IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0121395.html
   My bibliography  Save this article

IFI35, mir-99a and HCV Genotype to Predict Sustained Virological Response to Pegylated-Interferon Plus Ribavirin in Chronic Hepatitis C

Author

Listed:
  • Emilie Estrabaud
  • Kevin Appourchaux
  • Ivan Bièche
  • Fabrice Carrat
  • Martine Lapalus
  • Olivier Lada
  • Michelle Martinot-Peignoux
  • Nathalie Boyer
  • Patrick Marcellin
  • Michel Vidaud
  • Tarik Asselah

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.

Suggested Citation

  • Emilie Estrabaud & Kevin Appourchaux & Ivan Bièche & Fabrice Carrat & Martine Lapalus & Olivier Lada & Michelle Martinot-Peignoux & Nathalie Boyer & Patrick Marcellin & Michel Vidaud & Tarik Asselah, 2015. "IFI35, mir-99a and HCV Genotype to Predict Sustained Virological Response to Pegylated-Interferon Plus Ribavirin in Chronic Hepatitis C," PLOS ONE, Public Library of Science, vol. 10(4), pages 1-19, April.
  • Handle: RePEc:plo:pone00:0121395
    DOI: 10.1371/journal.pone.0121395
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121395
    Download Restriction: no

    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0121395&type=printable
    Download Restriction: no

    File URL: https://libkey.io/10.1371/journal.pone.0121395?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Amaia Lujambio & Scott W. Lowe, 2012. "The microcosmos of cancer," Nature, Nature, vol. 482(7385), pages 347-355, February.
    2. Dongliang Ge & Jacques Fellay & Alexander J. Thompson & Jason S. Simon & Kevin V. Shianna & Thomas J. Urban & Erin L. Heinzen & Ping Qiu & Arthur H. Bertelsen & Andrew J. Muir & Mark Sulkowski & John , 2009. "Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance," Nature, Nature, vol. 461(7262), pages 399-401, September.
    3. Gunter Meister & Thomas Tuschl, 2004. "Mechanisms of gene silencing by double-stranded RNA," Nature, Nature, vol. 431(7006), pages 343-349, September.
    4. Irene M. Pedersen & Guofeng Cheng & Stefan Wieland & Stefano Volinia & Carlo M. Croce & Francis V. Chisari & Michael David, 2007. "Interferon modulation of cellular microRNAs as an antiviral mechanism," Nature, Nature, vol. 449(7164), pages 919-922, October.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Xing Chen & Jun Yin & Jia Qu & Li Huang, 2018. "MDHGI: Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction," PLOS Computational Biology, Public Library of Science, vol. 14(8), pages 1-24, August.
    2. Jun Meng & Lin Shi & Yushi Luan, 2014. "Plant microRNA-Target Interaction Identification Model Based on the Integration of Prediction Tools and Support Vector Machine," PLOS ONE, Public Library of Science, vol. 9(7), pages 1-12, July.
    3. Xing Chen & Li Huang, 2017. "LRSSLMDA: Laplacian Regularized Sparse Subspace Learning for MiRNA-Disease Association prediction," PLOS Computational Biology, Public Library of Science, vol. 13(12), pages 1-28, December.
    4. Melissa Vos & Ruben Boers & Anne L M Vriends & Joachim Boers & Patricia F van Kuijk & Winan J van Houdt & Geert J L H van Leenders & Michal Wagrodzki & Wilfred F J van IJcken & Joost Gribnau & Dirk J , 2020. "MicroRNA expression and DNA methylation profiles do not distinguish between primary and recurrent well-differentiated liposarcoma," PLOS ONE, Public Library of Science, vol. 15(1), pages 1-16, January.
    5. Sean A. P. Clouston & Marcie S. Rubin & Jo C. Phelan & Bruce G. Link, 2016. "A Social History of Disease: Contextualizing the Rise and Fall of Social Inequalities in Cause-Specific Mortality," Demography, Springer;Population Association of America (PAA), vol. 53(5), pages 1631-1656, October.
    6. Chun-Yen Lin & Ji-Yih Chen & Tsung-Nan Lin & Wen-Juei Jeng & Chien-Hao Huang & Chang-Wen Huang & Su-Wei Chang & I-Shyan Sheen, 2011. "IL28B SNP rs12979860 Is a Critical Predictor for On-Treatment and Sustained Virologic Response in Patients with Hepatitis C Virus Genotype-1 Infection," PLOS ONE, Public Library of Science, vol. 6(3), pages 1-9, March.
    7. J. Fulneček, 2007. "Isolation and detection of small RNA molecules," Plant, Soil and Environment, Czech Academy of Agricultural Sciences, vol. 53(10), pages 451-455.
    8. Thomas R O'Brien & James E Everhart & Timothy R Morgan & Anna S Lok & Raymond T Chung & Yongwu Shao & Mitchell L Shiffman & Myhanh Dotrang & John J Sninsky & Herbert L Bonkovsky & Ruth M Pfeiffer & an, 2011. "An IL28B Genotype-Based Clinical Prediction Model for Treatment of Chronic Hepatitis C," PLOS ONE, Public Library of Science, vol. 6(7), pages 1-9, July.
    9. Erik Andrews & Yue Wang & Tian Xia & Wenqing Cheng & Chao Cheng, 2017. "Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome," PLOS Computational Biology, Public Library of Science, vol. 13(1), pages 1-20, January.
    10. Ming-Lung Yu & Chen-Hua Liu & Chung-Feng Huang & Tai-Chung Tseng & Jee-Fu Huang & Chia-Yen Dai & Zu-Yau Lin & Shinn-Cherng Chen & Liang-Yen Wang & Suh-Hang Hank Juo & Wan-Long Chuang & Jia-Horng Kao, 2012. "Revisiting the Stopping Rule for Hepatitis C Genotype 1 Patients Treated with Peginterferon Plus Ribavirin," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-8, December.
    11. Verónica Saludes & Elisabet Bascuñana & Elena Jordana-Lluch & Sònia Casanovas & Mercè Ardèvol & Esther Soler & Ramón Planas & Vicente Ausina & Elisa Martró, 2013. "Relevance of Baseline Viral Genetic Heterogeneity and Host Factors for Treatment Outcome Prediction in Hepatitis C Virus 1b-Infected Patients," PLOS ONE, Public Library of Science, vol. 8(8), pages 1-8, August.
    12. I-Cheng Lee & Yi-Hsiang Huang & Chien-Wei Su & Yuan-Jen Wang & Teh-Ia Huo & Kuei-Chuan Lee & Han-Chieh Lin, 2013. "CXCL9 Associated with Sustained Virological Response in Chronic Hepatitis B Patients Receiving Peginterferon Alfa-2a Therapy: A Pilot Study," PLOS ONE, Public Library of Science, vol. 8(10), pages 1-1, October.
    13. Eric R Londin & Margaret A Keller & Cathleen Maista & Gretchen Smith & Laura A Mamounas & Ran Zhang & Steven J Madore & Katrina Gwinn & Roderick A Corriveau, 2010. "CoAIMs: A Cost-Effective Panel of Ancestry Informative Markers for Determining Continental Origins," PLOS ONE, Public Library of Science, vol. 5(10), pages 1-12, October.
    14. Ester Aparicio & Mariona Parera & Sandra Franco & Nuria Pérez-Alvarez & Cristina Tural & Bonaventura Clotet & Miguel Angel Martínez, 2010. "IL28B SNP rs8099917 Is Strongly Associated with Pegylated Interferon-α and Ribavirin Therapy Treatment Failure in HCV/HIV-1 Coinfected Patients," PLOS ONE, Public Library of Science, vol. 5(10), pages 1-5, October.
    15. Helen Kovari & Stefan Russmann & Bruno Ledergerber & Daniel Müller & Margalida Rotger & Pablo Velli & Matthias Cavassini & Juan Ambrosioni & Andrea Bregenzer & Marcel Stöckle & Enos Bernasconi & Andri, 2015. "Ribavirin Concentrations Do Not Predict Sustained Virological Response in HIV/HCV-Coinfected Patients Treated with Ribavirin and Pegylated Interferon in the Swiss HIV Cohort Study," PLOS ONE, Public Library of Science, vol. 10(7), pages 1-11, July.
    16. Thanthima Suwanthawornkul & Thunyarat Anothaisintawee & Abhasnee Sobhonslidsuk & Ammarin Thakkinstian & Yot Teerawattananon, 2015. "Efficacy of Second Generation Direct-Acting Antiviral Agents for Treatment Naïve Hepatitis C Genotype 1: A Systematic Review and Network Meta-Analysis," PLOS ONE, Public Library of Science, vol. 10(12), pages 1-17, December.
    17. Arnaud Segers & Joachim Carpentier & Frédéric Francis & Rudy Caparros Megido, 2023. "Gene Silencing of laccase 1 Induced by Double-Stranded RNA in Callosobruchus maculatus (Fabricius 1775) (Coleoptera: Chrysomelidae) Suggests RNAi as a Potential New Biotechnological Tool for Bruchid’s," Agriculture, MDPI, vol. 13(2), pages 1-19, February.
    18. Sébastien L Floor & Aline Hebrant & Jaime M Pita & Manuel Saiselet & Christophe Trésallet & Frederick Libert & Guy Andry & Jacques E Dumont & Wilma C van Staveren & Carine Maenhaut, 2014. "MiRNA Expression May Account for Chronic but Not for Acute Regulation of mRNA Expression in Human Thyroid Tumor Models," PLOS ONE, Public Library of Science, vol. 9(11), pages 1-9, November.
    19. Thuc Duy Le & Junpeng Zhang & Lin Liu & Jiuyong Li, 2015. "Ensemble Methods for MiRNA Target Prediction from Expression Data," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-19, June.
    20. Deanna M. Santer & Daniel Li & Yanal Ghosheh & Muhammad Atif Zahoor & Dhanvi Prajapati & Bettina E. Hansen & D. Lorne J. Tyrrell & Jordan J. Feld & Adam J. Gehring, 2022. "Interferon-λ treatment accelerates SARS-CoV-2 clearance despite age-related delays in the induction of T cell immunity," Nature Communications, Nature, vol. 13(1), pages 1-12, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0121395. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.