Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA methylation analysis of cloned HCT116 cells treated with a DNA demethylating drug.

ABSTRACT: Epigenetic reprogramming using demethylating drugs is a promising approach for cancer therapy, but its efficacy is highly dependent on the dosing regimen. Low-dose treatment for a prolonged period shows a high therapeutic efficacy, despite its small demethylating effect. Here, we aimed to reveal the mechanisms of how such low-dose treatment shows high efficacy by focusing on epigenetic reprograming at the single-cell level. Single-cell RNA-sequencing of HCT116 cells treated with decitabine (DAC) revealed that up-regulated genes were highly variable at the single-cell level. To analyze functional consequences at the single-cell level, DAC-treated HCT116 cells were cloned. While only partial reduction of methylation levels was observed in bulk cells, complete demethylation of specific cancer-related genes was observed, depending upon clones. For example, p16 was completely demethylated in the H3-32 clone out of 9 clones, and this clone showed slower proliferation than other clones without demethylation. In addition, in this clone, the fraction of cells with tetraploid became much larger, indicating that cellular senescence was induced. These results showed that epigenetic reprogramming of specific cancer-related pathways at the single-cell level is likely to underlie the high efficacy of low-dose DNA demethylating therapy.

ORGANISM(S): Homo sapiens

PROVIDER: GSE149255 | GEO | 2020/10/02

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

scRNA-seq of DAC-treated and mock-treated HCT116.

Project description:Epigenetic reprogramming using demethylating drugs is a promising approach for cancer therapy, but its efficacy is highly dependent on the dosing regimen. Low-dose treatment for a prolonged period shows a high therapeutic efficacy, despite its small demethylating effect. Here, we aimed to reveal the mechanisms of how such low-dose treatment shows high efficacy by focusing on epigenetic reprograming at the single-cell level. Single-cell RNA-sequencing of HCT116 cells treated with decitabine (DAC) revealed that up-regulated genes were highly variable at the single-cell level. To analyze functional consequences at the single-cell level, DAC-treated HCT116 cells were cloned. While only partial reduction of methylation levels was observed in bulk cells, complete demethylation of specific cancer-related genes was observed, depending upon clones. For example, p16 was completely demethylated in the H3-32 clone out of 9 clones, and this clone showed slower proliferation than other clones without demethylation. In addition, in this clone, the fraction of cells with tetraploid became much larger, indicating that cellular senescence was induced. These results showed that epigenetic reprogramming of specific cancer-related pathways at the single-cell level is likely to underlie the high efficacy of low-dose DNA demethylating therapy.

2021-04-10 | GSE171429 | GEO

The impact of decitabine treatment in MDS-induced Tet2KD/KDEzh2Δ/Δ LSK HSPCs

Project description:To evaluate the impact of DNA demethylating agents on our mouse MDS model, we chose 5-aza-2’-deoxycytidine, decitabine (DAC), one of the DNA demethylating agents, which is incorporated into DNA but not RNA and has 10-fold more potency in DNA demethylation than 5-azacitidine. We transplanted Tet2KD/KDEzh2Δ/Δ MDS cells into lethally irradiated secondary recipients and treated them with DAC (low dose DAC at 0.25mg/kg, 3 times a week, intraperitoneal injection), then purified LSK HSPCs and evaluated the expression profiles.

2017-03-15 | GSE79204 | GEO

Generic drug screen identifies paracetamol as 5-aza-2’-deoxycytidine sensitizer in head and neck squamous cell carcinoma cells

Project description:Aberrant DNA methylation (5mC) is one of the key characteristics of many cancers including head and neck squamous cell carcinoma (HNSCC). The DNA demethylating agent 5-aza-2’-deoxycytidine (DAC) has anti-cancer therapeutic potential, but its clinical efficacy is currently hindered by dose-limiting side effects. Here we investigated the potential use of DAC in the treatment of HNSCC and show that its efficacy is primarily dependent on the ability of DAC to demethylate DNA. In order to establish whether HNSCC cells can be sensitized to DAC, a panel of 100 generic drugs were screened in combination with DAC. While the 100-drug panel did not sensitise DAC-resistant HNSCC cell lines to DAC treatment, the screen identified that paracetamol (acetaminophen), valproic acid and zinc acetate significantly enhanced DAC efficacy in the DAC-responsive cell lines. DAC and paracetamol were established to work in synergy, allowing DAC to be used at therapeutically relevant low doses (below 500nM). The mechanisms underlying the DAC-paracetamol synergy are multifactorial and encompass both effects of DAC on paracetamol action (alterations in the cyclooxygenase (COX) pathway and mimicry of paracetamol overdose) as well as decreased DNA methylation by paracetamol. Therefore, we propose DAC to be a potential therapeutic in a subset of HNSCC patients with its efficacy significantly increased by use of the common analgesic paracetamol. The DAC-paracetamol synergy should also be considered in cancers with an approved DAC treatment regime.

2018-11-02 | GSE110045 | GEO

Genome-wide DNA demethylation of HML58-3 (a derivative cell line of HCT116) after treatment of DAC, OR-2003, and OR-2100

Project description:A derivative cell line of HCT116, HML58-3, was established to detect DNA demethylating agents [Okochi-Takada E, Epigenetics. 2018;13:147-55.]. HML58-3 cells were treated with DNA demethylating agents (DAC, OR-2003, and OR-2100). Genome-wide DNA methylation was analyzed using the Infinium Human MethylationEPIC BeadChip.

2019-08-01 | GSE134293 | GEO

Optimal Anti-EGFR Treatment of mCRC Patients With Low-Frequency RAS Mutation

Project description:The present hypothesis is that anti-EGFR agents are active in tumors with low-level RAS mutation when the majority of tumor cells is still sensitive. While response rate may be high and may reflect sensitivity to anti-EGFR agents, PFS is anticipated to be shorter than in RAS wild-type patients due to the faster development of resistance when sensitive cells are eradicated and when the RAS-mutant anti-EGFR resistant clones become predominant. The characteristics of low-level RAS mutant tumors would be: * Objective response rate (ORR) high (reflecting the sensitive clone) * Progression-free survival (PFS) short (reflecting the more rapid outgrowth of RAS mutant clones)

| 2312021 | ecrin-mdr-crc

Genes regulated by miR-34b/c and DAC

Project description:We found frequent epigenetic silencing of microRNA-34b/c in human colorectal cancer. Introduction of miR-34b/c into a colorectal cancer cell line induced significant changes in gene expression profile. We also found overlap between the genes downregulated by miR-34b/c and those downregulated by DAC. Keywords: dose response A colorecal cancer cell line HCT116 was transfected with miR-34b or -c precursor or negative control. Also, HCT116 was treated with 5-aza-2'-deoxycytidine (DAC) or mock. Genes up- or downregulated by miR-34b/c and those by DAC was compared.

2008-04-30 | E-GEOD-10455 | biostudies-arrayexpress

Low-dose DNA demethylating therapy induces reprogramming of diverse cancer-related pathways at the single-cell level

Project description:Low-dose DNA demethylating therapy induces reprogramming of diverse cancer-related pathways at the single-cell level

| PRJNA720322 | ENA

Single-cell derived clones from human adipose stem cells present different immunomodulatory properties.

Project description:Human adipose mesenchymal stem cells are a heterogeneous population, where cell cultures derived from single cell-expanded clones present varying degrees of differential plasticity. This work focuses on the immunomodulatory/anti-inflammatory properties of these cells. To this end, 5 single cell clones were isolated (1.X and 3.X) from 2 volunteers. Regarding the expression level of the lineage-characteristic surface antigens, clones 1.10 and 1.22 expressed the lowest amounts, while clones 3.10 and 3.5 expressed more CD105 than the rest and clone 1.7 expressed higher amounts of CD73 and CD44. Regarding cytokine secretion, all clones were capable of spontaneously releasing high levels of IL-6 and low to moderate levels of IL-8. Furthermore, clone 3.X produced the highest amounts of pro-inflammatory cytokines such as IL-1β, while clones 1.10 and 1.22 highly expressed IL-4 and IL-5. These differences can be explained in part by the distinct DNA promoter methylation profile exhibited by the clones. The results of this work indicates that this stem cell population is heterogeneous in its secretion profile, and that isolation, characterization and selection of the appropriate cell clone is a more exact method for the possible treatment of different patients or pathologies.

2014-03-03 | GSE44222 | GEO

Somatic epimutations enable native single-cell clonal tracking on hematopoietic cell state landscapes across the murine and human lifespan

Project description:Current approaches to track stem cell clones through differentiation require genetic engineering or rely on sparse somatic DNA variants. Here, we show that targeted single-cell measurements of DNA methylation at single-CpG resolution deliver joint information about cellular differentiation state and clonal identities. We develop EPI-clone, a method for transgene-free lineage tracing based on microfluidic, targeted single-cell DNA methylation analysis. Applied to mouse and human hematopoiesis, we captured hundreds of clonal differentiation trajectories across tens of individuals and almost 400,000 single-cells. Using ground-truth genetic barcodes, we demonstrate that EPI-clone accurately identifies clonal lineages throughout hematopoietic differentiation while at the same time providing cell state resolution similar to transcriptomic data. Applied to unperturbed hematopoiesis in murine ageing, we demonstrate that myeloid bias and low output of old HSCs are restricted to a small number of expanded developmental clones, while many functionally young-like clones persist in old age. In human ageing, we demonstrate that clones carrying CHIP mutations are part of a spectrum of age-related expansions of low-output clones. EPI-clone is compatible with the multiplexed readout of surface protein, somatic variants and RNA from the same single cell. Taken together, EPI-clone enables accurate and transgene-free single-cell lineage tracing on hematopoietic cell state landscapes at scale.

2024-12-31 | GSE282971 | GEO

Comparison of endogenous gene expression of HCT116 colorectal cancer cells and HCT116-derived DAPK1 knockout (ko) clones.

Project description:Data were obtained via Nanostring nCounter Gene Expression Assay (PanCancer Progression Panel, XT_PGX_HuV1_CancerProg_CSO XT-CSO-PROG1-12, Cat. no. 115000152, Nanostring Technologies, Hamburg, Germany) We aimed to reveal Death-associated protein kinase 1 (DAPK1)-dependent gene expression in the context of tumor progression covering genes involved in extracellular matrix, epithelial-mesenchymal transition, metastasis and angiogenesis comparing HCT116 DAPK1 wt cells and three different monoclonal DAPK1 ko clones named clone 7/6, clone 10/8 and clone 21/9. DAPK1 ko clones were generated by CRISPR/Cas9-mediated genomic editing.

2019-05-01 | GSE130488 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data