A Prognostic Signature for Clear Cell Renal Cell Carcinoma Based on Ferroptosis-Related lncRNAs and Immune Checkpoints

Comprehensive analysis of a tryptophan metabolism-related model in the prognostic prediction and immune status for clear cell renal carcinoma

BACKGROUND

Clear cell renal cell carcinoma (ccRCC) is characterized as one of the most common types of urological cancer with high degrees of malignancy and mortality. Due to the limited effectiveness of existing traditional therapeutic methods and poor prognosis, the treatment and therapy of advanced ccRCC patients remain challenging. Tryptophan metabolism has been widely investigated because it significantly participates in the malignant traits of multiple cancers. The functions and prognostic values of tryptophan metabolism-related genes (TMR) in ccRCC remain virtually obscure.

METHODS

We employed the expression levels of 40 TMR genes to identify the subtypes of ccRCC and explored the clinical characteristics, prognosis, immune features, and immunotherapy response in the subtypes. Then, a model was constructed for the prediction of prognosis based on the differentially expressed genes (DEGs) in the subtypes from the TCGA database and verified using the ICGC database. The prediction performance of this model was confirmed by the receiver operating characteristic (ROC) curves. The relationship of Risk Score with the infiltration of distinct tumor microenvironment cells, the expression profiles of immune checkpoint genes, and the treatment benefits of immunotherapy and chemotherapy drugs were also investigated.

RESULTS

The two subtypes revealed dramatic differences in terms of clinical characteristics, prognosis, immune features, and immunotherapy response. The constructed 6-gene-based model showed that the high Risk Score was significantly connected to poor overall survival (OS) and advanced tumor stages. Furthermore, increased expression of CYP1B1, KMO, and TDO2 was observed in ccRCC tissues at the translation levels, and an unfavorable prognosis for these patients was also found.

CONCLUSION

We identified 2 molecular subtypes of ccRCC based on the expression of TMR genes and constructed a prognosis-related model that may be used as a powerful tool to guide the prediction of ccRCC prognosis and personalized therapy. In addition, CYP1B1, KMO, and TDO2 can be regarded as the risk prognostic genes for ccRCC.

Targeting ferroptosis in renal cell carcinoma: Potential mechanisms and novel therapeutics

Renal cell carcinoma (RCC) is an increasingly prevalent urologic malignancy that impacts human health worldwide. Surgery is an effective strategy for early RCC treatment, but advanced RCC is resistant to chemotherapy, thus development of other potential therapeutic strategies is urgent. Ferroptosis is a newly defined form of programmed cell death characterized by accumulation of iron-dependent lipid peroxides and plays a crucial role in the tumor progression and drug resistance. Recent studies have shown that ferroptosis participates in RCC progression and chemoresistance. Therefore, identifying the potential role of ferroptosis in RCC could develop novel therapeutic targets and clinical markers for this disease. This review concisely summarizes the regulatory role of iron, amino acid, and lipid metabolism in ferroptosis, as well as discusses the relationship between ferroptosis and RCC, and details the role of ferroptosis in tumor progression, which indicates that various ferroptosis regulators are dysregulated in RCC and exert paradoxical effects, either tumor-suppressive or oncogenic. These ferroptosis-related regulators are expected to be used as clinical markers for RCC prognosis. Thus, targeting these regulators to trigger ferroptosis may be the key to the development of potential therapeutic strategies for this disease.

B7-H7: A potential target for cancer immunotherapy

Cancer immunotherapy enhances the body's immunity against tumors by mitigating immune escape. Compared with traditional chemotherapy, immunotherapy has the advantages of fewer drugs, a wider range of action and fewer side effects. B7-H7 (also known as HHLA2, B7y) is a member of the B7 family of costimulatory molecules that was discovered more than 20 years ago. B7-H7 is mostly expressed in organs such as the breast, intestine, gallbladder and placenta and is detected predominantly in monocytes/macrophages in the immune system. Its expression is upregulated after stimulation by inflammatory factors such as lipopolysaccharide and interferon-γ. B7-H7/transmembrane and immunoglobulin domain containing 2 (TMIGD2) and killer cell immunoglobulin-like receptor, three Ig domains and long cytoplasmic tail 3 (KIR3DL3)-B7-H7 are the two currently confirmed signaling pathways for B7-H7. An increasing number of studies have demonstrated that B7-H7 is widely present in a variety of human tumor tissues, especially in programmed cell death-1 (PD-L1)-negative human tumors. B7-H7 promotes tumor progression, disrupts T-cell-mediated antitumor immunity, and inhibits immune surveillance. B7-H7 also triggers tumor immune escape and is associated with clinical stage, depth of tumor infiltration, metastasis, prognosis, and survival related to different tumor types. Multiple studies have shown that B7-H7 is a promising immunotherapeutic target. Herein, review the current literature on the expression, regulation, receptors and function of B7-H7 and its regulation/function in tumors.

Identification and Validation of a Novel Ferroptotic Prognostic Genes-Based Signature of Clear Cell Renal Cell Carcinoma

Simple Summary

Clear cell renal cell carcinoma (ccRCC) is one of the leading types of kidney malignancy and is closely related to ferroptosis that is an iron-dependent regulated cell death with lipid peroxide accumulation. A signature of nine ferroptotic genes was identified as an independent prognostic factor via construction in The Cancer Genome Atlas (TCGA) database and validation in the ArrayExpress database. This signature could successfully divide patients into low- and high-risk groups to predict survival rate. Compared with the other eight genes, glutaminase 2 (GLS2) played a crucial role during erastin-induced ferroptosis in ACHN and Caki-1 cells. It was discovered for the first time that GLS2 might be a ferroptotic suppressor in ccRCC.

Abstract

Renal cell carcinoma (RCC), as one of the primary urological malignant neoplasms, shows poor survival, and the leading pathological type of RCC is clear cell RCC (ccRCC). Differing from other cell deaths (such as apoptosis, necroptosis, pyroptosis, and autophagy), ferroptosis is characterized by iron-dependence, polyunsaturated fatty acid oxidization, and lipid peroxide accumulation. We analyzed the ferroptosis database (FerrDb V2), Gene Expression Omnibus database, The Cancer Genome Atlas database, and the ArrayExpress database. Nine genes that were differentially expressed and related to prognosis were involved in the ferroptotic prognostic model via the least absolute shrinkage and selection operator Cox regression analysis, which was established in ccRCC patients from the kidney renal clear cell carcinoma (KIRC) cohort in TCGA database, and validated in ccRCC patients from the E-MTAB-1980 cohort in the ArrayExpress database. The signature could be an independent prognostic factor for ccRCC, and high-risk patients showed worse overall survival. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were utilized to investigate the potential mechanisms. The nine genes in ccRCC cells with erastin or RSL3 treatment were validated to find the crucial gene. The glutaminase 2 (GLS2) gene was upregulated during ferroptosis in ccRCC cells, and cells with GLS2 shRNA displayed lower survival, a lower glutathione level, and a high lipid peroxide level, which illustrated that GLS2 might be a ferroptotic suppressor in ccRCC.

Immunization Combined with Ferroptosis Related Genes to Construct a New Prognostic Model for Head and Neck Squamous Cell Carcinoma

Simple Summary

Immunity combined with ferroptosis is being considered as a new tumor treatment modality, and its regulation in head and neck squamous cell carcinoma is still unknown. The purpose of this study was to look into the potential molecular biological roles of immune ferroptosis genes in head and neck squamous cell carcinoma. The 12-IFRM signatures were successfully constructed and classified into high- and low-risk groups using the TCGA database and related data resources. In patients with head and neck squamous cell carcinoma, feature-based risk scores were more predictive of survival than traditional clinicopathological features. Furthermore, the expression of CD8⁺T cells and macrophage M0 differed significantly between the two groups. The expression of TNFSF9 and CD44 in the high-risk groups was significantly increased compared with the low-risk groups. Next, we found a higher proportion of high-risk mutations than in the low-risk group. In addition, the high-risk group was more sensitive to some chemotherapy drugs. Finally, we performed correlation analysis on the model genes. In this paper, the 12-IFRM signatures was developed with promising application prospects for predicting the clinical outcomes and treatment outcomes in head and neck squamous cell carcinoma.

Abstract

Ferroptosis is a new type of programmed cell death that plays a pivotal role in a variety of tumors. Moreover, immunity is closely related to ferroptosis. However, immune-ferroptosis-related mRNAs (IFRMs) are still not fully understood in the regulation of head and neck squamous cell carcinoma (HNSC). The purpose of this paper was to investigate the IFRMs prediction of HNSC and its possible molecular biological role. RNA-Seq and related clinical data were mined from the TCGA database, ImmPort database, GeneCards database, FerrDb database, and previous data. In R software, the “DESeq2” package was used to analyze the differential expression of IFRMs. We used univariate Cox analysis to judge the prognosis of the IFRMs. Using the least absolute shrinkage and selection operator (LASSO) and Cox regression, a prediction model for 12 IFRMs was established. In this study, the Kaplan–Meier survival curve and receiver operating characteristic (ROC) curve analysis were used to evaluate the prediction results. Moreover, factors such as immune landscape, somatic mutations, and drug susceptibility are also discussed. We successfully constructed the signature of 12-IFRMs. The two risk groups were classified according to the risk score obtained by this signature. Compared with conventional clinicopathological features, the characteristic-based risk score was more predictive of survival in patients with HNSC. Furthermore, the expression of CD8⁺T cells and macrophage M0 differed significantly between the two groups. Moreover, the expression of TNFSF9 and CD44 in high-risk groups was significantly increased compared with the low-risk groups. Then, we found a higher proportion of high-risk mutations than in the low-risk group. Next, the high-risk group was more sensitive to chemotherapy drugs such as bosutinib, docetaxel, erlotinib, gefitinib, imatinib, lapatinib, and sorafenib. Finally, an in-depth analysis of the association and potential value of the 12 genes was performed. In summary, the 12-IFRM signatures established in this paper had good application prospects and could be effectively used to predict the clinical outcome and treatment response of head and neck squamous cell carcinoma.

Identification of Ferroptosis-Related lncRNA Pairs for Predicting the Prognosis of Head and Neck Squamous Cell Carcinoma

Background

Ferrogenesis was strongly associated with tumorigenesis and development, and activating the ferrogenic process was a novel regimen in treating cancer, especially conventional treatment-resistant cancers. The purpose of the article was to construct a ferroptosis-related long noncoding RNAs (FRlncRNAs) signature, regardless of expression levels to effectively predict prognosis and immunotherapeutic response for head and neck squamous cell carcinoma (HNSCC).

Methods

The RNA-seq data for HNSCC and corresponding clinical information were obtained in the TCGA database, and ferroptosis-related genes (FRGs) were extracted in the ferroptosis database. On this basis, differentially expressed FRlncRNAs (DEFRlncRNAs) pairs were identified through coexpression analysis, differential expression analysis, and a fresh pairing algorithm. Then, a risk assessment model was established with univariate Cox, LASSO, and multivariate Cox regression analysis. Finally, we evaluated the model from various aspects, including survival status, clinicopathological characteristics, infiltration status of immune cells, immune functions, chemotherapeutic sensitivity, immune checkpoint inhibitors (ICIs)-related molecules, and N6-methyladenosine (m⁶A) mRNA status.

Result

We established a signature of 11-DEFRlncRNA pairs related to the prognosis of HNSCC that had AUC values above 0.75 in the one-, three-, and five-year ROC curves, underscoring the high susceptibility and specifiability of predicting HNSCC prognosis. Survival rates were remarkably higher for the low-risk patients than for the high-risk patients, and the signature was significantly correlated with survival, clinical, T, and N stages. Finally, immune cell infiltration status, immune functions, chemotherapeutic sensitivity, and expression levels of ICIs-related and m⁶A-related molecules were statistically different among different groups.

Conclusion

Our study established a novel lncRNA signature, which is independent of specific expression levels, could predict patient prognosis, and might have promising clinical applications in HNCSS.