Prognosis and Immunotherapy Response With a Novel Golgi Apparatus Signature-Based Formula in Lung Adenocarcinoma

Jiang, Yupeng; Ouyang, Wenhao; Zhang, Chenzi; Yu, Yunfang

doi:10.3389/fcell.2021.817085

Cited by 8 publications

(6 citation statements)

References 43 publications

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“…It is urgent to devise a workable plan for an immune therapeutic application that is safe and efficient in light of all of these adverse occurrences. Therefore, finding new non-apoptotic pathways that control cell death and enhance the immune microenvironment of malignancies is crucial from a clinical and practical standpoint [ 37 ].…”

Section: Discussionmentioning

confidence: 99%

GAPDH Is a Novel Ferroptosis-Related Marker and Correlates with Immune Microenvironment in Lung Adenocarcinoma

et al. 2023

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Lung adenocarcinoma (LUAD) is a prevalent form of lung cancer with high morbidity and fatality rates. Ferroptosis is a type of programmed cell death that is iron-dependent. Recent findings have suggested that ferroptosis inducers have promising prospects for the therapy of LUAD. However, ferroptosis-related gene expression in LUAD and its relationship with the tumor prognosis and tumor immune microenvironment remain unknown. We identified a total of 638 ferroptosis-related genes, built a LUAD ferroptosis-related risk model (FRRM) with the help of Least Absolute Shrinkage Selection Operator (LASSO) regression analysis based on The Cancer Genome Atlas (TCGA) database, split LUAD patients into high- and low-risk clusters, and verified the model utilizing the Gene Expression Omnibus (GEO) database. The results of the FRRM’s principal component analysis (PCA) demonstrated its strong predictive power. Further, univariate and multivariate Cox and AUC curve analyses demonstrated that the model was independent of other clinical traits and served as an independent prognostic factor. The nomogram demonstrated strong predictive power for overall survival, according to calibration plots. We also explored variations in clinical characteristics, immune cell infiltration, immune-related function, and functional pathways between the high- and low-risk groups. Additionally, we used a protein–protein interaction (PPI) network of various genes in the two groups to search for potential target genes. GAPDH was then chosen for a follow-up investigation. An analysis was performed on the relationship between GAPDH and variations in survival prognosis, clinical traits, immune cell infiltration, immune checkpoints, and immunotherapy. In vitro tests further supported the probable functions of GAPDH as a ferroptosis marker in LUAD. In conclusion, a novel ferroptosis-related prognostic gene, GAPDH, was discovered, whose expression was connected to the tumor immune microenvironment. The combination of immunotherapy and the targeting of GAPDH to induce ferroptosis in LUAD may provide a novel therapeutical option.

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Section: Discussionmentioning

confidence: 99%

GAPDH Is a Novel Ferroptosis-Related Marker and Correlates with Immune Microenvironment in Lung Adenocarcinoma

et al. 2023

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“…Recently, many reports revealed the correlation between the gene expressed profiling and survival time in DLBCL 30 , 31 or other tumors 32 , 33 , but they only used one or two biological functions. However, ribosome participates in numerous bioprocesses such as translation, proliferation and tumorigenesis, we chose the RibGs to develop the prognostic model including these many cellular functions.…”

Section: Discussionmentioning

confidence: 99%

Prognostic Significance of Ribosome-related Genes Signature in Diffuse Large B Cell Lymphoma

Wang¹,

Jiang²,

Hu³

et al. 2023

J. Cancer

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Background:The diffuse large B-cell lymphoma (DLBCL) is a heterogeneous lymphoma with a dismal outcome, due to approximately 40% patients will be relapsed or refractory to the standard therapy of rituximab plus cyclophosphamide, doxorubicin, vincristine and prednisone (R-CHOP). Therefore, we need urgently to explore the approach to classify the risk of DLBCL patients accurately and accurately targeting therapy. The ribosome is a vital cellular organelle that is mainly responsible for translation mRNA into protein, moreover, more and more reports revealed that ribosome was associated with cellular proliferation and tumorigenesis. Therefore, our study aimed to construct a prognostic model of DLBCL patients using ribosome-related genes (RibGs). Method: We screened differentially expressed RibGs between healthy donors' B cells and DLBCL patients' malignant B cells in GSE56315 dataset. Next, we performed analyses of univariate Cox regression, the least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox regression analyses to establish the prognostic model consisting of 15 RibGs in GSE10846 training set. Then, we validated the model by a range of analyses including Cox regression, Kaplan-Meier survival, ROC curve, and nomogram in training and validation cohorts. Results: The RibGs model showed a reliably predictive capability. We found the upregulated pathways in high-risk group most associated with innate immune reaction such as interferon response, complement and inflammatory responses. In addition, a nomogram including age, gender, IPI score and risk score was constructed to help explain the prognostic model. We also discovered the high-risk patients were more sensitive to some certain drugs. Finally, knocking out the NLE1 could inhibit the proliferation of DLBCL cell lines. Conclusion:As far as we know, it is the first time to predict the prognosis of DLBCL using the RibGs and give a new sight for DLBCL treatment. Importantly, the RibGs model could be acted as a supplementary to the IPI in classifying the risk of DLBCL patients.

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“…“c5.go.symbols” and “c2.cp.kegg.symbols” gene sets were downloaded, and the R software “GSVA” package was used to perform the Gene Set Variation Analysis (GSVA) to explore the differences in molecular function, biological behavior, and signaling pathways of different phenotypes based on DRG-FRGs. Online website TIMER 2.0 ( ) including diverse algorithms ( Jiang et al, 2021 ) of TIMER, CIBERSORT, CIBERSORT-ABS, QUANTISEQ, MCPCOUNTER, XCELL, and EPIC was used to conduct analysis of immune cell infiltration, and a heatmap to display the differences. Single-sample gene set enrichment analysis (ssGSEA) plays a role in calculating the enrichment score that indicates the level at a gene is enriched in a particular gene set.…”

Section: Methodsmentioning

confidence: 99%

“…ssGSEA was performed using R software packages “GSVA” and “GSEABase” to calculate the concentration score of 23 immune cells in different clusters ( Xiong et al, 2023 ). The ESTIMATE algorithm is a method of calculating tumor purity ( Jiang et al, 2021 ). The R software “ESTIMATE” package was used to analyze the immune scores and stromal scores in different clusters to explore the infiltration of immune cells and stromal cells in TME.…”

Section: Methodsmentioning

confidence: 99%

Novel application of the ferroptosis-related genes risk model associated with disulfidptosis in hepatocellular carcinoma prognosis and immune infiltration

Wei,

Wang,

Chen

et al. 2024

PeerJ

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Hepatocellular carcinoma (HCC) stands as the prevailing manifestation of primary liver cancer and continues to pose a formidable challenge to human well-being and longevity, owing to its elevated incidence and mortality rates. Nevertheless, the quest for reliable predictive biomarkers for HCC remains ongoing. Recent research has demonstrated a close correlation between ferroptosis and disulfidptosis, two cellular processes, and cancer prognosis, suggesting their potential as predictive factors for HCC. In this study, we employed a combination of bioinformatics algorithms and machine learning techniques, leveraging RNA sequencing data, mutation profiles, and clinical data from HCC samples in The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and the International Cancer Genome Consortium (ICGC) databases, to develop a risk prognosis model based on genes associated with ferroptosis and disulfidptosis. We conducted an unsupervised clustering analysis, calculating a risk score (RS) to predict the prognosis of HCC using these genes. Clustering analysis revealed two distinct HCC clusters, each characterized by significantly different prognostic and immune features. The median RS stratified HCC samples in the TCGA, GEO, and ICGC cohorts into high-and low-risk groups. Importantly, RS emerged as an independent prognostic factor in all three cohorts, with the high-risk group demonstrating poorer prognosis and a more active immunosuppressive microenvironment. Additionally, the high-risk group exhibited higher expression levels of tumor mutation burden (TMB), immune checkpoints (ICs), and human leukocyte antigen (HLA), suggesting a heightened responsiveness to immunotherapy. A cancer stem cell infiltration analysis revealed a higher similarity between tumor cells and stem cells in the high-risk group. Furthermore, drug sensitivity analysis highlighted significant differences in response to antitumor drugs between the two risk groups. In summary, our risk prognostic model, constructed based on ferroptosis-related genes associated with disulfidptosis, effectively predicts HCC prognosis. These findings hold potential implications for patient stratification and clinical decision-making, offering valuable theoretical insights in this field.

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Prognosis and Immunotherapy Response With a Novel Golgi Apparatus Signature-Based Formula in Lung Adenocarcinoma

Cited by 8 publications

References 43 publications

GAPDH Is a Novel Ferroptosis-Related Marker and Correlates with Immune Microenvironment in Lung Adenocarcinoma

GAPDH Is a Novel Ferroptosis-Related Marker and Correlates with Immune Microenvironment in Lung Adenocarcinoma

Prognostic Significance of Ribosome-related Genes Signature in Diffuse Large B Cell Lymphoma

Novel application of the ferroptosis-related genes risk model associated with disulfidptosis in hepatocellular carcinoma prognosis and immune infiltration

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