Comprehensive gene expression analysis of 5'-end of mRNA identified novel intronic transcripts associated with hepatocellular carcinoma

Genomics

Volumn 95, Issue 4, 2010, Pages 217-223

  Hodo, Yuji ^a   Hashimoto, Shin Ichi ^b   Honda, Masao ^a   Yamashita, Taro ^a   Suzuki, Yutaka ^c   Sugano, Sumio ^c   Kaneko, Shuichi ^a   Matsushima, Kouji ^b  

^a KANAZAWA UNIVERSITY GRADUATE SCHOOL OF MEDICAL SCIENCE   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

Author keywords

5' end serial analysis of gene expression; Acyl coenzyme A oxidase 2; Hepatocellular carcinoma; Intron; Transcriptional start site

Indexed keywords

ACYL COENZYME A OXIDASE; MESSENGER RNA; TUMOR MARKER;

ADULT; ARTICLE; CASE REPORT; CONTROLLED STUDY; DATA BASE; GENE EXPRESSION REGULATION; GENE LIBRARY; GENE MAPPING; GENE SEQUENCE; GENOME; HUMAN; HUMAN TISSUE; INTRON; LIVER CELL CARCINOMA; MALE; PRIORITY JOURNAL; RNA STRUCTURE; SERIAL ANALYSIS OF GENE EXPRESSION; TRANSCRIPTION INITIATION; TRANSCRIPTION INITIATION SITE; UPREGULATION;

ACYL-COA OXIDASE; CARCINOMA, HEPATOCELLULAR; CELLS, CULTURED; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; INTRONS; LIVER; LIVER NEOPLASMS; MALE; MIDDLE AGED; RNA, MESSENGER; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION, GENETIC;

EID: 77950340458     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2010.01.004     Document Type: Article

References (29)

1. El-Serag H.B., Rudolph K.L. Hepatocellular carcinoma: epidemiology and molecular carcinogenesis. Gastroenterology 2007, 132:2557-2576.
2. Yokoi Y., Suzuki S., Baba S., Inaba K., Konno H., Nakamura S. Clinicopathological features of hepatocellular carcinomas (HCCs) arising in patients without chronic viral infection or alcohol abuse: a retrospective study of patients undergoing hepatic resection. J. Gastroenterol. 2005, 40:274-282.
3. Aravalli R.N., Steer C.J., Cressman E.N. Molecular mechanisms of hepatocellular carcinoma. Hepatology 2008, 48:2047-2063.
4. Duggan D.J., Bittner M., Chen Y., Meltzer P., Trent J.M. Expression profiling using cDNA microarrays. Nat. Genet. 1999, 21:10-14.
5. Velculescu V.E., Zhang L., Vogelstein B., Kinzler K.W. Serial analysis of gene expression. Science 1995, 270:484-487.
6. Yamashita T., Hashimoto S., Kaneko S., Nagai S., Toyoda N., Suzuki T., Kobayashi K., Matsushima K. Comprehensive gene expression profile of a normal human liver. Biochem. Biophys. Res. Commun. 2000, 269:110-116.
7. Hashimoto S., Nagai S., Sese J., Suzuki T., Obata A., Sato T., Toyoda N., Dong H.Y., Kurachi M., Nagahata T., Shizuno K., Morishita S., Matsushima K. Gene expression profile in human leukocytes. Blood 2003, 101:3509-3513.
8. Okabe H., Satoh S., Kato T., Kitahara O., Yanagawa R., Yamaoka Y., Tsunoda T., Furukawa Y., Nakamura Y. Genome-wide analysis of gene expression in human hepatocellular carcinomas using cDNA microarray: identification of genes involved in viral carcinogenesis and tumor progression. Cancer. Res. 2001, 61:2129-2137.
9. Shirota Y., Kaneko S., Honda M., Kawai H.F., Kobayashi K. Identification of differentially expressed genes in hepatocellular carcinoma with cDNA microarrays. Hepatology 2001, 33:832-840.
10. Yamashita T., Honda M., Kaneko S. Application of serial analysis of gene expression in cancer research. Curr. Pharm. Biotechnol. 2008, 9:375-382.
11. Suzuki Y., Taira H., Tsunoda T., Mizushima-Sugano J., Sese J., Hata H., Ota T., Isogai T., Tanaka T., Morishita S., Okubo K., Sakaki Y., Nakamura Y., Suyama A., Sugano S. Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. EMBO Rep. 2001, 2:388-393.
12. Kimura K., Wakamatsu A., Suzuki Y., Ota T., Nishikawa T., Yamashita R., Yamamoto J., Sekine M., Tsuritani K., Wakaguri H., Ishii S., Sugiyama T., Saito K., Isono Y., Irie R., Kushida N., Yoneyama T., Otsuka R., Kanda K., Yokoi T., Kondo H., Wagatsuma M., Murakawa K., Ishida S., Ishibashi T., Takahashi-Fujii A., Tanase T., Nagai K., Kikuchi H., Nakai K., Isogai T., Sugano S. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome. Res. 2006, 16:55-65.
13. Shiraki T., Kondo S., Katayama S., Waki K., Kasukawa T., Kawaji H., Kodzius R., Watahiki A., Nakamura M., Arakawa T., Fukuda S., Sasaki D., Podhajska A., Harbers M., Kawai J., Carninci P., Hayashizaki Y. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc. Natl. Acad. Sci. U. S. A. 2003, 100:15776-15781.
14. Hashimoto S., Suzuki Y., Kasai Y., Morohoshi K., Yamada T., Sese J., Morishita S., Sugano S., Matsushima K. 5'-end SAGE for the analysis of transcriptional start sites. Nat. Biotechnol. 2004, 22:1146-1149.
15. Yamashita T., Kaneko S., Hashimoto S., Sato T., Nagai S., Toyoda N., Suzuki T., Kobayashi K., Matsushima K. Serial analysis of gene expression in chronic hepatitis C and hepatocellular carcinoma. Biochem. Biophys. Res. Commun. 2001, 282:647-654.
16. Yamashita T., Honda M., Takatori H., Nishino R., Minato H., Takamura H., Ohta T., Kaneko S. Activation of lipogenic pathway correlates with cell proliferation and poor prognosis in hepatocellular carcinoma. J. Hepatol. 2009, 50:100-110.
17. Mattick J.S. Introns: evolution and function. Curr. Opin. Genet. Dev. 1994, 4:823-831.
18. Mattick J.S., Makunin I.V. Non-coding RNA. Hum. Mol. Genet. 2006, 15(Spec No 1):R17-29.
19. Louro R., Smirnova A.S., Verjovski-Almeida S. Long intronic noncoding RNA transcription: expression noise or expression choice?. Genomics 2009, 93:291-298.
20. Yu S., Rao S., Reddy J.K. Peroxisome proliferator-activated receptors, fatty acid oxidation, steatohepatitis and hepatocarcinogenesis. Curr. Mol. Med. 2003, 3:561-572.
21. Kondoh N., Wakatsuki T., Ryo A., Hada A., Aihara T., Horiuchi S., Goseki N., Matsubara O., Takenaka K., Shichita M., Tanaka K., Shuda M., Yamamoto M. Identification and characterization of genes associated with human hepatocellular carcinogenesis. Cancer. Res. 1999, 59:4990-4996.
22. Kobayashi Y., Higashi T., Nouso K., Nakatsukasa H., Ishizaki M., Kaneyoshi T., Toshikuni N., Kariyama K., Nakayama E., Tsuji T. Expression of MAGE, GAGE and BAGE genes in human liver diseases: utility as molecular markers for hepatocellular carcinoma. J. Hepatol. 2000, 32:612-617.
23. Minn A.H., Kayton M., Lorang D., Hoffmann S.C., Harlan D.M., Libutti S.K., Shalev A. Insulinomas and expression of an insulin splice variant. Lancet 2004, 363:363-367.
24. Stier H., Fahimi H.D., Van Veldhoven P.P., Mannaerts G.P., Volkl A., Baumgart E. Maturation of peroxisomes in differentiating human hepatoblastoma cells (HepG2): possible involvement of the peroxisome proliferator-activated receptor alpha (PPAR alpha). Differentiation 1998, 64:55-66.
25. Zha S., Ferdinandusse S., Hicks J.L., Denis S., Dunn T.A., Wanders R.J., Luo J., De Marzo A.M., Isaacs W.B. Peroxisomal branched chain fatty acid beta-oxidation pathway is upregulated in prostate cancer. Prostate 2005, 63:316-323.
26. Tokuoka K., Nakajima Y., Hirotsu K., Miyahara I., Nishina Y., Shiga K., Tamaoki H., Setoyama C., Tojo H., Miura R. Three-dimensional structure of rat-liver acyl-CoA oxidase in complex with a fatty acid: insights into substrate-recognition and reactivity toward molecular oxygen. J. Biochem. 2006, 139:789-795.
27. Meyer K., Jia Y., Cao W.Q., Kashireddy P., Rao M.S. Expression of peroxisome proliferator-activated receptor alpha, and PPARalpha regulated genes in spontaneously developed hepatocellular carcinomas in fatty acyl-CoA oxidase null mice. Int. J. Oncol. 2002, 21:1175-1180.
28. Tanaka N., Moriya K., Kiyosawa K., Koike K., Gonzalez F.J., Aoyama T. PPARalpha activation is essential for HCV core protein-induced hepatic steatosis and hepatocellular carcinoma in mice. J. Clin. Invest. 2008, 118:683-694.
29. Rubie C., Kempf K., Hans J., Su T., Tilton B., Georg T., Brittner B., Ludwig B., Schilling M. Housekeeping gene variability in normal and cancerous colorectal, pancreatic, esophageal, gastric and hepatic tissues. Mol. Cell. Probes. 2005, 19:101-109.