Population genotyping of the germline immunoglobulin repertoire in AIDS-designated rhesus macaque breeding colonies

项目总结 当代艾滋病毒疫苗研究的一个战略重点是开发广泛诱导的方法 能够中和不同病毒株的中和抗体(BNAbs)。发现bNAb的基石 是对HIV感染者的抗体进化进行准确的纵向研究的能力 突变并获得中和活性。目前，不可能进行类似的抗体进化 使用恒河猴(RMS)的追踪研究，由于缺乏明确的免疫球蛋白(IG)等位基因。这是最好的 我们团队最近的一项大规模疫苗研究就是例证，在这项研究中，我们对一个从头开始的基因组进行了测序 为了获得准确的IG基因座组装，使用长读测序对RM进行了分析。此参考文献 显著提高了跟踪由我们的疫苗策略引发的生殖系突变的准确性。 这一工具在破译导致自体中和或免疫优势的轨迹方面至关重要 和非中和反应。在其他工作中，我们开发了新的生物信息学方法学(种系 推断)以从免疫球蛋白谱系中鉴定未突变的生殖系抗体序列。这项工作有 导致了数百个新的推断的IG等位基因的鉴定。 R24建议的目标是通过表征IG等位基因和单倍型来建立这些发现的基础 在为主要艾滋病毒疫苗利益相关者服务的NHP灵长类中心，艾滋病患者被指定为RMS。目前， 免疫球蛋白基因座在RMS中的特征不佳，部分原因是技术挑战。免疫球蛋白基因分型目前没有 在将RMS纳入疫苗研究时用作标准。相比之下，RMS的MHC基因分型已经成为 疫苗研究的标准实践，是NPRC RM群体遗传管理的核心功能。这个 因此，缺乏关于RMIG基因座的遗传数据是一个重大的知识鸿沟，并削弱了我们评估 猴子体内抗体的进化接种了旨在诱导中和抗体的疫苗。目标是 R24提案的目的是解决这一战略需求，并建立一种资源，在该资源中，该遗传信息(IG 等位基因序列信息、单倍型和等位基因使用)可用于HIV疫苗和NHP研究 社区。

PROJECT SUMMARY A strategic priority for contemporary HIV vaccine research is the development of approaches to elicit broadly neutralizing antibodies (bNAbs) able to neutralize diverse strains of the virus. A cornerstone of bNAb discovery is the ability to conduct accurate, longitudinal studies of antibody evolution in HIV infected individual as they gain mutations and acquire neutralization activity. Currently, it is not possible to perform analogous antibody evolution tracing studies using rhesus macaques (RMs), due to a lack of defined immunoglobulin (IG) alleles. This is best exemplified by a recent study large scale vaccine study by our group in which we sequenced a de novo genome of a RM using long-read sequencing in order to obtain accurate assemblies of the IG loci. This reference significantly enhanced the accuracy of tracking the mutations from germline elicited by our vaccine strategies. This tool was critical in deciphering trajectories that led to either autologous neutralization or immunodominance and non-neutralizing responses. In other work, we have developed novel bioinformatics methodology (germline inference) to identify the unmutated germline antibody sequence from immunoglobulin repertoire. This work has led to identification of hundreds of novel inferred IG alleles. The goal of this R24 proposal is to build on these findings by characterizing the IG alleles and haplotypes in AIDS designated RMs at NHP primate centers that serve the major HIV vaccine stakeholders. Currently, the IG loci are poorly characterized in RMs, in part due to technical challenges. IG genotypes are not currently used as criteria when enrolling RMs into vaccine studies. In contrast, MHC genotyping of RMs has become standard practice for vaccine studies and is a core function in genetic management of NPRC RM colonies. The lack of genetic data on the RM IG loci is therefore a significant knowledge gap and impairs our ability to assess the evolution of antibodies in monkeys administered vaccines that aim to elicit neutralizing antibodies. The goal of this R24 proposal is to address this strategic need and build a resource in which this genetic information (IG allele sequence information, haplotype, and allele usage) is available to the HIV vaccine and NHP research communities.