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Application and prospect of live cell DNA-based molecular recorders in cell lineage tracing
- Synthetic Biology Journal Vol. 6, Issue 3, Pages: 651-668(2025)
- 作者机构：
北京大学定量生物学中心，北京 100871
- 作者简介：
- 基金信息：
DOI：10.12211/2096-8280.2024-082
CLC： Q816Received：27 November 2024，
Revised：2025-03-03，
Published：30 June 2025
- 稿件说明：
移动端阅览
姜百翼， 钱珑. 活细胞记录器在细胞谱系追踪中的应用和前景［J］. 合成生物学， 2025， 6（3）： 651-668
JIANG Baiyi， QIAN Long. Application and prospect of live cell DNA-based molecular recorders in cell lineage tracing［J］. Synthetic Biology Journal， 2025， 6（3）： 651-668
姜百翼， 钱珑. 活细胞记录器在细胞谱系追踪中的应用和前景［J］. 合成生物学， 2025， 6（3）： 651-668 DOI： 10.12211/2096-8280.2024-082.
JIANG Baiyi， QIAN Long. Application and prospect of live cell DNA-based molecular recorders in cell lineage tracing［J］. Synthetic Biology Journal， 2025， 6（3）： 651-668 DOI： 10.12211/2096-8280.2024-082.
摘要
基于DNA的活细胞分子记录器技术，通过诱导可遗传的DNA变异，为细胞历史的追溯提供了一种创新手段。作为新一代细胞谱系追踪方法的代表，该技术能够与单细胞测序、多组学测序等技术相集成，帮助科研人员重构细胞发育分化路径及肿瘤起源的谱系发生树，是探究这些核心生物学议题的有效平台。本综述系统性回顾了自2016年以来基于Cas9的分子记录器在谱系追踪领域的技术演变轨迹与应用进展，同时综合分析了一些新型分子记录器的研究动态，并对其优势与局限性进行了评估。自2016年以来，以CRISPR-Cas9系统为核心的分子记录器取得了显著进展，并逐渐成为该领域的主流技术，研究人员在优化编辑效率和增加记录位点等方面进行了充分的探索。尽管如此，以Cas9为基础的分子记录器仍面临CRISPR-Cas9系统固有的限制与挑战，例如DNA双链断裂带来碱基缺失，进而引起记录信息丢失。这促使研究者们探索开发新型分子记录器，以期作为谱系追踪的更高效精准的工具。先导编辑器、DNA结合蛋白融合碱基编辑器以及T7转录聚合酶融合碱基编辑器等基于新原理的分子记录器能够避免DNA双链断裂，以碱基替换而非碱基缺失的形式写入信息。相较于Cas9系统，它们展现出独特优势，同时也伴随着潜在的风险与挑战。先导编辑器可以以时间顺序的方式记录信息，但脱靶效应仍然是一个问题。DNA结合蛋白融合碱基编辑器提高了编辑效率和特异性，但它们在不同细胞类型中的有效性需要进一步探索。T7 RNA聚合酶融合碱基编辑器已经在体内定向进化系统中取得了成功，但它们目前在哺乳动物系统中的应用仍然有限。未来，基于DNA的分子记录器的研究应着重于优化编辑效率、降低信息丢失率、提高谱系恢复效率，并探索其在复杂生物系统中的应用潜力。
Abstract
Tracing the division and differentiation history of cells is a critical issue in organismal development and cancer research. Live cell DNA-based molecular recorders
a synthetic system that induces heritable DNA variations
offers an innovative approach for reconstructing cell lineage histories. As a representative for the new generation of cell lineage tracing method
this system can be integrated with high-throughput single-cell sequencing and multi-omics analysis
enabling the reconstruction of developmental differentiation pathways of cells and the phylogenetic trees of tumorigenesis as well. Live cell DNA-based molecular recorders serve as an effective platform for exploring these core biological processes. This review systematically analyzes the technological evolution of Cas9-based molecular recorders in lineage tracing since 2016 and its applications
while also analyzing the research trends of some novel molecular recorders and evaluating their advantages and limitations. Since 2016
molecular recorders based on the CRISPR-Cas9 system have made significant progress and gradually become the mainstream technology in this field. However
Cas9-based molecular recorders still suffer from several inherent limitations
such as the low lineage resolution due to insufficient editing efficiencies
the loss of recorded information caused by DNA double-strand breaks
and potential lineage merging due to barcode homoplasy. These limitations pose challenges for researchers to explore and develop new types of molecular recorders as more efficient and precise tools for cell lineage tracing. Novel molecular recorders based on new principles
such as prime editors
DNA-binding protein-fused base editors
and T7 RNA polymerase-fused base editors
can avoid DNA double-strand breaks and record information through base substitutions rather t
han deletions. Compared to the Cas9 system
they exhibit unique advantages but also come with potential risks and challenges. Prime editors can record information in a temporal sequential manner
but off-target effects remain a concern. DNA-binding protein-fused base editors offer high editing efficiencies and specificities
but their effectiveness across different cell types requires further exploration. T7 RNA polymerase-fused base editors have achieved success in
in vivo
directed evolution systems
but their application in mammalian systems is still limited. In the future
the research of DNA-based molecular recorders should focus on optimizing editing efficiency
reducing information loss
improving lineage recovery efficiency
and exploring their application potentials in complicated biological systems.
2
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