Fig. 1. CNS resident macrophage antigen presentation mediates neurodegeneration.

a Experimental paradigm for conditional Iab deletion from CX3CR1⁺ cells. Mice received tamoxifen and 4 weeks later were given AAV2-SYN. Four weeks post AAV2-SYN, flow cytometry and immunohistochemistry were performed. Six months post-AAV, unbiased stereology was performed to quantify neurodegeneration. b Quantification of recombination efficiency of CNS resident macrophages, including microglia (Mg) and border-associated macrophages (BAMs), or meningeal classical dendritic cells (cDCs) 6 weeks after tamoxifen treatment using the CX3CR1^CreERT2 mice crossed to TdTomato^fl/fl reporter mice. N = 4 mice, unpaired two-tailed T test. *p = 0.0169. Mean ± SEM is displayed. Representative results of two independent experiments are shown. c Quantification of ventral midbrain CD4⁺ T cells in (d). n = 5 CX3CR1+/− mice and 4 CX3CR1+/− Iab fl/fl mice, **p < 0.01. Mean ± SD is shown. d Representative scans of the ventral midbrain containing the SNpc of DAB staining for CD4⁺ T cells in CX3CR1^CreERT2/+ Iab^fl/fl or CX3CR1^CreERT2/+ mice. Zoomed images are below showing higher magnification of the boxed area. Numbers indicate if the zoomed image was from CX3CR1^CreERT2/+ or CX3CR1^CreERT2/+ Iab^fl/fl mice. Representative images from two independent experiments are shown. e Immunofluorescent images of CD4⁺ T cell infiltration in CX3CR1^CreERT2/+ Iab^fl/fl or CX3CR1^CreERT2/+ mice. Brains are labeled with AAV2-SYN (green), CD4 (red) and IBA1 (blue). Images are taken at ×40, scale bar is 50 μm (top) or images are digitally zoomed (bottom). Representative images from two independent experiments are shown. f Representative DAB images of the substantia nigra pars compacta in CX3CR1^CreERT2/+ Iab^fl/fl or CX3CR1^CreERT2/+ mice. Images are labeled with tyrosine hydroxylase (TH), and both the contralateral uninjected (left) and ipsilateral injected (right) sides of the brain are shown. Scale bar is 100 μm. Representative image from one experiment is shown. g Quantification of unbiased stereology of TH+ immunostained neurons in the SNpc of CX3CR1^CreERT2/+IAB^fl/fl or CX3CR1^CreERT2/+ control mice who received AAV2-SYN. Quantification is performed at 6 months post AAV transduction and neuron counts are normalized to the average of the group contralateral side. Two-way ANOVA, with Bonferonni multiple comparisons correction, n = 10 mice per group. **p = 0.0053, *p = 0.0105. Mean ± SD is shown. *Source data is provided in the “Source data” file.