美国纽约基因组中心Dan A. Landau等研究人员合作实现单细胞中基因型与染色质可及性图谱的映射。2024年5月8日，《自然》杂志在线发表了这项成果。

为了描绘体细胞突变如何破坏人类克隆外生长的表观遗传景观，研究人员开发了具有单细胞染色质可及性的目标位点基因分型（GoT-ChA）。这种高通量平台可在一次检测中将数千个细胞的基因型与单细胞分辨率染色质可及性联系起来。研究人员将GoT-ChA应用于骨髓增殖性肿瘤患者的CD34⁺细胞，这些细胞具有JAK2^V617F突变的造血功能。对野生型和JAK2^V617F突变型祖细胞的可及性差异分析表明，突变型造血前体中存在细胞内在和细胞状态特异性转变，包括造血干细胞中的细胞内在促炎症特征，以及巨核细胞祖细胞中独特的促纤维化炎症染色质景观。

线粒体基因组图谱和细胞表面蛋白表达测量的整合，通过归因法将基因分型扩展到DOGMA-seq，实现了基因型、染色质可及性、RNA表达和细胞表面蛋白表达的单细胞捕获。总之，该研究表明，JAK2^V617F突变会以细胞内在和细胞类型特异的方式导致表观遗传学重构，从而影响炎症状态和分化轨迹。研究人员设想，GoT-ChA将有助于未来对恶性和非恶性情况下，不同克隆群体中体细胞突变与表观遗传改变之间的重要联系进行广泛研究。

研究人员表示，在体细胞组织分化过程中，染色质可及性的变化决定着细胞命运的启动和前体确立。因此，体细胞突变很可能会改变染色质可及性模式，因为它们会破坏分化拓扑结构，导致异常克隆生长。然而，由于突变细胞和野生型细胞混杂在一起，要确定体细胞突变对人类样本表观基因组的影响具有挑战性。

附：英文原文

Title: Mapping genotypes to chromatin accessibility profiles in single cells

Author: Izzo, Franco, Myers, Robert M., Ganesan, Saravanan, Mekerishvili, Levan, Kottapalli, Sanjay, Prieto, Tamara, Eton, Elliot O., Botella, Theo, Dunbar, Andrew J., Bowman, Robert L., Sotelo, Jesus, Potenski, Catherine, Mimitou, Eleni P., Stahl, Maximilian, El Ghaity-Beckley, Sebastian, Arandela, JoAnn, Raviram, Ramya, Choi, Daniel C., Hoffman, Ronald, Chalign, Ronan, Abdel-Wahab, Omar, Smibert, Peter, Ghobrial, Irene M., Scandura, Joseph M., Marcellino, Bridget, Levine, Ross L., Landau, Dan A.

Issue&Volume: 2024-05-08

Abstract: In somatic tissue differentiation, chromatin accessibility changes govern priming and precursor commitment towards cellular fates1,2,3. Therefore, somatic mutations are likely to alter chromatin accessibility patterns, as they disrupt differentiation topologies leading to abnormal clonal outgrowth. However, defining the impact of somatic mutations on the epigenome in human samples is challenging due to admixed mutated and wild-type cells. Here, to chart how somatic mutations disrupt epigenetic landscapes in human clonal outgrowths, we developed genotyping of targeted loci with single-cell chromatin accessibility (GoT–ChA). This high-throughput platform links genotypes to chromatin accessibility at single-cell resolution across thousands of cells within a single assay. We applied GoT–ChA to CD34+ cells from patients with myeloproliferative neoplasms with JAK2V617F-mutated haematopoiesis. Differential accessibility analysis between wild-type and JAK2V617F-mutant progenitors revealed both cell-intrinsic and cell-state-specific shifts within mutant haematopoietic precursors, including cell-intrinsic pro-inflammatory signatures in haematopoietic stem cells, and a distinct profibrotic inflammatory chromatin landscape in megakaryocytic progenitors. Integration of mitochondrial genome profiling and cell-surface protein expression measurement allowed expansion of genotyping onto DOGMA-seq through imputation, enabling single-cell capture of genotypes, chromatin accessibility, RNA expression and cell-surface protein expression. Collectively, we show that the JAK2V617F mutation leads to epigenetic rewiring in a cell-intrinsic and cell type-specific manner, influencing inflammation states and differentiation trajectories. We envision that GoT–ChA will empower broad future investigations of the critical link between somatic mutations and

DOI: 10.1038/s41586-024-07388-y

Source: https://www.nature.com/articles/s41586-024-07388-y