HIV-1 and the host: A tale of two genomes!

In an insightful scientific article, Dr Partha P. Majumder and Dr Ankita Garg, National Institute of Biomedical Genomics, share their interesting perspective on the latest research efforts to track the Human Immunodeficiency Virus (HIV-1). Read on for details:  

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About Authors: 
Expert Image-Dr Partha P. MajumderPARTHA P. MAJUMDER is a Professor of Human Genetics in the Indian Statistical Institute, Kolkata, and the founder of the National Institute of Biomedical Genomics, Kalyani, West Bengal, where he is currently a Distinguished Professor.   He is also a Sir J.C. Bose National Fellow.  He has pioneered the development of many statistical methods in the analysis of human genome diversity and genetic epidemiology. His work on genetics of human populations in India has provided a deep insight into the peopling of the Indian subcontinent.
Expert Image-Dr Ankita GargANKITA GARG is an Assistant Professor at the National Institute of Biomedical Genomics, Kalyani, West Bengal. She has over 12 years of experience in translational research in the field of infectious diseases and immunology. .  Her work has centred around immune pathogenesis of M tuberculosis and HIV-1 with particular emphasis on developing novel approaches for diagnosis, treatment and risk factors associated with occult TB and HIV disease.

The clinical outcome of HIV-1 infection ranges from: rapid progressors, slow progressors, long term non-progressors (LTNP) to individuals remaining seronegative despite high risk/multiple HIV-1 exposure. This spectrum of clinical manifestation, along with the risk of HIV-1 acquisition, is directly or indirectly influenced by the genetic make-up of the host, i.e., the individual who is infected or exposed.
Over the past several years, population studies in HIV host genetics have unraveled a series of human gene variants that modulate the response to HIV exposure. Genetic studies have identified genetic variants in some chemokine receptors CCR5, CCR2, CX3CR1, CXCR1 and CXCR6 that are associated with HIV-1 acquisition and progression to Acquired Immunodeficiency Syndrome (AIDS). For example, a 32 base-pair deletion in CCR5 (see Figure 1) protects the host from being infected even if exposed to HIV-1.  Among European Caucasians, the proportion of individuals each with two copies of the deletion is only about 0.1%.  Even those with one copy of the deletion get some protection in terms of lower viral load; the proportion of such individuals is about 17%.
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Figure 1: Structure of the chemokine receptor CCR5.
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Figure 2: The 32-base pair deletion.
In India, the deletion allele is absent in most ethnic groups (Majumder PP and Dey B: European Jour Hum Genet 9: 794; 2001), Chemokines are natural ligands for receptors that HIV-1 uses to enter the cells; these chemokines compete with the virus for co-receptor binding and influence susceptibility to HIV-1. Several polymorphisms located in (1) regulatory regions of CCL5 (encoding CC-chemokine RANTES), and (2) coding and non-coding regions of MIP1α have been associated with both resistance to HIV-1 infection and progression. Polymorphisms resulting in increased expression of chemokines notably reduce the risk of acquiring HIV-1.
Even though, numerous host factors that support HIV-1 replication have been identified using large scale siRNA (small interfering RNA) screens, genetic variants of only tumor susceptibility gene 101 (TSG101: -183T>C and +181A>C) and peptidyl propyl isomerase A (PPLA) genes were confirmed to modulate HIV pathogenesis. In parallel to expression of HIV-1 supporting factors, human genome encodes molecules that are intrinsic inhibitors of HIV-1 replication: most notably TRIM5α and APOBEC3G. Of these, common variants of TRIM5α suggest that it has no or only modest influence on HIV-1 disease outcome. An H186R coding change in APOBEC3G is reported to be associated with accelerated progression to AIDS in African population; thorough analysis in Caucasians did not show any association with HIV-1 control.
Human genes critical to immunity or inflammation also play role in HIV-1 pathogenesis and have been of interest for genetic studies. Polymorphisms in the genes encoding cytokines, cytokine receptors have been associated with both resistance and disease progression. In this regard, variants in genes responsible for innate immunity to HIV-1 such as: (i) β-defensin 1 gene (DEFB1) are associated with higher level of HIV-1 RNA in breast milk, and (ii) mannose-binding lectin 2 protein (encoded by MBL2) with increased susceptibility to HIV-1 infection and/or accelerated disease progression, iii) polymorphisms in TLR-7 and -9 influence disease progression.
Since the identification of CCR5-D32, an allele of CCR5 with a 32 bp deletion responsible for resistance to R5-virus acquisition, human genetics has undergone massive transitions and has provided new insights in HIV-1 host genetics. The Genome-Wide Association Studies (GWAS) performed in populations of European ancestry and African-Americans have shown that HLA class I variants (notably HLA-B-*5701 and HLA-B-*5703, respectively) are the strongest determinants of viral control. HLA class I are fundamental in immune recognition process and generating cytotoxic T cell (CTL) response; homozygosity for class I alleles limits diversity in epitope recognition, impairing anti-HIV CTL response that leads to faster progression and higher viremia. In this regard, HIV control is observed to be better in individuals with HLA-B*27, B*51 and B*5801, but insufficient in individuals with HLA-B*5802 and alleles from HLA-B35Px group. Besides being key players in CTL activity, HLA class I molecules also serve as ligands for killer cell immunoglobulin-like receptors (KIRs), expressed on the surface of natural killer (NK) cells. KIRs regulate activating or inhibitory signals of NK cells thereby directly modulate the innate immune response of HIV-1 infection. Certain KIR genes and HLA class I allele combinations, particularly KIR3DL1 and KIR3DS1 along with HLA-Bw4 are associated with better HIV-1 control and delay disease progression.
Necessity to improve precision of transcriptome analysis
It is intriguing that besides the homozygosity in CCR5-D32 decreasing susceptibility to R5 HIV-1 infection, other genetic associations (CCR2-V64I, SDF1-3’A, RANTES-403A-28G or 28C, RANTES-In1.1C, DC-SIGN-7/6 or 7/8, DC-SIGNR-7/5, DC-SIGNR-7/7) are biologically still poorly understood. Surpassing the information obtained from genome wide studies, novel approaches including transcriptome and proteome analysis and siRNA screens have been utilized to understand the modulation of prominent anti-viral defense genes in pathogenic versus non-pathogenic infection and NCBI HIV-1 Human Protein Interaction Database summarizes over 3,000 protein interactions with almost 1,500 human genes. These still need to be validated across the disease spectrum and various human ethnic lineages.
Of the 1,000 proteins identified using siRNA transfection and shRNA transduction studies, minimal overlap across studies was investigated in genes potentially necessary for optimal viral replication. These investigations emphasize the necessity to improve precision of transcriptome analysis through added resolution of RNA-Seq. However, genes identified in two or more independent transfection screens belonged to nuclear pore machinery, components of NF-kB complex and key kinases. More recently, the use of CRISPR/Cas9 genome editing approach has also confirmed host CD4 and CCR5 along with ALCAM (responsible for cell aggregation required for cell-to-cell HIV transmission), TPST2 and SCL35B2 (facilitate CCR5 recognition) to be essential for HIV infection.
These new generation host genetic approaches are critical to functionally validate genome wide studies and identify therapeutic targets to control HIV infection. In conclusion, it is detrimental to undertake large cohort studies including individuals from multiple ethnic background and integrate different layers of data generated using multiple approaches.

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