Fig. 5: Targeting TEXterm single-state TFs enhances tumour control.
From: Atlas-guided discovery of transcription factors for T cell programming
a, Experimental design and tumour outcomes from adoptive transfer of P14 CD8+ T cells carrying CRISPR KOs of Zscan20 (TEXterm single-state TF gene) or Hic1 (multi-state TF gene active in TEXterm and TRM cells) into B16-GP33 melanoma-bearing mice. Tumour volumes and terminal weights are shown. b, Co-transfer design mixing Zscan20-KO or Hic1-KO Cas9+ P14 cells with scramble controls before transfer. c,d, Quantification of PD1+SLAMF6−TIM3+ exhausted subsets (c) and CX3CR1+ and GZMB+ effector populations (d) in Zscan20-KO and Hic1-KO cells. e, Human pan-cancer single-cell multi-omics and scRNA-seq datasets48,49,50,51,52,53,54,55 were integrated to assess TF expression and activity across CD8+ T cell states using scTaiji. BC, breast cancer; CHOL, cholangiocarcinoma; ESCA, oesophageal cancer; FTC, follicular thyroid cancer; MM, multiple myeloma; OV, ovarian cancer; PACA, pancreatic cancer; THCA, thyroid cancer; UCEC, uterine corpus endometrial carcinoma. f, Paired scRNA-seq and scATAC-seq were used to build regulatory networks and compute PageRank TF activity scores. Shown are normalized scores for TEXterm single-state TF genes (Fig. 1f) with conserved DNA-binding motifs in humans. g, mRNA expression of TEXterm TF genes across TEXterm and TRM clusters in human tumours; cross-species conserved TF genes are in bold. h, Human peripheral blood mononuclear cell (PMBC) KO design. ZSCAN20-KO or JDP2-KO CD8+ T cells were stimulated with anti-CD3/CD28 beads for 18 days to model chronic activation. i,j, Flow cytometry analysis of CCR7 (memory-like and stem-like) (i) and the inhibitory receptors LAG3, PD1 and TIM3 (j) in KO versus control cells. k, Frequencies of IFNγ+TNF+ and interleukin-2 (IL-2)+ cells. l, Polyfunctionality analysis of cytokine-producing cells. m, Schematic of adoptive transfer and anti-PD1 treatment testing synergy with TEXterm TF gene KO. Cas9+ P14 cells (±TF KO) were transferred into B16-GP33 tumours and treated with anti-PD1 or IgG2a. D7, day 7; D25, day 25. n,o, Tumour growth and weights for Zscan20-KO (n) and Jdp2-KO (o) versus controls. Data are mean ± s.e.m.; n ≥ 6 from at least two biological replicates. Statistics, two-way ANOVA with Tukey’s (tumour volume in a, n, o); one-way ANOVA with Dunnett’s (i–k, tumour weights in a, n, o); paired t-tests (c, d); two-way ANOVA with Dunnett’s (l). ****P < 0.0001, ***P < 0.001, **P < 0.01, *P < 0.05.
