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Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

Nature Genetics volume 48, pages 11931203 (2016) | Download Citation

Abstract

We define the chromatin accessibility and transcriptional landscapes in 13 human primary blood cell types that span the hematopoietic hierarchy. Exploiting the finding that the enhancer landscape better reflects cell identity than mRNA levels, we enable 'enhancer cytometry' for enumeration of pure cell types from complex populations. We identify regulators governing hematopoietic differentiation and further show the lineage ontogeny of genetic elements linked to diverse human diseases. In acute myeloid leukemia (AML), chromatin accessibility uncovers unique regulatory evolution in cancer cells with a progressively increasing mutation burden. Single AML cells exhibit distinctive mixed regulome profiles corresponding to disparate developmental stages. A method to account for this regulatory heterogeneity identified cancer-specific deviations and implicated HOX factors as key regulators of preleukemic hematopoietic stem cell characteristics. Thus, regulome dynamics can provide diverse insights into hematopoietic development and disease.

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Acknowledgements

We thank C. Mazumdar and A. Raj for assistance with RNA-seq, A. Newman for expert assistance with CIBERSORT, and our laboratory members for discussion. We thank the Stanford Hematology Division Tissue Bank and the patients for donating their samples. M.R.C. acknowledges NIH training grant R25CA180993 and NIH F31 Predoctoral fellowship F31CA180659. J.D.B. acknowledges National Science Foundation Graduate Research Fellowships and NIH training grant T32HG000044 for support. M.P.S. acknowledges the NIH and NHGRI for funding through 5U54HG00455805. Research was also supported by the NIH (P50HG007735 to H.Y.C., W.J.G., and M.P.S.), UH2AR067676 (H.Y.C.), the Stanford Cancer Center (H.Y.C.), the Howard Hughes Medical Institute (H.Y.C. and J.K.P.), the Stinehart-Reed Foundation (R.M.), the Ludwig Institute (R.M.), and the NIH (R01CA18805 to R.M.). R.M. is a New York Stem Cell Foundation Robertson Investigator.

Author information

Author notes

    • M Ryan Corces
    •  & Jason D Buenrostro

    These authors contributed equally to this work.

    • Jason D Buenrostro
    • , Ravindra Majeti
    •  & Howard Y Chang

    These authors jointly directed this work.

Affiliations

  1. Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA.

    • M Ryan Corces
    • , Julie L Koenig
    •  & Ravindra Majeti
  2. Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.

    • M Ryan Corces
    • , Julie L Koenig
    •  & Ravindra Majeti
  3. Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.

    • M Ryan Corces
    • , Jason D Buenrostro
    • , Michael P Snyder
    • , William J Greenleaf
    •  & Howard Y Chang
  4. Department of Genetics, Stanford University, Stanford, California, USA.

    • Jason D Buenrostro
    • , Beijing Wu
    • , Peyton G Greenside
    • , Michael P Snyder
    • , Jonathan K Pritchard
    • , Anshul Kundaje
    •  & William J Greenleaf
  5. Broad Institute of MIT and Harvard, Harvard University, Cambridge, Massachusetts, USA.

    • Jason D Buenrostro
  6. Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, California, USA.

    • Peyton G Greenside
  7. Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.

    • Steven M Chan
  8. Department of Biology, Stanford University, Stanford, California, USA.

    • Jonathan K Pritchard
  9. Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.

    • Jonathan K Pritchard
  10. Department of Computer Science, Stanford University, Stanford, California, USA.

    • Anshul Kundaje

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Contributions

M.R.C., J.D.B., R.M., and H.Y.C. conceived the project. M.R.C. performed all cell sorting, RNA-seq, and CIBERSORT analysis, AML cell culture experiments, and mouse experiments. J.D.B. performed all ATAC-seq data analysis and regulatory network analysis, and oversaw all ATAC-seq library generation and protocol optimization performed by B.W. M.R.C. and J.L.K. performed DNA genotyping for patients with AML. J.D.B., P.G.G., and A.K. performed GWAS correlation analyses. W.J.G., M.P.S., and J.K.P. assisted with sequencing and study design. S.M.C. collected patient follow-up data and performed all survival analyses. M.R.C., J.D.B., R.M., and H.Y.C. wrote the manuscript with input from all authors.

Competing interests

Stanford University has filed a provisional patent application on the methods described, and J.D.B., H.Y.C., and W.J.G. are named as inventors. H.Y.C. and W.J.G. are founders of Epinomics.

Corresponding authors

Correspondence to Ravindra Majeti or Howard Y Chang.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–14 and Supplementary Note.

Excel files

  1. 1.

    Supplementary Table 1

    Normal donor information, cell sorting strategies, and sort purities.

  2. 2.

    Supplementary Table 2

    Enhancer cytometry signature matrix used for cell type deconvolution via CIBERSORT.

  3. 3.

    Supplementary Table 3

    Transcription factor and GWAS deviations across hematopoiesis.

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    Supplementary Table 4

    Transcription factor motif–gene association table and correlation values of RNA-seq.

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    Supplementary Table 5

    Patient clinical follow-up and genotyping data.

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    Supplementary Table 6

    Enhancer cytometry–derived fractional contributions of normal cell regulomes to AML samples.

  7. 7.

    Supplementary Table 7

    shRNA sequences used in this study.

Zip files

  1. 1.

    Supplementary Data: Compiled archive of motif images for hematopoiesis motifs obtained from JASPAR.

    The motif images for all transcription factors used in this study are provided for reference.

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DOI

https://doi.org/10.1038/ng.3646

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