA were also reduced by genistein, providing an additional mechanism for the suppression of PG biological effects. Further, the growth stimulatory effects of both exogenous PGs and endogenous PGs derived from precursor arachidonic acid were attenuated by genistein. We also performed a pilot randomised double blind clinical study in which placebo or soy isoflavone supplements were given to PCa patients in the neo-adjuvant setting for 2 weeks before prostatectomy. Gene expression changes were measured in the prostatectomy specimens. In PCa patients ingesting isoflavones, we observed significant decreases in prostate COX-2 mRNA and increases in p21 mRNA. There were significant correlations between COX-2 mRNA suppression, p21 mRNA stimulation and serum isoflavone levels. We propose that the inhibition of the PG pathway contributes to the beneficial effect of soy isoflavones in PCa chemoprevention and/or treatment.

    View details for DOI 10.1002/ijc.24161

    View details for Web of Science ID 000264647600007

    View details for PubMedID 19127598

  • Recommendations for the reporting of surgically resected specimens of renal cell carcinoma The Association of Directors of Anatomic and Surgical Pathology HUMAN PATHOLOGY Higgins, J. P., McKenney, J. K., Brooksd, J. D., Argani, P., Epstein, J. I. 2009; 40 (4): 456-463

    Abstract

    A checklist based approach to reporting the relevant pathologic details of renal cell carcinoma resection specimens improves the completeness of the report. Karyotypic evaluation of renal neoplasms has refined but also complicated their classification. The number of diagnostic possibilities has increased and the importance of distinguishing different tumor types has been underscored by dramatic variation in prognosis and the development of targeted therapies for specific subtypes. The increasing number of recognized renal neoplasms has implications for handling renal resection specimens. Furthermore, the prognostic significance of other features of renal neoplasms related to grade and stage has been demonstrated. This guideline for the handling of renal resection specimens will focus on problem areas in the evolving practice of diagnosis, grading, and staging of renal neoplasms. The accompanying checklist will serve to ensure that all necessary details of the renal resection specimen are included in the surgical pathology report.

    View details for DOI 10.1016/j.humpath.2008.12.004

    View details for Web of Science ID 000264990200002

    View details for PubMedID 19289184

  • STEREOTACTIC BODY RADIOTHERAPY FOR LOCALIZED PROSTATE CANCER: INTERIM RESULTS OF A PROSPECTIVE PHASE II CLINICAL TRIAL INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS King, C. R., Brooks, J. D., Gill, H., Pawlicki, T., Cotrutz, C., Presti, J. C. 2009; 73 (4): 1043-1048

    Abstract

    The radiobiology of prostate cancer favors a hypofractionated dose regimen. We report results of a prospective Phase II clinical trial of stereotactic body radiotherapy (SBRT) for localized prostate cancer.Forty-one low-risk prostate cancer patients with 6 months' minimum follow-up received 36.25 Gy in five fractions of 7.25 Gy with image-guided SBRT alone using the CyberKnife. The early (<3 months) and late (>6 months) urinary and rectal toxicities were assessed using validated quality of life questionnaires (International Prostate Symptom Score, Expanded Prostate Cancer Index Composite) and the Radiation Therapy Oncology Group (RTOG) toxicity criteria. Patterns of prostate-specific antigen (PSA) response are analyzed.The median follow-up was 33 months. There were no RTOG Grade 4 acute or late rectal/urinary complications. There were 2 patients with RTOG Grade 3 late urinary toxicity and none with RTOG Grade 3 rectal complications. A reduced rate of severe rectal toxicities was observed with every-other-day vs. 5 consecutive days treatment regimen (0% vs. 38%, p = 0.0035). A benign PSA bounce (median, 0.4 ng/mL) was observed in 12 patients (29%) occurring at 18 months (median) after treatment. At last follow-up, no patient has had a PSA failure regardless of biochemical failure definition. Of 32 patients with 12 months minimum follow-up, 25 patients (78%) achieved a PSA nadir

    View details for DOI 10.1016/j.ijrobp.2008.05.059

    View details for Web of Science ID 000264257400013

    View details for PubMedID 18755555

  • Temporal Changes in Gene Expression Induced by Sulforaphane in Human Prostate Cancer Cells PROSTATE Bhamre, S., Sahoo, D., Tibshirani, R., Dill, D. L., Brooks, J. D. 2009; 69 (2): 181-190

    Abstract

    Prostate cancer is thought to arise as a result of oxidative stresses and induction of antioxidant electrophile defense (phase 2) enzymes has been proposed as a prostate cancer prevention strategy. The isothiocyanate sulforaphane, derived from cruciferous vegetables like broccoli, potently induces surrogate markers of phase 2 enzyme activity in prostate cells in vitro and in vivo. To better understand the temporal effects of sulforaphane and broccoli sprouts on gene expression in prostate cells, we carried out comprehensive transcriptome analysis using cDNA microarrays.Transcripts significantly modulated by sulforaphane over time were identified using StepMiner analysis. Ingenuity Pathway Analysis (IPA) was used to identify biological pathways, networks, and functions significantly altered by sulforaphane treatment.StepMiner and IPA revealed significant changes in many transcripts associated with cell growth and cell cycle, as well as a significant number associated with cellular response to oxidative damage and stress. Comparison to an existing dataset suggested that sulforaphane blocked cell growth by inducing G2/M arrest. Cell growth assays and flow cytometry analysis confirmed that sulforaphane inhibited cell growth and induced cell cycle arrest.Our data suggest that in prostate cells sulforaphane primarily induces cellular defenses and inhibits cell growth by causing G2/M phase arrest. Furthermore, based on the striking similarities in the gene expression patterns induced across experiments in these cells, sulforaphane appears to be the primary bioactive compound present in broccoli sprouts, suggesting that broccoli sprouts can serve as a suitable source for sulforaphane in intervention trials.

    View details for DOI 10.1002/pros.20869

    View details for Web of Science ID 000262701200008

    View details for PubMedID 18973173

  • CD 9 and vimentin distinguish clear cell from chromophobe renal cell carcinoma. BMC clinical pathology Williams, A. A., Higgins, J. P., Zhao, H., Ljunberg, B., Brooks, J. D. 2009; 9: 9-?

    Abstract

    Clear cell renal cell carcinoma (ccRCC) and chromophobe renal cell carcinoma (chRCC) can usually be distinguished by histologic characteristics. Occasionally, diagnosis proves challenging and diagnostic difficulty will likely increase as needle biopsies of renal lesions become more common.To identify markers that aid in differentiating ccRCC from chRCC, we used gene expression profiles to identify candidate markers that correlate with histology. 39 antisera and antibodies, including 35 for transcripts identified from gene expression profiling, were evaluated. Promising markers were tested on a tissue microarray (TMA) containing 428 renal neoplasms. Strength of staining of each core on the TMA was formally scored and the distribution of staining across different types of renal neoplasms was analyzed.Based on results from initial immunohistochemical staining of multitissue titer arrays, 23 of the antisera and antibodies were selected for staining of the TMA. For 7 of these markers, strength of staining of each core on the TMA was formally scored. Vimentin (positive in ccRCC) and CD9 (positive in chRCC) best distinguished ccRCC from chRCC. The combination of vimentin negativity and CD9 positivity was found to distinguish chRCC from ccRCC with a sensitivity of 100.0% and a specificity of 95.2%.Based on gene expression analysis, we identify CD9 and vimentin as candidate markers for distinguishing between ccRCC and chRCC. In difficult cases and particularly when the amount of diagnostic tissue is limited, vimentin and CD9 staining could serve as a useful adjunct in the differential diagnosis of ccRCC and chRCC.

    View details for DOI 10.1186/1472-6890-9-9

    View details for PubMedID 19922654

  • Comprehensive genomic characterization defines human glioblastoma genes and core pathways NATURE Chin, L., Meyerson, M., Aldape, K., Bigner, D., Mikkelsen, T., VandenBerg, S., Kahn, A., PENNY, R., Ferguson, M. L., Gerhard, D. S., Getz, G., Brennan, C., Taylor, B. S., Winckler, W., Park, P., Ladanyi, M., Hoadley, K. A., Verhaak, R. G., Hayes, D. N., Spellman, P. T., Absher, D., Weir, B. A., Ding, L., Wheeler, D., Lawrence, M. S., Cibulskis, K., Mardis, E., Zhang, J., Wilson, R. K., Donehower, L., Wheeler, D. A., Purdom, E., Wallis, J., Laird, P. W., Herman, J. G., Schuebel, K. E., Weisenberger, D. J., BAYLIN, S. B., Schultz, N., Yao, J., Wiedemeyer, R., WEINSTEIN, J., Sander, C., Gibbs, R. A., Gray, J., Kucherlapati, R., Lander, E. S., Myers, R. M., Perou, C. M., McLendon, R., Friedman, A., Van Meir, E. G., Brat, D. J., Mastrogianakis, G. M., Olson, J. J., Lehman, N., Yung, W. K., Bogler, O., Berger, M., Prados, M., Muzny, D., Morgan, M., Scherer, S., Sabo, A., Nazareth, L., Lewis, L., Hall, O., Zhu, Y., Ren, Y., Alvi, O., Yao, J., Hawes, A., Jhangiani, S., Fowler, G., San Lucas, A., Kovar, C., Cree, A., Dinh, H., Santibanez, J., Joshi, V., Gonzalez-Garay, M. L., Miller, C. A., Milosavljevic, A., Sougnez, C., Fennell, T., Mahan, S., Wilkinson, J., Ziaugra, L., Onofrio, R., Bloom, T., Nicol, R., Ardlie, K., Baldwin, J., Gabriel, S., Fulton, R. S., McLellan, M. D., Larson, D. E., Shi, X., Abbott, R., Fulton, L., Chen, K., Koboldt, D. C., Wendl, M. C., Meyer, R., Tang, Y., Lin, L., Osborne, J. R., Dunford-Shore, B. H., Miner, T. L., Delehaunty, K., Markovic, C., Swift, G., Courtney, W., Pohl, C., Abbott, S., Hawkins, A., Leong, S., Haipek, C., Schmidt, H., Wiechert, M., Vickery, T., Scott, S., Dooling, D. J., Chinwalla, A., Weinstock, G. M., O'Kelly, M., Robinson, J., Alexe, G., Beroukhim, R., Carter, S., Chiang, D., Gould, J., Gupta, S., Korn, J., Mermel, C., Mesirov, J., Monti, S., Nguyen, H., Parkin, M., Reich, M., Stransky, N., Garraway, L., Golub, T., Protopopov, A., Perna, I., Aronson, S., Sathiamoorthy, N., Ren, G., Kim, H., Kong, S. W., Xiao, Y., Kohane, I. S., Seidman, J., Cope, L., Pan, F., Van Den Berg, D., van Neste, L., Yi, J. M., Li, J. Z., Southwick, A., Brady, S., Aggarwal, A., Chung, T., Sherlock, G., Brooks, J. D., Jakkula, L. R., Lapuk, A. V., Marr, H., Dorton, S., Choi, Y. G., Han, J., Ray, A., Wang, V., Durinck, S., Robinson, M., Wang, N. J., Vranizan, K., Peng, V., Van Name, E., Fontenay, G. V., Ngai, J., Conboy, J. G., Parvin, B., Feiler, H. S., Speed, T. P., Socci, N. D., Olshen, A., Lash, A., Reva, B., Antipin, Y., Stukalov, A., Gross, B., Cerami, E., Wang, W. Q., Qin, L., Seshan, V. E., Villafania, L., Cavatore, M., Borsu, L., Viale, A., Gerald, W., Topal, M. D., Qi, Y., Balu, S., Shi, Y., Wu, G., Bittner, M., Shelton, T., Lenkiewicz, E., Morris, S., Beasley, D., Sanders, S., Sfeir, R., Chen, J., Nassau, D., Feng, L., Hickey, E., Schaefer, C., Madhavan, S., Buetow, K., Barker, A., Vockley, J., Compton, C., Vaught, J., Fielding, P., Collins, F., Good, P., Guyer, M., Ozenberger, B., Peterson, J., Thomson, E. 2008; 455 (7216): 1061-1068

    Abstract

    Human cancer cells typically harbour multiple chromosomal aberrations, nucleotide substitutions and epigenetic modifications that drive malignant transformation. The Cancer Genome Atlas (TCGA) pilot project aims to assess the value of large-scale multi-dimensional analysis of these molecular characteristics in human cancer and to provide the data rapidly to the research community. Here we report the interim integrative analysis of DNA copy number, gene expression and DNA methylation aberrations in 206 glioblastomas--the most common type of adult brain cancer--and nucleotide sequence aberrations in 91 of the 206 glioblastomas. This analysis provides new insights into the roles of ERBB2, NF1 and TP53, uncovers frequent mutations of the phosphatidylinositol-3-OH kinase regulatory subunit gene PIK3R1, and provides a network view of the pathways altered in the development of glioblastoma. Furthermore, integration of mutation, DNA methylation and clinical treatment data reveals a link between MGMT promoter methylation and a hypermutator phenotype consequent to mismatch repair deficiency in treated glioblastomas, an observation with potential clinical implications. Together, these findings establish the feasibility and power of TCGA, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer.

    View details for DOI 10.1038/nature07385

    View details for Web of Science ID 000260252600035

    View details for PubMedID 18772890

  • Identification of candidate prostate cancer genes through comparative expression-profiling of seminal vesicle PROSTATE Thompson, M., Lapointe, J., Choi, Y., Ong, D. E., Higgins, J. P., Brooks, J. D., Pollack, J. R. 2008; 68 (11): 1248-1256

    Abstract

    Prostate cancer is the most frequently diagnosed cancer among men in the United States. In contrast, cancer of the seminal vesicle is exceedingly rare, despite that the prostate and seminal vesicle share similar histology, secretory function, androgen dependency, blood supply, and (in part) embryonic origin. We hypothesized that gene-expression differences between prostate and seminal vesicle might inform mechanisms underlying the higher incidence of prostate cancer.Whole-genome DNA microarrays were used to profile gene expression of 11 normal prostate and 7 seminal vesicle specimens (including six matched pairs) obtained from radical prostatectomy. Supervised analysis was used to identify genes differentially expressed between normal prostate and seminal vesicle, and this list was then cross-referenced to genes differentially expressed between normal and cancerous prostate. Expression patterns of selected genes were confirmed by immunohistochemistry using a tissue microarray.We identified 32 genes that displayed a highly statistically significant expression pattern with highest levels in seminal vesicle, lower levels in normal prostate, and lowest levels in prostate cancer. Among these genes was the known candidate prostate tumor suppressor GSTP1 (involved in xenobiotic detoxification). The expression pattern of GSTP1 and four other genes, ABCG2 (xenobiotic transport), CRABP2 (retinoic acid signaling), GATA3 (lineage-specific transcription), and SLPI (immune response), was confirmed by immunohistochemistry.Our findings identify candidate prostate cancer genes whose reduced expression in prostate (compared to seminal vesicle) may be permissive to prostate cancer initiation. Such genes and their pathways may inform mechanisms of prostate carcinogenesis, and suggest new opportunities for prostate cancer prevention.

    View details for DOI 10.1002/pros.20792

    View details for Web of Science ID 000258021300012

    View details for PubMedID 18500686

  • Postoperative prostate-specific antigen velocity independently predicts for failure of salvage radiotherapy after prostatectomy INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS King, C. R., Presti, J. C., Brooks, J. D., Gill, H., Spiotto, M. T. 2008; 70 (5): 1472-1477

    Abstract

    Identification of patients most likely to benefit from salvage radiotherapy (RT) using postoperative (postop) prostate-specific antigen (PSA) kinetics.From 1984 to 2004, 81 patients who fit the following criteria formed the study population: undetectable PSA after radical prostatectomy (RP); pathologically negative nodes; biochemical relapse defined as a persistently detectable PSA; salvage RT; and two or more postop PSAs available before salvage RT. Salvage RT included the whole pelvic nodes in 55 patients and 4 months of total androgen suppression in 56 patients. The median follow-up was >5 years. All relapses were defined as a persistently detectable PSA. Kaplan-Meier and Cox proportional hazards multivariable analysis were performed for all clinical, pathological, and treatment factors predicting for biochemical relapse-free survival (bRFS).There were 37 biochemical relapses observed after salvage RT. The 5-year bRFS after salvage RT for patients with postop prostate-specific antigen velocity < or = 1 vs. >1 ng/ml/yr was 59% vs. 29%, p = 0.002. In multivariate analysis, only postop PSAV (p = 0.0036), pre-RT PSA level < or = 1 (p = 0.037) and interval-to-relapse >10 months (p = 0.012) remained significant, whereas pelvic RT, hormone therapy, and RT dose showed a trend (p = approximately 0.06). PSAV, but not prostate-specific antigen doubling time, predicted successful salvage RT, suggesting an association of zero-order kinetics with locally recurrent disease.Postoperative PSA velocity independently predicts for the failure of salvage RT and can be considered in addition to high-risk features when selecting patients in need of systemic therapy following biochemical failure after RP. For well-selected patients, salvage RT can achieve high cure rates.

    View details for DOI 10.1016/j.ijrobp.2007.08.014

    View details for Web of Science ID 000254660800028

    View details for PubMedID 17935902

  • hCAP-D3 expression marks a prostate cancer subtype with favorable clinical behavior and androgen signaling signature AMERICAN JOURNAL OF SURGICAL PATHOLOGY Lapointe, J., Malhotra, S., Higgins, J. P., Bair, E., Thompson, M., Salari, K., Giacomini, C. P., Ferrari, M., Montgomery, K., Tibshirani, R., van de Rijn, M., Brooks, J. D., Pollack, J. R. 2008; 32 (2): 205-209

    Abstract

    Growing evidence suggests that only a fraction of prostate cancers detected clinically are potentially lethal. An important clinical issue is identifying men with indolent cancer who might be spared aggressive therapies with associated morbidities. Previously, using microarray analysis we defined 3 molecular subtypes of prostate cancer with different gene-expression patterns. One, subtype-1, displayed features consistent with more indolent behavior, where an immunohistochemical marker (AZGP1) for subtype-1 predicted favorable outcome after radical prostatectomy. Here we characterize a second candidate tissue biomarker, hCAP-D3, expressed in subtype-1 prostate tumors. hCAP-D3 expression, assayed by RNA in situ hybridization on a tissue microarray comprising 225 cases, was associated with decreased tumor recurrence after radical prostatectomy (P=0.004), independent of pathologic tumor stage, Gleason grade, and preoperative prostate-specific antigen levels. Simultaneous assessment of hCAP-D3 and AZGP1 expression in this tumor set improved outcome prediction. We have previously demonstrated that hCAP-D3 is induced by androgen in prostate cells. Extending this finding, Gene Set Enrichment Analysis revealed enrichment of androgen-responsive genes in subtype-1 tumors (P=0.019). Our findings identify hCAP-D3 as a new biomarker for subtype-1 tumors that improves prognostication, and reveal androgen signaling as an important biologic feature of this potentially clinically favorable molecular subtype.

    View details for Web of Science ID 000252759900004

    View details for PubMedID 18223322

  • The impact of tumor volume on outcomes after radical prostatectomy: Implications for prostate cancer screening. The Open Prostate Cancer Journal James D. Brooks, Robert Tibshirani, Michelle Ferrari, Joseph C. Presti, Jr., Harcharan Gill, Christopher R. King 2008; 1: 1-8
  • Intrinsic androgen-dependent gene expression patterns revealed by comparison of genital fibroblasts from normal males and individuals with complete and partial androgen insensitivity syndrome BMC GENOMICS Holterhus, P., Deppe, U., Werner, R., Richter-Unruh, A., Bebermeier, J., Wuensch, L., Krege, S., Schweikert, H., Demeter, J., Riepe, F., Hiort, O., Brooks, J. D. 2007; 8

    Abstract

    To better understand the molecular programs of normal and abnormal genital development, clear-cut definition of androgen-dependent gene expression patterns, without the influence of genotype (46, XX vs. 46, XY), is warranted. Previously, we have identified global gene expression profiles in genital-derived fibroblasts that differ between 46, XY males and 46, XY females with complete androgen insensitivity syndrome (CAIS) due to inactivating mutations of the androgen receptor (AR). While these differences could be due to cell autonomous changes in gene expression induced by androgen programming, recent work suggests they could also be influenced by the location from which the fibroblasts were harvested (topology). To minimize the influence of topology, we compared gene expression patterns of fibroblasts derived from identical urogenital anlagen: the scrotum in normally virilized 46, XY males and the labia majora from completely feminized 46, XY individuals with CAIS.612 transcripts representing 440 unique genes differed significantly in expression levels between scrotum and CAIS labia majora, suggesting the effects of androgen programming. While some genes coincided with those we had identified previously (TBX3, IGFBP5, EGFR, CSPG2), a significant number did not, implying that topology had influenced gene expression in our previous experiments. Supervised clustering of gene expression data derived from a large set of fibroblast cultures from individuals with partial AIS revealed that the new, topology controlled data set better classified the specimens.Inactivating mutations of the AR, in themselves, appear to induce lasting changes in gene expression in cultured fibroblasts, independent of topology and genotype. Genes identified are likely to be relevant candidates to decipher androgen-dependent normal and abnormal genital development.

    View details for DOI 10.1186/1471-2164-8-376

    View details for Web of Science ID 000252779600001

    View details for PubMedID 17945006

  • Genomic profiling reveals alternative genetic pathways of prostate tumorigenesis CANCER RESEARCH Lapointe, J., Li, C., Giacomini, C. P., Salari, K., Huang, S., Wang, P., Ferrari, M., Hernandez-Boussard, T., Brooks, J. D., Pollack, J. R. 2007; 67 (18): 8504-8510

    Abstract

    Prostate cancer is clinically heterogeneous, ranging from indolent to lethal disease. Expression profiling previously defined three subtypes of prostate cancer, one (subtype-1) linked to clinically favorable behavior, and the others (subtypes-2 and -3) linked with a more aggressive form of the disease. To explore disease heterogeneity at the genomic level, we carried out array-based comparative genomic hybridization (array CGH) on 64 prostate tumor specimens, including 55 primary tumors and 9 pelvic lymph node metastases. Unsupervised cluster analysis of DNA copy number alterations (CNA) identified recurrent aberrations, including a 6q15-deletion group associated with subtype-1 gene expression patterns and decreased tumor recurrence. Supervised analysis further disclosed distinct patterns of CNA among gene-expression subtypes, where subtype-1 tumors exhibited characteristic deletions at 5q21 and 6q15, and subtype-2 cases harbored deletions at 8p21 (NKX3-1) and 21q22 (resulting in TMPRSS2-ERG fusion). Lymph node metastases, predominantly subtype-3, displayed overall higher frequencies of CNA, and in particular gains at 8q24 (MYC) and 16p13, and loss at 10q23 (PTEN) and 16q23. Our findings reveal that prostate cancers develop via a limited number of alternative preferred genetic pathways. The resultant molecular genetic subtypes provide a new framework for investigating prostate cancer biology and explain in part the clinical heterogeneity of the disease.

    View details for DOI 10.1158/0008-5472.CAN-07-0673

    View details for Web of Science ID 000249679500013

    View details for PubMedID 17875689

  • Placental S100 (S100P) and GATA3: Markers for transitional epithelium and urothelial carcinoma discovered by complementary DNA microarray AMERICAN JOURNAL OF SURGICAL PATHOLOGY Higgins, J. P., Kaygusuz, G., Wang, L., Montgomery, K., Mason, V., Zhu, S. X., Marinelli, R. J., Presti, J. C., van de Rijn, M., Brooks, J. D. 2007; 31 (5): 673-680

    Abstract

    The morphologic distinction between prostate and urothelial carcinoma can be difficult. To identify novel diagnostic markers that may aid in the differential diagnosis of prostate versus urothelial carcinoma, we analyzed expression patterns in prostate and bladder cancer tissues using complementary DNA microarrays. Together with our prior studies on renal neoplasms and normal kidney, these studies suggested that the gene for placental S100 (S100P) is specifically expressed in benign and malignant urothelial cells. Using tissue microarrays, a polyclonal antiserum against S100P protein stained 86% of 295 urothelial carcinomas while only 3% of 260 prostatic adenocarcinomas and 1% of 133 renal cell carcinomas stained. A commercially available monoclonal antibody against S100P stained 78% of 300 urothelial carcinomas while only 2% of 256 prostatic adenocarcinomas and none of 137 renal cell carcinomas stained. A second gene, GATA3, also showed high level expression in urothelial tumors by cDNA array. A commercially available monoclonal antibody against GATA3 stained 67% of 308 urothelial carcinomas, but none of the prostate or renal carcinomas. For comparison, staining was also performed for p63 and cytokeratin 5/6. p63 stained 87% of urothelial carcinomas whereas CK5/6 stained 54%. Importantly, when S100P and p63 were combined 95% of urothelial carcinomas were labeled by one or both markers. We conclude that the detection of S100P and GATA3 protein expression may help distinguish urothelial carcinomas from other genitourinary neoplasms that enter into the differential diagnosis.

    View details for Web of Science ID 000246135600003

    View details for PubMedID 17460449

  • A promoting role of androgen receptor in androgen-sensitive and -insensitive prostate cancer cells NUCLEIC ACIDS RESEARCH Li, T., Zhao, H., Peng, Y., Beliakoff, J., Brooks, J. D., Sun, Z. 2007; 35 (8): 2767-2776

    Abstract

    Although the vital role of the androgen receptor (AR) has been well demonstrated in primary prostate cancers, its role in the androgen-insensitive prostate cancers still remains unclear. Here, we used a small hairpin RNA approach to directly assess AR activity in prostate cancer cells. Reduction of AR expression in the two androgen-sensitive prostate cancer cell lines, LNCaP and LAPC4, significantly decreased AR-mediated transcription and cell growth. Intriguingly, in two androgen-insensitive prostate cell lines, LNCaP-C42B4 and CWR22Rv1, knockdown of AR expression showed a more pronounced effect on AR-induced transcription and cell growth than androgen depletion. Using cDNA microarrays, we also compared the transcriptional profiles induced by either androgen depletion or AR knockdown. Although a significant number of transcripts appear to be regulated by both androgen depletion and AR knockdown, we observed a subset of transcripts affected only by androgen depletion but not by AR knockdown, and vice versa. Finally, we demonstrated a direct role for AR in promoting tumor formation and growth in a xenograft model. Taken together, our results elucidate an important role for the AR in androgen-insensitive prostate cancer cells, and suggest that AR can be used as a therapeutic target for androgen-insensitive prostate cancers.

    View details for DOI 10.1093/nar/gkm198

    View details for Web of Science ID 000247239600029

    View details for PubMedID 17426117

  • A variant TMPRSS2 isoform and ERG fusion product in prostate cancer with implications for molecular diagnosis MODERN PATHOLOGY Lapointe, J., Kim, Y. H., Miller, M. A., Li, C., Kaygusuz, G., van de Rijn, M., Huntsman, D. G., Brooks, J. D., Pollack, J. R. 2007; 20 (4): 467-473

    Abstract

    Prostate cancer is the most commonly diagnosed cancer among men in the United States. Recently, fusion of TMPRSS2 with ETS family oncogenic transcription factors has been identified as a common molecular alteration in prostate cancer, where most often the rearrangement places ERG under the androgen-regulated transcriptional control of TMPRSS2. Here, we carried out rapid amplification of cDNA ends (RACE) on a prostate cancer specimen carrying an atypical aberration discovered by array-based comparative genomic hybridization (array CGH), suggesting an alternative fusion partner of ERG. We identified novel transcribed sequences fused to ERG, mapping 4 kb upstream of the TMPRSS2 start site. The sequences derive from an apparent second TMPRSS2 isoform, which we found also expressed in some prostate tumors, suggesting similar androgen-regulated control. In a reverse transcription-polymerase chain reaction (RT-PCR)-based survey of 63 prostate tumor specimens (54 primary and nine lymph node metastases), 44 (70%) cases expressed either the known or novel variant TMPRSS2-ERG fusion, 28 (44%) expressed both, 10 (16%) expressed only the known, and notably six (10%) expressed only the variant isoform fusion. In this specimen set, the presence of a TMPRSS2-ERG fusion showed no statistical association with tumor stage, Gleason grade or recurrence-free survival. Nonetheless, the discovery of a novel variant TMPRSS2 isoform-ERG fusion adds to the characterization of ETS-family rearrangements in prostate cancer, and has important implications for the accurate molecular diagnosis of TMPRSS2-ETS fusions.

    View details for DOI 10.1038/modpathol.3800759

    View details for Web of Science ID 000245271000007

    View details for PubMedID 17334351

  • Endothelin-1 promotes cell survival in renal cell carcinoma through the ETA receptor CANCER LETTERS Pflug, B. R., Zheng, H., Udan, M. S., D'Antonio, J. M., Marshall, F. F., Brooks, J. D., Nelson, J. B. 2007; 246 (1-2): 139-148

    Abstract

    Endothelin-1 (ET-1) is a potent vasoconstrictor that has been shown to significantly impact many benign and malignant tissues by signaling through its two cognate receptors: ET(A) and ET(B). As ET-1 has a role in both normal and diseased kidney, we initiated studies to investigate endothelin axis expression and function in renal cell carcinoma (RCC). In this study, relatively high levels of ET-1 were detected in all six human RCC cell lines investigated. RT-PCR and Southern analyses revealed that all six RCC cell lines expressed ET(A) receptor mRNA, while 3/6 cell lines also expressed ET(B) mRNA. High affinity ET-1 binding occurred in all but one RCC cell line and quantitative RT-PCR demonstrated ET(A) mRNA expression in all six cell lines. Methylation of the ET(B) promoter (EDNRB) in 4/6 RCC cell lines was observed, suggesting a mechanism for repressed ET(B) expression. Moreover, methylation occurred in 32/48 of renal tumors and in 27/55 of histologically normal adjacent tissue samples studied, while no methylation was evident in any normal tissue isolated from nephrectomy or at autopsy. Functionally, ET-1 significantly inhibited paclitaxel-induced apoptosis in RCC cells through binding ET(A) with the ET-1 signaling mediated via the PI3-kinase/Akt pathway. Collectively, these data support the therapeutic targeting of the ET(A) receptor as a novel treatment strategy for RCC.

    View details for DOI 10.1016/j.canlet.2006.02.007

    View details for Web of Science ID 000244154900017

    View details for PubMedID 16581180

  • Selenomethionine induced transcriptional programs in human prostate cancer cells JOURNAL OF UROLOGY Zhao, H., Brooks, J. D. 2007; 177 (2): 743-750

    Abstract

    We determined the effects of selenomethionine, the major organic selenium containing compound found in the diet and the form of selenium being used in the Selenium and Vitamin E Cancer Prevention Trial, on prostate cancer cells.We assessed global transcript profiles of selenomethionine treated LNCaP using cDNA microarrays and compared them to those of cells treated with methylselenic acid, a direct precursor of methylselenol, which is the active form of selenium in vivo.After treatment with selenomethionine 2,336 unique genes showed expression changes of at least 1.5-fold in at least 3 time points during 48 hours and 366 unique transcripts differed significantly between selenomethionine and methylselenic acid treated LNCaP. Approximately half of the 76 cell cycle regulated genes affected by selenomethionine were down-regulated and enriched for genes associated with the G2/M phase. Flow cytometry analysis showed that selenomethionine induced G2/M arrest in LNCaP at low concentrations. Selenomethionine also affected expression levels of 35 known androgen responsive genes and 18 of these transcripts showed changes that were the inverse of those seen after androgen stimulation. At high concentrations selenomethionine decreased prostate specific antigen promoter driven luciferase expression.Selenomethionine modulates transcript levels of genes involved in a number of biological processes, including cell cycle/apoptosis androgen signaling, signal transduction and transcriptional regulation. Although the pathways affected paralleled in many ways those that are modulated by methylselenic acid, distinct differences in transcript patterns and effects on cell cycle regulation suggest that different selenium compounds could exert unique effects in prostate cells.

    View details for DOI 10.1016/j.juro.2006.09.071

    View details for Web of Science ID 000243453900074

    View details for PubMedID 17222674

  • Distinctive gene expression of prostatic stromal cells cultured from diseased versus normal tissues JOURNAL OF CELLULAR PHYSIOLOGY Zhao, H., Ramos, C. F., Brooks, J. D., Peehl, D. M. 2007; 210 (1): 111-121

    Abstract

    To obtain a comprehensive view of the transcriptional programs in prostatic stromal cells of different histological/pathological origin, we profiled 18 adult human stromal cell cultures from normal transition zone (TZ), normal peripheral zone (PZ), benign prostatic hyperplasia (BPH), and prostate cancer (CA) using cDNA microarrays. A hierarchical clustering analysis of 714 named unique genes whose expression varied at least threefold from the overall mean abundance in at least three samples in all 18 samples demonstrated that cells of different origin displayed distinct gene expression profiles. Many of the differentially expressed genes are involved in biological processes known to be important in the development of prostatic diseases including cell proliferation and apoptosis, cell adhesion, and immune response. Significance Analysis of Microarrays (SAM) analysis identified genes that showed differential expression with statistical significance including 24 genes between cells from TZ versus BPH, 34 between BPH versus CA, and 101 between PZ versus CA. S100A4 and SULF1, the most up- and downregulated genes in BPH versus TZ, respectively, showed expression at the protein level consistent with microarray analysis. In addition, sulfatase assay showed that BPH cells have lower SULF1 activity compared to TZ cells. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis confirmed differential expression of ENPP2/autotoxin and six other genes between PZ versus CA, as well as differential expression of six genes between BPH versus CA. Our results support the hypothesis that prostatic stromal cells of different origin have unique transcriptional programs and point towards genes involved in actions of stromal cells in BPH and CA.

    View details for DOI 10.1002/jcp.20828

    View details for Web of Science ID 000242568200012

    View details for PubMedID 17044071

  • Cell-line and tissue-specific signatures of androgen receptor-coregulator transcription JOURNAL OF MOLECULAR MEDICINE-JMM Bebermeier, J., Brooks, J. D., DePrimo, S. E., Werner, R., Deppe, U., Demeter, J., Hiort, O., Holterhus, P. 2006; 84 (11): 919-931

    Abstract

    Normal genital skin fibroblasts (GSF) and the human prostate carcinoma cell line LNCaP have been used widely as cell culture models of genital origin to study androgen receptor (AR) signaling. We demonstrate that LNCaP shows a reproducible response to androgens as assessed using cDNA-microarrays representing approximately 32,000 unique human genes, whereas several independent GSF strains are virtually unresponsive. We show that LNCaP cells express markedly higher AR protein levels likely contributing to the observed differences of androgen responsiveness. However, previous data suggested that AR-expression levels alone do not determine androgen responsiveness of human GSF compared to LNCaP. We hypothesized that cell-specific differences in expression levels of AR coregulators might contribute to differences in androgen responsiveness and might be found by comparing LNCaP and GSFs. Using the Canadian McGill-database of AR coregulators ( http://www.mcgill.ca/androgendb ), we identified 61 AR-coregulator genes represented by 282 transcripts on our microarray platform that was used to measure transcript profiles of LNCaP and GSF cells. Baseline expression levels of 48 AR-coregulator transcripts representing 33 distinct genes showed significant differences between GSF and LNCaP, four of which we confirmed by reverse transcriptase polymerase chain reaction. Compared to LNCaP, GSFs displayed significant upregulation of AR coregulators that can function as repressors of AR-transactivation, such as caveolin 1. Analysis of a recently published comprehensive dataset of 115 microarrays representing 35 different human tissues revealed tissue-specific signatures of AR coregulators that segregated with ontogenetically related groups of tissues (e.g., lymphatic system and genital tissues, brain). Our data demonstrate the existence of cell-line and tissue-specific expression patterns of molecules with documented AR coregulatory functions. Therefore, differential expression patterns of AR coregulators could modify tissue-specificity and diversity of androgen actions in development, physiology, and disease.

    View details for DOI 10.1007/s00109-006-0081-1

    View details for Web of Science ID 000241589100005

    View details for PubMedID 16932916

  • Application of genomic technologies to human prostate cancer OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY Li, S., Bhamre, S., Lapointe, J., Pollack, J. R., Brooks, J. D. 2006; 10 (3): 261-275

    Abstract

    Prostate cancer is the most commonly diagnosed non-cutaneous malignancy in U.S. males and has a broad spectrum of clinical behavior ranging from indolent to lethal. Microarray technology has provided unprecedented opportunity to explore the genetic processes underlying prostate cancer by providing a comprehensive survey of a cell's transcriptional landscape. Prostate cancer, however, has posed significant challenges that have contributed to inconsistent results between studies and difficulty replicating findings. Despite these challenges, several important insights have been gained along with new clinical biomarkers of diagnosis and prognosis. Continued improvements in methods of tissue preparation, microarray technology and data analysis will overcome existing challenges and fuel future discoveries.

    View details for Web of Science ID 000241666200002

    View details for PubMedID 17069507

  • Reliability of small amounts of cancer in prostate biopsies to reveal pathologic grade UROLOGY King, C. R., McNeal, J. E., Gill, H., Brooks, J. D., Srinivas, S., Presti, J. C. 2006; 67 (6): 1229-1234

    Abstract

    To examine grade reliability when biopsies contain very small amounts of prostate cancer. Prostate biopsy findings are known to undergrade prostate cancer compared with the pathologic specimens yet remain the only grade guiding disease management.The presence of a clinically significant grade change from biopsy cores to matched prostatectomy specimens was examined in 371 patients. The biopsies were characterized for primary and secondary Gleason grade, number of positive cores, and total linear length of cancer. The pathologic specimens were characterized for cancer volume and relative percentage by grade. The rates of upgrading or downgrading were tested against all clinical and biopsy information for any significant predictive value.The overall rate of upgrading was 40.7% and downgrading was 16.1%. Upgrading was constant and independent of any clinical or biopsy tumor volume indexes. Specifically, when cancer was present in only one biopsy core and measured 2 mm or less (n = 48), it was just as predictive of the pathologic grade as that from any greater number of positive cores and any greater extent of cancer length present. Downgrading was less frequent for biopsies with small amounts of cancer.Histologic grading from small amounts of cancer in prostate biopsies is reliable and not more prone to grading errors. A repeat biopsy for these patients may not be indicated.

    View details for DOI 10.1016/j.urology.2005.12.031

    View details for Web of Science ID 000238390900026

    View details for PubMedID 16765184

  • Refractory hematuria from amyloidosis successfully treated by splenectomy UROLOGY Ma, J. F., Coutre, S. E., Curet, M. J., Brooks, J. D. 2006; 67 (5)

    Abstract

    Systemic amyloidosis can result in a coagulopathy that is associated with low levels of factor X. We present a case of intractable, life-threatening hematuria that was successfully managed with activated recombinant human factor VII and splenectomy.

    View details for DOI 10.1016/j.urology.2005.11.048

    View details for Web of Science ID 000238390800059

    View details for PubMedID 16698382

  • Modest induction of phase 2 enzyme activity in the F-344 rat prostate BMC CANCER Jones, S. B., Brooks, J. D. 2006; 6

    Abstract

    Prostate cancer is the most commonly diagnosed malignancy in men and is thought to arise as a result of endogenous oxidative stress in the face of compromised carcinogen defenses. We tested whether carcinogen defense (phase 2) enzymes could be induced in the prostate tissues of rats after oral feeding of candidate phase 2 enzyme inducing compounds.Male F344 rats were gavage fed sulforaphane, beta-naphthoflavone, curcumin, dimethyl fumarate or vehicle control over five days, and on the sixth day, prostate, liver, kidney and bladder tissues were harvested. Cytosolic enzyme activities of nicotinamide quinone oxidoreductase (NQO1), total glutathione transferase (using DCNB) and mu-class glutathione transferase (using CDNB) were determined in the treated and control animals and compared.In prostatic tissues, sulforaphane produced modest but significant increases in the enzymatic activities of NQO1, total GST and GST-mu compared to control animals. beta-naphthoflavone significantly increased NQO1 and GST-mu activities and curcumin increased total GST and GST-mu enzymatic activities. Dimethyl fumarate did not significantly increase prostatic phase 2 enzyme activity. Compared to control animals, sulforaphane also significantly induced NQO1 or total GST enzyme activity in the liver, kidney and, most significantly, in the bladder tissues. All compounds were well tolerated over the course of the gavage feedings.Orally administered compounds will induce modestly phase 2 enzyme activity in the prostate although the significance of this degree of induction is unknown. The 4 different compounds also altered phase 2 enzyme activity to different degrees in different tissue types. Orally administered sulforaphane potently induces phase 2 enzymes in bladder tissues and should be investigated as a bladder cancer preventive agent.

    View details for DOI 10.1186/1471-2407-6-62

    View details for Web of Science ID 000236547000001

    View details for PubMedID 16539699

  • Gene expression profiling predicts survival in conventional renal cell carcinoma PLOS MEDICINE Zhao, H. J., Ljungberg, B., Grankvist, K., Rasmuson, T., Tibshirani, R., Brooks, J. D. 2006; 3 (1): 115-124

    Abstract

    Conventional renal cell carcinoma (cRCC) accounts for most of the deaths due to kidney cancer. Tumor stage, grade, and patient performance status are used currently to predict survival after surgery. Our goal was to identify gene expression features, using comprehensive gene expression profiling, that correlate with survival.Gene expression profiles were determined in 177 primary cRCCs using DNA microarrays. Unsupervised hierarchical clustering analysis segregated cRCC into five gene expression subgroups. Expression subgroup was correlated with survival in long-term follow-up and was independent of grade, stage, and performance status. The tumors were then divided evenly into training and test sets that were balanced for grade, stage, performance status, and length of follow-up. A semisupervised learning algorithm (supervised principal components analysis) was applied to identify transcripts whose expression was associated with survival in the training set, and the performance of this gene expression-based survival predictor was assessed using the test set. With this method, we identified 259 genes that accurately predicted disease-specific survival among patients in the independent validation group (p < 0.001). In multivariate analysis, the gene expression predictor was a strong predictor of survival independent of tumor stage, grade, and performance status (p < 0.001).cRCC displays molecular heterogeneity and can be separated into gene expression subgroups that correlate with survival after surgery. We have identified a set of 259 genes that predict survival after surgery independent of clinical prognostic factors.

    View details for DOI 10.1371/journal.pmed.0030013

    View details for Web of Science ID 000236342700020

    View details for PubMedID 16318415

  • The retinoic acid synthesis gene ALDH1a2 is a candidate tumor suppressor in prostate cancer CANCER RESEARCH Kim, H., Lapointe, J., Kaygusuz, G., Ong, D. E., Li, C. D., van de Rijn, M., Brooks, J. D., Pollack, J. R. 2005; 65 (18): 8118-8124

    Abstract

    Prostate cancer is the most common cancer among men in the United States, and aberrant DNA methylation is known to be an early molecular event in its development. Here, we have used expression profiling to identify novel hypermethylated genes whose expression is induced by treatment of prostate cancer cell lines with the DNA methyltransferase inhibitor 5-Aza-2'-deoxycytidine (5-aza-dC). Of the 271 genes that were induced by 5-aza-dC treatment, 25 also displayed reduced expression in primary prostate tumors compared with normal prostate tissue, and the decreased expression of only one gene, aldehyde dehydrogenase 1 family, member A2 (ALDH1a2), was also associated with shorter recurrence-free survival. ALDH1a2 encodes an enzyme responsible for synthesis of retinoic acid (RA), a compound with prodifferentiation properties. By immunohistochemistry, we observed that ALDH1a2 was expressed in epithelia from normal prostate but not prostate cancer. Using bisulfite sequencing, we determined that the ALDH1a2 promoter region was significantly hypermethylated in primary prostate tumors compared with normal prostate specimens (P = 0.01). Finally, transfection-mediated reexpression of wild-type ALDH1a2 (but not a presumptive catalytically dead mutant) in the prostate cancer cell line DU145 resulted in decreased colony growth (P < 0.0001), comparable with treatment with either 5-aza-dC or RA. Taken together, our findings implicate ALDH1a2 as a candidate tumor suppressor gene in prostate cancer and further support a role of retinoids in the prevention or treatment of prostate cancer.

    View details for DOI 10.1158/0008-5472.CAN-04-4562

    View details for Web of Science ID 000231848800010

    View details for PubMedID 16166285

  • Preoperative PSA velocity is an independent prognostic factor for relapse after radical prostatectomy JOURNAL OF CLINICAL ONCOLOGY Patel, D. A., Presti, J. C., McNeal, J. E., Gill, H., Brooks, J. D., King, C. R. 2005; 23 (25): 6157-6162

    Abstract

    Preoperative prostate-specific antigen (PSA) velocity (PSAV), or the rate of PSA rise before diagnosis, predicts for risk of cancer death after radical prostatectomy (RP). We evaluated the relative merit of established preoperative factors, including biopsy indices and preoperative PSAV, for their impact on relapse after RP.The outcomes of 202 men who underwent RP were reviewed. Biopsies were characterized for grade, percentage positive cores, and total linear tumor length. Surgical specimens were characterized for cancer volume, relative percentage by grade, extracapsular extension, and margin status. Univariate and multivariate analyses were performed with respect to relapse-free survival after RP.Thirty-one patients relapsed after RP (defined as PSA > or = 0.2 ng/mL), with a median time to failure of 16 months. Median follow-up was 48 months. Kaplan-Meier relapse-free survival at 5 years was 89%, compared with 73% for PSAV < or = 2 v > 2 ng/mL/year (P = .003). On multivariate analysis, only the biopsy Gleason sum (P < .008; relative risk, > 4.8) and the preoperative PSAV (P < .04; relative risk, 3.0 to 4.7) remained significant. Patients with a PSAV of > 2 ng/mL/year were more likely to be pT3 (P = .007), have positive margins (P = .01), have tumors > 1 mL (P = .05), and possess > 10% grade 4/5 tumors (P = .04).The preoperative PSAV is a significant independent clinical factor predicting for relapse after RP and also predicts for larger, more aggressive, and more locally advanced tumors. Its inclusion will be useful in risk stratification, evaluation for alternatives to surgery, and patient selection for neoadjuvant or adjuvant therapies as part of randomized clinical trials.

    View details for DOI 10.1200/JCO.2005.01.2336

    View details for Web of Science ID 000231606300041

    View details for PubMedID 16135482

  • Genome-wide characterization of gene expression variations and DNA copy number changes in prostate cancer cell lines PROSTATE Zhao, H. J., Kim, Y., Wang, P., Lapointe, J., Tibshirani, R., Pollack, J. R., Brooks, J. D. 2005; 63 (2): 187-197

    Abstract

    The aim of this study was to characterize gene expression and DNA copy number profiles in androgen sensitive (AS) and androgen insensitive (AI) prostate cancer cell lines on a genome-wide scale.Gene expression profiles and DNA copy number changes were examined using DNA microarrays in eight commonly used prostate cancer cell lines. Chromosomal regions with DNA copy number changes were identified using cluster along chromosome (CLAC).There were discrete differences in gene expression patterns between AS and AI cells that were not limited to androgen-responsive genes. AI cells displayed more DNA copy number changes, especially amplifications, than AS cells. The gene expression profiles of cell lines showed limited similarities to prostate tumors harvested at surgery.AS and AI cell lines are different in their transcriptional programs and degree of DNA copy number alterations. This dataset provides a context for the use of prostate cancer cell lines as models for clinical cancers.

    View details for DOI 10.1002/pros.20158

    View details for Web of Science ID 000228400100007

    View details for PubMedID 15486987

  • Juvenile posttraumatic high-flow priapism: current management dilemmas JOURNAL OF PEDIATRIC SURGERY Marotte, J. B., Brooks, J. D., Sze, D., Kennedy, W. A. 2005; 40 (4)

    Abstract

    High-flow priapism results from disruption of the intercavernosal artery resulting in an arteriocavernosal fistula and is rarely encountered in the pediatric and adolescent population. Clinically it manifests as a painless, prolonged erection after perineal trauma. Treatment has ranged from expectant management to open surgical exploration with vessel ligation. Internal pudendal arteriogram and superselective embolization with autologous blood clot has emerged as a safe and effective treatment modality in the young male population. Here the authors present 3 patients with high-flow priapism and discuss management of this rare clinical entity.

    View details for DOI 10.1016/j.jpedsurg.2005.01.023

    View details for Web of Science ID 000229359300042

    View details for PubMedID 15852259

  • Reg IV: A promising marker of hormone refractory metastatic prostate cancer CLINICAL CANCER RESEARCH Gu, Z. N., Rubin, M. A., Yang, Y., DePrimo, S. E., Zhao, H. J., Horvath, S., Brooks, J. D., Loda, M., Reiter, R. E. 2005; 11 (6): 2237-2243

    Abstract

    The diagnosis and management of prostate cancer is hampered by the absence of markers capable of identifying patients with metastatic disease. In order to identify potential new markers for prostate cancer, we compared gene expression signatures of matched androgen-dependent and hormone refractory prostate cancer xenografts. One candidate gene overexpressed in a hormone refractory xenograft was homologous to the regenerating protein gene family, a group of secreted proteins expressed in the gastrointestinal tract and overexpressed in inflammatory bowel disease and cancer. This gene, Reg IV, was confirmed to be differentially expressed in the LAPC-9 hormone refractory xenograft. Consistent with its up-regulation in a hormone refractory xenograft, it is expressed in several prostate tumors after neoadjuvant hormone ablation therapy. As predicted by its sequence homology, it is secreted from transiently transfected cells. It is also expressed strongly in a majority of hormone refractory metastases represented on two high-density tissue microarrays. In comparison, it is not expressed by any normal prostate specimens and only at low levels in approximately 40% of primary tumors. These data support Reg IV as a candidate marker for hormone refractory metastatic prostate cancer.

    View details for Web of Science ID 000227770000019

    View details for PubMedID 15788672

  • Resveratrol-induced gene expression profiles in human prostate cancer cells CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Jones, S. B., DePrimo, S. E., Whitfield, M. L., Brooks, J. D. 2005; 14 (3): 596-604

    Abstract

    The transhydroxystilbene resveratrol is found at high levels in red wine and grapes, and red wine consumption may be inversely associated with prostate cancer risk. To gain insights into the possible mechanisms of action of resveratrol in human prostate cancer, we did DNA microarray analysis of the temporal transcriptional program induced by treatment of the human prostate cancer cell line LNCaP with resveratrol.Spotted DNA microarrays containing over 42,000 elements were used to obtain a global view of the effects of resveratrol on gene expression. Prostate-specific antigen (PSA) and androgen receptor (AR) expression were determined by Northern blot and immunoblot analyses. Cell proliferation was determined by the 3-(4, 5-dimethylthiazolyl-2)-2, 5-diphenyltetrazolium bromide assay and cell cycle analysis by flow cytometry.We observed time-dependent expression changes in >1,600 transcripts as early as 6 hours after treatment with resveratrol. Most striking was the modulation of a number of important genes in the androgen pathway including PSA and AR. Resveratrol also down-regulated expression of cell cycle and proliferation-specific genes involved in all phases of the cell cycle, induced negative regulators of proliferation, caused accumulation of cells at the sub-G1 and S phases of the cell cycle, and inhibited cell proliferation in a time- and dose-dependent manner.Resveratrol produces gene expression changes in the androgen axis and cell cycle regulators that may underlie its putative anticancer activities in prostate cancer.

    View details for Web of Science ID 000227545900011

    View details for PubMedID 15767336

  • Molecular targets of Doxazosin in human prostatic stromal cells PROSTATE Zhao, H. J., Lai, F., Nonn, L., Brooks, J. D., Peehl, D. M. 2005; 62 (4): 400-410

    Abstract

    We used cDNA microarray analysis to obtain insights into the mechanisms of action of doxazosin, an alpha(1)-adrenergic receptor antagonist used to treat benign prostatic hyperplasia (BPH).Hierarchical clustering analysis and significance analysis of microarray (SAM) were performed to identify genes differentially expressed between untreated stromal cells cultured from normal tissue and BPH, and changes in gene expression induced by doxazosin. Transcript levels of selected genes were validated by real-time reverse-transcription polymerase chain reaction (RT-PCR).Hierarchical clustering analyses separated untreated normal and BPH cells. Sixty-seven genes whose expression varied at least twofold after doxazosin treatment in both normal and BPH cells were identified, as were 93 genes differentially regulated in normal versus BPH cells. Molecular targets consistent with tumor necrosis factor (TNF)-alpha-related activity were identified.Normal versus BPH stromal cells differ in global gene transcription. Doxazosin induced gene expression changes relevant to proliferation/apoptosis, immune defense, cell-cell signaling/signal transduction, and transcriptional regulation.

    View details for DOI 10.1002/pros.20161

    View details for Web of Science ID 000226991500011

    View details for PubMedID 15378519

  • Positive family history of prostate cancer not associated with worse outcomes after radical prostatectomy UROLOGY Lee, K. L., Marotte, J. B., Ferrari, M. K., McNeal, J. E., Brooks, J. D., Presti, J. C. 2005; 65 (2): 311-315

    Abstract

    To determine the clinical outcomes in men with (FH) and without (NFH) a family history of prostate cancer after radical prostatectomy.We performed a retrospective analysis of 557 men with localized prostate cancer treated by radical prostatectomy between 1989 and 2000. We defined a positive FH as having one or more first-degree relatives such as a father or brother with prostate cancer. The clinical and pathologic features, as well as biochemical disease-free survival, defined as an undetectable prostate-specific antigen level (less than 0.2 ng/mL), were compared between the FH and NFH groups.Compared with the NFH group, the FH men were younger at surgery (median 62 years versus 64 years, P = 0.01), had a lower median preoperative prostate-specific antigen level (7.2 ng/mL versus 7.8 ng/mL, P = 0.05), and were more likely to have only low-grade disease at the final pathologic evaluation (26.2% versus 17.8%, P = 0.05). At a median follow-up of 7.5 years (mean 7.6 +/- 2.9 years), 17% of the FH group had biochemical disease recurrence compared with 30% in the NFH group. The actuarial disease-free survival rate at 5 and 10 years for the two groups was 86% and 80% compared with 73% and 66%, respectively (P = 0.01). When controlled for pathologic variables in a multivariate analysis, FH was not an independent predictor of disease-free survival.The association of improved disease-free survival in the FH patients may have been driven by an earlier age at diagnosis and more favorable pathologic features.

    View details for DOI 10.1016/j.urology.2004.09.005

    View details for Web of Science ID 000227307000021

    View details for PubMedID 15708044

  • Microarray Data Mining for Potential Selenium Targets in Chemoprevention of Prostate Cancer. Cancer genomics & proteomics Zhang, H., Dong, Y., Zhao, H., Brooks, J. D., Hawthorn, L., Nowak, N., Marshall, J. R., Gao, A. C., Ip, C. 2005; 2 (2): 97-114

    Abstract

    BACKGROUND: A previous clinical trial showed that selenium supplementation significantly reduced the incidence of prostate cancer. We report here a bioinformatics approach to gain new insights into selenium molecular targets that might be relevant to prostate cancer chemoprevention. MATERIALS AND METHODS: We first performed data mining analysis to identify genes which are consistently dysregulated in prostate cancer using published datasets from gene expression profiling of clinical prostate specimens. We then devised a method to systematically analyze three selenium microarray datasets from the LNCaP human prostate cancer cells, and to match the analysis to the cohort of genes implicated in prostate carcinogenesis. Moreover, we compared the selenium datasets with two datasets obtained from expression profiling of androgen-stimulated LNCaP cells. RESULTS: We found that selenium reverses the expression of genes implicated in prostate carcinogenesis. In addition, we found that selenium could counteract the effect of androgen on the expression of a subset obtained from androgen-regulated genes. CONCLUSIONS: The above information provides us with a treasure of new clues to investigate the mechanism of selenium chemoprevention of prostate cancer. Furthermore, these selenium target genes could also serve as biomarkers in future clinical trials to gauge the efficacy of selenium intervention.

    View details for PubMedID 18548127

  • A transcriptional profile of aging in the human kidney PLOS BIOLOGY Rodwell, G. E., Sonu, R., Zahn, J. M., Lund, J., Wilhelmy, J., Wang, L. L., Xiao, W. Z., Mindrinos, M., Crane, E., Segal, E., Myers, B. D., Brooks, J. D., Davis, R. W., Higgins, J., Owen, A. B., Kim, S. K. 2004; 2 (12): 2191-2201

    Abstract

    In this study, we found 985 genes that change expression in the cortex and the medulla of the kidney with age. Some of the genes whose transcripts increase in abundance with age are known to be specifically expressed in immune cells, suggesting that immune surveillance or inflammation increases with age. The age-regulated genes show a similar aging profile in the cortex and the medulla, suggesting a common underlying mechanism for aging. Expression profiles of these age-regulated genes mark not only age, but also the relative health and physiology of the kidney in older individuals. Finally, the set of aging-regulated kidney genes suggests specific mechanisms and pathways that may play a role in kidney degeneration with age.

    View details for DOI 10.1371/journal.pbio.0020427

    View details for Web of Science ID 000226099600020

    View details for PubMedID 15562319

  • Vascular invasion predicts recurrence after radical prostatectomy: Stratification of risk based on pathologic variables UROLOGY Ferrari, M. K., McNeal, J. E., Malhotra, S. M., Brooks, J. D. 2004; 64 (4): 749-753

    Abstract

    To determine whether vascular invasion (VI) is an independent predictor of prostate cancer recurrence and/or survival and to stratify risk of recurrence in patients with VI.Vascular invasion status was documented in 620 radical prostatectomy specimens with an average of 7.5 years of follow-up. The relationship between VI and other clinical and pathologic features was tested. Vascular invasion as an independent predictor of recurrence was investigated by logistic regression analysis. Survival analyses and stratification of VI patients was developed with Kaplan-Meier survival curves.Vascular invasion was identified in 110 patients (18%) and correlated significantly (P <0.0001) with high Gleason grade, extracapsular extension (EPE), seminal vesicle invasion, increasing cancer volumes, positive margins, and elevated preoperative prostate-specific antigen (PSA) levels. Logistic regression analysis demonstrated that VI was a strong and independent predictor for disease recurrence, when considered with grade, EPE, seminal vesicle invasion, lymph node involvement, cancer volume, preoperative PSA levels, and positive margins. At 12 years after radical prostatectomy, patients with VI demonstrated significantly lower disease-specific survival (P = 0.0005). Among patients with VI, stratification of grade, EPE, and the number of VI foci identified three significantly different prognostic groups.In long-term follow-up, VI was a significant predictor of prostate cancer recurrence and death after radical prostatectomy. In patients with VI, high Gleason grade, EPE, and more than five foci of VI are associated with poor prognosis.

    View details for DOI 10.1016/j.urology.2004.04.070

    View details for Web of Science ID 000224680300030

    View details for PubMedID 15491714

  • Molecular activity of 1,25-dihydroxyvitamin D-3 in primary cultures of human prostatic epithelial cells revealed by cDNA microarray analysis JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY Peehl, D. M., Shinghal, R., Nonn, L., Seto, E., Krishnan, A. V., Brooks, J. D., Feldman, D. 2004; 92 (3): 131-141

    Abstract

    1,25-Dihydroxyvitamin D(3) [1,25(OH)(2)D(3)] exerts anti-proliferative, differentiating and apoptotic effects on prostatic cells. These activities, in addition to epidemiologic findings that link Vitamin D to prostate cancer risk, support the use of 1,25(OH)(2)D(3) for prevention or therapy of prostate cancer. The molecular mechanisms by which 1,25(OH)(2)D(3) exerts antitumor effects on prostatic cells are not well-defined. In addition, there is heterogeneity among the responses of various prostate cell lines and primary cultures to 1,25(OH)(2)D(3) with regard to growth inhibition, differentiation and apoptosis. To understand the basis of these differential responses and to develop a better model of Vitamin D action in the prostate, we performed cDNA microarray analyses of primary cultures of normal and malignant human prostatic epithelial cells, treated with 50 nM of 1,25(OH)(2)D(3) for 6 and 24 h. CYP24 (25-hydroxyvitamin D(3)-24-hydroxylase) was the most highly upregulated gene. Significant and early upregulation of dual specificity phosphatase 10 (DUSP10), validated in five additional primary cultures, points to inhibition of members of the mitogen-activated protein kinase (MAPK) superfamily as a key event mediating activity of 1,25(OH)(2)D(3) in prostatic epithelial cells. The functions of other regulated genes suggest protection by 1,25(OH)(2)D(3) from oxidative stress. Overall, these results provide new insights into the molecular basis of antitumor activities of Vitamin D in prostate cells.

    View details for DOI 10.1016/j.jsbmb.2004.07.003

    View details for Web of Science ID 000226009000003

    View details for PubMedID 15555907

  • Radiotherapy after radical prostatectomy: Does transient androgen suppression improve outcomes? INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS King, C. R., Presti, J. C., Gill, H., Brooks, J., Hancock, S. L. 2004; 59 (2): 341-347

    Abstract

    The long-term biochemical relapse-free survival and overall survival were compared for patients receiving either radiotherapy (RT) alone or radiotherapy combined with a short-course of total androgen suppression for failure after radical prostatectomy.Between 1985 and 2001, a total of 122 patients received RT after radical prostatectomy at our institution. Fifty-three of these patients received a short-course of total androgen suppression (TAS) 2 months before and 2 months concurrent with RT with a nonsteroidal antiandrogen and an luteinizing hormone-releasing hormone (LHRH) agonist (combined therapy group); the remaining 69 patients received RT alone. Treatment failure was defined after postoperative RT as a detectable PSA >0.05 ng/mL. Clinical and treatment variables examined included: presurgical PSA, clinical T stage, pathologic Gleason sum (pGS), seminal vesicle (SV) involvement, lymph node involvement, surgical margins, pre-RT PSA, prostate dose, pelvic irradiation, indication for postoperative RT (salvage or adjuvant), and time interval between surgery and RT. Minimum follow-up after postoperative RT was 1 year and median follow-up was 5.9 years (maximum, 14 years) for patients receiving RT alone, and 3.9 years (maximum, 11 years) for patients receiving RT with TAS (combined therapy group). Kaplan-Meier analysis was performed for PSA failure-free survival (bNED) and for overall survival (OS). Cox proportional hazards multivariable analysis examined the influence all clinical and treatment variables predicting for bNED and OS.The median time to PSA failure after postoperative RT was 1.34 years for the combined therapy group and 0.97 years for the RT alone group (p = 0.19), with no failures beyond 5 years. At 5 years, the actuarial bNED rates were 57% for the combined therapy group compared with 31% for the RT alone group (p = 0.0012). Overall survival rates at 5 years were 100% for the combined therapy group compared with 87% for the RT alone group (p = 0.0008). For pGS or=8 the 5-year bNED rates were 65% for combined therapy and 17% for RT alone (p = 0.075). The 5-year OS rates for pGS or=8 was 100% for combined therapy and 54% for RT alone (p = 0.04). On multivariable analysis, only SV involvement (p = 0.0145) and the addition of short-course TAS to postoperative RT (p = 0.0019) were significant covariates predicting for bNED and, similarly, approached significance for overall survival (p = 0.0594 and p = 0.0856, respectively).Radiotherapy combined with a short-course TAS after radical prostatectomy appears to confer a PSA relapse-free survival advantage and possibly an overall survival advantage when compared with RT alone. The hypothesis that a transient course of androgen suppression with salvage or adjuvant RT after prostatectomy improves outcomes will need to be tested in a randomized trial.

    View details for DOI 10.1016/j.ijribp.2003.10.015

    View details for Web of Science ID 000221440800002

    View details for PubMedID 15145146

  • Lower body mass index is associated with a higher prostate cancer detection rate and less favorable pathological features in a biopsy population JOURNAL OF UROLOGY Presti, J. C., Lee, U., Brooks, J. D., Terris, M. K. 2004; 171 (6): 2199-2202

    Abstract

    Body mass index (BMI), calculated as weight in kg divided by the square of height in m, is used as an indicator of obesity. We assessed the relationship between BMI, and prostate cancer detection rates and biopsy features in a referral based biopsy population.A total of 787 consecutive patients referred for abnormal digital rectal examination and/or prostate specific antigen (PSA) greater than 4 ng/ml underwent systematic prostate biopsy. Three standard categories of BMI were considered, namely normal-less than 25, overweight-25 to 29.9 and obese-30 or greater kg/m. The presence or absence of cancer, percent of core involvement and tumor grade were correlated with BMI. Additional analyses controlled for patient age, PSA and prostate volume.For the entire population detection rates were highest in the normal BMI group compared to the overweight or obese group (52% vs 37% vs 42%, p = 0.0026). When stratified by age, this observation was true for men younger than 70 years (49% vs 32% vs 37%, p = 0.0042) but not for men 70 years or older. When only patients with PSA 10 ng/ml or less were considered, detection rates were highest in the normal BMI group (44% vs 28% vs 36%, p = 0.0061). This observation also persisted in patients younger than 70 years with PSA 10 ng/ml or less, or when only patients younger than 70 years with a total prostate volume of less than 50 cc were included. Of patients with cancer those with a normal BMI had a greater length of needle core involvement on biopsy.Normal BMI correlates with a higher cancer detection rate and larger cancers in men undergoing prostate biopsy.

    View details for DOI 10.1097/01.ju.0000124847.82541.60

    View details for Web of Science ID 000221510300018

    View details for PubMedID 15126785

  • Analysis of vitamin D-regulated gene expression in LNCaP human prostate cancer cells using cDNA microarrays PROSTATE Krishnan, A. V., Shinghal, R., Raghavachari, N., Brooks, J. D., Peehl, D. M., Feldman, D. 2004; 59 (3): 243-251

    Abstract

    1,25-dihydroxyvitamin D(3) [1,25(OH)2D3] exerts growth inhibitory, pro-differentiating, and pro-apoptotic effects on prostate cells. To better understand the molecular mechanisms underlying these actions, we employed cDNA microarrays to study 1,25(OH)2D3-regulated gene expression in the LNCaP human prostate cancer cells.mRNA isolated from LNCaP cells treated with vehicle or 50 nM 1,25(OH)2D3 for various lengths of time were hybridized to microarrays carrying approximately 23,000 genes. Some of the putative target genes revealed by the microarray analysis were verified by real-time PCR assays.1,25(OH)2D3 most substantially increased the expression of the insulin-like growth factor binding protein-3 (IGFBP-3) gene. Our analysis also revealed several novel 1,25(OH)2D3-responsive genes. Interestingly, some of the key genes regulated by 1,25(OH)2D3 are also androgen-responsive genes. 1,25(OH)2D3 also down-regulated genes that mediate androgen catabolism.The putative 1,25(OH)2D3 target genes appear to be involved in a variety of cellular functions including growth regulation, differentiation, membrane transport, cell-cell and cell-matrix interactions, DNA repair, and inhibition of metastasis. The up-regulation of IGFBP-3 gene has been shown to be crucial in 1,25(OH)2D3-mediated inhibition of LNCaP cell growth. 1,25(OH)2D3 regulation of androgen-responsive genes as well as genes involved in androgen catabolism suggests that there are interactions between 1,25(OH)2D3 and androgen signaling pathways in LNCaP cells. Further studies on the role of these genes and others in mediating the anti-cancer effects of 1,25(OH)2D3 may lead to better approaches to the prevention and treatment of prostate cancer.

    View details for DOI 10.1002/pros.20006

    View details for Web of Science ID 000220910600003

    View details for PubMedID 15042599

  • Time trends in pathologic features of radical prostatectomy - impact of family history UROLOGIC ONCOLOGY-SEMINARS AND ORIGINAL INVESTIGATIONS Marotte, J. B., Ferrari, M. K., McNeal, J. E., Brooks, J. D., Presti, J. C. 2004; 22 (3): 169-173

    Abstract

    We investigated whether the clinical or pathological features of patients with a family history of prostate cancer treated by radical prostatectomy differ from patients without a family history. A retrospective analysis of patients treated by radical prostatectomy between 1989 through 2000 was performed. The clinical and pathologic features of patients with a family history (defined as at least one first-degree relative with prostate cancer, N = 103) were compared with those with no family history (N = 456). In addition, the patients were stratified into two groups, those treated from 1989 through 1992 and those treated after 1992. In the entire cohort from 1989 through 2000, patients with a family history had a greater proportion of well-differentiated tumors than the NFH group (26.2% vs. 17.8%; P = 0.05). From 1989 to 1992 there was no statistical difference between patients with a family history (FH) and those without a family history (NFH) with respect to age, prostate specific antigen (PSA), PSA density, clinical or pathologic stage, Gleason grade, or total tumor volume. However, after 1992 the FH group tended to be younger than the NFH group (61.1 vs. 63.4; P = 0.02) and have a lower PSA (6.8 vs. 7.9; P = 0.01) at the time of diagnosis. We believe these differences are predominantly driven by more aggressive screening in patients with a family history of prostate cancer rather than any true genetic differences.

    View details for DOI 10.1016/j.urolonc.2004.04.003

    View details for Web of Science ID 000223195600002

    View details for PubMedID 15271309

  • Biochemical remission after resection of prostate cancer lung metastasis UROLOGY Chao, D. H., Higgins, J. P., Brooks, J. D. 2004; 63 (3)

    Abstract

    Once metastatic, prostate cancer was regarded as a systemic disease that is not amenable to surgical therapy. We present a case of a solitary pulmonary recurrence of prostate cancer after radical prostatectomy that was resected, resulting in 12 years of biochemical remission without additional therapy.

    View details for DOI 10.1016/j.urology.2003.10.069

    View details for Web of Science ID 000220223500041

    View details for PubMedID 15028469

  • Gene expression in the normal adult human kidney assessed by complementary DNA microarray MOLECULAR BIOLOGY OF THE CELL Higgins, J. P., Wang, L. L., Kambham, N., Montgomery, K., Mason, V., Vogelmann, S. U., Lemley, K. V., Brown, P. O., Brooks, J. D., van de Rijn, M. 2004; 15 (2): 649-656

    Abstract

    The kidney is a highly specialized organ with a complex, stereotyped architecture and a great diversity of functions and cell types. Because the microscopic organization of the nephron, the functional unit of the kidney, has a consistent relationship to the macroscopic anatomy of the kidney, knowledge of the characteristic patterns of gene expression in different compartments of the kidney could provide insight into the functions and functional organization of the normal nephron. We studied gene expression in dissected renal lobes of five adult human kidneys using cDNA microarrays representing approximately 30,000 different human genes. Total RNA was isolated from sections of the inner and outer cortex, inner and outer medulla, papillary tips, and renal pelvis and from glomeruli isolated by sieving. The results revealed unique and highly distinctive patterns of gene expression for glomeruli, cortex, medulla, papillary tips, and pelvic samples. Immunohistochemical staining using selected antisera confirmed differential expression of several cognate proteins and provided histological localization of expression within the nephron. The distinctive patterns of gene expression in discrete portions of the kidney may serve as a resource for further understanding of renal physiology and the molecular and cellular organization of the nephron.

    View details for DOI 10.1091/mbc.E03-06-0432

    View details for Web of Science ID 000188718900024

    View details for PubMedID 14657249

  • Diverse effects of methylseleninic acid on the transcriptional program of human prostate cancer cells MOLECULAR BIOLOGY OF THE CELL Zhao, H. J., Whitfield, M. L., Xu, T., Botstein, D., Brooks, J. D. 2004; 15 (2): 506-519

    Abstract

    Methylseleninic acid (MSA) has been shown to have potent anticancer activity and is an excellent compound for studying the anticancer effects of selenium in vitro. To gain insights into the effects of MSA in prostate cancer, we characterized the global transcriptional response of LNCaP, an androgen-sensitive human prostate cancer cell line, to MSA by using high-density cDNA microarrays. We identified 951 genes whose expression shows striking dose- and time-dependent changes in response to 3-30 microM MSA over the time course of 48 h. Transcript levels of many cell cycle-regulated genes change in response to MSA, suggesting that MSA inhibits proliferation. Consistent with these gene expression changes, cell proliferation, monitored by carboxyfluoroscein succinimidyl ester staining, was decreased after MSA treatment, and an accumulation of cells at G0/G1 phase was detected by flow cytometry. Surprisingly, MSA also modulated expression of many androgen-regulated genes, suppressed androgen receptor (AR) expression at both mRNA and protein level, and decreased levels of prostate specific antigen secreted into the medium. Low concentrations of MSA also induced significant increases in transcript levels of phase 2 detoxification enzymes and induced NADPH dehydrogenase, quinone 1 enzymatic activity, a surrogate marker of global phase 2 enzyme activity. Our results suggest that MSA may protect against prostate cancer by inhibiting cell proliferation, by modulating the expression of AR and AR-regulated genes and by inducing carcinogen defenses.

    View details for DOI 10.1091/mbc.E03-07-0501

    View details for Web of Science ID 000188718900012

    View details for PubMedID 14617803

  • Gene expression profiling identifies clinically relevant subtypes of prostate cancer PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Lapointe, J., Li, C., Higgins, J. P., van de Rijn, M., Bair, E., Montgomery, K., Ferrari, M., Egevad, L., Rayford, W., Bergerheim, U., Ekman, P., DeMarzo, A. M., Tibshirani, R., Botstein, D., Brown, P. O., Brooks, J. D., Pollack, J. R. 2004; 101 (3): 811-816

    Abstract

    Prostate cancer, a leading cause of cancer death, displays a broad range of clinical behavior from relatively indolent to aggressive metastatic disease. To explore potential molecular variation underlying this clinical heterogeneity, we profiled gene expression in 62 primary prostate tumors, as well as 41 normal prostate specimens and nine lymph node metastases, using cDNA microarrays containing approximately 26,000 genes. Unsupervised hierarchical clustering readily distinguished tumors from normal samples, and further identified three subclasses of prostate tumors based on distinct patterns of gene expression. High-grade and advanced stage tumors, as well as tumors associated with recurrence, were disproportionately represented among two of the three subtypes, one of which also included most lymph node metastases. To further characterize the clinical relevance of tumor subtypes, we evaluated as surrogate markers two genes differentially expressed among tumor subgroups by using immunohistochemistry on tissue microarrays representing an independent set of 225 prostate tumors. Positive staining for MUC1, a gene highly expressed in the subgroups with "aggressive" clinicopathological features, was associated with an elevated risk of recurrence (P = 0.003), whereas strong staining for AZGP1, a gene highly expressed in the other subgroup, was associated with a decreased risk of recurrence (P = 0.0008). In multivariate analysis, MUC1 and AZGP1 staining were strong predictors of tumor recurrence independent of tumor grade, stage, and preoperative prostate-specific antigen levels. Our results suggest that prostate tumors can be usefully classified according to their gene expression patterns, and these tumor subtypes may provide a basis for improved prognostication and treatment stratification.

    View details for DOI 10.1073/pnas.0304146101

    View details for Web of Science ID 000188555400023

    View details for PubMedID 14711987

  • Gene expression patterns in human embryonic stem cells and human pluripotent germ cell tumors PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Sperger, J. M., Chen, X., Draper, J. S., Antosiewicz, J. E., Chon, C. H., Jones, S. B., Brooks, J. D., Andrews, P. W., Brown, P. O., Thomson, J. A. 2003; 100 (23): 13350-13355

    Abstract

    Remarkably little is known about the transcriptional profiles of human embryonic stem (ES) cells or the molecular mechanisms that underlie their pluripotency. To identify commonalties among the transcriptional profiles of different human pluripotent cells and to search for clues into the genesis of human germ cell tumors, we compared the expression profiles of human ES cell lines, human germ cell tumor cell lines and tumor samples, somatic cell lines, and testicular tissue samples by using cDNA microarray analysis. Hierarchical cluster analysis of gene expression profiles showed that the five independent human ES cell lines clustered tightly together, reflecting highly similar expression profiles. The gene expression patterns of human ES cell lines showed many similarities with the human embryonal carcinoma cell samples and more distantly with the seminoma samples. We identified 895 genes that were expressed at significantly greater levels in human ES and embryonal carcinoma cell lines than in control samples. These genes are candidates for involvement in the maintenance of a pluripotent, undifferentiated phenotype.

    View details for DOI 10.1073/pnas.2235735100

    View details for Web of Science ID 000186573700044

    View details for PubMedID 14595015

  • Gene expression patterns in renal cell carcinoma assessed by complementary DNA microarray AMERICAN JOURNAL OF PATHOLOGY Higgins, J. P., Shinghal, R., Gill, H., Reese, J. H., Terris, M., Cohen, R. J., Fero, M., Pollack, J. R., van de Rijn, M., Brooks, J. D. 2003; 162 (3): 925-932

    Abstract

    Renal cell carcinoma comprises several histological types with different clinical behavior. Accurate pathological characterization is important in the clinical management of these tumors. We describe gene expression profiles in 41 renal tumors determined by using DNA microarrays containing 22,648 unique cDNAs representing 17,083 different UniGene Clusters, including 7230 characterized human genes. Differences in the patterns of gene expression among the different tumor types were readily apparent; hierarchical cluster analysis of the tumor samples segregated histologically distinct tumor types solely based on their gene expression patterns. Conventional renal cell carcinomas with clear cells showed a highly distinctive pattern of gene expression. Papillary carcinomas formed a tightly clustered group, as did tumors arising from the distal nephron and the normal kidney samples. Surprisingly, conventional renal cell carcinomas with granular cytoplasm were heterogeneous, and did not resemble any of the conventional carcinomas with clear cytoplasm in their pattern of gene expression. Characterization of renal cell carcinomas based on gene expression patterns provides a revised classification of these tumors and has the potential to supply significant biological and clinical insights.

    View details for Web of Science ID 000181215000023

    View details for PubMedID 12598325

  • Biochemical recurrence without PSA progression characterizes a subset of patients after radical prostatectomy. Prostate-specific antigen. Urology Shinghal, R., Yemoto, C., McNeal, J. E., Brooks, J. D. 2003; 61 (2): 380-385

    Abstract

    To characterize a subset of patients with biochemical recurrence after radical prostatectomy but with little, if any, subsequent rise in serum prostate-specific antigen (PSA) and no clinical progression during long-term follow-up.Of a series of 600 patients, 158 with biochemical recurrence after radical prostatectomy were examined. We identified a subset with measurable serum PSA levels during long-term follow-up, but with very low PSA velocity and no clinical recurrence. Serum PSA was measured with the ultrasensitive TOSOH assay with a PSA recurrence defined as a serum PSA of 0.07 ng/mL or greater.We identified 14 patients (8.8% of biochemical recurrences) with a detectable serum PSA level after radical prostatectomy yet without clinical or PSA progression at a mean follow-up after radical prostatectomy of 10.3 years. The mean time to PSA recurrence was 5.8 years, and the mean PSA velocity after recurrence was 0.028 ng/mL/yr. No clinical or pathologic features were found that could be used to identify this subset of patients.A subset of patients with biochemical recurrence after radical prostatectomy will not exhibit a progressive rise in serum PSA or clinical progression at 10 years follow-up. This suggests that serum PSA kinetics should be observed after biochemical recurrence before adjuvant hormonal therapy or radiotherapy.

    View details for PubMedID 12597952

  • Differential gene-expression patterns in genital fibroblasts of normal males and 46,XY females with androgen insensitivity syndrome: evidence for early programming involving the androgen receptor GENOME BIOLOGY Holterhus, P. M., Hiort, O., Demeter, J., Brown, P. O., Brooks, J. D. 2003; 4 (6)

    Abstract

    Androgen insensitivity syndrome (AIS) comprises a range of phenotypes from male infertility to complete feminization. Most individuals with AIS carry germline mutations of the androgen receptor (AR) that interfere with or ablate its function. As genital fibroblasts retain expression of the AR in vitro, we used genital skin fibroblasts from normal males and 46,XY females with complete AIS due to known AR mutations to gain insights into the role of the AR in human genital differentiation.Using DNA microarrays representing 32,968 different genes, we identified 404 transcripts with significant differences in transcription levels between genital skin fibroblasts cultured from normal and AIS-affected individuals. Gene-cluster analyses uncovered coordinated expression of genes involved in key processes of morphogenesis. On the basis of animal studies and human genetic syndromes, several of these genes are known to have specific roles in genital differentiation. Remarkably, genital fibroblasts from both normal and AIS-affected individuals showed no transcriptional response to dihydrotestosterone treatment despite expression of the AR.The results suggest that in addition to differences in the anatomic origin of the cells, androgen signaling during prenatal development contributes to setting long-lasting, androgen-independent transcriptional programs in genital fibroblasts. Our findings have broad implications in understanding the establishment and the stability of sexual dimorphism in human genital development.

    View details for Web of Science ID 000183720100007

    View details for PubMedID 12801411

  • Expression of FKBP12 in benign and malignant vascular endothelium - An immunohistochemical study on conventional sections and tissue microarrays AMERICAN JOURNAL OF SURGICAL PATHOLOGY Higgins, J. P., Montgomery, K., Wang, L. L., Domanay, E., Warnke, R. A., Brooks, J. D., van de Rijn, M. 2003; 27 (1): 58-64

    Abstract

    FKBP12 is a cytosolic FK506 binding protein that interacts with calcineurin and thereby mediates the immunosuppressive effects of FK506. Because initial immunohistochemical staining showed abundant expression of FKBP12 in vascular endothelial cells, we evaluated whether it could serve as a marker for vascular neoplasms. We performed immunohistochemical staining of conventional sections from formalin-fixed, paraffin-embedded tissue from 59 benign and malignant vascular neoplasms using a polyclonal rabbit antiserum against FKBP12. Western blot analysis of tissue from 6 angiosarcomas showed a single band at 12 kD, consistent with the published molecular weight for the FKBP12 protein. Together, CD31, CD34, and FKBP12 identified all 59 vascular neoplasms in this study. Specificity of immunohistochemical staining was assessed on 1,321 tissues represented on 7 tissue microarrays. All proteins were occasionally expressed in non-vascular tissue. Six of 8 vascular neoplasms represented on the arrays stained for FKBP12, as did normal vessels in numerous cores. The polyclonal antiserum shows comparable sensitivity (94.9%) and specificity (96.5%) to CD34 and CD31 and may be a useful additional marker for vascular differentiation. Because we have evaluated a large number of tissues by tissue microarray, we anticipate that our estimate of the specificity of immunostaining for FKBP12 as a marker for vascular endothelium will be accurate. In addition, our findings may explain the toxic effects of FK506 on vascular endothelium of the kidney.

    View details for Web of Science ID 000180144000007

    View details for PubMedID 12502928

  • Identification of potential prostate cancer preventive agents through induction of quinone reductase in vitro CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Brooks, J. D., Goldberg, M. F., Nelson, L. A., Wu, D., Nelson, W. G. 2002; 11 (9): 868-875

    Abstract

    Human prostate cancer is characterized by an early and near-universal loss of expression of the phase 2 enzyme glutathione S-transferase-pi (GSTP1). We hypothesize that a mechanism-based prostate cancer preventive strategy could involve induction of phase 2 enzymes within the prostate to compensate for the loss of GSTP1 expression. NAD[P]H:(quinone-acceptor) oxidoreductase (quinone reductase or QR) enzymatic activity, a surrogate of phase 2 enzyme response, was measured after treating the human prostate cancer cell line LNCaP with known phase 2 enzyme-inducing agents from 10 distinct chemical classes. QR enzymatic activity was assayed in microtiter plates using the menadione-coupled reduction of tetrazolium dye. Degree of induction was expressed as fold-increase over control and corrected for toxicity. Compounds were also tested in LNCaP-5-aza-C, an LNCaP subline selected in 5-aza-cytidine that expresses GSTP1, and in the human liver cell line HepG2. LNCaP showed robust induction of QR enzymatic activity after treatment with a subset of the phase 2 enzyme-inducing agents. All Michael acceptors were effective at inducing QR activity in LNCaP. Some phenolic antioxidants, heavy metal salts, and quinones also significantly increased QR activity, although inducer potency varied widely within these classes of compounds. Some of the isothiocyanates, mercaptans, bifunctional inducers, and trivalent arsenicals also produced modest QR induction, but peroxides and dithiolethiones were inactive. LNCaP-5-aza-C and LNCaP responded similarly to all compounds, but the pattern of response for HepG2 differed significantly. The differences in QR responsiveness between the prostate cell lines and HepG2 suggest that prostate tissues may have a unique pattern of response to phase 2-inducing agents distinct from other tissue types. Our data suggest that measurement of QR induction in prostate cancer cell lines may help identify potential cancer chemopreventive agents effective in the prostate.

    View details for Web of Science ID 000177967900011

    View details for PubMedID 12223431

  • Polymorphisms in the androgen receptor and type II 5 alpha-reductase genes and prostate cancer prognosis PROSTATE Shibata, A., Garcia, M. I., Cheng, I., Stamey, T. A., McNeal, J. E., Brooks, J. D., Henderson, S., Yemoto, C. E., Peehl, D. M. 2002; 52 (4): 269-278

    Abstract

    Cytosine-adenine-guanine repeat length of the androgen receptor gene and the A49T and V89L polymorphisms of the 5 alpha-reductase (SRD5A2) gene have been associated with prostate cancer.We investigated the relationship of the three genetic polymorphisms to tumor grade among 211 men who had undergone radical prostatectomy. Subjects had prostate cancer <3 cm(3) with a percentage of cancer represented by Gleason grade 4 or 5 (% Gleason grade 4/5) of either > or = 20% or < or = 5%. We also examined the association between those genetic markers and prostate specific antigen (PSA) failure among 112 subjects with > or = 20% Gleason grade 4/5.In cross-sectional analysis, none of the polymorphisms was a significant predictor of % Gleason grade 4/5. In longitudinal analysis, the LL genotype at the V89L site was associated with statistically significant four- to sixfold increase in PSA failure risk after adjustment for clinicopathologic variables.We observed poorer prognosis among men with the LL genotype at codon 89 of the SRD5A2 gene. Lack of consistency between studies must be resolved before clinical utility of this marker is established.

    View details for DOI 10.1002/pros.10119

    View details for Web of Science ID 000177541200003

    View details for PubMedID 12210487

  • Microarray analysis in prostate cancer research. Current opinion in urology Brooks, J. D. 2002; 12 (5): 395-399

    Abstract

    Microarray technologies are now being used to analyse prostate tumors and to gain insights into prostate cancer biology. This review provides a background on microarray technology, reviews recent applications of these techniques in prostate cancer research, and discusses the potential application of this technology to patient care.An analysis of genome-wide changes in expression has identified several hundred genes differentially expressed by normal and malignant prostate tissues. Some, such as hepsin, not only show increased expression in cancer, but can also provide prognostic information on prostate tumors based on their level of expression. Microarrays have also been used to characterize gene expression changes associated with androgen stimulation, the activation of EGR1 pathways, and prostate epithelial cellular senescence.Microarray analysis of gene expression in prostate cancer is in its infancy. Future work will probably yield new diagnostic and prognostic markers, provide insight into prostate cancer biology, and aid in identifying new therapeutic strategies.

    View details for PubMedID 12172426

  • Silencing of pi-class glutathione S-transferase in MDA PCa 2a and MDA PCa 2b cells PROSTATE Vidanes, G. M., Paton, V., Wallen, E., Peehl, D. M., Navone, N., Brooks, J. D. 2002; 51 (4): 225-230

    Abstract

    Loss of expression of the glutathione S-transferase-pi (GSTP1) is the most common genetic alteration described in human prostate cancer, occurring in virtually all tumors regardless of grade or stage. Of the available human prostate cancer cell lines, only LNCaP mirrors this phenotype. We investigated whether the prostate cancer cell lines MDA PCa 2a and MDA PCa 2b share this phenotype.GSTP1 protein and mRNA levels were assessed in the MDA PCa 2a and MDA PCa 2b cell lines by Western and Northern blot. DNA methylation was evaluated by Southern blot analysis of genomic DNA digested with the methylation-sensitive restriction enzymes BssHII, NotI, and SacII. Re-expression of GSTP1 was determined by RT-PCR following treatment with 5-azacytidine, a DNA methyltransferase inhibitor, and/or the histone deacetylase inhibitor trichostatin A (TSA).Like all human prostatic carcinomas in vivo, both the MDA PCa 2a and 2b cell lines lack protein and mRNA expression of GSTP1. This lack of expression is associated with methylation in the GSTP1 gene promoter. Treatment with the methyltransferase inhibitor 5-azacytidine resulted in re-expression of GSTP1. By itself, TSA did not result in re-expression of GSTP1, nor did it augment expression induced by 5-azacytidine.MDA PCa 2a and 2b appear to be useful models of human prostatic carcinoma in that they lack expression of GSTP1 due to gene silencing via promoter methylation. Inhibition of histone acetylation does not appear to affect GSTP1 expression.

    View details for DOI 10.1002/pros.10093

    View details for Web of Science ID 000175909900001

    View details for PubMedID 11987150

  • Novel pathways associated with bypassing cellular senescence in human prostate epithelial cells JOURNAL OF BIOLOGICAL CHEMISTRY Schwarze, S. R., DePrimo, S. E., Grabert, L. M., Fu, V. X., Brooks, J. D., Jarrard, D. F. 2002; 277 (17): 14877-14883

    Abstract

    Cellular senescence forms a barrier that inhibits the acquisition of an immortal phenotype, a critical feature in tumorigenesis. The inactivation of multiple pathways that positively regulate senescence are required for immortalization. To identify these pathways in an unbiased manner, we performed DNA microarray analyses to assess the expression of 20,000 genes in human prostate epithelial cells (HPECs) passaged to senescence. These gene expression patterns were then compared with those of HPECs immortalized with the human Papillomavirus 16 E7 oncoprotein. Senescent cells display gene expression patterns that reflect their nonproliferative, differentiated phenotype and express secretory proteases and extracellular matrix components. A comparison of genes transcriptionally up-regulated in senescence to those in which expression is significantly down-regulated in immortalized HPECs identified three genes: the chemokine BRAK, DOC1, and a member of the insulin-like growth factor axis, IGFBP-3. Expression of these genes is found to be uniformly lost in human prostate cancer cell lines and xenografts, and previously, their inactivation was documented in tumor samples. Thus, these genes may function in novel pathways that regulate senescence and are inactivated during immortalization. These changes may be critical not only in allowing cells to bypass senescence in vitro but in the progression of prostate cancer in vivo.

    View details for DOI 10.1074/jbc.M200373200

    View details for Web of Science ID 000175203000068

    View details for PubMedID 11836256

  • Anatomy of the rectourethralis muscle EUROPEAN UROLOGY Brooks, J. D., Eggener, S. E., Chao, W. M. 2002; 41 (1): 94-100

    Abstract

    To define the true anatomic structure of the rectourethralis muscle.Cross-sectional images of fresh tissues from the Visible Human Data set were reviewed. Three-dimensional computer reconstructions of the rectourethralis and surrounding structures were generated from these data using a high speed computer and imaging software. The structure of rectourethralis was confirmed by dissection of fresh cadavers.The rectourethralis arises deep within the substance of the smooth muscle of the rectal wall as two limbs of muscle which face posterolaterally. These limbs fuse into a single thick muscle which inserts into the perineal body.In contrast to all previous descriptions in the literature, the rectourethralis is a Y-shaped muscle which arises within the substance of the rectal wall deep to the outer longitudinal smooth muscle. This shape is consistent with the muscle's embryologic origin. Knowledge of the structure of the rectourethralis muscle will help urologists avoid rectal injuries during perineal approaches to the prostate.

    View details for Web of Science ID 000174457200021

    View details for PubMedID 11999473

  • Transcriptional programs activated by exposure of human prostate cancer cells to androgen GENOME BIOLOGY DePrimo, S. E., Diehn, M., Nelson, J. B., Reiter, R. E., Matese, J., Fero, M., Tibshirani, R., Brown, P. O., Brooks, J. D. 2002; 3 (7)

    Abstract

    Androgens are required for both normal prostate development and prostate carcinogenesis. We used DNA microarrays, representing approximately 18,000 genes, to examine the temporal program of gene expression following treatment of the human prostate cancer cell line LNCaP with a synthetic androgen.We observed statistically significant changes in levels of transcripts of more than 500 genes. Many of these genes were previously reported androgen targets, but most were not previously known to be regulated by androgens. The androgen-induced expression programs in three additional androgen-responsive human prostate cancer cell lines, and in four androgen-independent subclones derived from LNCaP, shared many features with those observed in LNCaP, but some differences were observed. A remarkable fraction of the genes induced by androgen appeared to be related to production of seminal fluid and these genes included many with roles in protein folding, trafficking, and secretion.Prostate cancer cell lines retain features of androgen responsiveness that reflect normal prostatic physiology. These results provide a broad view of the effect of androgen signaling on the transcriptional program in these cancer cells, and a foundation for further studies of androgen action.

    View details for Web of Science ID 000207581200008

    View details for PubMedID 12184806

  • Plasma selenium level before diagnosis and the risk of prostate cancer development JOURNAL OF UROLOGY Brooks, J. D., Metter, E. J., Chan, D. W., Sokoll, L. J., Landis, P., Nelson, W. G., Muller, D., Andres, R., Carter, H. B. 2001; 166 (6): 2034-2038

    Abstract

    Epidemiological studies and a randomized intervention trial suggest that the risk of prostate cancer may be reduced by selenium intake. We investigated whether plasma selenium level before diagnosis correlated with the risk of later developing prostate cancer.A case control study was performed on men from the Baltimore Longitudinal Study of Aging registry, including 52 with known prostate cancer and 96 age matched controls with no detectable prostatic disease. Plasma selenium was measured at an average time plus or minus standard deviation of 3.83 +/- 1.85 years before the diagnosis of prostate cancer by graphite furnace atomic absorption spectrophotometry. Adjusted odds ratio and 95% confidence interval were computed with logistic regression.After correcting for years before diagnosis, body mass index, and smoking and alcohol use history, higher selenium was associated with a lower risk of prostate cancer. Compared with the lowest quartile of selenium (range 8.2 to 10.7 microg./dl.), the odds ratios of the second (10.8 to 11.8), third (11.9 to 13.2) and fourth (13.3 to 18.2) quartiles were 0.15 (95% confidence interval 0.05 to 0.50), 0.21 (0.07 to 0.68) and 0.24 (0.08 to 0.77, respectively, p =0.01). Furthermore, plasma selenium decreased significantly with patient age (p <0.001).Low plasma selenium is associated with a 4 to 5-fold increased risk of prostate cancer. These results support the hypothesis that supplemental selenium may reduce the risk of prostate cancer. Because plasma selenium decreases with patient age, supplementation may be particularly beneficial to older men.

    View details for Web of Science ID 000172133900004

    View details for PubMedID 11696701

  • GSTP1 CpG island hypermethylation is responsible for the absence of GSTP1 expression in human prostate cancer cells AMERICAN JOURNAL OF PATHOLOGY Lin, X. H., Tascilar, M., Lee, W. H., Vles, W. J., Lee, B. H., Veeraswamy, R., Asgari, K., Freije, D., Van Rees, B., Gage, W. R., Bova, G. S., Isaacs, W. B., Brooks, J. D., DeWeese, T. L., De Marzo, A. M., Nelson, W. G. 2001; 159 (5): 1815-1826

    Abstract

    GSTP1 CpG island hypermethylation is the most common somatic genome alteration described for human prostate cancer (PCA); lack of GSTP1 expression is characteristic of human PCA cells in vivo. We report here that loss of GSTP1 function may have been selected during the pathogenesis of human PCA. Using a variety of techniques to detect GSTP1 CpG island DNA hypermethylation in PCA DNA, we found only hypermethylated GSTP1 alleles in each PCA cell in all but two PCA cases studied. In these two cases, CpG island hypermethylation was present at only one of two GSTP1 alleles in PCA DNA. In one of the cases, DNA hypermethylation at one GSTP1 allele and deletion of the other GSTP1 allele were evident. In the other case, an unmethylated GSTP1 allele was detected, accompanied by abundant GSTP1 expression. GSTP1 CpG island DNA hypermethylation was responsible for lack of GSTP1 expression by LNCaP PCA cells: treatment of the cells with 5-azacytidine (5-aza-C), an inhibitor of DNA methyltransferases, reversed the GSTP1 promoter DNA hypermethylation, activated GSTP1 transcription, and restored GSTP1 expression. GSTP1 promoter activity, assessed via transfection of GSTP1 promoter-CAT reporter constructs in LNCaP cells, was inhibited by SssI-catalyzed CpG dinucleotide methylation. Remarkably, although selection for loss of GSTP1 function may be inferred for human PCA, GSTP1 did not act like a tumor suppressor gene, as LNCaP cells expressing GSTP1, either after 5-aza-C treatment or as a consequence of transfection with GSTP1 cDNA, grew well in vitro and in vivo. Perhaps, GSTP1 inactivation may render prostatic cells susceptible to additional genome alterations, caused by electrophilic or oxidant carcinogens, that provide a selective growth advantage.

    View details for Web of Science ID 000171988000024

    View details for PubMedID 11696442

  • Potent induction of phase 2 enzymes in human prostate cells by sulforaphane CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Brooks, J. D., Paton, V. G., Vidanes, G. 2001; 10 (9): 949-954

    Abstract

    Two population-based, case-control studies have documented reduced risk of prostate cancer in men who consume cruciferous vegetables. Cruciferae contain high levels of the isothiocyanate sulforaphane. Sulforaphane is known to bolster the defenses of cells against carcinogens through up-regulation of enzymes of carcinogen defense (phase 2 enzymes). Prostate cancer is characterized by an early and near universal loss of expression of the phase 2 enzyme glutathione S-transferase (GST)-pi. We tested whether sulforaphane may act in prostatic cells by increasing phase 2 enzyme expression. The human prostate cancer cell lines LNCaP, MDA PCa 2a, MDA PCa 2b, PC-3, and TSU-Pr1 were treated with 0.1-15 microM sulforaphane in vitro. LNCaP was also treated with an aqueous extract of broccoli sprouts. Quinone reductase enzymatic activity, a surrogate of global phase 2 enzyme activity, was assayed by the menadione-coupled reduction of tetrazolium dye. Expression of NQO-1, GST-alpha, gamma-glutamylcysteine synthetase-heavy and -light chains, and microsomal GST was assessed by Northern blot analysis. Sulforaphane and broccoli sprout extract potently induce quinone reductase activity in cultured prostate cells, and this induction appears to be mediated by increased transcription of the NQO-1 gene. Sulforaphane also induces expression of gamma-glutamylcysteine synthetase light subunit but not the heavy subunit, and this induction is associated with moderate increases in intracellular glutathione levels. Microsomal and alpha-class glutathione transferases were also induced transcriptionally. Sulforaphane induces phase 2 enzyme expression and activity significantly in human prostatic cells. This induction is accompanied by, but not because of, increased intracellular glutathione synthesis. Our findings may help explain the observed inverse correlation between consumption of cruciferae and prostate cancer risk.

    View details for Web of Science ID 000170899000006

    View details for PubMedID 11535546

  • Prevention of prostate cancer HEMATOLOGY-ONCOLOGY CLINICS OF NORTH AMERICA DePrimo, S. E., Shinghal, R., Vidanes, G., Brooks, J. D. 2001; 15 (3): 445-?

    Abstract

    Strategies for reducing the occurrence of prostate cancers will be critical in limiting the morbidity and mortality of this disease. The long latency period of prostate tumors and improved understanding of prostate carcinogenesis suggest opportunities for effective preventive measures. Because androgen is integral to prostatic carcinogenesis, several preventive strategies under investigation target the androgen axis. Epidemiologic and basic studies implicate dietary factors in prostate cancer development and suggest that altering diet may influence prostate cancer risk and progression. Many of the micronutrients with preventive potential have antioxidant properties; cellular defenses against oxidative stresses are likely to be crucial in reducing prostate carcinogenesis. This article summarizes the current status and opportunities in prostate cancer prevention.

    View details for Web of Science ID 000170718000004

    View details for PubMedID 11525290

  • New molecular approaches for identifying novel targets, mechanisms, and biomarkers for prostate cancer chemopreventive agents. Urology Williams, E. D., Brooks, J. D. 2001; 57 (4): 100-102

    Abstract

    Recently developed complementary DNA (cDNA) microarray technology allows simultaneous assessment of expression on many hundreds or thousands of genes simultaneously. This technology holds great promise for providing new insights into prostate carcinogenesis that will reveal new targets for preventive intervention strategies. In addition, this technology will deepen understanding of the means by which putative preventive compounds exert their effects, generating molecular genetic biomarkers of treatment efficacy. Several putative preventive agents are currently under investigation, and development of novel preventive strategies poses significant challenges. High throughput approaches, such as cDNA microarrays, will speed discovery and progress in prostate cancer chemoprevention.

    View details for PubMedID 11295605

  • Role of cytologic criteria in the histologic diagnosis of gleason grade 1 prostatic adenocarcinoma HUMAN PATHOLOGY McNeal, J. E., Cohen, R. J., Brooks, J. D. 2001; 32 (4): 441-446

    Abstract

    Gleason grade 1 prostatic adenocarcinoma is defined by its gland architecture, which resembles that of benign prostate more than any other grade. It is characterized by closely spaced glands and expansile tumor border. Cytoplasm is clear to pale, superficially identical to benign nodular hyperplasia (BPH). However, there is recent evidence that prostatic "clear-cell carcinoma," including grade 1, has cytoplasm whose composition is distinctively different from BPH, being filled with lipid rather than with the protein-rich granules that characterize benign secretory cells or the nongranular protein matrix of other prostate cancers. We reasoned that grade 1 cancer might also have additional distinctive cellular features; we tested this hypothesis by observations on 17 grade 1 carcinoma foci found as components of transition zone clear-cell cancers. Unlike BPH secretory cells, cells of grade 1 cancer were uniformly large with even, straight borders laterally and luminally. Nuclei appeared sometimes benign but were fixed in a basal row dissimilar to the uneven distribution in BPH. Nuclear pyknotic foci, blue-tinged cytoplasm, and abundant dense luminal secretion were distinctively common. Immunostain for glutathione-S transferase was negative in grade 1 cancer but lightly positive in BPH secretory cells. These cytologic findings were proposed to be useful as diagnostic clues, especially in small-needle biopsy samples, in which architecture may be difficult to interpret. HUM PATHOL 32:441-446.

    View details for Web of Science ID 000168395100012

    View details for PubMedID 11331962

  • GSTP1 CpG island DNA hypermethylation in hepatocellular carcinomas INTERNATIONAL JOURNAL OF ONCOLOGY Tchou, J. C., Lin, X. H., Freije, D., Isaacs, W. B., Brooks, J. D., Rashid, A., De Marzo, A. M., Kanai, Y., Hirohashi, S., Nelson, W. G. 2000; 16 (4): 663-676

    Abstract

    Glutathione S-transferases, enzymes that defend cells against damage mediated by oxidant and electrophilic carcinogens, may be critical determinants of cancer pathogenesis. We report here that the pathogenesis of hepatocellular carcinoma (HCC), one of the most common cancers in the world, frequently involves an accumulation of somatic DNA methylation changes at GSTP1, the gene encoding the pi-class glutathione S-transferase. For our study, Hep3B HCC cells and a cohort of 20 HCC tissue specimens were subjected to analysis for GSTP1 expression and for somatic GSTP1 alterations. GSTP1 DNA hypermethylation in HCC DNA was assessed by Southern blot analysis, via a polymerase chain reaction (PCR) assay, and by using a genomic sequencing approach. Hep3B HCC cells failed to express GSTP1 mRNA or GSTP1 polypeptides. Similarly, HCC cells in 19 of 20 HCC cases were devoid of GSTP1 polypeptides. By Southern blot analysis, DNA from Hep3B HCC cells displayed abnormal GSTP1 hypermethylation. Treatment of Hep3B HCC cells in vitro with the DNA methyltransferase inhibitor 5-aza-deoxycytidine both reversed GSTP1 DNA hypermethylation and restored GSTP1 expression. Using a PCR assay, somatic GSTP1 DNA hypermethylation was also detected in HCC DNA from 17 of 20 HCC cases. Genomic sequencing analyses, undertaken to map 5-methyldeoxycytidine nucleotides located at the GSTP1 transcriptional regulatory region, frequently detected somatic DNA hypermethylation near the gene promoter in HCC DNA. The data indicate that GSTP1 DNA hypermethylation changes appear frequently in human HCC. In addition, the data raise the possibility that somatic GSTP1 inactivation, via hypermethylation, may contribute to the pathogenesis of HCC.

    View details for Web of Science ID 000085926100003

    View details for PubMedID 10717233

  • Absence of HinfI Restriction Abnormalities in Renal Oncocytoma Mitochondrial DNA. Molecular urology Brooks, J. D., Marshall, F. F., Isaacs, W. B., Johns, D. R. 1999; 3 (1): 1-3

    Abstract

    Renal oncocytomas are characterized by bland-appearing eosinophilic cells with a profusion of mitochondria. Previous work has suggested that these tumors possess a mutation in the 16.5-kbp circular mitochondrial DNA (mtDNA) manifested by an abnormal restriction fragment pattern after digestion with HinfI (Welter et al, Genes Chromosomes Cancer 1989;1:7-82). To better characterize this mtDNA abnormality in renal oncocytomas, we amplified the entire mitochondrial genome from five paired normal and oncocytoma specimens and subjected the amplified fragments to digestion with the restriction enzyme HinfI. No somatically acquired alterations were detected in the mtDNA from any of the five renal oncocytomas. One specimen displayed a known HinfI polymorphism in the mtDNA from both the normal and oncocytoma tissues. Our data do not support the existence of somatically acquired mitochondrial genome abnormalities in renal oncocytomas.

    View details for PubMedID 10851289

  • Potent induction of carcinogen defence enzymes with sulforaphane, a putative prostate cancer chemopreventive agent. Prostate cancer and prostatic diseases Brooks, J. D., Paton, V. 1999; 2 (S3): S8

    View details for PubMedID 12496788

  • Partial nephrectomy and caval thrombectomy for renal cell carcinoma in a solitary kidney with an accessory renal vein BJU INTERNATIONAL Pruthi, R. S., Angell, S. K., Brooks, J. D., Gill, H. 1999; 83 (1): 142-143

    View details for Web of Science ID 000079775000026

    View details for PubMedID 10233469

  • CG island methylation changes near the GSTP1 gene in prostatic intraepithelial neoplasia CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Brooks, J. D., WEINSTEIN, M., Lin, X. H., Sun, Y. H., Pin, S. S., Bova, G. S., Epstein, J. I., Isaacs, W. B., Nelson, W. G. 1998; 7 (6): 531-536

    Abstract

    Prostate intraepithelial neoplasia (PIN) is a purported prostate cancer precursor lesion and a candidate biomarker for efficacy assessment in prostate cancer chemoprevention trials. Loss of expression of the pi-class glutathione S-transferase enzyme GSTP1, which is associated with the hypermethylation of deoxycytidine residues in the 5'-regulatory CG island region of the GSTP1 gene, is a near-universal finding in human prostate cancer. GSTP1 expression was assessed by immunohistochemistry in 60 high-grade PIN samples adjacent to and distant from prostate adenocarcinoma. Whereas abundant enzyme polypeptide expression was evident in all normal prostatic tissues, all samples of high-grade PIN and adenocarcinoma were completely devoid of GSTP1. DNA from 10 high-grade PIN lesions was analyzed for GSTP1 CG island methylation changes using a PCR technique targeting a polymorphic (ATAAA)n repeat sequence in the promoter region of the GSTP1 gene. Somatic GSTP1 CG island methylation changes were detected in DNA from 7 of the 10 PIN lesions. Allele discrimination was possible for 5 of the 10 DNA samples: 2 of the 5 samples exhibited DNA methylation changes at both alleles; whereas 3 samples displayed no DNA methylation changes at either allele. GSTP1 CG island methylation changes were present in each of the five homozygous samples. Hypermethylation of the 5'-regulatory region of the GSTP1 gene may serve as an important molecular genetic biomarker for both prostate cancer and PIN. The finding of frequent GSTP1 methylation changes in PIN and prostate cancer supports a role for PIN lesions as a prostate cancer precursor and may provide insight to the molecular pathogenesis of prostate cancer.

    View details for Web of Science ID 000074029000013

    View details for PubMedID 9641498

  • Male pelvic anatomy reconstructed from the visible human data set JOURNAL OF UROLOGY Brooks, J. D., Chao, W. M., Kerr, J. 1998; 159 (3): 868-872

    Abstract

    To improve understanding of the male pelvic anatomy pertinent to urological surgery we performed computer generated, 3-dimensional reconstruction of the male pelvis from the Visible Human data set.A total of 18 discrete anatomical structures, including the prostate, bladder, urethra, rectum and pelvic musculature, was segmented from the Visible Human cross-sectional data obtained from the National Library of Medicine. Using high speed computing and rendering software, 3-dimensional models of each structure were generated and assembled into composite figures.These reconstructions offer a revised view of pelvic anatomy as it has been traditionally depicted. The lateral surfaces of the levator ani muscle are oriented vertically in the pelvis and directly applied to the entire lateral surface of the prostate. The bladder rests primarily anterior to the prostate rather than directly above it, as has been commonly depicted. In the cross-sectional data and reconstructions the trigone and anterior fibromuscular stroma of the prostate appear as a single unit in continuity, which may have functional implications for understanding the mechanisms of continence at the bladder neck. The striated urethral sphincter appears circular with abundant tissue posteriorly. This sphincteric muscle has greater length anteriorly than posteriorly.These 3-dimensional reconstructions provide unique insights into male pelvic anatomy. They are a useful teaching tool for investigation and virtual reality modeling of the male pelvis.

    View details for Web of Science ID 000071913700068

    View details for PubMedID 9474171

  • Differentiation of colonic metaplasia from adenocarcinoma of urinary bladder HUMAN PATHOLOGY JACOBS, L. B., Brooks, J. D., Epstein, J. I. 1997; 28 (10): 1152-1157

    Abstract

    Colonic metaplasia and primary bladder adenocarcinoma are relatively uncommon entities that can have similar gross clinical appearances. Examples of colonic metaplasia histologically mimicking cancer have only rarely been reported. We retrospectively analyzed 38 cases of cystitis glandularis (18 cases of colonic metaplasia), 12 cases of adenocarcinoma of urinary bladder (two well-differentiated, WDA), and one in situ adenocarcinoma from the surgical pathology files of Johns Hopkins Hospital. Nine patients with colonic metaplasia had widespread lesions. Two showed superficial muscularis propria involvement, mimicking adenocarcinoma; one of these cases had been diagnosed as infiltrating WDA at both an academic center and a community hospital. Dissecting mucin pools were focally seen in four cases of widespread colonic metaplasia, also mimicking cancer. One of the nine cases showed minimal cytological atypia, but no cases showed mitoses or signet ring cells. Distinguishing WDA from colonic metaplasia was the finding in WDA of infiltrative architectural pattern (two of two), extensive muscle invasion (two of two), moderate anaplasia (one of two), mitotic figures (two of two), and extensive mucinous pools (one of two). The diagnosis of adenocarcinoma in situ was based on anaplasia. Clinically, colonic metaplasia may resemble cancer. Histologically, colonic metaplasia may mimic cancer based on extensive involvement of the lamina propria, focal mucinous pools, focal muscularis propria involvement, focal mild cytological atypia, and rare mitoses. Despite overlapping features with colonic metaplasia, the diagnosis of WDA is based on the greater degree and extent of these atypical findings in cancer.

    View details for Web of Science ID A1997YD80100007

    View details for PubMedID 9343322

  • The Swedish prostate cancer paradox JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION Walsh, P. C., Brooks, J. D. 1997; 277 (6): 497-498

    View details for Web of Science ID A1997WG05400039

    View details for PubMedID 9020276

  • Methylation of the 5' CpG island of the endothelin B receptor gene is common in human prostate cancer CANCER RESEARCH Nelson, J. B., Lee, W. H., Nguyen, S. H., Jarrard, D. F., Brooks, J. D., Magnuson, S. R., Opgenorth, T. J., Nelson, W. G., Bova, G. S. 1997; 57 (1): 35-37

    Abstract

    Production of the potent vasoconstrictor endothelin-1 (ET-1) by human prostate cancer cells accompanies prostate cancer progression in vivo. The predominant endothelin receptor expressed by normal prostate epithelium, ETB, is not expressed by any of the established human prostate cancer cell lines, and ETB binding is decreased on prostate cancer tissues. ETB, which may mediate ET-1 clearance and may inhibit ET-1 secretion, is encoded by a gene that contains a 5' CpG island encompassing the transcriptional regulatory region. We examined this regulatory region of the ETB receptor gene (EDNRB) to determine whether hypermethylation of cytidine nucleotides accompanies decreased ETB expression in human prostate cancer. We found somatic methylation of CpG island sequences in EDNRB in 5 of 5 human prostate cancer cell lines, 15 of 21 primary prostate cancer tissues, and 8 of 14 prostate cancer metastases (70% of samples overall). Normal tissues contained only unmethylated EDNRB. Treatment of human prostatic carcinoma cell line cultures with 5-azacytidine induced ETB mRNA expression, suggesting that CpG island methylation changes might accompany the apparent transcriptional silencing of EDNRB in vivo.

    View details for Web of Science ID A1997WA69100009

    View details for PubMedID 8988036

  • An uncertain role for p53 gene alterations in human prostate cancers CANCER RESEARCH Brooks, J. D., Bova, G. S., Ewing, C. M., PIANTADOSI, S., Carter, B. S., Robinson, J. C., Epstein, J. I., Isaacs, W. B. 1996; 56 (16): 3814-3822

    Abstract

    Inactivation of the p53 gene has been implicated in prostate cancer progression. To determine the role of p53 inactivation in the progression of clinical prostatic carcinomas, we assessed 67 tumors derived from patients with clinically localized disease for chromosome 17p and p53 gene allelic loss, p53 gene mutations using single-strand conformational polymorphism and direct sequencing, and p53 protein expression using immunohistochemical staining. Of 55 informative tumors, 10 demonstrated loss of 17p or the p53 gene; however, only a single tumor had a mutation in its remaining p53 allele. Significant p53 overexpression was observed in 2 of 38 tumors, and 9 others had faint staining of a few nuclei ( < 1%). p53 overexpression occurred in no informative tumor with allelic loss or mutation. In a 1-7-year follow-up, positive immunohistochemical staining did not confer an increased risk of recurrence (risk of recurrence, 0.86, P = 0.78), whereas allelic loss of chromosome 17p appeared to be highly correlated with recurrence (risk of recurrence, 3.7, P = 0.003). In an unrelated group of 42 patients with metastatic prostate cancer, p53 overexpression was found in 26 tumors (62%), and 15(36%) had high grade staining. Neither the presence nor the degree of expression correlated with time to progression or time to death. This series suggests that p53 gene inactivation is rare in primary prostatic tumors, not essential to the development of prostate cancer metastases, and of limited use as a prognostic marker in patients with primary or metastatic disease. Another gene or genes on chromosome 17p may be involved in prostate cancer progression.

    View details for Web of Science ID A1996VB98600038

    View details for PubMedID 8706029

  • Epidemiologic and molecular features of prostate carcinogenesis as clues for new prostate cancer prevention strategies Canadian Journal of Urology Brooks JD, Lee WH, Nelson WG 1996; 3 (Supplement): 30-36
  • Molecular staging of prostate cancer Canadian Journal of Urology Lee WH, Brooks JD, Nelson WG 1996; 3 (Supplement): 80-88
  • UPJ obstruction: assessing minimally invasive therapies. Contemporary urology Moore, R. G., Brooks, J. D. 1995; 7 (12): 47-?

    View details for PubMedID 10172648

  • COMPARISON OF OPEN AND ENDOUROLOGICAL APPROACHES TO THE OBSTRUCTED URETEROPELVIC JUNCTION UROLOGY Brooks, J. D., Kavoussi, L. R., Preminger, G. M., Schuessler, W. W., Moore, R. G. 1995; 46 (6): 791-795

    Abstract

    To compare open pyeloplasty with three minimally invasive modalities: antegrade endopyelotomy, Acucise endopyelotomy (Applied Medical, Laguna Hills, Calif), and laparoscopic pyeloplasty.Forty-five adult patients with ureteropelvic junction obstruction were managed by one of the above four techniques. Success rates, analgesic use, length of hospital stay, recovery time, and complications were compared between each of the four groups.Successful relief of obstruction was achieved in 100% of patients undergoing open and laparoscopic dismembered pyeloplasty, 78% undergoing Acucise endopyelotomy, and 77% undergoing antegrade percutaneous endopyelotomy. Acucise endopyelotomy results in shorter convalescence (1 week) than antegrade endopyelotomy (4.7 weeks), laparoscopic pyeloplasty (2.3 weeks) or open pyeloplasty (10.3 weeks). Complication rates appear to be similar among all groups.Our limited data imply that Acucise endopyelotomy offers low morbidity with success rates comparable to antegrade pyeloplasty, whereas laparoscopic pyeloplasty is as effective as open pyeloplasty with diminished morbidity.

    View details for Web of Science ID A1995TJ34700007

    View details for PubMedID 7502417

  • ALLELIC LOSS OF THE RETINOBLASTOMA GENE IN PRIMARY HUMAN PROSTATIC ADENOCARCINOMAS PROSTATE Brooks, J. D., Bova, G. S., Isaacs, W. B. 1995; 26 (1): 35-39

    Abstract

    Inactivation of the retinoblastoma (Rb) gene has been implicated in the genesis and progression of a number of tumor types, including prostatic adenocarcinomas. We have analyzed a series of 46 surgically-resected human prostatic adenocarcinomas for allelic loss of the Rb gene with PCR amplification of a highly polymorphic region of the gene. 41 of 46 tumors (89%) were informative and 11 of these (27%) had lost one Rb allele. The relative frequency of this occurrence suggests that inactivation of the retinoblastoma gene may be an important event in prostate carcinogenesis.

    View details for Web of Science ID A1995QE72800007

    View details for PubMedID 7845865

  • FREQUENT LOSS OF CHROMOSOME ARMS 8P AND 13Q IN COLLECTING DUCT CARCINOMA (CDC) OF THE KIDNEY GENES CHROMOSOMES & CANCER Schoenberg, M., Cairns, P., Brooks, J. D., Marshall, F. F., Epstein, J. I., Isaacs, W. B., Sidransky, D. 1995; 12 (1): 76-80

    Abstract

    Collecting duct carcinoma (CDC) is a malignant renal neoplasm that is believed to arise from the epithelium of the ducts of Bellini in the distal nephron. These tumors are clinically aggressive and more often occur in a younger population than is typical of the more common clear cell renal carcinoma (RCC). Using highly informative polymorphic microsatellite markers on chromosome arms 3p, 5q, 6q, 9p, 9q, 11p, 13q, 17p, and 18q, we analyzed DNA from nonmalignant and tumor tissue in 6 cases of CDC. We found no evidence of 3p loss of heterozygosity (LOH) in these renal tumors by using multiple markers, a finding that distinguishes CDC from RCC in which 3p LOH has frequently been observed. We found LOH of 8p in 50% of the tumors examined; in addition, we observed LOH of 13q in 50% of the tumors studied. Interestingly, 8p LOH may be associated with high stage and poor clinical prognosis. These data suggest that the molecular events responsible for the development of CDC differ from those associated with the origin of RCC, and that tumor suppressor genes on 8p and 13q may be involved in the pathogenesis of CDC.

    View details for Web of Science ID A1995QU21600014

    View details for PubMedID 7534117

  • MOLECULAR-BIOLOGY OF PROSTATE-CANCER PROGRESSION CANCER SURVEYS Isaacs, W. B., Bova, G. S., Morton, R. A., Bussemakers, M. J., Brooks, J. D., Ewing, C. M. 1995; 23: 19-32

    Abstract

    A number of genetic changes have been documented in prostate cancer, ranging from allelic loss to point mutations and changes in DNA methylation patterns (summarized in Fig. 1). The most consistent changes seen are those of allelic loss events, with the majority of tumours examined showing loss of alleles from at least one chromosomal arm. The short arm of chromosome 8, followed by the long arm of chromosome 16, seem to be the most frequent regions of loss, suggesting the presence of novel tumour suppressor genes. Deletions of one copy of the RB and TP53 genes are less frequent as are mutations of the TP53 gene, and accumulating evidence suggests the presence of an additional tumour suppressor gene on chromosome 17p, which is frequently inactivated in prostate cancer. Alterations in the E-cadherin/alpha catenin mediated cell-cell adhesion mechanism appear to be present in almost half of all prostate cancers and may be critical to the acquisition of metastatic potential of aggressive prostate cancers. Finally, altered DNA methylation patterns have been found in the majority of prostate cancers examined, suggesting widespread alterations in methylation modulated gene expression. The presence of multiple changes in these tumours is consistent with the multistep nature of the transformation process. Finally, efforts to identify prostate cancer susceptibility loci are under way, which may elucidate critical early events in prostatic carcinogenesis.

    View details for Web of Science ID A1995RH96200003

    View details for PubMedID 7621457

  • Embryonal adenoma of the kidney: case report Journal of Urology Perlman EJ, Brooks J, Gordon AH, Griffin CA, Schoenberg M 1995; 154: 1473-1474
  • CYTIDINE METHYLATION OF REGULATORY SEQUENCES NEAR THE PI-CLASS GLUTATHIONE-S-TRANSFERASE GENE ACCOMPANIES HUMAN PROSTATIC CARCINOGENESIS PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Lee, W. H., Morton, R. A., Epstein, J. I., Brooks, J. D., Campbell, P. A., Bova, G. S., Hsieh, W. S., Isaacs, W. B., Nelson, W. G. 1994; 91 (24): 11733-11737

    Abstract

    Hypermethylation of regulatory sequences at the locus of the pi-class glutathione S-transferase gene GSTP1 was detected in 20 of 20 human prostatic carcinoma tissue specimens studied but not in normal tissues or prostatic tissues exhibiting benign hyperplasia. In addition, a striking decrease in GSTP1 expression was found to accompany human prostatic carcinogenesis. Immunohistochemical staining with anti-GSTP1 antibodies failed to detect the enzyme in 88 of 91 prostatic carcinomas analyzed. In vitro, GSTP1 expression was limited to human prostatic cancer cell lines containing GSTP1 alleles with hypomethylated promoter sequences; a human prostatic cancer cell line containing only hypermethylated GSTP1 promoter sequences did not express GSTP1 mRNA or polypeptides. Methylation of cytidine nucleotides in GSTP1 regulatory sequences constitutes the most common genomic alteration yet described for human prostate cancer.

    View details for Web of Science ID A1994PU28500092

    View details for PubMedID 7972132

  • MOLECULAR-BIOLOGY OF PROSTATE-CANCER SEMINARS IN ONCOLOGY Isaacs, W. B., Bova, G. S., Morton, R. A., Bussemakers, M. J., Brooks, J. D., Ewing, C. M. 1994; 21 (5): 514-521

    Abstract

    A number of genetic changes have been documented in prostate cancer, ranging from allelic loss to point mutations and changes in DNA methylation patterns (summarized in Fig 1). To date, the most consistent changes are those of allelic loss events, with the majority of tumors examined showing loss of alleles from at least one chromosomal arm. The short arm of chromosome 8, followed by the long arm of chromosome 16 appear to be the most frequent regions of loss, suggesting the presence of novel tumor suppressor genes. Deletions of one copy of the Rb and p53 genes are less frequent as are mutations of the p53 gene, and accumulating evidence suggests the presence of an additional tumor suppressor gene on chromosome 17p, which is frequently inactivated in prostate cancer. Alterations in the E-cadherin/alpha catenin mediated cell-cell adhesion mechanism appear to be present in almost half of all prostate cancers, and may be critical to the acquisition of metastatic potential of aggressive prostate cancers. Finally, altered DNA methylation patterns have been found in the majority of prostate cancers examined, suggesting widespread alterations in methylation-modulated gene expression. The presence of multiple changes in these tumors is consistent with the multistep nature of the transformation process. Finally, efforts to identify prostate cancer susceptibility loci are underway and will hopefully elucidate critical early events in prostatic carcinogenesis.

    View details for Web of Science ID A1994PM94000002

    View details for PubMedID 7939745

  • LAPAROSCOPIC MANAGEMENT OF TESTICULAR PAIN AFTER EMBOLOTHERAPY OF VARICOCELE JOURNAL OF ENDOUROLOGY Brooks, J. D., Moore, R. G., Kavoussi, L. R. 1994; 8 (5): 361-363

    Abstract

    We report a patient who underwent embolization of a varicocele for chronic testicular pain with Gianturco coils and developed increased bilateral pain. Complete pain relief was achieved by laparoscopic resection of both spermatic cords. The case provides insights into the pathophysiology of testicular pain and may suggest alternative therapies for chronic orchialgia.

    View details for Web of Science ID A1994PQ01200010

    View details for PubMedID 7858624

  • Mutations of the VHL tumour suppressor gene in renal carcinoma Nature Genetics Gnarra JR, Tory K, Weng Y, Schmidt L, Wei MH, Li H, Latif F, Liu S, Chen F, Duh FM, Lubensky I, Duan DR, Florence C, Pozzatti R, Walther MM, Bander NH, Grossman HB, Braunch H, Pomer S, Brooks JD, Isaacs WB, Lerman MI, Zbar B, Linehan WM 1994; 7: 85-90
  • TUMOR-SUPPRESSOR GENE ALLELIC LOSS IN HUMAN RENAL CANCERS JOURNAL OF UROLOGY Brooks, J. D., Bova, G. S., Marshall, F. F., Isaacs, W. B. 1993; 150 (4): 1278-1283

    Abstract

    It is now apparent that multiple genetic alterations, including oncogene activation and tumor suppressor gene inactivation, are necessary steps in carcinogenesis. We have studied this concept in renal cancers by looking at specific tumor suppressor genes implicated in several allelotyping studies. Primary, predominantly low stage renal tumors of varying grades and histologic subtypes were investigated for allelic loss of 3p, 17p and the p53 gene, the DCC gene and the Rb gene and its product. 3p loss occurred in 47% of tumors studied and was much more common in clear cell cancers (85%). 17p and p53 gene loss were relatively uncommon events with only 6 of 42 tumors demonstrating loss. None of the tumors with typical histologies had allelic loss of the DCC gene, though loss did occur in leiomyosarcoma and a collecting duct tumor. Allelic loss of the Rb gene occurred in one clear cell tumor, the leiomyosarcoma, and, interestingly, in both collecting duct tumors in this series. Allelic loss of the Rb gene was correlated with little or no RB protein expression as judged by immunohistochemistry. At all loci studied, allelic loss did not appear to correlate with tumor grade or stage. These results suggest that inactivation of the p53, Rb, and DCC genes by allelic loss are uncommon events in the early stages of renal carcinogenesis.

    View details for Web of Science ID A1993LX76200066

    View details for PubMedID 8371415

  • TUBULARIZED NEOURETHRA FOLLOWING RADICAL RETROPUBIC PROSTATECTOMY JOURNAL OF UROLOGY Steiner, M. S., Burnett, A. L., Brooks, J. D., Brendler, C. B., STUTZMAN, R. E., Carter, H. B. 1993; 150 (2): 407-409

    Abstract

    A 1.5 cm. tubularized neourethra was formed using an anterior bladder flap as part of bladder neck reconstruction after radical retropubic prostatectomy in 69 consecutive patients with clinically localized prostate cancer (study group). Postoperative continence (defined as requiring no protection for any activity) was assessed by history at 3 months (all men) and 6 months (45 of 69 men). Continence in the study group was compared to that of 45 men with 6 months of followup who underwent radical retropubic prostatectomy without tubularization of the anterior bladder (control group). At 3 months 38 of 69 men (55%) were continent in the study group and 14 of 45 (31%) were continent in the control group (p < 0.03). At 6 months 39 of 45 men (87%) were continent in the study group compared to 21 of 45 (47%) in the control group (p < 0.01). Upright cystograms performed on men with and without the tubularized neourethra after radical retropubic prostatectomy suggest that a neourethra proximal to the external sphincter may increase resistance in this area and result in early return of urinary control in men undergoing radical retropubic prostatectomy.

    View details for Web of Science ID A1993LM76500032

    View details for PubMedID 8326564

  • Regional DNA Hypermethylation at D17S5 precedes 17p structural changes in the progression of renal tumors Cancer Research Makos M, Nelkin BD, Reiter RE, Gnarra JR, Brooks J, Isaacs W, Linehan M, Baylin SB 1993; 53: 2719-2722
  • Genetic alterations in prostate cancer - prognostic implications? Akteulle Onkologie Isaacs WB, Bova GS, Brooks JD, Ewing CM, Morton RA, Robinson JC 1993; 78: 84-92
  • DOPAMINE UPTAKE BLOCKERS PROTECT AGAINST THE DOPAMINE DEPLETING EFFECT OF 1-METHYL-4-PHENYL-1,2,3,6-TETRAHYDROPYRIDINE (MPTP) IN THE MOUSE STRIATUM NEUROSCIENCE LETTERS Ricaurte, G. A., Langston, J. W., DeLanney, L. E., Irwin, I., Brooks, J. D. 1985; 59 (3): 259-264

    Abstract

    1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), a recently described neurotoxin, produces a marked dopamine (DA) depletion in the mouse striatum. In this study, a series of DA uptake blockers was tested for their ability to prevent this effect of MPTP. The agents tested (amfonelic acid, benztropine, bupropion and mazindol) completely protected against DA depletion in the mouse striatum when given before DA-depleting doses of MPTP were administered, whereas atropine and trihexyphenidyl (which were employed for comparative purposes) did not. DA uptake blocking agents appear to represent a second general class of compounds, monoamine oxidase inhibitors being the first, which protect against the biologic effects of MPTP in the mouse.

    View details for Web of Science ID A1985ASY5800005

    View details for PubMedID 3932903

Conference Proceedings


  • LONG-TERM OUTCOMES FROM A PROSPECTIVE TRIAL OF STEREOTACTIC BODY RADIOTHERAPY FOR LOW-RISK PROSTATE CANCER King, C. R., Brooks, J. D., Gill, H., Presti, J. C. ELSEVIER SCIENCE INC. 2012: 877-882

    Abstract

    Hypofractionated radiotherapy has an intrinsically different normal tissue and tumor radiobiology. The results of a prospective trial of stereotactic body radiotherapy (SBRT) for prostate cancer with long-term patient-reported toxicity and tumor control rates are presented.From 2003 through 2009, 67 patients with clinically localized low-risk prostate cancer were enrolled. Treatment consisted of 36.25 Gy in 5 fractions using SBRT with the CyberKnife as the delivery technology. No patient received hormone therapy. Patient self-reported bladder and rectal toxicities were graded on the Radiation Therapy Oncology Group scale (RTOG).Median follow-up was 2.7 years. There were no grade 4 toxicities. Radiation Therapy Oncology Group Grade 3, 2, and 1 bladder toxicities were seen in 3% (2 patients), 5% (3 patients), and 23% (13 patients) respectively. Dysuria exacerbated by urologic instrumentation accounted for both patients with Grade 3 toxicity. Urinary incontinence, complete obstruction, or persistent hematuria was not observed. Rectal Grade 3, 2, and 1 toxicities were seen in 0, 2% (1 patient), and 12.5% (7 patients), respectively. Persistent rectal bleeding was not observed. Low-grade toxicities were substantially less frequent with QOD vs. QD dose regimen (p = 0.001 for gastrointestinal and p = 0.007 for genitourinary). There were two prostate-specific antigen (PSA), biopsy-proven failures with negative metastatic workup. Median PSA at follow-up was 0.5 ± 0.72 ng/mL. The 4-year Kaplan-Meier PSA relapse-free survival was 94% (95% confidence interval, 85%-102%).Significant late bladder and rectal toxicities from SBRT for prostate cancer are infrequent. PSA relapse-free survival compares favorably with other definitive treatments. The current evidence supports consideration of stereotactic body radiotherapy among the therapeutic options for localized prostate cancer.

    View details for DOI 10.1016/j.ijrobp.2010.11.054

    View details for Web of Science ID 000299239900063

    View details for PubMedID 21300474

  • Preneoplastic prostate lesions - An opportunity for prostate cancer prevention Nelson, W. G., De Marzo, A. M., DeWeese, T. L., Lin, X. H., Brooks, J. D., Putzi, M. J., Nelson, C. P., Groopman, J. D., Kensler, T. W. NEW YORK ACAD SCIENCES. 2001: 135-144

    Abstract

    Environmental factors, especially the diet, play a prominent role in the epidemic of prostate cancer (PCA), in the United States. Many candidate dietary components have been proposed to influence human prostatic carcinogenesis, including fat, calories, fruits and vegetables, anti-oxidants, and various micronutrients, but the specific roles dietary agents play in promoting or preventing PCA remain controversial. We have collected evidence to suggest that GSTP1, the gene encoding the pi-class glutathione S-transferase (GST), may serve a "caretaker" function for prostatic cells. Although GSTP1 can be detected in normal prostatic epithelium, in almost all PCA cases, PCA cells fail to express GSTP1 polypeptides, and lack of GSTP1 expression most often appears to be the result of somatic "CpG island" DNA methylation changes. Loss of GSTP1 function also appears to be characteristic of prostatic epithelial neoplasia (PIN) lesions, thought to represent PCA precursors. We have recently learned that a new candidate early PCA precursor lesion, proliferative inflammatory atrophy (PIA), characterized by proliferating prostatic cells juxtaposed to inflammatory cells, contains epithelial cells that express high levels of GSTP1. These findings have formed the basis for a new model of prostatic carcinogenesis, in which prostatic cells in PIA lesions, subjected to a barrage of inflammatory oxidants, induce GSTP1 expression as a defense against oxidative genome damage. When cells with defective GSTP1 genes appear amongst the PIA cells, such cells become vulnerable to oxidants and electrophiles that inflict genome damage that tends to promote neoplastic transformation to PIN and PCA cells. Subsequently, PIN and PCA cells with defective GSTPI genes remain vulnerable to similar stresses tending to promote malignant progression. This new model for prostatic carcinogenesis has implications for the design of new prostate cancer prevention strategies. Rational prevention approaches might include: (i) restoration of GSTPI expression via treatment with inhibitors of CpG methylation, (ii) compensation for inadequate GSTPI activity via treatment with inducers of general GST activity, and (iii) abrogation of genome-damaging stresses via avoidance of exogenous carcinogens and/or reduction of endogenous carcinogenic (particularly oxidant) stresses.

    View details for Web of Science ID 000173778200012

    View details for PubMedID 11795433

  • MOLECULAR-GENETICS AND CHROMOSOMAL ALTERATIONS IN PROSTATE-CANCER Isaacs, W. B., Bova, G. S., Morton, R. A., Bussemakers, M. J., Brooks, J. D., Ewing, C. M. WILEY-LISS. 1995: 2004-2012
  • GENETIC ALTERATIONS IN PROSTATE-CANCER Isaacs, W. B., Bova, G. S., Morton, R. A., Bussemakers, M. J., Brooks, J. D., Ewing, C. M. COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT. 1994: 653-659

    Abstract

    A number of genetic changes have been documented in prostate cancer, ranging from allelic loss to point mutations and changes in DNA methylation patterns (summarized in Fig. 1). To date, the most consistent changes are those of allelic loss events, with the majority of tumors examined showing loss of alleles from at least one chromosomal arm. The short arm of chromosome 8, followed by the long arm of chromosome 16, appear to be the most frequent regions of loss, suggesting the presence of novel tumor suppressor genes. Deletions of one copy of the Rb and p53 genes are less frequent, as are mutations of the p53 gene, and accumulating evidence suggests the presence of an additional tumor suppressor gene on chromosome 17p, which is frequently inactivated in prostate cancer. Alterations in the E-cadherin/alpha-catenin-mediated cell-cell adhesion mechanism appear to be present in almost half of all prostate cancers and may be critical to the acquisition of metastatic potential of aggressive prostate cancers. Finally, altered DNA methylation patterns have been found in the majority of prostate cancers examined, suggesting widespread alterations in methylation-modulated gene expression. The presence of multiple changes in these tumors is consistent with the multistep nature of the transformation process. Finally, efforts to identify prostate cancer susceptibility loci are under way and may elucidate critical early events in prostatic carcinogenesis.

    View details for Web of Science ID A1994RH96600074

    View details for PubMedID 7587126

Stanford Medicine Resources: