This study analyzed the expression of 275 DDR genes in normal tumor samples from TCGA and GEO databases, and ultimately identified 19 DDR genes that were associated with prognosis. It appeared that they were related to CNV, with CHAF1A, CDC25A, DCLRE1B, and CHEK1 showing amplification according to CNV. POLD3, BRIP1, CUL4A, and BRCC3 exhibited significant CNV deletions at a high frequency in STAD. There have been numerous related studies on the mechanisms of these genes. For example, it was discovered that CDC25A degradation is regulated by NIMA-related kinase 11 (NEK11) and induces G2/M phase arrest [21]. It was also found that Pold3 is essential for genome stability and telomere integrity in embryonic stem cells and meiosis [22]. Subsequently, we conducted LASSO regression analysis and multivariate Cox regression analysis, and ultimately obtained a prognostic model of gastric cancer DDR score constructed with two genes (CHAF1A, PER1).
CHAF1A (CAF p150) is the main functional subunit of CAF-1, which promotes the rapid assembly of nucleosomes on newly replicated DNA and participates in DNA replication, gene expression regulation, and DNA mismatch repair[23]. Studies have shown that elevated CHAF1A expression is positively correlated with tumor progression and poor patient outcomes[24]. The co-expression gene network analysis conducted by Xia Sun et al revealed that CHAF1A is not only associated with cell proliferation, DNA repair, and cell apoptosis, but also with cancer metabolism, immune system function, and drug resistance. Notably, high levels of CHAF1A expression are positively correlated with an immune-suppressive microenvironment, resistance to endocrine therapy, and resistance to chemotherapy. The increased expression of CHAF1A in breast cancer tissues has been verified, suggesting that CHAF1A plays a crucial role as a cell cycle-related protein in the progression of esophageal cancer. These proteins have the potential to serve as important prognostic biomarkers and therapeutic targets for esophageal cancer. [25]
PER1 is one of the core components of the circadian clock gene [26], and participates in regulating many important physiological activities such as cell cycle and apoptosis. Current research suggests that PER1 is an important tumor suppressor. Overexpression of PER1 inhibits tumor growth, while also inhibiting glycolysis, proliferation, and the PI3K/AKT pathway [27]. Abnormal expression of PER1 is closely related to the occurrence and development of various cancers, including gastric cancer and non-small cell lung cancer (NSCLC) [28]. Xingya Guo et al have found that the RNA demethylase ALKBH5 prevents the progression of pancreatic cancer by transcriptionally activating PER1 in a m6A-YTHDF2-dependent manner[29]. This study is based on the gastric cancer DRR score constructed from the two genes CHAF1A and PER1. Through PCA analysis and further risk assessment, the low-risk group of patients selected showed significantly better progression-free survival and overall survival compared to the high-risk group, particularly in stage II-IV GC patients. This result is consistent with our consistent treatment outcomes for GC patients.
The advancement of research in the cancer microenvironment has greatly promoted the development of immunotherapy for advanced gastric cancer. Despite the advantages of immunotherapy in advanced gastric cancer, challenges such as poor clinical efficacy and immunotolerance hinder its widespread application. Through GSVA enrichment analysis and CIBERSORT estimation, this study evaluated the infiltration of immune cells and the corresponding immune checkpoint relevance in the high-risk and low-risk groups. The results also showed that the low-risk group had a more abundant presence of immune-promoting cells compared to the high-risk group. For example, the low-risk group had a more abundant presence of Tfh cells, which have been identified as the main producers of IL-21 in the TME of different human cancers and mouse models [30]. This cytokine plays an important role in mediating humoral responses by promoting B cell activation, class switch recombination, and anti-tumor IgG1 and IgG3 secretion[31].
PD-1 and PD-L1 inhibitors have been recommended in the guidelines of several countries for the treatment of gastric cancer, with Nivolumab and Pembrolizumab being recommended as first-line combination therapies for advanced gastric cancer by the NCCN guidelines[32]. However, immune checkpoint inhibitors do not guarantee effectiveness for every patient; for example, the PD-L1 immune checkpoint inhibitor Avelumab did not demonstrate superiority in maintenance therapy after first-line chemotherapy for gastric cancer [33]. In light of this, we can use a DNA repair mechanism prediction model to compare the immune characteristics of patients and predict the efficacy of immunotherapy for these patients. This study found that the low-risk group exhibited relatively higher scores in common inhibition aspects related to antigen-presenting cells, inflammation promotion, cytolytic activity, and MHC class I. The DDR score for TME and immune therapy prediction results indicated that the TIDE score in the low-risk group was lower than that of the high-risk group, suggesting that they are more likely to benefit from immunotherapy. With higher TIDE scores, the likelihood of immune escape in the high-risk group is greater. Taken together, the DDR score predicts that the low-risk group of gastric cancer patients has a TME with stronger immune responsiveness, indicating a greater potential for suitability for immunotherapy. However, caution must be exercised when applying the results from the IMvigor210 cohort, which comprised 298 urothelial cancer samples, as an external validation due to limitations stemming from the absence of datasets related to immunotherapy response in gastric cancer. Consequently, a comprehensive exploration of the role played by DNA damage repair genes in predicting the effectiveness of immunotherapy should be pursued within a gastric cancer cohort to ascertain its validity.
The interesting finding from the PCR results was that in the high-expression subgroup of CHAF1A, the proportion of T cell CD8, T cell CD4 memory activation, T cell follicular helper cells, resting NK cells, and M1 macrophages was significantly higher, while the low-expression subgroup had a richer proportion of immature B cells, resting T cell CD4, regulatory T cells (Tregs), monocytes, M2 macrophages, resting dendritic cells, and resting mast cells (p < 0.05). This seemingly indicates a more "hot tumor" phenotype in patients with high CHAF1A expression, but the higher proportions of these immune cells do not necessarily signify stronger immune responsiveness in these patients.
In this study, consensus clustering and k-means methods were further used to identify molecular subtypes of patients. A comparison of the immune characteristics of the two DDR subtypes revealed differential expression of 28 immune checkpoints, including CD44, CD86, and CD28. High expression of CD44 significantly contributes to enhancing tumor-promoting mechanisms, such as cell proliferation, migration, invasion, and stemness [34]. The endocytic function of CD86 is considered a key target for CTLA-4 immune regulation [35] and CD28 receptor, when linked to the T cell receptor (TCR), provides a critical second signal for the activation of naive T cells [36]. Furthermore, a comparison of immune cell infiltration between the two DDR subtypes revealed higher levels of immune cell infiltration in cluster 1 compared to cluster 2. Additionally, cluster 1 was closely associated with higher immune scores, ESTIMATE scores, and stromal scores, implying significant differences in the tumor microenvironment between the two DDR subtypes.
Currently, chemotherapy based on fluoropyrimidines, platinum agents, and taxanes is the main treatment for advanced gastric cancer [37–39]. However, chemotherapy is associated with issues of primary and acquired drug resistance and high toxicity. Perhaps, based on this stratification, we can try to identify the relationship between different subtypes and the efficacy of chemotherapy in treating gastric cancer. This study found that cluster 1 was associated with the IC50 of imatinib, nilotinib, sunitinib, and dasatinib, while cluster 2 was associated with the IC50 of afatinib, erlotinib, gemcitabine, and methotrexate. Therefore, we can use DDR scoring to identify appropriate chemotherapy or targeted drugs for different subtypes, guiding systemic treatment for gastric cancer.