The transcriptional landscape of αβ T cell differentiation

• Published in: Nature immunology Vol. 14; no. 6; pp. 619 - 632
• Main Authors: Mingueneau, Michael, Kreslavsky, Taras, Gray, Daniel, Heng, Tracy, Cruse, Richard, Ericson, Jeffrey, Bendall, Sean, Spitzer, Matthew H, Nolan, Garry P, Kobayashi, Koichi, von Boehmer, Harald, Mathis, Diane, Benoist, Christophe, Best, Adam J, Knell, Jamie, Goldrath, Ananda, Joic, Vladimir, Koller, Daphne, Shay, Tal, Regev, Aviv, Cohen, Nadia, Brennan, Patrick, Brenner, Michael, Kim, Francis, Nageswara Rao, Tata, Wagers, Amy, Rothamel, Katherine, Ortiz-Lopez, Adriana, Bezman, Natalie A, Sun, Joseph C, Min-Oo, Gundula, Kim, Charlie C, Lanier, Lewis L, Miller, Jennifer, Brown, Brian, Merad, Miriam, Gautier, Emmanuel L, Jakubzick, Claudia, Randolph, Gwendalyn J, Monach, Paul, Blair, David A, Dustin, Michael L, Shinton, Susan A, Hardy, Richard R, Laidlaw, David, Collins, Jim, Gazit, Roi, Rossi, Derrick J, Malhotra, Nidhi, Sylvia, Katelyn, Kang, Joonsoo, Fletcher, Anne, Elpek, Kutlu, Bellemare-Pelletier, Angelique, Malhotra, Deepali, Turley, Shannon
• Format: Journal Article
• Language: English
• Published: United States Nature Publishing Group 01.06.2013
• Subjects: Analysis; Animals; Antigens, CD; Antigens, CD - immunology; Antigens, CD - metabolism; Antigens, Differentiation, T-Lymphocyte; Antigens, Differentiation, T-Lymphocyte - immunology; Antigens, Differentiation, T-Lymphocyte - metabolism; CD4-Positive T-Lymphocytes; CD4-Positive T-Lymphocytes - immunology; CD4-Positive T-Lymphocytes - metabolism; CD8-Positive T-Lymphocytes; CD8-Positive T-Lymphocytes - immunology; CD8-Positive T-Lymphocytes - metabolism; Cell Differentiation; Cell Differentiation - genetics; Cell Differentiation - immunology; Cell Lineage; Cell Lineage - genetics; Cell Lineage - immunology; Cell Proliferation; Cells, Cultured; Cluster Analysis; Flow Cytometry; Genetic aspects; Genetic transcription; Histocompatibility Antigens; Histocompatibility Antigens - genetics; Histocompatibility Antigens - immunology; Histocompatibility Antigens - metabolism; Lectins, C-Type; Lectins, C-Type - immunology; Lectins, C-Type - metabolism; Life Sciences; Male; Mice; Mice, Inbred C57BL; Oligonucleotide Array Sequence Analysis; Phosphorylation; Phosphorylation - immunology; Physiological aspects; Receptors, Antigen, T-Cell, alpha-beta; Receptors, Antigen, T-Cell, alpha-beta - genetics; Receptors, Antigen, T-Cell, alpha-beta - immunology; Receptors, Antigen, T-Cell, alpha-beta - metabolism; T cells; Thymocytes; Thymocytes - cytology; Thymocytes - immunology; Thymocytes - metabolism; Transcriptome; Transcriptome - genetics; Transcriptome - immunology; United States
• ISSN: 1529-2908; 1529-2916
• DOI: 10.1038/ni.2590

The differentiation of αβT cells from thymic precursors is a complex process essential for adaptive immunity. Here we exploited the breadth of expression data sets from the Immunological Genome Project to analyze how the differentiation of thymic precursors gives rise to mature T cell transcriptomes. We found that early T cell commitment was driven by unexpectedly gradual changes. In contrast, transit through the CD4(+)CD8(+) stage involved a global shutdown of housekeeping genes that is rare among cells of the immune system and correlated tightly with expression of the transcription factor c-Myc. Selection driven by major histocompatibility complex (MHC) molecules promoted a large-scale transcriptional reactivation. We identified distinct signatures that marked cells destined for positive selection versus apoptotic deletion. Differences in the expression of unexpectedly few genes accompanied commitment to the CD4(+) or CD8(+) lineage, a similarity that carried through to peripheral T cells and their activation, demonstrated by mass cytometry phosphoproteomics. The transcripts newly identified as encoding candidate mediators of key transitions help define the 'known unknowns' of thymocyte differentiation.