Extending Lines from Epigenetic to Cancer: Long Non-coding RNAs

Year 2018, Volume: 40 Issue: 3, 114 - 121, 01.09.2018

Didem Turgut Coşan Emine Yağcı , Hülyam Kurt

https://doi.org/10.20515/otd.440958

Cited By: 1

Abstract

Transcripts that do not have
the protein coding capacity in the human genome are called non- coding RNAs
(ncRNAs). These non-coding RNAs are divided into two major categories as small
non-coding RNAs (sncRNA) and long non-coding RNAs (lncRNA), depending on their
length. LncRNAs are a group of non-coding RNAs of > 200 nucleotides. They
function through molecular and biochemical mechanisms, including cis and trans
regulation of gene expression, epigenetic modulation of the nucleus and post-transcriptional
control in the cytoplasm. LncRNAs may localize to part such as cytoplasm,
nucleus, and mitochondria in the cell, and may alter their function depending
on where they are localized. They have the ability to interact with various
chromatin modifying complexes to modulate the chromatin state. The ability of
collect and bind to chromatin to these complexes of lncRNAs can control gene
expression by altering epigenetic structure. Recent studies have shown that
lncRNAs may be an oncogenic or tumor suppressor function; suggesting that
lncRNAs play an important role in the development and progression of cancer.
LncRNAs play an important  role in many
types of cancer, and they may represent potential therapeutic targets because
they can be used as biomarkers to predict recurrence and prognosis. In this review, will refer to the general
characteristics, localizations, functions of lncRNAs, and cancer-related
lncRNAs. Thus, it is intended that readers will have different views on the
relationship between lncRNAs, which are thought to be important intermediates
in the progression of various cancers in the future, and some cancer mechanisms
that have not yet been fully exploited.

Keywords

Long non-coding RNAs, gene expression, cancer, epigenetic

Epigenetikten Kansere Uzanan Çizgiler: Uzun Kodlamayan RNA’lar

Abstract

İnsan genomununda protein
kodlama kapasitesine sahip olmayan transkriptler kodlamayan RNA (ncRNA) olarak
adlandırılmaktadır. Bu kodlamayan RNA’lar
uzunluklarına göre küçük kodlamayan RNA’lar (sncRNA) ve uzun kodlamayan RNA'lar
(lncRNA) olarak iki ana kategoriye ayrılır. LncRNA'lar, >200 nükleotidden
oluşan bir grup kodlamayan RNA'dır. Gen ekspresyonunun cis ve trans
regülasyonu, çekirdeğin epigenetik modülasyonu ve sitoplazmada
post-transkripsiyonel kontrolü de içeren moleküler ve biyokimyasal mekanizmalar
yoluyla işlev görürler. LncRNA’lar hücrede sitoplazma, çekirdek ve mitokondri
gibi alanlara lokalize olabilirler ve lokalize oldukları yere göre
fonksiyonları değişiklik gösterebilir. Kromatin durumunu modüle etmek için
çeşitli kromatin remodelingte rol oynayan komplekslerle etkileşme kapasitesine
sahiptirler. LncRNA'ların bu kabiliyeti, epigenetik yapıyı değiştirerek gen
ekspresyonunu kontrol edebilir. Son yıllarda yapılan çalışmalar, lncRNA'ların
onkojenik veya tümör baskılayıcı fonksiyonu olabileceğini göstermektedir; bu da
onların kanser gelişiminde ve ilerlemesinde önemli bir rol oynadığını ortaya
koymaktadır. LncRNA'lar birçok kanser türünde önemli rol oynar. Nüks ve
prognozu öngörmek için biyolojik belirteç olarak kullanılabileceklerinden
dolayı kanserde potansiyel terapötik hedefler olarak gösterebilirler. Bu derlemede, lncRNA'ların genel özellikleri,
lokalizasyonları, fonksiyonları ve kanser ile ilişkili olan lncRNA çeşitlerine
değinilecektir. Böylece okuyucularda, gelecekte çeşitli kanserlerin
progresyonunda önemli ara bileşenler olabileceği düşünülen lncRNA’larla, henüz
tam olarak açıklığa kavuşmamış bazı kanser mekanizmaları arasındaki ilişki
hakkında farklı bakış açılarının oluşturulması amaçlanmaktadır.

Keywords

Uzun kodlamayan RNA’lar, gen ekspresyonu, kanser, epigenetik

References

• 1. Djebali, S., et al., Landscape of transcription in human cells. Nature, 2012. 489(7414): p. 101-108.
• 2. Deniz, E. and B. Erman, Long noncoding RNA (lincRNA), a new paradigm in gene expression control. Functional & integrative genomics, 2016: p. 1-9.
• 3. Katayama, S., et al., Antisense transcription in the mammalian transcriptome. Science, 2005. 309(5740): p. 1564-1566.
• 4. Cabili, M.N., et al., Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes & development, 2011. 25(18): p. 1915-1927.
• 5. Groux, H., et al., A 19-kDa human erythrocyte molecule H19 is involved in rosettes, present on nucleated cells, and required for T cell activation. Comparison of the roles of H19 and LFA-3 molecules in T cell activation. The Journal of Immunology, 1989. 142(9): p. 3013-3020.
• 6. Brown, C.J. and A. Ballabio, A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature, 1991. 349(6304): p. 38.
• 7. Briggs, S.F. and R.A.R. Pera, X chromosome inactivation: recent advances and a look forward. Current opinion in genetics & development, 2014. 28: p. 78-82.
• 8. Laurent, G.S., C. Wahlestedt, and P. Kapranov, The Landscape of long noncoding RNA classification. Trends in Genetics, 2015. 31(5): p. 239-251.
• 9. Derrien, T., et al., The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome research, 2012. 22(9): p. 1775-1789.
• 10. Ponting, C.P., P.L. Oliver, and W. Reik, Evolution and functions of long noncoding RNAs. Cell, 2009. 136(4): p. 629-641.
• 11. Carlevaro-Fita, J., et al., Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells. RNA, 2016. 22(6): p. 867-882.
• 12. Noh, J.H., et al., HuR and GRSF1 modulate the nuclear export and mitochondrial localization of the lncRNA RMRP. Genes & development, 2016. 30(10): p. 1224-1239.
• 13. Wilk, R., et al., Diverse and pervasive subcellular distributions for both coding and long noncoding RNAs. Genes & development, 2016. 30(5): p. 594-609.
• 14. Chen, L.L. and G.G. Carmichael, Long noncoding RNAs in mammalian cells: what, where, and why? Wiley Interdisciplinary Reviews: RNA, 2010. 1(1): p. 2-21.
• 15. Zhang, R., et al., LncRNAs and cancer (Review). Oncology Letters, 2016. 12(2): p. 1233-1239.
• 16. Rutenberg-Schoenberg, M., A.N. Sexton, and M.D. Simon, The properties of long noncoding RNAs that regulate chromatin. Annual review of genomics and human genetics, 2016. 17: p. 69-94.
• 17. Fatica, A. and I. Bozzoni, Long non-coding RNAs: new players in cell differentiation and development. Nature Reviews Genetics, 2014. 15(1): p. 7-21.
• 18. Wang, K.C., et al., A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature, 2011. 472(7341): p. 120-124.
• 19. Cloonan, N., et al., Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nature methods, 2008. 5(7): p. 613-619.
• 20. Wilusz, J.E., H. Sunwoo, and D.L. Spector, Long noncoding RNAs: functional surprises from the RNA world. Genes & development, 2009. 23(13): p. 1494-1504.
• 21. Batista, P.J. and H.Y. Chang, Long noncoding RNAs: cellular address codes in development and disease. Cell, 2013. 152(6): p. 1298-1307.
• 22. Guttman, M. and J.L. Rinn, Modular regulatory principles of large non-coding RNAs. Nature, 2012. 482(7385): p. 339-346.
• 23. Khorkova, O., J. Hsiao, and C. Wahlestedt, Basic biology and therapeutic implications of lncRNA. Advanced drug delivery reviews, 2015. 87: p. 15-24.
• 24. Prensner, J.R. and A.M. Chinnaiyan, The emergence of lncRNAs in cancer biology. Cancer discovery, 2011. 1(5): p. 391-407.
• 25. WEIDLE, U.H., et al., Long Non-coding RNAs and their Role in Metastasis. Cancer Genomics-Proteomics, 2017. 14(3): p. 143-160.
• 26. Yen, K., et al., Genome-wide nucleosome specificity and directionality of chromatin remodelers. Cell, 2012. 149(7): p. 1461-1473.
• 27. Tano, K. and N. Akimitsu, Long non-coding RNAs in cancer progression. Frontiers in genetics, 2012. 3.
• 28. Cogill, S.B. and L. Wang, Co-expression network analysis of human lncRNAs and cancer genes. Cancer informatics, 2014(Suppl. 5): p. 49.
• 29. Hindorff, L.A., et al., Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proceedings of the National Academy of Sciences, 2009. 106(23): p. 9362-9367.
• 30. Gupta, R.A., et al., Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature, 2010. 464(7291): p. 1071-1076.
• 31. Guo, W., et al., Associations between polymorphisms of HOTAIR and risk of gastric cardia adenocarcinoma in a population of north China. Tumor Biology, 2015. 36(4): p. 2845-2854.
• 32. Loewen, G., et al., Functions of lncRNA HOTAIR in lung cancer. Journal of hematology & oncology, 2014. 7(1): p. 90.
• 33. You, Q.-Y., H. Tao, and B. Ling, Long noncoding RNA HOX transcript antisense intergenic RNA (HOTAIR) as a foe and novel potential therapeutic target for endometrial carcinoma. International Journal of Gynecological Cancer, 2014. 24(9): p. 1536.
• 34. Zhang, K., et al., Long non-coding RNA HOTAIR promotes glioblastoma cell cycle progression in an EZH2 dependent manner. Oncotarget, 2015. 6(1): p. 537.
• 35. Weng, A.P., et al., Activating mutations of NOTCH1 in human T cell acute lymphoblastic leukemia. Science, 2004. 306(5694): p. 269-271.
• 36. Trimarchi, T., et al., Genome-wide mapping and characterization of Notch-regulated long noncoding RNAs in acute leukemia. Cell, 2014. 158(3): p. 593-606.
• 37. Zhang, A., M. Xu, and Y.-Y. Mo, Role of the lncRNA–p53 regulatory network in cancer. Journal of molecular cell biology, 2014. 6(3): p. 181-191.
• 38. Gutschner, T., M. Hämmerle, and S. Diederichs, MALAT1—a paradigm for long noncoding RNA function in cancer. Journal of molecular medicine, 2013. 91(7): p. 791-801.
• 39. Ellis, M.J., et al., Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature, 2012. 486(7403): p. 353-360.
• 40. Du, Z., et al., Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer. Nature communications, 2016. 7.
• 41. Xu, Y., et al., Upregulation of the long noncoding RNA TUG1 promotes proliferation and migration of esophageal squamous cell carcinoma. Tumor Biology, 2015. 36(3): p. 1643-1651.
• 42. Li, Q., et al., Plasma long noncoding RNA protected by exosomes as a potential stable biomarker for gastric cancer. Tumor Biology, 2015. 36(3): p. 2007-2012.
• 43. Hu, Y., et al., Long noncoding RNA GAPLINC regulates CD44-dependent cell invasiveness and associates with poor prognosis of gastric cancer. Cancer research, 2014. 74(23): p. 6890-6902.
• 44. Ding, J., et al., Expression and clinical significance of the long non-coding RNA PVT1 in human gastric cancer. OncoTargets and therapy, 2014. 7: p. 1625.
• 45. Xu, T.-p., et al., Decreased expression of the long non-coding RNA FENDRR is associated with poor prognosis in gastric cancer and FENDRR regulates gastric cancer cell metastasis by affecting fibronectin1 expression. Journal of hematology & oncology, 2014. 7(1): p. 63.
• 46. Kang, L., et al., Aberrant allele-switch imprinting of a novel IGF1R intragenic antisense non-coding RNA in breast cancers. European journal of cancer, 2015. 51(2): p. 260-270.
• 47. Fidler, I.J., The pathogenesis of cancer metastasis: the'seed and soil'hypothesis revisited. Nature Reviews Cancer, 2003. 3(6): p. 453.
• 48. Langley, R.R. and I.J. Fidler, The seed and soil hypothesis revisited—The role of tumor‐stroma interactions in metastasis to different organs. International journal of cancer, 2011. 128(11): p. 2527-2535.
• 49. Poste, G. and I.J. Fidler, The pathogenesis of cancer metastasis. Nature, 1980. 283(5743): p. 139.
• 50. Chiang, A.C. and J. Massagué, Molecular basis of metastasis. New England Journal of Medicine, 2008. 359(26): p. 2814-2823.
• 51. Pencheva, N. and S.F. Tavazoie, Control of metastatic progression by microRNA regulatory networks. Nature cell biology, 2013. 15(6): p. 546.
• 52. Bouyssou, J.M., et al., Regulation of microRNAs in cancer metastasis. Biochimica et Biophysica Acta (BBA)-Reviews on Cancer, 2014. 1845(2): p. 255-265.
• 53. Ling, H., et al., CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer. Genome research, 2013. 23(9): p. 1446-1461.
• 54. Cai, Y., J. He, and D. Zhang, Long noncoding RNA CCAT2 promotes breast tumor growth by regulating the Wnt signaling pathway. OncoTargets and therapy, 2015. 8: p. 2657.
• 55. Redis, R.S., et al., CCAT2, a novel long non-coding RNA in breast cancer: expression study and clinical correlations. Oncotarget, 2013. 4(10): p. 1748.
• 56. Yang, F., et al., Long noncoding RNA high expression in hepatocellular carcinoma facilitates tumor growth through enhancer of zeste homolog 2 in humans. Hepatology, 2011. 54(5): p. 1679-1689.
• 57. Yang, F., et al., Repression of the long noncoding RNA-LET by histone deacetylase 3 contributes to hypoxia-mediated metastasis. Molecular cell, 2013. 49(6): p. 1083-1096.
• 58. Yuan, J.-h., et al., A long noncoding RNA activated by TGF-β promotes the invasion-metastasis cascade in hepatocellular carcinoma. Cancer cell, 2014. 25(5): p. 666-681.
• 59. Ikushima, H. and K. Miyazono, TGFβ signalling: a complex web in cancer progression. Nature reviews cancer, 2010. 10(6): p. 415.
• 60. Gregory, P.A., et al., The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1. Nature cell biology, 2008. 10(5): p. 593.
• 61. Butz, H., et al., Crosstalk between TGF-β signaling and the microRNA machinery. Trends in pharmacological sciences, 2012. 33(7): p. 382-393.
• 62. Tycowski, K.T., et al., Viral noncoding RNAs: more surprises. Genes & development, 2015. 29(6): p. 567-584.
• 63. Huarte, M., The emerging role of lncRNAs in cancer. Nature medicine, 2015. 21(11): p. 1253-1261.
• 64. Ling, H., M. Fabbri, and G.A. Calin, MicroRNAs and other non-coding RNAs as targets for anticancer drug development. Nature reviews Drug discovery, 2013. 12(11): p. 847-865.
• 65. Yarmishyn, A.A. and I.V. Kurochkin, Long noncoding RNAs: a potential novel class of cancer biomarkers. Frontiers in genetics, 2015. 6: p. 145.
• 66. Sun, M. and W.L. Kraus, From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease. Endocrine reviews, 2015. 36(1): p. 25-64.