Genome-wide transcriptome analysis identifies novel gene signatures implicated in human chronic liver disease

American Journal of Physiology - Gastrointestinal and Liver Physiology

Volumn 305, Issue 5, 2013, Pages

  Smalling, Rana V ^a   Delker, Don A ^a   Zhang, Yuxia ^a   Nieto, Natalia ^b   Mcguiness, Michael S ^a   Liu, Shuanghu ^a   Friedman, Scott L ^b   Hagedorn, Curt H ^a   Wang, Li ^a  

^a UNIVERSITY OF UTAH   (United States)

^b MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

C virus; Chronic hepatitis; Gene expression; Human chronic liver diseases; Knockout mice; Ribonucleic acid sequencing; Small heterodimer partner

Indexed keywords

DUAL SPECIFIC PHOSPHATASE 4; PEPTIDOGLYCAN RECOGNITION PROTEIN 2; PROTEIN; PROTEIN TYROSINE PHOSPHATASE SHP; SPARC RELATED MODULAR CALCIUM BINDING PROTEIN 2; TETRASPANIN 4; THROMBOSPONDIN 1; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ALCOHOL LIVER CIRRHOSIS; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; CHRONIC LIVER DISEASE; CONTROLLED STUDY; DISEASE COURSE; EXPERIMENTAL MODEL; FATTY LIVER; GENE EXPRESSION REGULATION; HEPATITIS; HEPATITIS C; HUMAN; HUMAN TISSUE; LIVER BIOPSY; LIVER CIRRHOSIS; LIVER FIBROSIS; LIVER INJURY; MALE; MICROARRAY ANALYSIS; MOUSE; NONALCOHOLIC FATTY LIVER; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; UPREGULATION;

EID: 84883324300     PISSN: 01931857     EISSN: 15221547     Source Type: Journal    
DOI: 10.1152/ajpgi.00077.2013     Document Type: Article

References (51)

1. Aktas B, Yilmaz Y, Eren F, Yonal O, Kurt R, Alahdab YO, Celikel CA, Ozdogan O, Imeryuz N, Kalayci C, Avsar E. Serum levels of vaspin, obestatin, and apelin-36 in patients with nonalcoholic fatty liver disease. Metab Clin Exp 60: 544-549, 2011.
2. Baker SS, Baker RD, Liu W, Nowak NJ, Zhu L. Role of alcohol metabolism in non-alcoholic steatohepatitis. PloS one 5: e9570, 2010.
3. Brunt EM. Nonalcoholic steatohepatitis. Semin Liver Dis 24: 3-20, 2004.
4. Choi YH, Hagedorn CH. Purifying mRNAs with a high-affinity eIF4E mutant identifies the short 3' poly(A) end phenotype. Proc Natl Acad Sci USA 100: 7033-7038, 2003.
5. Cubero FJ, Nieto N. Ethanol and arachidonic acid synergize to activate Kupffer cells and modulate the fibrogenic response via tumor necrosis factor alpha, reduced glutathione, and transforming growth factor betadependent mechanisms. Hepatology 48: 2027-2039, 2008.
6. Datta S, Wang L, Moore DD, Osborne TF. Regulation of 3-hydroxy-3-methylglutaryl coenzyme A reductase promoter by nuclear receptors liver receptor homologue-1 and small heterodimer partner: a mechanism for differential regulation of cholesterol synthesis and uptake. J Biol Chem 281: 807-812, 2006.
7. Deng YB, Nagae G, Midorikawa Y, Yagi K, Tsutsumi S, Yamamoto S, Hasegawa K, Kokudo N, Aburatani H, Kaneda A. Identification of genes preferentially methylated in hepatitis C virus-related hepatocellular carcinoma. Cancer Sci 101: 1501-1510, 2010.
8. Dziarski R, Gupta D. Mammalian peptidoglycan recognition proteins (PGRPs) in innate immunity. Innate Immunity 16: 168-174, 2010.
9. El-Youssef M, Mu Y, Huang L, Stellmach V, Crawford SE. Increased expression of transforming growth factor-beta1 and thrombospondin-1 in congenital hepatic fibrosis: possible role of the hepatic stellate cell. J Pediatr Gastroenterol Nutr 28: 386-392, 1999.
10. Elpek GO, Gokhan GA, Bozova S. Thrombospondin-1 expression correlates with angiogenesis in experimental cirrhosis. World J Gastroenterol 14: 2213-2217, 2008.
11. Fiorucci S, Antonelli E, Rizzo G, Renga B, Mencarelli A, Riccardi L, Orlandi S, Pellicciari R, Morelli A. The nuclear receptor SHP mediates inhibition of hepatic stellate cells by FXR and protects against liver fibrosis. Gastroenterology 127: 1497-1512, 2004.
12. He N, Park K, Zhang Y, Huang J, Lu S, Wang L. Epigenetic inhibition of nuclear receptor small heterodimer partner is associated with and regulates hepatocellular carcinoma growth. Gastroenterology 134: 793-802, 2008.
13. Huang da W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37: 1-13, 2009.
14. Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Prot 4: 44-57, 2009.
15. Huang J, Iqbal J, Saha PK, Liu J, Chan L, Hussain MM, Moore DD, Wang L. Molecular characterization of the role of orphan receptor small heterodimer partner in development of fatty liver. Hepatology 46: 147-157, 2007.
16. Huang J, Tabbi-Anneni I, Gunda V, Wang L. Transcription factor Nrf2 regulates SHP and lipogenic gene expression in hepatic lipid metabolism. Am J Physiol Gastrointest Liver Physiol 299: G1211-G1221, 2010.
17. Huang Q, Lin B, Liu H, Ma X, Mo F, Yu W, Li L, Li H, Tian T, Wu D, Shen F, Xing J, Chen ZN. RNA-Seq analyses generate comprehensive transcriptomic landscape and reveal complex transcript patterns in hepatocellular carcinoma. PloS one 6: e26168, 2011.
18. Jeschke MG, Klein D, Thasler WE, Bolder U, Schlitt HJ, Jauch KW, Weiss TS. Insulin decreases inflammatory signal transcription factor expression in primary human liver cells after LPS challenge. Mol Med 14: 11-19, 2008.
19. Jin T, Xu D, Ding Q, Zhang Y, Mao C, Pan Y, Wang Z, Chen Y. Identification of the topology and functional domains of PAQR10. Biochem J 443: 643-653, 2012.
20. Keyse SM. Dual-specificity MAP kinase phosphatases (MKPs) and cancer. Cancer Metastasis Rev 27: 253-261, 2008.
21. Kirby GM, Nichols KD, Antenos M. CYP2A5 induction and hepatocellular stress: an adaptive response to perturbations of heme homeostasis. Curr Drug Metab 12: 186-197, 2011.
22. Li Y, Wang L, Qiu J, Da L, Tiollais P, Li Z, Zhao M. Human tetraspanin transmembrane 4 superfamily member 4 or intestinal and liver tetraspan membrane protein is overexpressed in hepatocellular carcinoma and accelerates tumor cell growth. Acta Biochim Biophys Sinica 44: 224-232, 2012.
23. Lieber CS, DeCarli LM, Sorrell MF. Experimental methods of ethanol administration. Hepatology 10: 501-510, 1989.
24. Malone JH, Oliver B. Microarrays, deep sequencing and the true measure of the transcriptome (Abstract). BMC Biol 9: 34, 2011.
25. Martin JA, Wang Z. Next-generation transcriptome assembly. Nat Rev Genet 12: 671-682, 2011.
26. Matsukuma KE, Bennett MK, Huang J, Wang L, Gil G, Osborne TF. Coordinated control of bile acids and lipogenesis through FXR-dependent regulation of fatty acid synthase. J Lipid Res 47: 2754-2761, 2006.
27. Matsukuma KE, Wang L, Bennett MK, Osborne TF. A key role for orphan nuclear receptor liver receptor homologue-1 in activation of fatty acid synthase promoter by liver X receptor. J Biol Chem 282: 20164-20171, 2007.
28. Miele L, Forgione A, Hernandez AP, Gabrieli ML, Vero V, Di Rocco P, Greco AV, Gasbarrini G, Gasbarrini A, Grieco A. The natural history and risk factors for progression of non-alcoholic fatty liver disease and steatohepatitis. Eur Rev Med Pharmacol Sci 9: 273-277, 2005.
29. Nix DA, Courdy SJ, Boucher KM. Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks (Abstract). BMC Bioinformatics 9: 523, 2008.
30. Oler AJ, Alla RK, Roberts DN, Wong A, Hollenhorst PC, Chandler KJ, Cassiday PA, Nelson CA, Hagedorn CH, Graves BJ, Cairns BR. Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors. Nat Struct Mol Biol 17: 620-628, 2010.
31. Ondracek CR, Reese VC, Rushing CN, Oropeza CE, McLachlan A. Distinct regulation of hepatitis B virus biosynthesis by peroxisome proliferator-activated receptor gamma coactivator 1alpha and small heterodimer partner in human hepatoma cell lines. J Virol 83: 12545-12551, 2009.
32. Pan X, Zhang Y, Wang L, Hussain MM. Diurnal regulation of MTP and plasma triglyceride by CLOCK is mediated by SHP. Cell Metab 12: 174-186, 2010.
33. Papic N, Maxwell CI, Delker DA, Liu S, Heale BS, Hagedorn CH. RNA-sequencing analysis of 5' capped RNAs identifies many new differentially expressed genes in acute hepatitis C virus infection. Viruses 4: 581-612, 2012.
34. Park YJ, Qatanani M, Chua SS, LaRey JL, Johnson SA, Watanabe M, Moore DD, Lee YK. Loss of orphan receptor small heterodimer partner sensitizes mice to liver injury from obstructive cholestasis. Hepatology 47: 1578-1586, 2008.
35. Rocnik EF, Liu P, Sato K, Walsh K, Vaziri C. The novel SPARC family member SMOC-2 potentiates angiogenic growth factor activity. J Biol Chem 281: 22855-22864, 2006.
36. Ruffalo M, LaFramboise T, Koyuturk M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics 27: 2790-2796, 2011.
37. Saha S, Jing X, Park SY, Wang S, Li X, Gupta D, Dziarski R. Peptidoglycan recognition proteins protect mice from experimental colitis by promoting normal gut flora and preventing induction of interferongamma. Cell Host Microbe 8: 147-162, 2010.
38. Scholtes C, Diaz O, Icard V, Kaul A, Bartenschlager R, Lotteau V, Andre P. Enhancement of genotype 1 hepatitis C virus replication by bile acids through FXR. J Hepatol 48: 192-199, 2008.
39. Starley BQ, Calcagno CJ, Harrison SA. Nonalcoholic fatty liver disease and hepatocellular carcinoma: a weighty connection. Hepatology 51: 1820-1832, 2010.
40. Tiniakos DG, Vos MB, Brunt EM. Nonalcoholic fatty liver disease: pathology and pathogenesis. Ann Rev Pathol 5: 145-171, 2010.
41. Wang L, Han Y, Kim CS, Lee YK, Moore DD. Resistance of SHP-null mice to bile acid-induced liver damage. J Biol Chem 278: 44475-44481, 2003.
42. Wang L, Lee YK, Bundman D, Han Y, Thevananther S, Kim CS, Chua SS, Wei P, Heyman RA, Karin M, Moore DD. Redundant pathways for negative feedback regulation of bile acid production. Dev Cell 2: 721-731, 2002.
43. Wang YD, Chen WD, Moore DD, Huang W. FXR: a metabolic regulator and cell protector. Cell Res 18: 1087-1095, 2008.
44. Zhang DY, Friedman SL. Fibrosis-dependent mechanisms of hepatocarcinogenesis. Hepatology 56: 769-775, 2012.
45. Zhang Y, Andrews GK, Wang L. Zinc-induced Dnmt1 expression involves antagonism between MTF-1 and nuclear receptor SHP. Nucleic Acids Res 40: 4850-4860, 2012.
46. Zhang Y, Bonzo JA, Gonzalez FJ, Wang L. Diurnal regulation of the early growth response 1 (Egr-1) protein expression by hepatocyte nuclear factor 4alpha (HNF4alpha) and small heterodimer partner (SHP) cross-talk in liver fibrosis. J Biol Chem 286: 29635-29643, 2011.
47. Zhang Y, Hagedorn CH, Wang L. Role of nuclear receptor SHP in metabolism and cancer. Biochim Biophys Acta 1812: 893-908, 2011.
48. Zhang Y, Soto J, Park K, Viswanath G, Kuwada S, Abel ED, Wang L. Nuclear receptor SHP, a death receptor that targets mitochondria, induces apoptosis and inhibits tumor growth. Mol Cell Biol 30: 1341-1356, 2010.
49. Zhang Y, Wang L. Nuclear receptor SHP inhibition of Dnmt1 expression via ERRgamma. FEBS Lett 585: 1269-1275, 2011.
50. Zhang Y, Xu P, Park K, Choi Y, Moore DD, Wang L. Orphan receptor small heterodimer partner suppresses tumorigenesis by modulating cyclin D1 expression and cellular proliferation. Hepatology 48: 289-298, 2008.
51. Zhou T, Zhang Y, Macchiarulo A, Yang Z, Cellanetti M, Coto E, Xu P, Pellicciari R, Wang L. Novel polymorphisms of nuclear receptor SHP associated with functional and structural changes. J Biol Chem 285: 24871-24881, 2010.