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Comparison of genomic H3K9ac status in CD4 T cells with diverse progress of chronic hepatitis B

ABSTRACT: Histone 3 lysine 9 acetylation (H3K9ac) at transcription initiation sites is a well known marker for actively initiating and transcribing genes.The purpose of the present study was to investigate the association between H3K9ac and diverse progress of HBV infection. We employed chromatin immunoprecipitation microarray (ChIP-chip) technology to profile and compare the variations of genes H3K9ac in CD4 T cells of the CHB patients at the different clinic phases. The results showed there were lots of different genes with H3K9ac among the study groups.

ORGANISM(S): Homo sapiens

PROVIDER: GSE40365 | GEO | 2012/08/28

SECONDARY ACCESSION(S): PRJNA173885

REPOSITORIES: GEO

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Comparison of genomic H3K9ac status in CD4 T cells with diverse progress of chronic hepatitis B

Project description:Histone 3 lysine 9 acetylation (H3K9ac) at transcription initiation sites is a well known marker for actively initiating and transcribing genes.The purpose of the present study was to investigate the association between H3K9ac and diverse progress of HBV infection. We employed chromatin immunoprecipitation microarray (ChIP-chip) technology to profile and compare the variations of genes H3K9ac in CD4 T cells of the CHB patients at the different clinic phases. The results showed there were lots of different genes with H3K9ac among the study groups. Comparison of genomic H3K9ac status in CD4 T cells from CHB patients at the different clinic phases

2012-08-28 | E-GEOD-40365 | biostudies-arrayexpress

Quantitative Proteomic Analysis of Plasma Samples from Chronic Hepatitis B and Chronic Liver Failure Patients for Biomarker Discovery

Project description:Hepatitis B virus (HBV)-associated acute on chronic liver failure (HBV-ACLF), characterized by an acute deterioration of liver function in the patients with chronic hepatitis B (CHB), is lack of predicting biomarkers for prognosis. To explore potential biomarkers of HBV-ACLF for clinical applications, immuno-depletion of high-abundance plasma proteins followed by iTRAQ-based quantitative proteomic approach was employed to analyze plasma samples from 20 healthy control people, 20 CHB patients and 20 HBV-ACLF patients, respectively. As a result, a total of 427 proteins were identified and quantified from these samples, and 42 proteins were differentially expressed in HBV-ACLF patients as compared to both CHB patients and healthy controls. According to bioinformatics analysis results, 6 proteins related to immune response (MMR), inflammatory response (OPN, HPX), blood coagulation (ATIII) and lipid metabolism (APO-CII, GP73) were selected as biomarker candidates. Further ELISA analysis confirmed the significant up-regulation of GP73, MMR, OPN and down-regulation of ATIII, HPX, APO-CII in HBV-ACLF plasma samples (p<0.01). Moreover, receiver operating characteristic (ROC) curve analysis revealed high diagnostic value of these candidates in assessing HBV-ACLF. In conclusion, present quantitative proteomic study identified 6 novel HBV-ACLF biomarker candidates and might provide fundamental information for development of HBV-ACLF biomarker.

2018-10-23 | PXD007975 | Pride

Identification of differentially expressed microRNAs in liver tissue of Hepatitis B virus (HBV) infected hepatocellular carcinoma (HCC)

Project description:Global expression profiling of miRNAs in liver tissue of HBV infected HCC and chronic hepatitis B (CHB) with no fibrosis was evaluated. A total of 40 differentially expressed miRNAs were identified in HCC. Top 10 miRNAs are validated in more numbers of HCC tisuues by qRT PCR. Finally six miRNAs (miR-15a, miR-16, miR-21,miR-29b-3p, miR-126, miR-142-3p, miR-193a-5p) showed similar expression pattern in both microarray and qRT PCR Differential expression analysis of microRNAs in HBV infected HCC (n=4) compared to CHB patients with no fibrosis (n=8) as control.

2015-04-15 | E-GEOD-67882 | biostudies-arrayexpress

mRNA profile of CD8 T cells from chronic HBV patients

Project description:The low frequency of HBV-specific CD8+ T cells in the peripheral blood of CHB patients has limited studies of the mechanisms underlying HBV-induced T cell exhaustion. Similar to the expansion defect displayed in HBV-specific CD8+ T cells, TCR-induced proliferation of global CD8+ T cells is impaired in a fraction of chronic HBV (CHB) patients. Thus, examining the molecular regulation of global CD8+ T cell function in CHB patients may provide insight into the exhaustion of HBV-specific CD8+ T cells. We used microarrays to detail the global programme of gene expression of CD8 T cells from CHB patients who have not received anti-viral treatment. Fifteen milliliters of blood was drawn from eachof three CHB patients and three healthy donors. PBMCs were enriched using Ficoll, and CD8+ T cells were purified using positive selection beads to a purity of >95% (Miltenyi Biotec, Auburn, CA). Total RNA was extracted using a mirVana isolation kit (Life Technologies, Carlsbad, CA).

2016-07-01 | E-GEOD-51489 | biostudies-arrayexpress

Microarray gene expression from hepatitis B virus infection to hepatocellular carcinoma

Project description:Background: The pathogenesis of hepatitis B virus (HBV)-caused hepatocellular carcinoma (HCC) is complex and not fully understood. In clinical, the effective prevention and treatment of HCC rely on the accurate diagnosis. We developed a biology network approach to investigate the potential mechanisms and biomarkers of each stages from HBV infection to HCC. Methods Global gene profiling of healthy individuals (HC), HBV carriers (HBVC), chronic hepatitis B patients (CHB), liver cirrhosis (LC) and HCC was analyzed by gene array. Differentially expressed genes (DEG) were found by RVM (Random variance model) corrective ANOVA and STC (Series Test of Cluster) analysis.

2019-10-28 | GSE114783 | GEO

mRNA profile of CD8 T cells from chronic HBV patients

2016-07-01 | GSE51489 | GEO

Comparative Transcriptome Analysis of Peripheral Blood Mononuclear Cells Across Clinical Cohorts of Hepatitis B Virus Induced Hepatocellular Carcinoma and Chronic Asymptomatic Hepatitis B Infection in Nigeria

Project description:Hepatitis B Virus (HBV) infection affects about 20 million Nigerians and its most fatal complications is the hepatocellular carcinoma (HCC). Chronic hepatitis B (CHB) infection progresses to HCC which lacks sensitive and specific biomarkers at early stage for detection and subsequent treatment. Efforts in this study is therefore to assess the differential gene expression across clinical cohorts of HBV infection to identify the potential biomarkers of early-stage HCC. Total RNA was extracted and the peripheral blood mononuclear cells (PBMC) in 12 samples were sequenced through the bulk RNA sequencing modality. This was followed by bioinformatic analysis for differential gene expression studies using GALAXY, Qiagen RNA-Sequencing Analysis and DAVID pipelines. Transcriptomic analysis of the PBMC identified a total of 66,726 genes and transcripts. Among patients with HBV-Induced HCC vs CHB, a total of 3,204 genes were differentially expressed with 76 and 272 genes significantly upregulated and downregulated respectively. Across the clinical cohorts of HBV-induced HCC vs healthy controls, 4561 were dysregulated with 370 and 375 genes significantly upregulated and downregulated respectively. Across the significantly upregulated genes of the cohort HBV-induced HCC vs healthy controls, 86 Gene ontology (GO) terms were identified, 19 clustered, 103 terms did not cluster, while across the downregulated cohort, 255 GO terms were identified, 63 clustered, 335 did not. The mitogen-activated protein kinase (MAPK) signalling pathway, cell division cycle and microRNA pathways in the HCC cohort were dysregulated

2023-10-01 | GSE236281 | GEO

Optimized RNA Interference Therapeutics Combined with Interleukin-2 mRNA for Treating Hepatitis B Virus Infection

Project description:BACKGROUND & AIMS: This study aimed to develop a pan-genotypic and multifunctional small interfering RNA (siRNA) against hepatitis B virus (HBV) with an efficient delivery system for treating chronic hepatitis B (CHB), and explore combined RNA interference (RNAi) and immune modulatory modalities for better viral control. METHODS: Twenty synthetic siRNAs targeting consensus motifs distributed across the whole HBV genome were designed and evaluated. The lipid nanoparticle (LNP) formulation was optimized by adopting HO-PEG2000-DMG lipid and modifying the molar ratio of traditional polyethylene glycol (PEG) lipid in LNP prescriptions. The efficacy and safety of this formulation in delivering siHBV (tLNP/siHBV) along with the mouse IL-2 (mIL-2) mRNA (tLNP/siHBVIL2) were evaluated in the rAAV-HBV1.3 mouse model. RESULTS: A siRNA combination (terms “siHBV”) with a genotypic coverage of 98.55% was selected, chemically modified, and encapsulated within an optimized LNP (tLNP) of high efficacy and security to fabricate a therapeutic formulation for CHB. The results revealed that tLNP/siHBV significantly reduced the expression of viral antigens and DNA (up to 3log10 reduction) in dose- and time-dependent manners at single-dose or multi-dose frequencies, with satisfactory safety profiles. Further studies showed that tLNP/siHBVIL2 enables additive antigenic and immune control of the virus, via introducing potent HBsAg clearance through RNAi and triggering strong HBV-specific CD4+ and CD8+ T cell responses by expressed mIL-2 protein. CONCLUSIONS: By adopting tLNP as nucleic acid nanocarriers, the co-delivery of siHBV and mIL-2 mRNA enables synergistic antigenic and immune control of HBV, thus offering a promising translational therapeutic strategy for treating CHB.

2024-04-02 | GSE262515 | GEO

Expression data from PBMCs in patients with CHB or SC HBV

Project description:There were 3 patients with CHB and 3 patients with SC HBV in microarray analysis. As for the liver function parameters, the average HBsAg and HBeAg levels of CHB group were obviously higher than SC HBV group. The obtained RNAs expression profiles were analyzed by microarray analysis. A total of 513 lncRNAs, 256 mRNAs and 48 miRNAs were found to be differentially expressed (DE) in patients with CHB compared with patients with SC HBV (fold change > 1.2 and P < 0.05).

2023-02-03 | GSE224283 | GEO

Transcriptomic analysis of the woodchuck model of chronic hepatitis B: Liver gene expression in tumor and non-tumor samples from chronically infected woodchucks

Project description:The Eastern woodchuck (Marmota monax) is naturally infected with woodchuck hepatitis virus (WHV), a hepadnavirus closely related to the human hepatitis B virus (HBV). The woodchuck is used as an animal model for studying chronic hepatitis B (CHB) and HBV-associated hepatocellular carcinoma (HCC) in humans, but the lack of sequence information has hitherto precluded functional genomics analysis. To address this major limitation of the model, we report here the sequencing, assembly and annotation of the woodchuck transcriptome, together with the generation of custom woodchuck microarrays. Using this new platform, we characterized the transcriptional response to persistent WHV infection and WHV-induced HCC. This revealed that chronic WHV infection, like HBV, is associated with (i) a limited intrahepatic type I interferon response, (ii) intrahepatic induction of markers associated with T cell exhaustion, (iii) elevated levels of suppressor of cytokine signaling 3 (SOCS3) in the liver, and (iv) intrahepatic accumulation of neutrophils. Underscoring the translational value of the woodchuck model, this study also determined that WHV-induced HCC shares molecular characteristics with a subtype of human HCC with poor prognosis. Conclusion: Our data establish the translational value of the woodchuck model and provide new insights into immune pathways which may play a role either in the persistence of HBV infection or the sequelae of CHB. Custom microarrays, generated from sequences obtained in transcriptome sequencing of woodchuck liver and PBMCs, were used to examine non-tumor vs. tumor gene expression in liver samples obtained from animals chronically infected with WHV (n=13). Multiple technical replicates per woodchuck sample are included.

2012-04-10 | E-GEOD-36545 | biostudies-arrayexpress

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