DNA Damage Response and Repair Gene Alterations Increase Tumor Mutational Burden and Promote Poor Prognosis of Advanced Lung Cancer

Abstract

DNA damage response and repair (DDR) gene alterations increase tumor-infiltrating lymphocytes, genomic instability, and tumor mutational burden (TMB). Whether DDR-related alterations relate to therapeutic response and prognosis in lung cancer lacking oncogenic drivers remains unknown. Pretherapeutic cancer samples of 122 patients [86 non-small cell lung cancer and 36 small cell lung cancer (SCLC)] harboring no EGFR/ALK alterations were collected. Through whole-exome sequencing, we outlined DDR mutational landscape and determined relationships between DDR gene alterations and TMB or intratumoral heterogeneity. Then, we evaluated the impacts of DDR gene alterations on therapeutic response and prognosis and established a DDR-based model for prognosis prediction. In addition, we investigated somatic interactions of DDR genes and immunomodulatory genes, immune expression patterns, immune microenvironment, and immune infiltration characteristics between DDR-deficient and DDR-proficient samples. Samples from cBioportal datasets were utilized for verification. We found that deleterious DDR gene alterations were closely associated with higher TMB than proficient-types (p < 0.001). DDR mechanisms attach great importance to the determination of patients’ prognosis after chemotherapy, and alterations of base excision repair pathway in adenocarcinoma, nucleotide excision repair in squamous carcinoma, and homologous recombination pathway in SCLC tend to associate with worse progression-free survival to first-line chemotherapy (all p < 0.05). A predictive nomogram model was constructed incorporating DDR-related alterations, clinical stage, and smoking status, with the area under curve values of 0.692–0.789 for 1- and 2-year receiver operating characteristic curves in training and testing cohorts. Furthermore, DDR-altered tumors contained enhanced frequencies of alterations in various genes of human leukocyte antigen (HLA) class I pathway including TAP1 and TAP2 than DDR-proficient samples. DDR-deficient types had lower expressions of STING1 (p = 0.01), CD28 (p = 0.020), HLA-DRB6 (p = 0.014) in adenocarcinoma, lower TNFRSF4 (p = 0.017), and TGFB1 expressions (p = 0.033) in squamous carcinoma, and higher CD40 (p = 0.012) and TNFRSF14 expressions (p = 0.022) in SCLC. DDR alteration enhanced activated mast cells in adenocarcinoma (p = 0.044) and M2 macrophage in squamous carcinoma (p = 0.004) than DDR-proficient types. Collectively, DDR gene alterations in lung cancer without oncogenic drivers are positively associated with high TMB. Specific DDR gene alterations tend to associate with worse progression-free survival to initial chemotherapy.

Identification of a DNA damage repair gene‐related signature for lung squamous cell carcinoma prognosis

“…The other way round, LUSC generally exhibits relatively a higher somatic mutation frequency in contrast with different tumor types 15 . A high proportion occurred in genes that are involved in the maintenance of genome integrity through chromatin modification and DNA damage response and repair and specific DDR gene alterations tend to associate with worse progression‐free survival to initial chemotherapy 16 . For diagnosis and treatment, it is necessary to investigate further the predictive value resulting in the development of LUSC.…”

Pan-cancer Analyses Reveal Regulation and Clinical Outcome Association of the PCLAF in Human Tumors

“…It is generally believed that cancer is caused by genetic mutations, which biologically enhance the resistance of cancer cells to surrounding normal cells [31][32][33]. At present, advances in systems biology methods provide us with a large amount of data to identify molecular alterations and explore the heterogeneity of cancer cells [34][35][36].…”

Germline DNA damage response gene mutations as predictive biomarkers of immune checkpoint inhibitor efficacy

“…A total of 20 genes were identified as being associated with DDR and were grouped into different functional pathways from published resources ( Supplementary Table S1 ) ( 17 , 19 , 21 , 28 ). We considered all loss-of-function alterations deleterious, including nonsense mutations, splice site, deletions spanning multiple exons, and frameshift alterations ( Supplementary Table S2 ).…”