EOMES interacts with RUNX3 and BRG1 to promote innate memory cell formation through epigenetic reprogramming

Nicolas Istaces, Marion Splittgerber, Viviana Lima Silva, Muriel Nguyen, Séverine Thomas, Aurore Le, Younes Achouri, Emilie Calonne, Matthieu Defrance, François Fuks, Stanislas Goriely () and Abdulkader Azouz
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Nicolas Istaces: Institute for Medical Immunology (IMI)
Marion Splittgerber: Institute for Medical Immunology (IMI)
Viviana Lima Silva: Institute for Medical Immunology (IMI)
Muriel Nguyen: Institute for Medical Immunology (IMI)
Séverine Thomas: Institute for Medical Immunology (IMI)
Aurore Le: Institute for Medical Immunology (IMI)
Younes Achouri: Institut de Duve
Emilie Calonne: Laboratory of Cancer Epigenetics
Matthieu Defrance: Interuniversity Institute of Bioinformatics in Brussels (IB2)
François Fuks: Laboratory of Cancer Epigenetics
Stanislas Goriely: Institute for Medical Immunology (IMI)
Abdulkader Azouz: Institute for Medical Immunology (IMI)

Nature Communications, 2019, vol. 10, issue 1, 1-17

Abstract: Abstract Memory CD8+ T cells have the ability to provide lifelong immunity against pathogens. Although memory features generally arise after challenge with a foreign antigen, naïve CD8 single positive (SP) thymocytes may acquire phenotypic and functional characteristics of memory cells in response to cytokines such as interleukin-4. This process is associated with the induction of the T-box transcription factor Eomesodermin (EOMES). However, the underlying molecular mechanisms remain ill-defined. Using epigenomic profiling, we show that these innate memory CD8SP cells acquire only a portion of the active enhancer repertoire of conventional memory cells. This reprograming is secondary to EOMES recruitment, mostly to RUNX3-bound enhancers. Furthermore, EOMES is found within chromatin-associated complexes containing BRG1 and promotes the recruitment of this chromatin remodelling factor. Also, the in vivo acquisition of EOMES-dependent program is BRG1-dependent. In conclusion, our results support a strong epigenetic basis for the EOMES-driven establishment of CD8+ T cell innate memory program.

Date: 2019
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DOI: 10.1038/s41467-019-11233-6

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