Analysis of regulation of prognosis, immune infiltration, and ferroptosis in sarcoma based on stemness index model

doi:10.12307/2025.055

Abstract

Abstract: BACKGROUND: The stemness index may be associated with the prognosis and immune infiltration of sarcoma, but the specific regulatory mechanism and characteristic genes have yet to be fully elucidated.
OBJECTIVE: To investigate the correlation between stem cells and prognosis as well as immune infiltration in sarcoma employing the gene stemness index model and to identify the ferroptosis signature genes associated with sarcoma stem cells.
METHODS: The sarcoma RNA sequencing data and related clinical information were obtained from the Cancer Genome Atlas (TCGA). The sarcoma RNA sequencing data were grouped using the sarcoma stemness index. Survival data were used to analyze prognosis between groups. Differentially expressed genes were obtained for pathway enrichment and immune infiltration analysis. Ferroptosis-related differential genes were used to construct a protein interaction network and analyze prognostic correlation. Rhabdomyosarcoma cell lines were cultured and divided into adherent cell group and stem cell group. The adherent cell group received no intervention, while the stem cell group was treated with serum-free culture to enrich stem cells in rhabdomyosarcoma cells. qRT-PCR was used to evaluate stemness markers, ferroptosis-related genes, and mRNA expression of ferroptosis-related markers in the cells.
RESULTS AND CONCLUSION: (1) Patients were divided into high and low stemness index groups based on the median stemness index. The progression-free survival of patients in the high stemness index group was lower than that in the low stemness index group by disease risk prediction, suggesting poor prognosis. (2) According to GO and KEGG analysis, the groups with high and low stemness indices differed from one another. There were differences in immune infiltration between the high and low stemness index groups. Nine of the 23 ferroptosis-related genes in the differential genes have the potential to establish a highly correlated network of protein interactions. Patients with high expression of IDO1, IFNG, and AQP5 have a better prognosis, while those with high expression of CA9 have a poor prognosis. (3) The qRT-PCR results demonstrated a significant upregulation of stem cell-related markers NANOG, SOX2, and OCT4 mRNA expressions in the stem cell group compared to the adherent cell group (P < 0.05). Compared to the adherent cell group, the stem cell group exhibited decreased mRNA expression level of ferroptosis-related marker SLC7A11 (P < 0.05) while showing increased levels of ACSL4, GPX4, FTH1, and COX2 (P < 0.05). Compared to the adherent cell group, the stem cell group displayed decreased mRNA expression level of differentially expressed gene CA9 alongside elevated levels of IDO1, IFNG, and AQP5 (P < 0.05). Stem cells were strongly associated with sarcoma survival and ferroptosis by bioinformatics analysis and experimental verification. Sarcoma stem cells have aberrant expression of CA9, IDO1, IFNG, and AQP5, which may serve as new targets for sarcoma therapy as well as diagnostic indicators.

Key words: ">sarcoma, stem cell, stemness index, ferroptosis, survival prognosis, immune infiltration

CLC Number:

Wei Jingxian, Meng Lian, Sun Hao, Zhang Tiantian, Liu Chunxia. Analysis of regulation of prognosis, immune infiltration, and ferroptosis in sarcoma based on stemness index model[J]. Chinese Journal of Tissue Engineering Research, 2025, 29(19): 4151-4160.

Figures/Tables 5

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