Fig. 1.

Synthetic lethal interactions with FGFR inhibition are identified using a genome-wide RNA interference–based loss-of-function screen. (A) As described in the Materials and Methods, the HNSCC cell lines UMSCC25, CCL30, and 584-A2 were transduced with a genome-wide shRNA library and either treated with the FGFR inhibitor, AZ8010, or DMSO control for 72 hours. After recovering for an additional 72 hours, RNA was isolated from the cells and nested polymerase chain reaction was performed to isolate the shRNA sequences and to add Illumina adaptor sequences. Samples were submitted to Illumina sequencing and the reads were analyzed by BiNGS! (Bioinformatics for Next Generation Sequencing). (B) Tabular representation of the shRNA counts obtained by deep sequencing for the 10 most highly ranked SLATs in UMSCC25 cells as well as ERBB2. The intensity of red indicates the number of shRNA read counts in each replicate for both the control and AZ8010-treated groups. Each line corresponds to an independent shRNA targeting the indicated gene. The top 10 hits and the data for ERBB2 for UMSCC25 cells are shown. (C) Synthetic lethal hits (SLATs) (E value ≤ 20) among growth receptors and their common downstream signaling pathways. SLATs identified in the UMSCC25 cells are shaded red, SLATs in 584-A2 cells are shaded green, and SLATs in CCL30 cells are shaded blue. Pathway members that were not identified as SLATs in any cell line are unshaded. The number listed near each SLAT is the P value (see Materials and Methods).