Anurag Rathore

Role of Homozygous DC-SIGNR 5/5 Tandem Repeat Polymorphism in HIV-1 Exposed Seronegative North Indian Individuals

Despite multiple sexual exposures to HIV-1 virus, some individuals remain HIV-1 seronegative. Although several genetic factors have been related to HIV-1 resistance, the homozygosity for a mutation in CCR5 gene (the 32-bp deletion, i.e., CCR5-Delta32 allele) is presently considered the most relevant one. The C-type lectins, DC-SIGN (present on dendritic cells and macrophages) and DC-SIGNR (present on endothelial cells in liver and lymph nodes) efficiently bind and transmit HIV-1 to susceptible cell in trans, thereby augmenting the infection. A potential association of the DC-SIGN and DC-SIGNR neck domain repeat polymorphism and risk of HIV-1 infection is currently under debate. To determine the influence of host genetic factors on HIV-1 resistance, we conducted genetic risk association study in HIV-1-exposed seronegative (n = 47) individuals, HIV-1 seronegative (n = 262) healthy control, and HIV-1-infected seropositive patients (n = 168) for polymorphism in neck domain of DC-SIGN and DC-SIGNR genes. The DC-SIGN and DC-SIGNR genotypes were identified by polymerase chain reaction method in DNA extracted from peripheral blood and confirmed by sequencing. Fisher exact or χ2 test was used for static analysis. DC-SIGN genotype and allele distribution was fairly similar in HIV-1-exposed seronegative, HIV-1 seropositive, and HIV-1 seronegative control. There was no statistical significance in the differences in the distribution of DC-SIGN genotypes. A total of 13 genotypes were found in DC-SIGNR neck repeat region polymorphism. Among all the genotypes, only 5/5 homozygous showed significant reduced risk of HIV-1 infection in HIV-1-exposed seronegative individuals (p = 0.009). A unique genotype 8/5 heterozygous was also found in HIV-1 seropositive individual, which is not reported elsewhere.

Association of RANTES −403 G/A, −28 C/G and In1.1 T/C polymorphism with HIV‐1 transmission and progression among North Indians

The relationships between host immune factors and HIV‐1 disease progression are still in dispute. The RANTES SNPs exhibit distinct ethnic distribution and are associated with different effects on the course of HIV infection. Therefore, impact of RANTES gene polymorphism on HIV‐1 transmission and progression needs to be evaluated. The RANTES genotypes were identified by PCR‐RFLP method and confirmed by sequencing in HIV‐1 seronegative (HSN; n = 315), HIV‐1 exposed seronegative (HES; n = 47) and HIV‐1 seropositive (HSP; n = 196) patients classified into different clinical stages (i.e. Stages I, II, III). Fisher exact test was used for statistical analysis and Arlequin software for haplotype analysis. RANTES allele −403G, −28C and In1.1 T were the predominant allele in the subject studied. HSP group have higher frequency of RANTES In1.1 T allele compared with HSN (91.32% vs. 86.19%; P = 0.013) and HES (91.32% vs. 78.72%; P = 0.001). Higher frequency of RANTES In1.1 C allele in Stage III was observed, compared with Stage I (14.28% vs. 6.39%) and was significantly associated with high risk (P = 0.047, OR = 2.439, C.I. = 1.061–5.609). Haplotype II (ACT) was significantly higher in HSP compared with HSN (9.69% vs. 1.58%) and associated with high risk (P < 0.001, OR = 6.655, C.I. = 2.443–18.132). There were no significant differences in RANTES −403 A/G and −28 C/G genotype and allele distribution in all the groups compared. Our results implicate that RANTES In1.1 T allele and haplotype II (ACT) may be a risk factor for HIV‐1 transmission while RANTES In1.1 C allele may be risk factor for disease progression among North Indians. J. Med. Virol. 80: 1133–1141, 2008.

Genetic Association of IL-10 Gene Promoter Polymorphism and HIV-1 Infection in North Indians

IntroductionCytokines play a significant role in host immune defense. IL-10 is an anti-inflammatory, immunomodulatory cytokine that can both stimulate and suppress the immune response and inhibits HIV-1 replication in vivo. Interindividual variations in IL-10 production were genetically contributed to polymorphisms within IL-10 promoter region.AimsThe aim of this study was to investigate the association of IL-10 gene promoter −1082 G/A, −819 C/T, and 592 C/A polymorphism on HIV-1 transmission /progression in North Indian individuals.Patients and MethodsA total of 180 HIV-1 seropositive (HSP) stratified on the basis of disease severity (stage I, II, and III), 50 HIV-1 exposed seronegative (HES) and 305 HIV-1 seronegative (HSN) individuals were genotyped for IL-10 gene promoter by polymerase chain reaction-restriction fragment length polymorphism. A suggestive evidence of association was obtained for IL-10 592 C/A promoter polymorphism at the level of allele and genotype distribution. The frequency of IL-10 592 A allele and genotype was significantly increased in HSP compared to HSN (p = 0.013; OR = 1.412 and p = 0.034; OR = 1.685 respectively). Further comparison in between different clinical stages of HIV-1 infected patients of IL-10 592 A allele and genotype revealed a significant increase in its frequency in the stage III compared with those together in stage I (p = 0.004, OR = 2.181 and p = 0.002, OR = 4.156, respectively). This study reports for the first time that IL-10 gene promoter 592 C/A polymorphism may be a risk factor for HIV-1 transmission/progression in HIV-1 infected North Indian individuals.

Association of CCR5-59029 A/G and CCL3L1 Copy Number Polymorphism with HIV Type 1 Transmission/Progression among HIV Type 1-Seropositive and Repeatedly Sexually Exposed HIV Type 1-Seronegative North Indians

The CCR5Delta32 mutation does not account for HIV-1 resistance in the majority of persons who are repeatedly exposed to HIV-1 by high-risk activities but remain seronegative and uninfected. Therefore, we investigated the impact of CCR5 59029 A/G and CCL3L1 copy number polymorphism on HIV-1 disease susceptibility and progression among HIV-1-infected and HIV-1-exposed seronegative North Indians. HIV-1-seropositive (HSP, n = 196) patients, stratified on the basis of disease severity (Stages I, II, and III) and HIV-1-exposed seronegative (HES, n = 47) individuals were genotyped for CCR5-59029 A/G polymorphism by PCR-RFLP and CCL3L1 copy number by the real-time TaqMan PCR method. A group of ethnically matched HIV-1-seronegative (HSN, n = 315) healthy volunteers were also genotyped as controls. Statistical analysis was done by SPSS software. The CCR5-59029 AG genotype was significantly higher in the HES compared with the HSP group (57.44% vs. 37.24%, p = 0.014). The CCL3L1 mean copy number of HES was higher compared with the HSP groups (3.148 +/- 0.291 vs. 2.795 +/- 0.122, p = 0.212), but was not significant when compared with independent samples t test. Possession of CCL3L1 copies < or = 2 or >2 was not associated with enhanced or reduced risk of HIV-1 acquisition. Gene-gene interaction studies showed enrichment of the CCR5-59029AG*CCL3L1>2 genotype in the HES group when compared with the HSP group (31.91% vs. 15.81%, p = 0.021, OR = 0.401, CI = 0.194-0.826). The increased frequency of the CCR5-59029AG*CCL3L1>2 genotype among HES individuals led us to conclude that the CCR5-59029 AG genotype and CCL3L1 gene dose appeared to have synergistic or interactive effects and are expected to be involved in the host innate resistance to HIV-1 infection.

Chemokines and Chemokine Receptors in susceptibility to HIV-1 infection and progression to AIDS

A multitude of host genetic factors plays a crucial role in susceptibility to HIV-1 infection and progression to AIDS, which is highly variable among individuals and populations. This review focuses on the chemokine-receptor and chemokine genes, which were extensively studied because of their role as HIV co-receptor or co-receptor competitor and influences the susceptibility to HIV-1 infection and progression to AIDS in HIV-1 infected individuals.

Mannose-binding lectin (+54) exon-1 gene polymorphism influence human immunodeficiency virus-1 susceptibility in North Indians

Mannose-binding lectin (MBL) is a circulating pattern-recognition molecule involved in the innate immune system that mediates phagocytosis and activates complement by binding to carbohydrate motifs. MBL-2 allelic variants are associated with deficiencies in innate immunity and have been found to be correlated with human immunodeficiency virus (HIV) infection. The present study investigated the role of MBL-2 exon-1 gene polymorphism (A, B, C and D) in 180 HIV-1 seropositive (HSP) stratified on the basis of disease severity (stage I, II, III), 50 HIV-1 exposed seronegative (HES) and 305 HIV-1 seronegative (HSN) individuals as a possible factor in the susceptibility to HIV-1 infection and the influence on disease progression among North Indian individuals. In our population, gene frequencies of MBL-2 variants were 15%, 5% and 2% for B, C and D alleles, respectively. The frequency of A/O heterozygous genotype was higher (42.00%), mainly because of A/D in HES group compared with HSP (35.00%) and HSN (36.72%) group. Homozygous B/B genotype was more frequent in HSP (6.11%) group than in HSN (1.31%; P = 0.005; odds ratio (OR) = 4.898) and was significantly associated with fourfold risk of acquiring HIV-1 infection. Our findings indicate that homozygosity for the codon 54-allele associated with low MBL production in the exon-1 of the MBL-2 gene is associated with increased susceptibility to HIV-1 infection in the studied population.

Risk for HIV-1 infection is not associated with Repeat-Region polymorphism in the DC-SIGN neck domain and Novel Genetic DC-SIGN Variants among North Indians

Abstract Background Several genetic factors have been related to HIV-1 resistance, the homozygosity for a mutation in CCR5 gene (CCR5Δ 32 allele) is presently considered the most relevant one. The C-type lectin, DC-SIGN efficiently binds and transmits HIV-1 to susceptible cell in trans thereby augmenting the infection. A potential association of the DC-SIGN neck domain repeats polymorphism and risk of HIV-1 infection is currently under debate. Methods Genetic risk association study was conducted in HIV-1 exposed seronegative (HES; n =50) individuals, HIV-1 seronegative (HSN; n =314) healthy control and HIV-1 infected seropositive patients (HSP; n =190) for polymorphism in neck domain of DC-SIGN gene. The DC-SIGN genotypes were identified by PCR from DNA extracted from peripheral blood and confirmed by sequencing. Fisher exact or χ2 test was used for statistical analysis. Results One HSN and HSP individual who were heterozygous (7/8) with respect to DC-SIGN repeat regions were found. The DC-SIGN neck repeat polymorphism among North Indian individuals was not associated with susceptibility to HIV-1 infection. Furthermore, inheritance study of heterozygous mutation (7/8) in HSN individuals family showed that one parent, two brothers, one sister and one daughter were heterozygous (7/8) for DC-SIGN mutant allele. Sequence analyses of DC-SIGN exon 4 repeat region of randomly selected 25 North Indian individuals from HSP, HSN and HES revealed four conserved intronic mutations. These mutations were at nucleotide position 1283, 1306, 1308 upstream and 1906 downstream of the DC-SIGN exon 4 repeat region when compared with the wild type sequence (NCBI Acc. No. AF209479). Conclusion The polymorphism in DC-SIGN neck repeats region was rare and not associated with HIV-1 susceptibility among North Indians. Sequencing analysis of DC-SIGN gene confirmed four novel genetic variants in intronic region flanking exon 4 coding region.

Absence of H186R Polymorphism in Exon 4 of the APOBEC3G Gene among North Indian Individuals

AIDS restriction genes have been defined in which allelic variations have been shown to influence infection or disease progression. Members of the APOBEC family of cellular polynucleotide cytidine deaminases (e.g., APOBEC3G) have been identified as a host factor that inhibits HIV-1 replication. It deaminates cytidine to uridine in nascent minus-strand viral DNA, inducing G-to-A hypermutation in the plus-strand viral DNA. The impact of codon-changing variant APOBEC3G H186R polymorphism on HIV-1 susceptibility and progression is not clear. We conducted genetic risk association study in HIV-1-exposed seronegative (HES; n = 50) individuals, HIV-1 seronegative (HSN; n = 320) healthy control, and HIV-1 seropositive patients (HSP; n = 190). The APOBEC3G H186R genotypes were identified by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method in DNA extracted from peripheral blood and confirmed by direct sequencing the randomly selected 58 samples. Frequency of rare homozygous RR (mutant type) and HR (heterozygous mutant) genotype was 0% while HH (wild type) was 100% among North Indians. In conclusion, we demonstrated that no genetic H186R polymorphism in exon 4 of APOBEC3G gene is found and therefore neither associated with differential susceptibility to HIV-1 infection/progression among North Indians.

Association between Apolipoprotein B mRNA-editing Enzyme CatalyticPolypeptide-Like 3B (APOBEC3B) Deletion with HIV-1 Acquisition andAIDS among North Indian Population

Objective: Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-Like 3B (APOBEC3B) is involved in innate immune response, exhibiting insertion–deletion polymorphism across the world in human population. A naturally occurring 29.5 kb deletion removes complete APOBEC3B gene. Human APOBEC3B family of proteins restricts HIV- 1 replication. Very few studies have been conducted on this subject and the deductions regarding the effects of APOBEC3B deletion on HIV-1 susceptibility and pathogenesis have been largely inconsistent. Therefore, we studied the association of APOBEC3B deletion with HIV-1 in the North Indian population. Methods: Insertion (I)/Deletion (D) APOBEC3B polymorphism was analyzed using Polymerase chain reaction. Infection rates as wells as stages of HIV were compared among the three genotypes: deletion-homozygous (D/D), Insertionhomozygous (I/I) and hemizygous (I/D) in 150 HIV-1 seropositive (HSP) and 250 HIV-1 seronegative (HSN) subjects. Results and discussion: The genotypic analysis revealed insignificant associations among homozygous deletion (D/D) genotype (P=0.130, OR=1.93, 95% CI=0.95–4.30) and moderate associations among hemizygous (I/D) genotypes (P=0.057, OR=1.56, 95% CI-1.03–2.44) with HIV-1 susceptibility and also the single copy of variant allele was more susceptible to HIV-1 infection. The severity of HIV-1 infection on the basis of CD4 count was not associated significantly with the disease progression to AIDS. Conclusion: In conclusion, we found that the deletion genotype of APOBEC3B gene polymorphism does not play any significant role on HIV-1 susceptibility. Hence, further studies with the expansion of sample size are needed to validate the results.