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| Status |
Public on Aug 10, 2023 |
| Title |
GPX8 deficiency-induced oxidative stress reprogrammed m6A epitranscriptome of oral cancer cells |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
Glutathione peroxidase 8 (GPX8) is a key regulator of redox homeostasis. Whether its antioxidant activity participates in the regulation of m6A modification is a crucial issue, which has important application value in cancer treatment. MeRIP-seq was used to explore the characteristics of transcriptome-wide m6A modification in GPX8-deficient oral cancer cells in this study. Oxidative stress caused by lack of GPX8 resulted in 1,279 hyper- and 2,287 hypo-methylated m6A peaks and 2,036 differentially expressed genes in GPX8-KO cells. Twenty-eight differentially expressed genes were related to the cell response to oxidative stress, and half of them changed their m6A modification. In GPX8-KO cells, m6A regulators IGF2BP2 and IGF2BP3 were upregulated, while FTO, RBM15, VIRMA, ZC3H13 and YTHDC2 were downregulated. After H2O2 treatment, the expression changes of RBM15, IGF2BP2 and IGF2BP3 were further enhanced. These data indicated that GPX8-mediated redox homeostasis regulated m6A modification, thereby affecting the expression and function of downstream genes. This study highlights the possible significance of GPX8 and the corresponding m6A regulatory or regulated genes as novel targets for antioxidant intervention in cancer therapy
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| Overall design |
Transcriptome-wide methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) were performed as previously described. Briefly, total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). PolyA RNA was purified using DynabeadsOligo (dT)25-61005 (Thermo Fisher, CA, USA) and cleavedinto about 100nt fragments using Magnesium RNA Fragmentation Module (NEB, USA). One portion of the RNA fragments was used as input and the other portion wasimmunoprecipitated with m6A-specific antibody (Synaptic Systems, Germany) to enrich m6A-methylated RNA fragments. RNA sequence library was prepared and purified, and the paired-end sequencing (PE150) of libraries was performed on Illumina NovaSeq™ 6000 platform (LC-Bio Technology CO., Ltd., Hangzhou, China), following the manufacturer’s protocol.
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| Contributor(s) |
Chen X, Yuan L, Zhang L, Chen L |
| Citation(s) |
37170591 |
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| Submission date |
Feb 07, 2023 |
| Last update date |
Aug 11, 2023 |
| Contact name |
xun chen |
| E-mail(s) |
chenx598@mail2.sysu.edu.cn
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| Phone |
18924007421
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| Organization name |
Sun yat-sen University
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| Street address |
Linyuanxi Road 55
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| City |
guangzhou |
| State/province |
guangdong |
| ZIP/Postal code |
510055 |
| Country |
China |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA932268 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE224718_RAW.tar |
238.7 Mb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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