Extended Data Fig. 4: Deletion of KDM5B induces endogenous retroelement expression and forms dsRNA.
From: KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements
a,b, Immunofluorescence staining of dsRNA with J2 antibody (red) and DAPI (blue) in WT or Kdm5b−/− YUMMER1.7 cells, using a confocal microscope (a) (scale bar = 50 µm) and 1445 cells with Ctl shRNA or Kdm5b shRNA (b) (scale bar = 50 µm). c, Immunofluorescence staining of dsRNA with J2 antibody (red) and DAPI (blue) of WT or Kdm5b sg YUMMER1.7 tumors harvested 14 days after tumor injection (scale bar = 100 µm). d. Immunofluorescence staining (left) and quantification (right) of dsRNA with J2 antibody (red) and DAPI (blue) of representative patients as responder or non-responder to ICB (scale bar = 100 µm). MGLI= mean grey level intensity. e, Volcano plots comparing inverted repeats in YUMMER1.7 cells with Kdm5b sg vs YUMMER1.7 cells with Ctl sg. f, Western blot analyses of Kdm5b sg YUMMER1.7 cells treated with 20 µM of reverse transcriptase inhibitors (RTi) for 48h. For gel source data, see Supplementary Fig. 1. g, qPCR analyses of retroelements from DNA isolated from cytosolic (cyto) lysate versus from nuclear lysate. Data are mean ± SD. h, Relative copy number of mitochondrial (mito) DNA quantified by qPCR analyses with Dloop primers. Data are mean ± SD. i, RT-qPCR analyses of MMVL30-int, RLTR6_Mm and Isg15 in Kdm5b−/− cells with the indicated doxycycline (Dox) inducible shRNAs. Data are mean ± SEM. p values for g-i were calculated using unpaired two-sided Students’ t tests. n.s., not significant; **p<0.01; ***p<0.001; ****p<0.0001.
