VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma
VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma
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DOI：
10.3791/53215
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发表时间：
2015-12-01
影响因子：
1.2
通讯作者：
Elemento, Olivier
中科院分区：
文献类型：
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作者：
Jiang, Yanwen;Nie, Kui;Elemento, Olivier
了解肿瘤克隆性对于了解肿瘤发生和疾病进展的机制至关重要。此外，了解肿瘤内响应于某些微环境或治疗而发生的克隆组成变化可能会导致设计更复杂和有效的方法来根除肿瘤细胞。然而，由于缺乏可区分的标记物，追踪肿瘤克隆亚群一直具有挑战性。为了解决这个问题，创建了VDJ-seq方案，以通过利用VDJ重组和体细胞超突变（SHM）（B细胞淋巴瘤的两个独特特征）来追踪弥漫性大B细胞淋巴瘤（DLBCL）复发的克隆进化模式。从扩增的重排免疫球蛋白重链（IgH）构建具有索引潜力的下一代测序（NGS）文库，来自初步诊断和复发DLBCL样品对的VDJ区域。测序后平均每个样品获得超过50万个VDJ序列，其包含VDJ重排和SHM信息。此外，开发了定制的生物信息学管道，以充分利用序列信息来表征这些样品中的IgH-VDJ库。此外，该管道允许重建和比较个体肿瘤的克隆结构，这使得能够检查诊断肿瘤内的克隆异质性，并推断诊断和复发肿瘤对之间的克隆进化模式。当将这种分析应用于几个诊断-复发对时，我们发现了多种独特的肿瘤进化模式可能导致DLBCL复发的关键证据。此外，这种方法可以扩展到其他临床方面，例如识别微小残留病，监测复发进展和治疗反应，以及在非淋巴瘤背景下研究免疫库。
Understanding tumor clonality is critical to understanding the mechanisms involved in tumorigenesis and disease progression. In addition, understanding the clonal composition changes that occur within a tumor in response to certain micro-environment or treatments may lead to the design of more sophisticated and effective approaches to eradicate tumor cells. However, tracking tumor clonal sub-populations has been challenging due to the lack of distinguishable markers. To address this problem, a VDJ-seq protocol was created to trace the clonal evolution patterns of diffuse large B cell lymphoma (DLBCL) relapse by exploiting VDJ recombination and somatic hypermutation (SHM), two unique features of B cell lymphomas.In this protocol, Next-Generation sequencing (NGS) libraries with indexing potential were constructed from amplified rearranged immunoglobulin heavy chain (IgH) VDJ region from pairs of primary diagnosis and relapse DLBCL samples. On average more than half million VDJ sequences per sample were obtained after sequencing, which contain both VDJ rearrangement and SHM information. In addition, customized bioinformatics pipelines were developed to fully utilize sequence information for the characterization of IgH-VDJ repertoire within these samples. Furthermore, the pipeline allows the reconstruction and comparison of the clonal architecture of individual tumors, which enables the examination of the clonal heterogeneity within the diagnosis tumors and deduction of clonal evolution patterns between diagnosis and relapse tumor pairs. When applying this analysis to several diagnosis-relapse pairs, we uncovered key evidence that multiple distinctive tumor evolutionary patterns could lead to DLBCL relapse. Additionally, this approach can be expanded into other clinical aspects, such as identification of minimal residual disease, monitoring relapse progress and treatment response, and investigation of immune repertoires in non-lymphoma contexts.