Genome-wide transcriptional sequencing identifies novel mutations in metabolic genes in human hepatocellular carcinoma

Cancer Genomics and Proteomics

Volumn 11, Issue 1, 2014, Pages 1-12

  Meerzaman, Daoud M ^a   Yan, Chunhua ^a   Chen, Qing Rong ^a   Edmonson, Michael N ^a   Schaefer, Carl F ^a   Clifford, Robert J ^a   Dunn, Barbara K ^a   Dong, L I ^a   Finney, Richard P ^a   Cultraro, Constance M ^a   Hu, Ying ^a   Yang, Zhihui ^a   Nguyen, C U V ^a   Kelley, Jenny M ^a   Cai, Shuang ^a   Zhang, Hongen ^a   Zhang, Jinghui ^a,b   Wilson, Rebecca ^a   Messmer, Lauren ^a   Chung, Young Hwa ^c   Kim, Jeong A ^c   Park, Neung Hwa ^c   Lyu, Myung Soo ^c   Song, I L Han ^d   Komatsoulis, George ^a   Buetow, Kenneth H ^a   more..

^a NATIONAL CANCER INSTITUTE   (United States)

^b ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

^c University of Ulsan College of Medicine   (South Korea)

^d Dankook University   (South Korea)

Author keywords

Gene expression; Hepatocellular carcinoma (HCC); Mutation; RNA seq

Indexed keywords

3 HYDROXY 3 METHYLGLUTARYL COENZYME A SYNTHASE 1; ADENOSINE TRIPHOSPHATASE; ADENOSINE TRIPHOSPHATASE CLASS I TYPE 8B MEMBER 1; AURORA B KINASE; BETA CATENIN; CADHERIN ASSOCIATED PROTEIN BETA 1; CLUSTERIN; HYDROXYMETHYLGLUTARYL COENZYME A SYNTHASE; INSULIN RECEPTOR SUBSTRATE 1; PROTEIN ARGININE METHYLTRANSFERASE; PROTEIN ARGININE METHYLTRANSFERASE 6; PROTEIN P53; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR FOXM1; UNCLASSIFIED DRUG; DNA; RNA; TRANSCRIPTOME;

ARTICLE; DIABETES MELLITUS; GENE EXPRESSION; GENE MUTATION; GENE SEQUENCE; HUMAN; LIVER CELL CARCINOMA; MOLECULAR GENETICS; MOLECULAR PATHOLOGY; NUCLEOTIDE SEQUENCE; OBESITY; PREVALENCE; RNA SEQUENCE; TUMOR GENE; WNT SIGNALING PATHWAY; GENETIC ASSOCIATION; GENETICS; LIVER TUMOR; METABOLISM; MUTATION;

CARCINOMA, HEPATOCELLULAR; DNA MUTATIONAL ANALYSIS; DNA, NEOPLASM; GENE EXPRESSION; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LIVER NEOPLASMS; MUTATION; RNA, NEOPLASM; TRANSCRIPTOME;

EID: 84901444946     PISSN: 11096535     EISSN: 17906245     Source Type: Journal    
DOI: None     Document Type: Article

References (43)

1. Gomaa AI, Khan SA, Toledano MB, Waked I and Taylor-Robinson SD: Hepatocellular carcinoma: epidemiology, risk factors and pathogenesis. World J Gastroenterol 14: 4300-4308, 2008.
2. Lata J: Chronic liver diseases as liver tumor precursors. Dig Dis 28: 596-599, 2010.
3. Davila JA, Morgan RO, Shaib Y, McGlynn KA and El-Serag HB: Hepatitis C infection and the increasing incidence of hepatocellular carcinoma: a population-based study. Gastroenterology 127: 1372-1380, 2004. (Pubitemid 39457763)
4. El-Serag HB, Davila JA, Petersen NJ and McGlynn KA: The continuing increase in the incidence of hepatocellular carcinoma in the United States: an update. Ann Intern Med 139: 817-823, 2003.
5. Starley BQ, Calcagno CJ and Harrison SA: Nonalcoholic fatty liver disease and hepatocellular carcinoma: a weighty connection. Hepatology 51: 1820-1832, 2010.
6. Bugianesi E, Vanni E andMarchesini G: NASH and the risk of cirrhosis and hepatocellular carcinoma in type 2 diabetes. Curr Diab Rep 7: 175-180, 2007. (Pubitemid 46951914)
7. Qureshi K and Abrams GA: Metabolic liver disease of obesity and role of adipose tissue in the pathogenesis of nonalcoholic fatty liver disease. World J Gastroenterol 13: 3540-3553, 2007. (Pubitemid 47162261)
8. Mortazavi A, Williams BA, McCue K, Schaeffer L and Wold B: Mapping and quantifying mammalian transcriptomes by RNASeq. Nat Methods 5: 621-628, 2008. (Pubitemid 351911867)
9. Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF et al: Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5: 613-619, 2008. (Pubitemid 351911866)
10. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M et al : A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321: 956-960, 2008.
11. Roessler S, Jia HL, Budhu A, Forgues M, Ye QH, Lee JS, Thorgeirsson SS et al : A unique metastasis gene signature enables prediction of tumor relapse in early-stage hepatocellular carcinoma patients. Cancer Res 70: 10202-10212, 2010.
12. Edmonson MN, Zhang J, Yan C, Finney RP, Meerzaman DM and Buetow KH: Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format. Bioinformatics 27: 865-866, 2011.
13. Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM et al : VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25: 2283-2285, 2009.
14. Rozen S and Skaletsky H: Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386, 2000.
15. Ewing B, Hillier L, Wendl MC and Green P: Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175-185, 1998. (Pubitemid 28177229)
16. Clifford RJ, Edmonson MN, Nguyen C and Buetow KH: Largescale analysis of non-synonymous coding region single nucleotide polymorphisms. Bioinformatics 20: 1006-1014, 2004. (Pubitemid 38660336)
17. Ng PC and Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res 31: 3812-3814, 2003. (Pubitemid 37442253)
18. Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T and Buetow KH: PID: the Pathway Interaction Database. Nucleic Acids Res 37: D674-679, 2009.
19. Benjamini Y, Drai D, Elmer G, Kafkafi N and Golani I: Controlling the false discovery rate in behavior genetics research. Behav Brain Res 125 : 279-284, 2001. (Pubitemid 33000466)
20. Olshen AB, Venkatraman ES, Lucito R and Wigler M: Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5 : 557-572, 2004. (Pubitemid 41180205)
21. Boon K, Osorio EC, Greenhut SF, Schaefer CF, Shoemaker J, Polyak K, Morin PJ et al: An anatomy of normal and malignant gene expression. Proc Natl Acad Sci USA 99 : 11287-11292, 2002. (Pubitemid 34920918)
22. Davila JA, Morgan RO, Shaib Y, McGlynn KA and El-Serag HB: Diabetes increases the risk of hepatocellular carcinoma in the United States: a population based case control study. Gut 54: 533-539, 2005. (Pubitemid 40403031)
23. Sanyal A, Poklepovic A, Moyneur E and Barghout V: Population-based risk factors and resource utilization for HCC: US perspective. Curr Med Res Opin 26: 2183-2191, 2010.
24. Hayama S, Daigo Y, Yamabuki T, Hirata D, Kato T, Miyamoto M, Ito T et al : Phosphorylation and activation of cell division cycle associated 8 by aurora kinase B plays a significant role in human lung carcinogenesis. Cancer Res 67: 4113-4122, 2007. (Pubitemid 46815056)
25. Wierstra I and Alves J: FOXM1, a typical proliferation-associated transcription factor. Biol Chem 388 : 1257-1274, 2007. (Pubitemid 350135573)
26. Shimo A, Tanikawa C, Nishidate T, Lin ML, Matsuda K, Park JH, Ueki T et al : Involvement of kinesin family member 2C/mitotic centromere-associated kinesin overexpression in mammary carcinogenesis. Cancer Sci 99: 62-70, 2008. (Pubitemid 350239032)
27. Guo J, Cagatay T, Zhou G, Chan CC, Blythe S, Suyama K, Zheng L et al : Mutations in the human naked cuticle homolog NKD1 found in colorectal cancer alter Wnt/Dvl/beta-catenin signaling. PLoS One 4 : e7982, 2009.
28. Wang X, Quail E, Hung NJ, Tan Y, Ye H and Costa RH: Increased levels of forkhead box M1B transcription factor in transgenic mouse hepatocytes prevent age-related proliferation defects in regenerating liver. Proc Natl Acad Sci USA 98: 11468-11473, 2001. (Pubitemid 32928752)
29. Zhao WM and Fang G: MgcRacGAP controls the assembly of the contractile ring and the initiation of cytokinesis. Proc Natl Acad Sci USA 102 : 13158-13163, 2005.
30. Gammie AE, Kurihara LJ, Vallee RB and Rose MD: DNM1, a dynamin-related gene, participates in endosomal trafficking in yeast. J Cell Biol 130 : 553-566, 1995.
31. Camarero N, Mascaro C, Mayordomo C, Vilardell F, Haro D and Marrero PF: Ketogenic HMGCS2 Is a c-Myc target gene expressed in differentiated cells of human colonic epithelium and downregulated in colon cancer. Mol Cancer Res 4: 645-653, 2006. (Pubitemid 44497217)
32. Musi N and Goodyear LJ: Insulin resistance and improvements in signal transduction. Endocrine 29: 73-80, 2006. (Pubitemid 43780348)
33. Boden G: Fatty acid-induced inflammation and insulin resistance in skeletal muscle and liver. Curr Diab Rep 6: 177-181, 2006.
34. Longato L, de la Monte S, Califano S and Wands JR: Synergistic premalignant effects of chronic ethanol exposure and insulin receptor substrate-1 overexpression in liver. Hepatol Res 38: 940-953, 2008.
35. Ning J and Clemmons DR. AMP-activated protein kinase inhibits IGF-I signaling and protein synthesis in vascular smooth muscle cells via stimulation of insulin receptor substrate 1 S794 and tuberous sclerosis 2 S1345 phosphorylation. Mol Endocrinol 24 : 1218-1229, 2010.
36. Leclerc GM, Leclerc GJ, Fu G and Barredo JC: AMPK-induced activation of Akt by AICAR is mediated by IGF-1R dependent and independent mechanisms in acute lymphoblastic leukemia. J Mol Signal 5 : 15, 2010.
37. Horike N, Takemori H, Katoh Y, Doi J, Min L, Asano T, Sun XJ et al : Adipose-specific expression, phosphorylation of Ser794 in insulin receptor substrate-1, and activation in diabetic animals of salt-inducible kinase-2. J Biol Chem 278: 18440-18447, 2003. (Pubitemid 36799466)
38. Kim YD, Park CH, Kim HS, Choi SK, Rew JS, Kim DY, Koh YS et al : Genetic alterations of Wnt signaling pathway-associated genes in hepatocellular carcinoma. J Gastroenterol Hepatol 23 : 110-118, 2008. (Pubitemid 350265215)
39. Machida K, Cheng KT, Sung VM, Shimodaira S, Lindsay KL, Levine AM, Lai MY et al: Hepatitis C virus induces a mutator phenotype: enhanced mutations of immunoglobulin and protooncogenes. Proc Natl Acad Sci USA 101: 4262-4267, 2004. (Pubitemid 38405917)
40. Azzalin CM and Lingner J: The human RNA surveillance factor UPF1 is required for S phase progression and genome stability. Curr Biol 16 : 433-439, 2006. (Pubitemid 43259356)
41. Lee H, Sengupta N, Villagra A, Rezai-Zadeh N and Seto E: Histone deacetylase 8 safeguards the human ever-shorter telomeres 1B (hEST1B) protein from ubiquitin-mediated degradation. Mol Cell Biol 26 : 5259-5269, 2006. (Pubitemid 44036197)
42. Hussain SP, Schwank J, Staib F, Wang XW and Harris CC: TP53 mutations and hepatocellular carcinoma: insights into the etiology and pathogenesis of liver cancer. Oncogene 26: 2166-2176, 2007. (Pubitemid 46536641)
43. Imbeaud S, Ladeiro Y and Zucman-Rossi J: Identification of novel oncogenes and tumor suppressors in hepatocellular carcinoma. Semin Liver Dis 30 : 75-86, 2010.