Extended Data Figure 7: Extensive genetic and transcriptional variation across 23 strains of A549.
(a) Top: unsupervised hierarchical clustering of 23 A549 strains, based on their non-silent single nucleotide variant (SNV) profiles derived from deep targeted sequencing. Strains expected to cluster together based on their evolutionary history are highlighted in blue. Bottom: a corresponding heatmap, showing the mutation status of non-silent mutations across the 23 A549 strains. Shown are mutations identified only in a subset of the strains, which were detected in above 5% of the reads (allelic fraction>0.05). The presence of a mutation is shown in yellow, and its absence in gray. (b) The number of non-silent point-mutations shared by each number of A549 strains. (c) Top: unsupervised hierarchical clustering of 23 A549 strains, based on the allelic fractions of their non-silent SNVs. Bottom: a corresponding heatmap, showing the allelic fractions of non-silent mutations across the 23 A549 strains. Shown are mutations identified only in a subset of the strains. The presence of a mutation is shown in color according to its allelic fraction. (d) The allelic fractions of non-silent mutations in six selected genes across 23 A549 strains. Note the inactivating frameshift mutation in SMARCA4, one of the most frequently mutated genes in lung adenocarcinoma27,64,65, which was detected at an allelic fraction of ~1 in 9 of the strains, but was not detected at all in the other 14 strains. (e) The number of gene-level copy number alterations (CNAs) shared by each number of MCF7 strains. Copy number gains are shown in red, and copy number losses in blue. (f) CNA variation in the copy number of CDKN2A. Copy number gains are shown in red, and copy number losses in blue. Thresholds for relative gains/losses were set at +/−0.1, respectively. (g) Unsupervised hierarchical clustering of 23 A549 strains, based on their global gene expression profiles. Strains expected to cluster together based on their evolutionary history are highlighted in blue. (h) A tSNE plot of L1000-based gene expression profiles from multiple samples of nine cancer cell lines. The asterisk denotes the 23 A549 strains profiled in the current study. (i) Comparison of the L1000-based A549 expression profiles to microarray-based expression profiles from CCLE. Histograms present the distributions of the Spearman correlations between the 23 A549 strains and either A549 (light blue), other non-small cell lung cancer cell lines (purple), other lung cancer cell lines (green) or non-lung cancer cell lines (gray). The comparison is based on the 978 “landmark” genes directly measured in L1000. (j) The number of differentially expressed genes (DEGs) identified in all possible pairwise comparisons of A549 strains, using a two-fold change cutoff. LFC, log fold change; DEGs, differentially expressed genes. (k) Arm-level gains are associated with significant up-regulation, and arm-level losses are associated with significant down-regulation, of genes transcribed from the aberrant arms. For example, GSEA reveals up-regulation of the genes on chromosome 2q in strains that have gained a copy of that arm (left), and down-regulation of the genes on chromosome 9q in strains that have lost a copy of that arm (right). (l) Gene-level CNAs are associated with significant dysregulation of the perturbed pathways. For example, GSEA reveals up-regulation of the genes that are up-regulated, and down-regulation of the genes that are down-regulated, when TP53 is knocked-down in strains with MDM2 high-level copy number gain; and up-regulation or down-regulation of the G2/M cell cycle checkpoint signature in strains with CDKN2A copy number loss or CCND1 copy number gain, respectively. (m) Point mutations are associated with significant dysregulation of the perturbed pathways. For example, GSEA reveals down-regulation of two PRC2-related expression signatures in strains with an inactivating SMARCA4. (n) The 10 top gene sets identified by GSEA to be significantly enriched among the 100 genes that are most differentially expressed across the A549 strains. The six gene sets related to KRAS signaling are highlighted in red.