Dustin, M. L. The immunological synapse. Cancer Immunol. Res. 2, 1023–1033 (2014).
Pasqual, G. et al. Monitoring T cell-dendritic cell interactions in vivo by intercellular enzymatic labelling. Nature 553, 496–500 (2018).
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).
Sudhof, T. C. & Malenka, R. C. Understanding synapses: past, present, and future. Neuron 60, 469–476 (2008).
Victora, G. D. & Nussenzweig, M. C. Germinal centers. Annu. Rev. Immunol. 30, 429–457 (2012).
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).
Niec, R. E., Rudensky, A. Y. & Fuchs, E. Inflammatory adaptation in barrier tissues. Cell 184, 3361–3375 (2021).
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).
Moses, L. & Pachter, L. Museum of spatial transcriptomics. Nat. Methods 19, 534–546 (2022).
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).
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).
Ombrato, L. et al. Metastatic-niche labelling reveals parenchymal cells with stem features. Nature 572, 603–608 (2019).
Zhang, S. et al. Monitoring of cell-cell communication and contact history in mammals. Science 378, eabo5503 (2022).
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).
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).
Weizman, O. E. et al. Developing synthetic tools to decipher the tumor-immune interactome. Proc. Natl Acad. Sci. USA 120, e2306632120 (2023).
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).
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).
Dustin, M. L. & Depoil, D. New insights into the T cell synapse from single molecule techniques. Nat. Rev. Immunol. 11, 672–684 (2011).
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).
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).
Merkenschlager, J. et al. Dynamic regulation of TFH selection during the germinal centre reaction. Nature 591, 458–463 (2021).
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).
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).
Rubtsov, Y. P. et al. Stability of the regulatory T cell lineage in vivo. Science 329, 1667–1671 (2010).
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).
Shulman, Z. et al. T follicular helper cell dynamics in germinal centers. Science 341, 673–677 (2013).
Dogan, I. et al. Multiple layers of B cell memory with different effector functions. Nat. Immunol. 10, 1292–1299 (2009).
McDonald, B. D., Jabri, B. & Bendelac, A. Diverse developmental pathways of intestinal intraepithelial lymphocytes. Nat. Rev. Immunol. 18, 514–525 (2018).
el Marjou, F. et al. Tissue-specific and inducible Cre-mediated recombination in the gut epithelium. Genesis 39, 186–193 (2004).
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).
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).
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).
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).
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).
Pazirandeh, A. et al. Multiple phenotypes in adult mice following inactivation of the Coxsackievirus and Adenovirus Receptor (Car) gene. PLoS ONE 6, e20203 (2011).
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).
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).
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).
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).
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).
Stevens, A. J. et al. Programming multicellular assembly with synthetic cell adhesion molecules. Nature 614, 144–152 (2022).
Giladi, A. et al. Dissecting cellular crosstalk by sequencing physically interacting cells. Nat. Biotechnol. 38, 629–637 (2020).
Sujino, T. et al. Tissue adaptation of regulatory and intraepithelial CD4+ T cells controls gut inflammation. Science 352, 1581–1586 (2016).
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).
Engels, B. et al. Retroviral vectors for high-level transgene expression in T lymphocytes. Hum. Gene Ther. 14, 1155–1168 (2003).
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).
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).
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).
Schraml, B. U. et al. Genetic tracing via DNGR-1 expression history defines dendritic cells as a hematopoietic lineage. Cell 154, 843–858 (2013).
Shinnakasu, R. et al. Regulated selection of germinal-center cells into the memory B cell compartment. Nat. Immunol. 17, 861–869 (2016).
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).
Danciu, C. et al. A characterization of four B16 murine melanoma cell sublines molecular fingerprint and proliferation behavior. Cancer Cell Int. 13, 75 (2013).
Sanchez, A. B. & de la Torre, J. C. Rescue of the prototypic Arenavirus LCMV entirely from plasmid. Virology 350, 370–380 (2006).
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).
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).
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).
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).
Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).
Sturm, G. et al. Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data. Bioinformatics 36, 4817–4818 (2020).
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).
Setty, M. et al. Wishbone identifies bifurcating developmental trajectories from single-cell data. Nat. Biotechnol. 34, 637–645 (2016).
Storey, J. D. & Tibshirani, R. Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA 100, 9440–9445 (2003).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).
Ko, J., Park, H., Heo, L. & Seok, C. GalaxyWEB server for protein structure prediction and refinement. Nucleic Acids Res. 40, W294–W297 (2012).
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).
Paulick, M. G. & Bertozzi, C. R. The glycosylphosphatidylinositol anchor: a complex membrane-anchoring structure for proteins. Biochemistry 47, 6991–7000 (2008).
Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018).
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).
