Extended Data Fig. 7: EGLN1 and VHL are selectively essential in tRCC cells.
a, HIF1A mRNA level in ccRCC or tRCC tumours from three independent studies (TCGA, Motzer et al., Elias et al. (PDX))20,21,22. b, HIF1A mRNA level in tRCC cell lines (n = 3, UOK109, FU-UR-1, s-TFE) versus ccRCC cell lines (n = 7, A498, A704, 786-O, 769-P, Caki-1, Caki-2, OS-RC-2). c, OCR after knockout of VHL in UOK109 and s-TFE cell lines. Data are shown as mean -+ s.d. for n = 8 (UOK109 control sgRNA), n = 12 (UOK109 VHL sgRNA-1), n = 11 (UOK109 VHL sgRNA-2), n = 13 (s-TFE control sgRNA, s-TFE VHL sgRNA-1) and n = 10 (s-TFE VHL sgRNA-2) biological replicates. d, Genes whose knockout has been previously reported27 to confer sensitivity (422 genes) or resistance (79 genes) to NRF2 activation were compared for dependency in s-TFE cells vs. ccRCC cells (average of dependency score for 5 ccRCC cell lines, for each gene). e, Western blot showing the expression of EGLN1, VHL, HIF-1-α after knockout of VHL in ccRCC (786-O) and tRCC (UOK109, s-TFE and FU-UR-1) cell lines. f, Cell proliferation of tRCC cell lines (UOK109 and s-TFE) and ccRCC (786-O) cell lines after knockout of VHL. Data are shown as mean -+ s.d. for n = 3 (UOK109, 786-O) and n = 5 (s-TFE) biological replicates. g, Western blot showing the expression of EGLN1, VHL after knockout of EGLN1 or VHL in tRCC (FU-UR-1) cell line. h, Cell proliferation of FU-UR-1 cells after knockout of EGLN1 or VHL. Data are shown as mean -+ s.d. for n = 3 biological replicates. i, Western blot showing the expression of EGLN1, VHL after knockout of EGLN1 or VHL in ccRCC (Caki-1) cell line. j, Cell proliferation of Caki-1 cells (VHL preserved) after knockout of EGLN1 or VHL. Data are shown as mean -+ s.d. for n = 6 biological replicates. k, Western blot showing the HIF-1-α expression in UOK109 and s-TFE expressing sgRNA target HIF1A after treatment with EGLN inhibitor (FG4592). Western blot performed once. For (a) and (d), statistical significance was determined by two-sided Mann–Whitney test. Centre line, median; box limits, upper and lower quartiles; whiskers, 1.5 times the interquartile range. For (f), (h) and (j), statistical significance was determined by two-tailed Student’s t-test.
