Identification of a non-coding KLF4 transcript generated from intron retention and downregulated in human hepatocellular carcinoma

International Journal of Oncology

Volumn 47, Issue 4, 2015, Pages 1554-1562

  Zhou, Junwei ^a   Lai, Paul Bo San ^a   Tsui, Stephen Kwok Wing ^a  

^a CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

CpG island; Hepatocellular carcinoma; Hypermethylation; KLF4 003; Long non coding RNA

Indexed keywords

DECITABINE; GENOMIC DNA; KRUPPEL LIKE FACTOR 4; MESSENGER RNA; NUCLEAR RNA; KRUPPEL LIKE FACTOR; TUMOR MARKER; UNTRANSLATED RNA;

ADULT; ARTICLE; CANCER RECURRENCE; CANCER SIZE; CPG ISLAND; DEMETHYLATION; DIAGNOSTIC TEST ACCURACY STUDY; DIAGNOSTIC VALUE; DNA SEQUENCE; DOWN REGULATION; EXON; FEMALE; FOLLOW UP; HUMAN; HUMAN CELL; INTRON; INTRON RETENTION; LIVER CELL CARCINOMA; LIVER CIRRHOSIS; MAJOR CLINICAL STUDY; MALE; METHYLATION; OPEN READING FRAME; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; AGED; AREA UNDER THE CURVE; DNA METHYLATION; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETIC TRANSFECTION; GENETICS; LIVER TUMOR; MIDDLE AGED; RECEIVER OPERATING CHARACTERISTIC; SENSITIVITY AND SPECIFICITY; WESTERN BLOTTING;

ADULT; AGED; AREA UNDER CURVE; BIOMARKERS, TUMOR; BLOTTING, WESTERN; CARCINOMA, HEPATOCELLULAR; CPG ISLANDS; DNA METHYLATION; DOWN-REGULATION; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; INTRONS; KRUPPEL-LIKE TRANSCRIPTION FACTORS; LIVER NEOPLASMS; MALE; MIDDLE AGED; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, UNTRANSLATED; ROC CURVE; SENSITIVITY AND SPECIFICITY; TRANSCRIPTION, GENETIC; TRANSFECTION;

EID: 84941002199     PISSN: 10196439     EISSN: 17912423     Source Type: Journal    
DOI: 10.3892/ijo.2015.3104     Document Type: Article

References (33)

1. El-Serag HB and Rudolph KL: Hepatocellular carcinoma: Epidemiology and molecular carcinogenesis. Gastroenterology 132: 2557-2576, 2007.
2. Blum HE: Hepatocellular carcinoma: Therapy and prevention. World J Gastroenterol 11: 7391-7400, 2005.
3. Soini Y, Chia SC, Bennett WP, Groopman JD, Wang JS, DeBenedetti VM, Cawley H, Welsh JA, Hansen C, Bergasa NV, et al: An aflatoxin-associated mutational hotspot at codon 249 in the p53 tumor suppressor gene occurs in hepatocellular carcinomas from Mexico. Carcinogenesis 17: 1007-1012, 1996.
4. Donato F, Tagger A, Gelatti U, Parrinello G, Boffetta P, Albertini A, Decarli A, Trevisi P, Ribero ML, Martelli C, et al: Alcohol and hepatocellular carcinoma: The effect of lifetime intake and hepatitis virus infections in men and women. Am J Epidemiol 155: 323-331, 2002.
5. Wei D, Wang L, Kanai M, Jia Z, Le X, Li Q, Wang H and Xie K: KLF4α up-regulation promotes cell cycle progression and reduces survival time of patients with pancreatic cancer. Gastroenterology 139: 2135-2145, 2010.
6. Scherer SW, Cheung J, MacDonald JR, Osborne LR, Nakabayashi K, Herbrick JA, Carson AR, Parker-Katiraee L, Skaug J, Khaja R, et al: Human chromosome 7: DNA sequence and biology. Science 300: 767-772, 2003.
7. Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie R, Wakamatsu A, Hayashi K, Sato H, Nagai K, et al: Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet 36: 40-45, 2004.
8. Bartel DP: MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116: 281-297, 2004.
9. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, et al: MicroRNA expression profiles classify human cancers. Nature 435: 834-838, 2005.
10. Meltzer PS: Cancer genomics: Small RNAs with big impacts. Nature 435: 745-746, 2005.
11. Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, Petrocca F, Visone R, Iorio M, Roldo C, Ferracin M, et al: A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci USA 103: 2257-2261, 2006.
12. Erdmann VA, Barciszewska MZ, Szymanski M, Hochberg A, de Groot N and Barciszewski J: The non-coding RNAs as riboregulators. Nucleic Acids Res 29: 189-193, 2001.
13. Ji P, Diederichs S, Wang W, Böing S, Metzger R, Schneider PM, Tidow N, Brandt B, Buerger H, Bulk E, et al: MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene 22: 8031-8041, 2003.
14. O'Neill MJ: The influence of non-coding RNAs on allele-specific gene expression in mammals. Hum Mol Genet 14 (Suppl 1): R113-R120, 2005.
15. Steenman MJ, Rainier S, Dobry CJ, Grundy P, Horon IL and Feinberg AP: Loss of imprinting of IGF2 is linked to reduced expression and abnormal methylation of H19 in Wilms' tumour. Nat Genet 7: 433-439, 1994.
16. Lottin S, Adriaenssens E, Dupressoir T, Berteaux N, Montpellier C, Coll J, Dugimont T and Curgy JJ: Overexpression of an ectopic H19 gene enhances the tumorigenic properties of breast cancer cells. Carcinogenesis 23: 1885-1895, 2002.
17. Manoharan H, Babcock K, Willi J and Pitot HC: Biallelic expression of the H19 gene during spontaneous hepatocarcinogenesis in the albumin SV40 T antigen transgenic rat. Mol Carcinog 38: 40-47, 2003.
18. Hsu HT, Wu PR, Chen CJ, Hsu LS, Yeh CM, Hsing MT, Chiang YS, Lai MT and Yeh KT: High cytoplasmic expression of Krüppel-like factor 4 is an independent prognostic factor of better survival in hepatocellular carcinoma. Int J Mol Sci 15: 9894-9906, 2014.
19. Ponting CP, Oliver PL and Reik W: Evolution and functions of long noncoding RNAs. Cell 136: 629-641, 2009.
20. Calin GA, Liu CG, Ferracin M, Hyslop T, Spizzo R, Sevignani C, Fabbri M, Cimmino A, Lee EJ, Wojcik SE, et al: Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer Cell 12: 215-229, 2007.
21. Tsai MC, Spitale RC and Chang HY: Long intergenic noncoding RNAs: New links in cancer progression. Cancer Res 71: 3-7, 2011.
22. Hou J, Lin L, Zhou W, Wang Z, Ding G, Dong Q, Qin L, Wu X, Zheng Y, Yang Y, et al: Identification of miRNomes in human liver and hepatocellular carcinoma reveals miR-199a/b-3p as therapeutic target for hepatocellular carcinoma. Cancer Cell 19: 232-243, 2011.
23. Ji J, Shi J, Budhu A, Yu Z, Forgues M, Roessler S, Ambs S, Chen Y, Meltzer PS, Croce CM, et al: MicroRNA expression, survival, and response to interferon in liver cancer. N Engl J Med 361: 1437-1447, 2009.
24. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, et al; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group): The transcriptional landscape of the mammalian genome. Science 309: 1559-1563, 2005.
25. Boyes J and Bird A: DNA methylation inhibits transcription indirectly via a methyl-CpG binding protein. Cell 64: 1123-1134, 1991.
26. Compere SJ and Palmiter RD: DNA methylation controls the inducibility of the mouse metallothionein-I gene lymphoid cells. Cell 25: 233-240, 1981.
27. Kass SU, Landsberger N and Wolffe AP: DNA methylation directs a time-dependent repression of transcription initiation. Curr Biol 7: 157-165, 1997.
28. Siegfried Z, Eden S, Mendelsohn M, Feng X, Tsuberi BZ and Cedar H: DNA methylation represses transcription in vivo. Nat Genet 22: 203-206, 1999.
29. Hsieh CL: Stability of patch methylation and its impact in regions of transcriptional initiation and elongation. Mol Cell Biol 17: 5897-5904, 1997.
30. Watt F and Molloy PL: Cytosine methylation prevents binding to DNA of a HeLa cell transcription factor required for optimal expression of the adenovirus major late promoter. Genes Dev 2: 1136-1143, 1988.
31. Sarraf SA and Stancheva I: Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly. Mol Cell 15: 595-605, 2004.
32. Klose RJ and Bird AP: Genomic DNA methylation: The mark and its mediators. Trends Biochem Sci 31: 89-97, 2006.
33. Clark MB, Johnston RL, Inostroza-Ponta M, Fox AH, Fortini E, Moscato P, Dinger ME and Mattick JS: Genome-wide analysis of long noncoding RNA stability. Genome Res 22: 885-898, 2012.