title: Changes in gene expression in liver tissue from patients with fulminant hepatitis E.
abstract: OBJECTIVE
  To study host gene expression and number of immune cells in liver tissues from patients with fulminant hepatitis E (FH-E).
  
  
  METHODS
  Microarray-based expression profiling was done using Illumina Human WG-6_v3_BeadChip arrays on post-mortem liver tissue from 5 patients with FH-E, and compared with similar tissue from 6 patients with fulminant hepatitis B (FH-B; disease controls) and normal liver tissue from 6 persons. Differential expression was defined as ≥ 2.0-fold change with Benjamini-Hochberg false discovery rate below 0.05 using t-test in liver tissue from FH-B and FH-E, than healthy liver tissue. For some genes that showed differential expression in FH-E, microarray data were validated using quantitative reverse transcription PCR. Differentially expressed gene lists were then subjected to "Gene Ontology" analysis for biological processes, and pathway analysis using BioCarta database on the DAVID server. In addition, tissue sections were stained for CD4(+), CD8(+) and CD56(+) cells using indirect immunohistochemistry; cells staining positive for each of these markers were counted and compared between groups.
  
  
  RESULTS
  Compared to normal livers, those from patients with FH-E and FH-B showed differential expression of 3377 entities (up-regulated 1703, downregulated 1674) and 2572 entities (up 1164, down 1408), respectively. This included 2142 (up 896, down 1246) entities that were common between the two sets; most of these belonged to metabolic, hemostatic and complement pathways, which are active in normal livers. Gene expression data from livers of patients with FH-E but not those of FH-B showed activation of several immune response pathways, particularly those involving cytotoxic T cells. The fold-change values of mRNA for selected genes in livers from FH-E than in normal liver tissue determined using quantitative reverse transcription PCR showed excellent concordance with microarray analysis. At immunohistochemistry, CD8(+) T cells showed an increase in liver biopsies from both FH-E [median 53.4 per arbitrary unit area (range 31.2-99.9)] and FH-B [median 49.3 (19.3-51.0); P = 0.005] compared to control liver tissue [median 6.9 (3.1-14.9)].
  
  
  CONCLUSIONS
  FH-E patients show CD8(+) T cell infiltration and increased gene expression of cytotoxic T cell pathways in liver, suggesting a possible pathogenetic role for these cells.
authors.affiliation: Anshu Naik, Amit Goel, Aditya N Sarangi, Nanda Chhavi, Rakesh Aggarwal, Department of Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, India.
authors.forename: Anshu
authors.initials: A
authors.lastname: Naik
authors.affiliation: Anshu Naik, Amit Goel, Aditya N Sarangi, Nanda Chhavi, Rakesh Aggarwal, Department of Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, India.
authors.forename: Amit
authors.initials: A
authors.lastname: Goel
authors.affiliation: Anshu Naik, Amit Goel, Aditya N Sarangi, Nanda Chhavi, Rakesh Aggarwal, Department of Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, India.
authors.forename: Vinita
authors.initials: V
authors.lastname: Agrawal
authors.affiliation: Anshu Naik, Amit Goel, Aditya N Sarangi, Nanda Chhavi, Rakesh Aggarwal, Department of Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, India.
authors.forename: Aditya N
authors.initials: AN
authors.lastname: Sarangi
authors.affiliation: Anshu Naik, Amit Goel, Aditya N Sarangi, Nanda Chhavi, Rakesh Aggarwal, Department of Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, India.
authors.forename: Nanda
authors.initials: N
authors.lastname: Chhavi
authors.affiliation: Anshu Naik, Amit Goel, Aditya N Sarangi, Nanda Chhavi, Rakesh Aggarwal, Department of Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, India.
authors.forename: Vineeta
authors.initials: V
authors.lastname: Singh
authors.affiliation: Anshu Naik, Amit Goel, Aditya N Sarangi, Nanda Chhavi, Rakesh Aggarwal, Department of Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, India.
authors.forename: Shahid
authors.initials: S
authors.lastname: Jameel
authors.affiliation: Anshu Naik, Amit Goel, Aditya N Sarangi, Nanda Chhavi, Rakesh Aggarwal, Department of Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, India.
authors.forename: Rakesh
authors.initials: R
authors.lastname: Aggarwal
mesh_terms: D000293:Adolescent; D000328:Adult; D001707:Biopsy, Needle; D015496:CD4-Positive T-Lymphocytes / Q000737:chemistry; D019002:CD56 Antigen / Q000032:analysis; D018414:CD8-Positive T-Lymphocytes / Q000737:chemistry; D016022:Case-Control Studies; D019295:Computational Biology; D030541:Databases, Genetic; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation; D016751:Hepatitis E / Q000175:diagnosis / Q000235:genetics*; D006801:Humans; D007150:Immunohistochemistry; D008099:Liver / Q000737:chemistry* / Q000473:pathology / Q000821:virology; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D025341:Principal Component Analysis; D012333:RNA, Messenger / Q000032:analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D055815:Young Adult
chemical_list: D019002:CD56 Antigen; C522918:NCAM1 protein, human; D012333:RNA, Messenger
keywords: Cytotoxic T cells; Gene expression; Hepatitis E; Hepatitis E virus; Immune response; Liver biopsy; Microarray; Natural killer cells; Pathogenesis