A Tetra-Primer Amplification Refractory Mutation System–Polymerase Chain Reaction (T-ARMS-PCR) for Genotyping of rs8099917 & rs12979860 IL28B Polymorphisms and Its Correlation of Various Variables in Iranian HCV Patients

Main Article Content

Ali Bahari
Mohammad Hashemi
Gholam Reza Bahari
Tahereh Fakharian
Sina Gerayli
Abbas Esmail Zadeh
Hamid Reza Sima
Hooman Mosannan Mozaffari
Ali Reza Bakhshipour
Zohreh Bari

Abstract

Background: Selecting patients for new direct acting antiviral treatment of HCV has prompted a conflicting matter worldwide because of its high cost and limited availability. Genotyping of IL28B polymorphisms will aid clinical decision making for identifying priorities of urgent treatment in resource-limited countries.

Objectives: The aim of the present study was to design a simple tetra-primer amplification refractory mutation system–polymerase chain reaction (T-ARMS-PCR) for genotyping of the rs8099917 and rs12979860 IL28B gene polymorphisms. Furthermore, we identify the correlation of variables such as gender, serum ALT level, histology of liver and baseline viral load with these polymorphisms.

Patients and Methods: We efficiently designed a T-ARMS-PCR for detection of rs12979860 and rs8099917 IL28B gene polymorphisms. Using this method, we genotyped 148 hepatitis C patients. To ensure T-ARMS genotyping quality, we, regenotyped samples with the PCR- sequencing method.

Results: Results of genotyping of rs12979860 and rs8099917 by T-ARMS PCR method were 100% concordant with the sequencing results. Among these 148 patients with chronic hepatitis C, the frequency of the rs12979860 CT, TT and CC genotypes was 72.3%, 14.2% and 13.5%, respectively and the frequency of the rs8099917 TT, GT and GG genotypes was 58.1%, 38.5% and 3.4%. Low frequency (2.7%) of association of two unfavourable homozygous genotypes (TT rs12979860 / GG rs809917) as well as 56.7% of association of 3 or 4 favorable alleles could explain good response of Iranians to HCV treatment with interferon-based regimens. About correlation of polymorphisms with different variables, only high viral load showed a statistically significant correlation to unfavorable genotype of TT rs12979860 ( p value = 0/05 ) and there was no correlation of  serum ALT level, gender and  histology of liver to IL28B genotypes.

Conclusions: We report that rs8099917 polymorphisms could predict outcomes better than rs12979860 in Iranian HCV patients.

Keywords:
Hepatitis C, IL28B, single nucleotide polymorphism, Tetra-ARMS-PCR, Iranian.

Article Details

How to Cite
Bahari, A., Hashemi, M., Bahari, G. R., Fakharian, T., Gerayli, S., Zadeh, A. E., Sima, H. R., Mozaffari, H. M., Bakhshipour, A. R., & Bari, Z. (2020). A Tetra-Primer Amplification Refractory Mutation System–Polymerase Chain Reaction (T-ARMS-PCR) for Genotyping of rs8099917 & rs12979860 IL28B Polymorphisms and Its Correlation of Various Variables in Iranian HCV Patients. Journal of Pharmaceutical Research International, 32(29), 31-41. https://doi.org/10.9734/jpri/2020/v32i2930881
Section
Original Research Article

References

Alavian SM. Hepatitis C infection in Iran; A review article,” Iranian Journal of Clinical Infectious Diseases. 2009;4(1):13.

Ahlenstiel G, Booth DR, George J. IL28B in hepatitis C virus infection: translating pharmacogenomics into clinical practice. J Gastroenterol. 2010;45(9):903-10.

Cavalcante LN, Lyra AC. Predictive factors associated with hepatitis C antiviral therapy response. World J Hepatol. 2015;7(12):1617-31.

Mangia A, Thompson AJ, Santoro R, Piazzolla V, Tillmann HL, Patel K, Shianna KV, Mottola L, Petruzzellis D, Bacca D, Carretta V, Minerva N, Goldstein DB, McHutchison JG. An IL28B polymorphism determines treatment response of hepatitis C virus genotype 2 or 3 patients who do not achieve a rapid virologic response. Gastroenterology. 2010;139(3):821-7,827 e1.

Hashemi M, Moazeni-Roodi A, Bahari A, Taheri M. A tetra-primer amplification refractory mutation system-polymerase chain reaction for the detection of rs8099917 IL28B genotype. Nucleosides Nucleotides Nucleic Acids. 2012;31(1):55-60.

Sharafi H, Alavian SM. IL28B polymorphism, Explanation for Different Responses to Therapy in Hepatitis C Patients. Hepat Mon. 2011;11(12):958-9.

Zhang C, Liu Y, Ring BZ, Nie K, Yang M, Wang M, Shen H, Wu X, Ma X. A novel multiplex tetra-primer ARMS-PCR for the simultaneous genotyping of six single nucleotide polymorphisms associated with female cancers. PLoS One. 2013;8(4):e62126,

Wu AH, Khalili M. The birth and potential death of IL28B genotyping for hepatitis C therapy,” Personalized Medicine. 2015; 12(2):55-57.

Thompson AJ, McHutchison JG. Will IL28B polymorphism remain relevant in the era of direct-acting antiviral agents for hepatitis C virus? Hepatology. 2012;56(1):373-81.

Gane EJ, Roberts SK, Stedman CA, Angus PW, Ritchie B, Elston R, Ipe D, Morcos PN, Baher L, Najera I, Chu T, Lopatin U,. Berrey MM, Bradford W, Laughlin M, Shulman NS, Smith PF. Oral combination therapy with a nucleoside polymerase inhibitor (RG7128) and danoprevir for chronic hepatitis C genotype 1 infection (INFORM-1): A randomised, double-blind, placebo-controlled, dose-escalation trial. Lancet. 2010;376(9751): 1467-75.

Zeuzem S, Soriano V, Asselah T, et al. Virololgic Rresponse to an interferon- free regimen of BI201335 and BI207127, with and without rivavirin, in treatement-naive patients with chronic genotype-1 HCV infection: Week 12 interim results of the SOUND-C2 STUDY [Abstract LB-15]. Hepatology. 2011;54(Suppl): 1436A.

Lawitz E, Mangia A, Wyles D, Rodriguez-Torres M, Hassanein T, Gordon SC, Schultz M, Davis MN, Kayali Z, Reddy KR, Jacobson IM, Kowdley KV, Nyberg L, Subramanian GM, Hyland RH, Arterburn S, Jiang D, McNally J, Brainard D, Symonds WT, McHutchison JG, Sheikh AM, Younossi Z, Gane EJ. Sofosbuvir for previously untreated chronic hepatitis C infection,” N Engl J Med. 2013;368(20):1878-87.

Zeuzem S, Dusheiko GM, Salupere R, Mangia A, Flisiak R, Hyland RH, Illeperuma A, Svarovskaia E, Brainard DM, Symonds WT, Subramanian GM, McHutchison JG, Weiland O, Reesink HW, Ferenci P, Hezode C, Esteban R, Investigators V. Sofosbuvir and ribavirin in HCV genotypes 2 and 3. N Engl J Med. 2014;370(21):1993-2001.

Tamaki N, Kurosaki M, Higuchi M, Takada H, Nakakuki N, Yasui Y, Suzuki S, Tsuchiya K, Nakanishi H, Itakura J, Takahashi Y, Ogawa S, Tanaka Y, Asahina Y, Izumi N. Genetic Polymorphisms of IL28B and PNPLA3 Are Predictive for HCV Related Rapid Fibrosis Progression and Identify Patients Who Require Urgent Antiviral Treatment with New Regimens. Plos One. 2015;10(9):e0137351.

Noureddin M, Wright EC, Alter HJ, Clark S, Thomas E, Chen R, Zhao X, Conry-Cantilena C, Kleiner DE, Liang TJ, Ghany MG. Association of IL28B genotype with fibrosis progression and clinical outcomes in patients with chronic hepatitis C: A longitudinal analysis. Hepatology. 2013;58(5):1548-57.

Bochud PY, Bibert S, Kutalik Z, Patin E, Guergnon J, Nalpas B, Goossens N, Kuske L, Mullhaupt B, Gerlach T, Heim MH, Moradpour D, Cerny A, Malinverni R, Regenass S, Dollenmaier G, Hirsch H, Martinetti G, Gorgiewski M, Bourliere M, Poynard T, Theodorou I, Abel L, Pol S, Dufour JF, Negro F, Swiss Hepatitis CCSG, AHEGS Group. IL28B alleles associated with poor hepatitis C virus (HCV) clearance protect against inflammation and fibrosis in patients infected with non-1 HCV genotypes. Hepatology. 2012;55(2):384-94.

Petta S, Cabibbo G, Enea M, et al. Cost-effective of sofosbuvir-based triple therapy for untreated patients with genotype 1 chronic hepatitis C. Hepatology. 2014;59:1692–1705.

Ekstrom V, Kumar R, Zhao Y, Yee ML, Sung C, Toh D, Loh PY, Tan J, Teo EK, Chow WC. Real world experience with pegylated interferon and ribavirin in hepatitis C genotype 1 population with favourable IL28B polymorphism. Gastroenterology Report. 2016;5.

Hashemi M, Moazeni-Roodi A, Fazaeli A, Sandoughi M, Bardestani GR, Kordi-Tamandani DM, GS. Lack of association between paraoxonase-1 Q192R polymorphism and rheumatoid arthritis in southeast Iran. Genet Mol Res. 2010;9(1):333-9.

McHutchison JG. The role of genetic markers in hepatitis C virus therapy: a major step for individualized care. Liver Int. 2011;31(1):29-35.

Rauch A, Kutalik Z, Descombes P, Cai T, Di Iulio J, Mueller T, Bochud M, Battegay M, Bernasconi E, Borovicka J, Colombo S, Cerny A, Dufour JF, Furrer H, Gunthard HF, Heim M, Hirschel B, Malinverni R, Moradpour D, Mullhaupt B, Witteck A, Beckmann JS, Berg T, Bergmann S, Negro F, Telenti A, Bochud PY. Genetic variation in IL28B is associated with chronic hepatitis C and treatment failure: a genome-wide association study. Gastroenterology. 2010;138(4);1338-45,1345 e1-7.

Li S, Hu P, Zhang QQ, Liu YH, Hu HD, Zhang DZ, Ren H. Single nucleotide polymorphisms of the IL28B and sustained virologic response of patients with chronic hepatitis C to PEG-interferon/ribavirin therapy: A meta-analysis: Meta-analysis of IL28B. Hepat Mon. 2011;11(3):163-72.

Mahboobi N, Behnava B, Alavian SM. IL28B SNP genotyping among Iranian HCV-infected patients: A preliminary report. Hepat Mon. 2011;11(5):386-8.

Sharafi H, Pouryasin A, Alavian SM, Behnava B, Keshvari M, Mehrnoush L, Salimi S, Kheradvar O. Development and Validation of a Simple, Rapid and Inexpensive PCR-RFLP Method for Genotyping of Common IL28B Polymorphisms: A Useful Pharmacogenetic Tool for Prediction of Hepatitis C Treatment Response. Hepat Mon. 2012;12(3):190-5.

Sharafi H, Pouryasin A, Alavian SM, Behnava B, Keshvari M, Salimi S, Mehrnoush L, Fatemi A. Distribution of IL28B Genotypes in Iranian Patients with Chronic Hepatitis C and Healthy Individuals. Hepat Mon. 2012;12(12):e8387.

Ge D, Fellay J, Thompson AJ, Simon JS, Shianna KV, Urban TJ, Heinzen EL, Qiu P, Bertelsen AH, Muir AJ, Sulkowski M, McHutchison JG, Goldstein DB. Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance. Nature. 2009;461(7262):399-401.

AASLD. HCV Guidance: Recommendations for testing, managing, and treating hepatitis C. Unique patient populations: Patients with decompensated cirrhosis, Updated July 6, 2016. Cited July 20, 2016.

Chu TW, Kulkarni R, Gane EJ, Roberts SK, Stedman C, Angus PW, Ritchie B, Lu XY, Ipe D, Lopatin U, Germer S, Iglesias VA, Elston R, Smith PF, Shulman NS. Effect of IL28B genotype on early viral kinetics during interferon-free treatment of patients with chronic hepatitis C. Gastroenterology. 2012;142(4):790-5.

Zeuzem S, Soriano S, Asselah T, Bronowicki JP, Lohse A, et. al. SVR4 and SVR12 with an interferon-free regimen of BI201335 and BI207127, +/- ribavirin, in treatment-naive patients with chronic genotype-1 HCV infection: interim results of sound-C2. J. Hepatol. 2012;56:S45.

Vadwai V, Ranjan Das B. IL28B Genotyping: A Step towards HCV-Personalized Therapy. International Journal of Gastroenterology Research and Practice. 2014;2014:16.

Sezaki H. The impact of IL28B polymorphism and HCV NS5A resistance associated variants on treatment response with ledipasvir and sofosbuvir regimen in Japanese real-life settings,” AASLD Liver Learning, Abstract. 2016;1953:144845.

Lundbo LF, Clausen LN, Weis N, Schonning K, Rosenorn L, Benfield T, Christensen PB. Influence of hepatitis C virus and IL28B genotypes on liver stiffness. PLoS One. 2014;9(12):e115882,

Barreiro P, Pineda JA, Rallon N, Naggie S, Martin-Carbonero L, Neukam K, Rivero A, Benito JM, Caruz A, Vispo E, Camacho A, Medrano J, McHutchison J, Soriano V. Influence of interleukin-28B single-nucleotide polymorphisms on progression to liver cirrhosis in human immunodeficiency virus-hepatitis C virus-coinfected patients receiving antiretroviral therapy. J Infect Dis. 2011;203(11):1629-36.

Rembeck K, Lagging M. Impact of IL28B, ITPA and PNPLA3 genetic variants on therapeutic outcome and progression of hepatitis C virus infection. Pharmacogenomics. 2015;16(10);1179-88.

Marabita F, Aghemo A, De Nicola S, Rumi MG, Cheroni C, Scavelli R, Crimi M, Soffredini R, Abrignani S, De Francesco R, CM. Genetic variation in the interleukin-28B gene is not associated with fibrosis progression in patients with chronic hepatitis C and known date of infection. Hepatology. 2011;54(4):1127-34.

Grebely J, Grady B, Hajarizadeh B, Page K, Dore GJ, INCS Group. Disease progression during advanced fibrosis: IL28B genotype or HCV RNA levels? Hepatology. 2014;59(4):1650-1.

Boglione L, Cusato J, Allegra S, Cariti G, Di Perri G, D'Avolio A. Role of IL28B genotyping in patients with hepatitis C virus-associated mixed cryoglobulinemia and response to PEG-IFN and ribavirin treatment. Arch Virol. 2015;160(8):2009-17.