灵长类CCR5基因的序列进化与系统发育研究

国家自然科学基金;中国科学院基金

Sequence evolution of the CCR5 chemokine receptor gene in primates

The chemokine receptor CCR5 can serve as a coreceptor for M-tropic HIV-1 infection and both M-tropic and T-tropic SIV infection. We sequenced the entire CCR5 gene from 10 nonhuman primates: Pongo pygmaeus, Hylobates leucogenys, Trachypithecus francoisi, Trachypithecus phayrei, Pygathrix nemaeus, Rhinopithecus roxellanae, Rhinopithecus bieti, Rhinopithecus avunculus, Macaca assamensis, and Macaca arctoides. When compared with CCR5 sequences from humans and other primates, our results demonstrate that:(1) nucleotide and amino acid sequences of CCR5 among primates are highly homologous, with variations slightly concentrated on the amino and carboxyl termini; and (2) site Asp13, which is critical for CD4-independent binding of SIV gp120 to Macaca mulatta CCR5, was also present in all other nonhuman primates tested here, suggesting that those nonhuman primate CCR5s might also bind SIV gp120 without the presence of CD4. The topologies of CCR5 gene trees constructed here conflict with the putative opinion that the snub-nosed langurs compose a monophyletic group, suggesting that the CCR5 gene may not be a good genetic marker for low-level phylogenetic analysis. The evolutionary rate of CCR5 was calculated, and our results suggest a slowdown in primates after they diverged from rodents. The synonymous mutation rate of CCR5 in primates is constant, about 1.1 x 10(-9) synonymous mutations per site per year. Comparisons of K-a and K-s suggest that the CCR5 genes have undergone negative or purifying selection. K-a/K-s ratios from cercopithecines and colobines are significantly different, implying that selective pressures have played different roles in the two lineages.

Structure analysis of CCR5 from human and primates

It is well known that the chemokine receptor CCR5 plays very important roles in HIV-1 virus infection. A three-dimensional molecular model of human CCR5 was generated by SYBYL, a distance geometry-based homologous modeling package, using the corresponding transmembrane domain of bacteriorhodopsin as the template. On the basis of human CCR5 model, we also built 18 3D molecular models of CCR5 in primates from Pongo pygmaeus, Pygathrix nemaeus, Macaca assameniss, Trachy-pithecus phayrei, T. francoisi, M. arotoides, Rhinopithecus roxellance, R, bieti, R. avunculus, Hylobates leucogenys, Pan troglodytes, Gorilla gorilla, Cercopithecus aethiops 1, C. aethiops 2, Papio hamadryas M. mulatta, M. fascicularis and M. nemestrina. Structural analyses and statistics results suggested that the main-chains of the primate CCR5 were similar to that of the human CCR5 and that the fit-RMS deviation values of these primate CCR5 were less than 0.1 Angstrom. Moreover, the structures of these CCR5 proteins, except those of the African green monkey 1 (C.aet1), do not have a remarkable difference. It is proved that the 14th residue is possibly very important in the inhibition infections by M-tropic HIV-1, and it is also demonstrated that the 13th residue of human CCR5 was changed from asparagine into aspartic acid in all these primates. It means that the primate CCR5 no longer depend on CD4 for efficient entry, but human CCR5 may have evolved subsequently due to the use of CD4 as a receptor, allowing the high-affinity chemokine receptor-binding site of HIV to be sequestered from host immune surveillance. (C) 2000 Elsevier Science B.V. All rights reserved.

Intra- and interspecific variation of the CCR5 gene in higher primates

We have evaluated the molecular evolution of the chemokine receptor CCR5 in primates. The chemokine receptor CCR5 serves as a major co-receptor for human immunodeficiency virus/simian immunodeficiency virus (HIV/SIV) infection. Knowledge of evolution of the CCR5 molecule and selection on the CCR5 gene may shed light on its functional role. The comparison of differences between intraspecific polymorphisms and interspecific fixed substitutions provides useful information regarding modes of selection during the course of evolution. There is marked polymorphism in the CCR5 gene sequence within different primate species, whereas sequence divergence between different species is small. By using contingency tests, we compared synonymous (SS) and nonsynonymous (NS) CCR5 mutations occurring within and between a broad range of primates. Our results demonstrate that CCR5 evolution did not follow expectations, of strict neutrality at the level of the whole gene. The proportion of NS to SS at the intraspecific level was significantly higher than that observed at the interspecific level. These results suggest that most CCR5 NS polymorphisms are slightly deleterious. However, at domains more closely correlated with its known biological functions, there was no obvious evidence to support deviation from neutrality.

Molecular modeling on human CCR5 receptors and complex with CD4 antigens and HIV-1 envelope glycoprotein gp120

AIM: To investigate the interaction between human CCR5 receptors (CCR5) and HIV-1 envelope glycoprotein gp120 (HIV-1 gp120) and HIV-1 receptor CD4 antigens (CD4). METHODS: The structurally con served regions (SCR) of human CCR5 was built by the SYBYL/Biopolymer module using the corresponding transmembrane (TM) domain of bacteriorhodopsin (bR) as the template. The coordinates for amino-ter minal residue sequence, and carboxyl-terminal residue sequence, extracellular and cytoplasmic loops were generated using LOOP SEARCH algorithm. Subsequently the structural model was merged into the complex with HIV-1 gp120 and CD4. RESULTS: Human CCR5 interacted with both an HIV-1 gp120 and CD4. The N-terminal residues (especially Met1 and Gln4) of human CCR5, contacted with CD4 residues, mainly 7Nith one span (56 - 59) of CD4 in electrostatic interaction and hydrogen-bonds. The binding sites of human CCR5 were buried in a hydrophobic center surrounded by a highly basic periphery. On the other hand, direct interatomic contacts were made between ? CCR5 residues and 6 gp120 amino-acid residues, which included van der Waals contacts, hydrophobic interaction, and hydrogen bonds. CONCLUSION: The interaction model should be helpful for rational design of novel anti-HIV drugs.

Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.

Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

Distribution of CCR2-64I and SDF1-3 ' A alleles and HIV status in 7 ethnic populations of Cameroon

Limited information is available on the prevalence among rural Africans of host genetic polymorphisms conferring resistance to HIV-1 infection or slowing HIV disease progression.We report the allelic frequencies of the AIDS-related polymorphisms CCR2-64I, SDF1-3#A, and CCR5-D32 in 321 volunteers from 7 ethnic groups in Cameroon. Allelic frequencies differed among the 7 ethnic groups, ranging from 10.8% to 31.3% for CCR2-64I and 0.0% to 7.1% for SDF1-3#A. No CCR5-D32 alleles were found. HIV seroprevalence was 6.9% in the total population and peaked at younger ages in girls and women than in boys and men. Among 15- to 54-year-olds, HIV seroprevalence varied from 2.0% to 11.1% among the village populations. Conditional logistic regression analysis using data from boys and men aged 15 to 54 years showed the number of CCR2-64I alleles to be a significant risk factor for HIV seropositivity (odds ratio per allele adjusted for age and matched on ethnic group = 6.3, 95% confidence interval: 1.3–30.3); this association was not found in women. The findings are consistent with the hypothesis that CCR2-64I alleles may delay HIV disease progression without affecting susceptibility to infection among men. We did not observe this relation among women, and other factors, such as multiple pregnancies or maternal stressors (eg, breastfeeding), may have masked any protective effect of CCR2-64I alleles. Further study of this issue among women is warranted. SDF1-3#A did not differ between HIV-seropositive and HIV-seronegative individuals but wasassociated with increasing age among HIV-seronegative women, suggesting a protective effect against HIV-1 infection.

Neutrality tests using DNA polymorphism from multiple samples

The polymorphism of a gene or a locus is studied with increasing frequency by multiple laboratories or the same group at different times. Such practice results in polymorphism being revealed by different samples at different regions of the locus. Tests of neutrality have been widely conducted for polymorphism data but commonly used statistical tests cannot be applied directly to such data. This article provides a procedure to conduct a neutrality test and details are given for two commonly used tests. Applying the two new tests to the chemokine-receptor gene (CCR5) in humans, we found that the hypothesis that all mutations are selectively neutral cannot explain the observed pattern of DNA polymorphism.

一种抗人免疫缺陷病毒Ⅰ型p24蛋白的单克隆抗体及其应用

一种抗人免疫缺陷病毒I型(HIV-1)p24蛋白的单克隆抗体及其应用，属生物技术领域。单克隆抗体的免疫原为HIV-1B亚型p24基因工程重组蛋白；是由免疫小鼠的脾细胞与骨髓瘤细胞融合产生的杂交瘤p3JB9、p5F1和p6F4细胞系分泌产生；属于免疫球蛋白IgG1型；与猴免疫缺陷病毒SIVAGM、猴逆转录D型病毒SRV交叉反应；与CCR5 嗜性病毒株HIVAda-M和耐药株HIV74V反应；p5F1和p6F4能与临床分离株HIVKM018反应，而 p3JB9不能与临床分离株HIVKM018反应。单克隆抗体可以与其它单克隆抗体或多克隆抗体组合，或可作放射性同位素、酶、荧光素化合物、化学发光化合物或胶体金属离子的标记，用于制备定性或定量检测各种体液、培养上清或细胞、组织中p24抗原的试剂。具有制备方法简单，效价高；单克隆抗体特异性强，灵敏度高。

树ju免疫细胞体外感染Ⅰ型人免疫缺陷病毒的实验研究

报告以不同的HIV-1病毒株体外感染树ju免疫细胞的实验研究,结果表明树ju的这些免疫细胞在体外未能感染上HIV-1,可能的原因是树ju的这些免疫细胞的HIV-1受体(CD4)和辅助受体(CCR5或CXCR4)与人的免疫细胞差别较大。

东亚人群 LMBR1 基因 Intron 5的遗传多样性研究

人LMBR1(Limb region 1 homolog (mouse)) 基因位于染色体7q36区域，全长约210.2 kb，含17个外显子，编码一个由490个氨基酸构成的跨膜蛋白。研究表明，LMBR1 基因的表达活性与脊椎动物四肢的手指或脚趾数目变化有关；另外，发生在其重要元件——intron 5 内的许多变异与多种表型的轴前多指症((PPD, Preaxial polydactyly)存在相关性，这主要是因为LMBR1 intron 5 内含有一个与骨骼系统发育有关的基因（SHH(Sonic hedgehog)基因）的远程顺式调控元件。本研究旨在探究LMBR1基因 intron 5 内的遗传多样性，进而评估HapMap计划的样本选择策略，并检测该区域是否受自然选择的作用。 国际人类基因组单体型图计划(HapMap Project，The International Haplotype Map Project) 于2002年10月正式启动，该计划旨在构建人类基因组中常见变异的遗传图式。自其数据发布以来，广泛应用于生物医学、群体遗传学等领域，在复杂疾病的遗传机理研究、自然选择的检测等方面做出了前所未有的贡献；但是HapMap计划中样本的代表性有待评估。 本研究中，我们综合考虑地理来源信息及线粒体单倍型类群 (Haplogroup)信息选择了41个东亚人作为样本（以保证样本的代表性），测定位于LMBR1 基因intron 5 内的目的片段中存在的单核苷酸多态性(SNP, Singe nucleotide polymorphism)位点，通过所得数据与HapMap数据的比较，发现二者之间差异显著且HapMap数据不能覆盖所有我们得到的常见变异，因而我们认为：HapMap计划中国部分的样本选择策略有待进一步完善。 关于自然选择的研究不仅可以使我们了解生物的进化机制，同时还对复杂疾病的遗传机理研究具有重要的提示作用，因而，对于自然选择的检测，一直以来都是生物学研究的重点。平衡选择是一种维持遗传多态性的自然选择方式，现已发现很多与特定疾病或性状相关的基因或调控序列受平衡选择的作用，如 G6PD 基因、PTC 基因、FMO3 基因、FSHB 基因及 CCR5 基因5’端顺式调控区等我们对41个东亚样本中LMBR1 intron 5 内一段长为9256 bp (Chr7: 156280954-156271699 (Build36))的序列进行以 Tajima’s D 检验为主的群体遗传学分析，发现该区域在进化历程中受到平衡选择的作用。LMBR1 intron 5 内的多态位点与多种表型的多指症存在相关性，受其调控的 SHH 基因在骨骼系统发育中具有重要作用，人类骨骼系统的适应性进化等三方面的因素为该区域受平衡选择的作用提供了进一步的佐证。 总之，本研究对HapMap计划的样本选择策略和数据应用提供了一定的参考；同时还发现一个与骨骼系统发育有关的基因调控元件受平衡选择的作用。

调节性T细胞在SIVmac239感染中国恒河猴中的变化及其机制的初步研究

CD4+CD25+调节性T细胞是1995年才发现的一个具有免疫抑制功能的T细胞亚群，主要通过细胞与细胞间直接接触和分泌抑制性细胞因子发挥作用，在维持机体免疫自稳、防止自身免疫以及肿瘤免疫、移植免疫等方面起着重要作用。有关Treg HIV/SIV病毒感染及AIDS的进展关系密切，但却有两种不同的观点。一种认为Treg的数量和功能受到损伤，从而导致宿主免疫系统过度活化。另一种则认为Treg在早期抑制了针对HIV/SIV的特异性的免疫反应，从而导致机体无法清除感染的病毒。本文利用动物模型对CD4+CD25+调节性T细胞在SIV感染后的数量和功能做了动态的检测，并对其中的机制做了初步的探讨。我们首先建立了SIVmac239病毒株对中国起源的恒河猴感染的动物模型，建立了前病毒的检测方法、血浆病毒载量的测定方法、血浆病毒特异性抗体的测定方法，以及病毒的分离方法，并获得了早期感染的相关数据。在研究中我们发现，SIV感染后的1周后即可在恒河猴外周单个核细胞DNA中检测到前病毒。病毒血症也在1周后出现，并很快达到高峰。不同的个体对病毒感染的体液免疫不尽相同，血浆抗体很快出现，但是99003猴抗体下降很快，而99083猴则保持了一定数量的抗体。同时，伴随SIV的感染进程的还有T淋巴细胞的数量变化，CD4+T细胞数量持续下降，而CD8+T细胞数量则在增加，出现CD4/CD8倒置的现象。以上说明恒河猴被SIV所成功感染。在该动物模型的基础上，我们利用体内传代的SIVmac239病毒株，对4只健康恒河猴进行了感染，并对CD4+CD25+调节性T细胞（Treg）亚群在数量上的变化进行了检测，并对其中的机制做了初步探讨。我们在研究中发现，外周血中的Treg在SIV感染后无论是绝对数量还是在占CD4+T细胞中的相对数量均有增加，而且Treg仍然保持了对靶细胞的抑制功能。对腹部淋巴结的分析显示，SIV感染后的一段时期内，该部位FoxP3 mRNA的表达水平也在上升，TGF-β、IL-10的转录也显著增加。前者可以通过抑制树突状细胞间接抑制效应细胞，而后者则是一个抑制性的细胞因子，可以直接作用于靶细胞。因此，我们推测SIV引起免疫系统的过度活化可能不是由于Treg功能的受损，其中的机制需要深入研究。 Treg表达CCR5表面分子（HIV辅助受体之一），同时也有CD4分子的表达，因此推测HIV/SIV可以感染Treg。但是国内外这方面的文献很少。我们对Treg中前病毒的检测发现，SIV可以感染Treg，而且对Treg的感染比例高于CD4+CD25－T细胞。这个结果与Treg绝对数量的上升的结果说明，SIV感染Treg但可能却没有杀伤Treg，因此Treg在数量上有所增加。不过，其中的机制仍有待于进一步的研究。在对SIV引起的体液免疫的研究中还发现，机体针对SIV不同抗原的抗体有不同的模式。部分抗原很快就产生了比较强的反应，但是却不能维持高水平的表达。而针对p27蛋白的抗体产生比较晚，但却长时间维持在比较高的水平。是否这样高水平的抗体有助于控制病毒复制是个值得探讨的问题。

树突状细胞亚群在SIVmac239感染中国恒河猴中数量、表型和功能变化及其机制的研究

本论文主要由3 个相对独立的部分组成：中国恒河猴单核细胞来源的树突 状细胞的表型及功能研究；外周血DC 亚群在SIVmac239 感染的中国恒河猴中 数量及细胞因子的变化以及急性感染期SIVmac239 对中国恒河猴外周血DC 亚 群的凋亡和免疫表型的影响。 非人灵长类动物是人类的近亲，由于在组织结构、免疫、生理和代谢等诸 多方面与人类高度近似，科学界较普遍地利用非人灵长类作为动物模型来进行 艾滋病（AIDS）的发病机制和疫苗研究。中国恒河猴发病缓慢，更适合于HIV 感染的相关研究。在本研究中，我们在体外成功培养了中国恒河猴单核细胞来 源的树突状细胞（monocyte derived dendritic cells，MDDC），并测定其表型和免 疫刺激功能。通过GM-CSF 和IL-4 共同刺激培养单核细胞6 天以后便获得了未 成熟MDDC，随后加入IL-1β、PGE2、LPS 和TNF-α 联合刺激MDDC 成熟。 成熟的MDDC 上调了共刺激分子和CD83 的表达，具有很强的刺激T 淋巴细胞 增殖的能力并分泌大量的IL-12。本研究为后续的DC 疫苗研究奠定了基础。 我们实验室建立了SIVmac239 感染的中国恒河猴动物模型。以该模型为依 托，我们研究了外周血中DC 亚群在急性感染期以及慢性感染期的数量、表型 及功能变化。DC 作为最重要的连接先天免疫与获得性免疫的抗原递呈细胞， 在AIDS 发病进程中扮演着重要的角色。研究发现AIDS 患者血液和淋巴结中 髓样DC（myeloid DC，mDC）和浆细胞样DC（plasmacytoid DC，pDC）会随 着感染的进程而减少，并且伴随着功能损伤。本论文通过研究发现，中国恒河 猴的DC 亚群数量在感染后尽管波动十分剧烈，但并没有显著性地增加或减少， 中文摘要 2 在后期DC 数量能够回升到正常的范围之类，这种回升不同于印度恒河猴，很 可能是中国恒河猴缓慢发病的原因之一。进一步通过研究体外刺激DC 亚群分 泌的细胞因子，我们发现在急性感染期，pDC 分泌的IFN-α 显著提高，并很可 能刺激mDC 成熟并促进了IL-12 的分泌。早期大量细胞因子的分泌有助于控制 病毒复制，但同时也激起了整个免疫系统的活化，促进了疾病进程。而在整个 感染阶段，IFN-α 与CD4+ T 细胞呈正相关，而与病毒载量呈负相关，表明了 IFN-α 对于延缓疾病进程具有重要的意义。 我们测定了急性感染期DC 亚群受病毒影响而发生的表型变化，发现pDC 更容易受到病毒影响而发生凋亡，这可能与pDC 高表达SIV 受体CD4 和CCR5 有关。在感染过程中，尽管mDC 和pDC 都显著地下调了CD4 表达，而上调了 CCR5 的表达，不过仅发现pDC CD4 的表达与病毒载量呈负相关，而CCR5 的 表达与病毒载量呈正相关。在此过程中DC 亚群都会因为病毒的影响而活化， 继而提高CCR7 的表达。同时无论mDC 还是pDC，其表达的CD80 和CD86 都与病毒载量呈正相关。在早期感染中，DC 的活化促使整个免疫系统针对病 毒发挥免疫反应，对于控制疾病发展具有重要意义。