Identification of N6-Methyladenosine-Related lncRNAs as a Prognostic Signature in Glioma

Chen, Yujia; Guo, Yunbo; Li, Shenglun; Xu, Jiacheng; Wang, Xiang; Ning, Weihai; Ma, Lixin; Qu, Yanming; Zhang, Mingshan; Zhang, Hongwei

doi:10.3389/fonc.2022.789283

Cited by 9 publications

(10 citation statements)

References 57 publications

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“…At present, the signatures used to predict prognosis of patients with glioma are sub-optimal. Chen et al (2022) constructed prognostic signatures of N6-methyladenosine-related lncRNAs in gliomas, demonstrating the feasibility of applying prognostic signatures for patients with glioma. Maimaiti et al (2022) analyzed the relationships between clinical outcomes and methylation-related lncRNAs in LGG and the tumor microenvironment, and found that gliomas are characterized by the tumor microenvironment.…”

Section: Discussionmentioning

confidence: 99%

An m6A/m5C/m1A/m7G-Related Long Non-coding RNA Signature to Predict Prognosis and Immune Features of Glioma

Shao

Liu

et al. 2022

Front. Genet.

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Background: Gliomas are the most common and fatal malignant type of tumor of the central nervous system. RNA post-transcriptional modifications, as a frontier and hotspot in the field of epigenetics, have attracted increased attention in recent years. Among such modifications, methylation is most abundant, and encompasses N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1 methyladenosine (m1A), and 7-methylguanosine (m7G) methylation.Methods: RNA-sequencing data from healthy tissue and low-grade glioma samples were downloaded from of The Cancer Genome Atlas database along with clinical information and mutation data from glioblastoma tumor samples. Forty-nine m6A/m5C/m1A/m7G-related genes were identified and an m6A/m5C/m1A/m7G-lncRNA signature of co-expressed long non-coding RNAs selected. Least absolute shrinkage and selection operator Cox regression analysis was used to identify 12 m6A/m5C/m1A/m7G-related lncRNAs associated with the prognostic characteristics of glioma and their correlation with immune function and drug sensitivity analyzed. Furthermore, the Chinese Glioma Genome Atlas dataset was used for model validation.Results: A total of 12 m6A/m5C/m1A/m7G-related genes (AL080276.2, AC092111.1, SOX21-AS1, DNAJC9-AS1, AC025171.1, AL356019.2, AC017104.1, AC099850.3, UNC5B-AS1, AC006064.2, AC010319.4, and AC016822.1) were used to construct a survival and prognosis model, which had good independent prediction ability for patients with glioma. Patients were divided into low and high m6A/m5C/m1A/m7G-LS groups, the latter of which had poor prognosis. In addition, the m6A/m5C/m1A/m7G-LS enabled improved interpretation of the results of enrichment analysis, as well as informing immunotherapy response and drug sensitivity of patients with glioma in different subgroups.Conclusion: In this study we constructed an m6A/m5C/m1A/m7G-LS and established a nomogram model, which can accurately predict the prognosis of patients with glioma and provides direction toward promising immunotherapy strategies for the future.

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Section: Discussionmentioning

confidence: 99%

An m6A/m5C/m1A/m7G-Related Long Non-coding RNA Signature to Predict Prognosis and Immune Features of Glioma

Shao

Liu

et al. 2022

Front. Genet.

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“…The LINC00462 promotes pancreatic cancer invasiveness through the miR-665/TGFBR1-TGFBR2/SMAD2/3 pathway [ 46 ]. According to Yujia Chen, through bioinformatics and vitro experiments, demonstrated that the LNCTAM34A promotes the proliferation, migration, and epithelial-mesenchymal transition of glioma cells [ 47 ]. According to Feilong Yang, AC024022.1 is found in the cytoplasm and is a predictive biomarker in papillary renal cell cancer [ 48 ].…”

Section: Discussionmentioning

confidence: 99%

Potential biomarkers for predicting the overall survival outcome of kidney renal papillary cell carcinoma: an analysis of ferroptosis-related LNCRNAs

Huang

Cai

et al. 2022

BMC Urol

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Background Kidney renal papillary cell carcinoma (KIRP) is a dangerous cancer, which accounts for 15–20% of all kidney malignancies. Ferroptosis is a rare kind of cell death that overcomes medication resistance. Ferroptosis-related long non-coding RNAs (LNCRNAs) in KIRP, remain unknown. Method We wanted to express how ferroptosis-related LNCRNAs interact with immune cell infiltration in KIRP. Gene set enrichment analysis in the GO and KEGG databases were used to explore gene expression enrichment. The prognostic model was constructed using Lasso regression. In addition, we also analyzed the modifications in the tumor microenvironment (TME) and immunological association. Result The expression of LNCRNA was closely connected to the ferroptosis, according to co-expression analyses. CASC19, AC090197.1, AC099850.3, AL033397.2, LINC00462, and B3GALT1-AS1 were found to be significantly increased in the high-risk group, indicating that all of these markers implicates the malignancy processes for KIRP patients and may be cancer-promoting variables. LNCTAM34A and AC024022.1 were shown to be significantly elevated in the low-risk group; these might represent as the KIRP tumor suppressor genes. According to the TCGA, CCR, and inflammation-promoting genes were considered to be significantly different between the low-risk and high-risk groups. The expression of CD160, TNFSF4, CD80, BTLA, and TNFRSF9 was different in the two risk groups. Conclusion LNCRNAs associated with ferroptosis were linked to the occurrence and progression of KIRP. Ferroptosis-related LNCRNAs and immune cell infiltration in the TME may be potential biomarkers in KIRP that should be further investigated.

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“…In addition, worse outcomes of UCEC patients were discovered when occurence of TP53 mutation, and low levels of microRNA and LNCTAM34A. Nevertheless, other studies have shown that LNCTAM34A is seen as a malignant promoter in glioma [ 19 ]. When LNCTAM34A was knocked out, glioma cell proliferation was inhibited, migration was diminished, and EMT rates were relatively low [ 19 ].…”

Section: Discussionmentioning

confidence: 99%

“…Nevertheless, other studies have shown that LNCTAM34A is seen as a malignant promoter in glioma [ 19 ]. When LNCTAM34A was knocked out, glioma cell proliferation was inhibited, migration was diminished, and EMT rates were relatively low [ 19 ]. This contradictory conclusion may be due to the direct heterogeneity of the different types of neoplasms [ 32 ].…”

Section: Discussionmentioning

confidence: 99%

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Pan-Cancer Gene Analysis of m6A Modification and Immune Infiltration in Uterine Corpus Endometrial Carcinoma

Xie

Yan

Lin

et al. 2022

Computational Intelligence and Neuroscience

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Objective. This investigation was to test the potential role of m6A-related long non-coding RNAs (lncRNAs) and immune infiltration as crucial factors in the diagnosis and treatment of uterine corpus endometrial cancer (UCEC). Method. The UCEC RNA-seq data were downloaded in the Cancer Genome Atlas (TCGA, https://portal.gdc.cancer.gov/). There were 587 samples totally, containing 543 UCEC cases and 35 healthy cases. The clinical information of UCEC cases included survival time, survival status, gender, age, stage, and TMN stage. Twenty-three m6A-related genes were found in published journals. The RNA-seq documents of UCEC were downloaded in the Cancer Genome Atlas (TCGA). The hub gene data of UCEC were downloaded from GEPIA2 database. The different packages of R language were applied to calculate and analyze in this research. Results. Among 587 cases in our study, we discovered 3039 lncRNAs in the TCGA-UCEC database. After the differential analysis, 23 m6A-associated genetics were screened and twenty-one m6A-associated differential genetics were found. In the end, we obtained 20 m6A-related lncRNAs. LNCTAM34A was considered as a predictive gene through univariate and multivariate Cox regression analysis. In addition to the above, patients with high LNCTAM34A expression had better outcomes than those with low LNCTAM34A expression. The high-risk cohort had greater scores of activated dendritic cells (aDCs), B cells, and T cell regulatory (Tregs) than low-risk cohort; in the meanwhile, high-risk cohort had lower scores of DCs and iDCs. Then, the high-risk cohort displayed greater scores in the immune functions of MHC class I, para-inflammation, and type I IFN response than those of low-risk cohort. Among 27 immune-inducible genes, the level of CD244, KIR3DLI, NRP1, PDCD1LG2, and TNFRSF8 was reduced in UCEC samples and the level of CD27, CD28, CD70, CD80, CD86, HAVCR2, ICOS, IDO1, LAIR1, PDCD1, TIGIT, TNFRSF18, -25, -9, -14, and VTCN1 was increased in UCEC samples. Conclusion. The key role of M6A-related lncRNAs in immune microenvironment in high-risk patients of UCEC. The patients with strong expression of LNCTAM34A have a good prognosis, and LNCTAM34A can be used as a prognostic gene for UCEC. m6A-related lncRNAs can be used as a potential treatment for UCEC. Our observations can be used as a hypothetical basis for future in vitro and animal experiments.

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Identification of N6-Methyladenosine-Related lncRNAs as a Prognostic Signature in Glioma

Cited by 9 publications

References 57 publications

An m6A/m5C/m1A/m7G-Related Long Non-coding RNA Signature to Predict Prognosis and Immune Features of Glioma

An m6A/m5C/m1A/m7G-Related Long Non-coding RNA Signature to Predict Prognosis and Immune Features of Glioma

Potential biomarkers for predicting the overall survival outcome of kidney renal papillary cell carcinoma: an analysis of ferroptosis-related LNCRNAs

Pan-Cancer Gene Analysis of m6A Modification and Immune Infiltration in Uterine Corpus Endometrial Carcinoma

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