Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling.

IF 3.5 2区 生物学 Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY
Khang Lê Quý, Maria Chernigovskaya, Maria Stensland, Sachin Singh, Jinwoo Leem, Santiago Revale, David A Yadin, Francesca L Nice, Chelsea Povall, Danielle H Minns, Jacob D Galson, Tuula A Nyman, Igor Snapkow, Victor Greiff
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Abstract

Immunoglobulins (Ig), which exist either as B-cell receptors (BCR) on the surface of B cells or as antibodies when secreted, play a key role in the recognition and response to antigenic threats. The capability to jointly characterize the BCR and antibody repertoire is crucial for understanding human adaptive immunity. From peripheral blood, bulk BCR sequencing (bulkBCR-seq) currently provides the highest sampling depth, single-cell BCR sequencing (scBCR-seq) allows for paired chain characterization, and antibody peptide sequencing by tandem mass spectrometry (Ab-seq) provides information on the composition of secreted antibodies in the serum. Yet, it has not been benchmarked to what extent the datasets generated by these three technologies overlap and complement each other. To address this question, we isolated peripheral blood B cells from healthy human donors and sequenced BCRs at bulk and single-cell levels, in addition to utilizing publicly available sequencing data. Integrated analysis was performed on these datasets, resolved by replicates and across individuals. Simultaneously, serum antibodies were isolated, digested with multiple proteases, and analyzed with Ab-seq. Systems immunology analysis showed high concordance in repertoire features between bulk and scBCR-seq within individuals, especially when replicates were utilized. In addition, Ab-seq identified clonotype-specific peptides using both bulk and scBCR-seq library references, demonstrating the feasibility of combining scBCR-seq and Ab-seq for reconstructing paired-chain Ig sequences from the serum antibody repertoire. Collectively, our work serves as a proof-of-principle for combining bulk sequencing, single-cell sequencing, and mass spectrometry as complementary methods towards capturing humoral immunity in its entirety.

Abstract Image

人类 B 细胞受体基因组和抗体蛋白质组剖析的基准和整合。
免疫球蛋白(Ig)以 B 细胞受体(BCR)的形式存在于 B 细胞表面,或以抗体的形式分泌出来,在识别和应对抗原威胁方面发挥着关键作用。联合鉴定 BCR 和抗体库的能力对于了解人类适应性免疫至关重要。目前,外周血批量 BCR 测序(bulkBCR-seq)可提供最高的采样深度,单细胞 BCR 测序(scBCR-seq)可进行配对链表征,而抗体多肽串联质谱测序(Ab-seq)可提供血清中分泌抗体的组成信息。然而,这三种技术生成的数据集在多大程度上相互重叠和互补,目前还没有基准。为了解决这个问题,我们从健康的人类捐献者身上分离出外周血 B 细胞,除了利用公开的测序数据外,还在体细胞和单细胞水平上对 BCR 进行了测序。我们对这些数据集进行了综合分析,按重复和跨个体进行了解析。同时,还分离了血清抗体,用多种蛋白酶进行了消化,并用 Ab-seq 进行了分析。系统免疫学分析表明,在个体内部,批量和 scBCR-seq 数据集之间的基因库特征具有很高的一致性,尤其是在使用重复数据时。此外,Ab-seq利用大样本和scBCR-seq文库参考文献鉴定出了克隆型特异性肽段,证明了结合scBCR-seq和Ab-seq从血清抗体库中重建成对链Ig序列的可行性。总之,我们的工作证明了将批量测序、单细胞测序和质谱分析作为互补方法来捕捉整个体液免疫的原理。
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来源期刊
NPJ Systems Biology and Applications
NPJ Systems Biology and Applications Mathematics-Applied Mathematics
CiteScore
5.80
自引率
0.00%
发文量
46
审稿时长
8 weeks
期刊介绍: npj Systems Biology and Applications is an online Open Access journal dedicated to publishing the premier research that takes a systems-oriented approach. The journal aims to provide a forum for the presentation of articles that help define this nascent field, as well as those that apply the advances to wider fields. We encourage studies that integrate, or aid the integration of, data, analyses and insight from molecules to organisms and broader systems. Important areas of interest include not only fundamental biological systems and drug discovery, but also applications to health, medical practice and implementation, big data, biotechnology, food science, human behaviour, broader biological systems and industrial applications of systems biology. We encourage all approaches, including network biology, application of control theory to biological systems, computational modelling and analysis, comprehensive and/or high-content measurements, theoretical, analytical and computational studies of system-level properties of biological systems and computational/software/data platforms enabling such studies.
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