Mellman, I., Coukos, G. & Dranoff, G. Cancer immunotherapy comes of age. Nature 480, 480–489 (2011).
Shulman, Z. et al. Transendothelial migration of lymphocytes mediated by intraendothelial vesicle stores rather than by extracellular chemokine depots. Nat. Immunol. 13, 67–76 (2012).
Guo, X. et al. Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing. Nat. Med. 24, 978–985 (2018).
Zhang, L. et al. Lineage tracking reveals dynamic relationships of T cells in colorectal cancer. Nature 564, 268–272 (2018).
Yost, K. E. et al. Clonal replacement of tumor-specific T cells following PD-1 blockade. Nat. Med. 25, 1251–1259 (2019).
Schenkel, J. M. & Masopust, D. Tissue-resident memory T cells. Immunity 41, 886–897 (2014).
Mackay, L. K. et al. Hobit and Blimp1 instruct a universal transcriptional program of tissue residency in lymphocytes. Science 352, 459–463 (2016).
Kumar, B. V. et al. Human tissue-resident memory T cells are defined by core transcriptional and functional signatures in lymphoid and mucosal sites. Cell Rep. 20, 2921–2934 (2017).
Im, S. J. et al. Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy. Nature 537, 417–421 (2016).
Miller, B. C. et al. Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade. Nat. Immunol. 20, 326–336 (2019).
Balin, S. J. et al. Human antimicrobial cytotoxic T lymphocytes, defined by NK receptors and antimicrobial proteins, kill intracellular bacteria. Sci. Immunol. 3, eaat7668 (2018).
Thommen, D. S. et al. A transcriptionally and functionally distinct PD–1+ CD8+ T cell pool with predictive potential in non-small-cell lung cancer treated with PD-1 blockade. Nat. Med. 24, 994–1004 (2018).
Sun, Q., Hao, Q. & Prasanth, K. V. Nuclear long noncoding RNAs: key regulators of gene expression. Trends Genet. 34, 142–157 (2018).
Delmas, V., Stokes, D. G. & Perry, R. P. A mammalian DNA-binding protein that contains a chromodomain and an SNF2/SWI2-like helicase domain. Proc. Natl Acad. Sci. USA 90, 2414–2418 (1993).
Gaide, O. et al. Common clonal origin of central and resident memory T cells following skin immunization. Nat. Med. 21, 647–653 (2015).
Simoni, Y. et al. Bystander CD8+ T cells are abundant and phenotypically distinct in human tumour infiltrates. Nature 557, 575–579 (2018).
Scheper, W. et al. Low and variable tumor reactivity of the intratumoral TCR repertoire in human cancers. Nat. Med. 25, 89–94 (2019).
Mariathasan, S. et al. TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells. Nature 554, 544–548 (2018).
Fehrenbacher, L. et al. Atezolizumab versus docetaxel for patients with previously treated non-small-cell lung cancer (POPLAR): a multicentre, open-label, phase 2 randomised controlled trial. Lancet 387, 1837–1846 (2016).
McDermott, D. F. et al. Clinical activity and molecular correlates of response to atezolizumab alone or in combination with bevacizumab versus sunitinib in renal cell carcinoma. Nat. Med. 24, 749–757 (2018).
Tumeh, P. C. et al. PD-1 blockade induces responses by inhibiting adaptive immune resistance. Nature 515, 568–571 (2014).
Araujo, J. M. et al. Effect of CCL5 expression in the recruitment of immune cells in triple negative breast cancer. Sci. Rep. 8, 4899 (2018).
Chen, D. S. & Mellman, I. Elements of cancer immunity and the cancer-immune set point. Nature 541, 321–330 (2017).
Wherry, E. J. & Kurachi, M. Molecular and cellular insights into T cell exhaustion. Nat. Rev. Immunol. 15, 486–499 (2015).
Topalian, S. L., Drake, C. G. & Pardoll, D. M. Immune checkpoint blockade: a common denominator approach to cancer therapy. Cancer Cell 27, 450–461 (2015).
Khan, O. et al. TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion. Nature 571, 211–218 (2019).
Scott, A. C. et al. TOX is a critical regulator of tumour-specific T cell differentiation. Nature 571, 270–274 (2019).
Sade-Feldman, M. et al. Defining T cell states associated with response to checkpoint immunotherapy in melanoma. Cell 175, 998–1013 (2018).
Yan, Y. et al. CX3CR1 identifies PD-1 therapy-responsive CD8+ T cells that withstand chemotherapy during cancer chemoimmunotherapy. JCI Insight 3, e97828 (2018).
Schumacher, T. N. & Scheper, W. A liquid biopsy for cancer immunotherapy. Nat. Med. 22, 340–341 (2016).
Hogan, S. A. et al. Peripheral blood TCR repertoire profiling may facilitate patient stratification for immunotherapy against melanoma. Cancer Immunol. Res. 7, 77–85 (2019).
Zheng, G. X. Y. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 14049 (2017).
Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888–1902 (2019).
Aran, D. et al. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat. Immunol. 20, 163–172 (2019).
Del Carratore, F. et al. RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets. Bioinformatics 33, 2774–2775 (2017).
Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).
Diedenhofen, B. & Musch, J. cocor: a comprehensive solution for the statistical comparison of correlations. PLoS One 10, e0121945 (2015).
Chao, A. et al. Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies. Ecol. Monogr. 84, 45–67 (2014).
Therneau, T. M. & Grambsch, P. M. Modeling Survival Data: Extending the Cox Model (Springer, 2000).
McInnes, L. & Healy, J. UMAP: uniform manifold approximation and projection for dimension reduction. Preprint at https://arXiv.org/abs/1802.03426 (2018).
Becht, E. et al. Dimensionality reduction for visualizing single-cell data using UMAP. Nat. Biotechnol. 37, 38–44 (2019).
Zeileis, A. et al. colorspace: a toolbox for manipulating and assessing colors and palettes. Preprint at https://arXiv.org/abs/1903.06490 (2019).
Barter, R. L. & Yu, B. Superheat: an R package for creating beautiful and extendable heatmaps for visualizing complex data. J. Comput. Graph. Stat. 27, 910–922 (2018).
Morgan, M. T. & Davis, S. R. GenomicDataCommons: a bioconductor interface to the NCI Genomic Data Commons. Preprint at https://www.bioRxiv.org/content/10.1101/117200v1 (2017).
Davis, S. & Meltzer, P. S. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics 23, 1846–1847 (2007).
Shimizu, Y., Meunier, L. & Hendershot, L. M. pERp1 is significantly up-regulated during plasma cell differentiation and contributes to the oxidative folding of immunoglobulin. Proc. Natl Acad. Sci. USA 106, 17013–17018 (2009).
Andreani, V. et al. Cochaperone Mzb1 is a key effector of Blimp1 in plasma cell differentiation and β1-integrin function. Proc. Natl Acad. Sci. USA 115, E9630–E9639 (2018).
Beham, A. W. et al. A TNF-regulated recombinatorial macrophage immune receptor implicated in granuloma formation in tuberculosis. PLoS Pathog. 7, e1002375 (2011).
Fuchs, T. et al. Expression of combinatorial immunoglobulins in macrophages in the tumor microenvironment. PLoS One 13, e0204108 (2018).
Thul, P. J. et al. A subcellular map of the human proteome. Science 356, 820 (2017).
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).
Liberzon, A. et al. Molecular signatures database (MSigDB) 3.0. Bioinformatics 27, 1739–1740 (2011).
Irizarry, R. A., Wang, C., Zhou, Y. & Speed, T. P. Gene set enrichment analysis made simple. Stat. Methods Med. Res. 18, 565–575 (2009).
Shugay, M. et al. VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. Nucleic Acids Res. 46, D419–D427 (2018).
Li, B. et al. Landscape of tumor-infiltrating T cell repertoire of human cancers. Nat. Genet. 48, 725–732 (2016).
Shan, G. & Gerstenberger, S. Fisher’s exact approach for post hoc analysis of a chi-squared test. PLoS One 12, e0188709 (2017).
