Fig 2: Decitabine in combination with PD-1 inhibitor reduces tumor growth by stimulating antitumor T cell immunity. (A) Schematic outline of decitabine and anti-PD-1 treatment for tumors: MYC-overexpressing 4T1 mouse breast cancer cells were subcutaneously injected into BALB/c mice. when tumors reached 100–200 mm3, the mice were treated with isotype control, anti-PD-1 antibody (200 µg i.p. injection every 3 days) and/or decitabine (0.8 mg/kg i.p. once a day) (n=7 mice/group) until the mice met the treatment endpoint. (B) Growth of subcutaneous 4T1-MYC-oe tumors in the four groups. The black arrow indicates the treatments. (C) Representative images of the 4T1-MYC-oe subcutaneous breast tumors in each group. (D) Tumor weight of each group at the time of sacrifice. (E) Scatter plots showing the percentage of CD3+, CD8+ and CD8+granzyme B+ cells in the four treatment groups determined by flow cytometry. The data are presented as the mean±SEM (B, D, E); one-way ANOVA test after adjusting for multiple comparisons (B); two-tailed unpaired Student’s t-test (D, E). **P<0.01; ***P<0.001. ANOVA, analysis of variance; NS, not significant; PD-1, programmed cell death protein 1; SEM, standard error of mean.

Fig 3: Clonal expansion of CD8 T cells in psoriatic arthritis.a, b TCR beta-chain V and J-gene usage in PsA blood and synovial fluid generated from 10× 5' data of patients PSA1505, PSA1607 and PSA1801. V and J segments are represented by arcs, scaled in size to their combined usage by all patients within each sample type, and giving equal weight to each patient. V–J pairings are represented by ribbons. Plot generated using VDJtools (v1.2.1)36. c UMAP of PsA synovial fluid CD4 and CD8 T cells from three patients with clonally expanded cells highlighted in red. Clonally expanded cells in synovial fluid associated most strongly with HLA-DR-high CD8, cycling and ZNF683+ CD8 clusters (odds ratios 12.6, 4.73 and 3.66; adjusted p value 0, 8.7E-19 and 6.1E-64, respectively; two-sided Fisher’s exact test with Bonferroni correction using R stats package; Supplementary Data 7a). d–f Individual clonal expansion across blood and synovial fluid for three PsA patients based on 10× 5' data. Circles represent CD8 clonotypes, triangles represent CD4 clonotypes. Data points coloured red show significantly expanded clonotypes (adjusted p value ? 0.05). Two-sided Fisher’s exact test, Benjamini–Hochberg correction. g Cluster assignment of enriched CD8 clones in PsA synovial fluid from three patients (PSA1505, PSA1607 and PSA1801). h UMAP plot of integrated memory T cells from one donor (PSA1607), including cells from 5' 10× and SS2 datasets (Supplementary Fig. 8). Synovial CD8 T cells from the clone most enriched in synovial fluid for this patient are highlighted in blue for the 10× data set and red for the SS2 data set. Source data are provided as a Source Data file.

Fig 4: Changes in the lymphoid cell sub-populations in normal vs steatotic murine livers.Isolated CD45 positive cells from normal and steatotic livers were stained for lymphoid markers, subjected to flow cytometry and gated as a fraction of CD3e positive lymphocytic cells. CD3e+ cells were analyzed for changes in the total percentage of (A) CD4 positive helper T cells, (B) CD8 positive cytotoxic T cells, (C) CD25 positive regulatory T cells, and (D) CD62L negative activated T cells between normal and steatotic murine livers. Results only showed a significant increase in the overall CD25+ subpopulation of CD3e+ cells in the steatotic livers when compared to normal livers.

Fig 5: Identification of T cell diversity during the 2nd trimester of human fetal development(A) Suspension mass cytometry (CyTOF) was performed on PMA/ionomycin-stimulated fetal T cells. The UMAP projection shows all the fetal and adult organs and blood samples used for T cell analysis: fetal gut (7), fetal lung (9), fetal liver (5), fetal skin (6), fetal thymus (8), fetal mLN (3), adult gut (5), adult lung (2), fetal (4), cord (3), and adult blood (4). Numbers in parenthesis represent number of samples being analyzed.(B) UMAP projection of all the blood samples, along with individual projections of each sample type (fetal, cord, and adult blood): fetal blood (4), cord blood (3), adult blood (4).(C) UMAP projection of the T cells from fetal and adult organs, along with individual projections of each organ over the UMAP: fetal gut (7), fetal lung (9), fetal liver (5), fetal skin (6), fetal thymus (8), fetal mLN (3), adult gut (5), and adult lung (2).(D) UMAP projection of fetal versus adult organs (in orange and blue, respectively). CD4+ and CD8+ T cell clustering is also shown on the same UMAP projection, in both fetal and adult tissues. Tregs in CD4 compartment is also shown based on CD4+CD25+FOXP3+CD152+ markers.(E) UMAP feature projection of T cell markers (CD3, CD4, and CD8) and Treg-associated markers (CD25, FOXP3, and CD152) are shown on top and bottom panels, respectively.(F) Percentage of Tregs in fetal versus adult tissues and in blood samples (fetal, adult, and cord blood) as determined by mass cytometry analysis (input gating strategy and reference plots in Figures S1B and S1C). As shown, Tregs are enriched in fetal organs as compared to adult organs and blood.(G) TNF cytokine expression in CD4+ (top) and CD8+ (bottom) T cells as determined by mass cytometry analysis of fetal and adult tissues (input gating strategy and reference plots in Figure S1G).(H) Percentage of CD4+ (top) and CD8+ (bottom) CD45RO+ memory T cells in fetal and adult tissues and blood samples (input gating strategy and reference plots in Figure S1I).(I) Percentage of TNF+ cells in CD4+ (top) and CD8+ (bottom) CD45RO+ effector memory T (Tem) cells in fetal and adult tissues and blood samples.See also Table S1.