Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains
Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains
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DOI：
10.1073/pnas.1219320110
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发表时间：
2013-04-16
影响因子：
11.1
通讯作者：
Kwong, Peter D.
中科院分区：
文献类型：
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作者：
Zhu, Jiang;Ofek, Gilad;Kwong, Peter D.
对来自具有广泛中和抗体的HIV-1感染个体的抗体转录物进行下一代测序可以提供鉴定体细胞变异和表征其谱系的有效手段。在这里，我们使用454焦磷酸测序和身份/发散网格采样来分析来自供体N152的重链和轻链序列，供体N152是广泛中和抗体10 E8的来源。我们鉴定了氨基酸序列差异高达28%的变体。鉴定的10 E8变体的重链和轻链系统发育树显示相似的结构，并且从匹配和不匹配的系统发育分支重建的10 E8变体在匹配时显示显著较低的自身反应性。为了测试系统发育配对的一般性，我们分析了捐助者国际艾滋病疫苗倡议84，抗体PGT 141 -145的来源。PGT 141 -145体细胞变体的重链和轻链系统发育树也显示出非常相似的结构;在这种情况下，分支配对可以通过已知的PGT 141 -145抗体锚定。总而言之，我们的研究结果表明，重链和轻链的系统发育匹配可以提供一种近似自然配对的方法。
Next-generation sequencing of antibody transcripts from HIV-1-infected individuals with broadly neutralizing antibodies could provide an efficient means for identifying somatic variants and characterizing their lineages. Here, we used 454 pyrosequencing and identity/divergence grid sampling to analyze heavy- and light-chain sequences from donor N152, the source of the broadly neutralizing antibody 10E8. We identified variants with up to 28% difference in amino acid sequence. Heavy- and light-chain phylogenetic trees of identified 10E8 variants displayed similar architectures, and 10E8 variants reconstituted from matched and unmatched phylogenetic branches displayed significantly lower autoreactivity when matched. To test the generality of phylogenetic pairing, we analyzed donor International AIDS Vaccine Initiative 84, the source of antibodies PGT141-145. Heavy- and light-chain phylogenetic trees of PGT141-145 somatic variants also displayed remarkably similar architectures; in this case, branch pairings could be anchored by known PGT141-145 antibodies. Altogether, our findings suggest that phylogenetic matching of heavy and light chains can provide a means to approximate natural pairings.