Systematic Analysis of the Gene Expression in the Livers of Nonalcoholic Steatohepatitis: Implications on Potential Biomarkers and Molecular Pathological Mechanism

PLoS ONE

Volumn 7, Issue 12, 2012, Pages

  Zhang, Yida ^a   Baker, Susan S ^b   Baker, Robert D ^b   Zhu, Ruixin ^a   Zhu, Lixin ^b  

^a TONGJI UNIVERSITY   (China)

^b UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER;

ADH4 GENE; AMINO ACID METABOLISM; ARTICLE; BIOINFORMATICS; CATABOLISM; GENE; GENE EXPRESSION; GENETIC ASSOCIATION; MOLECULAR PATHOLOGY; NONALCOHOLIC FATTY LIVER; NUCLEOTIDE SEQUENCE; PATHOGENESIS; PREDICTION; RISK FACTOR; STATISTICAL ANALYSIS; UREA CYCLE;

BIOLOGICAL MARKERS; COMPUTATIONAL BIOLOGY; FATTY LIVER; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PATHOLOGY, MOLECULAR; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; SIGNAL TRANSDUCTION;

EID: 84871570353     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0051131     Document Type: Article

References (71)

1. Ekstedt M, Franzen LE, Mathiesen UL, Thorelius L, Holmqvist M, et al. (2006) Long-term follow-up of patients with NAFLD and elevated liver enzymes. Hepatology 44: 865-873.
2. Adams LA, Lymp JF, St Sauver J, Sanderson SO, Lindor KD, et al. (2005) The natural history of nonalcoholic fatty liver disease: a population-based cohort study. Gastroenterology 129: 113-121.
3. Erickson SK, (2009) Nonalcoholic fatty liver disease. Journal of lipid research 50: S412-S416.
4. Ludwig J, Viggiano TR, McGill DB, Oh BJ, (1980) Nonalcoholic steatohepatitis: Mayo Clinic experiences with a hitherto unnamed disease. Mayo Clin Proc 55: 434-438.
5. Hashimoto E, Farrell GC, (2009) Will non-invasive markers replace liver biopsy for diagnosing and staging fibrosis in non-alcoholic steatohepatitis? Journal of Gastroenterology and Hepatology 24: 501-503.
6. Vuppalanchi R, Chalasani N, (2009) Nonalcoholic Fatty Liver Disease and Nonalcoholic Steatohepatitis: Selected Practical Issues in Their Evaluation and Management. Hepatology 49: 306-317.
7. de Alwis NM, Day CP, (2008) Non-alcoholic fatty liver disease: the mist gradually clears. J Hepatol 48 Suppl 1: S104-112.
8. Dowman JK, Tomlinson JW, Newsome PN, (2011) Systematic review: the diagnosis and staging of non-alcoholic fatty liver disease and non-alcoholic steatohepatitis. Alimentary Pharmacology & Therapeutics 33: 525-540.
9. Martel C, Esposti DD, Bouchet A, Brenner C, Lemoine A, (2012) Non-alcoholic steatohepatitis: new insights from OMICS studies. Curr Pharm Biotechnol 13: 726-735.
10. Day CP, James OFW, (1998) Steatohepatitis: A tale of two "hits"? Gastroenterology 114: 842-845.
11. Tamimi TIA-R, Elgouhari HM, Alkhouri N, Yerian LM, Berk MP, et al. (2011) An apoptosis panel for nonalcoholic steatohepatitis diagnosis. Journal of Hepatology 54: 1224-1229.
12. Yilmaz Y, (2009) Cytokeratin-18 fragments and biomarkers of the metabolic syndrome in nonalcoholic steatohepatitis. World Journal of Gastroenterology 15: 4387.
13. Perez-Carreras M, Del Hoyo P, Martin MA, Rubio JC, Martin A, et al. (2003) Defective hepatic mitochondrial respiratory chain in patients with nonalcoholic steatohepatitis. Hepatology 38: 999-1007.
14. Valdecantos MP, Perez-Matute P, Prieto-Hontoria PL, Sanchez-Campayo E, Moreno-Aliaga MJ, et al. (2011) Erythrocyte antioxidant defenses as a potential biomarker of liver mitochondrial status in different oxidative conditions. Biomarkers 16: 670-678.
15. Caldwell SH, Swerdlow RH, Khan EM, Iezzoni JC, Hespenheide EE, et al. (1999) Mitochondrial abnormalities in non-alcoholic steatohepatitis. J Hepatol 31: 430-434.
16. Wei Y, (2008) Nonalcoholic fatty liver disease and mitochondrial dysfunction. World Journal of Gastroenterology 14: 193.
17. Banasch M, Ellrichmann M, Tannapfel A, Schmidt W, Goetze O, (2012) The non-invasive 13C-methionine breath test detects hepatic mitochondrial dysfunction as a marker of disease activity in non-alcoholic steatohepatitis. European Journal of Medical Research 16: 258.
18. Marchesini G, Brizi M, Morselli-Labate AM, Bianchi G, Bugianesi E, et al. (1999) Association of nonalcoholic fatty liver disease with insulin resistance. The American journal of medicine 107: 450-455.
19. Chitturi S, Farrell GC. Etiopathogenesis of nonalcoholic steatohepatitis; 2001. pp. 23-34.
20. Sanyal AJ, Campbell-Sargent C, Mirshahi F, Rizzo WB, Contos MJ, et al. (2001) Nonalcoholic steatohepatitis: association of insulin resistance and mitochondrial abnormalities. Gastroenterology 120: 1183-1192.
21. Ma X, Li Z, (2006) Pathogenesis of nonalcoholic steatohepatitis (NASH). Chinese Journal of Digestive Diseases 7: 7-11.
22. Bertola A, Bonnafous S, Anty R, Patouraux S, Saint-Paul MC, et al. (2010) Hepatic expression patterns of inflammatory and immune response genes associated with obesity and NASH in morbidly obese patients. PLoS One 5: e13577.
23. Baker SS, Baker RD, Liu W, Nowak NJ, Zhu L, (2010) Role of alcohol metabolism in non-alcoholic steatohepatitis. PLoS One 5: e9570.
24. McCullough AJ, (2006) Pathophysiology of nonalcoholic steatohepatitis. Journal of clinical gastroenterology 40: S17.
25. Zhu L, Baker SS, Liu W, Tao M-H, Patel R, et al. (2011) Lipid in the livers of adolescents with nonalcoholic steatohepatitis: combined effects of pathways on steatosis. Metabolism 60: 1001-1011.
26. Miller MH, Ferguson MAJ, Dillon JF, (2011) Systematic review of performance of non-invasive biomarkers in the evaluation of non-alcoholic fatty liver disease. Liver International 31: 461-473.
27. Baranova A, Younossi ZM, (2008) The future is around the corner: Noninvasive diagnosis of progressive nonalcoholic steatohepatitis. Hepatology 47: 373-375.
28. Liu W, Baker SS, Baker RD, Nowak NJ, Zhu L, (2011) Upregulation of hemoglobin expression by oxidative stress in hepatocytes and its implication in nonalcoholic steatohepatitis. PLoS One 6: e24363.
29. Gene Expression Omnibus website. Available: http://wwwncbinlmnihgov/geo/ Accessed 2010 Nov 11.
30. Tusher VG, (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proceedings of the National Academy of Sciences 98: 5116-5121.
31. Chu G, Narasimhan B, Tibshirani R, Tusher V, (2002) SAM "Significance Analysis of Microarrays": Users Guide and Technical Document. Stanford University.
32. Kadota K, Nakai Y, Shimizu K, (2008) A weighted average difference method for detecting differentially expressed genes from microarray data. Algorithms for Molecular Biology 3: 8.
33. Kadota K, Shimizu K, (2011) Evaluating methods for ranking differentially expressed genes applied to microArray quality control data. BMC Bioinformatics 12: 227.
34. Troyanskaya OG, Garber ME, Brown PO, Botstein D, Altman RB, (2002) Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics 18: 1454-1461.
35. Tsodikov A, Szabo A, Jones D, (2002) Adjustments and measures of differential expression for microarray data. Bioinformatics 18: 251-260.
36. Raychaudhuri S, Stuart JM, Liu X, Small PM, Altman RB, (2000) Pattern recognition of genomic features with microarrays: site typing of Mycobacterium tuberculosis strains. Proc Int Conf Intell Syst Mol Biol 8: 286-295.
37. Pihur V, Datta S, Datta S, (2009) RankAggreg, an R package for weighted rank aggregation. BMC Bioinformatics 10: 62.
38. Kang H, Sheng Z, Zhu R, Huang Q, Liu Q, et al. (2012) Virtual Drug Screen Schema Based on Multiview Similarity Integration and Ranking Aggregation. Journal of Chemical Information and Modeling 52: 834-843.
39. Pihur V, Datta S, (2007) Weighted rank aggregation of cluster validation measures: a Monte Carlo cross-entropy approach. Bioinformatics 23: 1607-1615.
40. Huang da W, Sherman BT, Lempicki RA, (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37: 1-13.
41. Huang DW, Sherman BT, Lempicki RA, (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4: 44-57.
42. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, et al. (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34: D354-357.
43. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36: D480-484.
44. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, et al. (1999) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic acids research 27: 29-34.
45. Masotti A, Alisi A, (2012) Integrated bioinformatics analysis of microRNA expression profiles for an in-depth understanding of pathogenic mechanisms in non-alcoholic fatty liver disease. J Gastroenterol Hepatol 27: 187-188.
46. Chuaqui RF, Bonner RF, Best CJM, Gillespie JW, Flaig MJ, et al. (2002) Post-analysis follow-up and validation of microarray experiments. Nature Genetics 32: 509-514.
47. Diehl AM, Goodman Z, Ishak KG, (1988) Alcohollike liver disease in nonalcoholics. A clinical and histologic comparison with alcohol-induced liver injury. Gastroenterology 95: 1056-1062.
48. Nosova T, Jokelainen K, Kaihovaara P, Jousimies-Somer H, Siitonen A, et al. (1996) Aldehyde dehydrogenase activity and acetate production by aerobic bacteria representing the normal flora of human large intestine. Alcohol Alcohol 31: 555-564.
49. Cope K, Risby T, Diehl AM, (2000) Increased gastrointestinal ethanol production in obese mice: implications for fatty liver disease pathogenesis. Gastroenterology 119: 1340-1347.
50. Baraona E, Julkunen R, Tannenbaum L, Lieber CS, (1986) Role of intestinal bacterial overgrowth in ethanol production and metabolism in rats. Gastroenterology 90: 103-110.
51. Lindinger W, Taucher J, Jordan A, Hansel A, Vogel W, (1997) Endogenous production of methanol after the consumption of fruit. Alcohol Clin Exp Res 21: 939-943.
52. Sofer W, Martin PF, (1987) Analysis of alcohol dehydrogenase gene expression in Drosophila. Annu Rev Genet 21: 203-225.
53. Medicinenet website. Alcohol and Nutrition. Available: http://www.medicinenet.com/alcohol_and_nutrition/article.htm. Accessed 2011 Jun 28.
54. Lieber CS, Schmid R, (1961) The effect of ethanol on fatty acid metabolism; stimulation of hepatic fatty acid synthesis in vitro. Journal of Clinical Investigation 40: 394.
55. Galli A, Price D, Crabb D, (1999) High-level expression of rat class I alcohol dehydrogenase is sufficient for ethanol-induced fat accumulation in transduced hela cells. Hepatology 29: 1164-1170.
56. Ma Y, Meregalli M, Hodges S, Davies N, Bogdanos DP, et al. (2005) Alcohol dehydrogenase: an autoantibody target in patients with alcoholic liver disease. Int J Immunopathol Pharmacol 18: 173-182.
57. Kaur I, Katyal A, (2012) Immunoproteomic identification of biotransformed self-proteins from the livers of female Balb/c mice following chronic ethanol administration. Proteomics 12: 2036-2044.
58. Stokkeland K, Ebrahim F, Ekbom A, (2010) Increased risk of esophageal varices, liver cancer, and death in patients with alcoholic liver disease. Alcoholism: Clinical and Experimental Research 34: 1993-1999.
59. Sarin SK, Sachdev G, Jiloha RC, Bhatt A, Munjal GC, (1988) Pattern of psychiatric morbidity and alcohol dependence in patients with alcoholic liver disease. Dig Dis Sci 33: 443-448.
60. Kojima H, Sakurai S, Uemura M, Takekawa T, Morimoto H, et al. (2005) Difference and Similarity Between Non-Alcoholic Steatohepatitis and Alcoholic Liver Disease. Alcoholism: Clinical and Experimental Research 29: 259S-263S.
61. Boström P, Wu J, Jedrychowski MP, Korde A, Ye L, et al. (2012) A PGC1-α-dependent myokine that drives brown-fat-like development of white fat and thermogenesis. Nature 481: 463-468.
62. Wu GY, (2009) Amino acids: metabolism, functions, and nutrition. Amino Acids 37: 1-17.
63. Rhoads JM, Wu GY, (2009) Glutamine, arginine, and leucine signaling in the intestine. Amino Acids 37: 111-122.
64. Riviere L, Moreau P, Allmann S, Hahn M, Biran M, et al. (2009) Acetate produced in the mitochondrion is the essential precursor for lipid biosynthesis in procyclic trypanosomes. Proceedings of the National Academy of Sciences of the United States of America 106: 12694-12699.
65. Connor SC, Hansen MK, Corner A, Smith RF, Ryan TE, (2010) Integration of metabolomics and transcriptomics data to aid biomarker discovery in type 2 diabetes. Molecular Biosystems 6: 909-921.
66. Freund HR, Ryan JA Jr, Fischer JE, (1978) Amino acid derangements in patients with sepsis: treatment with branched chain amino acid rich infusions. Annals of Surgery 188: 423.
67. Pozefsky T, Tancredi RG, Moxley RT, DuPre J, Tobin JD, (1976) Effects of brief starvation on muscle amino acid metabolism in nonobese man. Journal of Clinical Investigation 57: 444.
68. Fiehn O, Garvey WT, Newman JW, Lok KH, Hoppel CL, et al. (2010) Plasma Metabolomic Profiles Reflective of Glucose Homeostasis in Non-Diabetic and Type 2 Diabetic Obese African-American Women. PLoS One 5.
69. Sunny Nishanth E, Parks Elizabeth J, Browning Jeffrey D, Burgess Shawn C, (2011) Excessive Hepatic Mitochondrial TCA Cycle and Gluconeogenesis in Humans with Nonalcoholic Fatty Liver Disease. Cell Metabolism 14: 804-810.
70. Farrell GC, Larter CZ, (2006) Nonalcoholic fatty liver disease: From steatosis to cirrhosis. Hepatology 43: S99-S112.
71. Parola M, Robino G, (2001) Oxidative stress-related molecules and liver fibrosis. Journal of Hepatology 35: 297-306.