May 19, 2024
Mapping genotypes to chromatin accessibility profiles in single cells – Nature

Mapping genotypes to chromatin accessibility profiles in single cells – Nature

  • Corces, M. R. et al. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat. Genet. 48, 1193–1203 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Buenrostro, J. D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486–490 (2015).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ma, S. et al. Chromatin potential identified by shared single-cell profiling of RNA and chromatin. Cell 183, 1103–1116 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Izzo, F. et al. DNA methylation disruption reshapes the hematopoietic differentiation landscape. Nat. Genet. 52, 378–387 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nam, A. S. et al. Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation. Nat. Genet. 54, 1514–1526 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mullally, A. et al. Physiological Jak2V617F expression causes a lethal myeloproliferative neoplasm with differential effects on hematopoietic stem and progenitor cells. Cancer Cell 17, 584–596 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gerritsen, M. et al. RUNX1 mutations enhance self-renewal and block granulocytic differentiation in human in vitro models and primary AMLs. Blood Adv. 3, 320–332 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jaiswal, S. et al. Age-related clonal hematopoiesis associated with adverse outcomes. N. Engl. J. Med. 371, 2488–2498 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Levine, R. L. et al. Activating mutation in the tyrosine kinase JAK2 in polycythemia vera, essential thrombocythemia, and myeloid metaplasia with myelofibrosis. Cancer Cell 7, 387–397 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kralovics, R. et al. A gain-of-function mutation of JAK2 in myeloproliferative disorders. N. Engl. J. Med. 352, 1779–1790 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • James, C. et al. A unique clonal JAK2 mutation leading to constitutive signalling causes polycythaemia vera. Nature 434, 1144–1148 (2005).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Baxter, E. J. et al. Acquired mutation of the tyrosine kinase JAK2 in human myeloproliferative disorders. Lancet 365, 1054–1061 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Panteli, K. E. et al. Serum interleukin (IL)-1, IL-2, sIL-2Ra, IL-6 and thrombopoietin levels in patients with chronic myeloproliferative diseases. Br. J. Haematol. 130, 709–715 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jamieson, C. H. M. et al. The JAK2 V617F mutation occurs in hematopoietic stem cells in polycythemia vera and predisposes toward erythroid differentiation. Proc. Natl Acad. Sci. USA 103, 6224–6229 (2006).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Giustacchini, A. et al. Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia. Nat. Med. 23, 692–702 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rodriguez-Meira, A. et al. Unravelling intratumoral heterogeneity through high-sensitivity single-cell mutational analysis and parallel RNA sequencing. Mol. Cell 73, 1292–1305 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rodriguez-Meira, A., O’Sullivan, J., Rahman, H. & Mead, A. J. TARGET-seq: a protocol for high-sensitivity single-cell mutational analysis and parallel RNA sequencing. STAR Protoc. 1, 100125 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • van Galen, P. et al. Single-cell RNA-seq reveals AML hierarchies relevant to disease progression and immunity. Cell 176, 1265–1281 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nam, A. S. et al. Somatic mutations and cell identity linked by genotyping of transcriptomes. Nature 571, 355–360 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Morita, K. et al. Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics. Nat. Commun. 11, 5327 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Miles, L. A. et al. Single-cell mutation analysis of clonal evolution in myeloid malignancies. Nature 587, 477–482 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Van Egeren, D. et al. Reconstructing the lineage histories and differentiation trajectories of individual cancer cells in myeloproliferative neoplasms. Cell Stem Cell 28, 514–523 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Van Egeren, D. et al. Transcriptional differences between JAK2-V617F and wild-type bone marrow cells in patients with myeloproliferative neoplasms. Exp. Hematol. 107, 14–19 (2022).

    Article 
    PubMed 

    Google Scholar
     

  • Turkalj, S. et al. GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells. Cell Stem Cell 30, 722–740 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Mackinnon, R. N. et al. Genome organization and the role of centromeres in evolution of the erythroleukaemia cell line HEL. Evol. Med. Publ. Health 2013, 225–240 (2013).

    Article 

    Google Scholar
     

  • Stuart, T., Srivastava, A., Madad, S., Lareau, C. A. & Satija, R. Single-cell chromatin state analysis with Signac. Nat. Methods 18, 1333–1341 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mustjoki, S. et al. JAK2V617F mutation and spontaneous megakaryocytic or erythroid colony formation in patients with essential thrombocythaemia (ET) or polycythaemia vera (PV). Leuk. Res. 33, 54–59 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Schieber, M., Crispino, J. D. & Stein, B. Myelofibrosis in 2019: moving beyond JAK2 inhibition. Blood Cancer J. 9, 74 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pardanani, A. & Tefferi, A. Definition and management of ruxolitinib treatment failure in myelofibrosis. Blood Cancer J. 4, e268 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cervantes, F. et al. Three-year efficacy, safety, and survival findings from COMFORT-II, a phase 3 study comparing ruxolitinib with best available therapy for myelofibrosis. Blood 122, 4047–4053 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Mondet, J., Hussein, K. & Mossuz, P. Circulating cytokine levels as markers of inflammation in philadelphia negative myeloproliferative neoplasms: diagnostic and prognostic interest. Mediators Inflamm. 2015, 670580 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tefferi, A. et al. Circulating interleukin (IL)-8, IL-2R, IL-12, and IL-15 levels are independently prognostic in primary myelofibrosis: a comprehensive cytokine profiling study. J. Clin. Oncol. 29, 1356–1363 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Verstovsek, S. et al. A double-blind, placebo-controlled trial of ruxolitinib for myelofibrosis. N. Engl. J. Med. 366, 799–807 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vukotić, M. et al. Inhibition of proinflammatory signaling impairs fibrosis of bone marrow mesenchymal stromal cells in myeloproliferative neoplasms. Exp. Mol. Med. 54, 273–284 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dunbar, A. J. et al. CXCL8/CXCR2 signaling mediates bone marrow fibrosis and is a therapeutic target in myelofibrosis. Blood 141, 2508–2519 (2023).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hu, W.-H. et al. NIBP, a novel NIK and IKKβ-binding protein that enhances NF-κB activation. J. Biol. Chem. 280, 29233–29241 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jeanpierre, S. et al. The quiescent fraction of chronic myeloid leukemic stem cells depends on BMPR1B, Stat3 and BMP4-niche signals to persist in patients in remission. Haematologica 106, 111–122 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wu, Y. et al. The prognostic value of matrix metalloproteinase-7 and matrix metalloproteinase-15 in acute myeloid leukemia. J. Cell. Biochem. 120, 10613–10624 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ikeda, M., Chiba, S., Ohashi, K. & Mizuno, K. Furry protein promotes aurora A-mediated Polo-like kinase 1 activation. J. Biol. Chem. 287, 27670–27681 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Komorowska, K. et al. Hepatic leukemia factor maintains quiescence of hematopoietic stem cells and protects the stem cell pool during regeneration. Cell Rep. 21, 3514–3523 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ficara, F. et al. Pbx1 restrains myeloid maturation while preserving lymphoid potential in hematopoietic progenitors. J. Cell Sci. 126, 3181–3191 (2013).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ficara, F., Murphy, M. J., Lin, M. & Cleary, M. L. Pbx1 regulates self-renewal of long-term hematopoietic stem cells by maintaining their quiescence. Cell Stem Cell 2, 484–496 (2008).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kleppe, M. et al. JAK-STAT pathway activation in malignant and nonmalignant cells contributes to MPN pathogenesis and therapeutic response. Cancer Discov. 5, 316–331 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kleppe, M. et al. Dual targeting of oncogenic activation and inflammatory signaling increases therapeutic efficacy in myeloproliferative neoplasms. Cancer Cell 33, 785–787 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dunbar, A. J. et al. Jak2V617F reversible activation shows its essential requirement in myeloproliferative neoplasms. Cancer Discov. https://doi.org/10.1158/2159-8290.CD-22-0952 (2024).

  • Wernig, G. et al. Unifying mechanism for different fibrotic diseases. Proc. Natl Acad. Sci. USA 114, 4757–4762 (2017).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Burda, P., Laslo, P. & Stopka, T. The role of PU.1 and GATA-1 transcription factors during normal and leukemogenic hematopoiesis. Leukemia 24, 1249–1257 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zhang, P. et al. Negative cross-talk between hematopoietic regulators: GATA proteins repress PU.1. Proc. Natl Acad. Sci. USA 96, 8705–8710 (1999).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Basak, A. & Sankaran, V. G. Regulation of the fetal hemoglobin silencing factor BCL11A. Ann. N. Y. Acad. Sci. 1368, 25–30 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sankaran, V. G. et al. Human fetal hemoglobin expression is regulated by the developmental stage-specific repressor BCL11A. Science 322, 1839–1842 (2008).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Hoffman, R. et al. Fetal hemoglobin in polycythemia vera: cellular distribution in 50 unselected patients. Blood 53, 1148–1155 (1979).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Mimitou, E. P. et al. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells. Nat. Biotechnol. 39, 1246–1258 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Baum, C. M., Weissman, I. L., Tsukamoto, A. S., Buckle, A. M. & Peault, B. Isolation of a candidate human hematopoietic stem-cell population. Proc. Natl Acad. Sci. USA 89, 2804–2808 (1992).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Asch, A. S., Barnwell, J., Silverstein, R. L. & Nachman, R. L. Isolation of the thrombospondin membrane receptor. J. Clin. Invest. 79, 1054–1061 (1987).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Valet, C. et al. Adipocyte fatty acid transfer supports megakaryocyte maturation. Cell Rep. 32, 107875 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Mustjoki, S. & Young, N. S. Somatic mutations in “benign” disease. N. Engl. J. Med. 384, 2039–2052 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Martincorena, I. et al. Somatic mutant clones colonize the human esophagus with age. Science 362, 911–917 (2018).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Martincorena, I. et al. Tumor evolution. High burden and pervasive positive selection of somatic mutations in normal human skin. Science 348, 880–886 (2015).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Granja, J. M. et al. ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis. Nat. Genet. 53, 403–411 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mulè, M. P., Martins, A. J. & Tsang, J. S. Normalizing and denoising protein expression data from droplet-based single cell profiling. Nat. Commun. 13, 2099 (2022).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stoeckius, M. et al. Cell hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. Genome Biol. 19, 224 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Thibodeau, A. et al. AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data. Genome Biol. 22, 252 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888–1902 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cao, J. et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature 566, 496–502 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schep, A. N., Wu, B., Buenrostro, J. D. & Greenleaf, W. J. chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data. Nat. Methods 14, 975–978 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pliner, H. A. et al. Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data. Mol. Cell 71, 858–871 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34, 525–527 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Melsted, P. et al. Modular, efficient and constant-memory single-cell RNA-seq preprocessing. Nat. Biotechnol. 39, 813–818 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Gehring, J., Hwee Park, J., Chen, S., Thomson, M. & Pachter, L. Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins. Nat. Biotechnol. 38, 35–38 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lareau, C. A. et al. Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nat. Biotechnol. 39, 451–461 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ludwig, L. S. et al. Lineage tracing in humans enabled by mitochondrial mutations and single-cell genomics. Cell 176, 1325–1339 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Svetnik, V. et al. Random forest: a classification and regression tool for compound classification and QSAR modeling. J. Chem. Inf. Comput. Sci. 43, 1947–1958 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Satpathy, A. T. et al. Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion. Nat. Biotechnol. 37, 925–936 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Plummer, N. W. et al. Expanding the power of recombinase-based labeling to uncover cellular diversity. Development 142, 4385–4393 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ruzankina, Y. et al. Deletion of the developmentally essential gene ATR in adult mice leads to age-related phenotypes and stem cell loss. Cell Stem Cell 1, 113–126 (2007).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kozlov, A., Alves, J. M., Stamatakis, A. & Posada, D. CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data. Genome Biol. 23, 37 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

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