ChIP-seq in steatohepatitis and normal liver tissue identifies candidate disease mechanisms related to progression to cancer

BMC Medical Genomics

Volumn 6, Issue 1, 2013, Pages

  Bysani, Madhusudhan ^a   Wallerman, Ola ^a,d   Bornelöv, Susanne ^a   Zatloukal, Kurt ^b   Komorowski, Jan ^a,c   Wadelius, Claes ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b MEDICAL UNIVERSITY OF GRAZ   (Austria)

^c UNIVERSITY OF WARSAW   (Poland)

^d UPPSALA UNIVERSITY   (Sweden)

Author keywords

Cancer networks; ChIP seq; Steatohepatitis; Tissue samples

Indexed keywords

HISTONE H3; MESSENGER RNA; UPSTREAM STIMULATORY FACTOR 1;

ARTICLE; CASE REPORT; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; CORRELATION ANALYSIS; FATTY LIVER; GENE EXPRESSION; GENE SEQUENCE; GENETIC ASSOCIATION; GENOTYPE; HISTONE MODIFICATION; HUMAN; HUMAN TISSUE; LIVER CANCER; LIVER METABOLISM; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SINGLE NUCLEOTIDE POLYMORPHISM;

CARCINOMA, HEPATOCELLULAR; CHROMATIN IMMUNOPRECIPITATION; DISEASE PROGRESSION; FATTY LIVER, ALCOHOLIC; GENE ONTOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HISTONES; LIVER; LIVER NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE; TRANSCRIPTOME; UPSTREAM STIMULATORY FACTORS;

EID: 84887350546     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-6-50     Document Type: Article

References (40)

1. From Mallory to Mallory-Denk bodies: what, how and why? Zatloukal K, French SW, Stumptner C, Strnad P, Harada M, Toivola DM, Cadrin M, Omary MB, Exp Cell Res 2007 313 2033 2049 10.1016/j.yexcr.2007.04.024 17531973 (Pubitemid 46842981)
2. Human fatty liver disease: old questions and new insights. Cohen JC, Horton JD, Hobbs HH, Science 2011 332 1519 1523 10.1126/science.1204265 21700865
3. Role of alcohol metabolism in non-alcoholic steatohepatitis. Baker SS, Baker RD, Liu W, Nowak NJ, Zhu L, PLoS One 2010 5 9570 10.1371/journal.pone. 0009570 20221393
4. Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver disease. Romeo S, Kozlitina J, Xing C, Pertsemlidis A, Cox D, Pennacchio L, Boerwinkle E, Cohen JC, Hobbs HH, Nat Genet 2008 40 1461 1465 10.1038/ng.257 18820647
5. 2011. Speliotes EK, Yerges-Armstrong LM, Wu J, Hernaez R, Kim LJ, Palmer CD, Gudnason V, Eiriksdottir G, Garcia ME, Launer LJ, Nalls M, Clark JM, Mitchell BD, Shuldiner AR, Butler JL, Tomas M, Hoffmann U, Hwang S-J, Massaro JM, O'Donnell CJ, Sahani DV, Salomaa V, Schadt EE, Schwartz SM, Siscovick DS, Voight BF, Carr JJ, Feitosa MF, Harris TB, Fox CS, et al. PLoS Genet 2011 7 1001324 10.1371/journal.pgen.1001324 21423719
6. A chromatin landmark and transcription initiation at most promoters in human cells. Guenther MG, Levine SS, Boyer L, Jaenisch R, Young R, Cell 2007 130 77 88 10.1016/j.cell.2007.05.042 17632057 (Pubitemid 47031323)
7. Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders. Rada-Iglesias A, Ameur A, Kapranov P, Enroth S, Komorowski J, Gingeras TR, Wadelius C, Genome Res 2008 18 380 392 10.1101/gr.6880908 18230803 (Pubitemid 351347081)
8. Familial combined hyperlipidemia is associated with upstream transcription factor 1 (USF1). Pajukanta P, Lilja HE, Sinsheimer JS, Cantor RM, Lusis AJ, Gentile M, Duan XJ, Soro-Paavonen A, Naukkarinen J, Saarela J, Laakso M, Ehnholm C, Taskinen M-R, Peltonen L, Nat Genet 2004 36 371 376 10.1038/ng1320 14991056 (Pubitemid 38437259)
9. Upstream transcription factor 1 (USF1) in risk of type 2 diabetes: association study in 2000 Dutch Caucasians. Meex SJR, van Vliet-Ostaptchouk JV, van der Kallen CJH, van Greevenbroek MMJ, Schalkwijk CG, Feskens EJM, Blaak EE, Wijmenga C, Hofker MH, Stehouwer CD, de Bruin TW, Mol Genet Metab 2008 94 352 355 10.1016/j.ymgme.2008.03.011 18445538
10. Fast and accurate short read alignment with Burrows-Wheeler transform. Li H, Durbin R, Bioinformatics 2009 25 1754 1760 10.1093/bioinformatics/btp324 19451168
11. SICTIN: Rapid footprinting of massively parallel sequencing data. Enroth S, Andersson R, Wadelius C, Komorowski J, BioData Min 2010 3 4 10.1186/1756-0381-3-4 20707885
12. Ensembl 2009. Hubbard TJP, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Holland R, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Lawson D, Longden I, et al. Nucleic Acids Res 2009 37 Database issue 690 D697 19033362
13. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM, Fly (Austin) 2012 6 80 92 10.4161/fly.19695 22728672
14. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Wang K, Li M, Hakonarson H, Nucleic Acids Res 2010 38 164 10.1093/nar/gkq603 20601685
15. Transcription factor binding and modified histones in human bidirectional promoters. Lin JM, Collins PJ, Trinklein ND, Fu Y, Xi H, Myers RM, Weng Z, Genome Res 2007 17 818 827 10.1101/gr.5623407 17568000 (Pubitemid 46919717)
16. Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq. Motallebipour M, Ameur A, Reddy Bysani MS, Patra K, Wallerman O, Mangion J, Barker M, McKernan KJ, Komorowski J, Wadelius C, Genome Biol 2009 10 129 10.1186/gb-2009-10-11-r129 19919681
17. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Huang DW, Sherman BT, Lempicki R, Nat Protoc 2009 4 44 57 19131956
18. Liverome: a curated database of liver cancer-related gene signatures with self-contained context information. Lee L, Wang K, Li G, Xie Z, Wang Y, Xu J, Sun S, Pocalyko D, Bhak J, Kim C, Lee K-H, Jang YJ, Il YY, Yoo H-S, Hwang S, BMC Genomics 2011 12 Suppl 3 3 10.1186/1471-2164-12-S3-S3
19. Identification, using cDNA macroarray analysis, of distinct gene expression profiles associated with pathological and virological features of hepatocellular carcinoma. Delpuech O, Trabut J, Carnot F, Feuillard J, Oncogene 2002 2926 2937 (Pubitemid 34499393)
20. Identification of discriminators of hepatoma by gene expression profiling using a minimal dataset approach. Neo SY, Leow CK, Vega VB, Long PM, Islam AFM, Lai PBS, Liu ET, Ren EC, Hepatology 2004 39 944 953 10.1002/hep.20105 15057898 (Pubitemid 38428933)
21. Insight into hepatocellular carcinogenesis at transcriptome level by comparing gene expression profiles of hepatocellular carcinoma with those of corresponding noncancerous liver. Xu XR, Huang J, Xu ZG, Qian BZ, Zhu ZD, Yan Q, Cai T, Zhang X, Xiao HS, Qu J, Liu F, Huang QH, Cheng ZH, Li NG, Du JJ, Hu W, Shen KT, Lu G, Fu G, Zhong M, Xu SH, Gu WY, Huang W, Zhao XT, Hu GX, Gu JR, Chen Z, Han ZG, Proc Natl Acad Sci U S A 2001 98 15089 15094 10.1073/pnas.241522398 11752456 (Pubitemid 34013974)
22. Gene expression patterns in human liver cancers. Chen X, Cheung S, So S, Mol Biol Cell 2002 13 June 1929 1939 12058060 (Pubitemid 34651483)
23. An integrated data analysis approach to characterize genes highly expressed in hepatocellular carcinoma. Patil MA, Chua M-S, Pan K-H, Lin R, Lih C-J, Cheung S-T, Ho C, Li R, Fan S-T, Cohen SN, Chen X, So S, Oncogene 2005 24 3737 3747 10.1038/sj.onc.1208479 15735714 (Pubitemid 40826873)
24. Genetic profile of Egyptian hepatocellular-carcinoma associated with hepatitis C virus Genotype 4 by 15 K cDNA microarray: preliminary study. Zekri A-RN, Hafez MM, Bahnassy A, Hassan ZK, Mansour T, Kamal MM, Khaled HM, BMC Res Notes 2008 1 106 10.1186/1756-0500-1-106 18959789
25. Molecular-based prediction of early recurrence in hepatocellular carcinoma. Kurokawa Y, Matoba R, Takemasa I, Nagano H, Dono K, Nakamori S, Umeshita K, Sakon M, Ueno N, Oba S, Ishii S, Kato K, Monden M, J Hepatol 2004 41 284 291 10.1016/j.jhep.2004.04.031 15288478 (Pubitemid 39177633)
26. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z, BMC Bioinforma 2009 10 48 10.1186/1471-2105-10-48
27. Common inherited variation in mitochondrial genes is not enriched for associations with type 2 diabetes or related glycemic traits. Segrè AV, Groop L, Mootha VK, Daly MJ, Altshuler D, Consortium D, investigators M, PLoS Genet 2010 6 1001058 10.1371/journal.pgen.1001058 20714348
28. Alcoholic hepatitis. Lucey MR, Mathurin P, Morgan TR, N Engl J Med 2009 360 2758 2769 10.1056/NEJMra0805786 19553649
29. SNP alleles in human disease and evolution. Shastry BS, J Hum Genet 2002 47 561 566 10.1007/s100380200086 12436191 (Pubitemid 36083255)
30. Variation in transcription factor binding among humans. Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, Hong M-Y, Karczewski KJ, Huber W, Weissman SM, Gerstein MB, Korbel JO, Snyder M, Science 2010 328 232 235 10.1126/science. 1183621 20299548
31. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Ward LD, Kellis M, Nucleic Acids Res 2012 40 Database issue 930 D934 22064851
32. Annotation of functional variation in personal genomes using RegulomeDB. Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub M, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, Cherry JM, Snyder M, Genome Res 2012 22 1790 1797 10.1101/gr.137323.112 22955989
33. Enhanced linkage of a locus on chromosome 2 to premature coronary artery disease in the absence of hypercholesterolemia. Nsengimana J, Samani NJ, Hall AS, Balmforth AJ, Mangino M, Yuldasheva N, Maqbool A, Braund P, Burton P, Bishop DT, Ball SG, Barrett JH, Eur J Hum Genet 2007 15 313 319 10.1038/sj.ejhg. 5201752 17149386
34. Neonatal hepatic steatosis by disruption of the adenosine kinase gene. Boison D, Scheurer L, Zumsteg V, Rülicke T, Litynski P, Fowler B, Brandner S, Mohler H, Proc Natl Acad Sci U S A 2002 99 6985 6890 10.1073/pnas.092642899 11997462 (Pubitemid 34526244)
35. PPARgamma is essential for protection against nonalcoholic steatohepatitis. Wu CW, Chu ESH, Lam CNY, Cheng aSL, Lee CW, Wong VWS, Sung JJY, Yu J, Gene Ther 2010 17 790 798 10.1038/gt.2010.41 20376096
36. Histone modification levels are predictive for gene expression. Karlić R, Chung H-R, Lasserre J, Vlahovicek K, Vingron M, Proc Natl Acad Sci U S A 2010 107 2926 2931 10.1073/pnas.0909344107 20133639
37. Association between PPARGC1A polymorphisms and the occurrence of nonalcoholic fatty liver disease (NAFLD). Yoneda M, Hotta K, Nozaki Y, Endo H, Uchiyama T, Mawatari H, Iida H, Kato S, Hosono K, Fujita K, Yoneda K, Takahashi H, Kirikoshi H, Kobayashi N, Inamori M, Abe Y, Kubota K, Saito S, Maeyama S, Wada K, Nakajima A, BMC Gastroenterol 2008 8 27 10.1186/1471-230X-8-27 18588668 (Pubitemid 352025048)
38. Epigenetic regulation of insulin resistance in nonalcoholic fatty liver disease: impact of liver methylation of the peroxisome proliferator-activated receptor γ coactivator 1α promoter. Sookoian S, Rosselli MS, Gemma C, Burgueño AL, Fernández Gianotti T, Castaño GO, Pirola CJ, Hepatology 2010 52 1992 2000 10.1002/hep.23927 20890895
39. Pathogenesis of alcoholic liver disease: the role of nuclear receptors. Gyamfi MA, Wan Y-JY, Exp Biol Med (Maywood) 2010 235 547 560 10.1258/ebm.2009.009249 20463294
40. Genome-wide scan identifies variation in MLXIPL associated with plasma triglycerides. Kooner JS, Chambers JC, Aguilar-Salinas C, Hinds D, Hyde CL, Warnes GR, Gómez Pérez FJ, Frazer K, Elliott P, Scott J, Milos PM, Cox DR, Thompson JF, Nat Genet 2008 40 149 151 10.1038/ng.2007.61 18193046 (Pubitemid 351171393)