Potential of Long Non- coding RNA Molecules in Diagnosis of Tumors
Authors:
B. Gromesová; V. Kubaczkova; B. Bollova; L. Sedlaříková; S. Ševčíková
Authors‘ workplace:
Babákova myelomová skupina, Ústav patologické fyziologie, LF MU, Brno
Published in:
Klin Onkol 2016; 29(1): 20-28
Category:
Review
doi:
https://doi.org/10.14735/amko201620
Overview
Long non-coding RNA molecules (lncRNA) are defined as molecules over 200 nucleotides long that are localized in the nucleus and cytoplasm of cells. Although function of most lnRNA is not known, it is obvious that they are involved in various biological processes. LncRNA play a key role in transcriptional as well as post‑transcriptional regulatory pathways and are involved in important cell processes, such as proliferation, differentiation, apoptosis but also pathogenesis of various diseases. Their dysregulation is important in steps of tumor transformation. In this review, we will describe the nature, function and molecular basis of these molecules as well as their diagnostic potential. The main focus of this review is the usage of these molecules in the most often diagnosed tumors in the Czech population – colorectal carcinoma, breast and prostate carcinomas.
Key words:
long non-coding RNA molecules – tumor markers – lncRNA deregulation – solid tumors
This work was supported by the grant of the Czech Ministry of Health AZV 15-29508A.
The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study.
The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers.
Submitted:
23. 10. 2015
Accepted:
2. 12. 2015
Sources
1. International Human Genome Sequencing Consortium. Finishing the euchromatic semence of the human genome. Nature 2004; 431(21): 931– 945.
2. Bertone P, Stolc V, Royce TE et al. Global identification of human transcribed sequences with genome tiling arrays. Science 2004; 306(24): 2242– 2246.
3. Kapranov P, Cheng J, Dike S et al. RNA maps reveal new RNA classes and a possible fiction for pervasive transcription. Science 2007; 316(8): 1484– 1488.
4. Wang KC, Chang HY. Molecular mechanisms of long noncoding RNAs. Mol Cell 2011; 43(16): 904– 914. doi: 10.1016/ j.molcel.2011.08.018.
5. Calore F, Lovat F, Garofalo M. Non‑ coding RNAs and cancer. Int J Mol Sci 2013; 14(8): 17085– 17110. doi: 10.3390/ ijms140817085.
6. Ma L, Bajic VB, Zhang Z. On the classification of long non‑coding RNAs. RNA Biol 2013; 10(6): 924– 933. doi: 10.4161/ rna.24604.
7. Maruyama R, Suzuki H. Long noncoding RNA involvement in cancer. BMB Rep 2012; 45(11): 604– 611.
8. Ponjavic J, Ponting CP, Lunter G. Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res 2007; 17(5): 556– 565.
9. Šána J, Faltejsková P, Svoboda M et al. Dlouhé nekódující RNA a jejich význam u nádorových onemocnění. Klin Onkol 2012; 25(4): 246– 254.
10. Ayers D. Long non‑coding RNAs: novel emergent biomarkers for cancer diagnostics. J Cancer Res Treat 2013; 1(2): 31– 35.
11. Morceau F, Chateauvieux S, Gaigneaux A et al. Long and short non‑coding RNAs as regulators of hematopoietic differentiation. Int J Mol Sci 2013; 14(7): 14744– 14770. doi: 10.3390/ ijms140714744.
12. Knauss JL, Sun T. Regulatory mechanisms of long noncoding RNAs in vertebrate central nervous system development and function. Neuroscience 2013; 235(3): 200– 214. doi: 10.1016/ j.neuroscience.2013.01.022.
13. Ernst C, Morton CC. Identification and function of long non‑coding RNA. Front Cell Neurosci 2013; 7: 168. doi: 10.3389/ fncel.2013.00168.
14. Li CH, Chen Y. Targeting long non‑coding RNAs in cancer: progress and prospects. Int J Biochem Cell Biol 2013; 45(8): 1895– 1910. doi: 10.1016/ j.biocel.2013.05.030.
15. Derrien T, Johnson R, Bussotti G et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 2012; 22(9): 1775– 1789. doi: 10.1101/ gr.132159.111.
16. Esteller M. Non‑ coding RNAs in human disease. Nature 2011; 12(12): 861– 874. doi: 10.1038/ nrg3074.
17. Han BW, Chen YQ. Potencial pathological and functional links between long noncoding RNAs and hematopoiesis. Sci Signal 2013; 6(289): re5. doi: 10.1126/ scisignal.2004099.
18. Garitano‑ Trajola A, Agirre X, Prosper F et al. Long non‑coding RNA in haematological malignancies. Int J Mol Sci 2013; 14(8): 15386– 1522. doi: 10.3390/ ijms140815386.
19. Alvarez‑ Dominguez JR, Hu W, Gromatzky AA et al. Long noncoding RNAs during normal and malignit hematopoiesis. Int J Hematol 201; 99(5): 531– 541. doi: 10.1007/ s12185‑ 014‑ 1552‑ 8.
20. Guttman M, Amit I, Garber M et al. Chromatin signature reveals over a thousand highly conserved large non‑coding RNAs in mammals. Nature 2009; 458(7235): 223– 227.
21. Wilusz JE, JnBaptiste CK, Lu LY et al. A triple helix stabilizes the 3’ ends of long noncoding RNAs that lack poly(A) tails. Genes Dev 2012; 26(21): 2392– 2407.
22. Deng G, Sui G. Noncoding RNA in oncogenesis: a new era of identifying key players. Int J Mol Sci 2013; 14(9): 18319– 18349. doi: 10.3390/ ijms140918319.
23. Wang H, Wang L, Erdjument‑ Bromage H et al. Role of histone H2A ubiquitination in Polycomb silencing. Nature 2004; 431(7010): 873– 878.
24. Ørom UA, Derrien T, Beringer M et al. Long noncoding RNAs with enhancer‑like function in human cells. Cell 2010; 143(1): 46– 58. doi: 10.1016/ j.cell.2010.09.001.
25. Diederichs S. The four dimensions of nocoding RNA conservation. Trends Genet 2014; 30(4): 121– 123. doi: 10.1016/ j.tig.2014.01.004.
26. Zhang X, Rice K, Wang Y et al. Maternally expressed gene 3 (MEG3) noncoding ribonucleic acid: isoform structure, expression and functions. Endocrinology 2010; 151(3): 939– 947. doi: 10.1210/ en.2009‑ 0657.
27. Dinger ME, Amaral PP, Mercer TR et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 2008; 18(9): 1433– 1445. doi: 10.1101/ gr.078378.108.
28. Mercer TR, Dinger ME, Mattick JS. Long non‑coding RNAs: insights into functions. Nature 2009; 10(3): 155– 159. doi: 10.1038/ nrg2521.
29. Pandey RR, Mondal T, Mohammad F et al. Kcnq1ot1 antisense noncoding RNA mediates lineage‑ specific transcriptional silencing through chromatin‑level regulation. Mol Cell 2008; 32(2): 232– 246. doi: 10.1016/ j.molcel.2008.08.022.
30. Rinn JL, Kertesz M, Wang JK et al. Functional demarcation of aktive and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007; 129(7): 1311– 1323.
31. Hung T, Chang HY. Long noncoding RNA in genome regulation: prospects and mechanisms. RNA Biol 2010; 7(5): 582– 585.
32. Huarte M, Guttman M, Feldser D et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 2010; 142(3): 409– 419. doi: 10.1016/ j.cell.2010.06.040.
33. Guttman M, Donaghey J, Carey BW et al. LincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 2011; 477(7364): 295– 300. doi: 10.1038/ nature10398.
34. Khalil AM, Guttman M, Huarte M et al. Many human large intergenic noncoding RNAs associate with chromatin‑modifying complexes and affect gene expression. Proc Natl Acad Sci U S A 2009; 106(28): 11667– 11672. doi: 10.1073/ pnas.0904715106.
35. Tsai MC, Manor O, Wan Y et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science 2010; 329(5992): 689– 693. doi: 10.1126/ science.1192002.
36. Zhao J, Sun BK, Erwin J Aet al. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 2008; 322(5902): 750– 756. doi: 10.1126/ science.1163045.
37. Gibb EA, Vucic EA, Enfield KS et al. Human cancer long non‑coding RNA transcriptomes. PLoS One 2011; 6(10): e25915. doi: 10.1371/ journal.pone.0025915.
38. Guffanti A, Iacono M, Pelucchi P et al. A transcriptional sketch of a primary human breast cancer by 454 deep sequencing. BMC Genomics 2009; 10: 163. doi: 10.1186/ 1471‑ 2164‑ 10‑ 163.
39. Li L, Sun R, Liang Y et al. Association between polymorphisms in long non‑coding RNA PRNCR1 in 8q24 and risk of colorectal cancer. J Exp Clin Cancer Res 2013; 32: 104. doi: 10.1186/ 1756‑ 9966‑ 32‑ 104.
40. Barsyte‑ Lovejoy D, Lau SK, Boutros PC et al. The c‑ Myc onkogene directly induces the H19 noncoding RNA by allele‑ specific binding to potentiate tumorigenesis. Cancer Res 2006; 66(10): 5330– 5337.
41. Gupta RA, Shah N, Wang KC et al. Long non‑coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010; 464(7291): 1071– 1076. doi: 10.1038/ nature08975.
42. Kogo R, Shimamura T, Mimori K et al. Long noncoding RNA HOTAIR regulates polycomb‑ dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res 2011; 71(20): 6320– 6326. doi: 10.1158/ 0008‑ 5472.CAN‑ 11‑ 1021.
43. Ji P, Diederichs S, Wang W et al. MALAT‑ 1, a novel noncoding RNA, and thymosin β4 predict metastasis and survival in early‑stage non‑small cell lung cancer. Oncogene 2003; 22(39): 8031– 8041.
44. Hutchinson JN, Ensminger AW, Clemson CM et al. A screen for nuclear transcript identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics 2007; 8: 39.
45. Lin R, Maeda S, Liu C et al. A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas. Oncogene 2007; 26(6): 851–858.
46. Luo JH, Ren B, Keryanov S et al. Transcriptomic and genomic analysis of human hepatocellular carcinomas and hepatoblastomas. Hepatology 2006; 44(4): 1012– 1024.
47. Morrison LE, Jewell SS, Usha L et al. Effects of ERBB2 amplicon size and genomic alternations of chromosomes 1, 3, and 10 on patient response to transtuzumab in metastatic breast cancer. Genes Chromosomes Cancer 2007; 46(4): 397– 405.
48. Smedley D, Sidhar S, Birdsall S et al. Characterization of chromosome 1 abnormalities in malignant melanomas. Genes Chromosomes Cancer 2000; 28(1): 121– 125.
49. Huarte M, Rinn JL. Large non‑coding RNAs: missing links in cancer? Hum Mol Genet 2010; 19(2): 152– 161. doi: 10.1093/ hmg/ ddq353.
50. Májek O, Daneš J, Skovajsová M et al (eds). Mamo.cz – Program mamografického screeningu v České republice [online]. Masarykova univerzita, Brno; 2015. [citováno 26. září 2015]. Dostupné z: http://www.mamo.cz/.
51. Dušek L, Mužík J, Kubásek M et al (eds). Epidemiologie zhoubných nádorů v České republice [online]. Masarykova univerzita, Brno; 2005. [citováno 23. září 2015]. Dostupné z: http://www.svod.cz.
52. Askarian‑ Amiri ME, Crawford J, French JD et al. SNORD‑ host RNA Zfas1 is a regulator of mammary develop-ment and a potential marker for breast cancer. RNA 2011; 17(5): 878– 891. doi: 10.1261/ rna.2528811.
53. Cz.movember.com [internetová stránka]. The movember foundation – celosvětová charitativní organizace, Česká republika; [aktualizováno 2015; citováno 26. září 2015]. Dostupné z: http://cz.movember.com/.
54. Prensner JR, Iyer MK, Balbin OA et al. Transcriptome sequencing across a prostate cancer kohort identifies PCAT‑ 1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol 2011; 29(8): 742– 749. doi: 10.1038/ nbt.1914.
55. Bussemakers MJ, van Bokhoven A, Verhaegh GW et al. DD3: a new prostate‑ specific gene, highly overexpressed in prostate cancer. Cancer Res 1999; 59(23): 5975– 5979.
56. Kleer CG, Cao Q, Varambally S. EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proc Natl Acad Sci U S A 2003; 100(20): 11606– 11611.
57. Varambally S, Dhanasekaran SM, Zhou M et al. The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature 2002; 419(6907): 624– 629.
58. Meng FJ, Shan A, Jin L et al. The expression of a variant prostate‑ specific antigen in human prostate. Cancer Epidemiol Biomarkers Prev 2002; 11(3): 305– 309.
59. De Kok JB, Verhaegh GW, Roelofs RW et al. DD3PCA3, a very sensitive and specific marker to detect prostate tumors. Cancer Res 2002; 62(9): 2695– 2698.
60. Qi P, Xu M, Ni S et al. Low expression of LOC285194 is associated with poor prognosis in colorectal cancer. J Transl Med 2013; 11: 122. doi: 10.1186/ 1479‑ 5876‑ 11‑ 122.
61. Ge X, Chen Y, Liao X et al. Overexpression of long noncoding RNA PCAT‑ 1 is a novel biomarker of poor prognosis in patients with colorectal cancer. Med Oncol 2013; 30(32): 588. doi: 10.1007/ s12032‑ 013‑ 0588‑ 6.
62. Chung S, Nakagawa H, Uemura M et al. Association of a novel long non‑coding RNA in 8q24 with prostate cancer susceptibility. Cancer Sci 2011; 102(1): 245– 252. doi: 10.1111/ j.1349‑ 7006.2010.01737.x.
63. Pal P, Xi H, Guha S et al. Common variants in 8q24 are associated with risk for prostate cancer and tumor aggressiveness in men of European ancestry. Prostate 2009; 69(14): 1548– 1556. doi: 10.1002/pros.20999.
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Clinical Oncology
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