Comprehensive genomic characterization of squamous cell lung cancers

Abstract

Lung squamous cell carcinoma is a common type of lung cancer, causing approximately 400,000 deaths per year worldwide. Genomic alterations in squamous cell lung cancers have not been comprehensively characterized, and no molecularly targeted agents have been specifically developed for its treatment. As part of The Cancer Genome Atlas, here we profile 178 lung squamous cell carcinomas to provide a comprehensive landscape of genomic and epigenomic alterations. We show that the tumour type is characterized by complex genomic alterations, with a mean of 360 exonic mutations, 165 genomic rearrangements, and 323 segments of copy number alteration per tumour. We find statistically recurrent mutations in 11 genes, including mutation of TP53 in nearly all specimens. Previously unreported loss-of-function mutations are seen in the HLA-A class I major histocompatibility gene. Significantly altered pathways included NFE2L2 and KEAP1 in 34%, squamous differentiation genes in 44%, phosphatidylinositol-3-OH kinase pathway genes in 47%, and CDKN2A and RB1 in 72% of tumours. We identified a potential therapeutic target in most tumours, offering new avenues of investigation for the treatment of squamous cell lung cancers.

Figure 1. Significantly mutated genes in lung SqCC

Significantly mutated genes (q-value <0.1) identified by exome sequencing are listed vertically by q-value. The percentage of lung SqCC samples with a mutation detected by automated calling is noted at the left. Samples displayed as columns, with the overall number of mutations plotted at the top and samples arranged to emphasize mutual exclusivity among mutations.

Figure 2. Somatically altered pathways in squamous cell lung cancer

Left, Alterations in oxidative response pathway genes by somatic mutation as defined by somatic mutation, copy number alteration or up- or down-regulation. Frequencies of alteration are expressed as a percentage of all cases, with background in red for activated genes and blue for inactivated genes. Right, Alterations in genes that regulate squamous differentiation, as defined in the left panel.

Figure 3. Gene expression subtypes integrated with genomic alterations

Tumors are displayed as columns, grouped by gene expression subtype. Subtypes were compared by Kruskal-Wallis tests for continuous features and by Fisher’s exact tests for categorical features. Displayed features displayed showed significant association with gene expression subtype (P<0.05), except for CDKN2A alterations. deltaN expression percentage represents transcript isoform usage between the TP63 isoforms, deltaN and tap63, as determined by RNA-sequencing. Chromosomal instability (CIN) is defined by the mean of the absolute values of chromosome arm copy numbers from the GISTIC^, output. Absolute values are used so that amplification and deletion alterations are counted equally. Hypermethylation scores and iCluster assignments are described in Supplementary Figure S6.1 and S7.A1, respectively. CIN, methylation, gene expression, and deltaN values were standardized for display using z-score transformation.

Figure 4. Multi-faceted characterization of mechanisms of CDKN2A loss

a, Schematic view of the exon structure of CDKN2A demonstrating the types of alterations identified in the study. The locations of point mutation are denoted by black and green circles. b, CDKN2A expression (y-axis) versus CDKN2A copy number (x-axis). Samples are represented by circles and colored-coded by specific type of CDKN2A alteration. c, Diagram of the KIAA1797-CDKN2A fusion identified by whole genome sequencing. d, CDKN2A alterations and expression levels (binary) in each sample.

Figure 5. Alterations in targetable oncogenic pathways in lung SqCCs

Pathway diagram showing the percentage of samples with alterations in the PI3K/RTK/RAS pathways. Alterations are defined by somatic mutations, homozygous deletions, high-level, focal amplifications, and, in some cases, by significant up- or down-regulation of gene expression (AKT3, FGFR1, PTEN).