key: cord-0032139-t2slh27n
authors: Song, Siyuan; Shu, Peng
title: Expression of ferroptosis-related gene correlates with immune microenvironment and predicts prognosis in gastric cancer
date: 2022-05-24
journal: Sci Rep
DOI: 10.1038/s41598-022-12800-6
sha: ff53093bbff116cd64810e8664d1b08f718b4cdd
doc_id: 32139
cord_uid: t2slh27n

The study is to explore the role of ferroptosis-related genes (FRGs) in the occurrence and development of gastric cancer (GC), and to construct a new prognosis signature to predict the prognosis in GC. Clinical information and corresponding RNA data of GC patients were downloaded from TCGA and GEO databases. Consensus clustering was performed to identify new molecular subgroups. ESTIMATE, CIBERSORT, McpCounter and TIMER algorithm were used to analyze the infiltration of immune cells in two molecular subgroups. LASSO algorithm and multivariate Cox analysis were used to construct a prognostic risk signature. Functional analysis was conducted to elucidate the underlying mechanisms. Finally, the FRPGs were verified by Quantitative Real-Time PCR. We obtained 16 FRGs and divided GC patients into two subgroups by consistent clustering. Cluster C1 with a higher abundance of immune cell infiltration but lower probability in response to immunotherapy, it was reasonable to speculate that Cluster C1 was in accordance with the immune rejection type. Functional analysis showed that the biological process of DEGs in training cohort mainly included immune globulin, and human immune response mediated by circulating immune globulin. GSEA analysis showed that compared with Cluster C2, Cluster C1 showed lower expression in lipid metabolism. The nomogram combined with risk signature and clinical features can accurately predict the prognosis of GC patients. We identified two molecular subtypes, Clusters C1 and C2. In Cluster C1, patients with poor prognosis present with a hyperimmune status and low lipid metabolism, and we speculate that Cluster C1 was in accordance with the immune rejection type. The risk model based on FRPGs can accurately predict the prognosis of GC. These results indicated that ferroptosis is associated with TIME, and deserved considerable attention in determining immunotherapy treatment strategy for GC patients.

Immune analysis. Immunological analysis was used to explore the immune differences between the two subgroups. Estimate algorithm (estimation of violent and immune cells in malignant tumor organization using expression) is used to evaluate the proportion of immune-matrix components in TIME, include Stromal Score (reflecting the presence of matrix), Immune Score (reflecting the level of immune cell infiltration) and ESTI-MAT Score (comprehensive score of immunity and matrix) 26 . The higher the corresponding score, the larger the proportion of corresponding components in TIME. Using MCP Counter and TIMER databases 27 to calculate the abundance of immune infiltrating cells. CIBERSORT algorithm was used to estimate the data of tumor infiltrating immune cells 28 . www.nature.com/scientificreports/ Establishment of prognostic risk signature based on FRPGs. The "glmnet" R package 29 was used for LASSO analysis to further select hub prognostic markers, and the minimum lambda was defined as the optimal value. According to the risk score of the prognosis signature, GC patients were divided into high and low risk groups. Kaplan-Meier survival curve and time-dependent ROC curve were used to analyze and compare the survival situation between the two groups. Immunohistochemical (IHC) staining of hub FRPGs were examined by human protein atlas (HPA) (https:// www. prote inatl as. org/ about/ downl oad). Maftools was used to calculate the mutation of hub FRPGs, and "ggplot2" package 30 was used to draw the mutation distribution map.

Validation of prognostic risk signature. Multivariate Cox analysis and subgroup analysis were used to evaluate the independence of the prognosis signature and the clinical characteristics (including Gender, Age,Grade, and Stage) of patients. The GEO validation cohort was used to verify the accuracy of the established prognosis signature. Combining the prognosis signature and clinical features, nomogram was constructed to predict the 1,3 and 5-year survival rate of GC patients.

Functional enrichment analysis. Differentially expressed genes (DEGs) between the two clusters were identified using R package ''Limma'' 31 in the training cohort, the false discovery rate (FDR) was less than 0.05, and the difference multiple was 1.5 times as the screening standard. GSEA enrichment analysis was carried out according to DEGs. Metascape software was used to construct PPI network of DEGs 32 . Moreover, we also performed survival analysis on samples in the GEO validation cohorts, divided the samples into high and low risk groups according to risk scores, and screened out DEGs by "limma" R package 31 . Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis 33, 34 were performed to enrich associated pathways.

Cell culture. GC Statistical analysis. All statistical analysis in this paper was carried out by R software and GraphPad Prism.

Student's t-test was used for statistical analysis between two groups, and one-way ANOVA analysis was selected flexibly when there were three or more groups. P < 0.05 was considered to be statistically significant.

All methods were carried out in accordance with relevant guidelines and regulations. Ethical approval is not applicable for this study.

Identification of molecular subtypes based on FRGs. Through univariate Cox analysis, we obtained 2,381 GC prognosis-related genes, and 16 FRPGs were obtained by intersecting 2,381 GC prognosis-related genes with 259 ferroptosis genes ( Fig. 2A) . The consensus clustering approach was conducted to divide the GC patients in the training cohort. The optimal clustering stability was identified when K = 2 ( Fig. 2B -E). Cluster C1 included 210 patients, while Cluster C2 included 197 patients. The two subgroups were visualized by heatmap (Fig. 2F ). Kaplan-Meier survival curves of two different subgroups showed that Cluster C2 showed significant median survival advantage, while Cluster C1 showed poor prognosis (Fig. 2G ).

showed significantly higher ESTIMATE scores (P < 0.0001), higher Immune score (P < 0.01), and higher Stromal score (P < 0.0001) in Cluster C1 compared with Cluster C2 (Fig. 3A) . The MCPCounter algorithm showed that the expression levels of B-lineage (P < 0.00), Myoid-Dendritic-cells (P < 0.0001), Neutrophils (P < 0.01), Endothelial-cells (P < 0.0001) and Fibroblasts (P < 0.0001) in Cluster C1 were significantly higher than those in Cluster C2 (Fig. 3B ). The TIMER algorithm showed that fibrolasts (p = 7.80e−12), CD4 + T cells (p = 0.0009), and B cells (p = 0.0023) were significantly higher in Cluster C1 than in Cluster C2. Macrophases-M2 and Tregs in two Cluster was no significant difference ( These results demonstrated that the TIME and immune status of the two molecular subtypes differed significantly. Cluster C1 with a poor prognosis had a high immune status, so we speculate that Cluster C1 is immune rejection type. , thirteen genes were finally obtained, and three of them were risk genes with the risk ratio greater than 1 (Fig. 4A ). The established risk signature successfully classified the GC patients into high risk and low risk groups (Fig. 4B ). Kaplan-Meier analysis showed that patients in the low risk group had a better overall survival than those in the high risk group (Fig. 4C ). Based on the information such as the survival status and survival time of the patients, we drew the forest map for multivariate survival analysis of FRPGs (Fig. 4D ). ROC analysis showed that the risk signature constructed exhibited www.nature.com/scientificreports/ accurate prediction ability within 5 years, with AUC of 0.69, 0.80 and 0.81 for 1, 3 and 5 years (Fig. 4E) . Finally, the TIME of the two groups was evaluated using the ESTIMATE algorithm, and the results showed that the high risk group had a higher ESTIMATE score (P = 1.2e−4), higher Immune score (P = 4.8e−7), and higher Stromal score (P = 5.1e−7) (Fig. 4F ). The TIMER database was used to predict the relationship between the FRPGs and the infiltration level of immune cells, and it was found that the FRPGs were closely related to the infiltration of macrophages, B cells, T cells, dendritic cells, and neutrophils (Fig. 4G ). The CIBERSORT algorithm indicated that Macrophases-M1 (p < 0.01) and Macrophases-M2 (p < 0.001) were significantly higher in high risk groups than in low risk groups, while Dendritic-cells-activated was significantly higher in low risk groups than in high risk groups (Fig. 4H ), suggesting the TIME and immune status of the two groups differed significantly. These results indicated that the risk signature constructed had a strong potential for prognosis prediction of GC patients, and it was significantly correlated with TIME in GC. The HPA database examined the immunohistochemical (IHC) staining of FRPGs ( Fig. 5A -J), and found that the protein expressions of ZFP36, TUBE1, www.nature.com/scientificreports/ www.nature.com/scientificreports/ NFE2L2, GCH1, GABARAPL2, CHAC1, CAPG, ACSL4, ACO1, and SLC1A4 in GC and normal tissues were significantly different, there was no protein expression of NOX5, MIR9-3, and NOX4 in HPA. In addition, we observed mutations of FRPGs in the training cohort and found that TUBE1 was a dominant gene and therefore better targeted (Fig. 6 ).

Validation of prognostic risk signature. We assessed the differences in risk scores among the subgroups by age (Fig. 7A) , gender ( 7F ) and found no significant differences between the subgroups, indicating that the risk scores were not correlated with the clinical characteristics of the patient. Besides, when the patients were regrouped according to age (Fig. 7G,H) , and gender (Fig. 7I,J) , the risk signature still exhibited potent predictive performance and those patients with lower risk score enjoyed better prognosis. This indicated that the prognosis signature we constructed can be used to independently predict the prognosis of GC patients. www.nature.com/scientificreports/ To verify the stability of the prognostic signature developed in the training cohort, we calculated the risk score for each patient in the validation cohort using the same formula as in the build training cohort. Patients in the validation cohort were grouped into high (n = 216) and low risk (n = 293) groups (Fig. 8A) , and ROC analysis revealed AUC values of 0.63, 0.65, and 0.69 at 1, 3, and 5 years, respectively (Fig. 8B) . The Survival curve showed that the low risk group had a better prognosis than the high risk group (Fig. 8C ). In addition, the ESTIMATE algorithm was performed on high risk and low risk group in the validation cohort, and the results showed that the high risk group had higher Stromal score (p < 0.001), higher ESTIMATE score (p < 0.001), and lower Tumor Purity (p < 0.001) (Fig. 8D-G) . These results demonstrated that the established risk signature was correlated with TIME and prognosis in GC in the validation cohort. www.nature.com/scientificreports/ Finally, a nomogram integrating the risk signature and clinical features were constructed to predict the prognosis of the GC patients more precisely (Fig. 8H) . The 3 years survival rates observed with the nomogram were matched well to the actual survival rates (Fig. 8I) , and similar result was also observed in the validation cohort (Fig. 8J) , demonstrating that the nomogram could predict the prognosis of GC patients accurately.

A total of 570 DEGs were detected compared to Cluster C2, of which 465 genes were up regulated and 105 genes were down regulated in Cluster C1 (Fig. 9A,B) . GO enrichment analysis showed that the biological process (BP) of DEGs mainly included cell migration, immune globulin, human immune response mediated by circulating immune globulin. Cellular component (CC) was mainly enriched in the extracellular matrix, and extracellular region part. Molecular function (MF) mainly included immunoglobulin receptor binding, fibronectin binding, and growth factor binding ( Fig. 9C-G) . The KEGG enrichment analysis showed that DEGs was mainly enriched in the Cell cycle, p53 signaling pathway, IL-17 signaling pathway, MAPK signaling pathway, and PI3K-Akt signaling pathway (Fig. 9H-I) . To further explore the relationship between enrichment pathways and prognosis of GC patients, we performed GSEA analysis, and the results showed that compared with Cluster C2, Cluster C1 showed lower expression in lipid metabolism and glutathione metabolism, which might be related to the poor prognosis of GC patients (Fig. 9J ). All these results demonstrated that expression of FRPGs were correlated with immunity and ferroptosis, which may be involved in the poor prognosis of GC patients.

Compared with the DEGs in training cohort, a total of 71 DEGs were detected, of which 7 genes were up regulated and 64 genes were down regulated in validation cohort (Fig. 10A,B) . KEGG enrichment analysis showed that DEGs was mainly enriched in the Cell cycle, p53 signaling pathway, and MAPK signaling pathway, which consistent with the results in training cohort. In addition, DEGs in validation cohort was also enriched in the Jak-STAT signaling pathway, TNF signaling pathway (Fig. 10C-F) .

Quantitative Real-Time PCR. We found that the protein expressions of ZFP36, TUBE1, NFE2L2, GCH1, GABARAPL2, CHAC1, CAPG, ACSL4, ACO1, and SLC1A4 in GC and normal tissues were significantly different. Their expression levels were evaluated in GES-1 and HGC-27 by qRT-PCR. Consistently, compared with GES-1, GCH1 (p < 0.01), CAPG (p < 0.05), and TUBE1 (p < 0.05) were significantly upregulated in HGC-27, while ZFP36 (p < 0.05), GABARAPL2 (p < 0.05), NFE2L2 (p < 0.01), and ACSL4 (p < 0.05) were downregulated, but CHAC1, ACO1, and SLC1A4 were no significant difference (Fig. 11A-J) . In summary, the potential roles of the FRPGs could also be verified in cell line experiment.

In recent years, various prognostic signatures have been proposed to predict the prognosis and immune infiltration of malignant tumors 35 . Including predicting the immune status and prognosis of malignant tumors by screening immune-related genes or FRGs. Few studies have elucidated the effects of the FRGs on TIME and prognosis. Therefore, in order to further verify the effect of ferroptosis on TIME in GC and explore the prognostic value of FRPGs in patients with GC, we constructed a prognostic risk signature based on FRPGs and validated it in the validation cohort.

Firstly, we divided GC patients into two subgroups by consistent clustering. Cluster C2 showed a significant median survival advantage, while Cluster C1 showed a poor prognosis. Subsequently, we performed an immune analysis to explore the role of ferroptosis in TIME. TIME plays a vital role in the prognosis of patients because tumor progression is associated with changes in the surrounding matrix, of which immune cells are a key component 36 . Therefore, we applied ESTIMATE, MCPCounter, TIMER, and CIBERSORT algorithms to determinate the TIME of the two subgroups. Compared with Cluster C1, GC patients in Cluster C1 had significantly higher ESTIMATE scores, higher Immune score, and higher Stromal score. Our results indicated that Macrophases-M1, CD4 Memory Activated-T cells, NK cells, fibrolasts, CD4 + T cells, B cells were significantly higher in Cluster C1 than in Cluster C2. Macrophases-M2 and Tregs in two Cluster was no significant difference, suggesting a relatively high immune status in Cluster C1. M1 macrophages are linked to antitumor activity, www.nature.com/scientificreports/ whereas M2 macrophages are associated with cancer progression and metastasis 37 . These results demonstrated that the TIME and immune status of the two molecular subtypes differed significantly. TIME is generally divided into three categories: immune inflammation, immune rejection and immune desert 38 . In this study, according to the exhibitions that the TIME of the patients in the Cluster C1 with a higher abundance of immune cell infiltration but lower probability in response to immunotherapy, it was reasonable to speculate that Cluster C1 was in accordance with the immune rejection type. As a successful immunotherapy depends on the ability of innate and adaptive immune cells to penetrate into the tumor parenchyma and eradicate cancer cells. In addition, we also found that the high infiltration of immune cells was accompanied by the activation of the stroma, which could exclude the entry of CD8 + T cells from the tumor parenchyma to the peritumoral stroma rich in www.nature.com/scientificreports/ fibroblasts and collagen 39 . We speculated that the activation of the stroma might be one of the reasons for the poor prognosis of Cluster C1, which had high infiltration of immune cells. Therefore, the prognosis of high risk group was often poor. In order to further verify the effect of ferroptosis on TIME in GC and explore the prognostic value of FRPGs in patients with GC, we constructed a prognostic risk signature based on FRPGs and validated it in the validation cohort. The genes used to establish the risk signature in this study have been shown to be closely related to tumor development and progression. A study had shown that autophagy promotes ferroptosis by degrading anti-ferroptosis factors 40 , and ZFP36 was a key protein for autophagy and considered to be related to ferroptosis 41 . NFE2L2, a known transcription factor involved in the encoding of GC development, is overexpressed as a prognostic marker of GC 42 . OS rate in GC patients with NRF2 positive expression was significantly reduced 43 . The experiment conducted by Wei 44 proved that GCH1 induced immunosuppression through a 5-HTP-AHR-ID01-dependent mechanism, and that the combination of metabolic intervention and immunotherapy of this pathway might be a promising strategy for the treatment of triple-negative breast cancer (TNBC), and the GCH1 inhibitor could be used as an analgesic 45 . Members of the GABARAP family (GABARAP, GABARAPL1/GEC1 and GABARAPL2/ GATE-16) are one of the subfamilies of the ATG8 protein family, which are related to the receptor and autophagy pathway 46 . The high-expression of GABARAP is related to the good prognosis of tumors 47 . CHAC1 is an enzyme related to the activity of γ-glutamyl cyclotransferase that can degrade intracellular GSH and promote ferroptosis of tumor cells 48 , which has been proved to be related to glioma 49 and breast cancer 50 . CAPG is particularly abundant in macrophage expression 51 , and CAPG had been proved to be related to tumor cell invasion and tumorigenic 52 . SLC1A4 is one of the members of solute carrier family 1(SLC1), and SLC1A4 is one of the important roles of amino acid transporter 53 . SLC1A4 is highly expressed in pancreatic ductal adenocarcinoma and liver cancer cells, and some studies have suggested that SLC1A4 may promote the process of ferroptosis 54 . ACSL4, a long-chain fatty acyl coenzyme, is closely related to the proliferation and migration of tumor cells 55 . ACSL4 had been shown to be overexpressed in breast cancer 56 , GC 57 , and liver cancer 58 . ACO1(Cytoplasmic aconitic acid hydratase) is a protein that participates in cytoplasmic and mitochondrial metabolism and, when down regulated, leads to cell death 59 . NOX is a family of encoded oxidases, NOX4 is a catalytic subunit of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase complex, and NOX5 mainly encodes calcium-dependent NADPH oxidase, produces superoxide, and acts as a calcium-dependent proton channel. The ROS produced by NOX4 is involved in a variety of biological functions, including signal transduction, cell differentiation and tumor cell growth 60, 61 , and NOX4 plays an important role in the process of ferroptosis 62 . Inhibition of NOX4 can significantly block ferroptosis 63 . MiRNA plays an important role in tumors. MiR-9 is overexpressed in lung cancer tissues 64 , and MiR-9 acts as a biomarker for poor prognosis in lung cancer and thyroid papillary carcinoma 65 . There is no report about the relationship between TUBE1 and tumor in the literature. www.nature.com/scientificreports/ Survival analysis indicated that whether in training cohort or the validation cohort, the established risk signature showed effective predictive performance for the survival of GC patients. The ROC curve showed the reliability and stability of the risk signature. And the high risk groups were accompanied with higher Stromal score, higher ESTIMATE score, and lower Tumor Purity. The HPA database examined the IHC staining of FRPGs, and found that the protein expressions of ZFP36, TUBE1, NFE2L2, GCH1, GABARAPL2, CHAC1, CAPG, ACSL4, ACO1, and SLC1A4 in GC and normal tissues were significantly different. Finally, a nomogram integrating the risk score and clinical features was also established and calibrated, and it showed considerable property for predicting the survival. All these results confirmed the prognostic prediction role of FRPGs in GC and correlation between FRPGs and TIME.

Finally, functional analysis was performed to explore potential biological mechanisms. GO enrichment analysis showed that the biological process of DEGs in training cohort mainly included immune globulin, and human immune response mediated by circulating immune globulin. However, the detailed relationship between ferroptosis and immunity is still unclear. Therefore, we performed GSEA analysis to further elucidate the underlying mechanisms, and the results showed that compared with Cluster C2, Cluster C1 showed lower expression in lipid metabolism, which might be related to the poor prognosis of GC patients. These results suggested that the down regulated lipid metabolism resulted in the impairment of TIME, thereby leading to the poor prognosis in GC. Ferroptosis is a regulated oxidative form of cell death associated with the accumulation of lipid ROS due to enhanced lipid peroxidation 66 . Since Cluster C1 was associated with relatively low levels of ROS, a small proportion of cells die from ferroptosis. Therefore, Cluster C1 had a poor prognosis. Researchers identified that ferroptosis was related to the immune response process 67 . It is unclear whether and how ferroptosis is involved in T cell immunity and cancer immunotherapy. Studies have shown that immunotherapy-activated CD8 + T cells enhance the specific lipid peroxidation of ferroptosis in tumor cells and that increased ferroptosis contributes to the anti-tumor efficacy of immunotherapy 68 . CD8 + T cells and fatty acids orchestrate tumor ferroptosis and immunity via ACSL4. Clinically, tumor ACSL4 correlates with T cell signatures and improved survival in ICBtreated cancer patients 69 .

KEGG enrichment analysis showed that DEGs in training cohort were mainly enriched in the p53 signaling pathway, IL-17 signaling pathway, MAPK signaling pathway, and PI3K-Akt signaling pathway. Studies have found that these pathways are associated with immune response [70] [71] [72] [73] . p53 is a tumor suppressor gene, and p53 mutations have been reported in many cancers 74 . When p53 mutations occur, cells proliferate abnormally and transform into cancer cells. GC patients with p53 mutation have worse prognosis than those without mutation 75 . More and more evidences support the pathogenic role of IL-17 in cancer formation, including colon cancer 76 and lung cancer 77 . Wu 78 found that IL-17 could promote tumor angiogenesis by mediating the up-regulation of VEGF in GC through STAT3 pathway. It has been confirmed that MAPK and PI3K-Akt pathways are involved in many processes of the occurrence and development of GC [79] [80] [81] .

Although multiple studies have established relevant prognostic models for ferroptosis in GC 82,83 , our study shows unique advantages compared with previous studies. Firstly, the number of patients was significantly different from that of published article. Secondly, our work focused on ferroptosis in patients with GC and identified two significantly different molecular subtypes of prognosis and immune status by consensus clustering. Thirdly, genes were obtained in different ways, we have selected differential genes based on molecular subtypes and partially elucidated the underlying mechanisms. Fourthly, we used the GEO data set to validate the prognosis www.nature.com/scientificreports/ model. Fifthly, we elucidated the effects of ferroptosis on TIME and prognosis. Sixthly, we verified the mRNA expression of FRPGs by qRT-PCR. Seventhly, the prognostic model based on FRPGs we constructed different from the previous articles. Finally, we speculated that the down regulated lipid metabolism may result in the impairment of TIME, thereby leading to the poor prognosis in GC. The establishment of prognostic risk signature based on FRPGs provided new possibilities for us to predict the efficacy of immunotherapy, and promotes personalized treatment for GC patients in the future. However, this study has certain limitations. Our signature was constructed and validated based on retrospective data, without relevant clinical experimental verification.

In summary, in this study, we identified two molecular subtypes, Clusters C1 and C2. In Cluster C1, patients with poor prognosis present with a hyperimmune state and low lipid metabolism, and we speculated that Cluster C1 was in accordance with the immune rejection type. The risk model based on FRPGs can accurately predict the prognosis of GC. These results indicated that ferroptosis is associated with TIME, and the down regulated lipid metabolism may result in the impairment of TIME, thereby leading to the poor prognosis in GC.

The data used to support the findings of this study are included within the article.

Received: 6 January 2022; Accepted: 10 May 2022

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P.S. designed the research. S.S. analyzed the data and wrote the paper. All authors read and approved the submitted version.

The authors declare no competing interests.

The online version contains supplementary material available at https:// doi. org/ 10. 1038/ s41598-022-12800-6.Correspondence and requests for materials should be addressed to P.S.

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