Computational Identification of Immune- and Ferroptosis-Related LncRNA Signature for Prognosis of Hepatocellular Carcinoma

Ferroptosis and hepatocellular carcinoma: the emerging role of lncRNAs

Hepatocellular carcinoma is the most common form of primary liver cancer and poses a significant challenge to the medical community because of its high mortality rate. In recent years, ferroptosis, a unique form of cell death, has garnered widespread attention. Ferroptosis, which is characterized by iron-dependent lipid peroxidation and mitochondrial alterations, is closely associated with the pathological processes of various diseases, including hepatocellular carcinoma. Long non-coding RNAs (lncRNAs), are a type of functional RNA, and play crucial regulatory roles in a variety of biological processes. In this manuscript, we review the regulatory roles of lncRNAs in the key aspects of ferroptosis, and summarize the research progress on ferroptosis-related lncRNAs in hepatocellular carcinoma.

Cuproptosis-related lncRNAs predict the clinical outcome and immune characteristics of hepatocellular carcinoma

Cuproptosis, as a novel copper-dependent and non-apoptotic form of cell death, is induced by aggregation of lipoylated mitochondrial proteins and the instability of Fe-S cluster proteins. However, the role of cuproptosis-related long noncoding RNAs (CRLncRNAs) in hepatocellular carcinoma (HCC) has not been clearly elucidated. In this study, we identified and characterized cuproptosis-related lncRNAs in HCC. 343 HCC cases from The Cancer Genome Atlas (TCGA) with gene transcriptome data and clinical data were obtained for analysis after the screening. Univariate and multivariate Cox proportional hazards analyses were performed to establish a prognostic cuproptosis-related lncRNA signature (CRlncSig). We established a prognosis-related model consisting of nine cuproptosis-related lncRNAs: GSEC, AL158166.1, AC005479.2, AL365361.1, AC026412.3, AL031985.3, LINC00426, AC009974.2, AC245060.7, which was validated in the internal cohort. High-risk group stratified by the CRlncSig was significantly related to poor prognosis (p < 0.001). The area under the receiver operating characteristic curve (AUC) of 1 year, 3 years, and 5 years of survival were 0.813, 0.789, and 0.752, respectively. Furthermore, a prognostic nomogram including CRlncSig with clinicopathologic factors was built with favorable predictive power. In addition, GO and KEGG enrichment analysis suggested that CRlncSig was involved in many carcinogenesis and immune-related pathways. Additionally, we found that tumor microenvironment, immune infiltration, immune function, and drug response were significantly different between the high-risk and low-risk groups based on the risk model. These results highlight the value of cuproptosis-related lncRNAs on prognosis for HCC patients and provide insight into molecular and immune features underlying cuproptosis-related lncRNAs, which might play an important role in patient management and immunotherapy.

A Ferroptosis-Related LncRNA Signature Associated with Prognosis, Tumor Immune Environment, and Genome Instability in Hepatocellular Carcinoma

Background

Ferroptosis is an iron-dependent form of cell death. In this study, we identified ferroptosis-related long noncoding RNAs (FRlncRNAs) to investigate their association with hepatocellular carcinoma (HCC) in prognosis, tumor immune environment, and genome instability.

Methods

Transcriptome profile data of HCC were retrieved from a public database. FRlncRNAs were identified by co-expression analysis. Patients were randomly divided into training and test cohorts. Univariate Cox analysis and Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression were performed to construct a risk model. Patients were divided into high- and low-risk groups based on the risk model. AUC and C index were used to assess the risk model. Survival analysis, immune status, and genome instability were compared between the two groups.

Results

Sixteen FRlncRNAs were identified and used to construct an FRlncRNA signature for the risk model. The Kaplan-Meier analysis revealed that patients in the high-risk group had poorer overall survival than patients in the low-risk group. The area under curve of the risk model was 0.879, 0.809, and 0.757 in the training cohort and 0.635, 0.688, and 0.739 in the test cohort at 1, 2, and 3 years, respectively. The risk model was an independent prognostic predictor and showed excellent prediction of prognosis compared with clinicopathological features. For the differentially expressed ferroptosis-related genes, many enriched metabolic pathways were identified in the functional enrichment analysis. Immune cells such as CD8+ T cells, macrophages M1, natural killer cells, and B cells, which may be associated with antitumor immune responses, differed between the high- and low-risk groups. Genome instability based on the risk model was also explored. A total of 61 genes were differently mutated between the two risk groups, and among them, TP53, HECW2, TRIM66, MCTP2, and KIAA1551 had the most significant mutation frequency differences.

Conclusion

The FRlncRNA signature is closely related with overall survival, tumor immune environment, and genome instability in HCC.

A novel Cuproptosis-related LncRNA signature to predict prognosis in hepatocellular carcinoma

Increased intracellular toxicity due to an imbalance in copper homeostasis caused by copper ion accumulation could regulate the rate of cancer cell growth and proliferation. The goal of this study was to create a novel Cuproptosis-related lncRNA signature that may be utilized to predict survival and immunotherapy in HCC patients. Cuproptosis-associated lncRNAs and differentially expressed lncRNAs between HCC tumor tissue and normal tissue were discovered first. By LASSO-Cox analysis, the overlapping lncRNAs were then utilized to build a Cuproptosis-associated lncRNA signature, which might be used to predict patient prognosis and responsiveness to immune checkpoint blockade (ICB) therapy. Differences in the infiltration of immune cell subpopulations between high and low-risk score subgroups were also analyzed. Moreover, a nomogram based on the Cuproptosis-associated lncRNA signature and clinical features was developed and demonstrated to have good predictive potential. Finally, qRT-PCR was performed in HerpG2 and MHCC-97H cell lines to explore whether these lncRNAs were indeed involved in the process of Cuproptosis. In summary, we created a prognostic lncRNA profile linked to Cuproptosis to forecast response to immunotherapy, which may provide a new potential non-apoptotic therapeutic perspective for HCC patients.

Prediction of Prognosis and Molecular Mechanism of Ferroptosis in Hepatocellular Carcinoma Based on Bioinformatics Methods

Background

As an iron-dependent type of programmed cell death, ferroptosis plays an important role in the pathogenesis and progression of hepatocellular carcinoma (HCC). Long noncoding RNAs (lncRNAs) have been linked to the prognosis of patients with HCC in a number of studies. Nevertheless, the predictive value of lncRNAs (FRLs) associated with ferroptosis in HCC has not been fully elucidated.

Methods

Download RNA sequencing data and clinical profiles of HCC patients from The Cancer Genome Atlas (TCGA) database. The FRLs associated with prognosis were determined by Pearson's correlation analysis. After that, prognostic signature for FRLs was established using Cox and LASSO regression analyses. Meanwhile, survival analysis, correlation analysis of clinicopathological features, Cox regression, receiver operating characteristic (ROC) curve, and nomogram were used to analyze the FRL signature's predictive capacity. The relationship between signature risk score, immune cell infiltration, and chemotherapy drug sensitivity is further studied.

Results

In total, 93 FRLs were found to be of prognostic value in patients with HCC. A five-FRL signature comprising AC015908.3, LINC01138, AC009283.1, Z83851.1, and LUCAT1 was created in order to enhance the prognosis prediction with HCC patients. The signature demonstrated a good predictive potency, according to the Kaplan-Meier and ROC curves. The five-FRL signature was found to be a risk factor independent of various clinical factors using Cox regression and stratified survival analysis. The high-risk group was shown to be enriched in tumorigenesis and immune-related pathways according to GSEA analysis. Additionally, immune cell infiltration, immune checkpoint molecules, and half-inhibitory concentrations differed considerably between risk groups, implying that this signature could be used to evaluate the clinical efficacy of chemotherapy and immunotherapy.

Conclusion

The five-FRL risk signature is helpful for assessing the prognosis of HCC patients and improving therapy options, so it can be further applied clinically.

Ferroptosis in Hepatocellular Carcinoma: Mechanisms, Drug Targets and Approaches to Clinical Translation

Simple Summary

In recent decades, scientific discoveries brought up several new treatments and improvements for patients suffering from hepatocellular carcinoma (HCC). However, increasing resistance to current therapies, such as sorafenib, worsen the outcome of HCC patients, leading to a search for alternative therapeutic strategies. The term ferroptosis describes a novel form of regulated cell death, which is different from apoptosis and necroptosis in a mechanistical and morphological manner. The main mechanism, which leads to cell death, is lipid peroxidation, caused by iron overload and the accumulation of polyunsaturated fatty acids. Recent studies demonstrate that ferroptosis can hamper the carcinogenesis in several tumor entities and in HCC. Therefore, a better understanding and a deeper insight in the processes of ferroptosis in HCC and the possible application of it in the clinical practice are of extreme importance.

Abstract

Ferroptosis, an iron and reactive oxygen species (ROS)-dependent non-apoptotic type of regulated cell death, is characterized by a massive iron overload and peroxidation of polyunsaturated fatty acids (PUFAs), which finally results in cell death. Recent studies suggest that ferroptosis can influence carcinogenesis negatively and therefore may be used as a novel anti-cancer strategy. Hepatocellular carcinoma (HCC) is a deadly malignancy with poor chances of survival and is the second leading cause of cancer deaths worldwide. Diagnosis at an already late stage and general resistance to current therapies may be responsible for the dismal outcome. As the liver acts as a key factor in iron metabolism, ferroptosis is shown to play an important role in HCC carcinogenesis and, more importantly, may hold the potential to eradicate HCC. In this review, we summarize the current knowledge we have of the role of ferroptosis in HCC and the application of ferroptosis as a therapy option and provide an overview of the potential translation of ferroptosis in the clinical practice of HCC.