DNA repair mechanisms that promote insertion-deletion events during immunoglobulin gene diversification
DNA repair mechanisms that promote insertion-deletion events during immunoglobulin gene diversification
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DOI：
10.1126/sciimmunol.ade1167
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发表时间：
2023-03-01
影响因子：
24.8
通讯作者：
Yeap，Leng-Siew
中科院分区：
文献类型：
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作者：
Hao，Qian;Zhan，Chuanzong;Yeap，Leng-Siew
插入和缺失 (indels) 是低频有害的基因组 DNA 改变。尽管插入缺失很罕见，但插入缺失很常见，并且导致长互补决定区 3 (CDR3) 的插入对于针对病毒的广泛中和和多反应性抗体中的抗原结合功能至关重要。由于检测插入缺失的挑战，在免疫球蛋白多样化过程中产生插入缺失的机制仍然知之甚少。我们对插入缺失进行了超深入分析，并使用乘客-免疫球蛋白小鼠模型系统地剖析了潜在机制。我们发现，激活诱导的胞苷脱氨酶依赖性±1碱基对（bp）插入缺失是最常见的插入缺失事件，会产生有害结果，而较长的框内插入缺失，尤其是可以延长CDR3长度的插入，是罕见的结果。 ±1-bp 插入缺失是通过碱基切除修复引导的，但更长的插入缺失需要额外的 DNA 处理因子。 DNA 核酸外切酶的异位表达或 DNA 聚合酶平衡的扰动可以增加较长插入缺失的频率，从而为可以生成具有长 CDR3 的抗体的模型铺平道路。我们的研究揭示了在抗体体细胞超突变过程中产生有益和有害插入缺失的机制，并且对于理解包括肿瘤发生在内的各种条件下有害的基因组改变具有重要意义。
Insertions and deletions (indels) are low-frequency deleterious genomic DNA alterations. Despite their rarity, indels are common, and insertions leading to long complementarity-determining region 3 (CDR3) are vital for antigen-binding functions in broadly neutralizing and polyreactive antibodies targeting viruses. Because of challenges in detecting indels, the mechanism that generates indels during immunoglobulin diversification processes remains poorly understood. We carried out ultra-deep profiling of indels and systematically dissected the underlying mechanisms usingpassenger-immunoglobulinmouse models. We found that activation-induced cytidine deaminase–dependent ±1–base pair (bp) indels are the most prevalent indel events, biasing deleterious outcomes, whereas longer in-frame indels, especially insertions that can extend the CDR3 length, are rare outcomes. The ±1-bp indels are channeled by base excision repair, but longer indels require additional DNA-processing factors. Ectopic expression of a DNA exonuclease or perturbation of the balance of DNA polymerases can increase the frequency of longer indels, thus paving the way for models that can generate antibodies with long CDR3. Our study reveals the mechanisms that generate beneficial and deleterious indels during the process of antibody somatic hypermutation and has implications in understanding the detrimental genomic alterations in various conditions, including tumorigenesis.