DMF-DM-seq: Digital-Microfluidics Enabled Dual-Modality Sequencing of Single-Cell mRNA and microRNA with High Integration, Sensitivity, and Automation,Analytical Chemistry

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DMF-DM-seq: Digital-Microfluidics Enabled Dual-Modality Sequencing of Single-Cell mRNA and microRNA with High Integration, Sensitivity, and Automation
Analytical Chemistry ( IF 6.7 ) Pub Date : 2024-07-22 , DOI: 10.1021/acs.analchem.4c03378
Yingwen Chen ₁ , Xuanqun Wang ₁ , Xing Na ₁ , Yingkun Zhang ₁ , Linfeng Cai ₁ , Jia Song ₂ , Chaoyong Yang _{1,

3}

Affiliation

Multimodal measurement of single cells provides deep insights into the intricate relationships between individual molecular layers and the regulatory mechanisms underlying intercellular variations. Here, we reported DMF-DM-seq, a highly integrated, sensitive, and automated platform for single-cell mRNA and microRNA (miRNA) co-sequencing based on digital microfluidics. This platform first integrates the processes of single-cell isolation, lysis, component separation, and simultaneous sequencing library preparation of mRNA and miRNA within a single DMF device. Compared with the current half-cell measuring strategy, DMF-DM-seq enables complete separation of single-cell mRNA and miRNA via a magnetic field application, resulting in a higher miRNA detection ability. DMF-DM-seq revealed differential expression patterns of single cells of noncancerous breast cells and noninvasive and aggressive breast cancer cells at both mRNA and miRNA levels. The results demonstrated the anticorrelated relationship between miRNA and their mRNA targets. Further, we unravel the tumor growth and metastasis-associated biological processes enriched by miRNA-targeted genes, along with important miRNA-interaction networks involved in significant signaling pathways. We also deconstruct the miRNA regulatory mechanisms underlying different signaling pathways across different breast cell types. In summary, DMF-DM-seq offers a powerful tool for a comprehensive study of the expression heterogeneity of single-cell mRNA and miRNA, which will be widely applied in basic and clinical research.

中文翻译：

DMF-DM-seq：数字微流体支持单细胞 mRNA 和 microRNA 的双模态测序，具有高集成度、灵敏度和自动化

单细胞的多模态测量可以深入了解各个分子层之间的复杂关系以及细胞间变异背后的调节机制。在此，我们报道了 DMF-DM-seq，这是一个高度集成、灵敏且自动化的平台，用于基于数字微流控的单细胞 mRNA 和 microRNA (miRNA) 共测序。该平台首先将 mRNA 和 miRNA 的单细胞分离、裂解、组分分离以及同步测序文库制备过程集成在单个 DMF 设备中。与目前的半细胞测量策略相比，DMF-DM-seq能够通过磁场应用实现单细胞mRNA和miRNA的完全分离，从而获得更高的miRNA检测能力。 DMF-DM-seq揭示了非癌性乳腺癌细胞以及非侵袭性和侵袭性乳腺癌细胞的单细胞在mRNA和miRNA水平上的差异表达模式。结果证明了 miRNA 与其 mRNA 靶标之间存在反相关关系。此外，我们还揭示了 miRNA 靶向基因丰富的肿瘤生长和转移相关的生物过程，以及参与重要信号通路的重要 miRNA 相互作用网络。我们还解构了不同乳腺细胞类型的不同信号通路背后的 miRNA 调节机制。综上所述，DMF-DM-seq为全面研究单细胞mRNA和miRNA的表达异质性提供了有力的工具，将在基础和临床研究中得到广泛应用。

更新日期：2024-07-22

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