Figure 5.

Interpreting the tumor-infiltrated T cells via ProjectSVR. We projected tumor-infiltrated CD4+ (a–c) and CD8+ T (d–f) cells from patients with breast cancer responding or non-responding to anti-PD1 treatment on the pan-cancer T cell atlas using ProjectSVR. And then transferred the reference T cell subtypes to query cells using a 10-NN classifier on reference embeddings. A. Projection of CD4+ T cells from responders and non-responders of anti-PD1 treatment by ProjectSVR. Dots represent reference metacells colored by cell type obtained from the original study. (b) Volcano plot of differential cell subtypes of CD4+ T cells between responders (R) and non-responders (NR). The P values were calculated by Wilcoxon test. Dots colored by cell subtypes are shown in (a). (c) Boxplots comparing the frequency of two CD4 + T cell subtypes between responders (R) and non-responders (NR). The P values by Wilcoxon test are shown. (d–f) The same plot as in (a–c) was applied to CD8+ T cells. Tfh, follicular helper T cells; Th1, T helper 1 cells. Treg, regulatory T cells. Tex, exhausted T cells; ISG, interferon-stimulated genes; Temra, terminally differentiated effector memory or effector; Tem, effector memory T cells; Trm, tissue-resident memory T cells; Tn, naïve T cells; and KIR, killer cell immunoglobulin-like receptors.