Extended Data Fig. 3: Lung dysbiosis does not modify T cell activation and expression profile in the lung.
a–e, Lung EAE was induced in rats that were pre-treated i.tr. with neomycin or PBS for 7 days. a, Lung immunization induces reprogramming in the gene expression profile of TMBP cells. Volcano plots depicting the differential gene expression profiles of lung-derived TMBP cells from PBS- (left) or neomycin- (right) pre-treated rats between D1 and D0 after immunization. Red and blue dots represent significantly up- or downregulated genes (P < 0.05), respectively. Indicated are representative genes involved in cell division and cell cycle. b, c, Genes differentially expressed after immunization are mainly involved in cell cycle. b, Significantly regulated KEGG pathways for genes upregulated between D1 versus D0 after immunization in TMBP cells isolated from lung of PBS- (left) or neomycin-treated (right) rats. Bold, pathways significantly enriched in both treatments. c, Heat map of the 50 most upregulated genes in D1 versus D0 after immunization in PBS- and neomycin-treated rats. d, Lung immunization does not change effector T cell differentiation. Total reads of transcription factors, cytokines and chemokine receptors in TMBP cells isolated from lung of PBS- or neomycin-treated rats on D0 and D1 after immunization Mean ± s.e.m. n = 3 (all groups). e, I.tr. neomycin treatment does not impair TMBP cell activation and migratory program. Relative expression of chemokine receptors and genes involved in cell cycle and cell egress in TMBP cells isolated from the lung of PBS- or neomycin-pre-treated rats on D1 after immunization. Quantitative PCR. Mean ± s.e.m. Representative data of two independent experiments. n = 3 (PBS); n = 4 (Neo) per condition. d, e, Statistical significance determined by unpaired two-tailed t-test. *P < 0.05.
