Clinical and genomic features of non-small cell lung cancer occurring in families

Abstract

Background: Exposure to environmental carcinogens, such as through smoking, is a major factor in the carcinogenesis of non-small cell lung cancer (NSCLC). However, genetic factors may also contribute.

Methods: To identify candidate tumor suppressor genes for NSCLC, we included 23 patients (10 related pairs and 3 individuals) with NSCLC who had other NSCLC-affected first-degree relatives in a local hospital. Exome analyses for both germline and somatic (NSCLC specimens) DNA were performed for 17 cases. Germline exome data of these 17 cases revealed that most of the short variants were identical to the variants in 14KJPN (a Japanese reference genome panel of more than 14 000 individuals) and only a nonsynonymous variant in the DHODH gene, p.A347T, was shared between a pair of NSCLC patients in the same family. This variant is a known pathogenic variant of the gene for Miller syndrome.

Results: Somatic genetic alterations in the exome data of our samples showed frequent mutations in the EGFR and TP53 genes. Principal component analysis of the patterns of 96 types of single nucleotide variants (SNVs) suggested the existence of unique mechanisms inducing somatic SNVs in each family. Delineation of mutational signatures of the somatic SNVs with deconstructSigs for the pair of germline pathogenic DHODH variant-positive cases showed that the mutational signatures of these cases included SBS3 (homologous recombination repair defect), SBS6, 15 (DNA mismatch repair), and SBS7 (ultraviolet exposure), suggesting that disordered pyrimidine production causes increased errors in DNA repair systems in these cases.

Conclusion: Our results suggest the importance of the detailed collection of data on environmental exposure along with genetic information on NSCLC patients to identify the unique combinations that cause lung tumorigenesis in a particular family.

Keywords: DHODH; exome; mutational signature; non-small cell lung cancer; tumor suppressor gene.

FIGURE 1

Schematic diagram of the present study design. We collected paired non‐small cell lung cancer (NSCLC) patients in our hospital and added three more cases with a family history featuring NSCLC.

FIGURE 2

Histopathology of mucinous lung adenocarcinomas in a pair of sibling patients. Images of hematoxylin–eosin‐stained specimens are shown. Scale bars (50 μm) are indicated in the lower right corner of the images. The two cases differed in the smoking status (LC01‐1 and LC01‐2 were a nonsmoker and smoker, respectively), so the smoking deposit is only seen in the histopathology of LC01‐2.

FIGURE 3

Comparison of DHODH p.A347T and a known pathogenic variant in the 3D model. (a and b) Predicted positions of p.A347T and a known pathogenic variant, p.R346W, in DHODH, respectively. The variant amino acid residues are indicated with light‐blue spheres (indicated with red arrows). The images (PDB version) were obtained from the jMorp website (see main text).

FIGURE 4

Possible somatic pathogenic variants of non‐small cell lung cancer (NSCLC) in this study. (a) A list of genes with somatic mutations found more than once in our collection (17 cases). KRAS oncogene mutation was identified in only one case, so it is omitted from this list. The rows for the EGFR and TP53 gene are highlighted with red rectangles. (b) DAVID analyses of the somatic mutated genes in this study. The KEGG pathway analysis results are shown. The similarity between our mutated genes and NSCLC dataset in KEGG database shows statistical significance (indicated with a red rectangle).

FIGURE 5

Scatter plot of principal component analysis of 96 patterns of single‐nucleotide variations of somatic mutations in the 17 NSCLC cases. The first and second principal components were plotted. Each related pair is enclosed in an ellipse and connected with a dotted line. Data from FFPE specimens are indicated with a red circle.

FIGURE 6

Delineation of mutational signatures of two related pairs for somatic genetic alterations in NSCLC. (a and b) Results of deconstructSigs analyses for a sibling pair (LC04) sharing a possible pathogenic mutation of the DHODH gene and the most distant pair in the PCA analysis (LC09) for a and b, respectively. The top three bar graphs indicate the ratios of single‐nucleotide variants of samples on the vertical axis and 96 types of SNVs are on the horizontal axis. “Actual” is the ratio of variants observed. “Produced” is the ratio of each variant by delineation by deconstructSigs with 30 identified SBSs. “Differences” indicates the difference between “Actual” and “Produced.” The bottom pie graphs indicate the ratio of deduced SBSs for the patients. The possible causes of the mutational signatures are indicated in a rectangle.