Long noncoding RNA SNHG15: A promising target in human cancers DOI Creative Commons

Niu Zhang,

Tianyao Lei,

Tianwei Xu

et al.

Frontiers in Oncology, Journal Year: 2023, Volume and Issue: 13

Published: March 28, 2023

As oncogenes or tumor suppressor genes, lncRNAs played an important role in tumorigenesis and the progression of human cancers. The lncRNA SNHG15 has recently been revealed to be dysregulated malignant tumors, suggesting aberrant expression which contributes clinical features regulates various oncogenic processes. We have selected extensive literature focused on from electronic databases, including studies relevant its significance critical events cancer-related processes such as cell proliferation, apoptosis, autophagy, metastasis, drug resistance. This review summarized current understanding cancer, mainly focusing pathological features, known biological functions, underlying molecular mechanisms. Furthermore, well-documented effective diagnostic prognostic marker for offering novel therapeutic interventions specific subsets cancer cells.

Language: Английский

Identification of RNA Methylation-Related lncRNAs Signature for Predicting Hot and Cold Tumors and Prognosis in Colon Cancer DOI Creative Commons
Rong He, Changfeng Man, Jiabin Huang

et al.

Frontiers in Genetics, Journal Year: 2022, Volume and Issue: 13

Published: April 6, 2022

N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), and 7-methylguanosine (m7G) are the major forms of RNA methylation modifications, which closely associated with development many tumors. However, prognostic value methylation-related long non-coding RNAs (lncRNAs) in colon cancer (CC) has not been defined. This study summarised 50 m6A/m1A/m5C/m7G-related genes downloaded 41 normal 471 CC tumor samples RNA-seq data clinicopathological information from The Cancer Genome Atlas (TCGA) database. A total 1057 lncRNAs (RMlncRNAs) were identified Pearson correlation analysis. Twenty-three RMlncRNAs values screened using univariate Cox regression By consensus clustering analysis, patients classified into two molecular subtypes (Cluster 1 Cluster 2) different clinical outcomes immune microenvironmental infiltration characteristics. 2 was considered to be "hot tumor" a better prognosis, while cluster regarded as "cold poorer prognosis. Subsequently, we constructed seven-lncRNA signature least absolute shrinkage selection operator (LASSO) regression. In combination other traits, found that lncRNA (called "RMlnc-score") an independent factor for cancer. addition, infiltration, immunotherapy response half-maximum inhibitory concentration (IC50) showed low RMlnc-score group more sensitive immunotherapy, high chemotherapeutic agents. summary, developed could used predict response, drug sensitivity patients, guiding accurate, personalized treatment regimens.

Language: Английский

Citations

20
N1-methyladenosine formation, gene regulation, biological functions, and clinical relevance DOI Creative Commons
Weidong Xiong, Yongchao Zhao, Zilun Wei

et al.

Molecular Therapy, Journal Year: 2022, Volume and Issue: 31(2), P. 308 - 330

Published: Oct. 29, 2022

N1-methyladenosine (m1A) is an adenosine moiety whose N1-position methylated. m1A methylation a prevalent, abundant, and conserved internal post-transcriptional modification among prokaryotic eukaryotic RNAs, especially in higher cells. Numerous studies have revealed that plays critical role the biogenesis of various thereby regulating different biological functions pathogenesis. In this review, we systematically comprehensively summarize installation, removal, recognition highlight effects on metabolism RNAs. We emphasize importance both growth organisms pathogenesis diseases, particularly cancers. Finally, also focused fact excretion human urine strongly associated with progression variety suggest levels can be quantified for early diagnosis some diseases as well monitoring during disease evolution.

Language: Английский

Citations

19
RNA modifications in long non-coding RNAs and their implications in cancer biology DOI
Jiexin Li, Xiansong Wang, Hongsheng Wang

et al.

Bioorganic & Medicinal Chemistry, Journal Year: 2024, Volume and Issue: 113, P. 117922 - 117922

Published: Sept. 13, 2024

Language: Английский

Citations

4
Subtype cluster analysis unveiled the correlation between m6A- and cuproptosis-related lncRNAs and the prognosis, immune microenvironment, and treatment sensitivity of esophageal cancer DOI Creative Commons
Mingxing Zhang, Yani Su, Pengfei Wen

et al.

Frontiers in Immunology, Journal Year: 2025, Volume and Issue: 16

Published: Feb. 17, 2025

Objective Esophageal cancer (EC) is characterized by a high degree of malignancy and poor prognosis. N6-methyladenosine (m6A), prominent post-transcriptional modification mRNA in mammalian cells, plays pivotal role regulating various cellular biological processes. Similarly, cuproptosis has garnered attention for its potential implications biology. This study seeks to elucidate the impact m6A- cuproptosis-related long non-coding RNAs (m6aCRLncs) on prognosis patients with EC. Methods The EC transcriptional data corresponding clinical information were retrieved from Cancer Genome Atlas (TCGA) database, comprising 11 normal samples 159 samples. Data 23 m6A regulators 25 genes sourced latest literature. m6aCRLncs linked identified through co-expression analysis. Differentially expressed associated screened using limma package R univariate Cox regression Subtype clustering was performed classify patients, enabling investigation differences outcomes immune microenvironment across patient clusters. A risk prognostic model constructed least absolute shrinkage selection operator (LASSO) regression. Its robustness evaluated survival analysis, stratification curves, receiver operating characteristic (ROC) curves. Additionally, model’s applicability features molecular subtypes assessed. To further explore utility predicting microenvironment, single-sample gene set enrichment analysis (ssGSEA), cell infiltration checkpoint differential expression conducted. Drug sensitivity identify therapeutic agents Finally, levels lines validated reverse transcription quantitative polymerase chain reaction (RT-qPCR). Results We developed based five m6aCRLncs, namely ELF3-AS1, HNF1A-AS1, LINC00942, LINC01389, MIR181A2HG, predict characterize patients. Analysis revealed significant cluster distribution, disease stage, N stage between high- low-risk groups. Immune profiling distinct populations functional pathways scores, including positive correlations naive B resting CD4+ T plasma negative macrophages M0 M1. we key checkpoint-related groups, TNFRSF14, TNFSF15, TNFRSF18, LGALS9, CD44, HHLA2, CD40. Furthermore, nine candidate drugs efficacy identified: Bleomycin, Cisplatin, Cyclopamine, PLX4720, Erlotinib, Gefitinib, RO.3306, XMD8.85, WH.4.023. RT-qPCR validation demonstrated that ELF3-AS1 significantly upregulated KYSE-30 KYSE-180 compared esophageal epithelial cells. Conclusion elucidates shaping it identifies against These findings hold promise enhancing provide valuable insights inform decision-making management this disease.

Language: Английский

Citations

0
Analysis of human brain RNA-seq data reveals combined effects of 4 types of RNA modifications and 18 types of programmed cell death on Alzheimer’s disease DOI Creative Commons
Ke Ye, Xinyu Han, Maoyi Tian

et al.

Journal of Translational Medicine, Journal Year: 2025, Volume and Issue: 23(1)

Published: April 3, 2025

Language: Английский

Citations

0
Integrative analysis of m6A-SNPs and single-cell RNA sequencing reveals key drivers of endocrine combined with CDK4/6 inhibitor therapy resistance in ER+ breast cancer DOI Creative Commons

Ruijie Ming,

Han Zhang, Huan Wu

et al.

Frontiers in Pharmacology, Journal Year: 2025, Volume and Issue: 16

Published: April 15, 2025

Background Endocrine therapy combined with CDK4/6 inhibitors remains a standard treatment for ER+ breast cancer, yet resistance is prevalent challenge. This study explores the role of N6-methyladenosine (m6A) modifications, influenced by m6A-SNPs, in shaping resistance, utilizing single-cell RNA sequencing to delineate underlying molecular mechanisms. Methods We integrated genome-wide association data transcriptomic profiles from cancer patients, focusing on differences between resistant and sensitive responses inhibitors. m6A-SNPs were identified analyzed their impact gene expression interactions RNA-binding proteins, particular focus roles within key cellular pathways. Results The crucial associated resistance. Notably, changes FILIP1L TOM1L1, related these SNPs, mapped using pseudotime trajectory analysis, which traced evolution states. TOM1L1 exhibited dynamic along trajectory, correlating significant shifts cell fate decisions. These findings underscore potential as mediators development particularly through involvement PI3K-Akt Wnt signaling pathways, critical progression drug Conclusion Our emphasize importance influencing cancer. regulation developmental tumor cells sensitivity provides insights into complexity results pave way developing targeted therapies that modify m6A-driven offering new strategies counteract improve patient outcomes.

Language: Английский

Citations

0
Transcriptome-wide 1-methyladenosine functional profiling of messenger RNA and long non-coding RNA in bladder cancer DOI Creative Commons

Jianjian Yin,

Song Yan-liang,

Yufeng Guo

et al.

Frontiers in Genetics, Journal Year: 2024, Volume and Issue: 15

Published: Feb. 28, 2024

Introduction: Post-transcriptional RNA modifications are crucial regulators of tumor development and progression. In many biological processes, N 1 -methyladenosine (m A) plays a key role. However, little is known about the links between chemical messenger RNAs (mRNAs) long noncoding (lncRNAs) their function in bladder cancer (BLCA). Methods: Methylated immunoprecipitation sequencing were performed to profile mRNA lncRNA m A methylation expression BLCA cells, with or without stable knockdown methyltransferase tRNA 61A (TRMT61A). Results: The analysis differentially methylated gene sites identified 16,941 peaks, 6,698 mRNAs, 10,243 lncRNAs two groups. Gene ontology enrichment Kyoto Encyclopedia Genes Genomes pathway analyses expressed transcripts showed that A-regulated mainly related protein binding signaling pathways cancer. addition, genes also A-modified 14 mRNAs 19 lncRNAs. Next, these used construct lncRNA-microRNA-mRNA competing endogenous network, which included 118 miRNAs, 15 lncRNAs, 8 mRNAs. Finally, transcripts, SCN2B ENST00000536140, highly tissues, associated decreased overall patient survival. Discussion: This study revealed substantially different amounts distributions after TRMT61A predicted cellular functions may be involved, providing evidence implicates epitranscriptomic regulation tumorigenesis

Language: Английский

Citations

3
Role of N6‐methyladenosine RNA modification in cancer DOI Creative Commons
Yi Qu, Nannan Gao, Shengwei Zhang

et al.

MedComm, Journal Year: 2024, Volume and Issue: 5(9)

Published: Sept. 1, 2024

Abstract N6‐methyladenosine (m6A) is the most abundant modification of RNA in eukaryotic cells. Previous studies have shown that m6A pivotal diverse diseases especially cancer. corelates with initiation, progression, resistance, invasion, and metastasis However, despite these insights, a comprehensive understanding its specific roles mechanisms within complex landscape cancer still elusive. This review begins by outlining key regulatory proteins their posttranslational modifications (PTMs), as well role chromatin accessibility transcriptional activity Additionally, it highlights impact progression modulating programmed cell death affecting tumor microenvironment through various cancer‐associated immune Furthermore, discusses how microorganisms can induce enduring epigenetic changes oncogenic effect microorganism‐associated cancers altering modifications. Last, delves into immunotherapy, encompassing therapy, checkpoint blockade, cytokine adoptive transfer direct targeting regulators. Overall, this clarifies multifaceted explores targeted therapies aimed at manipulating modification, aiming to advance research improve patient outcomes.

Language: Английский

Citations

3
Integrated Analysis of N1-Methyladenosine Methylation Regulators-Related lncRNAs in Hepatocellular Carcinoma DOI Open Access

Danjun Song,

Xi Wang, Yining Wang

et al.

Cancers, Journal Year: 2023, Volume and Issue: 15(6), P. 1800 - 1800

Published: March 16, 2023

N1-methyladenosine (m1A) and long non-coding RNAs (lncRNAs) play significant roles in tumor progression hepatocellular carcinoma (HCC). However, their association with HCC is still unclear. In this study, lncRNAs related to m1A were extracted from the mRNA expression matrix The Cancer Genome Atlas (TCGA) database. Five m1A-related (AL031985.3, NRAV, WAC-AS1, AC026412.3, AC099850.4) identified based on lasso Cox regression they generated a prognostic signature of HCC. was as an independent prognosis factor patients. Moreover, achieved better performance than TP53 mutation status or mutational burden (TMB) scores stratification patient survival. immune landscape indicated that most checkpoint genes cells distributed differently between both risk groups. A higher IC50 chemotherapeutics (sorafenib, nilotinib, sunitinib, gefitinib) observed high-risk group, lower gemcitabine low-risk suggesting potential chemosensitivity. addition, fifty-five small molecular drugs found drug sensitivity NRAV expression. Together, five could be promising prediction approach therapeutic response assessment tool for

Language: Английский

Citations

7
Identification of a novel m5C/m6A-related gene signature for predicting prognosis and immunotherapy efficacy in lung adenocarcinoma DOI Creative Commons
Yiming Ma, Jun Yang,

Tiantai Ji

et al.

Frontiers in Genetics, Journal Year: 2022, Volume and Issue: 13

Published: Sept. 30, 2022

Lung adenocarcinoma (LUAD) is the most prevalent subtype of non-small cell lung cancer (NSCLC) and associated with high mortality rates. However, effective methods to guide clinical therapeutic strategies for LUAD are still lacking. The goals this study were analyze relationship between an m5C/m6A-related signature construct a novel model evaluating prognosis predicting drug resistance immunotherapy efficacy. We obtained data from patients Cancer Genome Atlas (TCGA) Gene Expression Omnibus (GEO) datasets. Based on differentially expressed genes, we identified distinct modification subtypes in by unsupervised clustering compared differences functions pathways different clusters. In addition, risk was constructed using multivariate Cox regression analysis based prognostic genes predict response. showed landscape 36 m5C/m6A regulators TCGA-LUAD samples 29 normal groups. Two genes. Compared cluster 2, 1 had lower regulator expression, higher OS (overall survival), immune activity, abundance infiltrating cells. Four gene signatures consisting HNRNPA2B1, IGF2BP2, NSUN4, ALYREF used model, high-risk group worse prognosis, checkpoint tumor mutational burden (TMB). treated immunotherapy, scores expression better immunotherapeutic efficacy than those low-risk scores. concluded that regulator-related could serve as biomarker sensitivity chemotherapy immunotherapy.

Language: Английский

Citations

12