Identification of new head and neck squamous cell carcinoma subtypes and development of a novel score system (PGSscore) based on variations in pathway activity between tumor and adjacent non-tumor samples

Zhang, Yufan; Liu, Ying; Huang, Junfei; Hu, Zhiqi; Miao, Yong

doi:10.1016/j.csbj.2022.08.057

Cited by 2 publications

(2 citation statements)

References 72 publications

(91 reference statements)

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“…Genes of the identified module and differentially expressed genes from the high and low mRNAsi subgroups of GSE103224 were intersected to identify genes responsible for malignant cell stemness. Multivariate Cox regression analysis was performed to construct the GSScore [33] , [34] , [35] , [36] . Differentially expressed genes from the high and low GSScore groups were identified using the Wilcoxon rank-sum test with thresholds of FDR < 0.01 and log2FoldChange > 1.…”

Section: Methodsmentioning

confidence: 99%

Machine learning-based identification of lower grade glioma stemness subtypes discriminates patient prognosis and drug response

Zhou

Chen

Zhang

et al. 2023

Computational and Structural Biotechnology Journal

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Section: Methodsmentioning

confidence: 99%

Machine learning-based identification of lower grade glioma stemness subtypes discriminates patient prognosis and drug response

Zhou

Chen

Zhang

et al. 2023

Computational and Structural Biotechnology Journal

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“…The Spearman's correlation coefficient was calculated to explore the correlation between MYC targets/TMB/MSI score and SLC2A2 expression. To predict the chemotherapeutic response associated with SLC2A2 expression, the IC 50 score was analyzed based on Genomics of Drug Sensitivity in Cancer (release-8.2; https://www.cancerrxgene.org/) (14). The 'pRRophetic' package (version 0.5; https://github.com/paulgeeleher/pRRophetic) was used for prediction and the IC 50 score was calculated using ridge regression.…”

Section: Functional Analysis Of Slc2a2 In Gcmentioning

confidence: 99%

Prediction and verification of the prognostic biomarker SLC2A2 and its association with immune infiltration in gastric cancer

Zhang,

Zhou,

Song

et al. 2023

Oncol Lett

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Gastric cancer (GC) is the fifth most common cause of cancer-associated deaths; however, its treatment options are limited. Despite clinical improvements, chemotherapy resistance and metastasis are major challenges in improving the prognosis and quality of life of patients with GC. Therefore, effective prognostic biomarkers and targets associated with immunological interventions need to be identified. Solute carrier family 2 member 2 ( SLC2A2 ) may serve a role in tumor development and invasion. The present study aimed to evaluate SLC2A2 as a prospective prognostic marker and chemotherapeutic target for GC. SLC2A2 expression in several types of cancer and GC was analyzed using online databases, and the effects of SLC2A2 expression on survival prognosis in GC were investigated. Clinicopathological parameters were examined to explore the association between SLC2A2 expression and overall survival (OS). Associations between SLC2A2 expression and immune infiltration, immune checkpoints and IC 50 were estimated using quantification of the tumor immune contexture from human RNA-seq data, the Tumor Immune Estimation Resource 2.0 database and the Genomics of Drug Sensitivity in Cancer database. Differential SLC2A2 expression and the predictive value were validated using the Human Protein Atlas, Gene Expression Omnibus, immunohistochemistry and reverse transcription-quantitative PCR. SLC2A2 expression was downregulated in most types of tumor but upregulated in GC. Functional enrichment analysis revealed an association between SLC2A2 expression and lipid metabolism and the tumor immune microenvironment. According to Gene Ontology term functional enrichment analysis, SLC2A2 -related differentially expressed genes were enriched predominantly in ‘chylomicron assembly’, ‘plasma lipoprotein particle assembly’, ‘high-density lipoprotein particle’, ‘chylomicron’, ‘triglyceride-rich plasma lipoprotein particle’, ‘very-low-density lipoprotein particle’. ‘intermembrane lipid transfer activity’, ‘lipoprotein particle receptor binding’, ‘cholesterol transporter activity’ and ‘intermembrane cholesterol transfer activity’. In addition, ‘cholesterol metabolism’, and ‘fat digestion and absorption’ were significantly enriched in the Kyoto Encyclopedia of Genes and Genomes pathway analysis. Patients with GC with high SLC2A2 expression had higher levels of neutrophil and M2 macrophage infiltration and a significant inverse correlation was observed between SLC2A2 expression and MYC targets, tumor mutation burden, microsatellite instability and immune checkpoints. Furthermore, patients with high SLC2A2 expression had worse prognosis, including OS, disease-specific survival and progression-free interval. Multivariate regres...

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Identification of new head and neck squamous cell carcinoma subtypes and development of a novel score system (PGSscore) based on variations in pathway activity between tumor and adjacent non-tumor samples

Cited by 2 publications

References 72 publications

Machine learning-based identification of lower grade glioma stemness subtypes discriminates patient prognosis and drug response

Machine learning-based identification of lower grade glioma stemness subtypes discriminates patient prognosis and drug response

Prediction and verification of the prognostic biomarker SLC2A2 and its association with immune infiltration in gastric cancer

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