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Transcriptome and chromatin landscape of iNKT cells are shaped by subset differentiation and antigen exposure

Author

Listed:
  • Mallory Paynich Murray

    (La Jolla Institute for Immunology)

  • Isaac Engel

    (La Jolla Institute for Immunology)

  • Grégory Seumois

    (La Jolla Institute for Immunology)

  • Sara Herrera-De la Mata

    (La Jolla Institute for Immunology)

  • Sandy Lucette Rosales

    (La Jolla Institute for Immunology)

  • Ashu Sethi

    (La Jolla Institute for Immunology)

  • Ashmitaa Logandha Ramamoorthy Premlal

    (La Jolla Institute for Immunology)

  • Goo-Young Seo

    (La Jolla Institute for Immunology)

  • Jason Greenbaum

    (La Jolla Institute for Immunology)

  • Pandurangan Vijayanand

    (La Jolla Institute for Immunology
    University of Southampton, Faculty of Medicine
    University of California San Diego)

  • James P. Scott-Browne

    (La Jolla Institute for Immunology
    National Jewish Health)

  • Mitchell Kronenberg

    (La Jolla Institute for Immunology
    University of California San Diego)

Abstract

Invariant natural killer T cells (iNKT cells) differentiate into thymic and peripheral NKT1, NKT2 and NKT17 subsets. Here we use RNA-seq and ATAC-seq analyses and show iNKT subsets are similar, regardless of tissue location. Lung iNKT cell subsets possess the most distinct location-specific features, shared with other innate lymphocytes in the lung, possibly consistent with increased activation. Following antigenic stimulation, iNKT cells undergo chromatin and transcriptional changes delineating two populations: one similar to follicular helper T cells and the other NK or effector like. Phenotypic analysis indicates these changes are observed long-term, suggesting that iNKT cells gene programs are not fixed, but they are capable of chromatin remodeling after antigen to give rise to additional subsets.

Suggested Citation

  • Mallory Paynich Murray & Isaac Engel & Grégory Seumois & Sara Herrera-De la Mata & Sandy Lucette Rosales & Ashu Sethi & Ashmitaa Logandha Ramamoorthy Premlal & Goo-Young Seo & Jason Greenbaum & Pandur, 2021. "Transcriptome and chromatin landscape of iNKT cells are shaped by subset differentiation and antigen exposure," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-21574-w
    DOI: 10.1038/s41467-021-21574-w
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