Dustin, M. L. The immunological synapse. Cancer Immunol. Res. 2, 1023–1033 (2014).
Google Scholar
Pasqual, G. et al. Monitoring T cell-dendritic cell interactions in vivo by intercellular enzymatic labelling. Nature 553, 496–500 (2018).
Google Scholar
Greenwald, I. & Rubin, G. M. Making a difference: the role of cell-cell interactions in establishing separate identities for equivalent cells. Cell 68, 271–281 (1992).
Google Scholar
Sudhof, T. C. & Malenka, R. C. Understanding synapses: past, present, and future. Neuron 60, 469–476 (2008).
Google Scholar
Victora, G. D. & Nussenzweig, M. C. Germinal centers. Annu. Rev. Immunol. 30, 429–457 (2012).
Google Scholar
Bilate, A. M. et al. T cell receptor is required for differentiation, but not maintenance, of intestinal CD4+ intraepithelial lymphocytes. Immunity 53, 1001–1014 (2020).
Google Scholar
Niec, R. E., Rudensky, A. Y. & Fuchs, E. Inflammatory adaptation in barrier tissues. Cell 184, 3361–3375 (2021).
Google Scholar
Mempel, T. R., Henrickson, S. E. & Von Andrian, U. H. T-cell priming by dendritic cells in lymph nodes occurs in three distinct phases. Nature 427, 154–159 (2004).
Google Scholar
Moses, L. & Pachter, L. Museum of spatial transcriptomics. Nat. Methods 19, 534–546 (2022).
Google Scholar
Efremova, M., Vento-Tormo, M., Teichmann, S. A. & Vento-Tormo, R. CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes. Nat. Protoc. 15, 1484–1506 (2020).
Google Scholar
Liu, D. S., Loh, K. H., Lam, S. S., White, K. A. & Ting, A. Y. Imaging trans-cellular neurexin-neuroligin interactions by enzymatic probe ligation. PLoS ONE 8, e52823 (2013).
Google Scholar
Ombrato, L. et al. Metastatic-niche labelling reveals parenchymal cells with stem features. Nature 572, 603–608 (2019).
Google Scholar
Zhang, S. et al. Monitoring of cell-cell communication and contact history in mammals. Science 378, eabo5503 (2022).
Google Scholar
Bechtel, T. J., Reyes-Robles, T., Fadeyi, O. O. & Oslund, R. C. Strategies for monitoring cell–cell interactions. Nat. Chem. Biol. 17, 641–652 (2021).
Google Scholar
Yassin, M. et al. Upregulation of PD-1 follows tumour development in the AOM/DSS model of inflammation-induced colorectal cancer in mice. Immunology 158, 35–46 (2019).
Google Scholar
Weizman, O. E. et al. Developing synthetic tools to decipher the tumor-immune interactome. Proc. Natl Acad. Sci. USA 120, e2306632120 (2023).
Google Scholar
Dorr, B. M., Ham, H. O., An, C., Chaikof, E. L. & Liu, D. R. Reprogramming the specificity of sortase enzymes. Proc. Natl Acad. Sci. USA 111, 13343–13348 (2014).
Google Scholar
Guimaraes, C. P. et al. Site-specific C-terminal and internal loop labeling of proteins using sortase-mediated reactions. Nat. Protoc. 8, 1787–1799 (2013).
Google Scholar
Dustin, M. L. & Depoil, D. New insights into the T cell synapse from single molecule techniques. Nat. Rev. Immunol. 11, 672–684 (2011).
Google Scholar
Madisen, L. et al. A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nat. Neurosci. 13, 133–140 (2010).
Google Scholar
Robertson, J. M., Jensen, P. E. & Evavold, B. D. DO11.10 and OT-II T cells recognize a C-terminal ovalbumin 323-339 epitope. J. Immunol. 164, 4706–4712 (2000).
Google Scholar
Merkenschlager, J. et al. Dynamic regulation of TFH selection during the germinal centre reaction. Nature 591, 458–463 (2021).
Google Scholar
Stoll, S., Delon, J., Brotz, T. M. & Germain, R. N. Dynamic imaging of T cell-dendritic cell interactions in lymph nodes. Science 296, 1873–1876 (2002).
Google Scholar
Frederico, B. et al. DNGR-1-tracing marks an ependymal cell subset with damage-responsive neural stem cell potential. Dev. Cell 57, 1957–1975 (2022).
Google Scholar
Rubtsov, Y. P. et al. Stability of the regulatory T cell lineage in vivo. Science 329, 1667–1671 (2010).
Google Scholar
Aghajani, K., Keerthivasan, S., Yu, Y. & Gounari, F. Generation of CD4CreERT2 transgenic mice to study development of peripheral CD4-T-cells. Genesis 50, 908–913 (2012).
Google Scholar
Shulman, Z. et al. T follicular helper cell dynamics in germinal centers. Science 341, 673–677 (2013).
Google Scholar
Dogan, I. et al. Multiple layers of B cell memory with different effector functions. Nat. Immunol. 10, 1292–1299 (2009).
Google Scholar
McDonald, B. D., Jabri, B. & Bendelac, A. Diverse developmental pathways of intestinal intraepithelial lymphocytes. Nat. Rev. Immunol. 18, 514–525 (2018).
Google Scholar
el Marjou, F. et al. Tissue-specific and inducible Cre-mediated recombination in the gut epithelium. Genesis 39, 186–193 (2004).
Google Scholar
Mucida, D. et al. Transcriptional reprogramming of mature CD4+ helper T cells generates distinct MHC class II-restricted cytotoxic T lymphocytes. Nat. Immunol. 14, 281–289 (2013).
Google Scholar
London, M., Bilate, A. M., Castro, T. B. R., Sujino, T. & Mucida, D. Stepwise chromatin and transcriptional acquisition of an intraepithelial lymphocyte program. Nat. Immunol. 22, 449–459 (2021).
Google Scholar
Cepek, K. L. et al. Adhesion between epithelial cells and T lymphocytes mediated by E-cadherin and the alpha E beta 7 integrin. Nature 372, 190–193 (1994).
Google Scholar
Zen, K. et al. Neutrophil migration across tight junctions is mediated by adhesive interactions between epithelial coxsackie and adenovirus receptor and a junctional adhesion molecule-like protein on neutrophils. Mol. Biol. Cell 16, 2694–2703 (2005).
Google Scholar
Cohen, C. J. et al. The coxsackievirus and adenovirus receptor is a transmembrane component of the tight junction. Proc. Natl Acad. Sci. USA 98, 15191–15196 (2001).
Google Scholar
Pazirandeh, A. et al. Multiple phenotypes in adult mice following inactivation of the Coxsackievirus and Adenovirus Receptor (Car) gene. PLoS ONE 6, e20203 (2011).
Google Scholar
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005).
Google Scholar
Oldstone, M. B. et al. Virus and immune responses: lymphocytic choriomeningitis virus as a prototype model of viral pathogenesis. Br. Med. Bull. 41, 70–74 (1985).
Google Scholar
Olson, M. R., McDermott, D. S. & Varga, S. M. The initial draining lymph node primes the bulk of the CD8 T cell response and influences memory T cell trafficking after a systemic viral infection. PLoS Pathog. 8, e1003054 (2012).
Google Scholar
Jakubzick, C. et al. Minimal differentiation of classical monocytes as they survey steady-state tissues and transport antigen to lymph nodes. Immunity 39, 599–610 (2013).
Google Scholar
Puglielli, M. T. et al. In vivo selection of a lymphocytic choriomeningitis virus variant that affects recognition of the GP33-43 epitope by H-2Db but not H-2Kb. J. Virol. 75, 5099–5107 (2001).
Google Scholar
Stevens, A. J. et al. Programming multicellular assembly with synthetic cell adhesion molecules. Nature 614, 144–152 (2022).
Google Scholar
Giladi, A. et al. Dissecting cellular crosstalk by sequencing physically interacting cells. Nat. Biotechnol. 38, 629–637 (2020).
Google Scholar
Sujino, T. et al. Tissue adaptation of regulatory and intraepithelial CD4+ T cells controls gut inflammation. Science 352, 1581–1586 (2016).
Google Scholar
Shin, K. S. et al. Monocyte-derived dendritic cells dictate the memory differentiation of CD8+ T cells during acute infection. Front. Immunol. 10, 1887 (2019).
Google Scholar
Engels, B. et al. Retroviral vectors for high-level transgene expression in T lymphocytes. Hum. Gene Ther. 14, 1155–1168 (2003).
Google Scholar
Kim, J. H. et al. High cleavage efficiency of a 2A peptide derived from porcine teschovirus-1 in human cell lines, zebrafish and mice. PLoS ONE 6, e18556 (2011).
Google Scholar
Argos, P. An investigation of oligopeptides linking domains in protein tertiary structures and possible candidates for general gene fusion. J. Mol. Biol. 211, 943–958 (1990).
Google Scholar
Lee, P. P. et al. A critical role for Dnmt1 and DNA methylation in T cell development, function, and survival. Immunity 15, 763–774 (2001).
Google Scholar
Schraml, B. U. et al. Genetic tracing via DNGR-1 expression history defines dendritic cells as a hematopoietic lineage. Cell 154, 843–858 (2013).
Google Scholar
Shinnakasu, R. et al. Regulated selection of germinal-center cells into the memory B cell compartment. Nat. Immunol. 17, 861–869 (2016).
Google Scholar
Barnden, M. J., Allison, J., Heath, W. R. & Carbone, F. R. Defective TCR expression in transgenic mice constructed using cDNA-based alpha- and beta-chain genes under the control of heterologous regulatory elements. Immunol. Cell Biol. 76, 34–40 (1998).
Google Scholar
Danciu, C. et al. A characterization of four B16 murine melanoma cell sublines molecular fingerprint and proliferation behavior. Cancer Cell Int. 13, 75 (2013).
Google Scholar
Sanchez, A. B. & de la Torre, J. C. Rescue of the prototypic Arenavirus LCMV entirely from plasmid. Virology 350, 370–380 (2006).
Google Scholar
Emonet, S. F., Garidou, L., McGavern, D. B. & de la Torre, J. C. Generation of recombinant lymphocytic choriomeningitis viruses with trisegmented genomes stably expressing two additional genes of interest. Proc. Natl Acad. Sci. USA 106, 3473–3478 (2009).
Google Scholar
Iwasaki, M., Ngo, N., Cubitt, B., Teijaro, J. R. & de la Torre, J. C. General molecular strategy for development of arenavirus live-attenuated vaccines. J. Virol. 89, 12166–12177 (2015).
Google Scholar
van der Heide, V. et al. Functional impairment of “helpless” CD8+ memory T cells is transient and driven by prolonged but finite cognate antigen presentation. Preprint at bioRxiv https://doi.org/10.1101/2024.01.22.576725 (2024).
Pasqual, G., Angelini, A. & Victora, G. D. Triggering positive selection of germinal center B cells by antigen targeting to DEC-205. Methods Mol. Biol. 1291, 125–134 (2015).
Google Scholar
Bilate, A. M. et al. Tissue-specific emergence of regulatory and intraepithelial T cells from a clonal T cell precursor. Sci. Immunol. 1, eaaf7471 (2016).
Google Scholar
Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).
Google Scholar
Sturm, G. et al. Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data. Bioinformatics 36, 4817–4818 (2020).
Google Scholar
Franzen, O., Gan, L. M. & Bjorkegren, J. L. M. PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data. Database 2019, baz046 (2019).
Google Scholar
Setty, M. et al. Wishbone identifies bifurcating developmental trajectories from single-cell data. Nat. Biotechnol. 34, 637–645 (2016).
Google Scholar
Storey, J. D. & Tibshirani, R. Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA 100, 9440–9445 (2003).
Google Scholar
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Google Scholar
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).
Google Scholar
Ko, J., Park, H., Heo, L. & Seok, C. GalaxyWEB server for protein structure prediction and refinement. Nucleic Acids Res. 40, W294–W297 (2012).
Google Scholar
Jo, S., Kim, T., Iyer, V. G. & Im, W. CHARMM-GUI: a web-based graphical user interface for CHARMM. J. Comput. Chem. 29, 1859–1865 (2008).
Google Scholar
Paulick, M. G. & Bertozzi, C. R. The glycosylphosphatidylinositol anchor: a complex membrane-anchoring structure for proteins. Biochemistry 47, 6991–7000 (2008).
Google Scholar
Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018).
Google Scholar
PyMOL v.2.4.0 (Schrödinger & DeLano, 2020).
Butler, A., Hoffman, P., Smibert, P., Papalexi, E. & Satija, R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat. Biotechnol. 36, 411–420 (2018).
Google Scholar