美国哥伦比亚大学Peter A. Sims研究组近日取得一项新成果。经过不懈努力，他们的研究开发出了来自单个细胞核的RNA和DNA的可扩展共测序。该项研究成果发表在2025年2月12日出版的《自然—方法学》上。

研究团队介绍了一种高度可扩展的方法，用于核小体耗尽（DEFND-seq）后的DNA和表达联合分析。在DEFND-seq中，细胞核被核小体耗尽，标记并分离成单个液滴，用于信使RNA和基因组DNA条形码。一旦核小体被耗尽，随后的步骤可以进行广泛使用的10x Genomics液滴微流控技术和商业试剂盒。研究小组展示了从细胞系的数千个单个细胞核生产高复杂性mRNA和gDNA测序文库，新鲜和存档的手术标本将基因表达与拷贝数和单核苷酸变异联系起来。

据悉，直接研究基因型和表型之间关系的理想技术是同时分析RNA和DNA的全基因组和单细胞分辨率；然而，现有的工具缺乏对复杂肿瘤和组织进行综合分析所需的吞吐量。

附：英文原文

Title: Scalable co-sequencing of RNA and DNA from individual nuclei

Author: Olsen, Timothy R., Talla, Pranay, Sagatelian, Romella K., Furnari, Julia, Bruce, Jeffrey N., Canoll, Peter, Zha, Shan, Sims, Peter A.

Issue&Volume: 2025-02-12

Abstract: The ideal technology for directly investigating the relationship between genotype and phenotype would analyze both RNA and DNA genome-wide and with single-cell resolution; however, existing tools lack the throughput required for comprehensive analysis of complex tumors and tissues. We introduce a highly scalable method for jointly profiling DNA and expression following nucleosome depletion (DEFND-seq). In DEFND-seq, nuclei are nucleosome-depleted, tagmented and separated into individual droplets for messenger RNA and genomic DNA barcoding. Once nuclei have been depleted of nucleosomes, subsequent steps can be performed using the widely available 10x Genomics droplet microfluidic technology and commercial kits. We demonstrate the production of high-complexity mRNA and gDNA sequencing libraries from thousands of individual nuclei from cell lines, fresh and archived surgical specimens for associating gene expression with both copy number and single-nucleotide variants.

DOI: 10.1038/s41592-024-02579-x

Source: https://www.nature.com/articles/s41592-024-02579-x