Fig 2: Systemic immune response during chronic pancreatitis in mice.Splenocytes were analyzed from control (con) and chronic pancreatitis (CP) mice. a T cell (CD4+) differentiation is shown by intracellular transcription factor staining of GATA3 for Th2 cells (p = 0.0016, con n = 4/CP n = 8), b TBET for Th1 cells, c ROR?t for Th17 cells and d FOXP3 in combination with CD25 to discriminate Treg cells (p = 0.0085, con n = 4/CP n = 8). e, f In contrast to GATA3+ Th2 cells an increase of CD206+ or CD163+ alternatively activated macrophages could not be observed. g Serum concentration of IL-4 was significantly increased (p = 0.0422, con n = 7/CP n = 15), whereas the rise of IL-10, IFN?, TNF, and IL-17A concentrations were not significant (con n = 7/CP n = 15). h The intracellular cytokine production of CD4+ T cells was analyzed by labeling for IL-4, IL-13, IFN?, TNF, and IL-10 after brefeldin a/monensin treatment. Th2 cytokines IL-4 (p = 0.0443, con n = 7/CP n = 15), IL-13 (p = 0.0455, con n = 7/CP n = 15) and IL-10 (p = 0.0294, con n = 7/CP n = 15) were elevated in CD4+ T cells, whereas of Th1 cytokines only IFN? (p = 0.0072, con n = 7/CP n = 15) was elevated but not TNF (con n = 7/CP n = 14). i Gene expression in splenocytes was also analyzed by RT-qPCR for Il4 (p = 0.0250, con n = 7/CP n = 15), Il13 (con n = 3/CP n = 13), Il10 (con n = 6/CP n = 15), Tnf (con n = 7/CP n = 15) and Ifng (con n = 6/CP n = 15) and confirmed the Th2 differentiation. Transcript levels as determined by RT-qPCR were normalized using Rn5s as internal calibrator gene and were related to the corresponding mRNA amounts in control mice. All data were presented as means ± SEM, statistically significant differences were tested by unpaired two-tailed students t-test for independent samples and significance levels of p < 0.05 are marked by an asterisk (a, d, g, h, i). Source data are provided as a Source Data file.

Fig 3: The effects of autophagy deficiency in Becn1+/- mice on the neuro-immune response in the spinal cord at 3 d post-injury. (A-C) Flow cytometry analysis showed increased numbers of CD45intCD11b+ microglia and CD45hiCD11b+ leukocyte infiltration in both WT and Becn1+/- mice following SCI. Representative dot plot of immune cells in the spinal cord of sham and injured mice are shown in A. Quantification of CD45intCD11b+ microglia counts and CD45hiCD11b+ leukocyte are indicated in B and C. (D-G) Proinflammatory cytokines TNF (D-E) and IL-1ß (F-G) in the microglia showed significant increase after SCI, with even higher levels in Becn1+/- mice. n = 5 (Sham/WT), 9 (SCI/WT), 6 (Sham/Becn1+/-), and 8 (SCI/Becn1+/-) mice. ***p < 0.001 vs. Sham groups. #p < 0.05 vs. SCI/WT. Two-way ANOVA followed by Tukey's multiple comparison.

Fig 4: AE-specific CD8+ T cells display an effector/memory phenotype in the CNS of mice with EAE.C57BL/6 mice (n = 8) were immunized with 100 µg MOG35-55 and 400 µg heat-killed M. tuberculosis in IFA at day 0, and received 200 ng PTX i.v. at days 0 and 2. After 28 days, spleens (SPL) and brains and spinal cords (CNS) were collected, and flow cytometry analysis was performed. A Cumulative analysis of CD8+ T cell frequency in SPL and CNS of MOG35-55-immunized or not immunized (CTRL, n = 4) mice. B Representative stainings with pooled dextramers (Dextr) to the 3 selected peptides, VIM66-74 (SAVRLRSSV), MYH9120-127 (VINPYKNL), MYH9761-768 (VFFRAGVL), in gated live single CD8+ T cells, from SPL and CNS of mice with EAE (upper panels). CD44 expression in gated dextramer+ (red) or dextramer– (black) CD8+ T cells (lower panels). C Cumulative analysis of dextramer+ cell percentage in SPL and CNS of MOG35-55-immunized or not immunized (CTRL, n = 4) mice. D Frequency of CD44+ CD62L– effector/memory cells in total or dextramer+ CD8+ T cells from SPL and CNS of MOG35-55-immunized mice. E Frequency of cells producing IFN-?, TNF or GM-CSF in gated CD44+ among total or dextramer+ CD8+ T cells from SPL and CNS of MOG35-55-immunized mice. Samples with insufficient numbers of dextramer+ events were not included in the analysis. F Spearman correlation between cytokine production in CD44+ dextramer+ cells and cumulative disease score. The data are from a single experiment representative of two independent experiments. Bars represent means ± SEM. *P < 0.05, **P < 0.01, ***P < 0.005, by Mann-Whitney test. nd, not determined. ns, not significant.

Fig 5: The effects of old age on the central immune response to TBI. A A representative dot plot of leukocyte populations in the brain at 48 h and 16 weeks after TBI. Quantification of CD45intCD11b+ microglia (B), CD45hiCD11b+ myeloid cells (C), and CD45hiCD11b- putative lymphocyte (D) cell counts are shown. Microglial proliferation as measured using cell cycle markers. A main effect of injury was seen in Ki67 (E) and PCNA (F) expression, driven largely by the increase at 48 h after TBI. Reactive oxygen species (ROS) and oxidative stress were measured using DCF. Main effects of age and injury were seen in microglial ROS levels (G). Pro-inflammatory cytokine production was assessed. The relative expression level of IL-1ß (H) and TNF (I) in microglia is shown. For all histograms, gray = FMO control, blue = young, red = old, sham = no outline/no fill, 48 h TBI = bold outline/no fill, and 16w TBI = bold outline/bold fill. N = 5–7/group. Data were analyzed using 2-way ANOVA group analysis with Tukey’s test for multiple comparisons. ***p < 0.001, **p < 0.01, *p < 0.05