Fig 6. Secondary screening identifies modifiers of the response to A3A in HMCES KO LXF-289 cells.

(A) Schematic of the secondary screen in LXF-289 A3A HMCES KO cells. (B) PC analysis of A3A conditional LFC scores for all genes across all 10 experimental conditions (see labels next to arrows, which show loadings of the conditions on PC1 and PC2; HMCES wt refers to the parental LXF-289 cell line). Top genes, defined as the top 10 genes from S3C Fig, plus those that pass at least 1 filter (specified in the legend of S11 Fig), as well as additional genes that pass the filters when they are relaxed, are highlighted on the figure for each indicated comparison: green, synthetic advantage; black, synthetic lethality; red synthetic lethal in HMCES wt. Gene-level LFCs and GO analysis results are included in S6 and S7 Tables, and additional epistasis analysis is included in S11 Fig. (C) Selected genes from panel B, sorted by a score calculated as the mean of the standardized sgRNA LFCs and standardized MLE beta score differences from the 4 DOX vs. control comparisons of HMCES KO samples, minus the mean obtained in the same way for the HMCES wt samples. A negative score (black squares, as in B) indicates likely synthetic lethality with A3A expression in HMCES KO but not in HMCES wt, and a positive score (green triangles, as in B) suggests that the gene confers a synthetic advantage with A3A expression in HMCES KO, but not in HMCES wt (e.g., UNG). Known TSGs or oncogenes are indicated (see key, data derived from COSMIC: https://cancer.sanger.ac.uk/census). Gene products that are known PIKK substrates or regulators (PIKK) and those that have been demonstrated to localize to active replication forks (Fork) are indicated [69–71]. Numerical data for panels B and C are provided in S6 Data. A3A, APOBEC3A; gDNA, guide DNA; GO, Gene Ontology; KO, knockout; LFC, log₂ fold change; PC, principal component; PIKK, PI-3 kinase-like kinase; sgRNA, single gRNA; TSG, tumor supressor gene; wt, wild-type.