Lindenhofer Dominik, Bauman Julia R, Hawkins John A, Fitzgerald Donnacha, Yildiz Umut, Jung Haeyeon, Korosteleva Anastasiia, Marttinen Mikael, Kueblbeck Moritz, Zaugg Judith B, Noh Kyung-Min, Dietrich Sascha, Huber Wolfgang, Stegle Oliver, Steinmetz Lars M
Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany.
Nat Methods. 2025 Sep 1. doi: 10.1038/s41592-025-02805-0.
Genetic variants (both coding and noncoding) can impact gene function and expression, driving disease mechanisms such as cancer progression. The systematic study of endogenous genetic variants is hindered by inefficient precision editing tools, combined with technical limitations in confidently linking genotypes to gene expression at single-cell resolution. We developed single-cell DNA-RNA sequencing (SDR-seq) to simultaneously profile up to 480 genomic DNA loci and genes in thousands of single cells, enabling accurate determination of coding and noncoding variant zygosity alongside associated gene expression changes. Using SDR-seq, we associate coding and noncoding variants with distinct gene expression in human induced pluripotent stem cells. Furthermore, we demonstrate that in primary B cell lymphoma samples, cells with a higher mutational burden exhibit elevated B cell receptor signaling and tumorigenic gene expression. SDR-seq provides a powerful platform to dissect regulatory mechanisms encoded by genetic variants, advancing our understanding of gene expression regulation and its implications for disease.
基因变异（包括编码和非编码变异）会影响基因功能和表达，推动诸如癌症进展等疾病机制。对内源性基因变异的系统研究受到低效精准编辑工具的阻碍，同时在将基因型与单细胞分辨率下的基因表达进行可靠关联方面存在技术限制。我们开发了单细胞DNA-RNA测序（SDR-seq）技术，可在数千个单细胞中同时分析多达480个基因组DNA位点和基因，能够准确确定编码和非编码变异的纯合性以及相关的基因表达变化。利用SDR-seq技术，我们将人类诱导多能干细胞中的编码和非编码变异与不同的基因表达相关联。此外，我们证明在原发性B细胞淋巴瘤样本中，具有较高突变负荷的细胞表现出更高的B细胞受体信号传导和致瘤基因表达。SDR-seq提供了一个强大的平台来剖析由基因变异编码的调控机制，增进我们对基因表达调控及其对疾病影响的理解。
