Abstract
Large-scale analysis of gene expression in prostate- cancer using gene expression microarrays has revolutionized our understanding of prostate cancer. By allowing analysis of gene expression changes of tens of thousands of genes simultaneously, this technique has facilitated discovery of key biological alterations in prostate cancer such as the TMPRSS2/ERG fusion gene. In addition, this approach has discovered novel diagnostic biomarkers such as alpha methyl-acyl CoA racemase. Careful attention to preanalytical variables such as tissue preservation, tumor purity, the anatomic site of tissue origin, and RNA integrity is critical. Careful attention to the analytical variables and data analysis is also required for optimal results. Currently, next-generation RNA sequencing is displacing gene expression arrays due to superior analytical performance and rapidly decreasing cost. Large-scale expression of gene expression will continue to be a major tool for discovery in prostate cancer for the foreseeable future.
References
Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, et al. What is a gene, post-ENCODE? History and updated definition. [Historical Article Research Support, N.I.H., Extramural Review]. Genome Res. 2007;17(6):669–81.
Ozen M, Creighton CJ, Ozdemir M, Ittmann M. Widespread deregulation of microRNA expression in human prostate cancer. Oncogene. 2008;27(12):1788–93.
Li JJ, Biggin MD. Gene expression. Statistics requantitates the central dogma. [Comment Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Science. 2015;347(6226):1066–7.
Yu W, Feng S, Dakhova O, Creighton CJ, Cai Y, Wang J, et al. FGFR-4 Arg(3)(8)(8) enhances prostate cancer progression via extracellular signal-related kinase and serum response factor signaling. Clin Cancer Res. 2011;17(13):4355–66.
Yang F, Chen Y, Shen T, Guo D, Dakhova O, Ittmann MM, et al. Stromal TGF-beta signaling induces AR activation in prostate cancer. Oncotarget. 2014;5(21):10854–69.
Yan J, Yu CT, Ozen M, Ittmann M, Tsai SY, Tsai MJ. Steroid receptor coactivator-3 and activator protein-1 coordinately regulate the transcription of components of the insulin-like growth factor/AKT signaling pathway. Cancer Res. [Research Support, N.I.H., Extramural.]. 2006;66(22):11039–46.
Chaib H, Cockrell EK, Rubin MA, Macoska JA. Profiling and verification of gene expression patterns in normal and malignant human prostate tissues by cDNA microarray analysis. Neoplasia. [Comparative Study Research Support, U.S. Gov’t, P.H.S.]. 2001;3(1):43–52.
Rhodes DR, Barrette TR, Rubin MA, Ghosh D, Chinnaiyan AM. Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res. 2002;62(15):4427–33.
Rubin MA, Zhou M, Dhanasekaran SM, Varambally S, Barrette TR, Sanda MG, et al. Alpha-Methylacyl coenzyme A racemase as a tissue biomarker for prostate cancer. JAMA. [Research Support, Non-US Gov’t Research Support, US Gov’t, PHS]. 2002;287(13):1662–70.
Lapointe J, Li C, Higgins JP, van de Rijn M, Bair E, Montgomery K, et al. Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci U S A. 2004;101(3):811–6.
Voss BL, Santiano K, Milano M, Mangold KA, Kaul KL. Integrity and amplification of nucleic acids from snap-frozen prostate tissues from robotic-assisted laparoscopic and open prostatectomies. Arch Pathol Lab Med. [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. 2013;137(4):525–30.
Esgueva R, Park K, Kim R, Kitabayashi N, Barbieri CE, Dorsey PJ Jr, et al. Next-generation prostate cancer biobanking: toward a processing protocol amenable for the International Cancer Genome Consortium. Diagn Mol Pathol. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. 2012;21(2):61–8.
Best S, Sawers Y, Fu VX, Almassi N, Huang W, Jarrard DF. Integrity of prostatic tissue for molecular analysis after robotic-assisted laparoscopic and open prostatectomy. Urology. [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t.]. 2007;70(2):328–32.
Dash A, Maine IP, Varambally S, Shen R, Chinnaiyan AM, Rubin MA. Changes in differential gene expression because of warm ischemia time of radical prostatectomy specimens. Am J Pathol. [Research Support, U.S. Gov’t, P.H.S.]. 2002;161(5):1743–8.
Stuart RO, Wachsman W, Berry CC, Wang-Rodriguez J, Wasserman L, Klacansky I, et al. In silico dissection of cell-type-associated patterns of gene expression in prostate cancer. Proc Natl Acad Sci U S A. [Research Support, U.S. Gov’t, PHS]. 2004;101(2):615–20.
Dakhova O, Ozen M, Creighton CJ, Li R, Ayala G, Rowley D, et al. Global gene expression analysis of reactive stroma in prostate cancer. Clin Cancer Res. 2009;15(12):3979–89.
Tomlins SA, Mehra R, Rhodes DR, Cao X, Wang L, Dhanasekaran SM, et al. Integrative molecular concept modeling of prostate cancer progression. Nat Genet. [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. 2007;39(1):41–51.
Dakhova O, Rowley D, Ittmann M. Genes upregulated in prostate cancer reactive stroma promote prostate cancer progression in vivo. Clin Cancer Res. [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. 2014;20(1):100–9.
Luo J, Dunn T, Ewing C, Sauvageot J, Chen Y, Trent J, et al. Gene expression signature of benign prostatic hyperplasia revealed by cDNA microarray analysis. Prostate. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, P.H.S.]. 2002;51(3):189–200.
Kosari F, Cheville JC, Ida CM, Karnes RJ, Leontovich AA, Sebo TJ, et al. Shared gene expression alterations in prostate cancer and histologically benign prostate from patients with prostate cancer. Am J Pathol. [Research Support, Non-U.S. Gov’t]. 2012;181(1):34–42.
Risk MC, Knudsen BS, Coleman I, Dumpit RF, Kristal AR, LeMeur N, et al. Differential gene expression in benign prostate epithelium of men with and without prostate cancer: evidence for a prostate cancer field effect. Clin Cancer Res. [Research Support, N.I.H., Extramural]. 2010;16(22):5414–23.
Chandran UR, Dhir R, Ma C, Michalopoulos G, Becich M, Gilbertson J. Differences in gene expression in prostate cancer, normal appearing prostate tissue adjacent to cancer and prostate tissue from cancer free organ donors. BMC Cancer. [Research Support, N.I.H., Extramural Research Support, U.S. Gov’t, Non-P.H.S. Research Support, U.S. Gov’t, P.H.S.]. 2005;5:45.
Varambally S, Dhanasekaran SM, Zhou M, Barrette TR, Kumar-Sinha C, Sanda MG, et al. The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature. 2002;419(6907):624–9.
Taylor BS, Schultz N, Hieronymus H, Gopalan A, Xiao Y, Carver BS, et al. Integrative genomic profiling of human prostate cancer. Cancer Cell. [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t.]. 2010;18(1):11–22.
Glinsky GV, Krones-Herzig A, Glinskii AB, Gebauer G. Microarray analysis of xenograft-derived cancer cell lines representing multiple experimental models of human prostate cancer. Mol Carcinog. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, P.H.S.]. 2003;37(4):209–21.
Sirotnak FM, She Y, Khokhar NZ, Hayes P, Gerald W, Scher HI. Microarray analysis of prostate cancer progression to reduced androgen dependence: studies in unique models contrasts early and late molecular events. Mol Carcinog. [Comparative Study Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, P.H.S.]. 2004;41(3):150–63.
Narita S, Tsuchiya N, Saito M, Inoue T, Kumazawa T, Yuasa T, et al. Candidate genes involved in enhanced growth of human prostate cancer under high fat feeding identified by microarray analysis. Prostate. [Research Support, Non-U.S. Gov’t]. 2008;68(3):321–35.
Acevedo VD, Gangula RD, Freeman KW, Li R, Zhang Y, Wang F, et al. Inducible FGFR-1 activation leads to irreversible prostate adenocarcinoma and an epithelial-to-mesenchymal transition. Cancer Cell. 2007;12(6):559–71.
Carstens JL, Shahi P, Van Tsang S, Smith B, Creighton CJ, Zhang Y, et al. FGFR1-WNT-TGF-beta signaling in prostate cancer mouse models recapitulates human reactive stroma. Cancer Res. [Research Support, N.I.H., Extramural.]. 2014;74(2):609–20.
Ittmann M, Huang J, Radaelli E, Martin P, Signoretti S, Sullivan R, et al. Animal models of human prostate cancer: the consensus report of the New York meeting of the Mouse Models of Human Cancers Consortium Prostate Pathology Committee. Cancer Res. [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. 2013;73(9):2718–36.
Berquin IM, Min Y, Wu R, Wu H, Chen YQ. Expression signature of the mouse prostate. J Biol Chem. [Research Support, N.I.H., Extramural Research Support, U.S. Gov’t, P.H.S.]. 2005;280(43):36442–51.
Aytes A, Mitrofanova A, Lefebvre C, Alvarez MJ, Castillo-Martin M, Zheng T, et al. Cross-species regulatory network analysis identifies a synergistic interaction between FOXM1 and CENPF that drives prostate cancer malignancy. Cancer Cell. [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t.]. 2014;25(5):638–51.
Irshad S, Bansal M, Castillo-Martin M, Zheng T, Aytes A, Wenske S, et al. A molecular signature predictive of indolent prostate cancer. Sci Transl Med. [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. 2013;5(202):202ra122.
Thompson VC, Day TK, Bianco-Miotto T, Selth LA, Han G, Thomas M, et al. A gene signature identified using a mouse model of androgen receptor-dependent prostate cancer predicts biochemical relapse in human disease. Int J Cancer. [Research Support, N.I.H., Extramural.]. 2012;131(3):662–72.
Imbeaud S, Graudens E, Boulanger V, Barlet X, Zaborski P, Eveno E, et al. Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces. Nucleic Acids Res. [Evaluation Studies Research Support, Non-U.S. Gov’t.]. 2005;33(6):e56.
Greytak SR, Engel KB, Bass BP, Moore HM. Accuracy of molecular data generated with FFPE biospecimens: lessons from the literature. Cancer Res. [Review]. 2015;75(8):1541–7.
Oberthuer A, Juraeva D, Li L, Kahlert Y, Westermann F, Eils R, et al. Comparison of performance of one-color and two-color gene-expression analyses in predicting clinical endpoints of neuroblastoma patients. Pharmacogenomics J. [Comparative Study Research Support, Non-U.S. Gov’t.]. 2010;10(4):258–66.
Lapuk AV, Volik SV, Wang Y, Collins CC. The role of mRNA splicing in prostate cancer. Asian J Androl. [Research Support, Non-U.S. Gov’t]. 2014;16(4):515–21.
Kwabi-Addo B, Ropiquet F, Giri D, Ittmann M. Alternative splicing of fibroblast growth factor receptors in human prostate cancer. Prostate. 2001;46(2):163–72.
Dehm SM, Schmidt LJ, Heemers HV, Vessella RL, Tindall DJ. Splicing of a novel androgen receptor exon generates a constitutively active androgen receptor that mediates prostate cancer therapy resistance. Cancer Res. 2008;68(13):5469–77.
Cuperlovic-Culf M, Belacel N, Culf AS, Ouellette RJ. Microarray analysis of alternative splicing. OMICS. [Research Support, Non-U.S. Gov’t Review]. 2006;10(3):344–57.
Steinhoff C, Vingron M. Normalization and quantification of differential expression in gene expression microarrays. Brief Bioinform. [Research Support, Non-U.S. Gov’t Review]. 2006;7(2):166–77.
Gusnanto A, Calza S, Pawitan Y. Identification of differentially expressed genes and false discovery rate in microarray studies. Curr Opin Lipidol. [Review]. 2007;18(2):187–93.
Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, Sun XW, et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science. [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S. Research Support, U.S. Gov’t, P.H.S.]. 2005;310(5748):644–8.
Tomlins SA, Rhodes DR, Yu J, Varambally S, Mehra R, Perner S, et al. The role of SPINK1 in ETS rearrangement-negative prostate cancers. Cancer Cell. [Meta-Analysis Multicenter Study Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-PHS]. 2008;13(6):519–28.
Saldanha AJ. Java Treeview – extensible visualization of microarray data. Bioinformatics. 2004;20(17):3246–8.
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545–50.
Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, Briggs BB, et al. Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia. 2007;9(2):166–80.
Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t.]. 2012;2(5):401–4.
Wang J, Cai Y, Ren C, Ittmann M. Expression of variant TMPRSS2/ERG fusion messenger RNAs is associated with aggressive prostate cancer. Cancer Res. 2006;66(17):8347–51.
Clark J, Merson S, Jhavar S, Flohr P, Edwards S, Foster CS, et al. Diversity of TMPRSS2-ERG fusion transcripts in the human prostate. Oncogene. [Research Support, Non-U.S. Gov’t.]. 2007;26(18):2667–73.
Yoshimoto M, Joshua AM, Chilton-Macneill S, Bayani J, Selvarajah S, Evans AJ, et al. Three-color FISH analysis of TMPRSS2/ERG fusions in prostate cancer indicates that genomic microdeletion of chromosome 21 is associated with rearrangement. Neoplasia. [Research Support, Non-U.S. Gov’t.]. 2006;8(6):465–9.
Rajput AB, Miller MA, De Luca A, Boyd N, Leung S, Hurtado-Coll A, et al. Frequency of the TMPRSS2:ERG gene fusion is increased in moderate to poorly differentiated prostate cancers. J Clin Pathol. 2007;60(11):1238–43.
Mehra R, Tomlins SA, Shen R, Nadeem O, Wang L, Wei JT, et al. Comprehensive assessment of TMPRSS2 and ETS family gene aberrations in clinically localized prostate cancer. Mod Pathol. 2007;20(5):538–44.
Nam RK, Sugar L, Wang Z, Yang W, Kitching R, Klotz LH, et al. Expression of TMPRSS2:ERG gene fusion in prostate cancer cells is an important prognostic factor for cancer progression. Cancer Biol Ther. 2007;6(1):40–5.
Demichelis F, Fall K, Perner S, Andren O, Schmidt F, Setlur SR, et al. TMPRSS2:ERG gene fusion associated with lethal prostate cancer in a watchful waiting cohort. Oncogene. [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t.]. 2007;26(31):4596–9.
Soller MJ, Isaksson M, Elfving P, Soller W, Lundgren R, Panagopoulos I. Confirmation of the high frequency of the TMPRSS2/ERG fusion gene in prostate cancer. Genes Chromosomes Cancer. 2006;45(7):717–9.
Attard G, Clark J, Ambroisine L, Fisher G, Kovacs G, Flohr P, et al. Duplication of the fusion of TMPRSS2 to ERG sequences identifies fatal human prostate cancer. Oncogene. [Research Support, Non-U.S. Gov’t.]. 2008;27(3):253–63.
Lin B, Ferguson C, White JT, Wang S, Vessella R, True LD, et al. Prostate-localized and androgen-regulated expression of the membrane-bound serine protease TMPRSS2. Cancer Res. 1999;59(17):4180–4.
Wang J, Cai Y, Yu W, Ren C, Spencer DM, Ittmann M. Pleiotropic biological activities of alternatively spliced TMPRSS2/ERG fusion gene transcripts. Cancer Res. [Research Support, N.I.H., Extramural Research Support, U.S. Gov’t, Non-P.H.S.]. 2008;68(20):8516–24.
Shao L, Tekedereli I, Wang J, Yuca E, Tsang S, Sood A, et al. Highly specific targeting of the TMPRSS2/ERG fusion gene using liposomal nanovectors. Clin Cancer Res. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. 2012;18(24):6648–57.
Leinonen KA, Tolonen TT, Bracken H, Stenman UH, Tammela TL, Saramaki OR, et al. Association of SPINK1 expression and TMPRSS2:ERG fusion with prognosis in endocrine-treated prostate cancer. Clin Cancer Res. 2010;16(10):2845–51.
Ateeq B, Tomlins SA, Laxman B, Asangani IA, Cao Q, Cao X, et al. Therapeutic targeting of SPINK1-positive prostate cancer. Sci Transl Med. 2011;3(72):72ra17.
Bismar TA, Yoshimoto M, Duan Q, Liu S, Sircar K, Squire JA. Interactions and relationships of PTEN, ERG, SPINK1 and AR in castration-resistant prostate cancer. Histopathology. 2012;60(4):645–52.
Grupp K, Diebel F, Sirma H, Simon R, Breitmeyer K, Steurer S, et al. SPINK1 expression is tightly linked to 6q15- and 5q21-deleted ERG-fusion negative prostate cancers but unrelated to PSA recurrence. Prostate. 2013;73(15):1690–8.
Jiang Z, Woda BA. Diagnostic utility of alpha-methylacyl CoA racemase (P504S) on prostate needle biopsy. Adv Anat Pathol. [Review]. 2004;11(6):316–21.
Jiang Z, Woda BA, Wu CL, Yang XJ. Discovery and clinical application of a novel prostate cancer marker: alpha-methylacyl CoA racemase (P504S). Am J Clin Pathol. [Review]. 2004;122(2):275–89.
Kumaresan K, Kakkar N, Verma A, Mandal AK, Singh SK, Joshi K. Diagnostic utility of alpha-methylacyl CoA racemase (P504S) & HMWCK in morphologically difficult prostate cancer. Diagn Pathol. [Evaluation Studies]. 2010;5:83.
Worschech A, Meirelles L, Billis A. Expression of alpha-methylacyl coenzyme A racemase in partial and complete focal atrophy on prostate needle biopsies. Anal Quant Cytol Histol. [Research Support, Non-U.S. Gov’t]. 2009;31(6):424–31.
Shah RB, Tadros Y, Brummell B, Zhou M. The diagnostic use of ERG in resolving an “atypical glands suspicious for cancer” diagnosis in prostate biopsies beyond that provided by basal cell and alpha-methylacyl-CoA-racemase markers. Hum Pathol. 2013;44(5):786–94.
Dabir PD, Ottosen P, Hoyer S, Hamilton-Dutoit S. Comparative analysis of three- and two-antibody cocktails to AMACR and basal cell markers for the immunohistochemical diagnosis of prostate carcinoma. Diagn Pathol. [Comparative Study Research Support, Non-U.S. Gov’t.]. 2012;7:81.
Tomlins SA, Palanisamy N, Siddiqui J, Chinnaiyan AM, Kunju LP. Antibody-based detection of ERG rearrangements in prostate core biopsies, including diagnostically challenging cases: ERG staining in prostate core biopsies. Arch Pathol Lab Med. [Evaluation Studies Research Support, N.I.H., Extramural.]. 2012;136(8):935–46.
Magi-Galluzzi C, Tsusuki T, Elson P, Simmerman K, LaFargue C, Esgueva R, et al. TMPRSS2-ERG gene fusion prevalence and class are significantly different in prostate cancer of Caucasian, African-American and Japanese patients. Prostate. 2011;71(5):489–97.
Rosen P, Pfister D, Young D, Petrovics G, Chen Y, Cullen J, et al. Differences in frequency of ERG oncoprotein expression between index tumors of Caucasian and African American patients with prostate cancer. Urology. [Research Support, N.I.H., Extramural]. 2012;80(4):749–53.
Laxman B, Morris DS, Yu J, Siddiqui J, Cao J, Mehra R, et al. A first-generation multiplex biomarker analysis of urine for the early detection of prostate cancer. Cancer Res. 2008;68(3):645–9.
Varambally S, Laxman B, Mehra R, Cao Q, Dhanasekaran SM, Tomlins SA, et al. Golgi protein GOLM1 is a tissue and urine biomarker of prostate cancer. Neoplasia. [Meta-Analysis Research Support, N.I.H., Extramural Research Support, U.S. Gov’t, Non-P.H.S.]. 2008;10(11):1285–94.
van Leenders GJ, Dukers D, Hessels D, van den Kieboom SW, Hulsbergen CA, Witjes JA, et al. Polycomb-group oncogenes EZH2, BMI1, and RING1 are overexpressed in prostate cancer with adverse pathologic and clinical features. Eur Urol. 2007;52(2):455–63.
Mucci LA, Pawitan Y, Demichelis F, Fall K, Stark JR, Adami HO, et al. Testing a multigene signature of prostate cancer death in the Swedish Watchful Waiting Cohort. Cancer Epidemiol Biomark Prev. 2008;17(7):1682–8.
Mucci LA, Pawitan Y, Demichelis F, Fall K, Stark JR, Adami HO, et al. Nine-gene molecular signature is not associated with prostate cancer death in a watchful waiting cohort. Cancer Epidemiol Biomarkers Prev. [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t.]. 2008;17(1):249–51.
Klein EA, Cooperberg MR, Magi-Galluzzi C, Simko JP, Falzarano SM, Maddala T, et al. A 17-gene assay to predict prostate cancer aggressiveness in the context of Gleason grade heterogeneity, tumor multifocality, and biopsy undersampling. Eur Urol. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. 2014;66(3):550–60.
Erho N, Crisan A, Vergara IA, Mitra AP, Ghadessi M, Buerki C, et al. Discovery and validation of a prostate cancer genomic classifier that predicts early metastasis following radical prostatectomy. PLoS One. [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t.]. 2013;8(6):e66855.
Sun Y, Goodison S. Optimizing molecular signatures for predicting prostate cancer recurrence. Prostate. [Comparative Study Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t.]. 2009;69(10):1119–27.
Glinsky GV, Glinskii AB, Stephenson AJ, Hoffman RM, Gerald WL. Gene expression profiling predicts clinical outcome of prostate cancer. J Clin Invest. 2004;113(6):913–23.
Yu YP, Landsittel D, Jing L, Nelson J, Ren B, Liu L, et al. Gene expression alterations in prostate cancer predicting tumor aggression and preceding development of malignancy. J Clin Oncol. [Research Support, U.S. Gov’t, P.H.S.]. 2004;22(14):2790–9.
Singh D, Febbo PG, Ross K, Jackson DG, Manola J, Ladd C, et al. Gene expression correlates of clinical prostate cancer behavior. Cancer Cell. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, P.H.S.]. 2002;1(2):203–9.
Cheville JC, Karnes RJ, Therneau TM, Kosari F, Munz JM, Tillmans L, et al. Gene panel model predictive of outcome in men at high-risk of systemic progression and death from prostate cancer after radical retropubic prostatectomy. J Clin Oncol. 2008;26(24):3930–6.
Chen X, Xu S, McClelland M, Rahmatpanah F, Sawyers A, Jia Z, et al. An accurate prostate cancer prognosticator using a seven-gene signature plus Gleason score and taking cell type heterogeneity into account. PLoS One. [Research Support, N.I.H., Extramural Research Support, U.S. Gov’t, Non-P.H.S.]. 2012;7(9):e45178.
Dhanasekaran SM, Barrette TR, Ghosh D, Shah R, Varambally S, Kurachi K, et al. Delineation of prognostic biomarkers in prostate cancer. Nature. [Research Support, Non-U.S. Gov’t.]. 2001;412(6849):822–6.
Jia Z, Rahmatpanah FB, Chen X, Lernhardt W, Wang Y, Xia XQ, et al. Expression changes in the stroma of prostate cancer predict subsequent relapse. PLoS One. [Clinical Trial Comparative Study Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. 2012;7(8):e41371.
Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000;403(6769):503–11.
Sorlie T. Molecular portraits of breast cancer: tumour subtypes as distinct disease entities. Eur J Cancer. 2004;40(18):2667–75.
Guo Y, Sheng Q, Li J, Ye F, Samuels DC, Shyr Y. Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data. PLoS One. [Comparative Study]. 2013;8(8):e71462.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer International Publishing AG
About this chapter
Cite this chapter
Ittmann, M. (2018). Gene Expression Analysis. In: Robinson, B., Mosquera, J., Ro, J., Divatia, M. (eds) Precision Molecular Pathology of Prostate Cancer. Molecular Pathology Library. Springer, Cham. https://doi.org/10.1007/978-3-319-64096-9_11
Download citation
DOI: https://doi.org/10.1007/978-3-319-64096-9_11
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-64094-5
Online ISBN: 978-3-319-64096-9
eBook Packages: MedicineMedicine (R0)