Frequent alterations in cytoskeleton remodelling genes in primary and metastatic lung adenocarcinomas

Abstract

The landscape of genetic alterations in lung adenocarcinoma derived from Asian patients is largely uncharacterized. Here we present an integrated genomic and transcriptomic analysis of 335 primary lung adenocarcinomas and 35 corresponding lymph node metastases from Chinese patients. Altogether 13 significantly mutated genes are identified, including the most commonly mutated gene TP53 and novel mutation targets such as RHPN2, GLI3 and MRC2. TP53 mutations are furthermore significantly enriched in tumours from patients harbouring metastases. Genes regulating cytoskeleton remodelling processes are also frequently altered, especially in metastatic samples, of which the high expression level of IQGAP3 is identified as a marker for poor prognosis. Our study represents the first large-scale sequencing effort on lung adenocarcinoma in Asian patients and provides a comprehensive mutational landscape for both primary and metastatic tumours. This may thus form a basis for personalized medical care and shed light on the molecular pathogenesis of metastatic lung adenocarcinoma.

Figure 1. Mutational signatures of lung adenocarcinoma.

Comparison of signatures between primary and metastatic lung adenocarcinomas in this study as well as lung adenocarcinomas derived from a previously published European cohort. Signatures were displayed according to the 96-substitution classification, with x-axes showed mutation types and y-axes showed trinucleotide frequency of each mutation type.

Figure 2. Somatic mutations and clinical association in lung adenocarcinomas.

(a) Recurrently mutated genes and mutant frequencies in the full discovery and validation cohorts, comprising 335 primary tumours and 35 metastatic tumours. Primary tumours were classified into two groups: samples with metastases in adjacent lymph nodes or distant organs on diagnosis or surgery (PM+, n=229), and samples which were metastasis free at the time for diagnosis (PM−, n=105). Gender, smoking status and tumour stages were listed at the bottom according to the samples, as well as mutation types. Asterisks indicate genes predicted to be significantly mutated by MutSig algorithm (FDR<0.1). (b) Associations of specific mutated genes with metastasis status, gender, smoking status and age. Asterisks were marked at the sides of sample sets with significantly higher mutant frequencies (P<0.05, Fisher's exact test).

Figure 3. Genomic copy number alterations and mRNA expression profiling.

(a) Landscape of genomic copy number alterations in Chinese lung adenocarcinomas. Amplifications and deletions across chromosome 1–22 and X were shown with y-axis presenting G-score altitude. CNV profiles in primary and metastatic tumours were shown with different colours. Putative cancer driver genes were marked in locations with peaks across the genome. (b) Cluster classification of 56 tumours indicated three clusters with different gene expression pattern, 464 representative genes are included. (c) Gene expression clusters integrated with genomic mutations. Tumours were ordered as three clusters shown in b. Alterations of selected genes were shown across clusters, revealing mutations (Mut.) of KRAS, KEAP1, FLT1 as well as copy number amplification (Amp.) of CEP72 were enriched in cluster 3. Cluster 3 was also characterized as having exceeded expression (Expr.) status in genes participating in PI3K–Akt pathway or cytoskeleton remodelling process.

Figure 4. Integrated characterizations of IQGAP3 alterations.

(a) Quantitative RT–PCR analysis of 132 lung adenocarcinoma patients showed significantly higher expression of IQGAP3 mRNA in tumours than in adjacent normal tissues in lung adenocarcinoma patients. Kaplan–Meier survival curves showed that patients with high IQGAP3 expression had shorter overall survival. (b) Three-dimensional model of IQGAP3 protein showing the somatic mutations affecting functional domains. qPCR analysis in patients harbouring these mutations showed no significant difference of IQGAP3 expression between tumour and normal tissues. (c) Tumours harbouring genomic amplifications of IQGAP3 in chromosome 1. QPCR analysis indicated higher expression of IQGAP3 in corresponding tumours with copy gain of IQGAP3 than in adjacent normal tissues.

Figure 5. Altered pathways and network in lung adenocarcinomas.

(a) Somatic mutations, copy umber alterations and genomic rearrangements affecting p53 signalling/cell cycle process, RTK/Ras/PI3K pathway, cytoskeleton remodelling regulation and histone/chromatin modification. Percentage presented alteration frequencies in 101 primary tumours and 35 metastatic tumours, respectively. (b) Network connection of genes involved in cytoskeleton remodelling regulation. Gene–gene interactions are inferred by CytoScape program.

Figure 6. Therapeutic targeting in lung adenocarcinomas.

Somatic mutations, copy number alterations and translocations affecting genes that are regarded as targets of specific antibodies or kinase inhibitors. Somatic mutations only consist of recurrent mutations in this cohort or mutations previously reported in the COSMIC database. Primary tumours and metastatic tumours with at least one alteration are shown.