GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells

• Published in: Cell stem cell Vol. 30; no. 5; pp. 722 - 740.e11
• Main Authors: Turkalj, Sven, Jakobsen, Niels Asger, Groom, Angus, Metzner, Marlen, Riva, Simone G., Gür, E. Ravza, Usukhbayar, Batchimeg, Salazar, Mirian Angulo, Hentges, Lance D., Mickute, Gerda, Clark, Kevin, Sopp, Paul, Davies, James O.J., Hughes, Jim R., Vyas, Paresh
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 04.05.2023
• Subjects: acute myeloid leukemia; cancer evolution; Chromatin; chromatin accessibility; clonal tracking; epigenomics; Gene Expression Regulation; Genomics; Genotype; Humans; leukemia stem cells; Leukemia, Myeloid, Acute; single-cell ATAC-seq; single-cell technologies; somatic mutation; Transposases - genetics; Transposases - metabolism; tumor heterogeneity; single-cell ATAC-seq; leukemia stem cells; acute myeloid leukemia; chromatin accessibility; single-cell technologies; epigenomics; cancer evolution; somatic mutation; tumor heterogeneity; clonal tracking
• ISSN: 1934-5909; 1875-9777; 1875-9777
• DOI: 10.1016/j.stem.2023.04.012

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 efficiently 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 accurate 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 evolution, 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. [Display omitted] •High-sensitivity genomic genotyping linked to scATAC-seq in single malignant cells•Characterization of epigenetic variation as preleukemic clones transform to leukemia•Differentiation of specific leukemic clones is delayed at an LSC-like chromatin state•Genomic elements perturbed in LSC-like clones relate to stemness and differentiation Turkalj, Jakobsen, et al. develop a method linking clonal identities of single cells to their chromatin accessibility and study how epigenetic landscapes change with clonal evolution in human acute myeloid leukemia, revealing altered accessibility of genes and transcription factor motifs linked to leukemia stemness downstream of cooperating somatic mutations.