UVB drives different stages of epigenome alterations during progression of skin cancer [Bisulfite-seq]
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PROVIDER: PRJNA504025 | ENA |
REPOSITORIES: ENA
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Project description:Exposure to UVB irradiation results in multitude of cellular responses including generation of reactive oxygen species (ROS) and DNA damage and is responsible for non-melanoma skin cancers (NMSCs). Although genetic mutation is well documented, the epi-mutation, the alteration in epigenetics, remains elusive. DNA methylation is a stable and heritable epigenetic change in the control of gene expression. Furthermore, it is unclear how the epigenomic DNA methylome would change during progression of UVB-induced carcinogenesis. In this study, we utilized CpG Methyl-seq to identify a genome-wide DNA CpG methylation, to profile the DNA methylation in ultraviolet B (UVB)-irradiated SKH-1 mouse skin epidermis and non-melanoma skin papillomas at various stages. Agilent mouse SureSelect Methyl-seq Kit was used for enrichment of about 3.3 million CpG sites in the mouse genome. Simultaneously, RNA-seq was performed to examine the corresponding transcriptome alterations. Bioinformatic analysis was utilized to identify differentially methylated and differentially expressed genes. The methylation profiles in mouse epidermis were altered by UVB-irradiation as time progresses. Comparing all epidermis samples at week-15 versus week-25, UVB had great impact on DNA methylome alteration. Examination of the differentially methylated regions (DMRs), most of the DMRs were located in the distal intragenic (>3 kb upstream of TSS or downstream of 3’ UTR) and the promoter regions. Interestingly, at week-25 the methylation profiles between the whole skin versus the tumor samples were different. Ingenuity Pathways Analysis (IPA) identified many cancer related pathways including PTEN, p53, Nrf2 and inflammatory signaling in UVB-irradiation induced carcinogenesis. Cell cycle regulation and cell growth related pathways including State3 signaling and estrogen-mediated S-phase entry were also identified. Additionally, some novel genes involved in skin carcinogenesis that were not previously reported were differentially methylated, including Enf2, Mgst2, Vegfa, and Cdk4. The methylation and expression of these genes were validated by pyrosequencing and qPCR. Taken together, the current study provides novel profiles of methylation and transcriptomic changes at different stages of carcinogenesis in UVB-irradiation induced NMSC and offer potential targets for prevention and treatment of NMSC at different stages of human skin cancer.
2019-03-20 | GSE122226 | GEO
Project description:Exposure to UVB irradiation results in multitude of cellular responses including generation of reactive oxygen species (ROS) and DNA damage and is responsible for non-melanoma skin cancers (NMSCs). Although genetic mutation is well documented, the epi-mutation, the alteration in epigenetics, remains elusive. DNA methylation is a stable and heritable epigenetic change in the control of gene expression. Furthermore, it is unclear how the epigenomic DNA methylome would change during progression of UVB-induced carcinogenesis. In this study, we utilized CpG Methyl-seq to identify a genome-wide DNA CpG methylation, to profile the DNA methylation in ultraviolet B (UVB)-irradiated SKH-1 mouse skin epidermis and non-melanoma skin papillomas at various stages. Agilent mouse SureSelect Methyl-seq Kit was used for enrichment of about 3.3 million CpG sites in the mouse genome. Simultaneously, RNA-seq was performed to examine the corresponding transcriptome alterations. Bioinformatic analysis was utilized to identify differentially methylated and differentially expressed genes. The methylation profiles in mouse epidermis were altered by UVB-irradiation as time progresses. Comparing all epidermis samples at week-15 versus week-25, UVB had great impact on DNA methylome alteration. Examination of the differentially methylated regions (DMRs), most of the DMRs were located in the distal intragenic (>3 kb upstream of TSS or downstream of 3’ UTR) and the promoter regions. Interestingly, at week-25 the methylation profiles between the whole skin versus the tumor samples were different. Ingenuity Pathways Analysis (IPA) identified many cancer related pathways including PTEN, p53, Nrf2 and inflammatory signaling in UVB-irradiation induced carcinogenesis. Cell cycle regulation and cell growth related pathways including State3 signaling and estrogen-mediated S-phase entry were also identified. Additionally, some novel genes involved in skin carcinogenesis that were not previously reported were differentially methylated, including Enf2, Mgst2, Vegfa, and Cdk4. The methylation and expression of these genes were validated by pyrosequencing and qPCR. Taken together, the current study provides novel profiles of methylation and transcriptomic changes at different stages of carcinogenesis in UVB-irradiation induced NMSC and offer potential targets for prevention and treatment of NMSC at different stages of human skin cancer.
2019-03-20 | GSE122225 | GEO
Project description: Not available
| S-EPMC6411449 | biostudies-literature
Project description:UVB drives different stages of epigenome alterations during progression of skin cancer
| PRJNA504022 | ENA
Project description:UVB drives different stages of epigenome alterations during progression of skin cancer [RNA-Seq]
| PRJNA504024 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2019-03-20 | GSE122227 | GEO
Project description:Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput bisulfite sequencing Whole genome shotgun bisulfite sequencing of wildtype Arabidopsis plants (Columbia-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer.
2008-04-21 | E-GEOD-10966 | biostudies-arrayexpress
Project description:Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput bisulfite sequencing
2008-04-21 | GSE10966 | GEO
Project description:In this study, GC-specific DNA methylation profiling was investigated in nine fresh frozen tissues which included non-tumor, intestinal metaplasia, and gastric tumor using whole genome bisulfite sequencing to deeply understanding epigenome change during gastric carcinogenesis
2023-01-04 | GSE166154 | GEO
Project description:Unprotected exposure to UVB radiation from the sun and the resulting DNA damage are thought to be responsible for physiological changes in the skin and for a variety of skin cancers, including basal cell and squamous cell carcinoma and malignant melanoma. Although the mutagenic effects of UVB have been well documented and studied mechanistically, there is only limited information as to whether UV light may also be responsible for inducing epigenetic changes in the genome of exposed cells. DNA methylation is a stable epigenetic modification involved in gene control. To study the effects of UVB radiation on DNA methylation, we repeatedly exposed normal human keratinocytes to a UVB light source. After a recovery period, we analyzed global DNA methylation patterns in the irradiated and control cells using the methylated-CpG island recovery assay (MIRA) method in combination with high-resolution microarrays. Bioinformatics analysis revealed only a limited number of possible differences between UVB-exposed and control cells. However, these minor apparent changes could not be independently confirmed by bisulfite sequencing-based approaches. This study reveals that UVB irradiation of keratinocytes has no recognizable global effect on DNA methylation patterns and suggests that changes in DNA methylation, as observed in skin cancers, are not immediate consequences of human exposure to solar UVB irradiation. DNA methylation analysis of control and UVB irradiated keratinocytes. The MIRA assay was used for enrichment of methylated DNA. NimbleGen CpG island plus promoter arrats were used.
2013-01-30 | E-GEOD-42943 | biostudies-arrayexpress