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Chen J, Zhang D, Yan W, Yang D, Shen B. Translational bioinformatics for diagnostic and prognostic prediction of prostate cancer in the next-generation sequencing era. BIOMED RESEARCH INTERNATIONAL 2013; 2013:901578. [PMID: 23957008 PMCID: PMC3727129 DOI: 10.1155/2013/901578] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 06/22/2013] [Indexed: 01/13/2023]
Abstract
The discovery of prostate cancer biomarkers has been boosted by the advent of next-generation sequencing (NGS) technologies. Nevertheless, many challenges still exist in exploiting the flood of sequence data and translating them into routine diagnostics and prognosis of prostate cancer. Here we review the recent developments in prostate cancer biomarkers by high throughput sequencing technologies. We highlight some fundamental issues of translational bioinformatics and the potential use of cloud computing in NGS data processing for the improvement of prostate cancer treatment.
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Affiliation(s)
- Jiajia Chen
- Center for Systems Biology, Soochow University, Suzhou 215006, China
- School of Chemistry, Biology and Material Engineering, Suzhou University of Science and Technology, Suzhou 215011, China
| | - Daqing Zhang
- Center for Systems Biology, Soochow University, Suzhou 215006, China
| | - Wenying Yan
- Center for Systems Biology, Soochow University, Suzhou 215006, China
| | - Dongrong Yang
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Bairong Shen
- Center for Systems Biology, Soochow University, Suzhou 215006, China
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2
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Maqungo M, Kaur M, Kwofie SK, Radovanovic A, Schaefer U, Schmeier S, Oppon E, Christoffels A, Bajic VB. DDPC: Dragon Database of Genes associated with Prostate Cancer. Nucleic Acids Res 2010; 39:D980-5. [PMID: 20880996 PMCID: PMC3013759 DOI: 10.1093/nar/gkq849] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Prostate cancer (PC) is one of the most commonly diagnosed cancers in men. PC is relatively difficult to diagnose due to a lack of clear early symptoms. Extensive research of PC has led to the availability of a large amount of data on PC. Several hundred genes are implicated in different stages of PC, which may help in developing diagnostic methods or even cures. In spite of this accumulated information, effective diagnostics and treatments remain evasive. We have developed Dragon Database of Genes associated with Prostate Cancer (DDPC) as an integrated knowledgebase of genes experimentally verified as implicated in PC. DDPC is distinctive from other databases in that (i) it provides pre-compiled biomedical text-mining information on PC, which otherwise require tedious computational analyses, (ii) it integrates data on molecular interactions, pathways, gene ontologies, gene regulation at molecular level, predicted transcription factor binding sites on promoters of PC implicated genes and transcription factors that correspond to these binding sites and (iii) it contains DrugBank data on drugs associated with PC. We believe this resource will serve as a source of useful information for research on PC. DDPC is freely accessible for academic and non-profit users via http://apps.sanbi.ac.za/ddpc/ and http://cbrc.kaust.edu.sa/ddpc/.
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Affiliation(s)
- Monique Maqungo
- South African National Bioinformatics Institute, University of the Western Cape, Private Bag-X17, Modderdam Road, Bellville, Cape Town, South Africa
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Hood L. A personal journey of discovery: developing technology and changing biology. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2008; 1:1-43. [PMID: 20636073 DOI: 10.1146/annurev.anchem.1.031207.113113] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
This autobiographical article describes my experiences in developing chemically based, biological technologies for deciphering biological information: DNA, RNA, proteins, interactions, and networks. The instruments developed include protein and DNA sequencers and synthesizers, as well as ink-jet technology for synthesizing DNA chips. Diverse new strategies for doing biology also arose from novel applications of these instruments. The functioning of these instruments can be integrated to generate powerful new approaches to cloning and characterizing genes from a small amount of protein sequence or to using gene sequences to synthesize peptide fragments so as to characterize various properties of the proteins. I also discuss the five paradigm changes in which I have participated: the development and integration of biological instrumentation; the human genome project; cross-disciplinary biology; systems biology; and predictive, personalized, preventive, and participatory (P4) medicine. Finally, I discuss the origins, the philosophy, some accomplishments, and the future trajectories of the Institute for Systems Biology.
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Affiliation(s)
- Lee Hood
- Institute for Systems Biology, Seattle, Washington 98103, USA.
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4
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Pascal LE, Deutsch EW, Campbell DS, Korb M, True LD, Liu AY. The urologic epithelial stem cell database (UESC) - a web tool for cell type-specific gene expression and immunohistochemistry images of the prostate and bladder. BMC Urol 2007; 7:19. [PMID: 18072977 PMCID: PMC2231381 DOI: 10.1186/1471-2490-7-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Accepted: 12/11/2007] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Public databases are crucial for analysis of high-dimensional gene and protein expression data. The Urologic Epithelial Stem Cells (UESC) database http://scgap.systemsbiology.net/ is a public database that contains gene and protein information for the major cell types of the prostate, prostate cancer cell lines, and a cancer cell type isolated from a primary tumor. Similarly, such information is available for urinary bladder cell types. DESCRIPTION Two major data types were archived in the database, protein abundance localization data from immunohistochemistry images, and transcript abundance data principally from DNA microarray analysis. Data results were organized in modules that were made to operate independently but built upon a core functionality. Gene array data and immunostaining images for human and mouse prostate and bladder were made available for interrogation. Data analysis capabilities include: (1) CD (cluster designation) cell surface protein data. For each cluster designation molecule, a data summary allows easy retrieval of images (at multiple magnifications). (2) Microarray data. Single gene or batch search can be initiated with Affymetrix Probeset ID, Gene Name, or Accession Number together with options of coalescing probesets and/or replicates. CONCLUSION Databases are invaluable for biomedical research, and their utility depends on data quality and user friendliness. UESC provides for database queries and tools to examine cell type-specific gene expression (normal vs. cancer), whereas most other databases contain only whole tissue expression datasets. The UESC database provides a valuable tool in the analysis of differential gene expression in prostate cancer genes in cancer progression.
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Affiliation(s)
- Laura E Pascal
- Department of Urology, and the Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle WA 98195, USA.
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An Antibody Targeting the Type I Insulin-like Growth Factor Receptor Enhances the Castration-Induced Response in Androgen-Dependent Prostate Cancer. Clin Cancer Res 2007; 13:6429-39. [DOI: 10.1158/1078-0432.ccr-07-0648] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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6
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Morrissey C, True LD, Roudier MP, Coleman IM, Hawley S, Nelson PS, Coleman R, Wang YC, Corey E, Lange PH, Higano CS, Vessella RL. Differential expression of angiogenesis associated genes in prostate cancer bone, liver and lymph node metastases. Clin Exp Metastasis 2007; 25:377-88. [DOI: 10.1007/s10585-007-9116-4] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Accepted: 10/10/2007] [Indexed: 11/28/2022]
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7
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Coleman IM, Kiefer JA, Brown LG, Pitts TE, Nelson PS, Brubaker KD, Vessella RL, Corey E. Inhibition of androgen-independent prostate cancer by estrogenic compounds is associated with increased expression of immune-related genes. Neoplasia 2006; 8:862-78. [PMID: 17032503 PMCID: PMC1715921 DOI: 10.1593/neo.06328] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The clinical utility of estrogens for treating prostate cancer (CaP) was established in the 1940s by Huggins. The classic model of the anti-CaP activity of estrogens postulates an indirect mechanism involving the suppression of androgen production. However, clinical and preclinical studies have shown that estrogens exert growth-inhibitory effects on CaP under low-androgen conditions, suggesting additional modes whereby estrogens affect CaP cells and/or the microenvironment. Here we have investigated the activity of 17beta estradiol (E2) against androgen-independent CaP and identified molecular alterations in tumors exposed to E2. E2 treatment inhibited the growth of all four androgen-independent CaP xenografts studied (LuCaP 35V, LuCaP 23.1AI, LuCaP 49, and LuCaP 58) in castrated male mice. The molecular basis of growth suppression was studied by cDNA microarray analysis, which indicated that multiple pathways are altered by E2 treatment. Of particular interest are changes in transcripts encoding proteins that mediate immune responses and regulate androgen receptor signaling. In conclusion, our data show that estrogens have powerful inhibitory effects on CaP in vivo in androgen-depleted environments and suggest novel mechanisms of estrogen-mediated antitumor activity. These results indicate that incorporating estrogens into CaP treatment protocols could enhance therapeutic efficacy even in cases of advanced disease.
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Affiliation(s)
- Ilsa M Coleman
- Fred Hutchinson Cancer Research Center, Seattle, Seattle, WA, USA
| | - Jeffrey A Kiefer
- Department of Urology, Medical School, University of Washington, Seattle, WA, USA
| | - Lisha G Brown
- Department of Urology, Medical School, University of Washington, Seattle, WA, USA
| | - Tiffany E Pitts
- Department of Urology, Medical School, University of Washington, Seattle, WA, USA
| | - Peter S Nelson
- Fred Hutchinson Cancer Research Center, Seattle, Seattle, WA, USA
| | - Kristen D Brubaker
- Department of Urology, Medical School, University of Washington, Seattle, WA, USA
| | - Robert L Vessella
- Department of Urology, Medical School, University of Washington, Seattle, WA, USA
| | - Eva Corey
- Department of Urology, Medical School, University of Washington, Seattle, WA, USA
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8
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Wu JD, Haugk K, Coleman I, Woodke L, Vessella R, Nelson P, Montgomery RB, Ludwig DL, Plymate SR. Combined In vivo Effect of A12, a Type 1 Insulin-Like Growth Factor Receptor Antibody, and Docetaxel against Prostate Cancer Tumors. Clin Cancer Res 2006; 12:6153-60. [PMID: 17062692 DOI: 10.1158/1078-0432.ccr-06-0443] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE A human type 1 insulin-like growth factor receptor antibody (A12) has been shown to effectively inhibit human xenograft tumor growth, including androgen-dependent and androgen-independent prostate tumors. Docetaxel, either as a single agent or combined with others, has shown a survival benefit in prostate cancer patients. Based on these data, we investigated the combined in vivo effect of A12 and docetaxel on human androgen-independent and osseous prostate tumor growth. EXPERIMENTAL DESIGN To study human androgen-independent prostate cancer model, LuCaP35V tumors were implanted s.c. into castrated severe combined immunodeficient mice. When tumors reached about 100 mm3, animals were treated with vehicle control docetaxel (10 or 20 mg/kg) and docetaxel in combination with A12 (40 microg/kg) for 4 weeks. To study human osseous prostate cancer model, LuCaP 23.1 tumors were implanted intratibiae. When serum prostate-specific antigen reached 5 to 10 ng/mL, treatments were initiated. RESULTS A12 markedly augmented the inhibition of docetaxel on tumor growth. When docetaxel is combined with A12, the inhibition of tumor growth continued after treatment cessation, which was associated with continued apoptosis and decreased proliferation of tumor cells. Gene expression profiles indicated that the posttreatment suppression of tumor growth may be due to enhanced negative regulation of cell cycle progression- and/or cell survival-associated genes, some of which have been shown to induce resistance to docetaxel. CONCLUSIONS Our findings suggest that targeting type 1 insulin-like growth factor receptor can enhance the therapeutic effect of docetaxel on advanced prostate cancer. Our findings also suggest a potential mechanism to improve the treatment efficacy of docetaxel in prostate cancer.
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Affiliation(s)
- Jennifer D Wu
- Department of Medicine, University of Washington, Seattle, WA 98104, USA.
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Clark NL, Swanson WJ. Pervasive adaptive evolution in primate seminal proteins. PLoS Genet 2006; 1:e35. [PMID: 16170411 PMCID: PMC1201370 DOI: 10.1371/journal.pgen.0010035] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2005] [Accepted: 08/04/2005] [Indexed: 11/30/2022] Open
Abstract
Seminal fluid proteins show striking effects on reproduction, involving manipulation of female behavior and physiology, mechanisms of sperm competition, and pathogen defense. Strong adaptive pressures are expected for such manifestations of sexual selection and host defense, but the extent of positive selection in seminal fluid proteins from divergent taxa is unknown. We identified adaptive evolution in primate seminal proteins using genomic resources in a tissue-specific study. We found extensive signatures of positive selection when comparing 161 human seminal fluid proteins and 2,858 prostate-expressed genes to those in chimpanzee. Seven of eight outstanding genes yielded statistically significant evidence of positive selection when analyzed in divergent primates. Functional clues were gained through divergent analysis, including several cases of species-specific loss of function in copulatory plug genes, and statistically significant spatial clustering of positively selected sites near the active site of kallikrein 2. This study reveals previously unidentified positive selection in seven primate seminal proteins, and when considered with findings in Drosophila, indicates that extensive positive selection is found in seminal fluid across divergent taxonomic groups. Proteins found in seminal fluid accompanying sperm show dramatic effects on reproduction, such as manipulating female behavior. Even in primates they participate in competition between sperm of different males, and serve to protect sperm from infection by pathogens. These types of roles require the proteins to constantly adapt to stay ahead of the competition. Such adaptive pressures on proteins leave characteristic signatures in the DNA sequences that encode them. The authors used these signatures to identify adaptive evolution in primate seminal proteins and found extensive signs of adaptation when comparing thousands of seminal genes between human and chimpanzee. They further characterized outstanding genes in several primate species, including a diversity of apes and monkeys. Several of these proteins have no known function, yet by visualizing the adaptation on their three-dimensional surfaces, the authors uncovered clues to what is driving their evolution. In addition, they found several cases in which certain species lost their functional copies of these genes. Interestingly, species that showed loss of function do not participate in sperm competition. Past studies found widespread adaptation in fruit fly seminal fluid, and this study reveals extensive adaptation in primate seminal proteins. Could this be a phenomenon common among animals?
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Affiliation(s)
- Nathaniel L Clark
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
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10
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Bavik C, Coleman I, Dean JP, Knudsen B, Plymate S, Nelson PS. The gene expression program of prostate fibroblast senescence modulates neoplastic epithelial cell proliferation through paracrine mechanisms. Cancer Res 2006; 66:794-802. [PMID: 16424011 DOI: 10.1158/0008-5472.can-05-1716] [Citation(s) in RCA: 312] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The greatest risk factor for developing carcinoma of the prostate is advanced age. Potential molecular and physiologic contributors to the frequency of cancer occurrence in older individuals include the accumulation of somatic mutations through defects in genome maintenance, epigenetic gene silencing, oxidative stress, loss of immune surveillance, telomere dysfunction, chronic inflammation, and alterations in tissue microenvironment. In this context, the process of prostate carcinogenesis can be influenced through interactions between intrinsic cellular alterations and the extrinsic microenvironment and macroenvironment, both of which change substantially as a consequence of aging. In this study, we sought to characterize the molecular alterations that occur during the process of prostate fibroblast senescence to identify factors in the aged tissue microenvironment capable of promoting the proliferation and potentially the neoplastic progression of prostate epithelium. We evaluated three mechanisms leading to cell senescence: oxidative stress, DNA damage, and replicative exhaustion. We identified a consistent program of gene expression that includes a subset of paracrine factors capable of influencing adjacent prostate epithelial growth. Both direct coculture and conditioned medium from senescent prostate fibroblasts stimulated epithelial cell proliferation, 3-fold and 2-fold, respectively. The paracrine-acting proteins fibroblast growth factor 7, hepatocyte growth factor, and amphiregulin (AREG) were elevated in the extracellular environment of senescent prostate fibroblasts. Exogenous AREG alone stimulated prostate epithelial cell growth, and neutralizing antibodies and small interfering RNA targeting AREG attenuated, but did not completely abrogate the growth-promoting effects of senescent fibroblast conditioned medium. These results support the concept that aging-related changes in the prostate microenvironment may contribute to the progression of prostate neoplasia.
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Affiliation(s)
- Claes Bavik
- Division of Human Biology, Fred Hutchinson Cancer Research Center, University of Washington, 1100 Fairview Avenue North, Seattle, WA 98109, USA
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11
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Kuruma H, Egawa S, Oh-Ishi M, Kodera Y, Maeda T. Proteome analysis of prostate cancer. Prostate Cancer Prostatic Dis 2005; 8:14-21. [PMID: 15477873 DOI: 10.1038/sj.pcan.4500764] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In this paper, we briefly review cancer proteomics in general, with particular attention to our proteome analyses of prostate cancer. Our efforts include development of new tools and novel approaches to discovering proteins potentially useful as cancer diagnostic and/or prognostic biomarkers or as therapeutic targets. To this end, we analyzed prostate cancer proteomes using two-dimensional gel electrophoresis employing agarose gels for the initial isoelectric focusing step (agarose 2-DE), with mass spectrometry used for protein identification. Agarose 2-DE offers advantages over the more widely used immobilized pH gradient 2-DE for separating high molecular mass proteins (15-500 kDa), thereby increasing its power to detect changes in the cancer's high-molecular mass proteomes.
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Affiliation(s)
- H Kuruma
- Department of Urology, Kitasato University School of Medicine, 1-15-1 Kitasato, Sagamihara, Kanagawa 228-8555, Japan
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12
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Moore S, Knudsen B, True LD, Hawley S, Etzioni R, Wade C, Gifford D, Coleman I, Nelson PS. Loss of stearoyl-CoA desaturase expression is a frequent event in prostate carcinoma. Int J Cancer 2005; 114:563-71. [PMID: 15609334 DOI: 10.1002/ijc.20773] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Prostate carcinogenesis is influenced by genetic alterations resulting in a biochemical condition that favors cell proliferation and survival. Studies of prostate carcinoma using comparative genomic hybridization and cDNA microarray analysis indicate that numerous biochemical processes may be affected during cellular transformation and progression to an invasive phenotype. Among the consistently observed tumor-associated changes are alterations in fatty acid metabolism that influence diverse cellular activities such as signaling, energy utilization, and membrane fluidity. Increases in fatty acid synthase (FAS) levels have been shown to be one of the earliest and most frequent molecular alterations in prostate carcinogenesis. We sought to identify tumor-associated changes in the expression of genes with functional roles associated with lipid metabolism. Defined populations of normal and neoplastic prostate epithelium were acquired by laser capture microdissection and transcript levels were measured by cDNA microarray hybridization. We determined that stearoyl-CoA desaturase (SCD) transcripts were downregulated in cancer relative to normal epithelium. These results were confirmed by quantitative PCR. Further analysis by immunohistochemical evaluation of radical prostatectomy samples employed a quantitative scoring system with a range of 0-300. The median SCD expression levels were 150, 45 and 10 for normal, PIN and carcinoma samples, respectively. Statistically significant differential SCD expression between normal and cancerous epithelium was determined at the p=0.001 level, and between PIN and prostate carcinoma at the p=0.03 level. Of these cases, 92% overexpressed fatty acid synthase (FAS) in cancerous cells and 84.7% exhibited the signature of FAS overexpression and SCD loss in prostate carcinoma as compared to normal prostate epithelium. These results indicate that loss of SCD expression is a frequent event in prostate adenocarcinoma, and further supports a role for altered lipid metabolism as a factor in the process of carcinogenesis.
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Affiliation(s)
- Stacy Moore
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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13
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York TP, Plymate SR, Nelson PS, Eaves LJ, Webb HD, Ware JL. cDNA microarray analysis identifies genes induced in common by peptide growth factors and androgen in human prostate epithelial cells. Mol Carcinog 2005; 44:242-51. [PMID: 16240454 DOI: 10.1002/mc.20139] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Prostate cancer cells initially require androgen for continued proliferation, but invariably become androgen independent or unresponsive and recur after treatment by androgen ablation. Exploitation of common signaling components downstream of their specific receptors (i.e., androgen receptor (AR), insulin-like growth factor 1 (IGF-1) receptor, and epidermal growth factor (EGF) receptor) could provide a mechanism by which androgen independent cells survive and proliferate. Our objective was to design and implement prostate enriched cDNA microarrays to identify genes induced in prostate epithelial cells in a similar temporal pattern by both androgen and IGF or EGF. AR positive and AR negative human prostate epithelial cells of the M12 line were exposed in parallel to DHT, EGF, or IGF for 0, 6, or 24 h. RNA extracted from each of these groups was analyzed by cDNA microarrays composed of a unique set of 6373 prostate-derived cDNA clones from the Prostate Expression Database (PEDB). We observed statistically significant changes in 20 genes induced in common after 6 and 24 h exposure to androgen or these growth factors, and validated the microarray results by RT-PCR for three or four of these genes: v-myc, isocitrate dehydrogenase, and calnexin. Androgen response element binding motifs were identified in the upstream sequence in 16 of these 20 genes. These results provide comprehensive and unique insights into potential mechanisms by which peptide growth factors provide alternate pathways to control prostate epithelial cell proliferation in malignant states.
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Affiliation(s)
- Timothy P York
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
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14
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Plymate SR, Tennant MK, Culp SH, Woodke L, Marcelli M, Colman I, Nelson PS, Carroll JM, Roberts CT, Ware JL. Androgen receptor (AR) expression in AR-negative prostate cancer cells results in differential effects of DHT and IGF-I on proliferation and AR activity between localized and metastatic tumors. Prostate 2004; 61:276-90. [PMID: 15368471 DOI: 10.1002/pros.20099] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Two features of the progression from organ-confined to metastatic prostate cancer are dysregulation of the androgen receptor (AR) and a decrease in insulin-like growth factor-type-I receptor (IGF-IR) expression. The purpose of this study was to determine the effect of changes in IGF-IR expression on AR activity. METHODS M12 human prostate cells were stably transfected with an AR expression construct to produce the M12-AR parental (PAR) cell line. PAR cells were implanted orthotopically into nude mice and M12-AR primary (PRI) cell lines were derived from intraprostatic tumors and metastatic cell lines (MET) were derived from PRI tumors that had metastasized to diaphragm or lung. RESULTS Tumor formation in the prostate by PAR cells was decreased significantly compared to M12 controls. PAR, PRI, and MET cells expressed equivalent amounts of AR protein; however, IGF-IR expression was increased significantly in PAR and PRI cells. IGF-IR expression decreased in MET lines to the levels seen in M12 control cells. IGF-I significantly enhanced dihydrotestosterone (DHT)-stimulated, but not basal, AR transcriptional activity in PRI cells. In MET cells, IGF-I significantly suppressed DHT-stimulated transcriptional activity. In MET cells in which the IGF-IR was re-expressed from a retroviral vector, the effects of DHT and IGF-I on AR activity were similar to those seen in PRI cells. CONCLUSIONS This study demonstrates that the changes in IGF-IR expression exhibited by this model of metastatic progression cause significant alterations in AR signaling and suggest that this interaction may be an important aspect of the changes seen in AR function in disease progression in vivo.
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MESH Headings
- Androgens/pharmacology
- Animals
- Cell Division/drug effects
- Cell Line, Transformed/cytology
- Cell Line, Transformed/drug effects
- Cell Line, Transformed/physiology
- Cell Survival/drug effects
- Dihydrotestosterone/pharmacology
- Enzyme Inhibitors/pharmacology
- Humans
- Insulin-Like Growth Factor I/pharmacology
- Male
- Mice
- Mice, Nude
- Mitogen-Activated Protein Kinases/antagonists & inhibitors
- Mitogen-Activated Protein Kinases/metabolism
- Phosphatidylinositol 3-Kinases/metabolism
- Phosphoinositide-3 Kinase Inhibitors
- Prostatic Neoplasms/physiopathology
- Prostatic Neoplasms/secondary
- Protein Serine-Threonine Kinases/antagonists & inhibitors
- Protein Serine-Threonine Kinases/metabolism
- Proto-Oncogene Proteins/antagonists & inhibitors
- Proto-Oncogene Proteins/metabolism
- Proto-Oncogene Proteins c-akt
- RNA, Messenger/analysis
- Receptor, IGF Type 1/genetics
- Receptors, Androgen/genetics
- Receptors, Androgen/metabolism
- Signal Transduction/drug effects
- Transcription, Genetic/drug effects
- Transcription, Genetic/physiology
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Affiliation(s)
- Stephen R Plymate
- Department of Medicine, University of Washington, Seattle, Washington, USA.
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15
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Clegg N, Abbott D, Ferguson C, Coleman R, Nelson PS. Characterization and comparative analyses of transcriptomes from the normal and neoplastic human prostate. Prostate 2004; 60:227-39. [PMID: 15176052 DOI: 10.1002/pros.20055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND The prostate gland is a highly specialized organ with functional attributes that serve to enhance the fertility of mammalian species. Pathological processes affecting the prostate include benign prostate hypertrophy and prostate carcinoma; diseases that account for major morbidity and mortality in middle-aged and elderly men. To facilitate studies of biological processes uniquely represented in the prostate and assess molecular alterations associated with prostate carcinoma, we sought to establish the diversity of gene expression in the normal and neoplastic prostate through the compilation and analysis of a prostate transcriptome. METHODS We assembled and annotated ESTs derived from prostate cDNA libraries that were either produced in our laboratory or available from public sequence repositories such as CGAP, dbEST, and Unigene. Determinations of differential gene expression between the normal prostate, other normal tissues, and neoplastic prostate tissues was performed using statistical algorithms. Confirmation of differential expression was performed by quantitative PCR and Northern analysis. RESULTS A total of 99,448 high-quality ESTs were assembled and annotated to produce a prostate transcriptome comprised of 24,580 distinct TUs. Comparative analyses of gene expression levels identified 61 TUs with exclusive expression in the prostate and 45 TUs with high levels of expression in the prostate relative to at least 25 other normal tissues (P > 0.99). Comparative analyses of ESTs derived from neoplastic prostate tissues identified 75 genes with dysregulated expression in cancer (P > 0.99). CONCLUSIONS The human prostate expresses a diverse repertoire of genes that reflect a functionally complex organ. The identification of genes with prostate-restricted or enhanced expression may provide additional insights into the biochemical processes that interact to form the developmental, signaling, and metabolic pathways of the normal and neoplastic gland.
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Affiliation(s)
- Nigel Clegg
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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16
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Lin B, White JT, Utleg AG, Wang S, Ferguson C, True LD, Vessella R, Hood L, Nelson PS. Isolation and characterization of human and mouse WDR19,a novel WD-repeat protein exhibiting androgen-regulated expression in prostate epithelium. Genomics 2003; 82:331-42. [PMID: 12906858 DOI: 10.1016/s0888-7543(03)00151-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Androgens regulate important processes involved in the normal development and function of the human and rodent prostate glands. Here we report the isolation and characterization of a new androgen-regulated gene, designated WDR19, that encodes repeating sequence motifs found in the WD-repeat family of proteins. The WD repeat is a conserved domain of approximately 40 amino acids that is typically bracketed by glycine-histidine and tryptophan-aspartic acid (WD) dipeptides. WD-repeat proteins are a large group of structurally related proteins that participate in a wide range of cellular functions, including transmembrane signaling, mRNA modification, vesicle formation, and vesicular trafficking. The WDR19 gene comprises 36 exons and is located on chromosome 4p15-4p11. The predicted protein contains six WD repeats, a clathrin heavy-chain repeat, and three transmembrane domains. Sequence analysis reveals that the WDR19 gene is conserved from Caenorhabditis elegans to human. WDR19 is expressed in normal and neoplastic prostate epithelium as demonstrated by RNA in situ hybridization and is regulated by androgenic hormones. WDR19 transcripts exhibit alternative splicing in which two isoforms appear to be prostate restricted, a property that could be exploited for designing diagnostic or therapeutic strategies for prostate carcinoma.
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Affiliation(s)
- Biaoyang Lin
- The Institute for Systems Biology, 1441 North 34th Street, Seattle, WA, 98103, USA.
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17
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Corey E, Quinn JE, Buhler KR, Nelson PS, Macoska JA, True LD, Vessella RL. LuCaP 35: a new model of prostate cancer progression to androgen independence. Prostate 2003; 55:239-46. [PMID: 12712403 DOI: 10.1002/pros.10198] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Generation of suitable in vivo models is critical for understanding of processes associated with development and progression of prostate cancer (CaP). METHODS Lymph nodes containing metastatic androgen-independent CaP were implanted into athymic mice. A xenograft designated LuCaP 35 and its hormone-independent variant LuCaP 35V were established and characterized. RESULTS LuCaP 35 is an androgen-sensitive, prostate-specific antigen (PSA)-producing xenograft. It expresses the wild-type androgen receptor and exhibits deletions in chromosome 8p, but not in chromosome 10. The response of LuCaP 35 to androgen ablation is similar to that observed in man. Using recurring LuCaP 35 tumors we have also established an androgen-insensitive variant of LuCaP 35. CONCLUSIONS The availability of hormone-dependent and -independent variants of LuCaP 35, which exhibit many properties analogous to those of CaP in man, provides an excellent model system to study the processes associated with development of androgen independence and to evaluate new treatment modalities.
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MESH Headings
- Aged
- Alleles
- Animals
- Cell Division/physiology
- Chromosome Deletion
- DNA, Neoplasm/chemistry
- DNA, Neoplasm/genetics
- Humans
- Loss of Heterozygosity
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Mice, SCID
- Neoplasm Transplantation
- Neoplasms, Hormone-Dependent/genetics
- Neoplasms, Hormone-Dependent/metabolism
- Neoplasms, Hormone-Dependent/pathology
- Orchiectomy
- Polymerase Chain Reaction
- Prostate-Specific Antigen/biosynthesis
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/pathology
- Receptors, Androgen/genetics
- Receptors, Androgen/metabolism
- Transplantation, Heterologous
- Tumor Cells, Cultured
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Affiliation(s)
- Eva Corey
- Department of Urology, University of Washington, Seattle, Washington 98195, USA.
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18
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Clegg N, Ferguson C, True LD, Arnold H, Moorman A, Quinn JE, Vessella RL, Nelson PS. Molecular characterization of prostatic small-cell neuroendocrine carcinoma. Prostate 2003; 55:55-64. [PMID: 12640661 DOI: 10.1002/pros.10217] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVES A subset of prostate carcinomas is composed predominantly, even exclusively, of neuroendocrine (NE) cells. In this report, we sought to characterize the gene expression profile of a prostate small cell NE carcinoma by assessing the diversity and abundance of transcripts in the LuCaP 49 prostate small cell carcinoma xenograft. METHODS We constructed a cDNA library (PRCA3) from the LuCap 49 prostate small cell xenograft. Single pass DNA sequencing of randomly selected cDNA clones followed by sequence assembly and annotation produced a library of Expressed Sequence Tags (ESTs) representing the LuCaP 49 transcriptome. Comparative sequence analysis with ESTs derived from prostate adenocarcinoma libraries was performed using statistical algorithms designed to identify differentially expressed sequences. Putative NE cell-specific genes were further examined by Northern analysis. RESULTS Sequence assembly and analysis identified 1,447 distinct genes expressed in the LuCaP 49 cDNA library. These include cDNAs encoding the NE markers secretogranin (SCG2), CD24, and ENO2. Northern analysis revealed that three additional genes, ASCL1, INA, and SV2B are expressed in LuCaP 49 but not in various prostate cancer cell lines or xenografts. Fifteen genes were identified with a statistical probability (P > 0.9) of being up-regulated in LuCaP 49 small cell carcinoma relative to prostate adenocarcinoma (two primary prostate adenocarcinomas and the LNCaP prostate adenocarcinoma cell line). CONCLUSIONS Prostate small cell carcinoma expresses a diverse repertoire of genes that reflect characteristics of their NE cell of origin. ASCL1, INA, and SV2B are potential molecular markers for small cell NE tumors and NE cells of the prostate. This small cell NE carcinoma gene expression profile may yield insights into the development, progression, and treatment of subtypes of prostate cancer.
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Affiliation(s)
- Nigel Clegg
- Division of Human Biology, Fred Hutchinson Cancer Research Center, University of Washington-Seattle, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA
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19
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Plymate SR, Haugk KH, Sprenger CC, Nelson PS, Tennant MK, Zhang Y, Oberley LW, Zhong W, Drivdahl R, Oberley TD. Increased manganese superoxide dismutase (SOD-2) is part of the mechanism for prostate tumor suppression by Mac25/insulin-like growth factor binding-protein-related protein-1. Oncogene 2003; 22:1024-34. [PMID: 12592389 DOI: 10.1038/sj.onc.1206210] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Increased expression of mac25/insulin-like growth factor binding-protein related protein-1 (IGFBP-rP1) in human breast and prostate epithelial cell lines results in the suppression of tumor growth. CDNA expression array analysis revealed increased manganese superoxide dismutase (SOD-2) expression in the mac25/IGFBP-rP1-transfected M12 human prostate cancer cell line compared to M12 control cells. SOD-2 has been postulated to be a tumor suppressor. SOD-2 was also increased in LNCaP cells stably transfected with mac25/IGFBP-rP1, but not in mac25/IGFBP-rP1-transfected PC-3 cells. Mac25 LNCaP cells had a marked decrease in tumor growth in nude mice compared to controls, but there was no difference in tumor growth in mac25 PC-3 cells compared to control. Phosphorylated Erk and Akt were increased in the M12 and LNCaP transfected mac25/IGFBP-rP1 cells but not PC-3 mac25. Inhibition of PI-3 kinase results in a marked decrease in viability of the M12-mac25 cells compared to M12 controls. Cells treated with H(2)O(2) result in an increase in phospho-ERK. Transfection of SOD-2 in M12 cells markedly decreased tumor growth, apoptosis, G1 delay in the cell cycle, and expression of senescence associated beta-galactosidase. These results suggest that one of the downstream mediators of the senescence-associated tumor suppression effect of mac25/IGFBP-rP1 is SOD-2.
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Affiliation(s)
- Stephen R Plymate
- Veterans Affairs Puget Sound Health Care System, University of Washington School of Medicine, Seattle, WA 98105, USA
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20
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Li LC, Zhao H, Shiina H, Kane CJ, Dahiya R. PGDB: a curated and integrated database of genes related to the prostate. Nucleic Acids Res 2003; 31:291-3. [PMID: 12520005 PMCID: PMC165455 DOI: 10.1093/nar/gkg008] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Prostate Gene Database (PGDB: http://www.ucsf.edu/pgdb) is a curated and integrated database of genes or genomic loci related to the human prostate and prostatic diseases. Currently, PGDB covers genes involved in a number of molecular and genetic events of the prostate including gene amplification, mutation, gross deletion, methylation, polymorphism, linkage and over-expression, as published in the literature. Genes that are specifically expressed in prostate, as evidenced by analysis of data from expressed sequence tags (ESTs) and serial analysis of gene expression (SAGE), are also included. There are a total of 165 unique entries in the database. Users can either browse or query the PGDB through a web interface. For each gene, in addition to basic gene information and rich cross-references to other databases, inclusive and relevant literature references are provided to support the inclusion of the gene in the database. Detailed expression data calculated from the UniGene and SAGEmap databases are also presented.
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Affiliation(s)
- Long-Cheng Li
- Department of Urology, Veterans Affairs Medical Center, and University of California San Francisco, 4150 Clement Street, San Francisco, CA 94121, USA
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21
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Nelson PS. Identifying immunotherapeutic targets for prostate carcinoma through the analysis of gene expression profiles. Ann N Y Acad Sci 2002; 975:232-46. [PMID: 12538168 DOI: 10.1111/j.1749-6632.2002.tb05955.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carcinoma of the prostate represents one of the most frequently diagnosed cancers in men. If detected at an early stage, prostate cancer is highly treatable. However, cancers identified at a late stage are rarely cured with contemporary medical therapies. Early detection strategies presently center on the identification of prostate-specific proteins in the serum, and emerging therapeutics have utilized genes and proteins with prostate-restricted expression for tissue-selective immunological regimens incorporating vaccines, dendritic cell therapy, gene therapy, and antibody-based cell targeting. In order to develop improved therapeutic procedures, efforts have been directed toward the identification of genes exhibiting prostate-restricted expression profiles, or altered expression levels in neoplastic cells relative to their normal counterparts. Comprehensive expression profiling approaches such as the analysis of oligonucleotide- or complementary DNA (cDNA)-microarrays have greatly enhanced these efforts. Genes and their cognate proteins identified using such methods offer additional diagnostic and therapeutic targets that may aid in the understanding and treatment of prostate carcinoma.
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Affiliation(s)
- Peter S Nelson
- The Divisions of Human Biology and Clinical Research Fred Hutchinson Cancer Research Center Seattle, Washington 98109-1024, USA.
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22
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Nelson PS, Clegg N, Arnold H, Ferguson C, Bonham M, White J, Hood L, Lin B. The program of androgen-responsive genes in neoplastic prostate epithelium. Proc Natl Acad Sci U S A 2002; 99:11890-5. [PMID: 12185249 PMCID: PMC129364 DOI: 10.1073/pnas.182376299] [Citation(s) in RCA: 350] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human prostate gland is an important target organ of androgenic hormones. Testosterone and dihydrotestosterone interact with the androgen receptor to regulate vital aspects of prostate growth and function including cellular proliferation, differentiation, apoptosis, metabolism, and secretory activity. Our objective in this study was to characterize the temporal program of transcription that reflects the cellular response to androgens and to identify specific androgen-regulated genes (ARGs) or gene networks that participate in these responses. We used cDNA microarrays representing about 20,000 distinct human genes to profile androgen-responsive transcripts in the LNCaP adenocarcinoma cell line and identified 146 genes with transcript alterations more than 3-fold. Of these, 103 encode proteins with described functional roles, and 43 represent transcripts that have yet to be characterized. Temporal gene expression profiles grouped the ARGs into four distinct cohorts. Five uncharacterized ARGs demonstrated exclusive or high expression levels in the prostate relative to other tissues studied. A search of available DNA sequence upstream of 28 ARGs identified 25 with homology to the androgen response-element consensus-binding motif. These results identify previously uncharacterized and unsuspected genes whose expression levels are directly or indirectly regulated by androgens; further, they provide a comprehensive temporal view of the transcriptional program of human androgen-responsive cells.
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Affiliation(s)
- Peter S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA.
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23
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True LD, Buhler K, Quinn J, Williams E, Nelson PS, Clegg N, Macoska JA, Norwood T, Liu A, Ellis W, Lange P, Vessella R. A neuroendocrine/small cell prostate carcinoma xenograft-LuCaP 49. THE AMERICAN JOURNAL OF PATHOLOGY 2002; 161:705-15. [PMID: 12163395 PMCID: PMC1850754 DOI: 10.1016/s0002-9440(10)64226-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/29/2002] [Indexed: 11/23/2022]
Abstract
The late stages of progression of prostate carcinoma are typically characterized by an androgen-insensitive, rapidly proliferative state. Some late-stage tumors are composed predominantly of neuroendocrine cells. Virtually no animal models of a neuroendocrine/small cell variant of prostate carcinoma are available for experimental studies. We report a human neuroendocrine/small cell prostate carcinoma xenograft that was developed from a nodal metastasis of a human prostate carcinoma and that has been propagated as serial subcutaneous implants in severe combined immunodeficient mice for >4 years. Designated LuCaP 49, all tumor passages exhibit a neuroendocrine/small cell carcinoma phenotype-insensitivity to androgen deprivation, expression of neuroendocrine proteins, lack of expression of prostate-specific antigen or androgen receptor, and an unusually rapid growth (a doubling time of 6.5 days) for prostate cancer xenografts. Genetically this tumor exhibits loss of heterozygosity for the short arm of chromosome 8 and has a complex karyotype. This xenograft should prove to be useful in the investigation of mechanisms underlying the androgen-insensitive state of progressive prostate carcinoma.
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Affiliation(s)
- Lawrence D True
- Department of Pathology, University of Washington, Seattle, Washington, USA.
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24
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Dasgupta P. Genomics and urology. BJU Int 2002; 89:638-9. [PMID: 11942987 DOI: 10.1046/j.1464-410x.2002.t01-4-02731.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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25
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Abstract
DNA microarray technology provides a means to examine large numbers of molecular changes related to a biological process in a high throughput manner. This review discusses plausible utilities of this technology in prostate cancer research, including definition of prostate cancer predisposition, global profiling of gene expression patterns associated with cancer initiation and progression, identification of new diagnostic and prognostic markers, and discovery of novel patient classification schemes. The technology, at present, has only been explored in a limited fashion in prostate cancer research. Some hurdles to be overcome are the high cost of the technology, insufficient sample size and repeated experiments, and the inadequate use of bioinformatics. With the completion of the Human Genome Project and the advance of several highly complementary technologies, such as laser capture microdissection, unbiased RNA amplification, customized functional arrays (eg, single-nucleotide polymorphism chips), and amenable bioinformatics software, this technology will become widely used by investigators in the field. The large amount of novel, unbiased hypotheses and insights generated by this technology is expected to have a significant impact on the diagnosis, treatment, and prevention of prostate cancer. Finally, this review emphasizes existing, but currently underutilized, data-mining tools, such as multivariate statistical analyses, neural networking, and machine learning techniques, to stimulate wider usage.
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Affiliation(s)
- Shuk-Mei Ho
- Department of Surgery, University of Massachusetts Medical School, Room S4-746, 55 Lake Avenue North, Worcester, MA 01655, USA.
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26
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Liu AY, Nelson PS, van den Engh G, Hood L. Human prostate epithelial cell-type cDNA libraries and prostate expression patterns. Prostate 2002; 50:92-103. [PMID: 11816017 DOI: 10.1002/pros.10036] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND Transcriptome analysis is a powerful approach to uncovering genes responsible for diseases such as prostate cancer. Ideally, one would like to compare the transcriptomes of a cancer cell and its normal counterpart for differences. METHODS Prostate luminal and basal epithelial cell types were isolated and cell-type-specific cDNA libraries were constructed. Sequence analysis of cDNA clones generated 505 luminal cell genes and 560 basal cell genes. These sequences were deposited in a public database for expression analysis. RESULTS From these sequences, 119 unique luminal expressed sequence tags (ESTs) were extracted and assembled into a luminal-cell transcriptome set, while 154 basal ESTs were extracted and assembled into a basal-cell set. Interlibrary comparison was performed to determine representation of these sequences in cDNA libraries constructed from prostate tumors, PIN, cell lines. CONCLUSIONS Our analysis showed that a significant number of epithelial cell genes were not represented in the various transcriptomes of prostate tissues, suggesting that they might be underrepresented in libraries generated from tissue containing multiple cell types. Although both luminal and basal cell types are epithelial, their transcriptomes are more divergent from each other than expected, underscoring their functional difference (secretory vs. nonsecretory). Tumor tissues show different expression of luminal and basal genes, with perhaps a trend towards expression of basal genes in advanced diseases.
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Affiliation(s)
- Alvin Y Liu
- Department of Urology, University of Washington, Seattle, Washington 98195, USA.
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27
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Abstract
Systems biology studies biological systems by systematically perturbing them (biologically, genetically, or chemically); monitoring the gene, protein, and informational pathway responses; integrating these data; and ultimately, formulating mathematical models that describe the structure of the system and its response to individual perturbations. The emergence of systems biology is described, as are several examples of specific systems approaches.
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Affiliation(s)
- T Ideker
- Institute for Systems Biology, Seattle, Washington 98105, USA.
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28
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Clegg N, Eroglu B, Ferguson C, Arnold H, Moorman A, Nelson PS. Digital expression profiles of the prostate androgen-response program. J Steroid Biochem Mol Biol 2002; 80:13-23. [PMID: 11867260 DOI: 10.1016/s0960-0760(01)00167-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The androgen receptor (AR) and cognate ligands regulate vital aspects of prostate cellular growth and function including proliferation, differentiation, apoptosis, lipid metabolism, and secretory action. In addition, the AR pathway also influences pathological processes of the prostate such as benign prostatic hypertrophy and prostate carcinogenesis. The pivotal role of androgens and the AR in prostate biology prompted this study with the objective of identifying molecular mediators of androgen action. Our approach was designed to compare transcriptomes of the LNCaP prostate cancer cell line under conditions of androgen depletion and androgen stimulation by generating and comparing collections of expressed sequence tags (ESTs). A total of 4400 ESTs were produced from LNCaP cDNA libraries and these ESTs assembled into 2486 distinct transcripts. Rigorous statistical analysis of the expression profiles indicated that 17 genes exhibited a high probability (P>0.9) of androgen-regulated expression. Northern analysis confirmed that the expression of KLK3/PSA, FKBP5, KRT18, DKFZP564K247, DDX15, and HSP90 is regulated by androgen exposure. Of these, only KLK3/PSA is known to be androgen-regulated while the other genes represent new members of the androgen-response program in prostate epithelium. LNCaP gene expression profiles defined by two independent experiments using the serial analysis of gene expression (SAGE) method were compared with the EST profiles. Distinctly different expression patterns were produced from each dataset. These results are indicative of the sensitivity of the methods to experimental conditions and demonstrate the power and the statistical limitations of digital expression analyses.
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Affiliation(s)
- Nigel Clegg
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
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29
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Nelson PS, Pritchard C, Abbott D, Clegg N. The human (PEDB) and mouse (mPEDB) Prostate Expression Databases. Nucleic Acids Res 2002; 30:218-20. [PMID: 11752298 PMCID: PMC99083 DOI: 10.1093/nar/30.1.218] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Prostate Expression Databases (PEDB and mPEDB) are online resources designed to allow researchers to access and analyze gene expression information derived from the human and murine prostate, respectively. Human PEDB archives more than 84 000 Expressed Sequence Tags (ESTs) from 38 prostate cDNA libraries in a curated relational database that provides detailed library information including tissue source, library construction methods, sequence diversity and sequence abundance. The differential expression of each EST species can be viewed across all libraries using a Virtual Expression Analysis Tool (VEAT), a graphical user interface written in Java for intra- and inter-library sequence comparisons. Recent enhancements to PEDB include (i) the development of a murine prostate expression database, mPEDB, that complements the human gene expression information in PEDB, (ii) the assembly of a non-redundant sequence set or 'prostate unigene' that represents the diversity of gene expression in the prostate, and (iii) an expanded search tool that supports both text-based and BLAST queries. PEDB and mPEDB are accessible via the World Wide Web at http://www.pedb.org and http://www.mpedb.org.
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Affiliation(s)
- Peter S Nelson
- Division of Human Biology and Division of Clinical Research, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA.
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30
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Grouse LH, Munson PJ, Nelson PS. Sequence databases and microarrays as tools for identifying prostate cancer biomarkers. Urology 2001; 57:154-9. [PMID: 11295616 DOI: 10.1016/s0090-4295(00)00963-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Identification, acquisition, and assessment of molecular markers that could be adopted as surrogate endpoints for evaluating a response to prostate cancer intervention strategies is highly desirable. Recent advances in the fields of genomics and biotechnology have dramatically increased the quantity and accessibility of molecular information that is relevant to the study of prostate carcinogenesis. One major advance involves the construction of comprehensive databases that archive gene sequences and gene expression data. This information is in a format suitable for virtual queries designed to distinguish the molecular differences between normal and cancer cells. A second major advance uses robotic tools to construct microarrays comprising thousands of distinct genes expressed in prostate tissues. Such arrays offer a powerful approach for monitoring the expression of thousands of genes simultaneously and provide access for techniques designed to assess patterns or "fingerprints" of gene expression that may ultimately be used as signatures of response to therapeutic intervention.
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Affiliation(s)
- L H Grouse
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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31
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Abstract
The development of drugs to prevent prostate cancer is underway, yet monitoring the potential efficacy of these agents during clinical trials relies on measuring intermediate endpoints. In this review, various candidate markers are presented that are under different stages of evaluation as intermediate endpoint biomarkers. In addition, the near future will bring an unprecedented wave of new potential biomarkers. For instance, through genomics-based methods many new genes are being discovered whose altered expression may be involved in different phases of prostate cancer development and progression. In the development of rational approaches for selecting which of these untested biomarkers may be useful to measure systematically, there must be an improved understanding of the mechanisms of prostatic carcinogenesis. We submit that this improved understanding will come through new knowledge of the biology of normal prostate epithelial cells, the determination of the precise target cells of transformation, and how their growth regulation is genetically and epigenetically perturbed during the phases of initiation and progression. In this review, therefore, we also present our recent immune-mediated oxidant injury and regeneration hypothesis of why and how the prostate is targeted for carcinogenesis.
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Affiliation(s)
- A M De Marzo
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA.
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32
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Abstract
The molecular processes contributing to cancer of the human prostate gland are under intensive investigation. Methods used for discovering genetic alterations involved in prostate neoplasia include family studies designed to map hereditary disease loci, chromosomal studies to identify aberrations that may locate oncogenes or tumor suppressor genes, and comprehensive gene expression studies. These studies determine how various molecular signaling pathways influence or reflect the process of carcinogenesis. However, a comprehensive overview of the cell is necessary to understand all of the dynamic interactions between genes, their protein products, and the network of cellular processes resulting in tumorigenesis. Unraveling the complexity of these systems in a timely manner involves the integration of computers, miniaturization, and automation into molecular biology. New biotechnologies such as the development of automated DNA sequencing and complementary DNA microarrays allow for a systematic, "discovery-driven" approach. These and other technologies afford a comprehensive view of biology and pathology that have the potential to fully characterize the processes involved in neoplasia and therefore provide potential targets for the therapy of prostate and other cancers.
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Affiliation(s)
- P E Li
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop D4-100, Seattle, WA 98109-1024, USA.
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33
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34
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35
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Christiano AP, Yoshida BA, Dubauskas Z, Sokoloff M, Rinker-Schaeffer CW. Development of markers of prostate cancer metastasis. Review and perspective. Urol Oncol 2000; 5:217-223. [PMID: 10973711 DOI: 10.1016/s1078-1439(00)00070-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- AP Christiano
- Section of Urology, Department of Surgery, University of Chicago, 60637, Chicago, IL, USA
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36
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Nelson PS, Han D, Rochon Y, Corthals GL, Lin B, Monson A, Nguyen V, Franza BR, Plymate SR, Aebersold R, Hood L. Comprehensive analyses of prostate gene expression: convergence of expressed sequence tag databases, transcript profiling and proteomics. Electrophoresis 2000; 21:1823-31. [PMID: 10870968 DOI: 10.1002/(sici)1522-2683(20000501)21:9<1823::aid-elps1823>3.0.co;2-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Several methods have been developed for the comprehensive analysis of gene expression in complex biological systems. Generally these procedures assess either a portion of the cellular transcriptome or a portion of the cellular proteome. Each approach has distinct conceptual and methodological advantages and disadvantages. We have investigated the application of both methods to characterize the gene expression pathway mediated by androgens and the androgen receptor in prostate cancer cells. This pathway is of critical importance for the development and progression of prostate cancer. Of clinical importance, modulation of androgens remains the mainstay of treatment for patients with advanced disease. To facilitate global gene expression studies we have first sought to define the prostate transcriptome by assembling and annotating prostate-derived expressed sequence tags (ESTs). A total of 55000 prostate ESTs were assembled into a set of 15953 clusters putatively representing 15953 distinct transcripts. These clusters were used to construct cDNA microarrays suitable for examining the androgen-response pathway at the level of transcription. The expression of 20 genes was found to be induced by androgens. This cohort included known androgen-regulated genes such as prostate-specific antigen (PSA) and several novel complementary DNAs (cDNAs). Protein expression profiles of androgen-stimulated prostate cancer cells were generated by two-dimensional electrophoresis (2-DE). Mass spectrometric analysis of androgen-regulated proteins in these cells identified the metastasis-suppressor gene NDKA/nm23, a finding that may explain a marked reduction in metastatic potential when these cells express a functional androgen receptor pathway.
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Affiliation(s)
- P S Nelson
- Fred Hutchinson Cancer Research Center, Department of Molecular Biotechnology, University of Washington, Seattle, USA.
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37
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Abstract
Bioinformatics has, out of necessity, become a key aspect of drug discovery in the genomic revolution, contributing to both target discovery and target validation. The author describes the role that bioinformatics has played and will continue to play in response to the waves of genome-wide data sources that have become available to the industry, including expressed sequence tags, microbial genome sequences, model organism sequences, polymorphisms, gene expression data and proteomics. However, these knowledge sources must be intelligently integrated.
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Nelson PS, Clegg N, Eroglu B, Hawkins V, Bumgarner R, Smith T, Hood L. The prostate expression database (PEDB): status and enhancements in 2000. Nucleic Acids Res 2000; 28:212-3. [PMID: 10592228 PMCID: PMC102457 DOI: 10.1093/nar/28.1.212] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/1999] [Accepted: 10/07/1999] [Indexed: 11/12/2022] Open
Abstract
The Prostate Expression Database (PEDB) is an online resource designed to access and analyze gene expression information derived from the human prostate. PEDB archives >55 000 expressed sequence tags (ESTs) from 43 cDNA libraries in a curated relational database that provides detailed library information including tissue source, library construction methods, sequence diversity and sequence abundance. The differential expression of each EST species can be viewed across all libraries using a Virtual Expression Analysis Tool (VEAT), a graphical user interface written in Java for intra- and inter-library species comparisons. Recent enhancements to PEDB include: (i) the functional categorization of annotated EST assemblies using a classification scheme developed at The Institute for Genome Research; (ii) catalogs of expressed genes in specific prostate tissue sources designated as transcriptomes; and (iii) the addition of prostate proteome information derived from two-dimensional electrophoreses and mass spectrometry of prostate cancer cell lines. PEDB may be accessed via the WWW at http://www.mbt.washington.edu/PEDB/
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Affiliation(s)
- P S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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