Construction on of a Ferroptosis-Related lncRNA-Based Model to Improve the Prognostic Evaluation of Gastric Cancer Patients Based on Bioinformatics

Pan, Jing; Zhang, Xinyue; Fang, Xuedong; Xin, Zhuoyuan

doi:10.3389/fgene.2021.739470

Cited by 20 publications

(17 citation statements)

References 43 publications

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“…In view of the potential value in lncRNAs and ferroptosis-associated immunity, previous investigations have also built other ferroptosis-associated lncRNA models to evaluate tumor prognosis. Based on 17 ferroptosis-associated lncRNAs, Pan et al developed a prognostic model for gastric cancer, which had AUCs of 0.747 and 0.751 in the test and control groups [ 15 ]. The AUC for lung squamous cell carcinoma- (LUSC-) related model was 0.658 at 1 year, 0.693 at 2 years, and 0.687 at 3 years.…”

Section: Discussionmentioning

confidence: 99%

Identification of Ferroptosis-Associated Long Noncoding RNA Prognostic Model and Tumor Immune Microenvironment in Thyroid Cancer

Lin

Gan

He³

et al. 2022

Journal of Immunology Research

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Background. Thyroid cancer (TC) is a rapidly increasing incidence of endocrine malignancies, occupying 3% of new cancer incidence, of which 10% has a heterogeneous prognosis. Ferroptosis is a form of cell death distinct from apoptosis, which involves antitumor drug-related research. Long noncoding RNAs (lncRNAs) could affect cancer prognosis by regulating the ferroptosis; thus, ferroptosis-associated lncRNAs are emerging as prospective biomarkers for cancer therapy and prognosis. However, the prognostic factors of ferroptosis-associated lncRNAs in this solid tumor and their mechanisms remain unknown. Methods. The TC lncRNA data were extracted from RNA sequencing files of The Cancer Genome Atlas (TCGA). Then, we performed a two-cluster analysis and grouped 502 patients with TC in a 7 : 3 ratio. Both the least absolute shrinkage and selection operator (LASSO) regression and Cox regression analysis were conducted to create and validate the ferroptosis-associated lncRNA prognostic model (Ferr-LPM). Based on the median Ferr-LPM-based risk score (LPM_score) of the training cohort, we categorized patients into high and low LPM_score groups, which were then subjected to prognostic correlation and difference analysis. We also created a nomogram and assessed its predictive ability. Furthermore, immune-related mechanisms were investigated by analyzing the tumor immune microenvironment (TIME) and applying algorithms such as CIBERSROT. Results. We built a highly accurate nomogram to promote the clinical applicability of Ferr-LPM. The area under the receiver operating characteristic curve (AUC-ROC) reached above 0.9. Survival analysis suggested that when the Ferr-LPM score was higher, the overall survival (OS) of patients within this group was shorter. Meanwhile, we found a strong association between Ferr-LPM and TIME. Interestingly, the LPM_score was inversely proportional to the tumor purity but positively related to immune checkpoint blockade (ICB) response. Conclusion. We constructed a novel ferroptosis-associated lncRNA nomogram that could highly predict the prognosis of TC patients. Ferroptosis-associated lncRNAs might possess potential functions in regulating TIME, and lncRNAs provide TC patients with new prognostic biomarkers and therapeutic targets.

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Section: Discussionmentioning

confidence: 99%

Identification of Ferroptosis-Associated Long Noncoding RNA Prognostic Model and Tumor Immune Microenvironment in Thyroid Cancer

Lin

Gan

He³

et al. 2022

Journal of Immunology Research

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“…Compared to other prognostic signatures, our study mainly focused on lncRNAs correlated with angiogenesis status, identified prognosis-related ARLncs, and developed a risk model of prognosis in patients with STAD. Previous studies have investigated several prognostic models based on lncRNA expression involved in the process of ferroptosis [ 25 ], N6-methyladenosine modification [ 26 ], or Helicobacter pylori infection [ 27 ], which induce and activate the protumor signaling pathway of gastric cancer. Thus, our risk signatures had dual roles as it predicted the prognosis of STAD and contributed to the selection of proper cohorts who may benefit from antiangiogenesis treatment.…”

Section: Discussionmentioning

confidence: 99%

Angiogenesis-related lncRNAs predict the prognosis signature of stomach adenocarcinoma

et al. 2021

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Background Stomach adenocarcinoma (STAD), which accounts for approximately 95% of gastric cancer types, is a malignancy cancer with high morbidity and mortality. Tumor angiogenesis plays important roles in the progression and pathogenesis of STAD, in which long noncoding RNAs (lncRNAs) have been verified to be crucial for angiogenesis. Our study sought to construct a prognostic signature of angiogenesis-related lncRNAs (ARLncs) to accurately predict the survival time of STAD. Methods The RNA-sequencing dataset and corresponding clinical data of STAD were acquired from The Cancer Genome Atlas (TCGA). ARLnc sets were obtained from the Ensemble genome database and Molecular Signatures Database (MSigDB, Angiogenesis M14493, INTegrin pathway M160). A ARLnc-related prognostic signature was then constructed via univariate Cox and multivariate Cox regression analysis in the training cohort. Survival analysis and Cox regression were performed to assess the performance of the prognostic signature between low- and high-risk groups, which was validated in the validation cohort. Furthermore, a nomogram that combined the clinical pathological characteristics and risk score conducted to predict the overall survival (OS) of STAD. In addition, ARLnc-mRNA coexpression pairs were constructed with Pearson’s correlation analysis and visualized to infer the functional annotation of the ARLncs by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The expression of four ARLncs in STAD and their correlation with the angiogenesis markers, CD34 and CD105, were also validated by RT–qPCR in a clinical cohort. Results A prognostic prediction signature including four ARLncs (PVT1, LINC01315, AC245041.1, and AC037198.1) was identified and constructed. The OS of patients in the high-risk group was significantly lower than that of patients in the low-risk group (p < 0.001). The values of the time-dependent area under the curve (AUC) for the ARLnc signature for 1-, 3-, and 5- year OS were 0.683, 0.739, and 0.618 in the training cohort and 0.671, 0.646, and 0.680 in the validation cohort, respectively. Univariate and multivariate Cox regression analyses indicated that the ARLnc signature was an independent prognostic factor for STAD patients (p < 0.001). Furthermore, the nomogram and calibration curve showed accurate prediction of the survival time based on the risk score. In addition, 262 mRNAs were screened for coexpression with four ARLncs, and GO analysis showed that mRNAs were mainly involved in biological processes, including angiogenesis, cell adhesion, wound healing, and extracellular matrix organization. Furthermore, correlation analysis showed that there was a positive correlation between risk score and the expression of the angiogenesis markers, CD34 and CD105, in TCGA datasets and our clinical sample cohort. Conclusion Our study constructed a prognostic signature consisting of four ARLnc genes, which was closely related to the survival of STAD patients, showing high efficacy of the prognostic signature. Thus, the present study provided a novel biomarker and promising therapeutic strategy for patients with STAD.

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“…Mounting evidence indicated that lncRNAs have an undeniable prognosis prediction function in GC cancer. Prognostic signatures based on ferroptosis-related lncRNA, immune-related lncRNA and helicobacter pylori infectionrelated lncRNA were proved to have preferable prognosis prediction functions in GC (Ma et al, 2021;Pan J. et al, 2021;Wei et al, 2021;Xin et al, 2021). Apart from this, lncRNAs could be used for subtype identification and therapy response prediction of GC Jiang et al, 2021b).…”

Section: Introductionmentioning

confidence: 99%

Identification and Comprehensive Prognostic Analysis of a Novel Chemokine-Related lncRNA Signature and Immune Landscape in Gastric Cancer

Liang

Zha

et al. 2022

Front. Cell Dev. Biol.

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Gastric cancer (GC) is a malignant tumor with poor survival outcomes. Immunotherapy can improve the prognosis of many cancers, including GC. However, in clinical practice, not all cancer patients are sensitive to immunotherapy. Therefore, it is essential to identify effective biomarkers for predicting the prognosis and immunotherapy sensitivity of GC. In recent years, chemokines have been widely reported to regulate the tumor microenvironment, especially the immune landscape. However, whether chemokine-related lncRNAs are associated with the prognosis and immune landscape of GC remains unclear. In this study, we first constructed a novel chemokine-related lncRNA risk model to predict the prognosis and immune landscape of GC patients. By using various algorithms, we identified 10 chemokine-related lncRNAs to construct the risk model. Then, we determined the prognostic efficiency and accuracy of the risk model. The effectiveness and accuracy of the risk model were further validated in the testing set and the entire set. In addition, our risk model exerted a crucial role in predicting the infiltration of immune cells, immune checkpoint genes expression, immunotherapy scores and tumor mutation burden of GC patients. In conclusion, our risk model has preferable prognostic performance and may provide crucial clues to formulate immunotherapy strategies for GC.

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Construction on of a Ferroptosis-Related lncRNA-Based Model to Improve the Prognostic Evaluation of Gastric Cancer Patients Based on Bioinformatics

Cited by 20 publications

References 43 publications

Identification of Ferroptosis-Associated Long Noncoding RNA Prognostic Model and Tumor Immune Microenvironment in Thyroid Cancer

Identification of Ferroptosis-Associated Long Noncoding RNA Prognostic Model and Tumor Immune Microenvironment in Thyroid Cancer

Angiogenesis-related lncRNAs predict the prognosis signature of stomach adenocarcinoma

Identification and Comprehensive Prognostic Analysis of a Novel Chemokine-Related lncRNA Signature and Immune Landscape in Gastric Cancer

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