Long noncoding RNAs as putative biomarkers for prostate cancer detection

Journal of Molecular Diagnostics

Volumn 16, Issue 6, 2014, Pages 615-626

  Lee, Bongyong ^a   Mazar, Joseph ^a   Aftab, Muhammad N ^a   Qi, Feng ^a   Shelley, John ^a   Li, Jian Liang ^a   Govindarajan, Subramaniam ^a   Valerio, Felipe ^b   Rivera, Inoel ^b   Thurn, Tadzia ^c   Tran, Tien Anh ^d   Kameh, Darian ^c   Patel, Vipul ^c   Perera, Ranjan J ^a  

^a BURNHAM INSTITUTE   (United States)

^b Florida Urology Associates   (United States)

^c Global Robotic Institute at Florida Hospital   (United States)

^d FLORIDA HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; LONG UNTRANSLATED RNA; SMALL INTERFERING RNA; TUMOR MARKER;

APOPTOSIS; ARTICLE; CANCER DIAGNOSIS; CELL INVASION; CELL PROLIFERATION; CONTROLLED STUDY; GENE EXPRESSION; GLEASON SCORE; HUMAN; HUMAN CELL; HUMAN TISSUE; IN SITU HYBRIDIZATION; LNCAP CELL LINE; PROSTATE ADENOCARCINOMA; PROSTATE CANCER; PROSTATE CANCER CELL LINE; PROSTATE EPITHELIUM; UPREGULATION; URINALYSIS; GENETICS; MALE; METABOLISM; PROSTATE TUMOR;

BIOMARKERS, TUMOR; HUMANS; IN SITU HYBRIDIZATION; MALE; PROSTATIC NEOPLASMS; RNA, LONG NONCODING;

EID: 84908092021     PISSN: 15251578     EISSN: 19437811     Source Type: Journal    
DOI: 10.1016/j.jmoldx.2014.06.009     Document Type: Article

References (63)

1. A.L. Potosky, E.J. Feuer, and D.L. Levin Impact of screening on incidence and mortality of prostate cancer in the United States Epidemiol Rev 23 2001 181 186
2. G.L. Lu-Yao, D. McLerran, J. Wasson, J.E. Wennberg The Prostate Patient Outcomes Research Team An assessment of radical prostatectomy: time trends, geographic variation, and outcomes JAMA 269 1993 2633 2636
3. R. Etzioni, R. Cha, E.J. Feuer, and O. Davidov Asymptomatic incidence and duration of prostate cancer Am J Epidemiol 148 1998 775 785
4. J.R. Prensner, M.A. Rubin, J.T. Wei, and A.M. Chinnaiyan Beyond PSA: the next generation of prostate cancer biomarkers Sci Transl Med 4 2012 127rv3
5. T.J. Wilt, M.K. Brawer, K.M. Jones, M.J. Barry, W.J. Aronson, S. Fox, J.R. Gingrich, J.T. Wei, P. Gilhooly, B.M. Grob, I. Nsouli, P. Iyer, R. Cartagena, G. Snider, C. Roehrborn, R. Sharifi, W. Blank, P. Pandya, G.L. Andriole, D. Culkin, and T. Wheeler Radical prostatectomy versus observation for localized prostate cancer N Engl J Med 367 2012 203 213
6. G. Ploussard, and A. de la Taille Urine biomarkers in prostate cancer Nat Rev Urol 7 2010 101 109
7. G. Ploussard, A. Haese, H. Van Poppel, M. Marberger, A. Stenzl, P.F. Mulders, H. Huland, L. Bastien, C.C. Abbou, M. Remzi, M. Tinzl, S. Feyerabend, A.B. Stillebroer, M.P. Van Gils, J.A. Schalken, and A. de La Taille The prostate cancer gene 3 (PCA3) urine test in men with previous negative biopsies: does free-to-total prostate-specific antigen ratio influence the performance of the PCA3 score in predicting positive biopsies? BJU Int 106 2010 1143 1147
8. J.B. de Kok, G.W. Verhaegh, R.W. Roelofs, D. Hessels, L.A. Kiemeney, T.W. Aalders, D.W. Swinkels, and J.A. Schalken DD3(PCA3), a very sensitive and specific marker to detect prostate tumors Cancer Res 62 2002 2695 2698
9. Consortium IHGS Finishing the euchromatic sequence of the human genome Nature 431 2004 931 945
10. T. Ravasi, H. Suzuki, K.C. Pang, S. Katayama, M. Furuno, R. Okunishi, S. Fukuda, K. Ru, M.C. Frith, M.M. Gongora, S.M. Grimmond, D.A. Hume, Y. Hayashizaki, and J.S. Mattick Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome Genome Res 16 2006 11 19
11. T.R. Mercer, M.E. Dinger, S.M. Sunkin, M.F. Mehler, and J.S. Mattick Specific expression of long noncoding RNAs in the mouse brain Proc Natl Acad Sci U S A 105 2008 716 721
12. M. Cesana, D. Cacchiarelli, I. Legnini, T. Santini, O. Sthandier, M. Chinappi, A. Tramontano, and I. Bozzoni A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA Cell 147 2011 358 369
13. J.N. Hutchinson, A.W. Ensminger, C.M. Clemson, C.R. Lynch, J.B. Lawrence, and A. Chess A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains BMC Genomics 8 2007 39
14. M. Sone, T. Hayashi, H. Tarui, K. Agata, M. Takeichi, and S. Nakagawa The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons J Cell Sci 120 2007 2498 2506
15. C.M. Clemson, J.N. Hutchinson, S.A. Sara, A.W. Ensminger, A.H. Fox, A. Chess, and J.B. Lawrence An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles Mol Cell 33 2009 717 726
16. Y.T. Sasaki, T. Ideue, M. Sano, T. Mituyama, and T. Hirose MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles Proc Natl Acad Sci U S A 106 2009 2525 2530
17. H. Sunwoo, M.E. Dinger, J.E. Wilusz, P.P. Amaral, J.S. Mattick, and D.L. Spector MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles Genome Res 19 2009 347 359
18. S. Blackshaw, S. Harpavat, J. Trimarchi, L. Cai, H. Huang, W.P. Kuo, G. Weber, K. Lee, R.E. Fraioli, S.H. Cho, R. Yung, E. Asch, L. Ohno-Machado, W.H. Wong, and C.L. Cepko Genomic analysis of mouse retinal development PLoS Biol 2 2004 E247
19. J.L. Rinn, M. Kertesz, J.K. Wang, S.L. Squazzo, X. Xu, S.A. Brugmann, L.H. Goodnough, J.A. Helms, P.J. Farnham, E. Segal, and H.Y. Chang Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs Cell 129 2007 1311 1323
20. M.E. Dinger, P.P. Amaral, T.R. Mercer, K.C. Pang, S.J. Bruce, B.B. Gardiner, M.E. Askarian-Amiri, K. Ru, G. Solda, C. Simons, S.M. Sunkin, M.L. Crowe, S.M. Grimmond, A.C. Perkins, and J.S. Mattick Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation Genome Res 18 2008 1433 1445
21. K.S. Pollard, S.R. Salama, N. Lambert, M.A. Lambot, S. Coppens, J.S. Pedersen, S. Katzman, B. King, C. Onodera, A. Siepel, A.D. Kern, C. Dehay, H. Igel, M. Ares Jr., P. Vanderhaeghen, and D. Haussler An RNA gene expressed during cortical development evolved rapidly in humans Nature 443 2006 167 172
22. M. Pheasant, and J.S. Mattick Raising the estimate of functional human sequences Genome Res 17 2007 1245 1253
23. J. Ponjavic, C.P. Ponting, and G. Lunter Functionality or transcriptional noise? evidence for selection within long noncoding RNAs Genome Res 17 2007 556 565
24. M. Guttman, I. Amit, M. Garber, C. French, M.F. Lin, D. Feldser, M. Huarte, O. Zuk, B.W. Carey, J.P. Cassady, M.N. Cabili, R. Jaenisch, T.S. Mikkelsen, T. Jacks, N. Hacohen, B.E. Bernstein, M. Kellis, A. Regev, J.L. Rinn, and E.S. Lander Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals Nature 458 2009 223 227
25. K.V. Prasanth, and D.L. Spector Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum Genes Dev 21 2007 11 42
26. J. Peters, and J.E. Robson Imprinted noncoding RNAs Mamm Genome 19 2008 493 502
27. H. Royo, and J. Cavaille Non-coding RNAs in imprinted gene clusters Biol Cell 100 2008 149 166
28. J. Zhao, B.K. Sun, J.A. Erwin, J.J. Song, and J.T. Lee Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome Science 322 2008 750 756
29. T.A. Allen, S. Von Kaenel, J.A. Goodrich, and J.F. Kugel The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock Nat Struct Mol Biol 11 2004 816 821
30. C.A. Espinoza, T.A. Allen, A.R. Hieb, J.F. Kugel, and J.A. Goodrich B2 RNA binds directly to RNA polymerase II to repress transcript synthesis Nat Struct Mol Biol 11 2004 822 829
31. P.D. Mariner, R.D. Walters, C.A. Espinoza, L.F. Drullinger, S.D. Wagner, J.F. Kugel, and J.A. Goodrich Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock Mol Cell 29 2008 499 509
32. T. Fejes, V. Sotirova, R. Sachidanandam, G. Assaf, G.J. Hannon, P. Kapranov, S. Foissac, A.T. Willinggham, R. Duttagupta, and E. Dumais Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs Nature 457 2009 1028 1032
33. N. Ishii, K. Ozaki, H. Sato, H. Mizuno, S. Saito, A. Takahashi, Y. Miyamoto, S. Ikegawa, N. Kamatani, M. Hori, S. Saito, Y. Nakamura, and T. Tanaka Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction J Hum Genet 51 2006 1087 1099
34. E. Pasmant, I. Laurendeau, D. Heron, M. Vidaud, D. Vidaud, and I. Bieche Characterization of a germ-line deletion, including the entire INK4/ARF locus, in a melanoma-neural system tumor family: identification of ANRIL, an antisense noncoding RNA whose expression coclusters with ARF Cancer Res 67 2007 3963 3969
35. M.A. Faghihi, F. Modarresi, A.M. Khalil, D.E. Wood, B.G. Sahagan, T.E. Morgan, C.E. Finch, G. St Laurent 3rd, P.J. Kenny, and C. Wahlestedt Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase Nat Med 14 2008 723 730
36. E. Sonkoly, Z. Bata-Csorgo, A. Pivarcsi, H. Polyanka, A. Kenderessy-Szabo, G. Molnar, K. Szentpali, L. Bari, K. Megyeri, Y. Mandi, A. Dobozy, L. Kemeny, and M. Szell Identification and characterization of a novel, psoriasis susceptibility-related noncoding RNA gene, PRINS J Biol Chem 280 2005 24159 24167
37. R.S. Daughters, D.L. Tuttle, W. Gao, Y. Ikeda, M.L. Moseley, T.J. Ebner, M.S. Swanson, and L.P. Ranum RNA gain-of-function in spinocerebellar ataxia type 8 PLoS Genet 5 2009 e1000600
38. T.R. Mercer, I.A. Qureshi, S. Gokhan, M.E. Dinger, G. Li, J.S. Mattick, and M.F. Mehler Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation BMC Neurosci 11 2010 14
39. A. Guffanti, M. Iacono, P. Pelucchi, N. Kim, G. Solda, L.J. Croft, R.J. Taft, E. Rizzi, M. Askarian-Amiri, R.J. Bonnal, M. Callari, F. Mignone, G. Pesole, G. Bertalot, L.R. Bernardi, A. Albertini, C. Lee, J.S. Mattick, I. Zucchi, and G. De Bellis A transcriptional sketch of a primary human breast cancer by 454 deep sequencing BMC Genomics 10 2009 163
40. C.J. Woo, and R.E. Kingston HOTAIR lifts noncoding RNAs to new levels Cell 129 2007 1257 1259
41. L. Pibouin, J. Villaudy, D. Ferbus, M. Muleris, M.T. Prosperi, Y. Remvikos, and G. Goubin Cloning of the mRNA of overexpression in colon carcinoma-1: a sequence overexpressed in a subset of colon carcinomas Cancer Genet Cytogenet 133 2002 55 60
42. X. Fu, L. Ravindranath, N. Tran, G. Petrovics, and S. Srivastava Regulation of apoptosis by a prostate-specific and prostate cancer-associated noncoding gene, PCGEM1 DNA Cell Biol 25 2006 135 141
43. G.A. Calin, C.G. Liu, M. Ferracin, T. Hyslop, R. Spizzo, C. Sevignani, M. Fabbri, A. Cimmino, E.J. Lee, S.E. Wojcik, M. Shimizu, E. Tili, S. Rossi, C. Taccioli, F. Pichiorri, X. Liu, S. Zupo, V. Herlea, L. Gramantieri, G. Lanza, H. Alder, L. Rassenti, S. Volinia, T.D. Schmittgen, T.J. Kipps, M. Negrini, and C.M. Croce Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas Cancer Cell 12 2007 215 229
44. R. Lin, S. Maeda, C. Liu, M. Karin, and T.S. Edgington A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas Oncogene 26 2007 851 858
45. D. Khaitan, M.E. Dinger, J. Mazar, J. Crawford, M.A. Smith, J.S. Mattick, and R.J. Perera The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion Cancer Res 71 2011 3852 3862
46. G.K. Smyth Linear models and empirical bayes methods for assessing differential expression in microarray experiments Stat Appl Genet Mol Biol 3 2004 Article3
47. Y. Benjamini, and Y. Hochberg Controlling the False Discovery Rate: a Practical and Powerful Approach to Multiple Testing J R Stat Soc Ser B (methodological) 57 1995 289 300
48. R.C. Gentleman, V.J. Carey, D.M. Bates, B. Bolstad, M. Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, J. Gentry, K. Hornik, T. Hothorn, W. Huber, S. Iacus, R. Irizarry, F. Leisch, C. Li, M. Maechler, A.J. Rossini, G. Sawitzki, C. Smith, G. Smyth, L. Tierney, J.Y. Yang, and J. Zhang Bioconductor: open software development for computational biology and bioinformatics Genome Biol 5 2004 R80
49. G. Draisma, R. Etzioni, A. Tsodikov, A. Mariotto, E. Wever, R. Gulati, E. Feuer, and H. de Koning Lead time and overdiagnosis in prostate-specific antigen screening: importance of methods and context J Natl Cancer Inst 101 2009 374 383
50. G.L. Andriole, E.D. Crawford, R.L. Grubb 3rd, S.S. Buys, D. Chia, T.R. Church, M.N. Fouad, E.P. Gelmann, P.A. Kvale, D.J. Reding, J.L. Weissfeld, L.A. Yokochi, B. O'Brien, J.D. Clapp, J.M. Rathmell, T.L. Riley, R.B. Hayes, B.S. Kramer, G. Izmirlian, A.B. Miller, P.F. Pinsky, P.C. Prorok, J.K. Gohagan, and C.D. Berg Mortality results from a randomized prostate-cancer screening trial N Engl J Med 360 2009 1310 1319
51. E.M. Bolton, A.V. Tuzova, A.L. Walsh, T. Lynch, and A.S. Perry Non-coding RNAs in prostate cancer: the long and the short of it Clin Cancer Res 20 2014 35 43
52. M.J. Bussemakers, A. van Bokhoven, G.W. Verhaegh, F.P. Smit, H.F. Karthaus, J.A. Schalken, F.M. Debruyne, N. Ru, and W.B. Isaacs DD3: a new prostate-specific gene, highly overexpressed in prostate cancer Cancer Res 59 1999 5975 5979
53. H. Nakanishi, J. Groskopf, H.A. Fritsche, V. Bhadkamkar, A. Blase, S.V. Kumar, J.W. Davis, P. Troncoso, H. Rittenhouse, and R.J. Babaian PCA3 molecular urine assay correlates with prostate cancer tumor volume: implication in selecting candidates for active surveillance J Urol 179 2008 1804 1809 discussion 9-10
54. E.J. Whitman, J. Groskopf, A. Ali, Y. Chen, A. Blase, B. Furusato, G. Petrovics, M. Ibrahim, S. Elsamanoudi, J. Cullen, I.A. Sesterhenn, S. Brassell, H. Rittenhouse, S. Srivastava, and D.G. McLeod PCA3 score before radical prostatectomy predicts extracapsular extension and tumor volume J Urol 180 2008 1975 1979
55. D. Hessels, M.P. van Gils, O. van Hooij, S.A. Jannink, J.A. Witjes, G.W. Verhaegh, and J.A. Schalken Predictive value of PCA3 in urinary sediments in determining clinico-pathological characteristics of prostate cancer Prostate 70 2010 10 16
56. M. Auprich, F.K.H. Chun, J.F. Ward, K. Pummer, R. Babaian, H. Augustin, F. Luger, S. Gutschi, L. Budus, M. Fisch, H. Huland, M. Graefen, and A. Haese Critical assessment of preoperative urinary prostate cancer antigen 3 on the accuracy of prostate cancer staging Eur Urol 59 2011 96 105
57. S.A. Tomlins, D.R. Rhodes, S. Perner, S.M. Dhanasekaran, R. Mehra, X.W. Sun, S. Varambally, X. Cao, J. Tchinda, R. Kuefer, C. Lee, J.E. Montie, R.B. Shah, K.J. Pienta, M.A. Rubin, and A.M. Chinnaiyan Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer Science 310 2005 644 648
58. L. Nie, H.J. Wu, J.M. Hsu, S.S. Chang, A.M. Labaff, C.W. Li, Y. Wang, J.L. Hsu, and M.C. Hung Long non-coding RNAs: versatile master regulators of gene expression and crucial players in cancer Am J Transl Res 4 2012 127 150
59. V. Srikantan, Z. Zou, G. Petrovics, L. Xu, M. Augustus, L. Davis, J.R. Livezey, T. Connell, I.A. Sesterhenn, K. Yoshino, G.S. Buzard, F.K. Mostofi, D.G. McLeod, J.W. Moul, and S. Srivastava PCGEM1, a prostate-specific gene, is overexpressed in prostate cancer Proc Natl Acad Sci U S A 97 2000 12216 12221
60. G. Petrovics, W. Zhang, M. Makarem, J.P. Street, R. Connelly, L. Sun, I.A. Sesterhenn, V. Srikantan, J.W. Moul, and S. Srivastava Elevated expression of PCGEM1, a prostate-specific gene with cell growth-promoting function, is associated with high-risk prostate cancer patients Oncogene 23 2004 605 611
61. M.P. van Gils, D. Hessels, O. van Hooij, S.A. Jannink, W.P. Peelen, S.L. Hanssen, J.A. Witjes, E.B. Cornel, H.F. Karthaus, G.A. Smits, G.A. Dijkman, P.F. Mulders, and J.A. Schalken The time-resolved fluorescence-based PCA3 test on urinary sediments after digital rectal examination; a Dutch multicenter validation of the diagnostic performance Clin Cancer Res 13 2007 939 943
62. U. Schmidt, S. Fuessel, R. Koch, G.B. Baretton, A. Lohse, S. Tomasetti, S. Unversucht, M. Froehner, M.P. Wirth, and A. Meye Quantitative multi-gene expression profiling of primary prostate cancer Prostate 66 2006 1521 1534
63. B. Laxman, D.S. Morris, J. Yu, J. Siddiqui, J. Cao, R. Mehra, R.J. Lonigro, A. Tsodikov, J.T. Wei, S.A. Tomlins, and A.M. Chinnaiyan A first-generation multiplex biomarker analysis of urine for the early detection of prostate cancer Cancer Res 68 2008 645 649