APOBEC3G Variant (rs6001417) CG and GG Genotypes and their protective feature against HIV-1 Infection in Pakistani Dwelled Community

Qaisar Ali, Arshad Jamal, Sajjad Ullah, Ahmed Bilal Waqar

Abstract


Background: APOBEC3G (Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G) gene is one of the genetic host factors, have been linked with HIV-1 AIDS predisposing and protection in different residence populations. The investigation of genetic marker (APOBEC3G) variant (rs6001417) CC, CG and GG genotypes in Pakistan.

Methods: The extraction of DNA, the DNA Rapid Salting-out method was used. Then the observed DNA with electrophoresis technique referred for quantitative real-time PCR to identify the APOBEC3G variant rs6001417 genotypes and Taq Man genotyping.  

Results: Three genotypes of rs6001417 (CC, CG and GG) were compared both in HIV-1 infected patients and healthy control groups (p=0.73, p=0.007, p=0.01 respectively). The rs6001417 CG and GG genotype demonstrated a significant involvement in both the healthy and infected individuals and portraying possible protective effect against HIV-1 infection with predictive value of 36.43% and 13.57% respectively.

Conclusion: APOBEC3G (rs6001417) CG and GG genotypes may have a protective feature in the progression of HIV-1 infection and we may use this as a preliminary predictive marker in the country for HIV-1 infected individuals as well.

Keywords: HIV-1; APOBEC3G; Predictive marker; Predictive value; Real-time PCR


Full Text:

PDF

References


Barré-Sinoussi F, Chermann J-C, Rey F, Nugeyre MT, Chamaret S, et al. Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). Science, (1983); 220(4599): 868-871.

Celerino da Silva R, Victor Campos Coelho A, Rodrigues de Moura R, Claudio Arraes L, Andre Cavalcanti Brandao L, Lima Guimarães R, Crovella S. CUL5 and APOBEC3G polymorphisms are partially implicated in HIV-1 infection and antiretroviral therapy in a Brazilian population. Current HIV Research. 2017;15(4):245-57.

Murray CJ, Ortblad KF, Guinovart C, Lim SS, Wolock TM, et al. Global, regional, and national incidence and mortality for HIV, tuberculosis, and malaria during 1990–2013: a systematic analysis for the Global Burden of Disease Study 2013. The Lancet, (2014); 384(9947): 1005-1070.

Kharsany AB, Karim QA. HIV infection and AIDS in Sub-Saharan Africa: current status, challenges and opportunities. The open AIDS journal, (2016); 10: p34.

Ali Q, Jamal A,, Ullah S, Waqar AB.Male predominant association with Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G variants (rs6001417, rs35228531, rs8177832) predict protection against HIV-1 infection. Advancement in life Science, (2020); 7(2): 91-97.

Oberle CS, Joos B, Rusert P, Campbell NK, Beauparlant D, et al. Tracing HIV-1 transmission: envelope traits of HIV-1 transmitter and

recipient pairs. Retrovirology, (2016); 13(1): p62.

An P, Bleiber G, Duggal P, Nelson G, May M, et al. APOBEC3G genetic variants and their influence on the progression to AIDS. Journal of virology, (2004); 78(20): 11070-11076.

An P, Penugonda S, Thorball CW, Bartha I, Goedert JJ, et al. Role of APOBEC3F gene variation in HIV-1 disease progression and pneumocystis pneumonia. PLoS genetics, (2016); 12(3): e1005921.

Dunn GP, Bruce AT, Ikeda H, Old LJ, Schreiber RD. Cancer immunoediting: from immunosurveillance to tumor escape. Nature immunology, (2002); 3(11): p991.

van Kooyk Y, Appelmelk B, Geijtenbeek TB. A fatal attraction: Mycobacterium tuberculosis and HIV-1 target DC-SIGN to escape immune surveillance. Trends in molecular medicine, (2003); 9(4): 153-159.

D'Urbano V, De EC, Re M. Host restriction factors and Human immunodeficiency Virus (HIV-1): a dynamic interplay involving all phases of the viral life cycle. Current HIV research, (2018); 16(3): 184-207.

Bataller R, North KE, Brenner DA. Genetic polymorphisms and the progression of liver fibrosis: a critical appraisal. Hepatology, (2003); 37(3): 493-503.

Janssen R, Bont L, Siezen CL, Hodemaekers HM, Ermers MJ, et al. Genetic susceptibility to respiratory syncytial virus bronchiolitis is predominantly associated with innate immune genes. Journal of Infectious Diseases, (2007); 196(6): 826-834.

Powell EE, Edwards‐Smith CJ, Hay JL, Clouston AD, Crawford DH, et al. Host genetic factors influence disease progression in chronic hepatitis C. Hepatology, (2000); 31(4): 828-833.

Piacentini L, Biasin M, Fenizia C, Clerici M. Genetic correlates of protection against HIV infection: the ally within. J Intern Med, (2009); 265(1): 110-124.

A Estrada-Aguirre J, G Cazarez-Salazar S, A Ochoa-Ramirez L, de J Acosta-Cota S, Zamora-Gómez R, et al. Protective effect of CCR5 Delta-32 allele against HIV-1 in Mexican women. Current HIV research, (2013); 11(6): 506-510.

Kenny-Walsh E. The natural history of hepatitis C virus infection. Clinics in liver disease, (2001); 5(4): 969-977.

Dolo A, Modiano D, Maiga B, Daou M, Dolo G, et al. Difference in susceptibility to malaria between two sympatric ethnic groups in Mali. The American journal of tropical medicine and hygiene, (2005); 72(3): 243-248.

Perera FP. Molecular epidemiology: insights into cancer susceptibility, risk assessment, and prevention. JNCI: Journal of the National Cancer Institute, (1996); 88(8): 496-509.

Duggal NK, Emerman M. Evolutionary conflicts between viruses and restriction factors shape immunity. Nature Reviews Immunology, (2012); 12(10): 687.

Kagoné TS, Bisseye C, Méda N, Testa J, Pietra V, et al. A variant of DC-SIGN gene promoter associated with resistance to HIV-1 in serodiscordant couples in Burkina Faso. Asian Pacific journal of tropical medicine, (2014); 7: S93-S96.

Harris RS, Liddament MT. Retroviral restriction by APOBEC proteins. Nature Reviews Immunology, (2004); 4(11): 868-877.

Merindol N, Berthoux L. Restriction factors in HIV-1 disease progression. Current HIV research, (2015); 13(6): 448-461.

Imran M, Manzoor S, Saalim M, Resham S, Ashraf J, et al. HIV-1 and hijacking of the host immune system: the current scenario. APMIS, (2016); 124(10): 817-831.

Ayinde D, Casartelli N, Schwartz O. Restricting HIV the SAMHD1 way: through nucleotide starvation. Nature Reviews Microbiology, (2012); 10(10): 675-680.

Mehle A, Strack B, Ancuta P, Zhang C, McPike M, et al. Vif overcomes the innate antiviral activity of APOBEC3G by promoting its degradation in the ubiquitin-proteasome pathway. Journal of Biological Chemistry, (2004); 279(9): 7792-7798.

Farrow MA, Sheehy AM. Vif and Apobec3G in the innate immune response to HIV: a tale of two proteins. Future Micrbiology, (2008); 3(2): 145-154.

Iwabu Y, Kinomoto M, Tatsumi M, Fujita H, Shimura M, et al. Differential anti-APOBEC3G activity of HIV-1 Vif proteins derived from different subtypes. Journal of Biological Chemistry, (2010); 285(46): 35350-35358.

Binka M, Ooms M, Steward M, Simon V. The activity spectrum of Vif from multiple HIV-1 subtypes against APOBEC3G, APOBEC3F, and APOBEC3H. Journal of virology, (2012); 86(1): 49-59.

Reddy K, Winkler C, Werner L, Mlisana K, Karim SA, et al. APOBEC3G expression is dysregulated in primary HIV-1 infection and a polymorphic variant influences CD4+ T cell counts and plasma viral load. AIDS (London, England), (2010); 24(2): p195.

Do H, Vasilescu A, Diop G, Hirtzig T, Heath SC, et al. Exhaustive genotyping of the CEM15 (APOBEC3G) gene and absence of association with AIDS progression in a French cohort. Journal of Infectious Diseases, (2005); 191(2): 159-163.

Valcke HS, Bernard NF, Bruneau J, Alary M, Tsoukas CM, et al. APOBEC3G genetic variants and their association with risk of HIV infection in highly exposed Caucasians. Aids, (2006); 20(15): 1984-1986.

Kalam, I., Ullah, S., Ali, Q., Jamal, A. and Waqar, A.B., 2018. Impact of IL28B gene variants (rs12979860) in peg-IFN therapy against Chronic Hepatitis B Pakistani patients. Advancements in Life Sciences, 6(1), pp.11-18.

Miller S, Dykes D, Polesky H. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic acids research, (1988); 16(3): p1215.

Dean M, Carrington M, Winkler C, Huttley GA, Smith MW, et al. Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Science, (1996); 273(5283): 1856-1862.

McNab F, Mayer-Barber K, Sher A, Wack A, O'garra A. Type I interferons in infectious disease. Nature Reviews Immunology, (2015); 15(2): 87.

An P, Bleiber G, Duggal P, Nelson G, May M, et al. APOBEC3G genetic variants and their influence on the progression to AIDS. Journal of Virol, (2004); 78(20): 11070-11076.

Do H, Vasilescu A, Diop G, Hirtzig T, Heath SC, et al. Exhaustive genotyping of the CEM15 (APOBEC3G) gene and absence of association with AIDS progression in a French cohort. Journal Infection Diseases, (2005); 191(2): 159-163.

Ali Q, Kalam I, Ullah S, Jamal A, Imran M, et al. Predictive value of IL-28B rs12979860 variants for peg-IFN, sofosbuvir plus ribavirin treatment of HCV infection in Pakistani population. Personalized medicine, (2018); 15(6).

Iqbal K, Imran M, Ullah S, Jamal M, Waheed Y, et al. Correlation of apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G genetic variant rs8177832 with HIV-1 predisposition in Pakistani Population. Current HIV research, (2018); 16(4): 297-301.

Compaore TR, Soubeiga ST, Ouattara AK, Obiri-Yeboah D, Tchelougou D, et al. APOBEC3G Variants and Protection against HIV-1 Infection in Burkina Faso. PloS one, (2016); 11(1): p.e0146386.

Compaore TR, Diarra B, Assih M, Obiri-Yeboah D, Soubeiga ST, et al. HBV/HIV co-infection and APOBEC3G polymorphisms in a population from Burkina Faso. BMC infectious diseases, (2016); 16(1): p336.

Ezzikouri S, Kitab B, Rebbani K, Marchio A, Wain‐Hobson S, et al. Polymorphic APOBEC 3 modulates chronic hepatitis B in M oroccan population. Journal of viral hepatitis, (2013); 20(10): 678-686.

De Maio FA, Rocco CA, Aulicino PC, Bologna R, Mangano A, et al. Effect of HIV-1 Vif variability on progression to pediatric AIDS and its association with APOBEC3G and CUL5 polymorphisms. Infection, Genetics and Evolution, (2011); 11(6): 1256-1262.

Ali Q, Jamal A, Imran M, Ullah S, Kalam I, Ullah S, Waqar AB. Correlation of IL28B rs12979860 genotype and gender with spontaneous clearance of HCV infection: a Pakistani cross-section study. Personalized medicine. 2018 Nov;15(6):495-502.


Refbacks

  • There are currently no refbacks.