A universal co‐expression gene network and prognostic model for hepatic–biliary–pancreatic cancers identified by integrative analyses

Zhang, Jing; Wang, Yixuan; Zheng, Xiao; Cui, Jiahuan; Wang, Chaochen

doi:10.1002/2211-5463.13478

Cited by 8 publications

(5 citation statements)

References 56 publications

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“…The R packages “GSVA” ( 21 ) and “GSEABase” ( 22 ) were employed to perform enrichment analysis on the DEGs. The focus of the analysis was to identify the enrichment levels of the anoikis-DEGs on KEGG (Kyoto Encyclopedia of Genes and Genomes) and GO (Gene Ontology) ( 23 ). In addition, we have applied Cytoscape software ( 24 ) and the STRING database ( https://cn.string-db.org/ ) to explore the protein-protein interactions ( 25 ).…”

Section: Methodsmentioning

confidence: 99%

Anoikis resistance regulates immune infiltration and drug sensitivity in clear-cell renal cell carcinoma: insights from multi omics, single cell analysis and in vitro experiment

Wen,

Hou,

et al. 2024

Front. Immunol.

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BackgroundAnoikis is a form of programmed cell death essential for preventing cancer metastasis. In some solid cancer, anoikis resistance can facilitate tumor progression. However, this phenomenon is underexplored in clear-cell renal cell carcinoma (ccRCC).MethodsUsing SVM machine learning, we identified core anoikis-related genes (ARGs) from ccRCC patient transcriptomic data. A LASSO Cox regression model stratified patients into risk groups, informing a prognostic model. GSVA and ssGSEA assessed immune infiltration, and single-cell analysis examined ARG expression across immune cells. Quantitative PCR and immunohistochemistry validated ARG expression differences between immune therapy responders and non-responders in ccRCC.ResultsARGs such as CCND1, CDKN3, PLK1, and BID were key in predicting ccRCC outcomes, linking higher risk with increased Treg infiltration and reduced M1 macrophage presence, indicating an immunosuppressive environment facilitated by anoikis resistance. Single-cell insights showed ARG enrichment in Tregs and dendritic cells, affecting immune checkpoints. Immunohistochemical analysis reveals that ARGs protein expression is markedly elevated in ccRCC tissues responsive to immunotherapy.ConclusionThis study establishes a novel anoikis resistance gene signature that predicts survival and immunotherapy response in ccRCC, suggesting that manipulating the immune environment through these ARGs could improve therapeutic strategies and prognostication in ccRCC.

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Section: Methodsmentioning

confidence: 99%

Anoikis resistance regulates immune infiltration and drug sensitivity in clear-cell renal cell carcinoma: insights from multi omics, single cell analysis and in vitro experiment

Wen,

Hou,

et al. 2024

Front. Immunol.

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“…The lower chamber was supplied with 15% fetal bovine serum to serve as a chemoattractant for the U2OS cells. The number of cells present in the lower chamber after 36 hours was quantified to gauge cellular migration capabilities ( 43 ).…”

Section: Methodsmentioning

confidence: 99%

Multi-omic validation of the cuproptosis-sphingolipid metabolism network: modulating the immune landscape in osteosarcoma

Li,

Fang,

Liu

et al. 2024

Front. Immunol.

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BackgroundThe current understanding of the mechanisms by which metal ion metabolism promotes the progression and drug resistance of osteosarcoma remains incomplete. This study aims to elucidate the key roles and mechanisms of genes involved in cuproptosis-related sphingolipid metabolism (cuproptosis-SPGs) in regulating the immune landscape, tumor metastasis, and drug resistance in osteosarcoma cells.MethodsThis study employed multi-omics approaches to assess the impact of cuproptosis-SPGs on the prognosis of osteosarcoma patients. Lasso regression analysis was utilized to construct a prognostic model, while multivariate regression analysis was applied to identify key core genes and generate risk coefficients for these genes, thereby calculating a risk score for each osteosarcoma patient. Patients were then stratified into high-risk and low-risk groups based on their risk scores. The ESTIMATE and CIBERSORT algorithms were used to analyze the level of immune cell infiltration within these risk groups to construct the immune landscape. Single-cell analysis was conducted to provide a more precise depiction of the expression patterns of cuproptosis-SPGs among immune cell subtypes. Finally, experiments on osteosarcoma cells were performed to validate the role of the cuproptosis-sphingolipid signaling network in regulating cell migration and apoptosis.ResultsIn this study, seven cuproptosis-SPGs were identified and used to construct a prognostic model for osteosarcoma patients. In addition to predicting survival, the model also demonstrated reliability in forecasting the response to chemotherapy drugs. The results showed that a high cuproptosis-sphingolipid metabolism score was closely associated with reduced CD8 T cell infiltration and indicated poor prognosis in osteosarcoma patients. Cellular functional assays revealed that cuproptosis-SPGs regulated the LC3B/ERK signaling pathway, thereby triggering cell death and impairing migration capabilities in osteosarcoma cells.ConclusionThe impact of cuproptosis-related sphingolipid metabolism on the survival and migration of osteosarcoma cells, as well as on CD8 T cell infiltration, highlights the potential of targeting copper ion metabolism as a promising strategy for osteosarcoma patients.

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“…Hepatic-Biliary-Pancreatic (HBP) cancers represent a formidable challenge within the broader spectrum of gastrointestinal malignancies ( 1 ). These cancers encompass a complex array of diseases affecting the liver, bile ducts, and pancreas.…”

Section: Introductionmentioning

confidence: 99%

Editorial: Biomarkers and immunotherapy of hepatic-biliary-pancreatic cancers

Qian,

Jia,

Liu

2023

Front. Oncol.

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A universal co‐expression gene network and prognostic model for hepatic–biliary–pancreatic cancers identified by integrative analyses

Cited by 8 publications

References 56 publications

Anoikis resistance regulates immune infiltration and drug sensitivity in clear-cell renal cell carcinoma: insights from multi omics, single cell analysis and in vitro experiment

Anoikis resistance regulates immune infiltration and drug sensitivity in clear-cell renal cell carcinoma: insights from multi omics, single cell analysis and in vitro experiment

Multi-omic validation of the cuproptosis-sphingolipid metabolism network: modulating the immune landscape in osteosarcoma

Editorial: Biomarkers and immunotherapy of hepatic-biliary-pancreatic cancers

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