Overview of distinct 8-Oxoguanine profiles of messenger RNA in normal and senescent cancer cells
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ABSTRACT:
PROVIDER: PRJNA1200754 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31782573_1.fastq.gz | Fastqsanger.gz | |||
| SRR31782573_2.fastq.gz | Fastqsanger.gz | |||
| SRR31782574_1.fastq.gz | Fastqsanger.gz | |||
| SRR31782574_2.fastq.gz | Fastqsanger.gz | |||
| SRR31782575_1.fastq.gz | Fastqsanger.gz |
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Project description:Background: Cellular senescence plays a key role in the development of cancer, but the underlying mechanisms are unknown.Recently, several recent studies have shown that RNA methylation is closely related to cancer cell aging. 8-Oxoguanine (o8G) is an important and widely distributed methylation modification whose role in cancer cell senescence is far from elucidated. Methods: In this study, senescent cancer cell models (CaCO2 cells) were constructed by knocking down the ADAR1 gene. RNA immunoprecipitation sequencing was used to identify the o 8 G peaks on messenger RNA (mRNA) of normal CaCO2 cells and senescent CaCO2 cells, and the distribution characteristics of mRNA o 8 G modification were identified. Further bioinformatics analysis of the sequencing data was performed to preliminarily elucidate the potential function of the o8G-modified mRNA. Results: There were significant differences in mRNA o 8 G modification distribution between normal and senescent CaCO2 cells.It is suggested that o8G modification may play a key role in inducing cancer cells or promoting cancer cell senescence. Gene ontology (GO) enrichment analysis showed that the genes modified by o 8 G were enriched in Cellular component organization or biogenesis, Focal adhesion,and RNA binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the genes modified by o8G areconcentrated in Focal adhesion signaling pathway, Small cell lung cancer signaling pathway and Proteoglycans in cancer signaling pathway. Conclusion: This study preliminarily revealed the different distribution patterns of o8G modification between normal CaCO2 cells and senescent CaCO2 cells. Our study established the link between o 8 G modification and cancer cell senescence, which provides a new insight into the mechanism of cancer cell senescence and a potential therapeutic target for subsequent cancer treatment.
2024-12-21 | GSE284992 | GEO
Project description:BackgroundCellular senescence plays a key role in the development of cancer, but the underlying mechanisms are unknown. Recently, several recent studies have shown that RNA methylation is closely related to cancer cell aging. 8-Oxoguanine (o8G) is an important and widely distributed methylation modification whose role in cancer cell senescence is far from elucidated.MethodsIn this study, senescent cancer cell models (CaCO2 cells) were constructed by knocking down the ADAR1 gene. RNA immunoprecipitation sequencing was used to identify the o8G peaks on messenger RNA (mRNA) of normal CaCO2 cells and senescent CaCO2 cells, and the distribution characteristics of mRNA o8G modification were identified. Further bioinformatics analysis of the sequencing data was performed to preliminarily elucidate the potential function of the o8G-modified mRNA.ResultsThere were significant differences in mRNA o8G modification distribution between normal and senescent CaCO2 cells. It is suggested that o8G modification may play a key role in inducing cancer cells or promoting cancer cell senescence. Gene ontology (GO) enrichment analysis showed that the mRNAs modified by o8G were enriched in Cellular component organization or biogenesis, Focal adhesion, and RNA binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the genes modified by o8G are concentrated in Focal adhesion signaling pathway, Small cell lung cancer signaling pathway and Proteoglycans in cancer signaling pathway.ConclusionThis study preliminarily revealed the different distribution patterns of o8G modification between normal CaCO2 cells and senescent CaCO2 cells. Our study established the link between o8G modification and cancer cell senescence, which provides a new insight into the mechanism of cancer cell senescence and a potential therapeutic target for subsequent cancer treatment.
| S-EPMC11906479 | biostudies-literature
Project description:Overview of distinct 5-methylcytosine profiles of messenger RNA in normal and knock-down NSUN2 colorectal cancer cells
| PRJNA938787 | ENA
Project description:8-oxoguanine is excised from DNA by 8-oxoguanine DNA glycosylase-1 during DNA base excision repair. We used microarrays to gain insight into the potential biological function of the excised, free 8-oxoguanine base. MRC5, human diploid fibroblasts were exposed to 8-oxoguanine and changes in gene expression compared to mock control were analyzed 6 hours after exposure. MRC5, human diploid fibroblasts were exposed to 8-oxoguanine and changes in gene expression compared to mock control were analyzed 12 hours after exposure.
2011-01-27 | E-GEOD-26813 | biostudies-arrayexpress
Project description:Background: Colorectal cancer (CRC) is a harmful cancer with high morbidity and poor prognosis. There is growing evidence that RNA methylation is closely related to the occurrence of cancer and its malignant biological behavior. N6-methyladenosine (m6A) methylation is the most common RNA modification in eukaryotes, and its multiple regulatory mechanisms in CRC have been elucidated from multiple perspectives. At the same time, the role of 5-methylcytosine (m5C), another important and widely distributed methylation modification, in CRC is far from being elucidated. Methods: In this study, we used RNA immunoprecipitation sequencing combined with bioinformatics methods to identify the m5C peaks on messenger RNA (mRNA) in HCT15 cells and sh-NSUN2 HCT15 cells, understand which transcripts are modified by m5C, and characterize the distribution of m5C modifications. In addition, we performed further bioinformatics analysis of the detected data to initially clarify the potential function of these m5C-modified transcripts. Results: We found significant differences in the distribution of m5C between HCT15 cells and sh-NSUN2 HCT15 cells, suggesting that m5C is likely to play a key role in the occurrence and development of CRC. Furthermore, Gene Ontology (GO) enrichment analysis showed that genes altered by m5C were mainly enriched in phylogeny, synaptic membrane, and transcription factor binding.The Kyoto Encyclopedia of Genes and Genomes（KEGG）pathway analysis showed that the genes altered by m5C are enriched in ECM receptor interaction pathway, the circadian pathway, and the cAMP signaling pathway. Conclusions: Here, our study preliminarily revealed the different distribution patterns of m5C between HCT15 cell and sh-NSUN2 HCT15 cell. Our results open a new window to understand the role of m5C RNA methylation of mRNA in the development of CRC.
2023-03-02 | GSE226129 | GEO
Project description:8-oxoguanine is excised from DNA by 8-oxoguanine DNA glycosylase-1 during DNA base excision repair. We used microarrays to gain insight into the potential biological function of the excised, free 8-oxoguanine base.
2011-01-27 | GSE26813 | GEO
Project description:Purpose: Use RNA-seq strategy to characterize the PD-L1 correlated genes in sorted PD-L1 negative and positive doxorubicin-induced senescent and normal human foreskin fibroblasts HCA2 cells to identify the upstream transcriptional network for regulating heterogeneous PD-L1 expression in senescent cells. Methods: Early passaged normal HCA2 cells and senescent HCA2 cells induced by 24 hours of 100 nM doxorubicin treatment were utilized for the preparation of bulk RNA-seq libraries. Among the senescent cells, PD-L1 positive and negative cells were separated by FACSorting.
2022-08-27 | GSE198396 | GEO
Project description:Background: Colorectal cancer (CRC) is a harmful cancer with high morbidity and poor prognosis. There is growing evidence that RNA methylation is closely related to the occurrence of cancer and its malignant biological behavior. N6-methyladenosine (m6A) methylation is the most common RNA modification in eukaryotes, and its multiple regulatory mechanisms in CRC have been elucidated from multiple perspectives. At the same time, the role of 5-methylcytosine (m5C), another important and widely distributed methylation modification, in CRC is far from being elucidated. Methods: In this study, we used RNA immunoprecipitation sequencing combined with bioinformatics methods to identify the m5C peaks on messenger RNA (mRNA) in HCT15 cells and sh-NSUN2 HCT15 cells, understand which transcripts are modified by m5C, and characterize the distribution of m5C modifications. In addition, we performed further bioinformatics analysis of the detected data to initially clarify the potential function of these m5C-modified transcripts. Results: We found significant differences in the distribution of m5C between HCT15 cells and sh-NSUN2 HCT15 cells, suggesting that m5C is likely to play a key role in the occurrence and development of CRC. Furthermore, Gene Ontology (GO) enrichment analysis showed that genes altered by m5C were mainly enriched in phylogeny, synaptic membrane, and transcription factor binding. The Kyoto Encyclopedia of Genes and Genomes (KEGG)pathway analysis showed that the genes altered by m5C are enriched in ECM receptor interaction pathway, the circadian pathway, and the cAMP signaling pathway. Conclusion: Here, our study preliminarily revealed the different distribution patterns of m5C between HCT15 cell and sh-NSUN2 HCT15 cell. Our results open a new window to understand the role of m5C RNA methylation of mRNA in the development of CRC.
| S-EPMC10166136 | biostudies-literature
Project description:Although N6-methyladenosine (m6A) modification is closely associated with the pathogenesis of osteoarthritis (OA), the mRNA profile of m6A modification in OA remains unknown. Therefore, our study aimed to identify common m6A features and novel m6A-related therapeutic targets in OA. In the present study, we identified 3962 differentially methylated genes (DMGs) and 2048 differentially expressed genes (DEGs) using methylated RNA immunoprecipitation next-generation sequencing (MeRIP-seq) and RNA-sequencing. A co-expression analysis of DMGs and DEGs showed that the expression of 805 genes was significantly affected by m6A methylation. Specifically, we obtained 28 hypermethylated and upregulated genes, 657 hypermethylated and downregulated genes, 102 hypomethylated and upregulated genes, and 18 hypomethylated and downregulated genes. The differential gene expression analysis based on GSE114007 revealed 2770 DEGs. The Weighted Gene Co-expression Network Analysis (WGCNA) based on GSE114007 identified 134 OA-related genes. By taking the intersection of these results, ten novel aberrantly expressed, m6A-modified and OA-related key genes were identified, including SKP2, SULF1, TNC, ZFP36, CEBPB, BHLHE41, SOX9, VEGFA, MKNK2 and TUBB4B. The present study may provide valuable insight into identifying m6A-related pharmacological targets in OA.
| S-EPMC10203613 | biostudies-literature
Project description:N6-methyladenosine (m6A) is the most prevalent modification of eukaryotic cells st post-transcriptional level. The goals of this study are to compare the N6-methyladenosine modification of transcripts in normal and senescent nucleus pulposus cells using Me-RIP-seq
2022-03-23 | GSE169484 | GEO