Long-term culture of alveolospheres
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PROVIDER: PRJNA573090 | ENA |
REPOSITORIES: ENA
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Project description:Organoids retain the morphological and molecular patterns of their tissue of origin, are self-organizing, relatively simple to handle and accessible to genetic engineering. Thus, they represent an optimal tool for studying mechanisms of tissue maintenance and aging. Long-term expansion under standard growth conditions, however, is accompanied by changes in growth pattern and kinetics. As a potential explanation of these alterations, epigenetic drifts in organoid culture have been suggested. Here, we study histone tri-methylation at lysine 4 (H3K4me3) and 27 (H3K27me3) and transcriptome profiles of intestinal organoids derived from mismatch repair (MMR)-deficient and control mice and cultured for 3 and 20 weeks, and compare them with data on their tissue of origin. We find that, besides the expected changes in short-term culture, organoids show profound changes in their epigenome also during long-term culture. The most prominent are epigenetic gene activation by H3K4me3 recruitment to previously unmodified genes and by H3K27me3 loss from originally bivalent genes. We show that long-term culture is linked to broad transcriptional changes that indicate an ongoing maturation and metabolic adaptation process. This process is disturbed in MMR-deficient mice, resulting in endoplasmic reticulum (ER)-stress and Wnt-activation. Our results can be explained in terms of a mathematical model assuming that epigenetic changes during long-term culture involve DNA de-methylation that ceases if the metabolic adaptation is disturbed.
2021-07-05 | GSE179237 | GEO
Project description:Epigenetic changes during long term intestinal organoid culture
| PRJNA742895 | ENA
Project description:Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) are rare and highly heterogeneous neoplasms whose incidence has
markedly increased over the last decades. A grading system based on the tumor cells' proliferation index predicts high-risk for G3
NETs. However, low-to-intermediate grade (G1/G2) NETs have an unpredictable clinical course that varies from indolent to highly
malignant. Cultures of human cancer cells enable to perform functional perturbation analyses that are instrumental to enhance our
understanding of cancer biology. To date, no tractable and reliable long-term culture of G1/G2 NET has been reported to permit
disease modeling and pharmacological screens. Here, we report of the first long-term culture of a G2 metastatic small intestinal
NET that preserves the main genetic drivers of the tumor and retains expression patterns of the endocrine cell lineage.
Replicating the tissue, this long-term culture showed a low proliferation index, and yet it could be propagated continuously
without dramatic changes in the karyotype. The model was readily available for pharmacological screens using targeted agents
and as expected, showed low tumorigenic capacity in vivo. Overall, this is the first long-term culture of NETs to faithfully
recapitulate many aspects of the original neuroendocrine tumor.
| EGAS00001007093 | EGA
Project description:We analyzed the difference of gene expression between the isolates havested from long-term cultures (Ma et.al. 2020). In this study, the paradaux cell line were cultured for over 40 days under different population control conditions (uncontrolled, negative feedback and paradoxical feedback. Isolates of each culture were harvested at the end of the long-term culture and preped for whole genomic RNA sequencing.
2021-12-03 | GSE189948 | GEO
Project description:Granulosa cells (GCs) have many endocrine functions. However, in long-term in vitro culture GCs can change their properties. GCs were collected from hyper-stimulated ovarian follicles from woman during IVF procedures. They were cultured in in vitro long-term culture. RNA was collected after 1, 7, 15 and 30 days of culture. Expression microarrays were used for analysis, which allowed to identify groups of genes characteristic for particular cellular processes. In this study, we demonstrated the gene expression profile of long time primary cultured human ovarian granulosa cells.
2019-04-17 | GSE129919 | GEO
Project description:Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) are rare and highly heterogeneous neoplasms whose incidence has
markedly increased over the last decades. A grading system based on the tumor cells' proliferation index predicts high-risk for G3
NETs. However, low-to-intermediate grade (G1/G2) NETs have an unpredictable clinical course that varies from indolent to highly
malignant. Cultures of human cancer cells enable to perform functional perturbation analyses that are instrumental to enhance our
understanding of cancer biology. To date, no tractable and reliable long-term culture of G1/G2 NET has been reported to permit
disease modeling and pharmacological screens. Here, we report of the first long-term culture of a G2 metastatic small intestinal
NET that preserves the main genetic drivers of the tumor and retains expression patterns of the endocrine cell lineage.
Replicating the tissue, this long-term culture showed a low proliferation index, and yet it could be propagated continuously
without dramatic changes in the karyotype. The model was readily available for pharmacological screens using targeted agents
and as expected, showed low tumorigenic capacity in vivo. Overall, this is the first long-term culture of NETs to faithfully
recapitulate many aspects of the original neuroendocrine tumor.
| EGAS00001007108 | EGA
Project description:Epigenetic drift during long-term culture of cells in vitro
| PRJNA603001 | ENA
Project description:Epigenetic drift during long-term culture of cells in vitro
| PRJNA478324 | ENA
Project description:Culture expansion of primary cells evokes highly reproducible DNA methylation (DNAm) changes at specific sites in the genome. These changes might be due to an directly regulated epigenetic process, or to gradual deregulation of the epigenetic state, which is often referred to as “epigenetic drift”. We have identified CG dinucleotides (CpGs) that become continuously hyper- or hypomethylated in the course of culture expansion of mesenchymal stem cells (MSCs) and other cell types. During reprogramming into induced pluripotent stem cells (iPSCs) the long-term culture-associated hypomethylation is reversed simultaneously with pluripotency-associated DNAm changes. Bisulfite barcoded amplicon sequencing (BBA-seq) demonstrated that upon passaging the DNAm patterns of neighboring CpGs become more complex without evidence of continuous pattern development and without association to dominant subclones at later passages. Circularized chromatin conformation capture (4C) revealed reproducible changes in nuclear organization between early and late passages, while there was no preferential interaction with other genomic regions that also harbor culture-associated DNAm changes. Chromatin immunoprecipitation of CTCF did not show significant differences during long-term culture of MSCs, however culture-associated hypermethylation was enriched at CTCF binding sites and hypomethylated CpGs were devoid of CTCF. Taken together, the DNAm changes during culture-expansion of cells cannot be attributed to cellular subsets, whereas they seem to resemble epigenetic drift in relation to chromatin conformation.
2021-05-26 | GSE144195 | GEO
Project description:Mesenchymal stromal cells (MSC) were isolated from human bone marrow. Here, we have compared gene expression profiles of MSC at early and late passages. Long-term culture associated gene expression changes were then correlated with DNA-methylation profiles. The goal of this study was to determine if senescence-associated DNA-methylation (SA-DNAm) changes are reflected by differential gene expression. Overall, genes with SA-DNAm changes (particularly with SA-hypomethylation) were detected at low level and seemed to be scarcely expressed at early and late passages. MSC were isolated from three different donors and culture expanded until replicative senescence. Gene expression profiles were compared at early and late passage using GeneChip Humang Gene 1.0 ST arrays (Affymetrix). Six hybridizations are included in this series.
2012-09-24 | E-GEOD-37065 | biostudies-arrayexpress