Extended Data Fig. 9: PSME4 depletion in KP1.9 cells increases MHC levels.

a, Lysates of KP1.9 cells with PSME4 knockdown (shK369 and shK428, shK569 or shK813) or control (shRFP) were blotted for PSME4 and β-Actin as a loading control. b, Quantification of PSME4 band intensity in KP1.9 cell line with PSME4 KD or Ctrl (shRFP) across independent samples per condition normalized to actin as a loading control and to shRFP (bars indicate mean ± s.d.; two-sided student’s T test, shK428 P = 0.018, shK569 P = 0.0054 or shK813 P = 0.0368). c, KP1.9 cells and healthy mouse lung tissue were blotted for PSME4. β-Actin was blotted as a loading control. d, qPCR shows the expression of PSME4 in KP1.9 cells transfected with a PSME4 overexpression plasmid (n = 3 independent experiments; bars indicate mean ± s.d.). e, KP1.9 cells transfected with a PSME4 overexpression plasmid (+) or GFP (-) as a control. Cell lysates were blotted for PSME4 or PSMA1-7. β-Actin was blotted as a loading control. f, Band intensities of e were quantified for PSME4 and normalized to actin as a loading control (two-sided paired student’s t-test *P = 0.0331; n = 3 independent samples). g, Median fluorescence intensity from flow cytometry analysis of MHC-I expression using a Kb or Db antibody on KP1.9 cells with PSME4 overexpression or control (n = 3 independent samples). Box plots span the first to third quartiles and whiskers show 1.5× interquartile range (Wilcox test). h,i, GO-term enrichment (of key markers from the plasmacytoid DC (h) or mature DCs enriched in immunoregulatory molecules (mregDCs; i) population. Significance determined by FDR corrected q-value.