Fig. 4. Enrichment of interferon response and inflammation-associated gene sets correlates with progression free survival in human lung tumor biopsies.

Lung tumor biopsy specimens from eight EGFR mutant lung cancer patients were collected prior to treatment (baseline) and after 2 weeks of treatment with an EGFR TKI (re-biopsy). a Representative CT images of two patients acquired pre-treatment and at re-biopsy are shown. The arrowheads indicate the lesion that underwent biopsy prior to and on treatment with EGFR TKIs. b Following RNAseq analysis of RNA purified from the biopsies, GSEA was performed using the Hallmark MSigDB gene sets. The mean Normalized Enrichment Scores (NES) for each Hallmark across the 8 biopsy pairs were used to rank the gene sets and the top 15 are presented as a heatmap (the full analysis is provided in Supplementary Table S2). The data are from one distinct sample per biopsy. c Pearson correlation analysis was used to compare the enrichment scores from the 50 Hallmark gene sets with the TTP for the 8 patients. The full analysis is presented in Supplementary Table S3. The patient biopsies from the two EGFR-L858R tumors are indicated with a circle containing an “x”.