Evidence map›Paper›PMID 40597017›Full record

ArticleBMC cancer2025

Bioinformatics identification and validation of m6A/m1A/m5C/m7G/ac4 C-modified genes in oral squamous cell carcinoma.

Cheng-Hui Lu, Xue-Lai Yin, Zhuo-Deng Huang, Si-Ang Lv, Jun Wu, Jie Wei

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PubMed Full text at PMC Publisher
In one paragraph

Article in BMC cancer, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

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2citing papers in PubMed
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1 · What the graph read from it

What it found

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2 · The registry

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3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

6 authors.

Cheng-Hui Lu *Department of Stomatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Core Unit of National Clinical Research Center for Oral Diseases, Shanghai, 200092, China.
Xue-Lai Yin *Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Center of Head and Neck Oncology Clinical and Translational Science, Shanghai, 200011, China.
Zhuo-Deng Huang *Department of Laboratory Medicine, Jiading Branch of Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201803, China.
Si-Ang LvDepartment of Laboratory Medicine, Jiading Branch of Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201803, China.
Jun WuDepartment of Laboratory Medicine, Jiading Branch of Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201803, China. jun.wu@shsmu.edu.cn.
Jie WeiDepartment of Stomatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Core Unit of National Clinical Research Center for Oral Diseases, Shanghai, 200092, China. weijie3645@shsmu.edu.cn.

Funding

Construction Project of the "Discipline Peak-Climbing Plan" of Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine XKPF2024B500Interdisciplinary Program of Shanghai Jiao Tong University YG2022QN053Key Discipline Construction project of Jiading District Health System XK202405National Natural Science Foundation of China 82072892Natural Science Foundation of Guangxi Zhuang Autonomous Region 2023GXNSFAA026276
6 · The paper itself

Abstract

backgroundRNA modifications, including m6A, m1A, m5C, m7G, and ac4C, may play a role in the occurrence and development of cancer, such as proliferation. However, the effects of RNA modification-related genes (RRGs) in the development of oral squamous cell carcinoma (OSCC) have not been fully elucidated. The present study aimed to evaluate the effects and mechanisms of RRGs on OSCC development progression.

methodsRNA-seq transcriptome data, along with clinical and prognostic information, were extracted for 328 patients with OSCC from the TCGA database. A total of 49 RRGs were analyzed for differential expression. We then performed Lasso analysis, as well as univariate and multivariate Cox regression analyses, followed by Kaplan-Meier survival analysis to identify relevant prognostic genes and establish a risk-prognosis model. Patients were categorized into high-risk and low-risk groups, and gene set enrichment analysis (GSEA) was conducted to analyze differences in gene signatures between these two groups, using data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases. RT-PCR was employed to validate the expression levels of differentially expressed genes in OSCC samples. The four most significantly differentially expressed genes were selected for further functional analysis, and small interfering RNA (siRNA) vectors targeting these genes were transfected into OSCC CAL27 cells. The Cell Counting Kit-8 (CCK-8) assay was used to evaluate cell proliferation. Additionally, a subcutaneous CAL27 xenograft model transfected with short hairpin RNA (shRNA), combined with Ki-67 immunohistochemical (IHC) staining and TUNEL assay, was used to investigate their underlying molecular mechanisms in vivo.

resultsAmong the 49 RRGs, four genes (IGF2BP2, HNRNPC, NAT10, and TRMT61B) were found to be associated with the development of OSCC. Based on various methodological validations, a risk score model was constructed using these four genes. The high-risk and low-risk groups of OSCC patients exhibited significantly different survival outcomes and clinicopathological characteristics. Patients in the low-risk group had longer overall survival (OS) and lower mortality rates compared to those in the high-risk group. The nomogram and decision curve analysis (DCA) demonstrated that our risk model accurately and reliably predicted the impact of risk factors on OS at 1-, 3-, and 5-year. Additionally, risk scores correlated with the infiltration of several immune cells, particularly CD8

conclusionIn this study, we established a risk model and nomogram based on four RRGs, which can be used for risk stratification and predicting survival outcomes in patients with OSCC. This provides a reliable reference for individualized therapy in OSCC patients.

Indexed as

Biomarkers, TumorCarcinoma, Squamous CellComputational BiologyMouth NeoplasmsSquamous Cell Carcinoma of Head and NeckAnimalsCell Line, TumorCell ProliferationFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticHumansMaleMiceMice, NudeMiddle AgedBiomarkers, TumorBioinformatics analysisBiomarkersOral squamous cell carcinomaPrognostic signatureRNA modification

Identifiers

PMID40597017
PMCPMC12211329

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.