Volume: 17, Issue: 2

Review Article

Progress and Challenges for Live-cell Imaging of Genomic Loci Using CRISPR-based Platforms

Xiaotian Wu, Shiqi Mao, Yachen Ying, Christopher J. Krueger, Antony K. Chen

Chromatin conformation, localization, and dynamics are crucial regulators of cellular behaviors. Although fluorescence in situ hybridization-based techniques have been widely utilized for investigating chromatin architectures in healthy and diseased states, the requirement for cell fixation precludes the comprehensive dynamic analysis necessary to fully understand chromatin activities. This has spurred the development and application of a variety of imaging methodologies for visualizing single chromosomal loci in the native cellular context. In this review, we describe currently-available approaches for imaging single genomic loci in cells, with special focus on clustered regularly interspaced short palindromic repeats (CRISPR)-based imaging approaches. In addition, we discuss some of the challenges that limit the application of CRISPR-based genomic imaging approaches, and potential solutions to address these challenges. We anticipate that, with continued refinement of CRISPR-based imaging techniques, significant understanding can be gained to help decipher chromatin activities and their relevance to cellular physiology and pathogenesis.
染色质的三维空间构象、核内定位以及动力学特征在调控真核细胞基因表达进而影响细胞行为方面发挥着重要作用,例如:染色质空间构象的变化可以促使增强子等调控元件与靶基因相互靠近,从而促进基因表达;染色质从核质迁移至核膜处会降低其运动速率及基因表达水平等。 尽管荧光原位杂交技术已经被广泛运用于特定染色质的标记,进而研究染色质在发育过程中或病理条件下的行为变化,但是由于需要进行细胞固定、探针清洗等操作,该技术难以帮助研究者全面、真实地了解染色质在活细胞中的动态活动信息。因此,开发并优化在活细胞环境中标记特定染色质位点的荧光成像方法具有重要的意义。本文综述了目前用于在活细胞中标记特定染色质位点的成像方法,重点介绍了基于Clustered regularly interspaced short palindromic repeats (CRISPR)系统的荧光成像方法。本文分别阐述了基于荧光蛋白、有机荧光染料以及纳米颗粒等不同发光元素的CRISPR 成像体系的工作原理,以及现阶段每个体系在活细胞标记特定染色质位点,观测其时程变化,并获取其动力学信息等方面的应用。本文最后列举了CRISPR 成像领域存在的挑战,并针对这些挑战提出了一些建议。我们期待,基于CRISPR系统的染色质标记技术的不断完善能够为破译染色质活动与细胞生理及病理的关系提供有力的支持。

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Original Research

Single-cell Analysis of CAR-T Cell Activation Reveals A Mixed TH1/TH2 Response Independent of Differentiation

Iva Xhangolli, Burak Dura, GeeHee Lee, Dongjoo Kim, Yang Xiao, Rong Fan

The activation mechanism of chimeric antigen receptor (CAR)-engineered T cells may differ substantially from T cells carrying native T cell receptor, but this difference remains poorly understood. We present the first comprehensive portrait of single-cell level transcriptional and cytokine signatures of anti-CD19/4-1BB/CD28/CD3ζ CAR-T cells upon antigen-specific stimulation. Both CD4+ helper T (TH) cells and CD8+ cytotoxic CAR-T cells are equally effective in directly killing target tumor cells and their cytotoxic activity is associated with the elevation of a range of TH1 and TH2 signature cytokines, e.g., interferon γ, tumor necrotic factor α, interleukin 5 (IL5), and IL13, as confirmed by the expression of master transcription factor genes TBX21 and GATA3. However, rather than conforming to stringent TH1 or TH2 subtypes, single-cell analysis reveals that the predominant response is a highly mixed TH1/TH2 function in the same cell. The regulatory T cell activity, although observed in a small fraction of activated cells, emerges from this hybrid TH1/TH2 population. Granulocyte-macrophage colony stimulating factor (GM-CSF) is produced from the majority of cells regardless of the polarization states, further contrasting CAR-T to classic T cells. Surprisingly, the cytokine response is minimally associated with differentiation status, although all major differentiation subsets such as naïve, central memory, effector memory, and effector are detected. All these suggest that the activation of CAR-engineered T cells is a canonical process that leads to a highly mixed response combining both type 1 and type 2 cytokines together with GM-CSF, supporting the notion that polyfunctional CAR-T cells correlate with objective response of patients in clinical trials. This work provides new insights into the mechanism of CAR activation and implies the necessity for cellular function assays to characterize the quality of CAR-T infusion products and monitor therapeutic responses in patients.

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