Background
As one of the most prevalent malignant tumors worldwide, gastric cancer (GC) has high morbidity and mortality rates, with stomach adenocarcinoma (STAD) as one of the major pathological subtypes [
1]. STAD accounts for 80–90% of all gastric cases [
2]. The 5-year survival rate of patients with STAD with advanced or metastatic disease is less than 30% [
3,
4]. Most patients worldwide are not diagnosed until the advanced stage owing to the absence of significant early symptoms and limitations in medical screening [
5,
6]. Therefore, the accurate prediction of biomarkers is crucial for clinical prognostication and treatment. Currently, surgical resection is the primary treatment for STAD [
7]. However, because of the recurrence and metastasis of STAD after surgery, its prognosis is poor [
8]. Immunoassay inhibitors of PD-L1 have positive effects on immunotherapy and targeted therapy, and they can significantly improve the prognosis of patients with stable microsatellite carcinomas [
9].
Increasing evidence suggests that the tumor microenvironment (TME) plays a role in anti-tumor activity and contributes to the prediction of immune checkpoint blockade (ICB) responses [
10‐
13]. However, gaining advantages from STAD is not common [
14]. The TME comprises tumor cells, fibroblasts, extracellular matrix elements, and diffusing cytokines [
15,
16]. Growing tumor cells can be recognized and destroyed by tumor-infiltrating immune cells. This defensive behavior may involve inflammation as tumor cells evade immune defense mechanisms by selecting more aggressive tumor clones [
17]. High levels of regulatory T cells are commonly found in patients with cancer and are associated with the prognosis of different types of STAD [
18].
Furthermore, treatment is influenced by T-cell therapy [
19]. However, these cellular treatments need to be improved further to improve the cure rate. To date, studies on T-cell function have mainly focused on the negative regulatory factors contributing to functional deficiency [
20]. The US Food and Drug Administration (FDA) approved the first chimeric antigen receptor T-cell (CAR-T) therapy [
21]. Nevertheless, the therapeutic effect of the chimeric antigen receptor on STAD did not meet expectations because of the failure of T cells to perform their effector function within the TME fully. Positive regulators reportedly have a positive effect on T-cell proliferation, activation, and secretion of key cytokines, thereby optimizing and improving T-cell function in STAD [
22], that may further improve the treatment of STAD.
In this work, we aim to build signatures to study the effect of certain genes on gastric cancer using LASSO and multivariate Cox regression analyses. Our findings underscore the significance of considering tumor-infiltrating immune cells and their interactions with the TME in prognostic assessment and treatment planning. Also, the identification of potential therapeutic targets such as CXCL12 and SERPINE2 presents opportunities for developing targeted interventions aimed at mitigating immune exhaustion and enhancing treatment efficacy.
Materials and methods
STAD data source and preprocessing
Data on STAD-related gene expression, prognosis, and clinicopathological characteristics were collected from comprehensive GEO (GSE38749, GSE84437, GSE34942, and GSE15459;
https://www.ncbi.nlm.nih.gov/geo/) and TCGA (
https://portal.gdc.cancer.gov/) datasets. Following this, the FPKM values were converted to TPM values within the composite matrix. The 37 T cell-related genes were derived from the latest research [
22]. Ten tumors and ten normal single-cell ribonucleic acid (scRNA) samples were obtained from GSE18394.
WGCNA co-expression network construction
The co-representation network of differentially expressed genes (DEG) is built by the “WGCNA”package in the R package (version xx; The R Foundation for Statistical Computing, Vienna, Austria). Subsequently, pairs of genes were subjected to Pearson’s correlation matrix analysis.
To further analyze sample clustering for outliers detection, we calculated the similarity of the characteristic genes within each module, selected the standard tangent value from the module tree, and merged specific modules. The module-feature relationship between modular feature genes and T cells was described within the characteristic gene network, and two modules related to specific traits were found.
DEGs identification and enrichment analyses
The parameter of “limma”in the R package (The R Foundation for Statistical Computing, Vienna, Austria) was set to 1.5, and the P-value was adjusted to be less than 0.05 to screen DEGs across different T-cell clusters. A total of 178 genes were identified as DEGs. Moreover, disease ontology (DO), gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to explore the characteristics of the DEGs [
23‐
25].
Construction of prognostic T cell-related signature
The signature score was calculated to express the properties of each cell type, and DEGs were identified from T-cell clusters using LASSO and multivariate Cox regression analyses. Univariate Cox regression, overall survival (OS) (p < 0.05), and heatmap analysis were used to verify the signature validity. The GSE38749, GSE84437, GSE34942, GSE15459, and TCGA-STAD cohorts were segmented into training (n = 522) and test (n = 521) datasets at a ratio of 1:1, and the former was used to establish risk characteristics. We analyzed the various trajectories of each variable and identified candidate genes using multivariate Cox analysis. The risk score was calculated using the following formula:
Risk score = Σ(Expi × Coefi).
Analysis of TME, immunological checkpoint, mutation, and drug susceptibility
Based on the data from TCIA and TIDE (
http://tide.dfci.harvard.edu/), a boxplot was used to visualize the differences between the two groups in the expression levels and treatment diversity of the PD-1 and CTLA-4 immunological checkpoints. Additionally, we examined drug susceptibility and mutation status in the high- and low-risk groups using the prophetic and maftools packages, respectively.
Validation of external cohort
Survival analysis was conducted on the external IMV210 cohort and GSE62254 for validation. This involved analyzing the binary response in risk scores among CR/PR and SD/PD, as well as Kaplan–Meier survival analysis between high-risk and low-risk score groups. For the scRNA data, we created a project using the Seurat package and set the following screening criteria: (1) Each gene was expressed in at least three cells; (2) The total number of molecules detected in each cell was > 1000; (3) The number of genes detected in each cell was > 200 and < 10,000; (4) The proportion of mitochondrial and ribosomal genes was < 20%. The first 2000 highly variable genes were selected for scale analysis, and PCA dimensionality reduction analysis was performed. Twenty PC were selected for unsupervised clustering and labeled according to the marker genes of different cell types. Four methods, Ucell, singscore, ssgsea, and addmoduleScore, were used to score the TME of both normal and tumor tissues. The scores obtained from the UCell, irGSEA, and GSVA packages were utilized to explore the differential expression of SEPRINE2 in T cells from normal and tumor groups.
Youjiang cohort and Immunohistochemical
OS with high and low SEPRINE2 expression in GC was verified using the Youjiang cohort, and immunohistochemistry was conducted to test the content of high or low-expression SEPRINE2 samples in formalin/PFA-fixed paraffin-embedded sections (n = 93). Human GC tissues were stained for SERPINE2/PN-1 using ab154591 at a dilution of 1/500.
Cell culture and transfection
Human GC cell lines AGS and BGC-823 were purchased from the Shanghai Institutes of Biological Sciences (Shanghai, China). AGS and BGC-823 cells were cultured in RPMI 1640 medium (Gibco, USA) supplemented with 1% penicillin-streptomycin (Gibco, USA) and 10% fetal bovine serum (Gibco, USA). BGC-823 cells were maintained in Dulbecco’s modified DMEM medium (Gibco, USA) supplemented with 1% penicillin-streptomycin (Gibco, USA) and 10% fetal bovine serum (Gibco, USA). All the cells were cultured at 37 °C and 5% CO2. Cell transfections were performed using Lipofectamine 3000 (Invitrogen, USA), with oligonucleotides as a control. After 48 h of transfection, cellular RNA and proteins were extracted.
Cell migration assays and proliferation
Stably transfected AGS and BGC-823 cells were seeded in 96-well plates at a density of 5 × 104 cells/mL. A Cell Counting Kit-8 (Dojindo, Japan) was used to test cellular proliferative capacity. On each of the subsequent 6 days, the optical density was evaluated at 450 nm using a microplate reader (TEAN, Switzerland). Additionally, a transwell migratory assay was conducted to study the migratory response of AGS and BGC-823. The cell density was standardized to 2 × 105 cells/mL, and a volume of 100 µL cell suspension was added to the upper chamber. Medium containing 20% fetal bovine serum was added to the lower chamber. After 24 h, AGS and BGC-823 cells within the lower chamber were washed in 4% polyoxymethylene for 15 min, followed by staining with 0.1% crystal violet and subsequent rinsing with deionized water for 30 min. Finally, the cells were counted under a microscope.
Statistical analyses
R (version 4.1.2, R Foundation for Statistical Computing, Vienna, Austria) (
https://www.r-project.org/) was applied for all analyses, and statistical significance was set at
p < 0.05.
Discussion
The incidence of STAD is decreasing in most developed countries [
34]; however, the number of deaths due to the disease is increasing [
35]. Currently, treatment for gastric cancer is not satisfactory [
36]. Moreover, more than half of the patients diagnosed with gastric cancer cannot be treated surgically at the time of diagnosis [
37]. The lack of treatment for gastric cancer also leads to rapid disease progression and increased mortality. Previous studies have investigated the correlation between genes and carcinogenesis in various cancers, including GC [
38,
39]. Multiple types of genomic damage, including the activation of oncogenes and inactivation of tumor suppressor genes, are factors that cause gastric cancer [
40]. Its anti-tumor effects are characterized by the highly coordinated actions of many genes. Owing to the inadequacy of current medical technology, only one or two genotypes have been evaluated [
41].
The present study aimed to build signatures to study the effect of certain genes on gastric cancer using LASSO and multivariate Cox regression analyses. In this study, LASSO and multivariate Cox regression analyses were applied to build signatures to study the effect of certain genes on gastric cancer. Six core genes (CD5, ABCA8, SERPINE2, ESM1, SERPINA5, and NMU) were selected from the DEGs to establish risk marker signatures. The results showed that The risk score of T cell Cluster C2 was significantly higher than that of T cell Cluster C1, and the prognosis of C2 was significantly better than that of CI. We also performed validation using an external cohort, which further confirmed that our phenotypic classification of T cell-associated gene mutations was meaningful. In addition, we preliminarily found that the signature genes were closely correlated with STAD, which provides valuable clues for further research on immunotherapy targets for STAD.
Initially, we selected four genes (IL12B, B2M, HLA-A, and CD19) for further study, among which CD19 and IL12B showed a significant survival advantage in the predictive analysis. Autologous CD19-targeted CAR T-cells could significantly help treat blood cancer [
42]. Epidemiological studies have shown that IL-12B is associated with an increased incidence of cervical cancer [
43]. The TME cannot be ignored during tumor development [
44] as it contains many different cell types, such as endothelial and fibroblast [
45]. Tumor-infiltrating immune cells can directly or indirectly participate in immune responses, thereby affecting the prognosis of patients with tumors [
46]. For example, dendritic cells can capture antigens emitted by tumors, while Effector T cells (CD8+) and TAMs can lyse and phagocytose tumor cells.
Additionally, helper T cells (CD4+) limit the immune response [
47]. Inhibition of these cytokines can strengthen the anti-tumor effect of tumor-infiltrating lymphocytes and further improve their clinical therapeutic effect [
48,
49]. A recent study also confirmed that T helper cells are effective prognostic immune cells, which is correlated with further studies on gastric cancer [
50]. Based on immunological and drug sensitivity analyses, we found that the high-risk group had a higher probability of immune escape and was generally resistant to first-line chemotherapy, indicating insensitivity to these treatment methods.
The scRNA results suggested that, compared to normal tissue, T-cell infiltration in GC was more abundant, mainly composed of differentiated CD4 + T cells and NK cells, while gamma delta T cells with higher differentiation potential were fewer, indicating T-cell exhaustion in the tumors. SERPINE2, which had the highest score in the signature, was highly expressed in T cells from GC. We found a significant positive correlation between SERPINE2 and the T cell-related factor CXCL12 in our dataset. Previous studies indicated that CXCL12 interacts with T cells to reduce OS in patients with GC [
51], while SERPINE2 promotes cell proliferation [
52]. Correspondingly, we tested the effects of CXCL12 downregulation on cell proliferation and migration and found that CXCL12 significantly reduces promotional and migration potential in GC cell lines. Survival analyses performed for patients with different CXCL12 expression levels confirmed that patients with high CXCL12 expression levels had poor survival probability. However, our study not only confirmed the effects of CXCL12 on tumor cell promotion and metathesis, but also showed the potential value of CXCL12 in tumor treatment. Therefore, we preliminarily speculated that SERPINE2 affects CXCL12 through a potential pathway, thereby promoting T-cell exhaustion.
Numerous methods were employed to assist our signature in this study; however, there were still some shortcomings. Environmental, racial, economic, predictive, and follow-up factors influence OS [
22]; this is a limitation of our study, and in a follow-up study, we will control for the variables for a further in-depth study.
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.