Differential TF activity analysis between SLE and healthy controls within regulon 0, which includes the HPSC clusters, showed increased predicted activity of the TFs IRF7 and IRF9 as regulators of transcriptomic changes in SLE (p < 0.05, Figure 4D; Supplementary Table 5), further supporting that HSPCs in SLE are targeted by IFNs. Here, IRF9 is linked to systemic lupus erythematosus.