Clinical significance of DNA damage response mutations in stage I and stage IIIa NSCLC

Abstract

Background: DNA damage response (DDR) pathways are essential to sustain genomic stability and play a critical role in cancer development and progression. Here, we investigated the profile of DDR gene mutations in early-stage non-small cell lung cancer (NSCLC) and their prognostic values.

Methods: We first examined 74 DDR genes involved in seven DDR pathways and then focused on six specific genes: ATM, BRCA1, BRCA2, CHEK1, BARD1, and BRIP1. A total of 179 stage I and IIIa NSCLC patients who received curative resection in Peking Union Medical College Hospital and their corresponding samples were collected for DNA sequencing, immunohistochemistry and survival analysis.

Results: A total of 167 eligible patients were finally analyzed. Mutation frequencies were 82% and 26.3% for the selected 74 genes and six genes, respectively. Mismatch repair (MMR) and nucleotide excision repair (NER) alterations were observed more frequently in lung squamous cell carcinoma (LUSC) and smokers were more likely to develop the selected six DDR gene mutations than those who never smoked. Deleterious mutations in the six genes were independent prognostic indicators of significantly longer disease-free survival and overall survival. No association was found between DDR gene status and PD-L1 expression, CD8 positive lymphocyte and tumor-associated macrophage infiltration in tumor area. However, numbers of mutations were significantly increased among patients with DDR alterations.

Conclusions: Deleterious mutations of these six genes were common in resected NSCLC and could serve as prognostic biomarkers.

Keywords: DNA damage response; mutation landscape; prognosis; resected NSCLC; tumor microenvironment.

FIGURE 1

Mutation profile of the 74 DDR genes in stage I and IIIa non‐small cell lung cancer (NSCLC) patients. (a) Mutation profile of the 74 DNA damage response (DDR) genes. (b) Distribution of LUAD or LUSC in individual DDR pathway mutate samples. LUSC patients were prone to NER and MMR mutations. (c–e) Males and smokers were more likely to develop HR alterations. Females were more likely to develop NHEJ mutations. LUAD, lung adenocarcinoma. LUSC, lung squamous cell carcinoma. NER, nucleotide excision repair. MMR, mismatch repair. NHEJ, nonhomologous end joining. HR, homologous recombination.

FIGURE 2

Mutation profile of the specified six genes in stage I and IIIa non‐small cell lung cancer (NSCLC) patients. (a) Mutation profile of ATM, BRCA1, BRCA2, CHEK1, BARD1 and BRIP1. (b) Comparison of driver mutation frequencies between the six‐gene wild group and the six‐gene mutant group. There was no difference in driver mutation frequency between the six‐gene wild group and the six‐gene mutant group. (c) Smokers were more likely to develop the specified six gene mutations. (d) Distribution of LUAD or LUSC in the specified six genes mutations samples. LUSC were more likely to develop BRCA2 mutations. LUAD, lung adenocarcinoma. LUSC, lung squamous cell carcinoma.

FIGURE 3

Prognostic values of the six gene mutations in patients with stage I and stage IIIa non‐small cell lung cancer (NSCLC). (a) Among all patients, no association between DNA damage response (DDR) gene status and OS or DFS was found. (b) Multivariate Cox proportional hazard regression analysis demonstrated that age younger than 65 years, stage I and harboring the identified six gene mutations were independent prognostic parameters for significantly longer DFS and OS. (c) Among stage IIIa patients, DDR‐mut subgroup showed a trend towards improved OS and a statistically significant improvement in DFS. No similar findings were found in stage I patients. Among stage IIIa patients, LUSC patients with DDR mutations experience extended DFS and OS, whereas no such benefits are observed in LUAD patients. LUAD, lung adenocarcinoma. LUSC, lung squamous cell carcinoma. OS, overall survival. DFS, disease‐free survival.

FIGURE 4

Association of DNA damage response (DDR) gene status with tumor microenvironment. (a–d) DDR gene status did not affect PD‐L1 expression and infiltration of CD8‐positive T lymphocytes, M1 and M2 macrophage in tumor area. (e–h) Different DDR pathway alterations indicate different immune cell infiltration. (i–k) The DDR‐mut group has higher numbers of mutation, whether for 74 genes and six genes. The same conclusion was maintained when the individual DDR pathways were analyzed separately. (l) TMB was significantly higher in the DDR‐mut subgroup in the Pan‐Lung cancer dataset, both for 74 DDR genes and the specified six genes.