m5C RNA Methylation Regulators Predict Prognosis and Regulate the Immune Microenvironment in Lung Squamous Cell Carcinoma

Pan, Junfan; Huang, Zhidong; Xu, Yiquan

doi:10.3389/fonc.2021.657466

Cited by 79 publications

(82 citation statements)

References 41 publications

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“…Finally, we analyzed the expression and conducted Kaplan-Meier survival analysis of the six SLC family genes in the TCGA and GSE72094 datasets. As shown in Figures 9A-F, compared to adjacent normal tissues, the expression of SLC15A2, SLC25A34, and SLC46A3 were significantly lower and the expression of SLC26A11, SLC16A13, and SLC2A1 significantly higher in LUAC tissues, which were consistent with the results analyzed in the UALCAN (http://ualcan.path.uab.edu/) online tool (Pan et al, 2021). K-M survival analysis indicated that lower expression of SLC15A2, SLC25A34, SLC46A3, and SLC26A11 and higher expression of SLC16A13 and SLC2A1 were associated with a worse prognosis in the TCGA cohort (Figures 9G-L).…”

Section: Expression and Survival Analysis Of The Six Slc Family Genessupporting

confidence: 87%

Identification of a Six-Gene SLC Family Signature With Prognostic Value in Patients With Lung Adenocarcinoma

Zhu

Mou

et al. 2021

Front. Cell Dev. Biol.

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Given the importance of solute carrier (SLC) proteins in maintaining cellular metabolic homeostasis and that their dysregulation contributes to cancer progression, here we constructed a robust SLC family signature for lung adenocarcinoma (LUAD) patient stratification. Transcriptomic profiles and relevant clinical information of LUAD patients were downloaded from the TCGA and GEO databases. SLC family genes differentially expressed between LUAD tissues and adjacent normal tissues were identified using limma in R. Of these, prognosis-related SLC family genes were further screened out and used to construct a novel SLC family-based signature in the training cohort. The accuracy of the prognostic signature was assessed in the testing cohort, the entire cohort, and the external GSE72094 cohort. Correlations between the prognostic signature and the tumor immune microenvironment and immune cell infiltrates were further explored. We found that seventy percent of SLC family genes (279/397) were differentially expressed between LUAC tissues and adjacent normal. Twenty-six genes with p-values < 0.05 in univariate Cox regression analysis and Kaplan-Meier survival analysis were regarded as prognosis-related SLC family genes, six of which were used to construct a prognostic signature for patient classification into high- and low-risk groups. Kaplan-Meier survival analysis in all internal and external cohorts revealed a better overall survival for patients in the low-risk group than those in the high-risk group. Univariate and multivariate Cox regression analyses indicated that the derived risk score was an independent prognostic factor for LUAD patients. Moreover, a nomogram based on the six-gene signature and clinicopathological factors was developed for clinical application. High-risk patients had lower stromal, immune, and ESTIMATE scores and higher tumor purities than those in the low-risk group. The proportions of infiltrating naive CD4 T cells, activated memory CD4 T cells, M0 macrophages, resting dendritic cells, resting mast cells, activated mast cells, and eosinophils were significantly different between the high- and low-risk prognostic groups. In all, the six-gene SLC family signature is of satisfactory accuracy and generalizability for predicting overall survival in patients with LUAD. Furthermore, this prognostics signature is related to tumor immune status and distinct immune cell infiltrates in the tumor microenvironment.

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Section: Expression and Survival Analysis Of The Six Slc Family Genessupporting

confidence: 87%

Identification of a Six-Gene SLC Family Signature With Prognostic Value in Patients With Lung Adenocarcinoma

Zhu

Mou

et al. 2021

Front. Cell Dev. Biol.

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“…Meanwhile, three different m 1 A modification patterns identified by Gao et al significantly affect relapse-free survival, overall survival and the number of tumor microenvironment infiltration cells in COAD patients. In addition, Pan et al found that m 1 A regulatory factor expression levels significantly differed between lung squamous cell carcinoma and normal tissues ( Pan et al, 2021 ).…”

Section: Adenine-related Rna Modification Regulation In Head and Neck Squamous Cell Carcinomamentioning

confidence: 99%

Roles of Major RNA Adenosine Modifications in Head and Neck Squamous Cell Carcinoma

et al. 2021

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Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer malignancy worldwide and is known to have poor prognosis. The pathogenesis behind the development of HNSCC is not fully understood. Modifications on RNA are involved in many pathophysiological processes, such as tumor development and inflammation. Adenosine-related RNA modifications have shown to be linked to cancer and may play a role in cancer occurrence and development. To date, there are at least 170 different chemical RNA modifications that modify coding and non-coding RNAs (ncRNAs). These modifications affect RNA stability and transcription efficiency. In this review, we focus on the current understanding of the four major RNA adenosine modifications (N6-Methyladenosine, N1-Methyladenosine, Alternative Polyadenylation Modification and A-to-I RNA editing) and their potential molecular mechanisms related to HNSCC development and progression. We also touch on how these RNA modifications affect treatment of HNSCCs.

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“…In addition, Gao et al ( Gao et al, 2019 ) found that high expression of NSUN2 could promote the proliferation and tumorigenesis of gallbladder carcinoma cells both in vitro and in vivo by closely cooperating with ribosomal protein L6. Recently, the role of m5C modification in cancers, including lung cancer, colon carcinoma, bladder cancer, and thyroid carcinoma, has been explored ( Pan et al, 2021a ; Pan et al, 2021b ; Chen et al, 2021 ; Gao et al, 2021 ; Geng et al, 2021 ; Gu et al, 2021 ; Hu et al, 2021 ; Li et al, 2021 ; Liu et al, 2021 ; Xu et al, 2021 ). In addition, He et al ( He et al, 2020a ) built a gene signature including 2 m5C regulators and found that it could effectively predict the prognosis of HCC.…”

Section: Introductionmentioning

confidence: 99%

Identification of the Expression Patterns and Potential Prognostic Role of 5-Methylcytosine Regulators in Hepatocellular Carcinoma

Liu

Zheng

Wang

et al. 2022

Front. Cell Dev. Biol.

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Background: Hepatocellular carcinoma (HCC) is the most common primary liver cancer with a poor prognosis. 5-methylcytosine (m5C) modification plays a nonnegligible role in tumor pathogenesis and progression. However, little is known about the role of m5C regulators in HCC.Methods: Based on 9 m5C regulators, the m5C modification patterns of HCC samples extracted from public databases were systematically evaluated and correlated with tumor immune and prognosis characteristics. An integrated model called the “m5Cscore” was constructed using principal component analysis, and its prognostic value was evaluated.Results: Almost all m5C regulators were differentially expressed between HCC and normal tissues. Through unsupervised clustering, three different m5Cclusters were ultimately uncovered; these clusters were characterized by differences in prognosis, immune cell infiltration, and pathway signatures. The m5Cscore was constructed to quantify the m5C modifications of individual patients. Subsequent analysis revealed that the m5Cscore was an independent prognostic factor of HCC and could be a novel indicator to predict the prognosis of HCC.Conclusion: This study comprehensively explored and systematically profiled the features of m5C modification in HCC. m5C modification patterns play a crucial role in the tumor immune microenvironment (TIME) and prognosis of HCC. The m5Cscore provides a more holistic understanding of m5C modification in HCC and provides a practical tool for predicting the prognosis of HCC. This study will help clinicians identify effective indicators of HCC to improve the poor prognosis of this disease.

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m5C RNA Methylation Regulators Predict Prognosis and Regulate the Immune Microenvironment in Lung Squamous Cell Carcinoma

Cited by 79 publications

References 41 publications

Identification of a Six-Gene SLC Family Signature With Prognostic Value in Patients With Lung Adenocarcinoma

Identification of a Six-Gene SLC Family Signature With Prognostic Value in Patients With Lung Adenocarcinoma

Roles of Major RNA Adenosine Modifications in Head and Neck Squamous Cell Carcinoma

Identification of the Expression Patterns and Potential Prognostic Role of 5-Methylcytosine Regulators in Hepatocellular Carcinoma

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