Both genes and lncRNAs can be used as biomarkers of prostate cancer by using high throughput sequencing data

European Review for Medical and Pharmacological Sciences

Volumn 18, Issue 22, 2014, Pages 3504-3510

  Cheng, W S ^a   Tao, H ^a   Hu, E P ^a   Liu, S ^a   Cai, H R ^a   Tao, X L ^a   Zhang, L ^a   Mao, J J ^a   Yan, D L ^a  

^a TAIZHOU MUNICIPAL HOSPITAL   (China)

Author keywords

DEG; DEL; lncRNA; Prostate cancer; RNA seq

Indexed keywords

BIOLOGICAL MARKER; LONG UNTRANSLATED RNA; RNA, LONG NONCODING; TRANSCRIPTOME; TUMOR MARKERS, BIOLOGICAL;

ANATOMICAL CONCEPTS; ARTICLE; CANCER SCREENING; CARCINOGENESIS; CELL MATURATION; CONTROLLED STUDY; DEVELOPMENT; DIAGNOSTIC VALUE; GENE EXPRESSION; GENE FUNCTION; GENE ONTOLOGY; GMEB2 GENE; HIGH THROUGHPUT SEQUENCING; HUMAN; MOLECULAR BIOLOGY; ORGANISMS; PROSTATE CANCER; PTK6 GENE; RNA SEQUENCE; STMN3 GENE; STUDENT T TEST; TUMOR GENE; UCKL1 GENE; ZNF512B GENE; BIOSYNTHESIS; GENETICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; METABOLISM; METHODS; PROSTATIC NEOPLASMS;

HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; PROSTATIC NEOPLASMS; RNA, LONG NONCODING; TRANSCRIPTOME; TUMOR MARKERS, BIOLOGICAL;

EID: 84940118426     PISSN: 11283602     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (29)

1. KANTOFF PW, HIGANO CS, SHORE ND , BERGER ER, SMALL EJ, PENSON DF, REDFERN CH, FERRARI AC, DREICER R, SIMS RB, XU Y, FROHLICH MW, SCHELLHAMMER PF; for the IMPACT Study Investigators. Sipuleucel-T immunotherapy for castration-resistant prostate cancer. N Engl J Med 2010; 363: 411-422.
2. BERGER MF, LAWRENCE MS, DEMICHELIS F, DRIER Y, CIBULSKIS K, SIVACHENKO AY, SBONER A, ESGUEVA R, PFLUEGER D, SOUGNEZ C, ONOFRIO R, CARTER SL, PARK K, HABEGGER L, AMBROGIO L, FENNELL T, PARKIN M, SAKSENA G, VOET D, RAMOS AH, PUGH TJ, WILKINSON J, FISHER S, WINCKLER W, MAHAN S, ARDLIE K, BALDWIN J, SIMONS JW, KI T ABAYASHI N, MACDONALD TY, KANTOFF PW, CHIN L, GABRIEL SB, GERSTEIN MB, GOLUB TR, MEYERSON M, TEWARI A, LANDER ES, GETZ G, RUBIN MA, GARRAWAY LA. The genomic complexity of primary human prostate cancer. Nature 2011; 470: 214-220.
3. AMUNDADOTTIR LT, THORVALDSSON S, GUDBJARTSSON DF, SULEM P, KRISTJANSSON K, ARNASON S, GULCHER JR, BJORNSSON J, KONG A, THORSTEINSDOTTIR U, STE FANSSON K. Cancer as a complex phenotype. pattern of cancer distribution within and beyond the nuclear family. PLoS Med 2004; 1: e65.
4. GUDMUNDSSON J, SULEM P, GUDBJARTSSON DF, MASSON G, AGN ARSSON BA, BENEDIKTSDOTTIR KR, SIGURDSSON A, MAGNUSSON OT, GUDJONSSON SA, MAGNUSDOTTIR DN, JOHANNSDOTTIR H, HELGADOTTIR HT, STACEY SN, JONASDOTTIR A, OLAFSDOTTIR SB, THORLEIFSSON G, JONASSON JG, TRYGGVAD O TTIR L, NAVARRETE S, FUERTES F, HELFAND BT, HU Q, CSIKI IE, MATES IN, JINGA V, ABEN KK, VAN OORT IM, VERMEULEN SH, DONOVAN JL, HAMDY FC, NG CF, CHIU PK, LAU KM, NG MC, GULCHER JR, KON G A, CATALONA WJ, MAYORDOMO JI, EINARSSON GV, BARKARDOTTIR RB, JONSSON E, MATES D, NEAL DE, KIEMENEY LA, THORSTEINSDOTTIR U, RAFNAR T, STEFANSSON K. A study based on wholegenome sequencing yields a rare vari ant at 8q24 associated with prostate cancer. Nat Genet 2012; 44: 1326-1329.
5. GRASSO CS, WU YM, ROBINSON DR, CAO X, DHANASEKARAN SM, KHAN AP, QUIST MJ, JING X, LONIGRO RJ, BRE NNER JC, ASANGANI IA, ATEEQ B, CHUN SY, SIDDIQUI J, SAM L, ANSTETT M, MEHRA R, PRENSNER JR, PALANISAMY N, RYSLIK GA, VANDIN F, RAPHAEL BJ, KUNJU LP, RHODES DR, PIENTA KJ, CHINNAIYAN AM, T OMLINS SA. The mutational landscape of lethal castration-resistant prostate cancer. Nature 2012; 487: 239-243.
6. QIAN J, JENKINS RB, BOSTWICK DG. Genetic and chromosomal alterations in prostati c intraepithelial neoplasia and carcinoma detected by fluorescence in situ hybridization. Eur Urol 1999; 35: 479-483.
7. MANI RS,TOMLINS SA,CALLAHAN K,GHOSH A,NYATI MK,VARAMBALLY S,PALANISAMY N,CHINNAIYAN AM. Induced chromosomal proximity and gene fusions in prostate cancer Science, 2009, 326, 12 30.
8. SOOD R, BONNER TI, MAKALOWSKA I, STEPHAN DA, ROBBINS CM, CONNORS TD, MORGENBESSER SD, SU K, FARUQUE MU, PINKETT H, GRAHAM C, BAXEVANIS AD, KLINGER KW, LANDES GM, TRENT JM , CARPTEN JD. Cloning and characterization of 13 novel transcripts and the human RGS8 gene from the 1q25 region encompassing the hereditary prostate cancer (HPC1) locus. Genomics 2001; 73: 211-222.
9. LA NGE EM, CHEN H, BRIERLEY K, PERRONE EE, BOCK CH, GILLANDERS E, RAY ME, COONEY KA. Linkage analysis of 153 prostate cancer families over a 30-cM region containing the putative susceptibility locus HPCX. Clin Cancer Res 1999; 5: 4013-4020.
10. MOUL JW. Angiogenesis, p53, bcl-2 and Ki-67 in the progression of prostate cancer after radical prostatectomy. Eur Urol 1999; 35: 399-407.
11. P RENSNER JR, IYER MK, BALBIN OA, DHANASEKARAN SM, CAO Q, BRENNER JC, LAXMAN B, ASANGANI IA, GRASSO CS, KOMINSKY HD, CAO X, JING X, WANG X, SIDDIQUI J, WEI JT, ROBINSON D, IYER HK, PALANISA M Y N, MAHER CA, CHINNAIYAN AM. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol 2011; 29: 742-749.
12. TRAPNELL C, PACHTER L, SALZBERG SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009; 25: 1105-1111.
13. CABILI MN, TRAPNELL C, GOFF L, KOZIOL M, TAZON-VEGA B, REGEV A, RINN JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 2011; 25: 1915-1927.
14. YOUNG MD, WAKEFIELD MJ, SMYTH GK, OSHLACK A. Gene ontology analysis for RNA-seq. accounting for selection bias. Genome Biol 2010; 11: R14.
15. GENTLEMAN RC, CAREY VJ, BATES DM, BOLSTAD B, DETTLING M, DUDOIT S, ELLIS B, GAUTIER L, GE Y, GENTRY J, HORNIK K, HOTHORN T, HUBER W, IACUS S, IRIZARRY R, LEISCH F, LI C, MAECHLER M, ROSSINI AJ, SAWITZKI G, SMITH C, SMYTH G, TIERNEY L, YANG JY, ZHANG J. Bioconductor. open software development for computational biology and bioinformatics. Genome Biol 2004; 5: R80.
16. ULKUS L, WU M, CRAMER SD. Stem cell models for functional validation of prostate cancer genes. In. Stem Cells and Prostate Cancer. Springer, 2013; pp. 149-173.
17. GALBIATI M, O NESTO E, ZITO A, CRIPPA V, RUSMINI P, MARIOTTI R, BENTIVOGLIO M, BENDOTTI C, POLETTI A. The anabolic/androgenic steroid nandrolone exacerbates gene expression modifications induced by mutant SOD1 in muscles of mice models of amyotrophic lateral sclerosis. Pharmacol Res 2012; 65: 221-230.
18. TILI E, MICHAILLE JJ. Resveratrol, MicroRNAs, Inflammation, and Cancer. J Nucleic Acids 2011; 2011: 102431.
19. LIDEREAU R, DRIOUCH K, LANDEMAINE T. Method for predicting the occurrence of metastasis in breast cancer patients. In: Google Patents, 2008.
20. GEIGER T, MADDEN SF, GALLAGHE R WM, COX J, MANN M. Proteomic portrait of human breast cancer progression identifies novel prognostic markers. Cancer Res 2012; 72: 2428-2439.
21. WALTER-YOHRL ING J, CAO X, CALLAHAN M, WEBER W, MORGENBESSER S, MADDEN SL, WANG C, TEICHER BA. Identification of genes expressed in malignant cells that promote invasion. Cancer Res 2003; 63: 8939-8947.
22. CHARBAUT E, CURMI PA, OZON S, LACHKAR S, REDEKER V, SOBEL A. Stathmin family proteins display specific molecular and tubulin binding properties. J Biol Chem 2001; 276: 16146-16154.
23. JENKINS RB, WRENSCH MR, JOHNSON D, FRIDLEY BL, DECKER PA, XIAO Y, KOLLMEYER TM, RYNEARSON AL, FINK S, RICE T, MCCOY LS, HALDER C, KOSEL ML, GIANNINI C, TIHAN T, O'NEILL BP, LACHAN CE DH, YANG P, WIEMELS J, WIENCKE JK. Distinct germ line polymorphisms underlie glioma morphologic heterogeneity. Cancer Genet 2011; 204: 13-18.
24. KAUL S, BLACKFORD JA, JR., CHO S, SIMONS SS, JR. Ubc9 is a novel modulator of the induction properties of glucocorticoid receptors. J Biol Chem 2002; 277: 12541-12549.
25. JUTRAS S, BACHVAROVA M, KEITA M, BASCANDS JL, MESMAS SON AM, STEWART JM, GERA L, BACHVAROV D. Strong cytotoxic effect of the bradykinin antagonist BKM-570 in ovarian cancer cells-Analysis of the molecular mechanisms of its antiproliferative action. FEBS J 2010; 277: 5 146-5160.
26. BRAUER PM, TYNER AL. Building a better understanding of the intracellular tyrosine kinase PTK6-BRK by BRK. Biochim Biophys Acta 2010; 1806: 66-73.
27. SINGH AP, BAFNA S, CHAU DHARY K, VENKATRAMAN G, SMITH L, EUDY JD, JOHANSSON SL, LIN MF, BATRA SK. Genome-wide expression profiling reveals transcriptomic variation and perturbed gene networks in androgen-dependent and androgen-independent prostate ca ncer cells. Cancer Lett 2008; 259: 28-38.
28. YANO K. Gene expression correlation analysis predicts involvement of high-And low-confidence risk genes in different stages of prostate carcinogenesis Prostate 2010 70 1746-1759.
29. PRITCHARD CC, NELSON PS. Gene expression profiling in the developing prostate. Differentiation 2008; 76: 624-640.