Epigenetic changes during long term intestinal organoid culture
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PROVIDER: PRJNA742895 | 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: Not available
| S-EPMC8305684 | biostudies-literature
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: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:Human intestinal epithelial organoid models are rapidly emerging as novel experimental tools to investigate intestinal epithelial biology. A necessary aspect of organoid use is the passaging of cells and long term maintenance in culture. DNA methylation has been demonstrated to play a key role in regulating gene expression and cellular function. Here we explore the effect of culture duration, proinflammatory cytokine stimulation and differentiation on organoid DNA methylation. The experiment consists of RNA-seq of intestinal organoid cultures from paediatric ileum and colon.
2022-08-31 | E-MTAB-11548 | biostudies-arrayexpress
Project description:We report the establishment of a stable 3D in vitro organoid culture procedure from human fallopian tube samples and confirming experimentally the existence of adult stem cells in this epithelial tissue. Long term growth and the differentiation of the organoids depend on the interplay between the paracrine signaling pathways Wnt, NOTCH and BMP, since R spondin 1 and Wnt3a are required for preservation of stemness in concert with continuous suppression of TGF-beta activity. Microarray analysis revealed that inhibition of NOTCH signaling by the gamma-secretase inhibitor DBZ leads to down-regulation of a gene cluster associated with pluripotency, as the adult stem cell signature is significantly enriched in the list of downregulated targets. Microarray experiments were performed as dual-color hybridizations on Agilent human whole genome catalog 44K arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.
2015-01-01 | E-GEOD-60919 | biostudies-arrayexpress
Project description:Human intestinal epithelial organoid models are rapidly emerging as novel experimental tools to investigate intestinal epithelial biology. A necessary aspect of organoid use is the passaging of cells and long term maintenance in culture. DNA methylation has been demonstrated to play a key role in regulating gene expression and cellular function. Here we explore the effect of culture duration, proinflammatory cytokine stimulation and differentiation on organoid DNA methylation. The experiment consists of genome-wide DNA methylation profiling by Infinium HumanMethylationEPIC BeadChip of intestinal organoid cultures from paediatric ileum and colon. Our genome wide DNA methylation datasets represent a unique resource, which can be used by other researchers to validate their model systems.
2022-08-31 | E-MTAB-11545 | biostudies-arrayexpress
Project description:Long-term culture of alveolospheres
| PRJNA573090 | ENA
Project description:characterization of organoid culture
| PRJNA576369 | ENA
Project description:We report the establishment of a stable 3D in vitro organoid culture procedure from human fallopian tube samples and confirming experimentally the existence of adult stem cells in this epithelial tissue. Long term growth and the differentiation of the organoids depend on the interplay between the paracrine signaling pathways Wnt, NOTCH and BMP, since R spondin 1 and Wnt3a are required for preservation of stemness in concert with continuous suppression of TGF-beta activity. Microarray analysis revealed that inhibition of NOTCH signaling by the gamma-secretase inhibitor DBZ leads to down-regulation of a gene cluster associated with pluripotency, as the adult stem cell signature is significantly enriched in the list of downregulated targets.
2015-01-01 | GSE60919 | GEO