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. 2019 Aug 27;8:e43668. doi: 10.7554/eLife.43668

Figure 2. Examining global gene expression changes caused by combination of PI3K and MAPK activation using RNA-SEQ.

(A) Tumors were adenovirally induced in cohorts of BrafCAT/+ and BrafCAT/+;Pik3caLAT-H1047R/+ mice with AT2 specific CRE expression. Mice harvested at 2 or 6 weeks were induced with 107 PFU of Ad5-SpC-CRE, whereas mice harvested at 12 weeks were induced with 106 PFU of Ad5-SpC-CRE. (B) Tumor cells were harvested from each genotype at 2 weeks, 6 weeks, and 12 weeks post tumor induction via tissue dissociation and FACS. (C) GSEA analyses profiling cells sorted from BRAFV600E/PI3KαH1047R driven tumor bearing mice compared to BRAFV600E driven tumor bearing mice, showing all ‘Hallmark’ gene sets along with gene sets constructed from the most specific markers of the cell types of the distal lung epithelium. Black bars indicate adjP <.05, gray bars indicate Benjamini-Hochberg corrected enrichment statistic adjP ≥. 05. Here all time points combined within genotype. (D) GSEA mountain plot showing broad activation of PI3K signaling in BRAFV600E/PI3KαH1047R driven tumor bearing mice; adjP is Benjamini-Hochberg corrected enrichment statistic. (E) GSEA mountain plot showing broad activation of EMT in BRAFV600E/PI3KαH1047R driven tumor bearing mice; adjP is Benjamini-Hochberg corrected enrichment statistic. (F) GSEA mountain plot showing widespread loss of AT2 identity in BRAFV600E/PI3KαH1047R driven tumor bearing mice; adjP is Benjamini-Hochberg corrected enrichment statistic.

Figure 2—source code 1. R script to perform gene set enrichment analysis on Figure 2—source data 1–2, as well as plot these results.
elife-43668-fig2-code1.r (4.1KB, r)
DOI: 10.7554/eLife.43668.007
Figure 2—source data 1. DEseq2 output of differentially expressed genes comparing BRAFV600E/PI3KαH1047R and BRAFV600E driven tumors – all weeks pooled.
elife-43668-fig2-data1.tds (3.1MB, tds)
DOI: 10.7554/eLife.43668.008
Figure 2—source data 2. DEseq2 output of differentially expressed genes comparing BRAFV600E/PI3KαH1047R and BRAFV600E driven tumors – weeks separated.
elife-43668-fig2-data2.zip (3.3MB, zip)
DOI: 10.7554/eLife.43668.009

Figure 2.

Figure 2—figure supplement 1. Examining global gene expression changes caused by combination of PI3K and MAPK activation using RNA-SEQ.

Figure 2—figure supplement 1.

(A) Expanded view of GSEA analyses comparing results at each individual time point. Point size inversely proportional to adjusted enrichment statistic p value, color indicates time point at which comparison was performed. (B) In depth gating strategy used for isolation of all FACS sorted tumor cells in this study.