Philip, M. & Schietinger, A. CD8+ T cell differentiation and dysfunction in cancer. Nat. Rev. Immunol. 22, 209–223 (2022).
Propper, D. J. & Balkwill, F. R. Harnessing cytokines and chemokines for cancer therapy. Nat. Rev. Clin. Oncol. 19, 237–253 (2022).
Holder, P. G. et al. Engineering interferons and interleukins for cancer immunotherapy. Adv. Drug Deliv. Rev. 182, 114112 (2022).
Yoshida, H. & Hunter, C. A. The immunobiology of interleukin-27. Annu. Rev. Immunol. 33, 417–443 (2015).
Fabbi, M., Carbotti, G. & Ferrini, S. Dual roles of IL-27 in cancer biology and immunotherapy. Mediat. Inflamm. 2017, 3958069 (2017).
Pagano, G. et al. Interleukin-27 potentiates CD8+ T-cell-mediated antitumor immunity in chronic lymphocytic leukemia. Haematologica 108, 3011–3024 (2023).
Liu, Z. et al. Epstein-Barr virus-induced gene 3-deficiency leads to impaired antitumor T-cell responses and accelerated tumor growth. OncoImmunology 4, e989137 (2015).
Liu, Z. et al. IL‐27 enhances the survival of tumor antigen‐specific CD8+ T cells and programs them into IL‐10‐producing, memory precursor‐like effector cells. Eur. J. Immunol. 43, 468–479 (2013).
Zhu, J. et al. IL-27 gene therapy induces depletion of Tregs and enhances the efficacy of cancer immunotherapy. JCI Insight 3, e98745 (2018).
Ding, M. et al. IL‐27 improves adoptive CD8+ T cells’ antitumor activity via enhancing cell survival and memory T cell differentiation. Cancer Sci. 113, 2258–2271 (2022).
Chihara, N. et al. Induction and transcriptional regulation of the co-inhibitory gene module in T cells. Nature 558, 454–459 (2018).
DeLong, J. H. et al. IL-27 and TCR stimulation promote T cell expression of multiple inhibitory receptors. ImmunoHorizons 3, 13–25 (2019).
Clemente, C. G. et al. Prognostic value of tumor infiltrating lymphocytes in the vertical growth phase of primary cutaneous melanoma. Cancer 77, 1303–1310 (1996).
Huang, A. C. & Zappasodi, R. A decade of checkpoint blockade immunotherapy in melanoma: understanding the molecular basis for immune sensitivity and resistance. Nat. Immunol. 23, 660–670 (2022).
Georgiev, P. et al. Reverse translating molecular determinants of anti-programmed death 1 immunotherapy response in mouse syngeneic tumor models. Mol. Cancer Ther. 21, 427–439 (2022).
Pflanz, S. et al. IL-27, a heterodimeric cytokine composed of EBI3 and p28 protein, induces proliferation of naive CD4+ T cells. Immunity 16, 779–790 (2002).
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).
Awasthi, A. et al. A dominant function for interleukin 27 in generating interleukin 10-producing anti-inflammatory T cells. Nat. Immunol. 8, 1380–1389 (2007).
Batten, M. et al. IL-27 supports germinal center function by enhancing IL-21 production and the function of T follicular helper cells. J. Exp. Med. 207, 2895–2906 (2010).
Yadav, M. et al. Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing. Nature 515, 572–576 (2014).
Ngiow, S. F. et al. A threshold level of intratumor CD8+ T-cell PD1 expression dictates therapeutic response to anti-PD1. Cancer Res. 75, 3800–3811 (2015).
Juneja, V. R. et al. PD-L1 on tumor cells is sufficient for immune evasion in immunogenic tumors and inhibits CD8 T cell cytotoxicity. J. Exp. Med. 214, 895–904 (2017).
Pflanz, S. et al. WSX-1 and glycoprotein 130 constitute a signal-transducing receptor for IL-27. J. Immunol. 172, 2225–2231 (2004).
Hirahara, K. et al. Asymmetric action of STAT transcription factors drives transcriptional outputs and cytokine specificity. Immunity 42, 877–889 (2015).
Duhen, T. et al. Co-expression of CD39 and CD103 identifies tumor-reactive CD8 T cells in human solid tumors. Nat. Commun. 9, 2724 (2018).
DeLong, J. H. et al. Cytokine- and TCR-mediated regulation of T cell expression of Ly6C and Sca-1. J. Immunol. 200, 1761–1770 (2018).
Bailey, C. M. et al. Targeting HIF-1α abrogates PD-L1-mediated immune evasion in tumor microenvironment but promotes tolerance in normal tissues. J. Clin. Investig. 132, e150846 (2022).
Hos, B. J. et al. Identification of a neo-epitope dominating endogenous CD8 T cell responses to MC-38 colorectal cancer. OncoImmunology 9, 1673125 (2020).
Xu, W.-D., Wang, D.-C., Zhao, M. & Huang, A.-F. An updated advancement of bifunctional IL-27 in inflammatory autoimmune diseases. Front. Immunol. 15, 1366377 (2024).
Maekawa, Y. et al. Notch2 integrates signaling by the transcription factors RBP-J and CREB1 to promote T cell cytotoxicity. Nat. Immunol. 9, 1140–1147 (2008).
Müller, S. I. et al. A folding switch regulates interleukin 27 biogenesis and secretion of its α-subunit as a cytokine. Proc. Natl Acad. Sci. USA 116, 1585–1590 (2019).
Zhang, G., Budker, V. & Wolff, J. A. High levels of foreign gene expression in hepatocytes after tail vein injections of naked plasmid DNA. Hum. Gene Ther. 10, 1735–1737 (1999).
Liu, F., Song, Y. K. & Liu, D. Hydrodynamics-based transfection in animals by systemic administration of plasmid DNA. Gene Ther. 6, 1258–1266 (1999).
Hirahara, K. et al. Interleukin-27 priming of T cells controls IL-17 production in trans via induction of the ligand PD-L1. Immunity 36, 1017–1030 (2012).
Kleffel, S. et al. Melanoma cell-intrinsic PD-1 receptor functions promote tumor growth. Cell 162, 1242–1256 (2015).
Langlais, D., Barreiro, L. B. & Gros, P. The macrophage IRF8/IRF1 regulome is required for protection against infections and is associated with chronic inflammation. J. Exp. Med. 213, 585–603 (2016).
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).
Castiglioni, A. et al. Combined PD-L1/TGFβ blockade allows expansion and differentiation of stem cell-like CD8 T cells in immune excluded tumors. Nat. Commun. 14, 4703 (2023).
Andreatta, M. et al. Interpretation of T cell states from single-cell transcriptomics data using reference atlases. Nat. Commun. 12, 2965 (2021).
Das, K. M. P. et al. Hypoxia-inducible lipid droplet-associated protein inhibits adipose triglyceride lipase. J. Lipid Res. 59, 531–541 (2018).
McIntyre, A. & Harris, A. L. Metabolic and hypoxic adaptation to anti‐angiogenic therapy: a target for induced essentiality. EMBO Mol. Med. 7, 368–379 (2015).
Agresta, L., Hoebe, K. H. N. & Janssen, E. M. The emerging role of CD244 signaling in immune cells of the tumor microenvironment. Front. Immunol. 9, 2809 (2018).
McLane, L. M., Abdel-Hakeem, M. S. & Wherry, E. J. CD8 T cell exhaustion during chronic viral infection and cancer. Annu. Rev. Immunol. 37, 457–495 (2019).
Zhao, M. et al. Rapid in vitro generation of bona fide exhausted CD8+ T cells is accompanied by Tcf7 promotor methylation. PLoS Pathog. 16, e1008555 (2020).
Vardhana, S. A. et al. Impaired mitochondrial oxidative phosphorylation limits the self-renewal of T cells exposed to persistent antigen. Nat. Immunol. 21, 1022–1033 (2020).
Cheng, J. et al. IL-27 induces IFN/STAT1-dependent genes and enhances function of TIGIT+ HIVGag-specific T cells. iScience 25, 103588 (2022).
Riaz, N. et al. Tumor and microenvironment evolution during immunotherapy with nivolumab. Cell 171, 934–949 (2017).
Schober, K. et al. Orthotopic replacement of T-cell receptor α- and β-chains with preservation of near-physiological T-cell function. Nat. Biomed. Eng. 3, 974–984 (2019).
Johnston, R. J. et al. The immunoreceptor TIGIT regulates antitumor and antiviral CD8+ T cell effector function. Cancer Cell 26, 923–937 (2014).
Martin, E. et al. Role of IL-27 in Epstein–Barr virus infection revealed by IL-27RA deficiency. Nature 628, 620–629 (2024).
Zhu, C. et al. An IL-27/NFIL3 signalling axis drives Tim-3 and IL-10 expression and T-cell dysfunction. Nat. Commun. 6, 6072 (2015).
Ahn, E. et al. Role of PD-1 during effector CD8 T cell differentiation. Proc. Natl Acad. Sci. USA 115, 4749–4754 (2018).
Xiong, H. et al. Coexpression of inhibitory receptors enriches for activated and functional CD8+ T cells in murine syngeneic tumor models. Cancer Immunol. Res. 7, 963–976 (2019).
Gerhardt, L., Hong, M. M. Y., Yousefi, Y., Figueredo, R. & Vareki, S. M. IL-12 and IL-27 promote CD39 expression on CD8+ T cells and differentially regulate the CD39+CD8+ T cell phenotype. J. Immunol. 210, 1598–1606 (2023).
Blank, C. U. et al. Defining ‘T cell exhaustion’. Nat. Rev. Immunol. 19, 665–674 (2019).
Rudloff, M. W. et al. Hallmarks of CD8+ T cell dysfunction are established within hours of tumor antigen encounter before cell division. Nat. Immunol. 24, 1527–1539 (2023).
Pennock, N. D., Gapin, L. & Kedl, R. M. IL-27 is required for shaping the magnitude, affinity distribution, and memory of T cells responding to subunit immunization. Proc. Natl Acad. Sci. USA 111, 16472–16477 (2014).
Huang, Z. et al. IL-27 promotes the expansion of self-renewing CD8+ T cells in persistent viral infection. J. Exp. Med. 216, 1791–1808 (2019).
Miyagawa, F. et al. Interferon regulatory factor 8 integrates T-cell receptor and cytokine-signaling pathways and drives effector differentiation of CD8 T cells. Proc. Natl Acad. Sci. USA 109, 12123–12128 (2012).
Collison, L. W. et al. The inhibitory cytokine IL-35 contributes to regulatory T-cell function. Nature 450, 566–569 (2007).
Haribhai, D. et al. Regulatory T cells dynamically control the primary immune response to foreign antigen. J. Immunol. 178, 2961–2972 (2007).
Lin, W. et al. Regulatory T cell development in the absence of functional Foxp3. Nat. Immunol. 8, 359–368 (2007).
Hogquist, K. A. et al. T cell receptor antagonist peptides induce positive selection. Cell 76, 17–27 (1994).
Chen, Q. et al. Development of Th1-type immune responses requires the type I cytokine receptor TCCR. Nature 407, 916–920 (2000).
Clausen, B. E., Burkhardt, C., Reith, W., Renkawitz, R. & Förster, I. Conditional gene targeting in macrophages and granulocytes using LysMcre mice. Transgenic Res. 8, 265–277 (1999).
Schraml, B. U. et al. Genetic tracing via DNGR-1 expression history defines dendritic cells as a hematopoietic lineage. Cell 154, 843–858 (2013).
Gaublomme, J. T. et al. Nuclei multiplexing with barcoded antibodies for single-nucleus genomics. Nat. Commun. 10, 2907 (2019).
Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888–1902 (2019).
Korsunsky, I. et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat. Methods 16, 1289–1296 (2019).
Gupta, N. T. et al. Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. Bioinformatics 31, 3356–3358 (2015).
R Core Team (2021). R: A language and environment for statistical computing (R Foundation for Statistical Computing, 2021); www.R-project.org/.
Kotliar, D. et al. Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-seq. eLife 8, e43803 (2019).
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).
Lun, A. T. L., Chen, Y. & Smyth, G. K. It’s DE-licious: a recipe for differential expression analyses of RNA-seq experiments using quasi-likelihood methods in edgeR. Methods Mol. Biol. 1418, 391–416 (2016).
Oh, S. A., Seki, A. & Rutz, S. Ribonucleoprotein transfection for CRISPR/Cas9‐mediated gene knockout in primary T cells. Curr. Protoc. Immunol. 124, e69 (2019).
Oh, S. A. et al. High-efficiency nonviral CRISPR/Cas9-mediated gene editing of human T cells using plasmid donor DNA. J. Exp. Med. 219, e20211530 (2022).
Pau, G. & Reeder, J. HTSeqGenie: a NGS analysis pipeline. R package version 4.32.0 (2023); https://bioconductor.org/packages/HTSeqGenie.
Wu, T. D., Reeder, J., Lawrence, M., Becker, G. & Brauer, M. J. GMAP and GSNAP for genomic sequence alignment: enhancements to speed, accuracy, and functionality. Methods Mol. Biol. 1418, 283–334 (2016).
Kolde, R. pheatmap: pretty Heatmaps. R package version 1.0.12 (2019); CRAN.R-project.org/package=pheatmap.
Gu, Z., Eils, R. & Schlesner, M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32, 2847–2849 (2016).
Korotkevich, G. et al. Fast gene set enrichment analysis. Preprint at bioRxiv https://doi.org/10.1101/060012 (2021).
Holland, C. H., Szalai, B. & Saez-Rodriguez, J. Transfer of regulatory knowledge from human to mouse for functional genomics analysis. Biochim. Biophys. Acta 1863, 194431 (2020).
Rosenberg, J. E. et al. Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: a single-arm, multicentre, phase 2 trial. Lancet 387, 1909–1920 (2016).
Powles, T. et al. Atezolizumab versus chemotherapy in patients with platinum-treated locally advanced or metastatic urothelial carcinoma (IMvigor211): a multicentre, open-label, phase 3 randomised controlled trial. Lancet 391, 748–757 (2018).
Rittmeyer, A. et al. Atezolizumab versus docetaxel in patients with previously treated non-small-cell lung cancer (OAK): a phase 3, open-label, multicentre randomised controlled trial. Lancet 389, 255–265 (2017).
Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).
Bagaev, A. et al. Conserved pan-cancer microenvironment subtypes predict response to immunotherapy. Cancer Cell 39, 845–865 (2021).
Li, X. et al. Automated tumor immunophenotyping predicts clinical benefit from anti-PD-L1 immunotherapy. J. Pathol. 263, 190–202 (2024).
Huseni, M. A. et al. CD8+ T cell-intrinsic IL-6 signaling promotes resistance to anti-PD-L1 immunotherapy. Cell Rep. Med. 4, 100878 (2023).