Fig 1: PAPSS1 and PAPSS2 are novel synthetic lethal paralogs detected by TCGADEPMAP.a, Rank plot of target-level GI scores in H1299 cells, including the top ten synthetic lethalities (table insert). The novel synthetic lethality, PAPSS1/PAPSS2, is highlighted in blue. All CRISPR screens were performed as n = 3 biological replicates per cell line. b, Spheroid size of H1299 cells with single or dual PAPSS1 and PAPSS2 knockouts, normalized to NT control spheroids; n = 4 biological replicates per condition. Data show mean ± s.d. *P < 0.05 and **P < 0.01 as per unpaired, two-tailed t-test. c, Flow cytometry histogram overlay plots of viable H1299 and UMUC3 cells (DAPI−) showing expression of cell surface sulfonated HSPGs as measured by antibody clone 10E4-FITC. Dual loss of PAPSS1/PAPSS2 leads to total loss of sulfonation comparable to heparinase III treatment (HepIII*) which specifically cleaves sulfonated HS chains. d, Growth defects of UMUC3 spheroids following deletion of PAPSS1 (yellow bars) were partially rescued by the addition of 10 μg ml−1 and 50 μg ml−1 of exogenous HS as compared to NT control spheroids (green bars); n = 4 biological replicates for the untreated control and n = 3 biological replicates per treated condition. Data are mean ± s.d. *P < 0.05 as per unpaired, two-tailed t-test. e, Diagram showing tumor volumes over time (d, days) after in vivo implantation of 1 × 106 UMUC3 NT or PAPSS1-KO cells in SCID/beige mice. Each dot represents an individual mouse (n = 5 mice per condition); ***P < 0.001, as determined by unpaired, two-tailed t-test of the final data point. f, Kaplan–Meier plot of TCGADEPMAP patients with a predicted PAPSS1/PAPSS2 synthetic lethality has a worse outcome compared to the rest of the cohort, as determined by a Cox log-rank test. DAPI, 4,6-diamidino-2-phenylindole.Source data