DNA Methylation, Stem Cells and Cancer

Background: Cancer stem cells (CSCs) are considered the main cause of cancer recurrence and metastasis, and DNA methylation is involved in the maintenance of CSCs. However, the methylation profile of esophageal CSCs remains unknown. Methods: Side population (SP) cells were isolated from esophageal squamous cell carcinoma (ESCC) cell lines KYSE150 and EC109. Sphere-forming cells were collected from human primary esophageal cancer cells. SP cells and sphere-forming cells were used as substitutes for cancer stem-like cells. We investigated the genome-wide DNA methylation profile in esophageal cancer stem-like cells using reduced representation bisulfite sequencing (RRBS). Results: Methylated cytosine (mC) was found mostly in CpG dinucleotides, located mostly in the intronic, intergenic, and exonic regions. Forty intersected differentially methylated regions (DMRs) were identified in these 3 groups of samples. Thirteen differentially methylated genes with the same alteration trend were detected; these included OTX1, SPACA1, CD163L1, ST8SIA2, TECR, CADM3, GRM1, LRRK1, CHSY1, PROKR2, LINC00658, LOC100506688, and NKD2. DMRs covering ST8SIA2 and GRM1 were located in exons. These differentially methylated genes were involved in 10 categories of biological processes and 3 cell signaling pathways. Conclusions: When compared to non-CSCs, cancer stem-like cells have a differential methylation status, which provides an important biological base for understanding esophageal CSCs and developing therapeutic targets for esophageal cancer.

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Overexpression of CDKN2B (p15INK4B) and altered global DNA methylation status in mesenchymal stem cells of high-risk myelodysplastic syndromes

Leukemia ◽

10.1038/leu.2014.197 ◽

2014 ◽

Vol 28 (11) ◽

pp. 2241-2244 ◽

Cited By ~ 8

Author(s):

A Poloni ◽

G Maurizi ◽

D Mattiucci ◽

S Amatori ◽

B Fogliardi ◽

...

Keyword(s):

Dna Methylation ◽

Stem Cells ◽

Mesenchymal Stem Cells ◽

High Risk ◽

Myelodysplastic Syndromes ◽

Methylation Status ◽

Global Dna Methylation

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DNA methylation on N6-adenine in mammalian embryonic stem cells

Nature ◽

10.1038/nature17640 ◽

2016 ◽

Vol 532 (7599) ◽

pp. 329-333 ◽

Cited By ~ 291

Author(s):

Tao P. Wu ◽

Tao Wang ◽

Matthew G. Seetin ◽

Yongquan Lai ◽

Shijia Zhu ◽

...

Keyword(s):

Dna Methylation ◽

Stem Cells ◽

Embryonic Stem Cells ◽

Embryonic Stem

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Accumulation of DNA methylation alterations in paediatric glioma stem cells following fractionated dose irradiation

Clinical Epigenetics ◽

10.1186/s13148-020-0817-8 ◽

2020 ◽

Vol 12 (1) ◽

Cited By ~ 2

Author(s):

Anna Danielsson ◽

Kristell Barreau ◽

Teresia Kling ◽

Magnus Tisell ◽

Helena Carén

Keyword(s):

Dna Methylation ◽

Stem Cells ◽

Cellular Response ◽

Glioma Stem Cells ◽

Proliferation And Differentiation ◽

Radiation Resistant ◽

Radiation Induced ◽

Induced Changes ◽

Regulatory Functions

Abstract Background Radiation is an important therapeutic tool. However, radiotherapy has the potential to promote co-evolution of genetic and epigenetic changes that can drive tumour heterogeneity, formation of radioresistant cells and tumour relapse. There is a clinical need for a better understanding of DNA methylation alterations that may follow radiotherapy to be able to prevent the development of radiation-resistant cells. Methods We examined radiation-induced changes in DNA methylation profiles of paediatric glioma stem cells (GSCs) in vitro. Five GSC cultures were irradiated in vitro with repeated doses of 2 or 4 Gy. Radiation was given in 3 or 15 fractions. DNA methylation profiling using Illumina DNA methylation arrays was performed at 14 days post-radiation. The cellular characteristics were studied in parallel. Results Few fractions of radiation did not result in significant accumulation of DNA methylation alterations. However, extended dose fractionations changed DNA methylation profiles and induced thousands of differentially methylated positions, specifically in enhancer regions, sites involved in alternative splicing and in repetitive regions. Radiation induced dose-dependent morphological and proliferative alterations of the cells as a consequence of the radiation exposure. Conclusions DNA methylation alterations of sites with regulatory functions in proliferation and differentiation were identified, which may reflect cellular response to radiation stress through epigenetic reprogramming and differentiation cues.

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DAXX safeguards pericentromeric heterochromatin formation in embryonic stem cells

10.1101/2021.04.28.441827 ◽

2021 ◽

Author(s):

Antoine Canat ◽

Adeline Veillet ◽

Robert Illingworth ◽

Emmanuelle Fabre ◽

Pierre Therizols

Keyword(s):

Dna Methylation ◽

Stem Cells ◽

Dna Damage ◽

Embryonic Stem Cells ◽

Embryonic Stem ◽

Pericentric Heterochromatin ◽

Dna Demethylation ◽

Pericentromeric Heterochromatin ◽

Major Satellite ◽

Heterochromatin Formation

AbstractDNA methylation is essential for heterochromatin formation and repression of DNA repeat transcription, both of which are essential for genome integrity. Loss of DNA methylation is associated with disease, including cancer, but is also required for development. Alternative pathways to maintain heterochromatin are thus needed to limit DNA damage accumulation. Here, we find that DAXX, an H3.3 chaperone, protects pericentromeric heterochromatin and is essential for embryonic stem cells (ESCs) maintenance in the ground-state of pluripotency. Upon DNA demethylation-mediated damage, DAXX relocalizes to pericentromeric regions, and recruits PML and SETDB1, thereby promoting heterochromatin formation. In the absence of DAXX, the 3D-architecture and physical properties of pericentric heterochromatin are disrupted, resulting in derepression of major satellite DNA. Using epigenome editing tools, we demonstrate that H3.3, and specifically H3.3K9 modification, directly contribute to maintaining pericentromeric chromatin conformation. Altogether, our data reveal that DAXX and H3.3 unite DNA damage response and heterochromatin maintenance in ESCs.

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Haploinsufficiency of Dnmt1 Impairs Leukemia Stem Cell Function Through Derepression of Bivalent Chromatin Domains,

Blood ◽

10.1182/blood.v118.21.3459.3459 ◽

2011 ◽

Vol 118 (21) ◽

pp. 3459-3459

Author(s):

Jennifer J. Trowbridge ◽

Amit U. Sinha ◽

Scott A. Armstrong ◽

Stuart H. Orkin

Keyword(s):

Dna Methylation ◽

Stem Cells ◽

Dna Methyltransferase ◽

Cell Function ◽

Gene Signature ◽

Conditional Knockout ◽

Specific Gene ◽

Epigenetic Mechanisms ◽

Chromatin Domains ◽

Hematopoietic Stem

Abstract Abstract 3459 Leukemia stem cells (LSCs) are an attractive target in treatment of many types of blood cancers. There remains an incomplete understanding of the epigenetic mechanisms driving LSC formation and maintenance, and how this compares to the epigenetic regulation of normal hematopoietic stem cells (HSCs). One of the major epigenetic modifications, DNA methylation, is catalyzed by the DNA methyltransferase enzymes Dnmt1, Dnmt3a and Dnmt3b. We observed decreased expression of Dnmt3a and Dnmt3b in LSCs isolated from a model of MLL-AF9-induced acute myeloid leukemia (AML) compared to normal HSCs. In contrast, expression of Dnmt1 was maintained in LSCs compared to HSCs, suggesting that Dnmt1 may have a critical function in the formation and maintenance of LSCs. Supporting this hypothesis, we found that conditional knockout of Dnmt1 fully ablates the development of AML. Furthermore, haploinsufficiency of Dnmt1 (Dnmt1fl/+ Mx-Cre) was sufficient to delay progression of leukemogenesis and impair LSC self-renewal. Strikingly, haploinsufficiency of Dnmt1 did not functionally alter normal hematopoiesis or HSCs, suggesting an enhanced dependence of LSCs on DNA methylation. Mechanistically, we observed that haploinsufficiency of Dnmt1 in LSCs resulted in derepression of genes that had been silenced by MLL-AF9-mediated transformation and marked by bivalent H3K27me3/H3K4me3 chromatin domains. These results suggest that the formation and maintenance of LSCs depends not only upon activation of a leukemogenic program, but also upon silencing of a specific gene signature that is active in HSCs through crosstalk between two epigenetic mechanisms, polycomb-mediated repression and DNA methylation-mediated repression. This silenced gene signature includes known and candidate tumor suppressor genes as well as genes involved in lineage restriction. These studies present evidence that distinct epigenetic regulatory mechanisms are dominant in LSCs compared to HSCs and provide novel gene candidates for targeted reactivation in AML therapy. Disclosures: Armstrong: Epizyme: Consultancy.

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