Mapping genotypes to chromatin accessibility profiles in single cells.

TitleMapping genotypes to chromatin accessibility profiles in single cells.
Publication TypeJournal Article
Year of Publication2024
AuthorsIzzo F, Myers RM, Ganesan S, Mekerishvili L, Kottapalli S, Prieto T, Eton EO, Botella T, Dunbar AJ, Bowman RL, Sotelo J, Potenski C, Mimitou EP, Stahl M, Ghaity-Beckley SEl, Arandela JA, Raviram R, Choi DC, Hoffman R, Chaligne R, Abdel-Wahab O, Smibert P, Ghobrial IM, Scandura JM, Marcellino B, Levine RL, Landau DA
JournalNature
Volume629
Issue8014
Pagination1149-1157
Date Published2024 May
ISSN1476-4687
KeywordsAnimals, Antigens, CD34, Cell Differentiation, Chromatin, Clone Cells, Epigenesis, Genetic, Epigenome, Female, Genome, Mitochondrial, Genotype, Genotyping Techniques, Hematopoiesis, Hematopoietic Stem Cells, Humans, Inflammation, Janus Kinase 2, Male, Megakaryocytes, Membrane Proteins, Mice, Mutation, Myeloproliferative Disorders, RNA, Single-Cell Analysis
Abstract

In somatic tissue differentiation, chromatin accessibility changes govern priming and precursor commitment towards cellular fates1-3. 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 epigenetic alterations across clonal populations in malignant and non-malignant contexts.

DOI10.1038/s41586-024-07388-y
Alternate JournalNature
PubMed ID38720070
PubMed Central IDPMC11139586
Grant ListR33 CA267219 / CA / NCI NIH HHS / United States
UG3 NS132139 / NS / NINDS NIH HHS / United States
P01 CA108671 / CA / NCI NIH HHS / United States
RM1 HG011014 / HG / NHGRI NIH HHS / United States
P50 CA254838 / CA / NCI NIH HHS / United States
R01 HL157387 / HL / NHLBI NIH HHS / United States
K08 HL163489 / HL / NHLBI NIH HHS / United States
T32 GM007739 / GM / NIGMS NIH HHS / United States

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