scRNAseq defines the early differentiation state and lack of Th1 terminal effector CD4 T cells in NCan mice. (A) UMAPs of the lung CD4 T cell subset from n = 4 male mice from two canonical strains (C57BL/6 and CC011) and two NCan strains (PWK/PhJ and CC024) with GEX for cluster-defining markers from one experiment. (B) Proportion of lung CD4 T cells per cluster. Significance assessed by Mann–Whitney U test with Benjamini–Hochberg correction. (C and D) (C) Representative flow plots of KLRG1 (bottom) and CX3CR1 (top) staining in lung vasculature (CD45i.v.⁺) or lung parenchymal (CD45i.v.⁻) compartments with (D) quantification of percent of CD4⁺KLRG1⁺CX3CR1⁺CD45i.v.⁺ T cells. Data are pooled from two independent experiments (n = 3–4 mice per strain per experiment), with PWK/PhJ and CC024 representing NCan mice and C57BL/6 and CC011 representing canonical mice. Significance assessed by Mann–Whitney U test. (E) Violin plots of the type II IFN signature score from Moreira-Teixeira et al. (2020) for the naïve lung CD4 T cell clusters. Significance assessed by Mann–Whitney U test with Benjamini–Hochberg correction (ns = not significant [P > 0.05], *P < 0.05, **P < 0.01, ***P < 0.001). Treg, regulatory T cell; Tfh, T follicular helper cell.