GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells
GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells
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DOI：
10.1016/j.stem.2023.04.012
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发表时间：
2023-05-04
期刊：
影响因子：
23.9
通讯作者：
Vyas, Paresh
中科院分区：
文献类型：
--
作者：
Turkalj, Sven;Jakobsen, Niels Asger;Vyas, Paresh
了解克隆进化和癌症发展需要实验方法来表征基因调控的体细胞突变的后果。然而，目前还不存在将高含量染色质可及性与单细胞中的高置信度基因分型有效联系起来的方法。为了解决这一问题，我们开发了转座酶可降解染色质检测试剂盒（GTAC）的基因分型，实现了多个扩增位点的准确突变检测，以及强大的染色质可及性读数。我们将GTAC应用于原发性急性髓系白血病，获得了88%细胞中多突变的高质量染色质可及性谱和克隆身份。我们追踪了整个克隆进化过程中的染色质变化，显示了不同克隆对不同分化阶段的限制。此外，我们确定了与驱动突变的特定组合相关的转录因子基序可及性的开关，该开关使转化的祖细胞偏向白血病干细胞样染色质状态。GTAC是一个强大的工具，研究克隆异质性在广泛的癌前病变和肿瘤条件。
Understanding clonal evolution and cancer development requires experimental approaches for characterizing the consequences of somatic mutations on gene regulation. However, no methods currently exist that effi-ciently link high-content chromatin accessibility with high-confidence genotyping in single cells. To address this, we developed Genotyping with the Assay for Transposase-Accessible Chromatin (GTAC), enabling accu-rate mutation detection at multiple amplified loci, coupled with robust chromatin accessibility readout. We applied GTAC to primary acute myeloid leukemia, obtaining high-quality chromatin accessibility profiles and clonal identities for multiple mutations in 88% of cells. We traced chromatin variation throughout clonal evolu-tion, showing the restriction of different clones to distinct differentiation stages. Furthermore, we identified switches in transcription factor motif accessibility associated with a specific combination of driver mutations, which biased transformed progenitors toward a leukemia stem cell-like chromatin state. GTAC is a powerful tool to study clonal heterogeneity across a wide spectrum of pre-malignant and neoplastic conditions.