SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [KG1a DAC scTEM-seq]
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PROVIDER: PRJNA718185 | ENA |
REPOSITORIES: ENA
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Project description:Global changes in DNA methylation are observed in several developmental and disease contexts, and single-cell analyses are beginning to reveal the heterogeneous regulation of these processes. However, these studies are limited by the poor alignment rates and high sequencing demands associated with single-cell analysis of DNA methylation. We present single-cell transposable element methylation sequencing (scTEM-seq) for cost-effective estimation of global DNA methylation levels. By targeting high-copy LINE-1 and SINE Alu elements, we achieve amplicon bisulphite sequencing with thousands of annotated loci covered in each scTEM-seq library. Parallel transcriptome analysis of the same single cell is also performed to link global DNA methylation heterogeneity with transcriptional consequences. We apply scTEM-seq to KG1a acute myeloid leukaemia (AML) cells, and primary cells from an AML patient. Treatment of KG1a cells with the hypomethylating agent, decitabine, induces global DNA methylation heterogeneity associated with altered expression of viral response pathways. We also compare global levels of DNA methylation to expression of transposable elements and find a predominance of negative correlations in both the KG1a and patient cells. Finally, we observe co-ordinated upregulation of many transposable elements in a sub-set of decitabine treated KG1a cells. These observations suggest that viral mimicry processes important for epigenetic therapy and tumour immunogenicity are variably active in AML cells. By linking global DNA methylation heterogeneity with transcriptional consequences, scTEM-seq will refine our understanding of epigenetic regulation in cancer and beyond.
2022-04-13 | GSE171025 | GEO
Project description:Global changes in DNA methylation are observed in several developmental and disease contexts, and single-cell analyses are beginning to reveal the heterogeneous regulation of these processes. However, these studies are limited by the poor alignment rates and high sequencing demands associated with single-cell analysis of DNA methylation. We present single-cell transposable element methylation sequencing (scTEM-seq) for cost-effective estimation of global DNA methylation levels. By targeting high-copy LINE-1 and SINE Alu elements, we achieve amplicon bisulphite sequencing with thousands of annotated loci covered in each scTEM-seq library. Parallel transcriptome analysis of the same single cell is also performed to link global DNA methylation heterogeneity with transcriptional consequences. We apply scTEM-seq to KG1a acute myeloid leukaemia (AML) cells, and primary cells from an AML patient. Treatment of KG1a cells with the hypomethylating agent, decitabine, induces global DNA methylation heterogeneity associated with altered expression of viral response pathways. We also compare global levels of DNA methylation to expression of transposable elements and find a predominance of negative correlations in both the KG1a and patient cells. Finally, we observe co-ordinated upregulation of many transposable elements in a sub-set of decitabine treated KG1a cells. These observations suggest that viral mimicry processes important for epigenetic therapy and tumour immunogenicity are variably active in AML cells. By linking global DNA methylation heterogeneity with transcriptional consequences, scTEM-seq will refine our understanding of epigenetic regulation in cancer and beyond.
2022-04-13 | GSE171028 | GEO
Project description:Global changes in DNA methylation are observed in several developmental and disease contexts, and single-cell analyses are beginning to reveal the heterogeneous regulation of these processes. However, these studies are limited by the poor alignment rates and high sequencing demands associated with single-cell analysis of DNA methylation. We present single-cell transposable element methylation sequencing (scTEM-seq) for cost-effective estimation of global DNA methylation levels. By targeting high-copy LINE-1 and SINE Alu elements, we achieve amplicon bisulphite sequencing with thousands of annotated loci covered in each scTEM-seq library. Parallel transcriptome analysis of the same single cell is also performed to link global DNA methylation heterogeneity with transcriptional consequences. We apply scTEM-seq to KG1a acute myeloid leukaemia (AML) cells, and primary cells from an AML patient. Treatment of KG1a cells with the hypomethylating agent, decitabine, induces global DNA methylation heterogeneity associated with altered expression of viral response pathways. We also compare global levels of DNA methylation to expression of transposable elements and find a predominance of negative correlations in both the KG1a and patient cells. Finally, we observe co-ordinated upregulation of many transposable elements in a sub-set of decitabine treated KG1a cells. These observations suggest that viral mimicry processes important for epigenetic therapy and tumour immunogenicity are variably active in AML cells. By linking global DNA methylation heterogeneity with transcriptional consequences, scTEM-seq will refine our understanding of epigenetic regulation in cancer and beyond.
2022-04-13 | GSE171027 | GEO
Project description:Global changes in DNA methylation are observed in several developmental and disease contexts, and single-cell analyses are beginning to reveal the heterogeneous regulation of these processes. However, these studies are limited by the poor alignment rates and high sequencing demands associated with single-cell analysis of DNA methylation. We present single-cell transposable element methylation sequencing (scTEM-seq) for cost-effective estimation of global DNA methylation levels. By targeting high-copy LINE-1 and SINE Alu elements, we achieve amplicon bisulphite sequencing with thousands of annotated loci covered in each scTEM-seq library. Parallel transcriptome analysis of the same single cell is also performed to link global DNA methylation heterogeneity with transcriptional consequences. We apply scTEM-seq to KG1a acute myeloid leukaemia (AML) cells, and primary cells from an AML patient. Treatment of KG1a cells with the hypomethylating agent, decitabine, induces global DNA methylation heterogeneity associated with altered expression of viral response pathways. We also compare global levels of DNA methylation to expression of transposable elements and find a predominance of negative correlations in both the KG1a and patient cells. Finally, we observe co-ordinated upregulation of many transposable elements in a sub-set of decitabine treated KG1a cells. These observations suggest that viral mimicry processes important for epigenetic therapy and tumour immunogenicity are variably active in AML cells. By linking global DNA methylation heterogeneity with transcriptional consequences, scTEM-seq will refine our understanding of epigenetic regulation in cancer and beyond.
2022-04-13 | GSE171026 | GEO
Project description:SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells
| PRJNA718180 | ENA
Project description:SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [PBAT]
| PRJNA718186 | ENA
Project description:SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [RNA-seq]
| PRJNA718187 | ENA
Project description:SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [AML01 scTEM-seq]
| PRJNA718184 | ENA
Project description:Reversal of gene promoter DNA hypermethylation and associated abnormal gene silencing is an attractive approach to cancer therapy. The DNA methylation inhibitor, decitabine (5-aza-2'-deoxycitidine), is proving efficacious for hematological neoplasms especially at lower, less toxic, doses. Experimentally, high doses induce rapid DNA damage and cytotoxicity, but these may not explain the prolonged time to response seen in patients. Transient exposure of leukemic and solid tumor cells to clinically-relevant nanomolar doses, without causing immediate cytotoxicity or apoptosis, produces sustained reduced tumorigenicity, and for leukemia cells, diminished long-term self-renewal. These effects appear triggered by cellular reprogramming and include sustained decreases in promoter DNA methylation with associated gene re-expression, and anti-tumor changes in multiple key cellular regulatory pathways, most of which are high priority targets for pharmacologic anti-cancer strategies. Thus, low dose decitabine regimens appear to have broad applicability for cancer management. [Gene expression profiling] Leukemia cell lines Kasumi-1 and KG1A are treated with 10nM DAC during 72 hours and gene expression was assayed at day 3, 7 and 14 after the start of the treatment. Appropriate mock treated samples were used as control in each case. In addition, Kasumi-1 cells were also treated with a higher dose of DAC (500nM), 100nM ARA-C and 300 nM TSA, again controlled against mock treated Kasumi-1 cells, to separate dose and agent dependent effects. MCF7 was studied as an example of a solid tumor cell line. Therefore MCF7 cells were treated with 100nM DAC and results were assayed at day 1, day 3 and day 10. [Methylation profiling] The effects of the demethylating agent DAC were studied in the leukemia cell line Kasumi-1 over a 28 day time course. Intermediate time points were studied at days 3, 7, 14 and 21. These results were verfied in KG1A and KG1 leukemia cell lines, at one selected time point. The effects on one primary sample were also studied. Four normal leukemia samples (PL1, 2, 4 and 5) were used as general controls. The effect of DAC was compared to ARA-C, TSA. Both mock treated and day 3 DAC treated Kasumi-1 cells were repeated. These results were verified at one selected time point for the DAC treated MCF7 breast cancer cell line.
2012-03-21 | E-GEOD-20945 | biostudies-arrayexpress
Project description:Primary outcome(s): The detection rates of epigenetic heterogeneity in primary tumor and plasma from colorectal cancer patients with Methylation-sensitive high resolution melt(MS-HRM).
| 2636460 | ecrin-mdr-crc