Samples localized to disease pseudotime positions ‘beyond the SPIP’ showed a significant decrease in the abundance of urothelial cells, accompanied by an increase in the abundance of activated macrophages and fibroblasts (Fig. 3C and Fig. S5G; p < 0.003), a transition from naive to memory CD4 + T-cells (Fig. 3C and Fig. S5G; p < 0.05) and no significant change in basal tumor cells (Fig. S5G–H; p > 0.1). The gene discussed is CD4; the disease is neoplasm.