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

项目摘要 当代艾滋病毒疫苗研究的一个战略优先事项是发展广泛的方法， 中和抗体（bNAb）能够中和不同的病毒株。bNAb发现的基石 是能够进行准确的，纵向研究抗体的演变，在艾滋病毒感染者的个人，因为他们获得 突变并获得中和活性。目前，不可能进行类似的抗体进化 由于缺乏确定的免疫球蛋白（IG）等位基因，使用恒河猴（RM）进行追踪研究。这是最好 我们小组最近的一项大规模疫苗研究就是一个例子， 为了获得IG基因座的准确组装，使用长读序测序对RM进行测序。该参考 显著提高了追踪我们的疫苗策略引起的种系突变的准确性。 这一工具在破译导致自体中和或免疫显性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（种系 推断）以从免疫球蛋白库中鉴定未突变的种系抗体序列。这项工作 导致鉴定了数百种新的推断的IG等位基因。 这项R24提案的目标是通过表征IG等位基因和单倍型来建立这些发现 在艾滋病方面，NHP灵长类中心指定了RM，为主要的艾滋病毒疫苗利益相关者服务。目前， IG基因座在RM中的特征不佳，部分原因是技术上的挑战。IG基因型目前还没有 在将RM纳入疫苗研究时用作标准。相比之下，RM的MHC基因分型已成为 疫苗研究的标准实践，是NPRC RM菌落遗传管理的核心功能。的 因此，缺乏关于RM IG基因座的遗传数据是一个重大的知识缺口，并损害了我们评估 猴子接种疫苗后抗体的演变，目的是引发中和抗体。目标 这项R24提案的目的是解决这一战略需求，并建立一个资源IG 等位基因序列信息、单体型和等位基因使用）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.