Whole Exome Sequencing Identifies Frequent Somatic Mutations in Cell-Cell Adhesion Genes in Chinese Patients with Lung Squamous Cell Carcinoma

Abstract

Lung squamous cell carcinoma (SQCC) accounts for about 30% of all lung cancer cases. Understanding of mutational landscape for this subtype of lung cancer in Chinese patients is currently limited. We performed whole exome sequencing in samples from 100 patients with lung SQCCs to search for somatic mutations and the subsequent target capture sequencing in another 98 samples for validation. We identified 20 significantly mutated genes, including TP53, CDH10, NFE2L2 and PTEN. Pathways with frequently mutated genes included those of cell-cell adhesion/Wnt/Hippo in 76%, oxidative stress response in 21%, and phosphatidylinositol-3-OH kinase in 36% of the tested tumor samples. Mutations of Chromatin regulatory factor genes were identified at a lower frequency. In functional assays, we observed that knockdown of CDH10 promoted cell proliferation, soft-agar colony formation, cell migration and cell invasion, and overexpression of CDH10 inhibited cell proliferation. This mutational landscape of lung SQCC in Chinese patients improves our current understanding of lung carcinogenesis, early diagnosis and personalized therapy.

Figure 1. Significantly mutated genes in lung SQCC.

Significantly mutated genes (Qvalue < 0.1) identified by exome and target capture sequencing of 198 lung SQCCs are listed vertically by Q-value. The percentage of individuals with mutations of each gene is shown on the left. Samples displayed as columns and the overall number of mutations is plotted at the top. SMGs identified by both algorithms are marked with red font color. Samples screened by whole exome sequencing are marked with green font color, samples screened by target capture sequencing are marked with orange font color. Syn., synonymous; WES, whole exome sequencing; TCS, target capture sequencing.

Figure 2. Mutually exclusive/concurrent mutated genes and somatic mutations in CDH10 in lung SQCCs.

(a) Concurrent and mutually exclusive mutations observed in frequently mutated genes in lung SQCCs. For each gene (row), tumors (columns) with or without mutations are labeled in red or blue, respectively. (b–c) Totally mutual exclusive (no mutations from the two genes in one sample) in several pairs of gene, such as KEAP1 and NFE2L2, CDH10 and CTNNA2, are shown. (d) Somatic mutations in CDH10. The types and relative positions of somatic mutations are shown in the transcripts of CDH10 using the following symbols: red stars, nonsense mutations; bullets, missense mutations; blue diamonds, mutations at splice sites. Domains and motifs in each encoded protein product are also indicated.

Figure 3. Significantly mutated pathways in lung SQCC.

Somatic mutations in lung SQCC frequently occurred in genes of the (a) Cell-Cell adhesion/Wnt/Hippo/YAP, (b) Oxidative stress response, (c) PI3K/RTK/RAS signaling pathways. Oncogenes are indicated in pink to red and tumor suppressor proteins are shown in light to dark blue. The darkness of the colors is positively correlated to the percentage of tumors with genetic alterations. The frequency of genetic alterations for each of these pathway members in 198 tumors is indicated.

Figure 4. Mutation diversity of SMGs in Chinese lung SQCCs and other cancer types from TCGA data.

Percentages of samples mutated in each cancer types and Pan-Cancer are shown, and the highest percentage in each gene is shown in bold. BLCA, bladder urothelial carcinoma; BRCA, breast adenocarcinoma; COAD,READ, colon and rectal carcinoma; GBM, glioblastomamultiforme; HNSC, head and neck squamous cell carcinoma; KIRC, kidney renal clear cell carcinoma; LAML, acute myeloid leukaemia; OV, ovarian serous carcinoma; UCEC, uterine corpus endometrial carcinoma; LUAD, lung adenocarcinoma; LUSC, lung squamous cell carcinoma (TCGA study); LUSQCC, lung squamous cell carcinoma (the present study).