Comprehensive Analysis of N6-Methylandenosine-Related Long Non-Coding RNAs Signature in Prognosis and Tumor Microenvironment of Bladder Cancer

Chen, Kang; Zhu, Shaoming; Ye, Weimin; Xia, Yuqi; Ji, Xing; Geng, Jie

doi:10.3389/fonc.2022.774307

Cited by 5 publications

(2 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…LncRNAs are important in multi-gene regulatory networks, and they can be utilized to diagnose and predict survival in a variety of cancers (14). Multiple lncRNAs signature have been researched in bladder cancer (15)(16)(17). However, the role of ERS-related lncRNA in bladder cancer remains to be studied.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive analysis of the endoplasmic reticulum stress-related long non-coding RNA in bladder cancer

Wang

Yan

et al. 2022

Front. Oncol.

View full text Add to dashboard Cite

BackgroundBladder cancer is ranked the second most frequent tumor among urological malignancies. The research strived to establish a prognostic model based on endoplasmic reticulum stress (ERS)-related long non-coding RNA (lncRNA) in bladder cancer.MethodsWe extracted the ERS-related genes from the published research and bladder cancer data from the Cancer Genome Atlas database. ERS-related lncRNAs with prognostic significance were screened by univariate Cox regression, least absolute shrinkage and selection operator regression analysis and Kaplan-Meier method. Multivariate Cox analysis was leveraged to establish the risk score model. Moreover, an independent dataset, GSE31684, was used to validate the model’s efficacy. The nomogram was constructed based on the risk score and clinical variables. Furthermore, the biological functions, gene mutations, and immune landscape were investigated to uncover the underlying mechanisms of the ERS-related signature. Finally, we employed external datasets (GSE55433 and GSE89006) and qRT-PCR to investigate the expression profile of these lncRNAs in bladder cancer tissues and cells.ResultsSix ERS-related lncRNAs were identified to be closely coupled with patients’ prognosis. On this foundation, a risk score model was created to generate the risk score for each patient. The ERS-related risk score was shown to be an independent prognostic factor. And the results of GSE31684 dataset also supported this conclusion. Then, a nomogram was constructed based on risk scores and clinical characteristics, and proven to have excellent predictive value. Moreover, the gene function analysis demonstrated that ERS-related lncRNAs were closely linked to fatty extracellular matrix, cytokines, cell adhesion, and tumor pathways. Further analysis revealed the association of the 6-lncRNAs signature with gene mutations and immunity in bladder cancer. Finally, the external datasets and qRT-PCR verified high expressions of the ERS-related lncRNAs in bladder cancer tissues and cells.ConclusionsOverall, our findings indicated that ERS-related lncRNAs, which may affect tumor pathogenesis in a number of ways, might be exploited to assess the prognosis of bladder cancer patients.

show abstract

Section: Introductionmentioning

confidence: 99%

Comprehensive analysis of the endoplasmic reticulum stress-related long non-coding RNA in bladder cancer

Wang

Yan

et al. 2022

Front. Oncol.

View full text Add to dashboard Cite

show abstract

“…m6A modifications have been reported to play a crucial role in diverse biological processes. The development of various tumors is accompanied by m6A methylation modifications, including in colorectal cancer, 17 bladder cancer, 18 and prostate cancer 19 . Moreover, m6A modifications has been found in many CNS diseases 15 .…”

Section: Introductionmentioning

confidence: 99%

Comprehensive analysis of m6A methylation modification in chronic spinal cord injury in mice

Liu

Zhao

Qin

et al. 2022

Journal Orthopaedic Research

View full text Add to dashboard Cite

Chronic spinal cord injury (CSCI) is a catastrophic disease of the central nervous system (CNS), resulting in partial or complete loss of neurological function. N6-methyladenosine (m6A) is the most common form of reversible posttranslational modi cation at the RNA level. However, the role of m6A modi cation in CSCI remains unknown. In this study, we established a CSCI model using a water-absorbable polyurethane polymer, with behavioral assessment, electrophysiological analysis, and histochemical staining for validation. Methylated RNA immunoprecipitation sequencing (meRIP-seq) and mRNA sequencing (mRNA-seq) were jointly explored to compare the differences in CSCI spinal tissue and normal spinal tissue. Furthermore, qRT-PCR, western blotting, and immuno uorescence staining were used to analyze m6A modi cation-related proteins. We found that water-absorbable polyurethane polymer well simulated chronic spinal cord compression. BMS scores and electrophysiological analysis showed continuous neurological function decline after chronic compression of the spinal cord. meRIP-seq identi ed 642 differentially modi ed m6A genes, among which 263 genes were downregulated and 379 genes were upregulated. mRNA-seq showed that 1544 genes were upregulated and 290 genes were downregulated after CSCI. Gene Ontology (GO) terms and enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were also identi ed. qRT-PCR, western blotting, and immuno uorescence staining showed that Mettl14 was signi cantly upregulated after CSCI. Our study revealed a comprehensive pro le of m6A modi cations in CSCI and may provide a valuable tool for further research on CSCI. study showed that mettl14 was signi cantly overexpressed after CSCI and mainly expressed in neurons, which was further validated by qRT-PCR, western blotting, and immuno uorescence.Our study is not without limitations. First, we obtained whole spinal tissue for meRIP-seq and mRNA-seq. Although the total m6A modi cations were assessed, it was di cult to distinguish m6A methylation changes in speci c cell types. In further in-depth research, extracting speci c cells for veri cation of m6A modi cation and exploring its function would be meaningful. Second, we performed preliminary analyses of differentially expressed genes and enriched GO and KEGG pathways, but their roles in CSCI require further validation through extensive experiments.Collectively, our study analyzed m6A methylation modi cations in spinal cord tissue after CSCI. The results indicated that m6A plays an important role in the process of CSCI. Our research may provide new insights for further study of the CSCI pathological process and potential treatment options. DeclarationsAuthor contributions JH, YC and HL designed the study. CL and JZ carried out most of the experiments and data analysis. YJ, TQ, CD and TW assisted in experiments and data analysis. CL drafted the manuscript, and JH and YC revised the manuscript.

show abstract

Identification of key genes and lncRNAs based on M6A methylation regulators and Ferroptosis related genes for the slow flow/no reflow phenomenon

Zhang

Zhao

Shi

et al. 2023

Preprint

View full text Add to dashboard Cite

Differentially expressed lncRNAs (DELncs) between treat (STEMI-A and STEMI-B groups) and control group and between STEMI-A (used as control group) and STEMI-B group were obtained by differential analysis. 29 common DELncs were obtained using Venn diagram by intersecting the two DELncs sets. Subsequently, four key lncRNAs based on the treat and control group (ABC-KLncs) with the highest correlation degree (|cor| > 0.8 and p < 0.05) with MMRs and FRGs were obtained, including FAM230B, lnc-EVI2A-3, lnc-PZP-6, and lnc-PLGLB2-5. Through differential analysis and correlation analysis, and 544 DEGs between the treat and control groups with |cor| > 0.3 were identified, and a PPI network was further constructed. MCODE algrithm and Cytohubba algrithm were applied and sifted out four key genes based on the treat and control group (ABC-KGs), consisting of ATP2B3, SUMO2, PPIA, and DNM1. Differential analysis, correlation analysis, PPI network, MCODE algrithm, and Cytohubba algrithm were also performed on the STEMI-A and STEMI-B groups. Moreover, four 4 key lncRNAs based on STEMI-A and STEMI-B groups (AB-KLncs) consisting of LINC00907, lnc-ZNF583-4, RP11-566J3.4, and lnc-USP28-6, and three key genes based the STEMI-A and STEMI-B groups (AB-KGs) consisting of TXN, ASPM, and MYLK were filtered out. In conclusion, this study obtained four ABC-KLncs, four ABC-KGs, four AB-KLncs, and three AB-KGs, these can inform the diagnosis and further study of STEMI as well as the phenomenon of slow flow/no reflow.

show abstract

Comprehensive Analysis of N6-Methylandenosine-Related Long Non-Coding RNAs Signature in Prognosis and Tumor Microenvironment of Bladder Cancer

Cited by 5 publications

References 54 publications

Comprehensive analysis of the endoplasmic reticulum stress-related long non-coding RNA in bladder cancer

Comprehensive analysis of the endoplasmic reticulum stress-related long non-coding RNA in bladder cancer

Comprehensive analysis of m6A methylation modification in chronic spinal cord injury in mice

Identification of key genes and lncRNAs based on M6A methylation regulators and Ferroptosis related genes for the slow flow/no reflow phenomenon

Contact Info

Product

Resources

About