To test their association with SLE, we applied a Covarying Neighborhood Analysis (CNA) (28), which demonstrated that ICOS+ Ki67+ Tph/Tfh cells, Tregs, and granzyme K+ CD4 T cells were significantly enriched in SLE patients compared to controls (Figure 4B, Extended Data Figure 3D). This evidence concerns the gene TPH1 and systemic lupus erythematosus.