Fig 2: Immune Parameter Changes during the First Weeks of Life(A) The TDA parameter landscape subdivided into five developmental stages.(B and C) Interindividual distances for plasma protein profiles (B) (Euclidean) and cell composition (C) (Atchinson’s) across the five stages.(D) Plasma concentration (log2 NPX) of cytokines IL-27 and IL-10.(E) Plasma concentration (log2 NPX) of PIgR.(F) Plasma concentration (log2 NPX) of IL-8 (CXCL8) and cytokines IL-17A and IL-12B.(G) The frequency of CD8+ T cell cluster #1 as a fraction of all cells.(H) bhSNE plots showing cluster localization among CD8+ T cells and CD3, CD8a, CD161, and CD38 expression. All p values from KS tests comparing distributions of stages 2–3 combined versus stage 5.(I) Differentially regulated genes week 12 versus week 1 associated with the GO: positive reg. of immune system process. Genes ordered by absolute log2 (week 12/week 1) (x axis) and actual log2 (week 12/week 1) (y axis).See also Figure S5 and Table S1.

Fig 3: HOXA11-AS1 knockdown suppressed PD-L1 expression and immune escape, proliferation, and metastasis of HSCC cells. FaDu and Detroit cells were transfected with two specific shRNAs, shHOXA11-AS1-1 and shHOXA11-AS1-2. (A) Transfection efficiencies were measured by RT-qPCR. (B,C) PD-L1 levels were detected after silencing HOXA11-AS1 by Western blot and immunofluorescence. Anti-PD-L1 antibodies restored the cytotoxic effect of T lymphocytes. Treated FaDu and Detroit cells were pretreated with or without anti-PD-L1 antibodies for 1 h and co-cultured with PBMCs for 72 h (Representative images (400×) are shown, bars = 100 µm.), then (D) the percentage of CD8+ and (E) CD4+ T cells was analyzed by flow cytometry, and (F) the concentration of IFN-γ was measured by enzyme-linked immunosorbent assay (ELISA). Viability, colony formation, migration, and invasion of FaDu and Detroit cells were measured by (G) CCK-8, (H) colony formation, (I) wound healing, and (J) transwell assays after knockdown of HOXA11-AS1. Representative images (200×) are shown. * p < 0.05, ** p < 0.01, *** p < 0.001. Original Blots see Supplementary File Figure S1.

Fig 4: ACPA+ RA blood CD8+ T cells upregulate activation and cytotoxic markers in response to citrullinated antigens.a Stimulation of fresh blood from ACPA+ RA (n = 8, red bars) or HCs (n = 7, blue bars) with anti-CD3/28 Abs, NP/pp65, cit- or native vimentin for 6 h with addition of Golgi inhibitor for the last 5 h. Quantification of CD69+ and GzmB+IFNγ+ CD8+ T cells, and IFNγ+ CD4+ T cells. For CD69+CD8+, *P = 0.049, +P = 0.0397, **P = 0.001, ##P = 0.009, or ###P = 0.0008. For GzmB+IFNγ+CD8+, +P = 0.0175, **P = 0.0071, ##P = 0.0071, or ##P = 0.0037. For IFNγ+CD4+, ++P = 0.0065, +P = 0.0489, *P = 0.0155, #P = 0.0351, or ##P = 0.0038. b PBMCs of ACPA+ RA patients (n = 10) were incubated with anti-CD3/28 Abs, NP/pp65 (50 μM of each), individual citrullinated proteins (100 μM), all citrullinated proteins (20 μM each), or all native proteins (20 μM each) for 16 h. Percentage of IFNγ or Granzyme B (GzmB) expressing CD8+ T cells measured by intracellular staining. c Quantification of IFNγ+ or GzmB+IFNγ+ expressing CD8+ T cells in ACPA+ RA PBMCs treated with cit- or native vimentin in a dose-dependent manner (1, 10 or 100 μM) (n = 7). d Quantitative analysis of IFNγ+ or GzmB+IFNγ+ expressing CD8+ T cells in ACPA+ RA PBMCs stimulated with cit-vimentin in the presence or absence of anti-CD8 and/or HLA class I-blocking antibody (n = 10). Data are presented as means ± SEM. For a, two-tailed unpaired t-test: *P < 0.05 or **P < 0.01 versus no treatment in ACPA+ RA; +P < 0.05, or ++P < 0.01 versus no treatment in HC; and #P < 0.05, ##P < 0.01, or ###P < 0.001 versus cit-vimentin in ACPA+ RA. For b, two-tailed unpaired t-test: *P < 0.05, **P < 0.01, or ***P < 0.001 versus no treatment; #P < 0.05, or ##P < 0.01 versus all native proteins. For c, two-tailed unpaired t-test: *P < 0.05, or **P < 0.01 versus no treatment; #P < 0.05 for cit-vimentin 1 μM versus vimentin 1 μM; $P < 0.05 for cit-vimentin 10 μM versus native vimentin 10 μM by two-tailed unpaired t-test; +P < 0.05 for cit-vimentin 100 μM versus native vimentin 100 μM. For d, by two-tailed unpaired t-test: *P < 0.05, or **P < 0.01 versus no treatment; #P < 0.05, or ##P < 0.01 versus cit-vimentin 100 μM. Source data are provided as a Source Data file. HC healthy control, ACPA anti-citrullinated protein antibodies, RA rheumatoid arthritis, Cit-Vim citrullinated vimentin.

Fig 5: Adaptive immune response readouts associated with disease severity(A–C) Frequencies of T cell populations by hospitalization: inpatient (n = 6), outpatient (n = 24), and outpatient/inpatient (n = 10).(A) Frequency of CD38+/CD57+ CD8 T cells at V3; ∗∗∗p = 0.0007.(B) Frequency of CD38+/CD57+ dengue+ CD8 cells at V3; ∗∗∗p = 0.0003, ∗∗∗∗p < 0.0001.(C) Frequency of effector memory (EM) CD4+ T cells at V4; ∗p = 0.0408, ∗∗p = 0.0028.(D) Correlation of frequency of EM CD4+ T cells at V4 with frequency of CD38+ CD57+ CD8+ T cells at V3.(E) Frequencies of total dengue tetramer+ T cells by hospitalization groups. Mixed-effects analysis with Geisser-Greenhouse correction.(F) Frequency of CD57+ cytotoxic T /CD4 cells at V5 for patients with dengue fever (DF) but no WSs (DF without WS) and patients with DF and WSs (DF with WS). Each symbol represents 1 patient: primary (blue), secondary (red), empty symbols represent severe dengue (SD) cases.(G) Frequency of CD1c+IgM+ cells among CD19+ B cells at V3 by hospitalization: inpatient (n = 9), outpatient (n = 24), and outpatient/inpatient (n = 13); ∗p = 0.0108.(H) Frequency of plasmablasts (CD38+CD27+) among CD19+ B cells at V2 by hospitalization: inpatient (n = 9), outpatient (n = 24), and outpatient/inpatient (n = 13); ∗p = 0.0335.(I) Neutralization antibody titer (NT50) against DENV-2 at V4 for patients with DF without WS and patients with DF with WS. Empty symbols represent SD cases. ∗∗p = 0.0012, Mann-Whitney test. LLoQ: lowest limit of quantification.(J) LDA plot of features selected by Boruta feature selection that was performed on all-visit data and classified by hospitalization status (n = 29).(K) LDA plot of data selected by Boruta feature selection that was performed on V2 data and classified by hospitalization (n = 24).(L) LDA plot of data selected by Boruta feature selection that was performed on V2 data and classified by final hospitalization status (n = 24). Mann-Whitney test.(M) Frequencies of CD38+/CXCR5+ B cells over time by hospitalization status.(N) Frequencies of CD38+/CXCR5+ B cells over time by final hospitalization status.For all graphs, except where specified otherwise: error bars indicate means ± SD. Kruskal-Wallis with Dunn’s multiple comparison test.