An Evaluation of Long Non-coding RNAs in Cancer

Öz

Long non-coding RNAs (lncRNAs) gradually play significant roles in many fundamental biological functions. These genetic elements are considered major components of transcripts and critical components of cancer cells. Most genetic alterations in cancer cells occur in comparatively long, non-protein-encoding areas typically translated into lncRNAs. LncRNAs have essential functions in the pathophysiology of human diseases, particularly in the genesis, advancement, and metastasis of tumors, acting as either tumor suppressor genes or oncogenes. As a correlation, understanding the function and dynamic activity of lncRNAs is thought of as de novo and a promising biomarker for cancer therapeutics. The existence of differentially expressed lncRNAs with functional diversity in diverse anaplastic changes makes them valid elements in monitoring cancer cells. The application of sophisticated genetic tools such as next-gene sequencing on cancer transcriptomes has discovered multiple lncRNA functions in the context of anaplastic changes. Various lncRNAs expressed in different phenotypic situations have been found using the following and third-generation sequencing methods; however, many still need to be appropriately identified. This review summarizes and discusses previous studies on the role of lncRNAs in cancer cells, and underscores the therapeutic strategies associated with cancer-related lncRNAs.

Anahtar Kelimeler

• Long non-coding RNAs
• Gene expression
• Prognosis
• Cancer

Kaynakça

1. Atianand MK, Hu W, Satpathy AT, Shen Y, Ricci EP, Alvarez-Dominguez JR, Bhatta A, Schattgen SA, Mcgowan JD, Blin J. 2016. A long noncoding RNA lincRNA-EPS acts as a transcriptional brake to restrain inflammation. Cell, 165: 1672-1685.
2. Au PCK, Zhu Q-H, Dennis ES, Wang M-B. 2011. Long non-coding RNA-mediated mechanisms independent of the RNAi pathway in animals and plants. RNA Biol, 8: 404-414.
3. Baldassarre A, Masotti A. 2012. Long non-coding RNAs and p53 regulation. Int J Mol Sci, 13: 16708-16717.
4. Barsyte-Lovejoy D, Lau SK, Boutros PC, Khosravi F, Jurisica I, Andrulis IL, Tsao MS, Penn LZ. 2006. The c-Myc oncogene directly induces the H19 noncoding RNA by allele-specific binding to potentiate tumorigenesis. Cancer Res, 66: 5330-5337.
5. Bartonicek N, Maag JLV, Dinger ME. 2016. Long noncoding RNAs in cancer: mechanisms of action and technological advancements. Molec Cancer, 15: 1-10.
6. Campos EI, Reinberg D. 2009. Histones: annotating chromatin. Annu Rev Genet, 43: 559-599.
7. Cheetham S, Gruhl F, Mattick J, Dinger M. 2013. Long noncoding RNAs and the genetics of cancer. Br J Cancer, 108: 2419-2425.
8. Cuykendall TN, Rubin MA, Khurana E. 2017. Non-coding genetic variation in cancer. Curr Opin Syst Biol, 1: 9-15.

9. Da Rocha ST, Boeva V, Escamilla-Del-Arenal M, Ancelin K, Granier C, Matias NR, Sanulli S, Chow J, Schulz E, Picard C. 2014. Jarid2 is implicated in the initial Xist-induced targeting of PRC2 to the inactive X chromosome. Mol Cell, 53: 301-316.
10. Dinger ME, Pang KC, Mercer TR, Mattick JS. 2008. Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLoS Comput Biol, 4: e1000176.
11. Fatima R, Akhade VS, Pal D, Rao SM. 2015. Long noncoding RNAs in development and cancer: potential biomarkers and therapeutic targets. Mol Cell Biol, 3: 1-19.
12. Ghosal S, Das S, Chakrabarti J. 2013. Long noncoding RNAs: new players in the molecular mechanism for maintenance and differentiation of pluripotent stem cells. Stem Cells Dev, 22: 2240-2253.
13. Gofrit ON, Benjamin S, Halachmi S, Leibovitch I, Dotan Z, Lamm DL, Ehrlich N, Yutkin V, Ben-Am M, Hochberg A. 2014. DNA based therapy with diphtheria toxin-A BC-819: a phase 2b marker lesion trial in patients with intermediate risk nonmuscle invasive bladder cancer. J Urol, 191: 1697-1702.
14. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai M-C, Hung T, Argani P, Rinn JL. 2010. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature, 464: 1071-1076.
15. Hanahan D, Weinberg RA. 2000. The hallmarks of cancer. Cell, 100: 57-70.
16. Hanahan D, Weinberg RA. 2011. Hallmarks of cancer: the next generation. Cell, 144: 646-674.
17. Hibi K, Nakamura H, Hirai A, Fujikake Y, Kasai Y, Akiyama S, Ito K, Takagi H. 1996. Loss of H19 imprinting in esophageal cancer. Cancer Res, 56: 480-482.
18. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. 2009. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci, 106: 9362-9367.
19. Hu W, Yuan B, Flygare J, Lodish HF. 2011. Long noncoding RNA-mediated anti-apoptotic activity in murine erythroid terminal differentiation. Genes Dev, 25: 2573-2578.
20. Huarte M. 2015. The emerging role of lncRNAs in cancer. Nature Med, 21: 1253-1261.
21. Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, Khalil AM, Zuk O, Amit I, Rabani M. 2010. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell, 142: 409-419.
22. Hung T, Wang Y, Lin MF, Koegel AK, Kotake Y, Grant GD, Horlings HM, Shah N, Umbricht C, Wang P. 2011. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet, 43: 621-629.
23. Jarroux J, Morillon A, Pinskaya M. 2017. History, discovery, and classification of lncRNAs. Long non coding RNA biology, Adv Exp Med Biol, 1008: 1-46.
24. Jendrzejewski J, He H, Radomska HS, Li W, Tomsic J, Liyanarachchi S, Davuluri RV, Nagy R, De La Chapelle A. 2012. The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type. Proc Natl Acad Sci, 109: 8646-8651.
25. Jiang MC, Ni JJ, Cui WY, Wang BY, Zhuo W. 2019. Emerging roles of lncRNA in cancer and therapeutic opportunities. Am J Cancer Res, 9: 1354-1366.
26. Kalyana-Sundaram S, Kumar-Sinha C, Shankar S, Robinson DR, Wu Y-M, Cao X, Asangani IA, Kothari V, Prensner JR, Lonigro RJ. 2012. Expressed pseudogenes in the transcriptional landscape of human cancers. Cell, 149: 1622-1634.
27. Kanhere A, Viiri K, Araújo CC, Rasaiyaah J, Bouwman RD, Whyte WA, Pereira CF, Brookes E, Walker K, Bell GW. 2010. Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2. Mol Cell, 38: 675-688.
28. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, Van Oudenaarden A. 2009. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natil Acad Sci, 106: 11667-11672.
29. Kim WY, Sharpless NE. 2006. The regulation of INK4/ARF in cancer and aging. Cell, 127: 265-275.
30. Kotake Y, Nakagawa T, Kitagawa K, Suzuki S, Liu N, Kitagawa M, Xiong Y. 2011. Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15INK4B tumor suppressor gene. Oncogene, 30: 1956-1962.
31. Krappinger JC, Bonstingl L, Pansy K, Sallinger K, Wreglesworth NI, Grinninger L, Deutsch A, El-Heliebi A, Kroneis T, Mcfarlane RJ. 2021. Non-coding natural antisense transcripts: Analysis and application. J Biotechnol, 340: 75-101.
32. Liu YX, Wang L, Liu WJ, Zhang HT, Xue JH, Zhang ZW, Gao CJ. 2016. MiR-124-3p/B4GALT1 axis plays an important role in SOCS3-regulated growth and chemo-sensitivity of CML. J Hematol Oncol, 9: 1-12.
33. Liu Y, He A, Liu B, Huang Z, Mei H. 2019. Potential role of lncRNA H19 as a cancer biomarker in human cancers detection and diagnosis: a pooled analysis based on 1585 subjects. BioMed Res Int, 1: 1-11.
34. Liz J, Portela A, Soler M, Gomez A, Ling H, Michlewski G, Calin GA, Guil S, Esteller M. 2014. Regulation of pri-miRNA processing by a long noncoding RNA transcribed from an ultraconserved region. Mol Cell, 55: 138-147.
35. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, Mccarthy MI, Ramos EM, Cardon LR, Chakravarti A. 2009. Finding the missing heritability of complex diseases. Nature, 461: 747-753.
36. Matouk IJ, Degroot N, Mezan S, Ayesh S, Abu-Lail R, Hochberg A, Galun E. 2007. The H19 non-coding RNA is essential for human tumor growth. PloS one, 2: e845.
37. Mattick JS. 2001. Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep, 2: 986-991.
38. Mattick JS, Gagen MJ. 2001. The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms. Mol Biol Evol, 18: 1611-1630.
39. Mercer TR, Dinger ME, Mariani J, Kosik KS, Mehler MF, Mattick JS. 2008a. Noncoding RNAs in long-term memory formation. Neurosci, 14: 434-445.
40. Mercer TR, Dinger ME, Mattick JS. 2009. Long non-coding RNAs: insights into functions. Nat Rev Genet, 10: 155-159.
41. Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS. 2008b. Specific expression of long noncoding RNAs in the mouse brain. Proc. Natl Acad Sci, 105: 716-721.
42. Mitra SA, Mitra AP, Triche TJ. 2012. A central role for long non-coding RNA in cancer. Front Genet, 3: 17.
43. Ohtsuka T, Mitsuno M, Kitajima Y, Ide T, Lee SW, Miyazaki K. 2008. Role of ASC in hypoxia-mediated cell death in pancreatic cancer. Mol Med Rep, 1: 827-831.
44. Papait R, Kunderfranco P, Stirparo GG, Latronico MV, Condorelli G. 2013. Long noncoding RNA: a new player of heart failure? J Cardiovasc Transl Res, 6: 876-883.
45. Pasmant E, Sabbagh A, Masliah-Planchon J, Ortonne N, Laurendeau I, Melin L, Ferkal S, Hernandez L, Leroy K, Valeyrie-Allanore L. 2011. Role of noncoding RNA ANRIL in genesis of plexiform neurofibromas in neurofibromatosis type 1. J Natl Cancer Inst, 103: 1713-1722.
46. Patra CR, Ahmad I, Ayaz M, Khalil AT, Mukherjee S, Ovais M. 2021. Biogenic nanoparticles for cancer theranostics. Elsevier, Netherlands, 1st ed., pp: 143.
47. Pearson TA, Manolio TA. 2008. How to interpret a genome-wide association study. Jama, 299: 1335-1344.
48. Pintacuda G, Wei G, Roustan C, Kirmizitas BA, Solcan N, Cerase A, Castello A, Mohammed S, Moindrot B, Nesterova TB. 2017. hnRNPK recruits PCGF3/5-PRC1 to the Xist RNA B-repeat to establish polycomb-mediated chromosomal silencing. Mol Cell, 68: 955-969. e10.
49. Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP. 2010. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature, 465: 1033-1038.
50. Pontier DB, Gribnau J. 2011. Xist regulation and function explored. Hum Genet, 130: 223-236.
51. Ponting CP, Oliver PL, Reik W. 2009. Evolution and functions of long noncoding RNAs. Cell, 136: 629-641.
52. Qian Y, Shi L, Luo Z. 2020. Long non-coding RNAs in cancer: implications for diagnosis, prognosis, and therapy. Front Med, 7: 612393.
53. Ren, S, Peng Z, Mao J, Yu Y, Sun Y. 2012. RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings, Cell Res, 22:806–821.
54. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E. 2007. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell, 129: 1311-1323.
55. Schmitz SU, Grote P, Herrmann BG. 2016. Mechanisms of long noncoding RNA function in development and disease. Cell Mol Life Sci, 73: 2491-2509.
56. Smaldone MC, Davies BJ. 2010. BC-819, a plasmid comprising the H19 gene regulatory sequences and diphtheria toxin A, for the potential targeted therapy of cancers. Curr Opin Mol Ther, 12: 607-616.
57. Smolle MA, Bauernhofer T, Pummer K, Calin GA, Pichler M. 2017. Current insights into long non-coding RNAs (LncRNAs) in prostate cancer. Int J Mol Sci, 18: 473.
58. Tay Y, Kats L, Salmena L, Weiss D, Tan SM, Ala U, Karreth F, Poliseno L, Provero P, Di Cunto F. 2011. Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell, 147: 344-357.
59. Ulitsky I, Bartel DP. 2013. lincRNAs: genomics, evolution, and mechanisms. Cell, 154: 26-46.
60. Wang KC, Chang HY. 2011. Molecular mechanisms of long noncoding RNAs. Mol Cell, 43: 904-914.
61. Zhang X, Zhou Y, Mehta KR, Danila DC, Scolavino S, Johnson SR, Klibanski A. 2003. A pituitary-derived MEG3 isoform functions as a growth suppressor in tumor cells. J Clin Endocrinol Metab, 88: 5119-5126.
62. Zhao J, Sun BK, Erwin JA, Song J-J, Lee JT. 2008. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Sci, 322: 750-756.
63. Zhao Y, Li H, Fang S, Kang Y, Wu W, Hao Y, Li Z, Bu D, Sun N, Zhang MQ. 2016. NONCODE 2016: an informative and valuable data source of long non-coding RNAs. Nucleic Acids Res, 44: D203-D208.