Pyroptosis-Related Signature and Tumor Microenvironment Infiltration Characterization in Head and Neck Squamous Cell Carcinoma

Wu, Zeng-Hong; Wu, Bing-Fei; Li, Cheng; Zhang, Youjing; Zhou, Tao

doi:10.3389/fcell.2022.702224

Cited by 6 publications

(5 citation statements)

References 31 publications

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“…Previous studies have suggested that OSER1-DT is downregulated in non-small cell lung cancer (NSCLC) and hepatocellular carcinoma (HCC) and acts as a tumor suppressor by regulating the expression of genes such as Smad2, Rab23, and ELAVL1 through microRNA sponging or competitive binding [ 43 ]. Additionally, OSER1-DT may modulate the expression of GPX4, a key regulator of ferroptosis, which is another form of regulated cell death that is distinct from necroptosis but may share some common regulators or modulators [ 44 ]. In this study, we found that the expression of OSER1-DT was positively correlated with plasma cell infiltration and the activation of most immune pathways, particularly the B-cell receptor pathway.…”

Section: Discussionmentioning

confidence: 99%

RETRACTED ARTICLE: Identification and assessment of differentially expressed necroptosis long non-coding RNAs associated with periodontitis in human

He,

Zheng,

et al. 2023

BMC Oral Health

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Background Periodontitis is the most common oral disease and is closely related to immune infiltration in the periodontal microenvironment and its poor prognosis is related to the complex immune response. The progression of periodontitis is closely related to necroptosis, but there is still no systematic study of long non-coding RNA (lncRNA) associated with necroptosis for diagnosis and treatment of periodontitis. Material and methods Transcriptome data and clinical data of periodontitis and healthy populations were obtained from the Gene Expression Omnibus (GEO) database, and necroptosis-related genes were obtained from previously published literature. FactoMineR package in R was used to perform principal component analysis (PCA) for obtaining the necroptosis-related lncRNAs. The core necroptosis-related lncRNAs were screened by the Linear Models for Microarray Data (limma) package in R, PCA principal component analysis and lasso algorithm. These lncRNAs were then used to construct a classifier for periodontitis with logistic regression. The receiver operating characteristic (ROC) curve was used to evaluate the sensitivity and specificity of the model. The CIBERSORT method and ssGSEA algorithm were used to estimate the immune infiltration and immune pathway activation of periodontitis. Spearman’s correlation analysis was used to further verify the correlation between core genes and periodontitis immune microenvironment. The expression level of core genes in human periodontal ligament cells (hPDLCs) was detected by RT-qPCR. Results A total of 10 core necroptosis-related lncRNAs (10-lncRNAs) were identified, including EPB41L4A-AS1, FAM30A, LINC01004, MALAT1, MIAT, OSER1-DT, PCOLCE-AS1, RNF144A-AS1, CARMN, and LINC00582. The classifier for periodontitis was successfully constructed. The Area Under the Curve (AUC) was 0.952, which suggested that the model had good predictive performance. The correlation analysis of 10-lncRNAs and periodontitis immune microenvironment showed that 10-lncRNAs had an impact on the immune infiltration of periodontitis. Notably, the RT-qPCR results showed that the expression level of the 10-lncRNAs obtained was consistent with the chip analysis results. Conclusions The 10-lncRNAs identified from the GEO dataset had a significant impact on the immune infiltration of periodontitis and the classifier based on 10-lncRNAs had good detection efficiency for periodontitis, which provided a new target for diagnosis and treatment of periodontitis.

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Section: Discussionmentioning

confidence: 99%

RETRACTED ARTICLE: Identification and assessment of differentially expressed necroptosis long non-coding RNAs associated with periodontitis in human

He,

Zheng,

et al. 2023

BMC Oral Health

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“…Previous studies combined genomic data from bladder cancer and head and neck squamous cell carcinomas to classify pyroptosis into different subtypes. The results further confirmed prognosis and immunotherapy sensitivity differences between patients with different tumor subtypes [ 49 , 50 ]. This finding corroborates the findings of the present study.…”

Section: Discussionsupporting

confidence: 69%

Screening of novel tumor-associated antigens for lung adenocarcinoma mRNA vaccine development based on pyroptosis phenotype genes

Zhou,

Wang,

Wang

et al. 2024

BMC Cancer

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This study aimed to identify new pyroptosis-associated tumor antigens for use in mRNA vaccines and the screening of sensitive LUAD populations suitable for vaccination. The association between tumor immune infiltrating cell abundance and potential tumor antigens was investigated and visualized using the analysis modules of gene expression, clinical outcomes, and somatic copy number variation. In addition, the pyroptosis-related genes (PRGs) were clustered, the relative pyroptosis subtypes (PSs) and gene modules were identified, and the prognostic value of the PSs was examined. The expression of key PRGs in two lung adenocarcinoma cell lines was verified by RT-qPCR. Four tumor pyroptosis-associated antigens, CARD8, NAIP, NLRP1, and NLRP3, were screened as potential candidates for LUAD mRNA vaccine development. In the construction of consensus clusters for PRGs, two PSs, PS1 and PS2, were classified, in which patients with PS1 LUAD had a better prognosis. In contrast, patients with PS2 LUAD may have better responsiveness to mRNA vaccine treatment. The key PRGs can be regarded as biomarkers to predict the LUAD prognosis and identify patients suitable for mRNA vaccines. The RT-qPCR results showed that the expression levels of CSMD3, LRP1B, MUC16 and TTN were significantly increased in the two lung adenocarcinoma cell lines, while the expression levels of CARD8, TP53 and ZFHX4 were significantly reduced. The antigens CARD8, NAIP, NLRP1, and NLRP3, which are associated with tumor pyroptosis, could be candidate molecules for LUAD mRNA vaccine development. Patients with PS2 LUAD may be suitable candidates for mRNA vaccine treatment.

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“…In fact, the use of bioinformatics to find biomarkers to predict the prognosis of patients by different characteristics of tumors is very common in many types of tumors (46)(47)(48). However, due to the many influencing factors involved, it is often difficult to summarize the results with deterministic significance.…”

Section: Discussionmentioning

confidence: 99%

A necroptosis-related lncRNA signature was identified to predict the prognosis and immune microenvironment of IDH-wild-type GBM

Zhu¹,

Gu²,

Wang³

et al. 2022

Front. Oncol.

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IntroductionNecroptosis-related genes are essential for the advancement of IDH-wild-type GBM. However, the putative effects of necroptosis-related lncRNAs (nrlncRNAs) in IDH-wild-type GBM remain unknown.MethodsBy using the TCGA and GTEx databases, a nrlncRNA prognostic signature was created using LASSO Cox regression. The median risk score was used to categorize the patients into low and high-risk groups. To confirm the validity, univariate, multivariate Cox regression and ROC curves were used. Furthermore, by enrichment analysis, immune correlation analysis, and drug sensitivity analysis, the targeted lncRNAs were selected for further verification. As the highest upregulated expression in tumor than peritumor specimens, RP11-131L12.4 was selected for phenotype and functional experiments in primary GBM cells.ResultsSix lncRNAs were proved to be closely related to necroptosis in IDH-1-wild-type GBM, which were used to create a new signature. For 1-, 2-, and 3-year OS, the AUCs were 0.709, 0.645 and 0.694, respectively. Patients in the low-risk group had a better prognosis, stronger immune function activity, and more immune cell infiltration. In contrast, enrichment analysis revealed that the malignant phenotype was more prevalent in the high-risk group. In vitro experiments indicated that RP11-131L12.4 increased the tumor proliferation, migration and invasion, but decreased the necroptosis. Moreover, this nrlncRNA was also proved to be negatively associated with patient prognosis.ConclusionThe signature of nrlncRNAs may aid in the formulation of tailored and precise treatment for individuals with IDH-wild-type GBM. RP11-131L12.4 may play indispensable role in necroptosis suppression.

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Pyroptosis-Related Signature and Tumor Microenvironment Infiltration Characterization in Head and Neck Squamous Cell Carcinoma

Cited by 6 publications

References 31 publications

RETRACTED ARTICLE: Identification and assessment of differentially expressed necroptosis long non-coding RNAs associated with periodontitis in human

RETRACTED ARTICLE: Identification and assessment of differentially expressed necroptosis long non-coding RNAs associated with periodontitis in human

Screening of novel tumor-associated antigens for lung adenocarcinoma mRNA vaccine development based on pyroptosis phenotype genes

A necroptosis-related lncRNA signature was identified to predict the prognosis and immune microenvironment of IDH-wild-type GBM

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