Conserved cell-lineage controlled epigenetic regulation in human and mouse glioblastoma stem cells determines functionally distinct subgroups

AbstractThere is ample support for developmental regulation of glioblastoma stem cells (GSCs). To examine how cell lineage controls GSC function we have performed a cross-species epigenome analysis of mouse and human GSC cultures. We have analyzed and compared the chromatin-accessibility landscape of nine mouse GSC cultures of defined cell of origin and 60 patient-derived GSC cultures by assay for transposase-accessible chromatin using sequencing (ATAC-seq). This uncovered a variability of both mouse and human GSC cultures that was different from transcriptome analysis and better at predicting functional subgroups. In both species the chromatin accessibility-guided clusters were predominantly determined by distal regulatory element (DRE) regions, displayed contrasting sets of transcription factor binding motifs, and exhibited different functional and drug-response properties. Cross-species analysis of DRE regions in accessible chromatin revealed conserved epigenetic regulation of mouse and human GSCs. Human ATAC-seq data produced three distinct clusters with significant overlap to our previous mouse cell of origin- based stratification, where two of the clusters displayed significantly different patient survival. We conclude that epigenetic regulation of GSCs primarily is dictated by developmental origin which controls key GSC properties and affects therapeutic response.

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ECOA-7. Conserved cell-lineage controlled chromatin accessibility in human and mouse glioblastoma stem cells predicts functionally distinct subgroups

Neuro-Oncology Advances ◽

10.1093/noajnl/vdab070.007 ◽

2021 ◽

Vol 3 (Supplement_2) ◽

pp. ii2-ii2

Author(s):

Xi Lu ◽

Naga Prathyusha Maturi ◽

Malin Jarvius ◽

Linxuan Zhao ◽

Yuan Xie ◽

...

Keyword(s):

Stem Cells ◽

Epigenetic Regulation ◽

Regulatory Element ◽

Cell Lineage ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Cell Of Origin ◽

Glioblastoma Stem Cells ◽

Transcription Factor Motif ◽

Accessible Chromatin

Abstract There is ample support for developmental control of glioblastoma stem cells (GSCs), and a deeper knowledge of their epigenetic regulation could be central to more efficient glioblastoma (GBM) therapies. For this purpose, we analyzed the chromatin-accessibility landscape of nine mouse GSC cultures of defined cell of origin and 60 patient-derived GSC cultures by assay for transposase-accessible chromatin using sequencing (ATAC-seq). This uncovered an epigenetic variability of both mouse and human GSC cultures that differed from transcriptome clusters. Both mouse and human chromatin accessibility-guided clusters were predominantly determined by distal regulatory elements, displayed unique sets of transcription factor motif enrichment, and exhibited different functional and drug-response properties. Cross-species analysis of distal regulatory element regions in accessible chromatin of mouse and human cultures revealed conserved epigenetic regulation of GSCs.

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Analysis of accessible chromatin landscape in the inner cell mass and trophectoderm of human blastocysts

MHR Basic science of reproductive medicine ◽

10.1093/molehr/gaaa048 ◽

2020 ◽

Vol 26 (9) ◽

pp. 702-711

Author(s):

Min Yang ◽

Xin Tao ◽

Shiny Titus ◽

Tianhua Zhao ◽

Richard T Scott ◽

...

Keyword(s):

Epigenetic Regulation ◽

Inner Cell Mass ◽

Cell Mass ◽

Cell Lineage ◽

Distal Region ◽

Chromatin Accessibility ◽

Early Embryo ◽

Preimplantation Embryos ◽

Accessible Chromatin ◽

Human Preimplantation Embryos

Abstract Early embryonic development is characterized by drastic changes in chromatin structure that affects the accessibility of the chromatin. In human, the chromosome reorganization and its involvement in the first linage segregation are poorly characterized due to the difficulties in obtaining human embryonic material and limitation on low input technologies. In this study, we aimed to explore the chromatin remodeling pattern in human preimplantation embryos and gain insight into the epigenetic regulation of inner cell mass (ICM) and trophectoderm (TE) differentiation. We optimized ATAC-seq (an assay for transposase-accessible chromatin using sequencing) to analyze the chromatin accessibility landscape for low DNA input. Sixteen preimplantation human blastocysts frozen on Day 6 were used. Our data showed that ATAC peak distributions of the promoter regions (<1 kb) and distal regions versus other regions were significantly different between ICM versus TE samples (P < 0.01). We detected that a higher percentage of accessible binding loci were located within 1 kb of the transcription start site in ICM compared to TE (P < 0.01). However, a higher percentage of accessible regions was detected in the distal region of TE compared to ICM (P < 0.01). In addition, eight differential peaks with a false discovery rate <0.05 between ICM and TE were detected. This is the first study to compare the landscape of the accessible chromatin between ICM and TE of human preimplantation embryos, which unveiled chromatin-level epigenetic regulation of cell lineage specification in early embryo development.

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Isolation of Lineage Specific Nuclei Based on Distinct Endoreduplication Levels and Tissue-Specific Markers to Study Chromatin Accessibility Landscapes

Plants ◽

10.3390/plants9111478 ◽

2020 ◽

Vol 9 (11) ◽

pp. 1478

Author(s):

Ezgi Süheyla Karaaslan ◽

Natalie Faiß ◽

Chang Liu ◽

Kenneth Wayne Berendzen

Keyword(s):

High Efficiency ◽

Cell Lineage ◽

Light Response ◽

Chromatin Accessibility ◽

Tissue Layer ◽

Great Precision ◽

Ploidy Levels ◽

Epidermal Tissue ◽

Transcriptional Changes ◽

Accessible Chromatin

The capacity for achieving immense specificity and resolution in science increases day to day. Fluorescence-activated nuclear sorting (FANS) offers this great precision, enabling one to count and separate distinct types of nuclei from specific cells of heterogeneous mixtures. We developed a workflow to collect nuclei from Arabidopsis thaliana by FANS according to cell lineage and endopolyploidy level with high efficiency. We sorted GFP-labeled nuclei with different ploidy levels from the epidermal tissue layer of three-day, dark-grown hypocotyls followed by a shift to light for one day and compared them to plants left in the dark. We then accessed early chromatin accessibility patterns associated with skotomorphogenesis and photomorphogenesis by the assay for transposase-accessible chromatin using sequencing (ATAC-seq) within primarily stomatal 2C and fully endoreduplicated 16C nuclei. Our quantitative analysis shows that dark- and light-treated samples in 2C nuclei do not exhibit any different chromatin accessibility landscapes, whereas changes in 16C can be linked to transcriptional changes involved in light response.

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Exploiting the Complexities of Glioblastoma Stem Cells: Insights for Cancer Initiation and Therapeutic Targeting

International Journal of Molecular Sciences ◽

10.3390/ijms21155278 ◽

2020 ◽

Vol 21 (15) ◽

pp. 5278

Author(s):

Joana Vieira de Castro ◽

Céline S. Gonçalves ◽

Adília Hormigo ◽

Bruno M. Costa

Keyword(s):

Stem Cells ◽

Research Field ◽

Tumor Type ◽

Cell Of Origin ◽

Glioblastoma Stem Cells ◽

Open Questions ◽

Cancer Initiation ◽

Heterogeneous Nature ◽

New Strategies

The discovery of glioblastoma stem cells (GSCs) in the 2000s revolutionized the cancer research field, raising new questions regarding the putative cell(s) of origin of this tumor type, and partly explaining the highly heterogeneous nature of glioblastoma (GBM). Increasing evidence has suggested that GSCs play critical roles in tumor initiation, progression, and resistance to conventional therapies. The remarkable oncogenic features of GSCs have generated significant interest in better defining and characterizing these cells and determining novel pathways driving GBM that could constitute attractive key therapeutic targets. While exciting breakthroughs have been achieved in the field, the characterization of GSCs is a challenge and the cell of origin of GBM remains controversial. For example, the use of several cell-surface molecular markers to identify and isolate GSCs has been a challenge. It is now widely accepted that none of these markers is, per se, sufficiently robust to distinguish GSCs from normal stem cells. Finding new strategies that are able to more efficiently and specifically target these niches could also prove invaluable against this devastating and therapy-insensitive tumor. In this review paper, we summarize the most relevant findings and discuss emerging concepts and open questions in the field of GSCs, some of which are, to some extent, pertinent to other cancer stem cells.

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Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation

10.1101/2020.01.29.924878 ◽

2020 ◽

Author(s):

Matt J. Barter ◽

Kathleen Cheung ◽

Julia Falk ◽

Andreas C. Panagiotopoulos ◽

Caitlin Cosimini ◽

...

Keyword(s):

Gene Expression ◽

High Throughput Sequencing ◽

Regulatory Element ◽

Interleukin 1 ◽

Chromatin Modification ◽

Chromatin Accessibility ◽

Open Chromatin ◽

Enhancer Activity ◽

Cytokine Stimulation ◽

Accessible Chromatin

AbstractGenome-wide methods for examining chromatin modification provide detailed information on regulatory regions of the genome. Dynamic modifications of chromatin allow rapid access of the gene regulatory machinery to condensed genomic regions facilitating subsequent gene expression. Inflammatory cytokine stimulation of cells can cause rapid gene expression changes through direct signalling pathway-mediated transcription factor activation and regulatory element binding.Here we used the Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) to assess regions of the genome that are differentially accessible following treatment of cells with interleukin-1 (IL-1). We identified 126,483 open chromatin regions, with 241 regions significantly differentially accessible following stimulation, with 64 and 177 more or less accessible, respectively. These differentially accessible regions predominantly correspond to regions of the genome marked as enhancers. Motif searching identified an overrepresentation of a number of transcription factors, most notably RelA in the regions becoming more accessible, with analysis of ChIP-seq data confirmed RelA binding to these regions. A significant correlation in differential chromatin accessibility and gene expression was also observed.Functionality in regulating gene expression was confirmed using CRISPR/Cas9 genome-editing to delete regions for that became more accessible following stimulation in the genes MMP13, IKBKE and C1QTNF1. These same regions were also accessible for activation using a dCas9-transcriptional activator and showed enhancer activity in a cellular model.Together, these data describe and functionally validate a number of dynamically accessible chromatin regions involved in inflammatory signalling.

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