RNA-seq analyses generate comprehensive transcriptomic landscape and reveal complex transcript patterns in hepatocellular carcinoma

PLoS ONE

Volumn 6, Issue 10, 2011, Pages

  Huang, Qichao ^a   Lin, Biaoyang ^b,c   Liu, Hanqiang ^a   Ma, Xi ^a   Mo, Fan ^b   Yu, Wei ^b   Li, Lisha ^b   Li, Hongwei ^a   Tian, Tian ^d   Wu, Dong ^e   Shen, Feng ^e   Xing, Jinliang ^a   Chen, Zhi Nan ^a  

^a FOURTH MILITARY MEDICAL UNIVERSITY   (China)

^b ZHEJIANG UNIVERSITY   (China)

^c UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^d BEIJING JIAOTONG UNIVERSITY   (China)

^e SECOND MILITARY MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; TRANSCRIPTOME; ISOPROTEIN; MESSENGER RNA;

ANILLIN ACTIN BINDING PROTEIN GENE; ARTICLE; ATAD2 GENE; CANCER TISSUE; CELL GROWTH; CELL METABOLISM; CHROMOSOME 8Q; CONTROLLED STUDY; EXON; G 2 AND S PHASE EXPRESSED 1 GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC VARIABILITY; HEPATITIS B; HUMAN; IMMUNE RESPONSE; KINESIN FAMILY MEMBER 14 GENE; LIVER CARCINOGENESIS; LIVER CELL CARCINOMA; MACROPHAGE RECEPTOR WITH COLLAGENOUS GENE; MAJOR CLINICAL STUDY; PROSTAGLANDIN 12 SYNTHASE GENE; RNA SEQUENCE; RNA SPLICING; SEQUENCE ALIGNMENT; TISSUE FACTOR PATHWAY INHIBITOR 2 GENE; TRANSCRIPTOMICS; TUMOR GENE; UPREGULATION; GENETICS; LIVER TUMOR; PATHOLOGY; SEQUENCE ANALYSIS;

HEPATITIS B VIRUS;

CARCINOMA, HEPATOCELLULAR; EXONS; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; LIVER NEOPLASMS; PROTEIN ISOFORMS; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 80054771709     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0026168     Document Type: Article

References (55)

1. But DY, Lai CL, Yuen MF, (2008) Natural history of hepatitis-related hepatocellular carcinoma. World J Gastroenterol 14: 1652-1656.
2. Patil MA, Gutgemann I, Zhang J, Ho C, Cheung ST, et al. (2005) Array-based comparative genomic hybridization reveals recurrent chromosomal aberrations and Jab1 as a potential target for 8q gain in hepatocellular carcinoma. Carcinogenesis 26: 2050-2057.
3. Xu XR, Huang J, Xu ZG, Qian BZ, Zhu ZD, et al. (2001) Insight into hepatocellular carcinogenesis at transcriptome level by comparing gene expression profiles of hepatocellular carcinoma with those of corresponding noncancerous liver. Proc Natl Acad Sci U S A 98: 15089-15094.
4. Liang CR, Leow CK, Neo JC, Tan GS, Lo SL, et al. (2005) Proteome analysis of human hepatocellular carcinoma tissues by two-dimensional difference gel electrophoresis and mass spectrometry. Proteomics 5: 2258-2271.
5. Nam SW, Park JY, Ramasamy A, Shevade S, Islam A, et al. (2005) Molecular changes from dysplastic nodule to hepatocellular carcinoma through gene expression profiling. Hepatology 42: 809-818.
6. Lee JS, Chu IS, Heo J, Calvisi DF, Sun Z, et al. (2004) Classification and prediction of survival in hepatocellular carcinoma by gene expression profiling. Hepatology 40: 667-676.
7. Iizuka N, Oka M, Yamada-Okabe H, Mori N, Tamesa T, et al. (2002) Comparison of gene expression profiles between hepatitis B virus- and hepatitis C virus-infected hepatocellular carcinoma by oligonucleotide microarray data on the basis of a supervised learning method. Cancer Res 62: 3939-3944.
8. Pawitan Y, Michiels S, Koscielny S, Gusnanto A, Ploner A, (2005) False discovery rate, sensitivity and sample size for microarray studies. Bioinformatics 21: 3017-3024.
9. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y, (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18: 1509-1517.
10. Mardis ER, (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24: 133-141.
11. Wang Z, Gerstein M, Snyder M, (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
12. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349.
13. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B, (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628.
14. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, et al. (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321: 956-960.
15. Berger MF, Levin JZ, Vijayendran K, Sivachenko A, Adiconis X, et al. (2010) Integrative analysis of the melanoma transcriptome. Genome Res 20: 413-427.
16. Li R, Yu C, Li Y, Lam TW, Yiu SM, et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966-1967.
17. Mo F, Hong X, Gao F, Du L, Wang J, et al. (2008) A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data. BMC Bioinformatics 9: 537.
18. Robinson MD, McCarthy DJ, Smyth GK, (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
19. Burchard J, Zhang C, Liu AM, Poon RT, Lee NP, et al. (2010) microRNA-122 as a regulator of mitochondrial metabolic gene network in hepatocellular carcinoma. Mol Syst Biol 6: 402.
20. De Preter K, Barriot R, Speleman F, Vandesompele J, Moreau Y, (2008) Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions. Nucleic Acids Res 36: e43.
21. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102: 15545-15550.
22. De Bona F, Ossowski S, Schneeberger K, Ratsch G, (2008) Optimal spliced alignments of short sequence reads. Bioinformatics 24: i174-180.
23. Au KF, Jiang H, Lin L, Xing Y, Wong WH, (2010) Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res 38: 4570-4578.
24. Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, et al. (2010) MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res 38: e178.
25. Trapnell C, Pachter L, Salzberg SL, (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
26. Wu TD, Nacu S, (2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26: 873-881.
27. Jean G, Kahles A, Sreedharan VT, De Bona F, Ratsch G, (2010) RNA-Seq read alignments with PALMapper. Curr Protoc Bioinformatics Chapter 11: Unit 11 16.
28. Livak KJ, Schmittgen TD, (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25: 402-408.
29. Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN, (2010) RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics 26: 493-500.
30. Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, et al. (2002) Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A 99: 4465-4470.
31. Jongeneel CV, Delorenzi M, Iseli C, Zhou D, Haudenschild CD, et al. (2005) An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Res 15: 1007-1014.
32. Wong N, Lai P, Lee SW, Fan S, Pang E, et al. (1999) Assessment of genetic changes in hepatocellular carcinoma by comparative genomic hybridization analysis: relationship to disease stage, tumor size, and cirrhosis. Am J Pathol 154: 37-43.
33. Kusano N, Shiraishi K, Kubo K, Oga A, Okita K, et al. (1999) Genetic aberrations detected by comparative genomic hybridization in hepatocellular carcinomas: their relationship to clinicopathological features. Hepatology 29: 1858-1862.
34. Smith MW, Yue ZN, Geiss GK, Sadovnikova NY, Carter VS, et al. (2003) Identification of novel tumor markers in hepatitis C virus-associated hepatocellular carcinoma. Cancer Res 63: 859-864.
35. Sugarbaker DJ, Richards WG, Gordon GJ, Dong L, De Rienzo A, et al. (2008) Transcriptome sequencing of malignant pleural mesothelioma tumors. Proc Natl Acad Sci U S A 105: 3521-3526.
36. Nakatsura T, Yoshitake Y, Senju S, Monji M, Komori H, et al. (2003) Glypican-3, overexpressed specifically in human hepatocellular carcinoma, is a novel tumor marker. Biochem Biophys Res Commun 306: 16-25.
37. Oya H, Sato Y, Yamamoto S, Nakatsuka H, Kobayashi T, et al. (2006) Comparison between human-telomerase reverse transcriptase mRNA and alpha-fetoprotein mRNA as a predictive value for recurrence of hepatocellular carcinoma in living donor liver transplantation. Transplant Proc 38: 3636-3639.
38. Ohmachi Y, Murata A, Matsuura N, Yasuda T, Yasuda T, et al. (1993) Specific expression of the pancreatic-secretory-trypsin-inhibitor (PSTI) gene in hepatocellular carcinoma. Int J Cancer 55: 728-734.
39. Kang YH, Ji NY, Lee CI, Lee HG, Kim JW, et al. (2010) ESM-1 silencing decreased cell survival, migration, and invasion and modulated cell cycle progression in hepatocellular carcinoma. Amino Acids.
40. Yang JD, Roberts LR, (2010) Hepatocellular carcinoma: A global view. Nat Rev Gastroenterol Hepatol 7: 448-458.
41. Morgan ET, (1993) Down-regulation of multiple cytochrome P450 gene products by inflammatory mediators in vivo. Independence from the hypothalamo-pituitary axis. Biochem Pharmacol 45: 415-419.
42. Parmiani G, Anichini A, (2006) T cell infiltration and prognosis in HCC patients. J Hepatol 45: 178-181.
43. Yeligar S, Tsukamoto H, Kalra VK, (2009) Ethanol-induced expression of ET-1 and ET-BR in liver sinusoidal endothelial cells and human endothelial cells involves hypoxia-inducible factor-1alpha and microrNA-199. J Immunol 183: 5232-5243.
44. Chan KY, Lai PB, Squire JA, Beheshti B, Wong NL, et al. (2006) Positional expression profiling indicates candidate genes in deletion hotspots of hepatocellular carcinoma. Mod Pathol 19: 1546-1554.
45. Crawley JJ, Furge KA, (2002) Identification of frequent cytogenetic aberrations in hepatocellular carcinoma using gene-expression microarray data. Genome Biol 3: RESEARCH0075.
46. Schmidt EV, (1999) The role of c-myc in cellular growth control. Oncogene 18: 2988-2996.
47. Payton M, Coats S, (2002) Cyclin E2, the cycle continues. Int J Biochem Cell Biol 34: 315-320.
48. Wang X, Narayanan M, Bruey JM, Rigamonti D, Cattaneo E, et al. (2006) Protective role of Cop in Rip2/caspase-1/caspase-4-mediated HeLa cell death. Biochim Biophys Acta 1762: 742-754.
49. Wong N, Chan A, Lee SW, Lam E, To KF, et al. (2003) Positional mapping for amplified DNA sequences on 1q21-q22 in hepatocellular carcinoma indicates candidate genes over-expression. J Hepatol 38: 298-306.
50. Chun HK, Chung KS, Kim HC, Kang JE, Kang MA, et al. (2010) OIP5 is a highly expressed potential therapeutic target for colorectal and gastric cancers. BMB Rep 43: 349-354.
51. Kaur R, Yuan X, Lu ML, Balk SP, (2008) Increased PAK6 expression in prostate cancer and identification of PAK6 associated proteins. Prostate 68: 1510-1516.
52. Venables JP, Klinck R, Koh C, Gervais-Bird J, Bramard A, et al. (2009) Cancer-associated regulation of alternative splicing. Nat Struct Mol Biol 16: 670-676.
53. Bemmo A, Benovoy D, Kwan T, Gaffney DJ, Jensen RV, et al. (2008) Gene expression and isoform variation analysis using Affymetrix Exon Arrays. BMC Genomics 9: 529.
54. Ciro M, Prosperini E, Quarto M, Grazini U, Walfridsson J, et al. (2009) ATAD2 is a novel cofactor for MYC, overexpressed and amplified in aggressive tumors. Cancer Res 69: 8491-8498.
55. Zou JX, Guo L, Revenko AS, Tepper CG, Gemo AT, et al. (2009) Androgen-induced coactivator ANCCA mediates specific androgen receptor signaling in prostate cancer. Cancer Res 69: 3339-3346.