Hitoshi Ohtani

Natural selection in the TLR-related genes in the course of primate evolution

The innate immune system constitutes the front line of host defense against pathogens. Toll-like receptors (TLRs) recognize molecules derived from pathogens and play crucial roles in the innate immune system. Here, we provide evidence that the TLR-related genes have come under natural selection pressure in the course of primate evolution. We compared the nucleotide sequences of 16 TLR-related genes, including TLRs (TLR1–10), MYD88, TILAP, TICAM1, TICAM2, MD2, and CD14, among seven primate species. Analysis of the non-synonymous/synonymous substitution ratio revealed the presence of both strictly conserved and rapidly evolving regions in the TLR-related genes. The genomic segments encoding the intracellular Toll/interleukin 1 receptor domains, which exhibited lower rates of non-synonymous substitution, have undergone purifying selection. In contrast, TLR4, which carried a high proportion of non-synonymous substitutions in the part of extracellular domain spanning 200 amino acids, was found to have been the suggestive target of positive Darwinian selection in primate evolution. However, sequence analyses from 25 primate species, including eight hominoids, six Old World monkeys, eight New World monkeys, and three prosimians, showed no evidence that the pressure of positive Darwinian selection has shaped the pattern of sequence variations in TLR4 among New World monkeys and prosimians.

Impact of novel TRIM5α variants, Gly110Arg and G176del, on the anti-HIV-1 activity and the susceptibility to HIV-1 infection

Objective:TRIM5α is one of the factors contributing to intracellular defense mechanisms against HIV-1 infection. We investigated the association of TRIM5α sequence variations with the susceptibility to HIV-1 infection in Japanese and Indian. Design:Sequence variations in TRIM5α were investigated in HIV-1-infected patients and ethnic-matched controls. Functional alterations caused by rare variants were analyzed. Methods:We sequenced TRIM5α-exon 2 in both Japanese (94 HIV-1-infected patients and 487 controls) and Indian (101 HIV-1-infected patients and 99 controls). Frequency of variants and haplotypes were compared between the HIV-1-infected patients and controls. Functional analyses were performed for two rare variants, Gly110Arg and G176del. Results:The frequency of 43Tyr-allele in the Indian HIV-1-infected patients was significantly lower than that in the ethnic-matched controls (odds ratio = 0.52, 95% confidence interval = 0.31–0.89, P = 0.015). A similar tendency was observed in Japanese sample, although it was not statistically significant (odds ratio = 0.67, 95% confidence interval = 0.43–1.05, P = 0.095). On the other hand, haplotype analyses revealed that the haplotype carrying the 43Tyr-allele was significantly associated with the reduced susceptibility to HIV-1 infection in both ethnic groups. Functional analysis revealed that Gly110Arg variant weakened the anti-HIV-1 and anti-HIV-2 activities of human TRIM5α, whereas the truncated G176del-TRIM5 enhanced the antiviral activity of coexpressed TRIM5α. Epidemiological data were consistent in that Gly110Arg and G176del were associated with the susceptibility to and protection from HIV-1 infection, respectively. Conclusion:Both common and rare variants of TRIM5α are associated with the susceptibility to HIV-1 infection.

TIM1 haplotype may control the disease progression to AIDS in a HIV-1-infected female cohort in Thailand

Objective:To investigate association of TIM1 sequence variations with HIV/AIDS progression. Introduction:HIV-1 infected individuals have wide variations in disease progression including AIDS. T cell immunoglobulin and mucin 1 (TIM1) is a cell surface protein involved in the regulation of Th1/Th2 immune response. Materials and methods:We sequenced the highly polymorphic exon 4 of TIM1 from 246 individuals of HIV-1 infected Thai female cohort to determine their TIM1 haplotypes. Associations of TIM1 haplotypes with baseline clinical data (sero-status, plasma viral load, CD4 cell count, and symptomatic AIDS) and survival status during 3 years of follow-up were evaluated. Results:Seven TIM1 haplotypes, D3-A, D4, D3-C, D1, W-A, W-C, and D3-C*, were found in the cohort. Patients possessing the D3-A haplotype showed trends towards higher CD4+ cell count (P = 0.06) and lower proportion of AIDS-related symptoms (P = 0.022) than the other patients at the baseline. Kaplan–Meier analysis demonstrated that patients carrying the D3-A haplotype had a better survival rates (P = 0.019) than the others. D3-A haplotypes was tightly linked to the lower expression levels of TIM1. Conclusion:TIM1 D3-A haplotype is associated with the delay of disease progression to AIDS in the HIV-1 infected Thai females.

No Evidence of an Association between the APOBEC3B Deletion Polymorphism and Susceptibility to HIV Infection and AIDS in Japanese and Indian Populations

Japanese 0.937 (0.653–1.343) .791 0.650 (0.275–1.538) .426 1.031 (0.645–1.648) .995 I/I 45 (47.4) 128 (48.1) I/D 43 (45.3) 109 (41.0) D/D 7 (7.4) 29 (10.9) I 133 (70.0) 365 (68.6) D 57 (30.0) 167 (31.4) Indian 0.907 (0.637–1.291) .651 1.215 (0.425–3.473) .796 0.853 (0.569–1.281) .508 I/I 181 (72.1) 139 (68.8) I/D 61 (24.3) 57 (28.2) D/D 9 (3.6) 6 (3.0) I 423 (84.3) 335 (82.9) D 79 (15.7) 69 (17.1)

Validation of eight genetic risk factors in East Asian populations replicated the association of BRAP with coronary artery disease.

Coronary artery disease (CAD) is caused by a thrombotic occlusion or spasm of the coronary artery. Association of genetic variants with susceptibility to CAD has been reported in various populations, but the association should be replicated in other populations to establish the role of genetic variants in CAD. We conducted a case–control study with a total of 1480 CAD cases and 2115 controls from two East Asian populations, Japanese and Korean, to validate the associations of CAD with eight single nucleotide polymorphisms (SNPs) in eight loci, which were identified from large-scale whole-genome association studies in Europeans or East Asians. Among the tested SNPs, one SNP in BRAP (rs11066001) showed a significant association in allele frequency distribution with CAD in both the Japanese (Odds ratio (OR)=1.63, 95% confidence interval (CI); 1.41–1.89, P=5.0 × 10−11, corrected P (Pc)=4.0 × 10−10) and Korean populations (OR=1.68, 95% CI; 1.41–2.00, P=6.5 × 10−9, Pc=5.2 × 10−9), and a meta-analysis showed a significant association in the East Asian populations (OR=1.65, 95% CI; 1.48–1.85, P=1.8 × 10−18, Pc=1.4 × 10−17), whereas no evidence of association was found for the other SNPs. In addition, a combined analysis of BRAP and another CAD locus on 9p21 suggested that these loci had a synergistic role in the susceptibility. Failure to replicate the association with the other SNPs, which were reported in the European populations, suggested that their contributions to CAD were not large enough to be readily captured in the East Asian populations.

APOBEC3H polymorphisms and susceptibility to HIV-1 infection in an Indian population.

Human APOBEC3H (A3H) is a member of APOBEC cytidine deaminase family intensively constraining the HIV-1 replication. A3H is known to be polymorphic with different protein stability and anti-HIV-1 activity in vitro. We recently reported that A3H haplotypes composed of two functional polymorphisms, rs139292 (N15del) and rs139297 (G105R), were associated with the susceptibility to HIV-1 infection in Japanese. To confirm the association of A3H and HIV-1 infection in another ethnic group, a total of 241 HIV-1-infected Indian individuals and ethnic-matched 286 healthy controls were analyzed for the A3H polymorphisms. The frequency of 15del allele was high in the HIV-1-infected subjects as compared with the controls (0.477 vs 0.402, odds ratio (OR)=1.36, P=0.014). Haplotype analysis showed that the frequencies of 15del–105R was high (0.475 vs 0.400, OR=1.36, permutation P=0.037) in the HIV-1-infected subjects, confirming the association of A3H polymorphisms with the susceptibility to HIV-1 infection.

Status of TIM-1 exon 4 haplotypes and CD4+T cell counts in HIV-1 seroprevalent North Indians.

The TIM (T cell/transmembrane, immunoglobulin and mucin) proteins are crucial regulators of Th1/Th2 immune responses and have been implicated in several diseases including HIV-1/AIDS. The TIM1 exon 4 that codes for mucin domain is highly diverse, with sequence variants associated with varying phenotypes. In this study, TIM1 exon 4 was sequenced among 227 HIV-1 seroprevalent and 288 healthy non infected individuals from North Indian population and haplotypes established. A novel but rare haplotype D1(∗) was identified among the healthy and differed from D1 by a synonymous substitution G>T at Thr208Thr. The TIM1 haplotype diversity showed no association with susceptibility to HIV-1 infection. The seroprevalent individuals carrying D3A had relatively higher median CD4+T cell counts (368/μl) than those without (313/μl; p=0.02). A comparison of CD4+T counts between D3-A individuals on ART or ART naïve did not show any significant difference plausibly due to confounding nature of ART and other factors.

Lineage-specific evolution of T-cell immunoglobulin and mucin domain 1 gene in the primates

T-cell immunoglobulin domain and mucin domain containing protein 1 (TIM1), also known as a cellular receptor for hepatitis A virus (HAVCR1) or a molecule induced by ischemic injury in the kidney (KIM1), is involved in the regulation of immune responses. We investigated a natural selection history of TIM1 by comparative sequencing analysis in 24 different primates. It was found that TIM1 had become a pseudogene in multiple lineages of the New World monkey. We also investigated T cell lines originated from four different New World monkey species and confirmed that TIM1 was not expressed at the mRNA level. On the other hand, there were ten amino acid sites in the Ig domain of TIM1 in the other primates, which were suggested to be under positive natural selection. In addition, mucin domain of TIM1 was highly polymorphic in the Old World monkeys, which might be under balanced selection. These data suggested that TIM1 underwent a lineage-specific evolutionary pathway in the primates.

Molecular evolution of immunoglobulin superfamily genes in primates.

Genes of the immunoglobulin superfamily (IgSF) have a wide variety of cellular activities. In this study, we investigated molecular evolution of IgSF genes in primates by comparing orthologous sequences of 249 IgSF genes among human, chimpanzee, orangutan, rhesus macaque, and common marmoset. To evaluate the non-synonymous/synonymous substitution ratio (ω), we applied Bn-Bs program and PAML program. IgSF genes were classified into 11 functional categories based on the Gene Ontology (GO) database. Among them, IgSF genes in three functional categories, immune system process (GO:0002376), defense response (GO:0006952), and multi-organism process (GO:0051704), which are tightly linked to the regulation of immune system had much higher values of ω than genes in the other GO categories. In addition, we estimated the average values of ω for each primate lineage. Although each primate lineage had comparable average values of ω, the human lineage showed the lowest ω value for the immune-related genes. Furthermore, 11 IgSF genes, SIGLEC5, SLAMF6, CD33, CD3E, CEACAM8, CD3G, FCER1A, CD48, CD4, TIM4, and FCGR2A, were implied to have been under positive selective pressure during the course of primate evolution. Further sequence analyses of CD3E and CD3G from 23 primate species suggested that the Ig domains of CD3E and CD3G underwent the positive Darwinian selection.