Kaech, S. M. & Cui, W. Transcriptional control of effector and memory CD8+ T cell differentiation. Nat. Rev. Immunol. 12, 749–761 (2012).
Philip, M. & Schietinger, A. CD8+ T cell differentiation and dysfunction in cancer. Nat. Rev. Immunol. 22, 209–223 (2022).
Zhou, L., Chong, M. M. & Littman, D. R. Plasticity of CD4+ T cell lineage differentiation. Immunity 30, 646–655 (2009).
Aliahmad, P., Seksenyan, A. & Kaye, J. The many roles of TOX in the immune system. Curr. Opin. Immunol. 24, 173–177 (2012).
Wilkinson, B. et al. TOX: an HMG box protein implicated in the regulation of thymocyte selection. Nat. Immunol. 3, 272–280 (2002).
Aliahmad, P. & Kaye, J. Development of all CD4 T lineages requires nuclear factor TOX. J. Exp. Med. 205, 245–256 (2008).
Aliahmad, P. et al. TOX is required for development of the CD4 T cell lineage gene program. J. Immunol. 187, 5931–5940 (2011).
Seehus, C. R. et al. The development of innate lymphoid cells requires TOX-dependent generation of a common innate lymphoid cell progenitor. Nat. Immunol. 16, 599–608 (2015).
Page, N. et al. Expression of the DNA-binding factor TOX promotes the encephalitogenic potential of microbe-induced autoreactive CD8+ T cells. Immunity 48, 937–950 (2018).
Scott, A. C. et al. TOX is a critical regulator of tumour-specific T cell differentiation. Nature 571, 270–274 (2019).
Alfei, F. et al. TOX reinforces the phenotype and longevity of exhausted T cells in chronic viral infection. Nature 571, 265–269 (2019).
Khan, O. et al. TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion. Nature 571, 211–218 (2019).
Yao, C. et al. Single-cell RNA-seq reveals TOX as a key regulator of CD8+ T cell persistence in chronic infection. Nat. Immunol. 20, 890–901 (2019).
Wang, X. et al. TOX promotes the exhaustion of antitumor CD8+ T cells by preventing PD1 degradation in hepatocellular carcinoma. J. Hepatol. 71, 731–741 (2019).
Seo, H. et al. TOX and TOX2 transcription factors cooperate with NR4A transcription factors to impose CD8+ T cell exhaustion. Proc. Natl Acad. Sci. USA 116, 12410–12415 (2019).
Heim, K. et al. TOX defines the degree of CD8+ T cell dysfunction in distinct phases of chronic HBV infection. Gut 70, 1550–1560 (2020).
Sekine, T. et al. TOX is expressed by exhausted and polyfunctional human effector memory CD8+ T cells. Sci. Immunol. 5, eaba7918 (2020).
Maurice, N. J. et al. Inflammatory signals are sufficient to elicit TOX expression in mouse and human CD8+ T cells. JCI Insight 6, e150744 (2021).
Xu, W. et al. The transcription factor Tox2 drives T follicular helper cell development via regulating chromatin accessibility. Immunity 51, 826–839 (2019).
CJ, W. et al. MiR-23~27~24-mediated control of humoral immunity reveals a TOX-driven regulatory circuit in follicular helper T cell differentiation. Sci. Adv. 5, eaaw1715 (2019).
Canaria, D. A. et al. Tox induces T cell IL-10 production in a BATF-dependent manner. Front. Immunol. 14, 1275423 (2023).
Rumble, J. & Segal, B. M. In vitro polarization of T-helper cells. Methods Mol. Biol. 1193, 105–113 (2014).
Boyden, A. W., Legge, K. L. & Waldschmidt, T. J. Pulmonary infection with influenza A virus induces site-specific germinal center and T follicular helper cell responses. PLoS ONE 7, e40733 (2012).
Kumar, S. et al. Specialized Tfh cell subsets driving type-1 and type-2 humoral responses in lymphoid tissue. Cell Discov. 10, 64 (2024).
Arroyo-Díaz, N. M. et al. Interferon-γ production by Tfh cells is required for CXCR3+ pre-memory B cell differentiation and subsequent lung-resident memory B cell responses. Immunity 56, 2358–2372 (2023).
Thierfelder, W. E. et al. Requirement for Stat4 in interleukin-12-mediated responses of natural killer and T cells. Nature 382, 171–174 (1996).
Athie-Morales, V. et al. Sustained IL-12 signaling is required for Th1 development. J. Immunol. 172, 61–69 (2004).
Holden, N. S. et al. Phorbol ester-stimulated NF-κB-dependent transcription: roles for isoforms of novel protein kinase C. Cell Signal. 20, 1338–1348 (2008).
Chatila, T. et al. Mechanisms of T cell activation by the calcium ionophore ionomycin. J. Immunol. 143, 1283–1289 (1989).
Flanagan, W. M. et al. Nuclear association of a T-cell transcription factor blocked by FK-506 and cyclosporin A. Nature 352, 803–807 (1991).
Jain, J. et al. The T-cell transcription factor NFATp is a substrate for calcineurin and interacts with Fos and Jun. Nature 365, 352–355 (1993).
Pardoll, D. M. & Topalian, S. L. The role of CD4+ T cell responses in antitumor immunity. Curr. Opin. Immunol. 10, 588–594 (1998).
Swain, S. L., McKinstry, K. K. & Strutt, T. M. Expanding roles for CD4+ T cells in immunity to viruses. Nat. Rev. Immunol. 12, 136–148 (2012).
Quezada, S. A. et al. Tumor-reactive CD4+ T cells develop cytotoxic activity and eradicate large established melanoma after transfer into lymphopenic hosts. J. Exp. Med. 207, 637–650 (2010).
Oh, H. & Ghosh, S. NF-κB: roles and regulation in different CD4+ T-cell subsets. Immunol. Rev. 252, 41–51 (2013).
Kano, S. et al. The contribution of transcription factor IRF1 to the interferon-gamma-interleukin 12 signaling axis and TH1 versus TH-17 differentiation of CD4+ T cells. Nat. Immunol. 9, 34–41 (2008).
Yang, Y. et al. T-bet and eomesodermin play critical roles in directing T cell differentiation to Th1 versus Th17. J. Immunol. 181, 8700–8710 (2008).
Cardenas, M. A. et al. Differentiation fate of a stem-like CD4 T cell controls immunity to cancer. Nature 636, 224–232 (2024).
Guo, M. et al. Molecular, metabolic, and functional CD4 T cell paralysis in the lymph node impedes tumor control. Cell Rep. 42, 113047 (2023).
Schoenborn, J. R. et al. Comprehensive epigenetic profiling identifies multiple distal regulatory elements directing transcription of the gene encoding interferon-gamma. Nat. Immunol. 8, 732–742 (2007).
Balasubramani, A. et al. Regulation of the Ifng locus in the context of T-lineage specification and plasticity. Immunol. Rev. 238, 216–232 (2010).
Collier, S. P. et al. Regulation of the Th1 genomic locus from Ifng through Tmevpg1 by T-bet. J. Immunol. 193, 3959–3965 (2014).
Collier, S. P. et al. Cutting edge: influence of Tmevpg1, a long intergenic noncoding RNA, on the expression of Ifng by Th1 cells. J. Immunol. 189, 2084–2088 (2012).
Chandra, A. et al. Quantitative control of Ets1 dosage by a multi-enhancer hub promotes Th1 cell differentiation and protects from allergic inflammation. Immunity 56, 1451–1467 (2023).
Kiani, A. et al. Regulation of interferon-gamma gene expression by nuclear factor of activated T cells. Blood 98, 1480–1488 (2001).
Grenningloh, R., Kang, B. Y. & Ho, I. C. Ets-1, a functional cofactor of T-bet, is essential for Th1 inflammatory responses. J. Exp. Med. 201, 615–626 (2005).
Harhaj, E. W. & Sun, S. C. The serine/threonine phosphatase inhibitor calyculin A induces rapid degradation of IκBβ. Requirement of both the N- and C-terminal sequences. J. Biol. Chem. 272, 5409–5412 (1997).
Safford, M. et al. Egr-2 and Egr-3 are negative regulators of T cell activation. Nat. Immunol. 6, 472–480 (2005).
Chen, Y. et al. Pik3ip1 is a negative immune regulator that inhibits antitumor T-cell immunity. Clin. Cancer Res. 25, 6180–6194 (2019).
Schuster, M. et al. Atypical IκB proteins – nuclear modulators of NF-κB signaling. Cell Commun. Signal. 11, 23 (2013).
Badia-i-Mompel, P. et al. decoupleR: ensemble of computational methods to infer biological activities from omics data. Bioinformatics Adv. 2, vbac016 (2022).
Qiu, S. et al. TOX: a potential new immune checkpoint in cancers by pancancer analysis. Discov. Oncol. 15, 354 (2024).
Guo, L. et al. TOX correlates with prognosis, immune infiltration, and T cells exhaustion in lung adenocarcinoma. Cancer Med. 9, 6694–6709 (2020).
Kim, K. et al. Single-cell transcriptome analysis reveals TOX as a promoting factor for T cell exhaustion and a predictor for anti-PD-1 responses in human cancer. Genome Med. 12, 22 (2020).
Magen, A. et al. Intratumoral dendritic cell-CD4+ T helper cell niches enable CD8+ T cell differentiation following PD-1 blockade in hepatocellular carcinoma. Nat. Med. 29, 1389–1399 (2023).
Oh, D. Y. et al. Intratumoral CD4+ T cells mediate anti-tumor cytotoxicity in human bladder cancer. Cell 181, 1612–1625 (2020).
Marshall, N. B. & Swain, S. L. Cytotoxic CD4 T cells in antiviral immunity. J. Biomed. Biotechnol. 2011, 954602 (2011).
Bae, H. R. et al. Cytotoxic CD4⁺ T cells exhibit an immunosuppressive shift in checkpoint immunotherapy resistance in melanoma patients. Cancer Immunol. Immunother. 74, 297 (2025).
Cachot, A. et al. Tumor-specific cytolytic CD4 T cells mediate immunity against human cancer. Sci. Adv. 7, eabe3348 (2021).
Zhang, L. et al. Lineage tracking reveals dynamic relationships of T cells in colorectal cancer. Nature 564, 268–272 (2018).
Sato, Y. et al. Stem-like CD4+ T cells in perivascular tertiary lymphoid structures sustain autoimmune vasculitis. Sci. Transl. Med. 15, eadh0380 (2023).
Anderson, M. S. & Bluestone, J. A. The NOD mouse: a model of immune dysregulation. Annu. Rev. Immunol. 23, 447–485 (2005).
Delong, T. et al. Pathogenic CD4 T cells in type 1 diabetes recognize epitopes formed by peptide fusion. Science 351, 711–714 (2016).
Aljobaily, N. et al. Autoimmune CD4+ T cells fine-tune TCF1 expression to maintain function and survive persistent antigen exposure during diabetes. Immunity 57, 2583–2596 (2024).
Mitchell, J. S. et al. CD4+ T cells reactive to a hybrid peptide from insulin-chromogranin A adopt a distinct effector fate and are pathogenic in autoimmune diabetes. Immunity 57, 2399–2415 (2024).
Hatton, R. D. et al. A distal conserved sequence element controls Ifng gene expression by T cells and NK cells. Immunity 25, 717–729 (2006).
Gomez, J. A. et al. The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-gamma locus. Cell 152, 743–754 (2013).
Gearty, S. V. et al. An autoimmune stem-like CD8 T cell population drives type 1 diabetes. Nature 602, 156–161 (2022).
Espinosa-Carrasco, G. et al. Intratumoral immune triads are required for immunotherapy-mediated elimination of solid tumors. Cancer Cell 42, 1202–1216 (2024).
Philip, M. et al. Chromatin states define tumour-specific T cell dysfunction and reprogramming. Nature 545, 452–456 (2017).
Schietinger, A. et al. Tumor-specific T cell dysfunction is a dynamic antigen-driven differentiation program initiated early during tumorigenesis. Immunity 45, 389–401 (2016).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).
Harrow, J. et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 22, 760–774 (2012).
Love, M. I. et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Korotkevich, G. et al. Fast gene set enrichment analysis. Preprint at bioRxiv https://doi.org/10.1101/060012 (2021).
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 5545–5550 (2005).
Liberzon, A. et al. The Molecular Signatures Database Hallmark Gene Set Collection. Cell Syst. 1, 417–425 (2015).
Wu, T. et al. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation 2, 100141 (2021).
Müller-Dott, S. et al. Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities. Nucleic Acids Res. 51, 10934–10949 (2023).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Liu, T. Use model-based analysis of ChIP-seq (MACS) to analyze short reads gen. Methods Mol. Biol. 1150, 81–95 (2014).
Stark, R. & Brown, G. DiffBind: differential binding analysis of ChIP-seq peak data. Bioconductor http://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf (2011).
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).
Amezquita, R. A. marge: API for HOMER in R for Genomic Analysis using Tidy Conventions. R package version 0.0.4.9999 (2024).
Wang, Q. et al. Exploring epigenomic datasets by ChIPseeker. Curr. Protoc. 2, e585 (2022).
Lun, A. T. L., McCarthy, D. J. & Marioni, J. C. A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor. F1000Res. 5, 2122 (2016).
McCarthy, D. J. et al. Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. Bioinformatics 33, 1179–1186 (2016).
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587 (2021).
Bunis, D. G. et al. dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit. Bioinformatics 36, 5535–5536 (2020).
Dolgalev, I. babelgene: gene orthologs for model organisms in a tidy data format. R package version 22.9 https://CRAN.R-project.org/package=babelgene/ (2022).
Andreatta, M. & Carmona, S. J. UCell: robust and scalable single-cell gene signature scoring. Comput. Struct. Biotechnol. J. 19, 3796–3798 (2021).
Cheshire, C. et al. nf-core/cutandrun: nf-core/cutandrun v3.2.2 Iridium Ibis (3.2.2). Zenodo https://doi.org/10.5281/zenodo.10606804 (2024).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Kent, W. J. et al. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics 26, 2204–2207 (2010).
Zhu, L. J. et al. ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics 11, 237 (2010).