Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2015 Apr 6;10(4):e0121395.
doi: 10.1371/journal.pone.0121395. eCollection 2015.

IFI35, mir-99a and HCV genotype to predict sustained virological response to pegylated-interferon plus ribavirin in chronic hepatitis C

Emilie Estrabaud  1 , Kevin Appourchaux  1 , Ivan Bièche  2 , Fabrice Carrat  3 , Martine Lapalus  1 , Olivier Lada  1 , Michelle Martinot-Peignoux  1 , Nathalie Boyer  1 , Patrick Marcellin  1 , Michel Vidaud  2 , Tarik Asselah  1
Affiliations

IFI35, mir-99a and HCV genotype to predict sustained virological response to pegylated-interferon plus ribavirin in chronic hepatitis C

Emilie Estrabaud et al. PLoS One. .

Abstract

Although, the treatment of chronic hepatitis C (CHC) greatly improved with the use of direct antiviral agents, pegylated-interferon (PEG-IFN) plus ribavirin remains an option for many patients, worldwide. The intra-hepatic level of expression of interferon stimulated genes (ISGs) and the rs12979860 CC genotype located within IFNL3 have been associated with sustained virological response (SVR), in patients with CHC. The aim of the study was to identify micro-RNAs associated with SVR and to build an accurate signature to predict SVR. Pre-treatment liver biopsies from 111 patients, treated with PEG-IFN plus ribavirin, were studied. Fifty-seven patients had SVR, 36 non-response (NR) and 18 relapse (RR). The expression of 851 human miRNAs and 30 selected mRNAs, including ISGs, was assessed by RT-qPCR. In the first group of patients (screen), 20 miRNAs out of the 851 studied were deregulated between NRs and SVRs. From the 4 miRNAs validated (mir-23a, mir-181a*, mir-217 and mir-99a), in the second group of patients (validation), 3 (mir-23a, mir-181a* and mir-99a) were down-regulated in NRs as compared to SVRs. The ISGs, studied, were accumulated in SVRs and IFNL3 rs12979860 CT/TT carriers compared respectively to NRs and CC carriers. Combining, clinical data together with the expression of selected genes and micro-RNAs, we identified a signature (IFI35, mir-99a and HCV genotype) to predict SVR (AUC:0.876) with a positive predictive value of 86.54% with high sensibility (80%) and specificity (80.4%). This signature may help to characterize patients with low chance to respond to PEG-IFN/ribavirin and to elucidate mechanisms of NR.

PubMed Disclaimer

Conflict of interest statement

Competing Interests: The authors have declare that no competing interests exist.

Figures

Fig 1
Fig 1. Modification of miRNAs expression in SVRs and NRs.
Total RNAs was extracted and analyzed for miRNAs content by RT q-PCR. The ΔCt for each miRNA was calculated and normalized to the ΔCt value of SNORD44, in each biopsy. The histograms represent the mean expression of miRNAs/SNORD44 within the groups of patients NRs, SVRs and RRs normalized to the expression of the same miRNA within the group of normal patients. The association of miRNAs expression with viral response was calculated using the Wald test. 1A- Out of 851 miRNAs, 20 miRNAs were particularly deregulated between NRs and SVRs in the screen group (p<0.05 with at least a 2-fold difference between NRs and SVRs or p<0.01). 1B- The expression of the 20 miRNAs previously selected was assessed by RT q-PCR, in the validation group, independently. N = normal non-infected patients, NR = non-responders, RR = responders-relapsers, SVR = sustained virological responders.
Fig 2
Fig 2. Identification of a 3 miRNAs signature (mir-99a, mir-23a and mir-181a*) predictor of SVR and selective analysis of miRNAs expression in NRs and SVRs.
2A- The receiver Operator Curves (ROC) were calculated for each miRNAs and for the signature based on the combination of the 3 miRNAs. 2B- The sensibility (Se), specificity (Spe), positive predictive value (PPV) and negative predictive value (NPV) were calculated for each miRNA isolated and for the combination of the 3 miRNAs. 2C- The expression of mir-122, mir-196b, mir-296-5p, mir-448, mir-431 and mir-128 was analyzed by RT q-PCR in the total group of patients (n = 111). The ΔCp (ΔCpt = 2ΔCpsample) for each miRNAs was calculated and normalized to the ΔCp value of SNORD44 in each biopsy. The histograms represent the mean expression of miRNA/SNORD44 within the groups of patients NRs, SVRs and RRs normalized to the expression of the same miRNA within the group of normal patients. The association of mRNAs expression with viral response was calculated using the Wald test. N = normal un-infected patients, NR = non-responders, RR = responders-relapsers, SVR = sustained virological responders.
Fig 3
Fig 3. Modification of miRNAs expression in the serum of patients with chronic hepatitis C.
3A- Mir-23a, mir-99a, mir-181a*, mir-217 and mir-122 were detected by RT-q-PCR in 68 serums (NR = 26, RR = 10, RR = 32). The ΔCt for each miRNAs were calculated and normalized to the ΔCt value of c.elegans mir-39. The histograms represent the mean expression of miRNAs/mir-39 within the groups of patients NRs, RRs and SVRs. 3B- Correlation between mir-122 and alanine amino transferase, in the serum. The correlation was assessed using the Spearman correlation test. NR = non-responders, RR = responders-relapsers, SVR = sustained virological responders.
Fig 4
Fig 4. Differential mRNAs expression in NRs and SVRs prior to treatment.
4A- The hepatic expression of 25 mRNAs was assessed in the total group of patients by RT q-PCR. The ΔCp (ΔCpt = 2ΔCpsample) value was calculated for each mRNA expression and normalized to the ΔCp value of RPLP0 in each liver biopsy. The histograms represent the mean value of the expression of mRNA in NRs, SVRs and RRs. The expression values were compared by non-parametric test. 4B- High expression of ISGs is associated with IFNL3 TT genotype. The intra-hepatic expression of 25 mRNAs was analyzed by RT-qPCR from total RNAs extracts. IFNL3 rs12979860 polymorphism was determined by direct sequencing. The ΔCp (ΔCpt = 2ΔCpsample) value was calculated for each mRNA expression and normalized to the ΔCp value of RPLP0 in each liver biopsy. The histograms represent the mean value of the ratio of each mRNA expression in TT + CT /CC patients. ISGs: Interferon stimulated genes non- ISGs: other type of genes. NR = non-responders, RR = responders-relapsers, SVR = sustained virological responders.
Fig 5
Fig 5. Identification of a signature predicting SVR.
Clinical, miRNAs and mRNAs expression data were analyzed by multivariate analysis. 5A- ORs are presented for the 3 variables of the signature: mir-99a, IFI35 and HCV genotype 1. 5B- Receiver Operator Curves for prediction of viral response of the signature (AUC 0.876) (genotype 1, IFI35 and mir-99a expression) based on IFI35 expression (AUC 0.777) and mir-99a (AUC 0.688). 5C- Schematic representation of the prediction of SVR. Patients with genotype non-1 had high SVR rates when they express low level of IFI35 (l for low, < mean IFI35 expression). HCV genotype 1 infected patients with low level of IFI35 and high level of mir-99a (h for high, > mean mir-99a expression) showed high SVR rates.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Marcellin P, Asselah T, Boyer N. Fibrosis and disease progression in hepatitis C. Hepatology. 2002; 36: S47–56. - PubMed
    1. Seeff LB. Natural history of chronic hepatitis C. Hepatology. 2002; 36: S35–46. - PubMed
    1. Asselah T, Marcellin P. Second-wave IFN-based triple therapy for HCV genotype 1 infection: simeprevir, faldaprevir and sofosbuvir. Liver Int. 2014; 34 Suppl 1: 60–68. 10.1111/liv.12424 - DOI - PubMed
    1. Schinazi R, Halfon P, Marcellin P, Asselah T. HCV direct-acting antiviral agents: the best interferon-free combinations. Liver Int. 2014; 34 Suppl 1: 69–78. 10.1111/liv.12423 - DOI - PMC - PubMed
    1. Estrabaud E, Vidaud M, Marcellin P, Asselah T. Genomics and HCV infection: progression of fibrosis and treatment response. J Hepatol. 2012; - PubMed

Publication types

MeSH terms

Grants and funding

EE fellowship was supported by the french national agency for research on AIDS and viral hepatitis (ANRS). The study was supported by fundings from the french national agency for research on AIDS and viral hepatitis (ANRS). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

LinkOut - more resources