Interferon signaling related gene expression and clinical outcome of chronic hepatitis C
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE20119 | GEO | 2010/02/11
SECONDARY ACCESSION(S): PRJNA124257
REPOSITORIES: GEO
Similar Datasets
Project description:Chronic hepatitis C (CH) frequently developed liver cirrhosis and hepatocellular carcinoma without suitable treatment. However, peginterferon(IFN) and ribavirin therapy (combination therapy), which is present standard therapy, is imperfect effect because of several side effect. We attempt to catalog IFN related gene expression profile according to the response of combination therapy in to predict the outcome of drug-response before administration and establish the adequate treatment according to the individual clinical information. Chip1 [GPL9960-related Samples]: We quantified expression profile of 200 IFN related genes by microarray in the liver biopsy specimen from 88 CH patients without history of anti-viral therapy, 10 fatty liver patients without HCV infection were also enrolled. Chip2 [GPL9962-related Samples]: We quantified expression profile of 37 IFN related genes by microarray in the liver biopsy specimen from 88 CH patients without history of anti-viral therapy, 10 fatty liver patients without HCV infection were also enrolled.
2010-02-10 | E-GEOD-20119 | biostudies-arrayexpress
Project description:Background/Aims: Ribavirin improves treatment response to pegylated-interferon (PEG-IFN) in chronic hepatitis C but the mechanism remains controversial. We studied correlates of response and mechanism of action of ribavirin in treatment of hepatitis C. Methods: 70 treatment-naïve patients were randomized to 4 weeks of ribavirin (1000-1200 mg/d) or none, followed by PEG-IFN alfa-2a and ribavirin at standard doses and durations. Patients were randomized to undergo a liver biopsy either 24 hours before, or 6 hours after starting PEG-IFN. Hepatic gene expression was assessed by microarray and interferon-stimulated gene (ISG) expression quantified by the nCounter platform. Temporal changes in ISG expression were assessed by qPCR in peripheral-blood mononuclear cells (PBMC) and by serum levels of IP-10. Results: After four weeks of ribavirin monotherapy, HCV levels decreased by 0.5±0.5 log10 (p=0.009 vs. controls) and ALT by 33% (p<0.001). Ribavirin pretreatment, while modestly augmenting the induction of ISGs by PEG-IFN, did not modify the virological response to subsequent PEG-IFN and ribavirin treatment. However, biochemical, but not virological response to ribavirin monotherapy predicted response to subsequent combination treatment (rapid virological response, 71% in biochemical responders vs. 22% non-responders, p=0.01; early virological response, 100% vs. 68%, p=0.03, sustained virological response 83% vs. 41%, p=0.053). Ribavirin monotherapy lowered serum IP-10 levels but had no effect on ISG expression in PBMC. Conclusion: Ribavirin is a weak antiviral but its clinical effect in combination with PEG-IFN seems to be mediated by a separate, indirect mechanism, which may act to reset the interferon responsiveness in HCV-infected liver. Ribavirin pretreatment does not alter the clinical outcome of subsequent combination therapy. Analysis of liver biopsy samples from 52 patients under 4 different treatment conditions.
2013-03-08 | E-GEOD-38663 | biostudies-arrayexpress
Project description:Background/Aims: Ribavirin improves treatment response to pegylated-interferon (PEG-IFN) in chronic hepatitis C but the mechanism remains controversial. We studied correlates of response and mechanism of action of ribavirin in treatment of hepatitis C. Methods: 70 treatment-naïve patients were randomized to 4 weeks of ribavirin (1000-1200 mg/d) or none, followed by PEG-IFN alfa-2a and ribavirin at standard doses and durations. Patients were randomized to undergo a liver biopsy either 24 hours before, or 6 hours after starting PEG-IFN. Hepatic gene expression was assessed by microarray and interferon-stimulated gene (ISG) expression quantified by the nCounter platform. Temporal changes in ISG expression were assessed by qPCR in peripheral-blood mononuclear cells (PBMC) and by serum levels of IP-10. Results: After four weeks of ribavirin monotherapy, HCV levels decreased by 0.5±0.5 log10 (p=0.009 vs. controls) and ALT by 33% (p<0.001). Ribavirin pretreatment, while modestly augmenting the induction of ISGs by PEG-IFN, did not modify the virological response to subsequent PEG-IFN and ribavirin treatment. However, biochemical, but not virological response to ribavirin monotherapy predicted response to subsequent combination treatment (rapid virological response, 71% in biochemical responders vs. 22% non-responders, p=0.01; early virological response, 100% vs. 68%, p=0.03, sustained virological response 83% vs. 41%, p=0.053). Ribavirin monotherapy lowered serum IP-10 levels but had no effect on ISG expression in PBMC. Conclusion: Ribavirin is a weak antiviral but its clinical effect in combination with PEG-IFN seems to be mediated by a separate, indirect mechanism, which may act to reset the interferon responsiveness in HCV-infected liver. Ribavirin pretreatment does not alter the clinical outcome of subsequent combination therapy.
2013-03-08 | GSE38663 | GEO
Project description:Time series of gene expression arrays before and during treatment of Hepatitis C; days 0, 1, 2, 7, 14 and 28 for 69 participants (IDs 1 through 69 are used). Treating chronic hepatitis C using peginterferon alpha and ribavirin leads to sustained clearance of virus and clinical improvement in approximately 50% of patients. Response rates are lower among patients with genotype 1 than with genotypes 2 and 3 and among African American ( AA) compared to Caucasian (CA) patients. Using DNA microarrays, gene expression was assessed in a group of 33 African American and 36 Caucasian American patients with chronic hepatitis C, genotype 1 during the first 28 days of treatment. Results were examined with respect to treatment responses and to race. Patients showed a response to treatment at the gene expression level in RNA isolated from PBMC irrespective of degree of decrease in hepatitis C virus (HCV) RNA levels. However, gene expression responses were relatively blunted in patients with poor viral response (< 1.5 log10 IU/ml decrease at 28 days) compared to those in patients with a marked (> 3.5 log10 decrease) or intermediate (1.5 to 3.5 log10 decrease) response. The number of genes that were up- or down-regulated by peginterferon and ribavirin treatment was fewer in patients with a poor response compared to those with an intermediate or marked viral response. However AA patients had a stronger interferon response than CA patients in general. The induced levels of known ISGs such as OAS, MX1, IRF-7 and the toll like receptor TLR-7 was lower in poor response patients than in marked or intermediate response patients. Thus, the relative lack of viral response to interferon therapy of hepatitis C is associated with blunted interferon cell signaling. No specific regulatory gene could be identified as responsible for this global blunting or racial differences. Experiment Overall Design: Eligible patients were naïve to interferon and ribavirin treatment, had detectable HCV RNA in serum, and nearly all had a liver biopsy performed within the previous 18 months showing chronic hepatitis. Only patients who were born in the United States and designated themselves as âAfrican American/Blackâ or âCaucasian/Whiteâ were eligible. The clinical protocol called for participants to be treated for up to 48 weeks with peginterferon alpha-2a (Pegasysâ¢, Roche Pharmaceuticals Nutley, NJ) in a dose of 180 µg weekly by self-administered subcutaneous injection and ribavirin (Copegusâ¢, Roche) orally in a dose of 1000 or 1200 mg daily based on body weight of less than 75 kg or equal to or greater than 75 kg. Peripheral blood mononuclear cells (PBMC) were collected from patients before treatment (day 0) and on days 1 (after the initial supervised injection of peginterferon), 2, 7, 14 and 28. From the Virahep-C cohort, 72 patients who did not have dose reductions of either peginterferon or ribavirin in the first 28 days of treatment were selected such that 12 patients were included in each race (CA, AA) by virological response category. The three categories of response were: marked, defined as a decrease in HCV RNA levels of more than 3.5 log10 IU/ml or to undetectable on day 28; intermediate, defined as a decrease of 1.4 to 3.5 log10 IU/ml on day 28; and poor, defined as less than 1.4 log10 IU/ml decline on day 28 relative to baseline. These definitions were made a priori in an attempt to analyze the biological basis for virological responses. Of these, adequate RNA was not obtained from 3 patients to provide gene expression information. Of these 72, 69 were analyzed.
2008-06-16 | E-GEOD-7123 | biostudies-arrayexpress
Project description:The combination of peginterferon and ribavirin is the standard treatment for chronic hepatitis C. Our recent clinical study suggests that ribavirin augments the induction of interferon stimulated genes (ISGs) in patients treated for HCV infection [1]. In order to further characterize the mechanisms of action of ribavirin, we examined the effect of ribavirin treatment on ISG induction in cell culture. In addition, the effect of ribavirin on infectious HCV cell culture systems was also studied. Similar to interferon-alpha, ribavirin potently inhibits JFH-1 infection of Huh7.5.1 cells in a dose-dependent manner, which spans the physiological concentration of ribavirin in vivo. Microarray analysis and subsequent quantitative PCR assays demonstrated that ribavirin treatment resulted in the induction of a distinct set of ISGs. These ISGs, including IRF7 and IRF9 are known to play an important role in anti-HCV responses. When ribavirin is used in conjunction with interferon, induction of specific ISGs is synergistic when compared to either drug applied separately. Direct up-regulation of these antiviral genes by ribavirin is mediated by a novel mechanism different from those associated with interferon signaling and intracellular double stranded RNA sensing pathways such as RIG-I and MDA5. RNA interference studies excluded the activation of the Toll-like receptor and NF-KappaB pathways in the action of ribavirin. In conclusion, our study suggests that ribavirin, acting via a novel innate mechanism, potentiates the anti-HCV effect of interferon. Understanding the mechanism of action of ribavirin would be valuable in identifying novel antivirals.
2012-01-01 | GSE23031 | GEO
Project description:The combination of peginterferon and ribavirin is the standard treatment for chronic hepatitis C. Our recent clinical study suggests that ribavirin augments the induction of interferon stimulated genes (ISGs) in patients treated for HCV infection [1]. In order to further characterize the mechanisms of action of ribavirin, we examined the effect of ribavirin treatment on ISG induction in cell culture. In addition, the effect of ribavirin on infectious HCV cell culture systems was also studied. Similar to interferon-alpha, ribavirin potently inhibits JFH-1 infection of Huh7.5.1 cells in a dose-dependent manner, which spans the physiological concentration of ribavirin in vivo. Microarray analysis and subsequent quantitative PCR assays demonstrated that ribavirin treatment resulted in the induction of a distinct set of ISGs. These ISGs, including IRF7 and IRF9 are known to play an important role in anti-HCV responses. When ribavirin is used in conjunction with interferon, induction of specific ISGs is synergistic when compared to either drug applied separately. Direct up-regulation of these antiviral genes by ribavirin is mediated by a novel mechanism different from those associated with interferon signaling and intracellular double stranded RNA sensing pathways such as RIG-I and MDA5. RNA interference studies excluded the activation of the Toll-like receptor and NF-KappaB pathways in the action of ribavirin. In conclusion, our study suggests that ribavirin, acting via a novel innate mechanism, potentiates the anti-HCV effect of interferon. Understanding the mechanism of action of ribavirin would be valuable in identifying novel antivirals. RNA from three samples were treated with Ribavirin and compared to three PBS treated samples
2012-01-01 | E-GEOD-23031 | biostudies-arrayexpress
Project description:We attempt to catalog the microRNA (miRNA) expression profile according to the response of combination therapy in order to predict the outcome of drug-response before administration and clarify the relationship between aberrant expression of miRNAs and chronic liver disease. We quantified expression profile of 474 mature miRNAs by microarray in the liver biopsy specimen from 99 CH patients without history of anti-viral therapy.
2010-12-30 | E-GEOD-16922 | biostudies-arrayexpress
Project description:Predicting Treatment response to Hepatitis C, PEG-IFN/Ribavirin
2010-01-04 | PRD000181 | Pride
Project description:Study of PBMC gene expression during the first 10 weeks of therapy with Pegylated-interferon-alfa2b (PegIntronTM) and ribavirin (administered by weight) in HCV patients. This study compared the kinetics of gene expression during the first 10 weeks of therapy with Pegylated-interferon-alfa2b (PegIntronTM) and ribavirin (administered by weight) in HCV patients with the recently completed Virahep C study (9999) in which Peginterferon-alfa2a and ribavirin was administered. RNA was isolated from peripheral blood monocytes from twenty treatment-naïve patients just before treatment (day 0,) and at days 3, 6, 10, 13, 27, 42 and 70 days after treatment. Gene expression at each time was compared to that of day 0 using Affymetrix DNA-micro-arrays. Focusing upon genes that changed at least 1.5-fold and p<0.001, the numbers were high at day 3 (300 probes) and 10 (255) but dropped at days 6 (128) and 13 (142) but were steady at later time points. A large number of genes continued to be up regulated throughout the trial period. A second group of genes, including CXCL10, chemokine receptor 1, TRAIL, IL1 R and genes associated with complement and lipid metabolism, were transiently induced. CDKN1C (cyclin kinase inhibitor 1) was induced early but repressed at later times. Genes induced at later times were mostly related to blood chemistry and oxygen transport. Genes down regulated were related to ribosomal proteins and eukaryotic translation complexes. By week 10, 50% of the patients demonstrated a positive response to therapy. Conclusions: The response to pegintron/ribavirin was similar to that reported for Pegasys/ribavirin, although the extent of gene induction was less. No differences were found between patients responding to treatment or non-responders during this period. Our data suggest that more than once a week dosing might be desirable early on during treatment. Keywords: Time Course, gene expression
2009-04-21 | GSE11342 | GEO
Project description:Study of PBMC gene expression during the first 10 weeks of therapy with Pegylated-interferon-alfa2b (PegIntronTM) and ribavirin (administered by weight) in HCV patients. This study compared the kinetics of gene expression during the first 10 weeks of therapy with Pegylated-interferon-alfa2b (PegIntronTM) and ribavirin (administered by weight) in HCV patients with the recently completed Virahep C study (9999) in which Peginterferon-alfa2a and ribavirin was administered. RNA was isolated from peripheral blood monocytes from twenty treatment-naïve patients just before treatment (day 0,) and at days 3, 6, 10, 13, 27, 42 and 70 days after treatment. Gene expression at each time was compared to that of day 0 using Affymetrix DNA-micro-arrays. Focusing upon genes that changed at least 1.5-fold and p<0.001, the numbers were high at day 3 (300 probes) and 10 (255) but dropped at days 6 (128) and 13 (142) but were steady at later time points. A large number of genes continued to be up regulated throughout the trial period. A second group of genes, including CXCL10, chemokine receptor 1, TRAIL, IL1 R and genes associated with complement and lipid metabolism, were transiently induced. CDKN1C (cyclin kinase inhibitor 1) was induced early but repressed at later times. Genes induced at later times were mostly related to blood chemistry and oxygen transport. Genes down regulated were related to ribosomal proteins and eukaryotic translation complexes. By week 10, 50% of the patients demonstrated a positive response to therapy. Conclusions: The response to pegintron/ribavirin was similar to that reported for Pegasys/ribavirin, although the extent of gene induction was less. No differences were found between patients responding to treatment or non-responders during this period. Our data suggest that more than once a week dosing might be desirable early on during treatment. Experiment Overall Design: Time course, 20 individuals, samples taken before first treatment (day 0) and days 3, 6, 10, 13, 27, 42 and 70.
2009-05-03 | E-GEOD-11342 | biostudies-arrayexpress