Bioinformatics-based identification of ferroptosis-related biomarkers and immune infiltration in retinoblastoma
Highlight box
Key findings
• Three ferroptosis-related genes (FRGs; NFE2L2, HSPB1, JUN) were identified as potential diagnostic biomarkers for retinoblastoma (RB).
• These genes correlate with immune cell infiltration (e.g., CD8+ T cells, macrophages) and show distinct drug sensitivity patterns (AUY922, AG.014699, AMG.706).
• Reverse transcription-quantitative real-time polymerase chain reaction confirmed downregulation of all three genes in RB Y79 cells vs. retinal pigment epithelial cells.
What is known and what is new?
• Ferroptosis is involved in cancer progression and therapy resistance and RB lacks effective prognostic markers.
• This study provides the first integrative analysis linking FRGs to immune microenvironment and drug sensitivity in RB, using bioinformatics approaches.
What is the implication, and what should change now?
• NFE2L2, HSPB1, and JUN may serve as diagnostic biomarkers and therapeutic targets.
• Their association with immune infiltration suggests potential for immunotherapy combinations.
• Future experimental validation in RB cell lines and patient samples is warranted.
Introduction
Retinoblastoma (RB) is the most common primary intraocular malignancy in children (1). Surgical excision is generally performed when tumors present with high-risk clinical features. RB is primarily driven by mutations in the tumor suppressor gene RB1, which encodes the retinoblastoma protein (pRB) (2). Mortality rates remain high in developing countries, where approximately 55% of patients undergo enucleation. In contrast, in developed nations, timely chemotherapy combined with surgery increases survival rates to 95–98% (3,4). Recent advances, such as intra-arterial chemotherapy and intravitreal injection of chemotherapeutic agents, have reduced enucleation rates (5), but these therapies may still induce tumor metastasis and chemotherapy-related toxicities. The molecular mechanisms underlying RB pathogenesis remain incompletely understood.
Ferroptosis is a regulated, iron-dependent form of cell death characterized by phospholipid peroxidation, accumulation of reactive oxygen species (ROS), and polyunsaturated fatty acid-containing phospholipids (PUFA-PLs). Unlike apoptosis or necrosis, ferroptosis is not blocked by conventional inhibitors of these pathways, but can be mitigated by radical-trapping antioxidants (RTAs) such as ferrostatin-1 (Fer-1) (6). RB1 deletion and TP53 mutations are critical in RB pathogenesis, and both are implicated in ferroptosis regulation. Recent studies suggest that drug-tolerant RB cells can be eliminated by inducing autophagy-dependent ferroptosis (7), and that lipid peroxidation-mediated oxidative cell death may represent a promising strategy against drug-resistant RB (8). These findings highlight a potential role for ferroptosis in RB initiation and progression.
The tumor microenvironment (TME) encompasses non-malignant cells and acellular components within the tumor niche. Cytokine secretion induced by oncogenic alterations influences both malignant and stromal cells, including immune cells, fibroblasts, and vasculature. Interactions between RB cells and the TME are critical for tumor initiation, progression, metastasis, and therapeutic response (9).
Bioinformatics approaches provide powerful tools to identify candidate biomarkers in RB. In this study, we analyzed the Gene Expression Omnibus (GEO) dataset to identify differentially expressed genes (DEGs) between RB and healthy tissues. Ferroptosis-related DEGs were obtained by intersecting DEGs with a curated ferroptosis gene set. Key genes were further investigated through single-gene gene set enrichment analysis (GSEA), gene set variation analysis (GSVA), immune infiltration profiling, and drug sensitivity prediction. A schematic overview of the study design is shown in Figure 1. Assessing immune cell subtype distribution in RB tissues may enhance understanding of RB progression and enable the development of more precise diagnostic and therapeutic strategies. Collectively, this study provides new molecular insights into RB progression and identifies potential ferroptosis-related therapeutic targets. We present this article in accordance with the TRIPOD and MDAR reporting checklists (available at https://tcr.amegroups.com/article/view/10.21037/tcr-2025-aw-2568/rc).
Methods
Date collection
Data on RB patients were obtained from the GEO database (http://www.ncbi.nlm.nih.gov/geo), a public repository of gene expression datasets. The raw data of GSE166173 were downloaded for single-cell analysis, and four samples with complete expression profiles were included. For the single-cell dataset GSE166173, this dataset contains RB tissue samples, where the “normal” cells refer to non-malignant cell types identified through unsupervised clustering [such as cone cells, retinal pigment epithelial (RPE) cells, etc.]. These cells were used as intra-tumoral normal references for cell communication and trajectory analysis. For bulk transcriptome analysis, three datasets were used: GSE110811 (training set; 3 normal retinal tissue samples and 28 RB samples), GSE156657 (3 normal retinal tissue samples and 7 RB samples), and GSE97508 (3 normal retinal tissue samples and 6 RB samples). This study was conducted in accordance with the Declaration of Helsinki and its subsequent amendments.
Identification of RB cell marker genes by single-cell RNA sequencing (scRNA-seq) analysis
scRNA-seq data were analyzed using the R packages Seurat and SingleR. Data were normalized with the NormalizeData function in Seurat using the “LogNormalize” method, and a Seurat object was created from the normalized matrix. Principal component analysis (PCA) was performed on the top 1,500 variable genes using the RunPCA function. Significant principal components (PCs) were identified by JackStraw analysis, and the first 15 PCs were selected for downstream analyses. Cell clustering was performed with the FindNeighbors and FindClusters functions in Seurat, where Euclidean distance was used to construct a k-nearest neighbor graph. Dimensionality reduction was visualized using t-distributed stochastic neighbor embedding (t-SNE) with the RunTSNE function. DEGs for each cluster were identified with the FindAllMarkers function using the Wilcoxon rank-sum test, applying thresholds of |log2 [fold change (FC)]| >1 and adjusted P<0.01. Cluster annotation was performed using marker information from the CellMarker and PanglaoDB databases, supplemented by literature review to assign cell identities.
Model construction
Candidate genes were selected and least absolute shrinkage and selection operator (LASSO) regression was used to further build prediction correlation models. After incorporating the expression value of each specific gene, a risk score formula for each patient was constructed and weighted by its estimated regression coefficient in a LASSO regression analysis. According to the risk score formula, with the median risk score value as the cut-off point, patients were divided into low-risk groups and high-risk groups, and the receiver operating characteristic (ROC) curve was used to study the accuracy of model prediction.
Functional enrichment analysis of the ferroptosis-related genes (FRGs) (GSVA + GSEA)
GSEA was performed using the R package clusterProfiler, with significance defined as P<0.05. GSVA was conducted with the GSVA algorithm to systematically evaluate each gene set and identify potential functional alterations across samples.
Immune cell infiltration analysis
Immune cell infiltration in RB tissues was compared with healthy controls. Infiltration levels of 22 immune cell types were estimated using the CIBERSORT algorithm. Correlations among immune cell populations were visualized with the corrplot package. The Wilcoxon rank-sum test was applied to identify statistically significant differences in immune cell infiltration between groups. Visualization of infiltration patterns was conducted using the ggplot2, vioplot packages. Finally, Spearman’s rank correlation analysis was used to examine associations between FRGs and immune cell infiltration levels.
Drug sensitivity analysis
The Genomics of Drug Sensitivity in Cancer (GDSC) database, developed by the Sanger Institute (UK), was used to obtain information on tumor cell drug sensitivity. The R package pRRophetic was applied to predict chemotherapy sensitivity of each tumor sample by estimating the half-maximal inhibitory concentration (IC50) values through regression analysis.
Quantitative real-time polymerase chain reaction (qRT-PCR)
Total RNA was extracted from RB (Y79 line) and RPE (ARPE-19 line) cells using TRIzol reagent (Takara). For the culture and passaging details of the two cells, please see Appendix 1. cDNA was synthesized with the PrimeScript RT Master Mix Kit with gDNA Eraser (Takara, RR047A). qRT-PCR was performed and on a LightCycler 480 system (Roche, Penzberg, Germany) using SYBR Green Master Mix (for more details about qRT-PCR methodology, please see Appendix 1). Relative mRNA expression was calculated using the 2−ΔΔCT method, with GAPDH as the internal control. Primers for GAPDH, JUN, HSPB1, and NFE2L2 are listed in Table S1 (accurate biology).
Statistical analysis
All statistical analyses were performed using R software (version 4.2.0) and GraphPad Prism 9.0. DEGs were identified using the Wilcoxon rank-sum test with thresholds of |log2(FC)| >1 and adjusted P<0.01. LASSO regression was conducted using the glmnet package with 10-fold cross-validation to select optimal lambda. ROC curves were generated using the pROC package, and area under the curve (AUC) values were calculated. Correlations between gene expression and immune cell infiltration or metastasis-related genes were assessed using Spearman’s rank correlation coefficient. For qRT-PCR data, comparisons between two groups were analyzed using two‑tailed Student’s t-test. A P value <0.05 was considered statistically significant.
Results
Basic profiling for single cell data
Single cell level analysis in scRNA-Seq data
We processed the expression profiles using the Seurat package and filtered out low-quality cells based on the thresholds nFeature_RNA >500, nCount_RNA >1,000, percent.mt <15, nFeature_RNA <6,000, and nCount_RNA <25,000. After quality control, a total of 10,137 cells were retained. We visualized the filtering results by violin plots and scatterplots (Figure 2A,2B). We then performed data standardization, normalization, PCA, and Harmony analysis, which demonstrated clear clustering and batch correction across samples (Figure 2C-2E).
Next, we performed t-SNE analysis to determine the positional relationships among cells and identified 16 distinct clusters. These clusters were further classified into eight major cell types (Figure 3A,3B). We compared the proportions of these cell types between normal and RB groups (Figure 3C). By integrating differences in cell number and gene expression, we characterized the contribution of specific subpopulations to RB pathogenesis.
Annotation of cell subpopulations and their contribution to RB
We identified the top 266 DEGs (logFC >1) between RB and control groups to characterize transcriptional changes during this process. Cone cells were found to contribute most prominently to RB progression (Figure 4A,4B). We further reconstructed the developmental trajectories of different cone cell subtypes (Figure 4C-4E).
Identification of key genes and related analysis
Construction of prediction model and identification of key genes
The marker genes of cone cells (logFC >1) were selected to intersect with FRGs, and a total of 15 intersection genes were obtained (Figure 5A). We downloaded the RB-related dataset GSE110811 from the GEO database as the training set, and used datasets GSE156657 and GSE97508 as validation sets. LASSO regression was performed to screen for characteristic features among the 15 intersecting genes. The results showed that LASSO regression identified three genes as feature genes (Figure 5B-5D), which were designated as key genes for subsequent studies and used to construct a predictive model. The model formula is: RiskScore = NFE2L2 × (−0.0532820821590078) + HSPB1 × (0.0054879682205842) + JUN × (0.0494556842030953). The results demonstrated that the predictive model constructed with the three genes had good diagnostic efficacy, with an area under the AUC curve of 0.95 (Figure 5E). External datasets were used to further validate the diagnostic model, and the results showed that the model possessed strong stability, with AUC values of 0.86 and 0.89 for the two validation sets, respectively (Figure 5F,5G).
Analysis of key genes GSEA and GSVA
GSEA revealed that NFE2L2 was enriched in pathways related to DNA replication, necroptosis, and NOD-like receptor signaling (Figure 6A,6B). HSPB1 was mainly associated with cytokine-receptor interaction, neuroactive ligand-receptor interaction, and phototransduction (Figure 6C,6D). JUN was linked to DNA replication, the relaxin signaling pathway, and retinol metabolism (Figure 6E,6F).
GSVA further showed that high HSPB1 expression was enriched in the ROS pathway and allograft rejection (Figure 7A). Elevated JUN expression was associated with angiogenesis and Wnt/β-catenin signaling (Figure 7B), while NFE2L2 was enriched in PI3K-AKT-mTOR signaling and downregulation of ultraviolet (UV) response pathways (Figure 7C). These findings suggest that the three key genes may contribute to RB progression through distinct signaling mechanisms.
The correlation between key genes and metastasis-related genes
Aberrant activation of the RAS signaling pathway is closely associated with tumorigenesis and metastasis in multiple cancers. To explore its relevance in RB, we obtained RAS pathway-related genes from the GSEA database (https://www.gsea-msigdb.org/gsea/index.jsp) and analyzed their correlations with the key genes. NFE2L2 showed significant positive correlations with CHUK and RHOA, but a negative correlation with HRAS. HSPB1 was positively correlated with RALA and RHOA, while JUN demonstrated a positive correlation with RALGDS (Figure 8).
Drug sensitivity
Early-stage RB is commonly managed with surgery combined with chemotherapy, and assessing drug sensitivity may help optimize therapeutic efficacy. Using the R package pRRophetic with drug sensitivity data from the GDSC database, we predicted chemotherapy responses in each tumor sample and examined associations between key genes and commonly used chemotherapeutic agents. NFE2L2 expression was significantly correlated with sensitivity to ABT-888, AICAR, and AUY922 (Figure 9A). HSPB1 expression was associated with sensitivity to AG-014699 (Figure 9B), while JUN expression correlated with sensitivity to AKT inhibitor VIII and AMG-706 (Figure 9C). It should be noted that since the drug sensitivity predictions are based on the GDSC database, which mainly contains drug sensitivity data from other tumor types and may not be fully applicable to RB. Therefore, the predicted results should be interpreted with caution and require validation using RB-specific cell lines or organoid models.
Link between key genes and TME
Immune cell infiltration analysis
The distribution of immune infiltration levels and intercellular relationships was visualized by heatmaps (Figure 10A,10B). Notably, the proportions of CD8+ T cells and activated mast cells were significantly increased in RB samples compared with controls (Figure 10C). We further examined the correlations between key genes and immune cell populations. NFE2L2 showed strong positive correlations with naïve B cells, M0 macrophages, M2 macrophages, naïve CD4+ T cells, and CD8+ T cells. HSPB1 was positively correlated with M1 macrophages, resting NK cells, neutrophils, and resting memory CD4+ T cells, while displaying a negative correlation with memory B cells (Figure 10D).
We further analyzed the associations between the three key genes and a spectrum of immune-related factors, including immunosuppressive molecules, immunostimulatory molecules, chemokines, and chemokine receptors. These analyses revealed significant correlations, suggesting that the key genes are closely linked to immune cell infiltration and may play critical roles in shaping the immune microenvironment of RB (Figure 11).
The relationship between key genes and immune metabolic pathways
We next examined the expression abundance of the three key genes (NFE2L2, HSPB1, and JUN) across multiple cell types, including cone cells, endothelial cells, corneal epithelial cells, microglia, natural killer T (NKT) cells, RPE cells, fibroblasts, and cycling cone cells (Figure 12A-12C). We further analyzed their roles in immunometabolic regulation at the single-cell level (Figure 12D). The results showed that all three genes positively influenced immunity, metabolism, and signal transduction pathways, while exhibiting negative associations with cell proliferation pathways.
qRT-PCR results
Reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) analysis confirmed that the mRNA expression levels of NFE2L2, JUN, and HSPB1 were significantly reduced in RB Y79 cells compared with normal RPE cells (Figure 13). Since RB originates from cone precursor cells, the ideal control should be healthy cone cells. However, since primary cone cells are difficult to obtain and cannot be expanded in vitro, we initially selected RPE cells as the control. To more closely approximate the biological context, in subsequent studies we will supplement with another RB cell line, WERI-Rb-1, as well as another normal retinal control cell—human retinal progenitor cells (HRPC) as controls. In future research, we will collect clinical samples to validate the expression of these three genes and their relationship with patient prognosis at the tissue level using techniques such as immunohistochemistry and in situ hybridization.
Discussion
RB is a rare pediatric intraocular malignancy with an incidence of approximately 1 in 18,000 live births (10). While early detection and timely treatment can cure the disease, delayed intervention often leads to life-threatening progression. Current therapies—including systemic chemotherapy, enucleation, thermotherapy, and cryotherapy—have improved outcomes in developed countries, yet their efficacy remains limited and patient prognosis is often unsatisfactory (11). According to the Knudson “two-hit” hypothesis, biallelic inactivation of the RB1 gene is the initiating event in RB, and subsequent studies have identified additional molecular pathways and biomarkers that may provide opportunities for targeted intervention (12-14). Thus, further elucidation of RB’s molecular mechanisms is crucial for improving early diagnosis and therapy.
Ferroptosis, an iron-dependent form of regulated cell death characterized by lipid peroxidation, has recently gained attention for its potential to overcome therapy resistance in cancer (15,16) Emerging evidence supports its relevance in ocular diseases (17). For example, ferroptosis induction has been shown to inhibit RB proliferation, enhance chemosensitivity, and overcome multidrug resistance (18-20). Zhang et al. demonstrated that lactate metabolism in the TME promotes RB tumorigenesis and confers resistance to ferroptosis through MCT1-mediated lactate transport, highlighting metabolic vulnerabilities as therapeutic targets (21). Nevertheless, research directly linking ferroptosis to RB remains limited. Our findings contribute to this growing field by identifying three ferroptosis-associated genes—NFE2L2, HSPB1, and JUN—as potential diagnostic biomarkers and regulators of RB progression.
Each of these genes plays diverse roles in cancer biology and ferroptosis. NFE2L2 (Nrf2) is a master regulator of antioxidant responses and detoxification pathways. Persistent activation of NFE2L2 promotes RB1 protein degradation and contributes to tumor progression and drug resistance (22-24). While NFE2L2-mediated ferroptosis regulation has been studied in cataract, diabetic retinopathy, and age-related macular degeneration (25-30), its role in RB remains unexplored. JUN, a transcription factor involved in cell proliferation and stress responses, has been implicated in ferroptosis sensitivity across several cancers (31,32). Although evidence in ocular diseases is scarce, one study suggested JUN as a biomarker in retinal neurodegeneration via ferroptosis (33). HSPB1 (HSP27), expressed in multiple ocular tissues, has protective roles in RB, glaucoma, and cataract (34,35), and functions as a negative regulator of ferroptosis (36,37). Together, these results suggest that NFE2L2, JUN, and HSPB1 may influence RB development by modulating ferroptosis-related signaling networks.
Beyond ferroptosis, our study highlights the interplay between these genes and the RB immune microenvironment. The RB TME consists of diverse immune cells, including dendritic cells, macrophages, and T lymphocytes, which influence tumor growth and therapeutic response (38,39). Recent single-cell transcriptomic analyses by Zhang et al. have systematically characterized TME heterogeneity in RB, revealing distinct subclusters of tumor-associated macrophages (TAMs) and astrocyte-like cells that correlate with invasive phenotypes (40). This study demonstrated that cell-cell communications within the TME, particularly between TAMs and tumor cells, play pivotal roles in RB progression and metastasis. Our results demonstrate that NFE2L2, JUN, and HSPB1 are significantly correlated with immune infiltration patterns and immune-related molecules, suggesting that they may shape the immune landscape of RB. Given that immunotherapy remains underutilized in RB, dissecting these immune interactions could help identify new strategies to enhance anti-tumor immunity. Emerging approaches such as circRNA-based immunomodulation and TAM-directed therapies represent promising frontiers for RB treatment (41,42).
This study provides new insights into ferroptosis and immune regulation in RB; however, several limitations must be acknowledged. First, the analyses relied on publicly available datasets with relatively small sample sizes and variable clinical annotations, which may introduce bias. Second, while our integrative bioinformatics approach identified robust candidate genes, functional validation is still required. It is worth noting that the core findings of this study are based on correlation analysis, which can only reveal trends of association between variables but cannot establish causality. The three key genes (NFE2L2, HSPB1, JUN) did not show significant commonalities in their associations with immune regulation and metastasis-related genes, suggesting that they may function through independent signaling pathways—a speculation that requires validation through subsequent in vitro and in vivo functional experiments. Moreover, larger patient cohorts are needed to validate their diagnostic and therapeutic potential.
Conclusions
The dysregulated expression of NFE2L2, JUN, and HSPB1, together with distinct patterns of immune cell infiltration, appears to contribute to RB progression. These genes may serve as ferroptosis-related biomarkers and potential therapeutic targets in RB. Collectively, our findings provide novel insights that could aid in the prevention, monitoring, and precision treatment of RB.
Acknowledgments
The authors appreciate the GEO database. The authors thank Zhihui Gene Technology Co., Ltd. for their technical assistance and consultation on the bioinformatics analysis.
Footnote
Reporting Checklist: The authors have completed the TRIPOD and MDAR reporting checklists. Available at https://tcr.amegroups.com/article/view/10.21037/tcr-2025-aw-2568/rc
Data Sharing Statement: Available at https://tcr.amegroups.com/article/view/10.21037/tcr-2025-aw-2568/dss
Peer Review File: Available at https://tcr.amegroups.com/article/view/10.21037/tcr-2025-aw-2568/prf
Funding: This work was supported by
Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://tcr.amegroups.com/article/view/10.21037/tcr-2025-aw-2568/coif). The authors have no conflicts of interest to declare.
Ethical Statement: The authors are accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. This study was conducted in accordance with the Declaration of Helsinki and its subsequent amendments.
Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0/.
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