Abstract

T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide–major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4+ T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy.

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Acknowledgements

We thank members of the Chang, Davis and Greenleaf laboratories, including Y. Shen and K. Qu, for helpful discussions. We thank X. Ji, D. Wagh and J. Coller at the Stanford Functional Genomics Facility. This work was supported by the Parker Institute for Cancer Immunotherapy (A.T.S., H.Y.C. and M.M.D.), the US National Institutes of Health (NIH) grants P50HG007735 (H.Y.C. and W.J.G.), 5U19AI057229 (M.M.D.), and U19AI057266 (W.J.G), and the Scleroderma Research Foundation (H.Y.C.). A.T.S. was supported by a Parker Bridge Scholar Award from the Parker Institute for Cancer Immunotherapy and a Cancer Research Institute Irvington Fellowship from the Cancer Research Institute. N.S. was supported by the National Multiple Sclerosis Society Postdoctoral Fellowship. J.D.B. acknowledges the Broad Institute Fellows and Harvard Society of Fellows programs for funding. M.R.C. was supported by a grant from the Leukemia and Lymphoma Society Career Development Program. W.J.G. is a Chan Zuckerberg Biohub investigator. M.M.D. is an investigator of the Howard Hughes Medical Institute. Sequencing was performed by the Stanford Functional Genomics Facility (which is supported by NIH grant S10OD018220).

Author information

Author notes

  1. These authors contributed equally: Ansuman T. Satpathy, Naresha Saligrama, Jason D. Buenrostro.

  2. These authors jointly supervised this work: Mark M. Davis, Howard Y. Chang.

Affiliations

  1. Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA

    • Ansuman T. Satpathy
    • , Yuning Wei
    • , Jeffrey M. Granja
    • , Rui Li
    • , Yanyan Qi
    • , Kevin R. Parker
    • , Maxwell R. Mumbach
    • , David G. Gennert
    • , Alicia N. Schep
    • , M. Ryan Corces
    •  & Howard Y. Chang
  2. Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA

    • Ansuman T. Satpathy
  3. Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA

    • Naresha Saligrama
    • , William S. Serratelli
    •  & Mark M. Davis
  4. Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA

    • Jason D. Buenrostro
    •  & Caleb A. Lareau
  5. Harvard Society of Fellows, Harvard University, Cambridge, MA, USA

    • Jason D. Buenrostro
  6. Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA

    • Yuning Wei
    • , Adam J. Rubin
    • , Rui Li
    • , Yanyan Qi
    • , Kevin R. Parker
    • , M. Ryan Corces
    • , Youn H. Kim
    • , Paul A. Khavari
    •  & Howard Y. Chang
  7. Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA

    • Beijing Wu
    • , Jeffrey M. Granja
    • , Maxwell R. Mumbach
    • , David G. Gennert
    • , Alicia N. Schep
    • , William J. Greenleaf
    •  & Howard Y. Chang
  8. Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA

    • Jeffrey M. Granja
  9. Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA

    • Michael S. Khodadoust
  10. Department of Applied Physics, Stanford University, Stanford, CA, USA

    • William J. Greenleaf
  11. Chan Zuckerberg Biohub, San Francisco, CA, USA

    • William J. Greenleaf
  12. Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA

    • Mark M. Davis
  13. Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA

    • Mark M. Davis

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Contributions

A.T.S., N.S., M.M.D. and H.Y.C. conceived the project; A.T.S, N.S. and J.D.B. performed experiments and analyzed data; B.W. and Y.Q. performed T-ATAC-seq experiments; R.L., J.M.G., M.R.M. and D.G.G. performed ensemble ATAC-seq experiments and analyzed data; W.S.S. performed TCR-seq experiments; Y.W., A.J.R., K.R.P., C.A.L., A.N.S. and M.R.C. analyzed data; M.S.K. and Y.H.K. obtained clinical specimens; H.Y.C, M.M.D, W.J.G. and P.A.K. guided experiments and data analysis; and A.T.S, M.M.D. and H.Y.C. wrote the manuscript with input from all of the authors.

Competing interests

H.Y.C. and W.J.G. are founders of Epinomics and members of its scientific advisory board. H.Y.C. is a founder of Accent Therapeutics and a member of its scientific advisory board. H.Y.C. is a member of the scientific advisory board of Spring Discovery.

Corresponding authors

Correspondence to Mark M. Davis or Howard Y. Chang.

Supplementary information

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