Ferroptosis suppressor genes are highly expressed in esophageal cancer to inhibit tumor cell ferroptosis

doi:10.12122/j.issn.1673-4254.2024.07.19

Abstract

Abstract:

Objective To explore the role of ferroptosis-related genes in regulating ferroptosis of esophageal squamous cell carcinoma (ESCC). Methods ESCC datasets GSE161533 and GSE20347 were downloaded from the Gene Expression Omnibus (GEO) to identify the differentially expressed genes (DEGs) using R software. ESCC ferroptosis-related genes obtained by intersecting the DEGs with ferroptosis-related genes from FerrDb were analyzed using GO and KEGG analyses, protein-protein interaction (PPI) network analysis, and core gene identification through Cytoscape. The identified ferroptosis suppressor genes were validated using TCGA database, and their expression levels were detected using RT-qPCR in cultured normal esophageal cells and ESCC cells. Six ferroptosis suppressor genes (RRM2, GCLC, TFRC, TXN, SLC7A11, and EZH2) were downregulated with siRNA in ESCC cells, and the changes in cell proliferation and apoptosis were assessed with CCK8 assay and flow cytometry; Western blotting was performed to examine the changes in ferroptosis progression of the cells. Results We identified a total of 58 ESCC ferroptosis-related genes, which involved such biological processes as glutathione transmembrane transport, iron ion transport, and apoptosis and the ferroptosis, glutathione metabolism, and antifolate resistance pathways. The PPI network included 54 nodes and 74 edges with a clustering coefficient of 0.522 and PPI enrichment P<0.001. Cytoscape identified 6 core ferroptosis suppressor genes (RRM2, TFRC, TXN, EZH2, SLC7A11, and GCLC), which were highly expressed in ESCC tissues in the TCGA dataset and in ESCC cell lines. Downregulating these genes in ESCC TE1 cells significantly inhibited cell proliferation, promoted cell apoptosis, reduced the expression levels of ferroptosis markers GPX4 and FIH1, and increased the expression of ACSL4. Conclusion High expression of ferroptosis suppressor genes in ESCC may cause arrest of ferroptosis progression to facilitate tumor development, and inhibiting these genes can restore ferroptosis and promote cell apoptosis, suggesting their value as potential therapeutic targets for ESCC.

Key words: esophageal squamous cell carcinoma, ferroptosis, apoptosis

Yuanguo WANG, Peng ZHANG. Ferroptosis suppressor genes are highly expressed in esophageal cancer to inhibit tumor cell ferroptosis[J]. Journal of Southern Medical University, 2024, 44(7): 1389-1396.

Figures/Tables 7

Tab.1 Sequences of the primers for the ferroptosis suppressor genes and GAPDH

Primer	Primer sequence (5'-3')	Product length (bp)
RRM2	Forward Primer:GAACTTATTAGCAGAGATGAGG Reverse Primer:TTCTATCCGAACAGCATTGA	123
GCLC	Forward Primer:TCTCCAGGTGACATTCCAA Reverse Primer:TGACACATAGCCTCGGTAA	127
TFRC	Forward Primer:CTTCCTTCAATCACACTCAG Reverse Primer:ACAGTCTCCTTCCATATTCC	119
TXN	Forward Primer:AGCAGATCGAGAGCAAGA Reverse Primer:GAAGCAACATCCTGACAGT	193
SLC7A11	Forward Primer:CCTGTTGTGTCCACCATC Reverse Primer:AAGATTCCTGCTCCAATGAT	176
EZH2	Forward Primer:AAGGATACAGACAGTGATAGG Reverse Primer:ACATTCTCAGGAGGTTCAAT	164
GAPDH	Forward Primer:GAAGGTGAAGGTCGGAGTC Reverse Primer:GGGTGGAATCATATTGGAAC	152

Fig.1 Volcano map of the DEGs. Blue color represents the downregulated genes (log2FC<-1.0, P<0.05) and red the upregulated genes (log2FC>1.0, P<0.05) in GSE20347 and GSE161533 datasets.

Fig.2 Venn diagram of GSE161533 and GSE20347 DEGs and ferroptosis genes.

Fig.3 GO and KEGG functional enrichment map and PPI network map. A: Bubble diagram of GO analysis of BP, MF and CC functions. B: Bubble diagram of KEGG analysis of the main signaling pathways. C: PPI network (red indicates up-regulated and green down-regulated genes). D: Core gene network diagram screened by the "Degree" module.

Fig.4 Expression levels of 6 ferroptosis suppressor genes in TCGA esophageal cancer dataset. **P<0.01, ***P<0.001.

Fig.5 Expression levels of 6 ferroptosis suppressor genes in different esophageal cancer cell line. *P<0.05, **P<0.01, ***P<0.001.

Fig.6 Effect of ferroptosis suppressor gene knock-down on proliferation and apoptosis of esophageal carcinoma cells. A, B: Effect of knocking down ferroptosis suppressor genes on TE1 cell apoptosis and proliferation. C-F: Effect of knocking down ferroptosis suppressor genes on GPX4, FIH1 and ACSL4 proteins. *P<0.05 vs Control and Negative group.

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