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Transcript-indexed ATAC-seq for precision immune profiling

Nature Medicine volume 24, pages 580–590 (2018)Cite this article

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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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Fig. 1: T-ATAC-seq generates open chromatin and TCR profiles in single T cells.
Fig. 2: T-ATAC-seq identifies epigenomic signatures of clonal Jurkat T cells.
Fig. 3: Epigenomic landscape of ensemble human CD4+ T cell subtypes.
Fig. 4: Single-cell epigenomic and TCR profiling of human CD4+ T cells.
Fig. 5: T-ATAC-seq identifies epigenomic signatures of clonal leukemic T cells in patient samples.

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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).

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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.

Authors and 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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  1. Ansuman T. Satpathy
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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.

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

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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.

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Satpathy, A.T., Saligrama, N., Buenrostro, J.D. et al. Transcript-indexed ATAC-seq for precision immune profiling. Nat Med 24, 580–590 (2018). https://doi.org/10.1038/s41591-018-0008-8

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