A Novel Ferroptosis-Associated Gene Signature to Predict Prognosis in Patients with Uveal Melanoma

Assessment of ferroptosis as a promising candidate for metastatic uveal melanoma treatment and prognostication

Uveal melanoma (UM) is the most common primary intraocular tumour in adults. Local resection, radiation therapy, and enucleation are the current first-line, primary UM treatments. However, regardless of the treatment received, around 50% of UM patients will develop metastatic disease within five to 7 years. In the largest published series of unselected patients with metastatic UM (mUM), the median survival time after diagnosis of metastasis was 3.6 months, with less than 1% of patients surviving beyond 5 years. Approved drugs for treatment of mUM include systemic treatment with tebentafusp-tebn or isolated hepatic perfusion (IHP) with melphalan. However, these drugs are only available to a subset of patients and improve survival by only a few months, highlighting the urgent need for new mUM treatments. Accurately predicting which patients are at high risk for metastases is also crucial. Researchers are developing gene expression signatures in primary UM to create reliable prognostic models aimed at improving patient follow-up and treatment strategies. In this review we discuss the evidence supporting ferroptosis, a non-apoptotic form of cell death, as a potential novel treatment target and prognosticator for UM.

A novel arginine methylation-associated lncRNA signature effectively predicts prognosis in breast cancer patients

Breast cancer (BC) is a disease highly associated with epigenetic modification, and arginine methylation is particularly important in its genetic regulation. However, the role of arginine methylation related lncRNAs in breast cancer has not been studied. First, we identified the related lncRNAs (from TCGA database) according to the differentially expressed genes related to arginine methylation in breast cancer. Then the lncRNAs related to protein arginine methylation were obtained by regression analysis, and the risk score model was constructed. Finally, the cell experiment and subcutaneous tumor model verified that the arginine methylation related lncRNA z68871.1 in the model had a significant effect on the proliferation and invasion of breast cancer cells. In conclusion, we successfully constructed an arginine methylation related lncRNA model, which has strong predictive ability. At the same time, this study provides an experimental basis for exploring the mechanism of arginine methylation in BC and helps to find new biomarkers of BC.

Construction of oxidative phosphorylation-related prognostic risk score model in uveal melanoma

BACKGROUND

Uveal melanoma (UVM) is a malignant intraocular tumor in adults. Targeting genes related to oxidative phosphorylation (OXPHOS) may play a role in anti-tumor therapy. However, the clinical significance of oxidative phosphorylation in UVM is unclear.

METHOD

The 134 OXPHOS-related genes were obtained from the KEGG pathway, the TCGA UVM dataset contained 80 samples, served as the training set, while GSE22138 and GSE39717 was used as the validation set. LASSO regression was carried out to identify OXPHOS-related prognostic genes. The coefficients obtained from Cox multivariate regression analysis were used to calculate a risk score, which facilitated the construction of a prognostic model. Kaplan-Meier survival analysis, logrank test and ROC curve using the time "timeROC" package were conducted. The immune cell frequency in low- and high-risk group was analyzed through Cibersort tool. The specific genomic alterations were analyzed by "maftools" R package. The differential expressed genes between low- or high-risk group were analyzed and performed Gene Ontology (GO) and GSEA. Finally, we verified the function of CYC1 in UVM by gene silencing in vitro.

RESULTS

A total of 9 OXPHOS-related prognostic genes were identified, including NDUFB1, NDUFB8, ATP12A, NDUFA3, CYC1, COX6B1, ATP6V1G2, ATP4B and NDUFB4. The UVM prognostic risk model was constructed based on the 9 OXPHOS-related prognostic genes. The prognosis of patients in the high-risk group was poorer than low-risk group. Besides, the ROC curve demonstrated that the area under the curve of the model for predicting the 1 to 5-year survival rate of UVM patients were all more than 0.88. External validation in GSE22138 and GSE39717 dataset revealed that these 9 genes could also be utilized to evaluate and predict the overall survival of patients with UVM. The risk score levels related to immune cell frequency and specific genomic alterations. The DEGs between the low- and high- risk group were enriched in tumor OXPHOS and immune related pathway. In vitro experiments, CYC1 silencing significantly inhibited UVM cell proliferation and invasion, induced cell apoptosis.

CONCLUSION

In sum, a prognostic risk score model based on oxidative phosphorylation-related genes in UVM was developed to enhance understanding of the disease. This prognostic risk score model may help to find potential therapeutic targets for UVM patients. CYC1 acts as an oncogene role in UVM.

1,4-dihydroxy quininib activates ferroptosis pathways in metastatic uveal melanoma and reveals a novel prognostic biomarker signature

Uveal melanoma (UM) is an ocular cancer, with propensity for lethal liver metastases. When metastatic UM (MUM) occurs, as few as 8% of patients survive beyond two years. Efficacious treatments for MUM are urgently needed. 1,4-dihydroxy quininib, a cysteinyl leukotriene receptor 1 (CysLT1) antagonist, alters UM cancer hallmarks in vitro, ex vivo and in vivo. Here, we investigated the 1,4-dihydroxy quininib mechanism of action and its translational potential in MUM. Proteomic profiling of OMM2.5 cells identified proteins differentially expressed after 1,4-dihydroxy quininib treatment. Glutathione peroxidase 4 (GPX4), glutamate-cysteine ligase modifier subunit (GCLM), heme oxygenase 1 (HO-1) and 4 hydroxynonenal (4-HNE) expression were assessed by immunoblots. Biliverdin, glutathione and lipid hydroperoxide were measured biochemically. Association between the expression of a specific ferroptosis signature and UM patient survival was performed using public databases. Our data revealed that 1,4-dihydroxy quininib modulates the expression of ferroptosis markers in OMM2.5 cells. Biochemical assays validated that GPX4, biliverdin, GCLM, glutathione and lipid hydroperoxide were significantly altered. HO-1 and 4-HNE levels were significantly increased in MUM tumor explants from orthotopic patient-derived xenografts (OPDX). Expression of genes inhibiting ferroptosis is significantly increased in UM patients with chromosome 3 monosomy. We identified IFerr, a novel ferroptosis signature correlating with UM patient survival. Altogether, we demontrated that in MUM cells and tissues, 1,4-dihydroxy quininib modulates key markers that induce ferroptosis, a relatively new type of cell death driven by iron-dependent peroxidation of phospholipids. Furthermore, we showed that high expression of specific genes inhibiting ferroptosis is associated with a worse UM prognosis, thus, the IFerr signature is a potential prognosticator for which patients develop MUM. All in all, ferroptosis has potential as a clinical biomarker and therapeutic target for MUM.

Identification and validation of an immune-relevant risk signature predicting survival outcome and immune infiltration in uveal melanoma

PURPOSE

The current study aimed to reveal a novel immune-related signature to evaluate immune infiltration status and the survival outcome for patients with uveal melanoma (UM).

METHODS

Based on 80 UM samples from the Cancer Genome Atlas, the transcriptome gene expression and clinical characteristics were analyzed to identify immune-related genes that contributed most to prognosis based on LASSO Cox regression. By combining the gene expression level with the corresponding regression coefficient, a risk score was calculated and all patients were divided into high- and low-risk groups. Survival, tumor-infiltrating immune cell abundance, dysregulated signaling pathways, immunophenoscore and tumor mutation burden were compared between two groups. Validation of the risk signature was performed in GSE22138 and GSE44295 cohort. For evaluating the immunotherapy efficacy, 348 advanced urothelial cancer patients treated with immune checkpoint inhibitor (ICI) were used for external validation.

RESULTS

Nine immune-related prognostic genes were identified under the LASSO Cox regression in the TCGA cohort; they are ACKR2, AREG, CCL5, CLEC11A, IGKV1-33, IL36B, NROB1, TRAV8-4 and TRBV28. Better prognosis, elevated immune cell infiltration, decreased immune-suppressive cell infiltration, immune response-related pathways and higher immunophenoscore were found in low-risk patients, with better ICI treatment response rate.

CONCLUSION

The identified immune risk signature was demonstrated to be associated with the favorable immune infiltration, prognosis and immunotherapeutic efficacy, which may provide clues for survival evaluation and immune treatment.

Impact of curcumin on ferroptosis-related genes in colorectal cancer: Insights from in-silico and in-vitro studies

Colorectal cancer (CRC) is responsible for a significant number of cancer-related fatalities worldwide. Researchers are investigating the therapeutic potential of ferroptosis, a type of iron-dependent controlled cell death, in the context of CRC. Curcumin, a natural compound found in turmeric, exhibits anticancer properties. This study explores the effects of curcumin on genes related to ferroptosis (FRGs) in CRC. To gather CRC data, we used the Gene Expression Profiling Interactive Analysis (GEPIA) and Gene Expression Omnibus (GEO) databases, while FRGs were obtained from the FerrDb database and PubMed. We identified 739 CRC differentially expressed genes (DEGs) in CRC and discovered 39 genes that were common genes between FRGs and CRC DEGs. The DEGs related to ferroptosis were enriched with various biological processes and molecular functions, including the regulation of signal transduction and glucose metabolism. Using the Drug Gene Interaction Database (DGIdb), we predicted drugs targeting CRC-DEGs and identified 17 potential drug targets. Additionally, we identified eight essential proteins related to ferroptosis in CRC, including MYC, IL1B, and SLC1A5. Survival analysis revealed that alterations in gene expression of CDC25A, DDR2, FABP4, IL1B, SNCA, and TFAM were associated with prognosis in CRC patients. In SW480 human CRC cells, treatment with curcumin decreased the expression of MYC, IL1B, and EZH2 mRNA, while simultaneously increasing the expression of SLCA5 and CAV1. The findings of this study suggest that curcumin could regulate FRGs in CRC and have the potential to be utilized as a therapeutic agent for treating CRC.

A Newly Established Cuproptosis-Related Gene Signature for Predicting Prognosis and Immune Infiltration in Uveal Melanoma

Uveal melanoma (UVM) is the most common primary ocular malignancy in adults and involves several types of regulated cell death. Cuproptosis is a novel method of regulating cell death by binding lipoylated TCA cycle proteins. There is still no research on the relationship between cuproptosis-related genes (CRGs) and UVM. Here, we aimed to develop a prognostic CRG signature for UVM. After a prognostic CRG signature was constructed, we determined the relationship between the signature and immune infiltration, bioinformatics analysis and experimental validation. Finally, a prognostic cuproptosis-related three-gene (CRTG) signature was constructed, which comprised ORAI2, ACADSB and SLC47A1. The risk score of the CRTG signature was negatively correlated with the overall survival (OS) and progression-free survival (PFS) of patients, which revealed strong predictive ability and its independent prognostic value. In addition, we found that the risk score was negative for chromosomes 3 and 6p, and positive for 8q, and high-risk UVM patients showed an increase in protumor immune infiltrates and a high expression of immune checkpoints. Finally, experimental validation verified that the migratory ability of MUM-2B cells was suppressed by the knockdown of the identified genes in vitro. We constructed a CRTG signature that is helpful in predicting prognosis and guiding treatment for patients with UVM.

Ferroptosis induced by DCPS depletion diminishes hepatic metastasis in uveal melanoma

Hepatic metastasis develops in ∼50% of uveal melanoma (UM) patients with scarcely effective treatment resulting in lethality. The underlying mechanism of liver metastasis remains elusive. Ferroptosis, a cell death form characterized by lipid peroxide, in cancer cells may decrease metastatic colonization. In the present study, we hypothesized that decapping scavenger enzymes (DCPS) impact ferroptosis by regulating mRNA decay during the metastatic colonization of UM cells to liver. We found that inhibition of DCPS by shRNA or RG3039 induced gene transcript alteration and ferroptosis through reducing the mRNA turnover of GLRX. Ferroptosis induced by DCPS inhibition eliminates cancer stem-like cells in UM. Inhibition of DCPS hampered the growth and proliferation both in vitro and in vivo. Furthermore, targeting DCPS diminished hepatic metastasis of UM cells. These findings may shed light on the understanding of DCPS-mediated pre-mRNA metabolic pathway in UM by which disseminated cells gain enhanced malignant features to promote hepatic metastasis, providing a rational target for metastatic colonization in UM.

Identification and validation of immunogenic cell death-related score in uveal melanoma to improve prediction of prognosis and response to immunotherapy

BACKGROUND

Immunogenic cell death (ICD) could activate innate and adaptive immune response. In this work, we aimed to develop an ICD-related signature in uveal melanoma (UVM) patients and facilitate assessment of their prognosis and immunotherapy.

METHODS

A set of machine learning methods, including non-negative matrix factorization (NMF) method and least absolute shrinkage and selection operator (LASSO) logistic regression model, and bioinformatics analytic tools were integrated to construct an ICD-related risk score (ICDscore). CIBERSORT and ESTIMATE algorithms were used to evaluate the infiltration of immune cells. The Genomics of Drug Sensitivity in Cancer (GDSC), cellMiner and tumor immune dysfunction and exclusion (TIDE) databases were used for therapy sensitivity analyses. The predictive performance between ICDscore with other mRNA signatures was also compared.

RESULTS

The ICDscore could predict the prognosis of UVM patients in both the training and four validating cohorts. The ICDscore outperformed 19 previously published signatures. Patients with high ICDscore exhibited a substantial increase in immune cell infiltration and expression of immune checkpoint inhibitor-related genes, leading to a higher response rate to immunotherapy. Furthermore, the downregulation of poly (ADP-ribose) polymerase family member 8 (PARP8), a critical gene involved in the development of the ICDscore, resulted in decreased cell proliferation and slower migration of UVM cells.

CONCLUSION

In conclusion, we developed a robust and powerful ICD-related signature for evaluating the prognosis and benefits of immunotherapy that could serve as a promising tool to guide decision-making and surveillance for UVM patients.

Overexpression of ferroptosis-related genes FSP1 and CISD1 is related to prognosis and tumor immune infiltration in gastric cancer

PURPOSE

Gastric cancer (GC) is one of the highest incidence rate cancers worldwide and the search for new biomarkers remains urgent due to its relatively poor prognosis and limited treatment methods. Ferroptosis suppressor protein 1 (FSP1) and iron sulfur domain 1 (CISD1) promoted malignant tumor progression as ferroptosis suppressors in a variety of tumors, but their study in GC remains to be explored.

METHODS

In our study, FSP1 and CISD1 expression were predicted through different databases and confirmed by qRT-PCR, immunohistochemistry and western blotting. Enrichment analyses were exploited to explore the potential functions of FSP1 and CISD1. Finally, their relationship with immune infiltration was determined by Tumor Immune Estimation Resource and ssGSEA algorithm.

RESULTS

The expression of FSP1 and CISD1 was higher in GC tissues. Their strongly positive immunostaining was associated with increased tumor size, degree of differentiation, depth of invasion and lymph node metastasis in GC patients. Up-regulated FSP1 and CISD1 predicted poorer overall survival of patients with GC. Furthermore, FSP1 and CISD1 as ferroptosis inhibitors were predicted to be involved in GC immune cell infiltration.

CONCLUSIONS

Our study suggested that FSP1 and CISD1 acted as biomarkers of poor prognosis and promising immunotherapeutic targets for GC.

Single cell sequencing analysis constructed the N7-methylguanosine (m7G)-related prognostic signature in uveal melanoma

BACKGROUND

Uveal melanoma is a highly malignant tumor in the eye. Its recurrence and metastasis are common, and the prognosis is poor.

METHODS

The transcriptome data of UVM were downloaded from TCGA database, and the single cell sequencing dataset GSE139829 was downloaded from GEO database. Weighted co-expression network analysis was used to explore the modules associated with m7G. Lasso regression was used to construct M⁷G-related prognostic signature. Immune infiltration analysis was used to explore the significance of the model in the tumor immune microenvironment. Finally, cell assays were used to explore the function of key genes in the MUM-2B and OCM-1 cell lines of UVM.

RESULTS

The prognostic signature was constructed by Cox regression and Lasso regression. Patients could be divided into high-risk group and low-risk group by this signature, and the high-risk group had worse prognosis (P<0.05). Cell experiments showed that the proliferation, invasion and migration ability of UVM cell lines were significantly decreased after the knockdown of PAG1, a key gene in signature, which proved that PAG1 might be a potential target of UVM.

CONCLUSIONS

Our study explored the significance of m⁷G in UVM, provided biomarkers for its diagnosis and treatment.

A Novel Cuprotosis-Related lncRNA Signature Effectively Predicts Prognosis in Glioma Patients

Cuprotosis is a novel and different cell death mechanism from the existing known ones that can be used to explore new approaches to treating cancer. Just like ferroptosis and pyroptosis, cuprotosis-related genes regulate various types of tumorigenesis, invasion, and metastasis. However, the relationship between cuprotosis-related long non-coding RNA (cuprotosis-related lncRNA) in glioma development and prognosis has not been investigated. We obtained relevant data from the Genotype-Tissue Expression (GTEx), Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA), and published articles. First, we identified 365 cuprotosis-related lncRNAs based on 10 cuprotosis-related differential genes (|R²|> 0.4, p < 0.001). Then using Lasso and Cox regression analysis methods, 12 prognostic cuprotosis-related lncRNAs were obtained and constructed the CuLncSigi risk score formula. Our next step was to divide the tumor gliomas into two groups (high risk and low risk) based on the median risk score, and we found that patients in the high-risk group had a significantly worse prognosis. We used internal and external validation methods to simultaneously analyze and validate that the risk score model has good predictive power for patients with glioma. Next, we also performed enrichment analyses such as GSEA and aaGSEA and evaluated the relationship between immune-related drugs and tumor treatment. In conclusion, we successfully constructed a formula of cuprotosis-related lncRNAs with a powerful predictive function. More importantly, our study paves the way for exploring cuprotosis mechanisms in glioma occurrence and development and helps to find new relevant biomarkers for glioma early identification and diagnosis and to investigate new therapeutic approaches.

Comprehensive pan-cancer analysis and the regulatory mechanism of AURKA, a gene associated with prognosis of ferroptosis of adrenal cortical carcinoma in the tumor micro-environment

Background: The only curative option for patients with locally or locally advanced adrenocortical carcinoma is primary tumor curative sexual resection (ACC). However, overall survival remains low, with most deaths occurring within the first 2 years following surgery. The 5-year survival rate after surgery is less than 30%. As a result, more accurate prognosis-related predictive biomarkers must be investigated urgently to detect patients' disease status after surgery. Methods: Data from FerrDb were obtained to identify ferroptosis-related genes, and ACC gene expression profiles were collected from the GEO database to find differentially expressed ACC ferroptosis-related genes using differential expression analysis. The DEFGs were subjected to Gene Ontology gene enrichment analysis and KEGG signaling pathway enrichment analysis. PPI network building and predictive analysis were used to filter core genes. The expression of critical genes in ACC pathological stage and pan-cancer was then investigated. In recent years, immune-related factors, DNA repair genes, and methyltransferase genes have been employed in diagnosing and prognosis of different malignancies. Cancer cells are mutated due to DNA repair genes, and highly expressed DNA repair genes promote cancer. Dysregulation of methyltransferase genes and Immune-related factors, which are shown to be significantly expressed in numerous malignancies, also plays a crucial role in cancer. As a result, we investigated the relationship of AURKA with immunological checkpoints, DNA repair genes, and methyltransferases in pan-cancer. Result: The DEGs found in the GEO database were crossed with ferroptosis-related genes, yielding 42 differentially expressed ferroptosis-related genes. Six of these 42 genes, particularly AURKA, are linked to the prognosis of ACC. AURKA expression was significantly correlated with poor prognosis in patients with multiple cancers, and there was a significant positive correlation with Th2 cells. Furthermore, AURKA expression was positively associated with tumor immune infiltration in Lung adenocarcinoma (LUAD), Liver hepatocellular carcinoma (LIHC), Sarcoma (SARC), Esophageal carcinoma (ESCA), and Stomach adenocarcinoma (STAD), but negatively correlated with the immune score, matrix score, and calculated score in these tumors. Further investigation into the relationship between AURKA expression and immune examination gene expression revealed that AURKA could control the tumor-resistant pattern in most tumors by regulating the expression level of specific immune examination genes. Conclusion: AURKA may be an independent prognostic marker for predicting ACC patient prognosis. AURKA may play an essential role in the tumor microenvironment and tumor immunity, according to a pan-cancer analysis, and it has the potential to be a predictive biomarker for multiple cancers.

Ferroptosis Biomarkers for Predicting Prognosis and Immunotherapy Efficacy in Adrenocortical Carcinoma

BACKGROUND

Numerous studies have suggested that ferroptosis plays an important regulatory role in cancer cell death. Nonetheless, the potential effects of ferroptosis regulators on the prognosis, the expression of immunomodulatory factors in the tumor microenvironment and on the efficacy of immunotherapy in adrenocortical carcinoma (ACC) remain largely unknown.

METHODS

Public ACC datasets were used to investigate the relationship between ferroptosis regulators and prognosis and clinical features. A ferroptosis scoring system was established for individual cases of ACC using principal component analysis algorithms. Hub ferroptosis-related genes involved in immunoregulation and immunotherapy efficacy in ACC were further identified.

RESULTS

Twenty ferroptosis regulators were differentially expressed in ACC and 17 ferroptosis regulators were closely related to prognosis in ACC. A ferroptosis scoring system was developed based on ACSL4, FANCD2, and SLC7A1 expression, and the ferroptosis regulators could serve as an independent prognostic factor for ACC. Further analyses indicated that the ferroptosis score integrated with the tumor mutation burden (TMB), and immune-checkpoint gene expression could predict prognosis in ACC. RNA isolation and reverse transcription‑quantitative polymerase chain reaction (RT-qPCR) demonstrated significant differences in the expression levels of ACSL4, FANCD2, and SLC7A1 between ACC and normal tissues. Furthermore, FANCD2 was significantly related to immunotherapy efficacy and prognosis in ACC.

CONCLUSION

Our study demonstrated that ferroptosis was significantly associated with prognosis, clinical characteristics, immune-checkpoint gene expression, and tumor microenvironment immune cell infiltration in ACC. The current study provides comprehensive evidence for further research on ferroptosis regulators in ACC and provides new insight into the epigenetic regulation of the antitumor immune response.

Integrative analysis of enrichment and prognostic value of ferroptosis-related genes and pathways in multiple myeloma

Ferroptosis is a non-apoptotic form of cell death caused by excessive iron exposure. The role played by the ferroptosis-related genes and pathways in multiple myeloma (MM) is poorly understood. Here, we show that the ferroptosis-related pathways might be involved in tumorigenesis and are closely correlated with the prognosis of MM. The ferroptosis suppressor genes are progressively enriched with the progression of plasma cell dyscrasias. Furthermore, high expression of ferroptosis suppressor genes is correlated with high International Staging System and Revised-ISS staging of MM, as well as the poor outcomes of poor outcomes in progression-free survival and overall survival . The ferroptosis driver genes and the ferroptosis suppressor genes have the opposite effects on the progression and prognosis of MM. Moreover, we reveal that ferroptosis-related genes are associated with cytogenetic abnormalities in MM. The ferroptosis-related pathways and genes might impact the osteogenic differentiation of mesenchymal stromal cells in MM patients. A better understanding of the participation of ferroptosis in MM will pave the way for design of new therapies.

STEAP3 can predict the prognosis and shape the tumor microenvironment of clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is a common malignant tumor of the urinary system characterized by poor prognosis and difficult treatment. It has been reported that iron metabolism dysregulation is a common phenomenon in ccRCC and is closely related to the process of ccRCC. But still now, the exact function and underlying mechanisms of iron metabolism dysregulation in ccRCC have not been fully elucidated. In this study, we comprehensively investigated the prognostic value and potential role of STEAP3 (an iron metabolism-related gene) in ccRCC. STEAP3 is significantly up-regulated in ccRCC. High STEAP3 expression is associated with gender, hemoglobin level, pathological grade, tumor stage and significantly predicts an unfavorable prognosis of ccRCC patients. Functional enrichment analysis and evaluation of the tumor microenvironment indicated that STEAP3 was involved in the remodeling of tumor extracellular matrix and the shaping of an immune-suppressive tumor microenvironment to promote tumor metastasis and evade immune killing. Besides, the expression of STEAP3 is also associated with the expression of various immune checkpoint molecules and the IC50 of targeted drugs. Finally, we verified STEAP3 by RT-qPCR and IHC staining. In conclusion, we found that STEAP3 can serve as a candidate prognostic biomarker for ccRCC, and targeting STEAP3 and its biological processes may provide new references for the individualized treatment of ccRCC.

GPX4-independent ferroptosis—a new strategy in disease’s therapy

Ferroptosis is a form of programmed cell death characterized by intracellular iron accumulation and lipid peroxidation, and earlier studies identified glutathione peroxidase 4 (GPX4) as an essential regulator of this process. Ferroptosis plays an essential role in tumors, degenerative diseases, and ischemia-reperfusion injury. However, researchers have found that inhibition of GPX4 does not entirely suppress ferroptosis in certain diseases, or cells express resistance to ferroptosis agonists that inhibit GPX4. As research progresses, it has been discovered that there are multiple regulatory pathways for ferroptosis that are independent of GPX4. The study of GPX4-independent ferroptosis pathways can better target ferroptosis to prevent and treat various diseases. Here, the currently inhibited pulmonary GPX4-dependent ferroptosis pathways will be reviewed.

Heme Oxygenase-1 Overexpression Promotes Uveal Melanoma Progression and Is Associated with Poor Clinical Outcomes

Uveal melanoma (UM) is the most common primary intraocular tumor in adults. To date, the main strategies to counteract its progression consist of focal radiation on the tumor site and ocular enucleation. Furthermore, many UM patients develop liver metastasis within 10 years following diagnosis, eventually resulting in a poorer prognosis for those patients. Dissecting the molecular mechanism involved in UM progression may lead to identify novel prognostic markers with significative clinical applications. The aim of the present study was to evaluate the role of Heme Oxygenase 1 (HO-1) in regulating UM progression. UM cell lines (92.1) were treated with Hemin (CONC e time), a strong inducer of HO-1, and VP13/47, a selective inhibitor of its enzymatic activity. Interestingly, our results showed an enhanced 92.1 cellular proliferation and wound healing ability following an HO-1 increase, overall unveiling the role played by this protein in tumor progression. Similar results were obtained following treatment with two different CO releasing molecules (CORM-3 and CORM-A1). These results were further confirmed in a clinical setting using our UM cohort. Our results demonstrated an increased median HO-1 expression in metastasizing UM when compared to nonmetastasizing patients. Overall, our results showed that HO-1 derived CO plays a major role in UM progression and HO-1 protein expression may serve as a potential prognostic and therapeutical factor in UM patients.

EZH2-mediated H3K27me3 is a predictive biomarker and therapeutic target in uveal melanoma

Although gene mutations and aberrant chromosomes are associated with the pathogenesis and prognosis of uveal melanoma (UM), potential therapeutic targets still need to be explored. We aim to determine the predictive value and potential therapeutic target of EZH2 in uveal melanoma. Eighty-five uveal melanoma samples were recruited in our study, including 19 metastatic and 66 nonmetastatic samples. qRT-PCR, immunohistochemistry staining, and western blotting were applied to detect the expression of EZH2 and H3K27me3. We found that EZH2 (41/85, 48.24%) and H3K27me3 (49/85, 57.65%) were overexpressed in uveal melanoma. The expression of EZH2 was not significantly associated with metastasis. High H3K27me3 expression was correlated with poor patient prognosis. UNC 1999, an EZH2 inhibitor, can downregulate H3K27me3 expression and has the most potency to inhibit OMM1 cell growth by the cell cycle and ferroptosis pathway. These results indicate that H3K27me3 can be a biomarker predicting a poor prognosis of UM. EZH2 is the potential therapeutic target for UM.

A ferroptosis associated gene signature for predicting prognosis and immune responses in patients with colorectal carcinoma

Background: Colorectal carcinoma (CRC) is one of the most prevalent malignancies globally. Ferroptosis, a novel type of cell death, is critical in the development and treatment of tumors.

Objective: This study was designed to establish a genetic signature for ferroptosis which has a predictive effect on the outcomes and immunotherapeutic response of CRC.

Methods: Data of CRC patients were retrieved from TCGA and GEO databases. The genes associated with ferroptosis were obtained from GeneCards. The genetic signature for ferroptosis was identified by performing Cox regression analysis. Kaplan–Meier and ROC analysis were performed to assess the prognosis role of the genetic signature. CIBERSORT tool was used to identify a potential association of the genetic signature with the immune cells. The potential immunotherapeutic signatures and drug sensitivity prediction targeting this signature were also discussed. Immunohistochemistry was used to detect expression of ferroptosis-associated genes in CRC tissues and adjacent tissues.

Results: A ferroptosis-associated gene signature comprised of three genes (CDKN2A, FDFT1, and ACSL6) was developed for prediction of prognosis and evaluation of immune responses in CRC. Patients in the high-risk group tended to have a poor prognosis. In CRC, the ferroptosis-associated gene signature may function as independent predictors. Additionally, the expressional levels of the immune checkpoint proteins PD-L1 and CTLA-4 were substantially increased in the high-risk group. Moreover, we can distinguish between patients based on their immunotherapeutic responses more effectively if we categorize them by this signature. Additionally, candidate compounds were identified for the differentiation of CRC subtypes.

Conclusion: The ferroptosis-associated gene signature identified in this study is effective in predicting the prognosis and evaluating immunotherapeutic response in CRC patients, and provides us with novel insights into the potential effect of ferroptosis targeted treatment on CRC.

Prediction of Prognosis in Patients With Endometrial Carcinoma and Immune Microenvironment Estimation Based on Ferroptosis-Related Genes

Background: Ferroptosis, a form of non-apoptotic cell death, has aroused worldwide interest in cancer researchers. However, the current study about the correlation between ferroptosis-related genes (FRGs) and endometrial cancer (EC) remains limited.

Methods: First, the transcriptome profiling and clinical data of EC patients were downloaded from The Cancer Genome Atlas (TCGA) and Clinical Proteomic Tumor Analysis Consortium (CPTAC) program as the training group and testing group, respectively. FRGs were acquired through literature mining. Then, we used R 4.1.1 software to screen the differently expressed FRGs from TCGA, which was also connected with the prognosis of EC patients. Subsequently, the risk score of each tumor sample was identified by LASSO regression analysis, and we classified these samples into the high- and low-risk groups in the light of the median risk score. Receiver operating characteristic (ROC) curve analysis and Kaplan-Meier analysis were performed to assess the accuracy of this signature. Significantly, the data from CPTAC was used to validate the prediction model externally. Furthermore, we evaluated the immune microenvironment in this model via single-sample gene set enrichment analysis (ssGSEA).

Results: Among the 150 FRGs, 6 differentially expressed genes (DEGs) based on TCGA had a relationship with the prognosis of EC patients, namely, TP53, AIFM2, ATG7, TLR4, PANX1 and MDM2. The survival curve indicated a higher survival probability in the low-risk group. Moreover, the FRGs-based signature acted well in the prediction of overall survival (OS). The results of external verification confirmed the prediction model we established. Finally, ssGSEA revealed significant differences in the abundance of 16 immune cells infiltration and the activity of 13 immune functions between different risk groups.

Conclusion: We identified a novel ferroptosis-related gene signature which could concisely predict the prognosis and immunotherapy in EC patients.

Ferroptosis Associates With Diagnosis and Prognosis by Promoting Antitumor Immune Response in Melanoma

Immunotherapy has greatly improved the clinical benefits of cancer treatment, especially in melanoma. Ferroptosis is a novel mechanism of cell death which relates to immunity. This study aimed at understanding the potential link between ferroptosis and cancer immunocompetent in melanoma using multiple bioinformatics analyses. By the WGCNA assay, we first constructed a key module–gene of ferroptosis, which was strongly correlated with the diagnosis, prognosis, and infiltration of immune cells in melanoma. The elevated module–gene could effectively distinguish melanoma from normal tissues and acted as a good prognostic marker. The module–gene of ferroptosis was positively correlated with the infiltration of immune cells. In particular, the module was positively correlated with the expression of PD-L1 and sensitively increased after effective anti-PD-1 treatment. Furthermore, the differential expression of the module–gene between normal and tumor tissues was observed in pan-cancer. The similarity correlations of the module–gene with infiltration of immune cells and the expressions of PD-L1 were confirmed in the pan-cancer level. Our study demonstrated that the key module–gene of ferroptosis was closely related with diagnosis, prognosis, and anti-immune response in melanoma, as well as in pan-cancer.

A Ferroptosis Molecular Subtype-Related Signature for Predicting Prognosis and Response to Chemotherapy in Patients with Chronic Lymphocytic Leukemia

Ferroptosis is a type of regulated cell death catalyzed by the iron-dependent accumulation of lipid hydroperoxides to lethal levels. Chronic lymphocytic leukemia (CLL) is a chronic lymphoproliferative disorder. However, the understanding of ferroptosis in CLL remains largely poor. In this study, we investigated the stratification and prognostic role of ferroptosis-related genes in CLL patients of ICGC cohort. We obtained fourteen genes with prognostic value by screening 110 ferroptosis-related genes (FRGs). Based on the expression profiles of these 14 genes, we classified CLL patients into two clusters. Most of the FRGs were highly expressed in cluster 1, and cluster 1 was associated with better overall survival (OS). Subsequently, we developed an eight-gene signature (TP63, STEAP3, NQO1, ELAVL1, PRKAA1, HELLS, FANCD2, and CDKN2A) by using LASSO analysis. This risk signature divided CLL patients into high- and low-risk groups. We used Cox regression analysis and ROC analysis demonstrated the risk signature was reliable and robust. And we validated the risk model in an external cohort (GSE22762). We also conducted enrichment analysis and genomic mutation analysis. Finally, we explored the potential effect of chemotherapy between the two risk groups. Our study contributed to understanding the role of ferroptosis in CLL and facilitated personalized and precision treatment.

Development and Validation of a Novel Metabolic Signature-Based Prognostic Model for Uveal Melanoma

Purpose

Uveal melanoma (UM) is the most common primary malignant tumor with poor prognosis. The role of metabolism-related genes in the prognosis of UM remains unrevealed. This study aimed to establish and validate a prognostic prediction model for UM based on metabolism-related genes.

Methods

Gene expression profiles and clinicopathological information were downloaded from The Cancer Genome Atlas, and the Gene Expression Omnibus database. Univariable Cox regression, least absolute shrinkage and selection operator Cox regression, and stepwise regression were performed to establish the model. Kaplan-Meier survival analysis, receiver operating characteristic (ROC) curve analysis, and calibration and discrimination analyses were used to evaluate the prognostic model.

Results

Three metabolism-related genes, carbonic anhydrase 12, acyl-CoA synthetase long-chain family member 3, and synaptojanin 2, and three clinicopathological parameters (i.e., age, gender, and metastasis staging) were identified to establish the model. The risk score was found to be an independent prognostic factor for UM survival. High-risk patients demonstrated significantly poorer prognosis than low-risk patients. ROC analysis suggested the promising prognostic efficiency of the model. The calibration curve manifested satisfactory agreement between the predicted and observed risk. A nomogram and online survival calculator were developed to predict the survival probability.

Conclusions

The novel metabolism-based prognostic model could accurately predict the prognosis of UM patients, which facilitates the prediction of the survival probability by both ophthalmologists and patients with the online dynamic nomogram.

Translational Relevance

The dynamic nomogram links gene expression profiles to clinical prognosis of UM and is useful to evaluate the survival probability.

Extraction and Prioritization of a Gene-Cancer-By-Survival Network Involved in Homeostasis of Intracellular Calcium Concentrations Using TCGA PANCAN Data

Regulation of intracellular calcium concentrations, [Ca++]i is important in maintaining the viability of normal as well as cancer cells and can be mediated by tumor microenvironment. Calcium release-activated calcium channel protein (ORAI) calcium channels on the plasma membrane (PM) become physically connected by stromal interaction molecules (STIMs) to the endoplasmic reticulum (ER), on which paralogous receptors of inositol phosphate and of ryanodine are also present along with ATP2A/SERCA (sarco/endoplasmic reticulum calcium ATPases) subunits (also known as PM-ER geneset). Proper expression of this functionally and physically interconnected geneset is essential for the maintenance of [Ca++]i , yet has not been interrogated as a whole for its role in cancer prognosis using multivariable Cox regression. In the present study, we examined whether the expression profile of the PM-ER geneset exhibited prognostic significance across different cancers found in The Cancer Genome Atlas (TCGA) by generating gene-cancer-by-survival networks, in which the nodes represented either genes or cancers and the edges, the logarithmically transformed hazard ratios for overall survival (OS). We then applied network clustering to identify the gene-cancer subnetworks with high connectivity, among which uveal melanoma (UVM) emerged exhibiting the highest degree of genes (k = 10). BAP1, a well-known [Ca++]i regulator and a tumor suppressor, was not found to be significant in predicting OS by PM-ER geneset for UVM, yet it was for several others, including mesothelioma (MESO). Moreover, the best subset of the PM-ER geneset obtained by lasso predicted OS in the TCGA UVM cohort with an area under the receiver operating characteristics (AUC) of 91.4%, comparable to or better than previous prognostic signatures in the literature. Our findings indicate that homeostasis of [Ca++]i is an essential determinant of prognosis in multiple cancers and particularly in UVM. The proposed gene-cancer-by-survival network approach can be extended with other gene sets as well as different survival types.

PGM5P3-AS1 regulates MAP1LC3C to promote cell ferroptosis and thus inhibiting the malignant progression of triple-negative breast cancer

PURPOSE

Triple-negative breast cancer (TNBC) represents an aggressive subtype of breast cancer characteristic of high recurrence rate and poor prognosis. According to previous studies and bioinformatics prediction, PGM5P3-AS1 has been found to be significantly down-regulated in TNBC cells. In addition, cell ferroptosis has become a hotspot in breast cancer research and TNBC has been reported to be more sensitive to ferroptosis than receptor positive breast cancer. Hence, we aim at exploring the molecular mechanism of PGM5P3-AS1 in TNBC cells and further explore whether PGM5P3-AS1 can inhibit TNBC progression via promoting cell ferroptosis.

METHODS

The expression of genes in TNBC cells was verified by RT-qPCR assay. Functional assays were taken to evaluate the impact PGM5P3-AS1 may exert on TNBC progression. The regulatory pattern of PGM5P3-AS1 on cell ferroptosis in TNBC was validated through mechanism assays.

RESULTS

PGM5P3-AS1 was proved to be down-regulated in TNBC cells and suppressed TNBC cell proliferation as well as migration. PGM5P3-AS1 promoted cell ferroptosis in TNBC by recruiting RNA-binding protein (RBP) NOP58 to stabilize MAP1LC3C mRNA, and thus inhibiting TNBC progression.

CONCLUSION

PGM5P3-AS1 regulated MAP1LC3C to promote cell ferroptosis and thus inhibiting the malignant progression of TNBC.

Comprehensive analysis of ferroptosis-related genes and prognosis of cutaneous melanoma

BACKGROUND

Cutaneous Melanoma (CM) is a malignant disease with increasing incidence and high mortality. Ferroptosis is a new kind of cell death and related to tumor blood and lymphatic metastasis. This study aims at using bioinformatics technology to construct a prognostic signature and identify ferroptosis-related biomarkers to improve the prognosis and treatment of cutaneous melanoma.

METHODS

We used bioinformatics tools to analyze RNA sequencing expression data with clinical information from multiple databases, utilized varieties of statistical methods to construct a ferroptosis-related prognostic signature of cutaneous melanoma and screened out specific genes with independent prognostic ability.

RESULTS

We obtained 22 ferroptosis-related (P < 0.05) prognostic DEGs in the uniCox regression analysis, among which 10 high-expressed genes (ATG5, CHAC1, FANCD2, FBXL5, HMOX2, HSPB1, NQO1, PEBP1, PRNP, SLC3A2) were screened out by LASSO regression analysis to establish a predictive model. Meanwhile, the ferroptosis-related signature and the nomogram we drew performed an excellent performance based on Kaplan-Meier (K-M), Receiver operating characteristic (ROC) and calibration curves. Univariate and multivariable cox analyses displayed that our model was greater than other prognostic features. GO and KEGG analyses revealed that 10-biomarker signature was mainly related to epidermis differentiation and immunity. ssGSEA analysis indicated that the immune status between the two risk groups was highly different. Besides, we found that two genes (CP, ZEB1) had independent prognostic ability and can be applied for drug research. Both genes were highly related to immunity. GSEA illustrated that ZEB1 may be involved in cellular functions such as proliferation, apoptosis, and migration, while CP was closely connected to immune cell related functions.

CONCLUSION

The present study suggested a 10-biomarker signature can be clinically used to predict the prognosis of cutaneous melanoma, which was better than conventional factors. CP and ZEB1 were independent prognostic genes and can be applied to guide treatment. In addition, ZEB1 mutation was highly related to overall survival in cutaneous melanoma, while CP may be associated with tumor progression. Our study comprehensively analyzed the relationship between iron metabolism, ferroptosis-related genes, and the prognosis of cutaneous melanoma, provided new insight for molecular mechanisms and treatment of ferroptosis and cutaneous melanoma.

Construction and validation of a novel gene signature for predicting the prognosis of osteosarcoma

Osteosarcoma (OS) is the most common type of primary malignant bone tumor. The high-throughput sequencing technology has shown potential abilities to illuminate the pathogenic genes in OS. This study was designed to find a powerful gene signature that can predict clinical outcomes. We selected OS cases with gene expression and survival data in the TARGET-OS dataset and GSE21257 datasets as training cohort and validation cohort, respectively. The univariate Cox regression and Kaplan–Meier analysis were conducted to determine potential prognostic genes from the training cohort. These potential prognostic genes underwent a LASSO regression, which then generated a gene signature. The harvested signature’s predictive ability was further examined by the Kaplan–Meier analysis, Cox analysis, and receiver operating characteristic (ROC curve). More importantly, we listed similar studies in the most recent year and compared theirs with ours. Finally, we performed functional annotation, immune relevant signature correlation identification, and immune infiltrating analysis to better study he functional mechanism of the signature and the immune cells’ roles in the gene signature’s prognosis ability. A seventeen-gene signature (UBE2L3, PLD3, SLC45A4, CLTC, CTNNBIP1, FBXL5, MKL2, SELPLG, C3orf14, WDR53, ZFP90, UHRF2, ARX, CORT, DDX26B, MYC, and SLC16A3) was generated from the LASSO regression. The signature was then confirmed having strong and stable prognostic capacity in all studied cohorts by several statistical methods. We revealed the superiority of our signature after comparing it to our predecessors, and the GO and KEGG annotations uncovered the specifically mechanism of action related to the gene signature. Six immune signatures, including PRF1, CD8A, HAVCR2, LAG3, CD274, and GZMA were identified associating with our signature. The immune-infiltrating analysis recognized the vital roles of T cells CD8 and Mast cells activated, which potentially support the seventeen-gene signature’s prognosis ability. We identified a robust seventeen-gene signature that can accurately predict OS prognosis. We identified potential immunotherapy targets to the gene signature. The T cells CD8 and Mast cells activated were identified linked with the seventeen-gene signature predictive power.

miR-3587 Inhibitor Attenuates Ferroptosis Following Renal Ischemia-Reperfusion Through HO-1

Renal ischemia-reperfusion (IR) is frequently observed in patients who are critically ill, yet there are no reliable or effective approaches for the treatment of this condition. Ferroptosis, a form of programmed cell death, is regulated by key genes such as glutathione peroxidase 4 (GPX4) and heme oxygenase-1 (HMOX1) and participates in the injury of renal tubular epithelial cells during IR. This study aimed to investigate the miRNA-mRNA regulatory networks involved in ferroptosis following renal IR. Using bioinformatics analysis, HMOX1 was found to be significantly upregulated during the early stages of renal IR injury, and microRNA-3587 (miR-3587) was identified as a putative regulator of HMOX1. When a miR-3587 inhibitor was applied in a hypoxia-reoxygenation (HR) model system using renal tubular epithelial cells, HO-1 protein (encoded by HMOX1) expression was significantly increased relative to that observed in the HR group, with concomitant increases in GPX4 protein levels, enhanced cell viability, a reduction in malondialdehyde content, decreased Fe²⁺ level, and the restoration of normal mitochondrial membrane potential. Transmission electron microscopy showed a reduced or absent mitochondrial crest and a damaged mitochondrial outer membrane. Targeting of HMOX1 by miR-3587 was confirmed by luciferase reporter gene assay. In conclusion, these preliminary results indicate that inhibition of miR-3587 promotes HO-1 upregulation, thereby protecting renal tissues from IR-induced ferroptosis.

Identification and Validation of an Immune and Ferroptosis-Combined Index for Non-Small Cell Lung Cancer

Background: Non-small cell lung cancer (NSCLC) is among the major health problems around the world. Reliable biomarkers for NSCLC are still needed in clinical practice. We aimed to develop a novel ferroptosis- and immune-based index for NSCLC. Methods: The training and testing datasets were obtained from TCGA and GEO databases, respectively. Immune- and ferroptosis-related genes were identified and used to establish a prognostic model. Then, the prognostic and therapeutic potential of the established index was evaluated. Results: Intimate interaction of immune genes with ferroptosis genes was observed. A total of 32 prognosis-related signatures were selected to develop a predictive model for NSCLC using LASSO Cox regression. Patients were classified into the high- and low-risk group based on the risk score. Patients in the low-risk group have better OS in contrast with that in the high-risk group in independent verification datasets. Besides, patients with a high risk score have shorter OS in all subgroups (T, N, and M0 subgroups) and pathological stages (stage I, II, and III). The risk score was positively associated with Immune Score, Stromal Score, and Ferroptosis Score in TCGA and GEO cohorts. A differential immune cell infiltration between the high-risk and the low-risk groups was also observed. Finally, we explored the significance of our model in tumor-related pathways, and different enrichment levels in the therapeutic pathway were observed between the high- and low-risk groups. Conclusion: The present study developed an immune and ferroptosis-combined index for the prognosis of NSCLC.

A New Ferroptosis-Related lncRNA Signature Predicts the Prognosis of Bladder Cancer Patients

Background: Ferroptosis is closely related to the occurrence and development of cancer. An increasing number of studies have induced ferroptosis as a treatment strategy for cancer. However, the predictive value of ferroptosis-related lncRNAs in bladder cancer (BC) still need to be further elucidated. The purpose of this study was to construct a predictive signature based on ferroptosis-related long noncoding RNAs (lncRNAs) to predict the prognosis of BC patients.

Methods: We downloaded RNA-seq data and the corresponding clinical and prognostic data from The Cancer Genome Atlas (TCGA) database and performed univariate and multivariate Cox regression analyses to obtain ferroptosis-related lncRNAs to construct a predictive signature. The Kaplan-Meier method was used to analyze the overall survival (OS) rate of the high-risk and low-risk groups. Gene set enrichment analysis (GSEA) was performed to explore the functional differences between the high- and low-risk groups. Single-sample gene set enrichment analysis (ssGSEA) was used to explore the relationship between the predictive signature and immune status. Finally, the correlation between the predictive signature and the treatment response of BC patients was analyzed.

Results: We constructed a signature composed of nine ferroptosis-related lncRNAs (AL031775.1, AL162586.1, AC034236.2, LINC01004, OCIAD1-AS1, AL136084.3, AP003352.1, Z84484.1, AC022150.2). Compared with the low-risk group, the high-risk group had a worse prognosis. The ferroptosis-related lncRNA signature could independently predict the prognosis of patients with BC. Compared with clinicopathological variables, the ferroptosis-related lncRNA signature has a higher diagnostic efficiency, and the area under the receiver operating characteristic curve was 0.707. When patients were stratified according to different clinicopathological variables, the OS of patients in the high-risk group was shorter than that of those in the low-risk group. GSEA showed that tumor- and immune-related pathways were mainly enriched in the high-risk group. ssGSEA showed that the predictive signature was significantly related to the immune status of BC patients. High-risk patients were more sensitive to anti-PD-1/L1 immunotherapy and the conventional chemotherapy drugs sunitinib, paclitaxel, cisplatin, and docetaxel.

Conclusion: The predictive signature can independently predict the prognosis of BC patients, provides a basis for the mechanism of ferroptosis-related lncRNAs in BC and provides clinical treatment guidance for patients with BC.

A Novel Ferroptosis-Related Gene Signature to Predict Prognosis in Patients with Head and Neck Squamous Cell Carcinoma

The clinical TNM staging system is currently used to evaluate the prognosis of head and neck squamous cell carcinoma (HNSCC). The 5-year survival rate for patients with HNSCC is less than 50%, which is attributed to the lack of reliable prognostic biomarkers. Ferroptosis-related genes (FRGs) regulate cancer initiation and progression. Therefore, we analyzed the correlation between FRGs and the clinical outcomes of patients with HNSCC. A typical prognostic model of FRGs for HNSCC was constructed using bioinformatics tools and data from public databases, including The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and GeneCards. The model was generated based on the following six FRGs: ATG5, PRDX6, OTUB1, FTH1, SOCS1, and MAP3K5. The accuracy of model prediction was analyzed systematically. The overall survival (OS) of the high-risk group was significantly lower than that of the low-risk group. The AUC for 1-year, 3-year, and 5-year survival were 0.645, 0.721, and 0.737, respectively, in the training set (TCGA cohort) and 0.726, 0.620, and 0.584, respectively, in the validation set (GSE65858). The multivariate Cox regression analysis revealed that the risk score was an independent prognostic factor for HNSCC. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that six FRGs were enriched in the ferroptosis pathway. A novel FRG prognostic signature model was established for HNSCC. The findings of this study reveal that FRGs are potential biomarkers for HNSCC.

Identifying a Ferroptosis-Related Gene Signature for Predicting Biochemical Recurrence of Prostate Cancer

Ferroptosis induced by lipid peroxidation is closely related to cancer biology. Prostate cancer (PCa) is not only a malignant tumor but also a lipid metabolic disease. Previous studies have identified ferroptosis as an important pathophysiological pathway in PCa development and treatment, but its role in the prognosis of PCa is less well known. In this study, we constructed a nine-ferroptosis-related gene risk model that demonstrated strong prognostic and therapeutic predictive power. The higher risk score calculated by the model was significantly associated with a higher ferroptosis potential index, higher Ki67 expression, higher immune infiltration, higher probability of biochemical recurrence, worse clinicopathological characteristics, and worse response to chemotherapy and antiandrogen therapy in PCa. The mechanisms identified by the gene set enrichment analysis suggested that this signature can accurately distinguish high- and low-risk populations, which is possibly closely related to variations in steroid hormone secretion, regulation of endocrine processes, positive regulation of humoral immune response, and androgen response. Results of this study were confirmed in two independent PCa cohorts, namely, The Cancer Genome Atlas cohort and the MSK-IMPACT Clinical Sequencing Cohort, which contributed to the body of scientific evidence for the prediction of biochemical recurrence in patients with PCa. In addition, as the main components of this signature, the effects of the AIFM2 and NFS1 genes on ferroptosis were evaluated and verified by in vivo and in vitro experiments, respectively. The above findings provided new insights and presented potential clinical applications of ferroptosis in PCa.

Development and Validation of a Ferroptosis-Related Gene Signature and Nomogram for Predicting the Prognosis of Esophageal Squamous Cell Carcinoma

Esophageal squamous cell carcinoma (ESCC) is a common malignant tumor with high mortality and poor prognosis. Ferroptosis is a newly discovered form of cell death induced by iron-catalyzed excessive peroxidation of polyunsaturated fatty acids (PUFAs). However, the prognostic value of ferroptosis-related genes (FRGs) for ESCC remains unclear. Based on the ESCC dataset from the Gene Expression Omnibus (GEO) database, we identified 39 prognostic FRGs through univariate Cox regression analysis. After LASSO regression and multivariate Cox regression analyses, a multigene signature based on 10 prognostic FRGs was constructed and successfully divided ESCC patients into two risk groups. Patients in the low-risk group showed a significantly better prognosis than patients in the high-risk group. In addition, we combined the risk score with clinical predictors to construct a nomogram for ESCC. The predictive ability of the nomogram was further verified by ROC curves and calibration plots in both the training and validation sets. The predictive power of the nomogram was demonstrated to be better than that of either the risk score or clinical variable alone. Furthermore, functional analysis revealed that the 10-FRG signature was mainly associated with ferroptosis, differentiation and immune response. Connectivity map analysis identified potential compounds capable of targeting FRGs in ESCC. Finally, we demonstrated the prognostic value of SRC gene in ESCC using the clinical samples and found that SRC inhibition sensitized ESCC cells to ferroptosis inducers by in vitro experiments. In conclusion, we identified and verified a 10-FRG prognostic signature and a nomogram, which provide individualized prognosis prediction and provide insight into potential therapeutic targets for ESCC.

Ferroptosis-Associated Classifier and Indicator for Prognostic Prediction in Cutaneous Melanoma

Ferroptosis plays a critical role in different types of cancers, but the prognostic impact of ferroptosis in cutaneous melanoma remains lacking. Therefore, ferroptosis-related genes (FRGs) were firstly obtained from the FerrDb database and the differentially expressed FRGs were identified by the “limma” algorithm. Next, the prognostic differentially expressed FRGs were screened out by univariate Cox regression, which were subsequently used to cluster melanomas into two subtypes (clusters A and B). Besides, the Boruta algorithm and principal component analysis (PCA) were performed to build a 15-FRGs indicator, which can robustly predict patients' overall survival (OS) and be considered as an independent prognostic factor in melanoma. The melanoma patients were further divided into high- and low-FRGs score groups. The high score group have a good prognosis, with higher T cell immune infiltrating and lower mutation frequencies in NRAS, KRAS, and NF1. Finally, we discovered that many immune processes and several chemotherapy drugs were closely associated with FRGs score. Thus, our study provides a novel ferroptosis-associated classifier and indicator to predict the prognosis of melanoma. Besides, we identified several potential chemotherapy drugs to induce ferroptosis and could supply additional effective treatments.

A novel pyroptosis-associated gene signature for immune status and prognosis of cutaneous melanoma

Background

Cutaneous melanoma (CM) is a life-threatening destructive malignancy. Pyroptosis significantly correlates with programmed tumor cell death and its microenvironment through active host-tumor crosstalk. However, the prognostic value of pyroptosis-associated gene signatures in CM remains unclear.

Methods

Gene profiles and clinical data of patients with CM were downloaded from The Cancer Genome Atlas (TCGA) to identify differentially expressed genes associated with pyroptosis and overall survival (OS). We constructed a prognostic gene signature using LASSO analysis, then applied immune cell infiltration scores and Kaplan-Meier, Cox, and pathway enrichment analyses to determine the roles of the gene signature in CM. A validation cohort was collected from the Gene Expression Omnibus (GEO) database.

Results

Four pyroptosis-associated genes were identified and incorporated into a prognostic gene signature. Integrated bioinformatics findings showed that the signature correlated with patient survival and was associated with tumor growth and metastasis. The results of Gene Set Enrichment Analysis of a risk signature indicated that several enriched pathways are associated with cancer and immunity. The risk signature for immune status significantly correlated with tumor stem cells, the immune microenvironment, immune cell infiltration and immune subtypes. The expression of four pyroptosis genes significantly correlated with the OS of patients with CM and was related to the sensitivity of cancer cells to several antitumor drugs. A signature comprising four genes associated with pyroptosis offers a novel approach to the prognosis and survival of patients with CM and will facilitate the development of individualized therapy.

An Original Ferroptosis-Related Gene Signature Effectively Predicts the Prognosis and Clinical Status for Colorectal Cancer Patients

Background

Colorectal cancer (CRC) is one of the most common malignant tumors in the world. Ferroptosis is a newly defined form of cell death, distinguished by different morphology, biochemistry, and genetics, and involved in CRC progression and treatment. This study aims to establish a predictive model to elucidate the relationship between ferroptosis and prognosis of CRC patients, to explore the potential value of ferroptosis in therapeutic options.

Methods

The ferroptosis-related genes were obtained from the GeneCards and FerrDb websites. The limma R package was used to screen the differential ferroptosis-related genes (DEGs) in CRC from The Cancer Genome Atlas (TCGA) dataset. The least absolute shrinkage and selection operator (LASSO) and multivariate Cox regressions were to establish the 10-gene prognostic signature. The survival and receiver operating characteristic (ROC) curves were illustrated to evaluate the predictive effect of the signature. Besides, independent prognostic factors, downstream functional enrichment, drug sensitivity, somatic mutation status, and immune feature were analyzed. Moreover, all these conclusions were verified by using multiple datasets in International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO).

Results

Ten ferroptosis-related gene signature (TFAP2C, SLC39A8, NOS2, HAMP, GDF15, FDFT1, CDKN2A, ALOX12, AKR1C1, ATP6V1G2) was established to predict the prognosis of CRC patients by Lasso cox analysis, demonstrating a good performance on Receiver operating characteristic (ROC) and Kaplan–Meier (K–M) analyses. The CRC patients in the high- or low-risk group showed significantly different fractions of immune cells, such as macrophage cells and CD8+ T cells. Drug sensitivity and somatic mutation status like TP53 were also closely associated with the risk scores.

Conclusions

In this study, we identified a novel ferroptosis-related 10-gene signature, which could effectively predict the prognosis and survival time of CRC patients, and provide meaningful clinical implications for targeted therapy or immunotherapy. Targeting ferroptosis is a good therapeutic option for CRC patients. Further studies are needed to reveal the underlying mechanisms of ferroptosis in CRC.

Identification of a Ferroptosis-Related Signature Associated with Prognosis and Immune Infiltration in Adrenocortical Carcinoma

Adrenocortical carcinoma (ACC) is a rare malignant tumor with poor prognosis. Ferroptosis, a new form of cell death, differs from other forms of cell death and plays a vital role in tumor progress. Our study aimed to establish a ferroptosis-related signature with prognostic value in ACC. RNA-seq data and corresponding clinical characteristics for ACC were downloaded from TCGA and GEO databases. Genes included in ferroptosis risk signature were assessed by univariable and multivariable Cox regression analysis as well as lasso regression analysis. The prognostic value of the ferroptosis risk signature was assessed using K-M and ROC curves. Furthermore, we performed GSEA to discover the enriched gene sets in high-risk group. Additionally, TIMER website was applied to detect a possible connection between the signature and immune cells infiltration. ssGSEA was performed to evaluate scores of immune cells and immune-related pathways in two groups. A ferroptosis signature comprised of six genes (SLC7A11, TP53, HELLS, ACSL4, PCBP2, and HMGB1) was constructed to predict prognosis and reflect the immune infiltration in ACC. Patients in high-risk group were inclined to have worse prognosis. The ferroptosis model performed well in predicting prognosis and could be served as an independent indicator in ACC. GSEA revealed that gene sets correlated with biological processes including cell cycle, DNA replication, base excision repair, and P53 signaling pathway were highly enriched in high-risk group. In addition, we discovered that the expressional levels of hub genes were linked to six immune cells' infiltration in ACC tumor. ssGSEA revealed that contents of most immune cells significantly decreased in the high-risk group. In conclusion, the novel ferroptosis risk signature could be useful in predicting prognosis and reflecting immune infiltration in ACC. It also brings us new insights into the possible value of targeting ferroptosis during the therapy of ACC.