Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA304768 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2973260_1.fastq.gz | Fastqsanger.gz | |||
| SRR2973260_2.fastq.gz | Fastqsanger.gz | |||
| SRR2973261_1.fastq.gz | Fastqsanger.gz | |||
| SRR2973261_2.fastq.gz | Fastqsanger.gz | |||
| SRR2973262_1.fastq.gz | Fastqsanger.gz |
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Project description:A new 3D culture system to identify disease-relevant genes in colorectal cancer
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Project description:A new 3D culture system to identify disease-relevant genes in colorectal cancer [Microarray expression]
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Project description:To better understand and develop treatments for lung cancer, it is important to have reliable and physiologically relevant culture models. Traditional methods of growing lung cancer cells in two-dimensional monolayers have limitations in mimicking the complex architecture and microenvironment of lung tumors in vivo, limiting their value as reliably informative disease models. In this study, we introduce a new cell culture platform called "tumoroids," which involves growing HCC827 lung cancer cells in three-dimensional configurations for more accurately predicting how cell-cell orientation and signaling affects the cancer-driving properties of lung cancer. By comparing transcriptional profiles of HCC827 cells grown as tumoroids versus the same cells grown in two-dimensional monolayers, we investigate how cell-cell orientation and signaling impact the cancer-driving properties of lung cancer. We examine key features associated with cancer progression, such as epithelial mesenchymal transition, replicative ability, and induction of angiogenesis. Additionally, we assess the functional characteristics of the 3D tumoroid culture system by subjecting the cells to irradiation. Through comparing the gene expression profiles of the 3D tumoroid cultures with those of primary human lung adenocarcinoma, we find that the 3D tumoroid cultures closely resemble the characteristics of primary human lung cancer. This suggests that the 3D tumoroid culture platform can serve as a valuable in vitro model for studying lung cancer, offering greater clinical relevance compared to traditional 2D cultures. Overall, this study highlights the importance of using advanced culture models like 3D tumoroids to improve our understanding of lung cancer and facilitate the development of effective treatments.
2025-12-31 | GSE241845 | GEO
Project description:Background: Three-dimensional (3D) in vitro culture systems using human induced pluripotent stem cells (hiPSCs) represent impactful platforms to model neurodegenerative disease biology in physiologically relevant microenvironments. Though many successful biomaterials-based 3D model systems have been established for other neurogenerative diseases, such as Alzheimer’s Disease, relatively few exist for Parkinson’s Disease (PD) research. Methods: We employed tissue engineering approaches to construct a 3D silk scaffold-based platform for the culture of hiPSC-dopaminergic (DA) neurons derived from healthy individuals and PD patients harboring LRRK2 G2019S or GBA N370S mutations. We then compared results from protein, gene expression and metabolic analyses obtained from two-dimensional (2D) and 3D culture systems. Results: The 3D platform enabled the formation of dense dopamine neuronal network architectures and developed biological profiles both similar and distinct from 2D culture systems in healthy and PD disease lines. 3D PD cultures showed elevated levels of α-synuclein and alterations in purine metabolite profiles. Furthermore, computational network analysis of transcriptome networks nominated several novel molecular interactions occurring in neurons from patients with mutations in LRRK2 and GBA. Conclusion: The brain-like 3D system presented here is a realistic platform to interrogate molecular mechanisms underlying PD biology. The key advantages of silk-based bioengineering technology include long-term culture and the ability to incorporate multiple brain-relevant cell types to parse cell-cell interactions in development, disease, and aging.
2022-03-16 | GSE172409 | GEO
Project description:Tumor cell response to irradiation also depends on their microenvironment. Therefore ongoing investigation of three-dimensional (3D) cell culture models provide researchers with essential data studying and remodeling radiotherapeutic implications in cancer treatment. 3D culture models were shown to mimic in vivo cell microenvironment more accurately than the standard two-dimensional cell monolayer (2D) cultures. Growing evidence suggests that 2D and 3D cultured cell gene expression pattern discrepancies following irradiation is highly dependent on cell-ECM interactions. It has been shown that laminin-rich-extracellular matrix (lr-ECM) used in 3D cultures not only alters cancer cell phenotype and response to external stimuli but also affects their differentiation, migration and survivability. Thus, a change in these fundamental cell properties demands us to reconsider data previously collected using 2D in vitro models. RNA was harvested from two colorectal cancer cell lines cultivated under 3D cell culture conditions, 4h after treatment of single (2 Gy or 10 Gy) or fractionated (5x2 Gy) ionizing radiation dose.
2015-12-12 | E-GEOD-75915 | biostudies-arrayexpress
Project description:Gene expression profile of two reporgrammed cell lines iPSC CRL1831 (induced pluripotent stem cells) and CSC DLD1 (cancer stem-like cells) derived from normal colon CRL1831 and colorectal cancer DLD-1 cells, after transfer to 3D cell culture conditions and cell lines treated with single or fractionated ionizing radiation doses under 3D cell culture conditions. There are no data that cancer metastases arise due to specific mutations of cancer cells. Therefore ongoing investigation of reprogrammed cancer cells grown in three-dimensional (3D) cell culture models might provide researchers with essential data studying tumor oncogenesis and metastases formation. 3D culture models were shown to mimic in vivo cell microenvironment more accurately than the standard two-dimensional cell monolayer (2D) cultures. Also, growing evidence suggests that 2D and 3D cultured cells gene expression pattern variance following irradiation is highly dependent on cancer cell state and their interaction with microenvironment.
2017-01-07 | GSE93228 | GEO
Project description:<p>Three-dimensional (3D) cell culture technologies, which more closely mimic the complex microenvironment of tissue, are being increasingly evaluated as a tool for the preclinical screening of clinically promising new molecules, and studying of tissue metabolism. Studies of metabolites released into the extracellular space (secretome) allow understanding the metabolic dynamics of tissues and changes caused by therapeutic interventions. Although quite advanced in the field of proteomics, studies on the secretome of low molecular weight metabolites (< 1500 Da) are still very scarce. We present an untargeted metabolomic protocol based on the hybrid technique of liquid chromatography coupled with high-resolution mass spectrometry for the analysis of low-molecular-weight metabolites released into the culture medium by 3D cultures and co-culture (secretome model). For that we analyzed HT-29 human colon carcinoma cells and 3T3-L1 preadipocytes in 3D-monoculture and 3D-co-culture. The putative identification of the metabolites indicated a sort of metabolites, among them arachidonic acid, glyceric acid, docosapentaenoic acid and beta-Alanine which are related to cancer and obesity. This protocol represents a possibility to list metabolites released in the extracellular environment in a comprehensive and untargeted manner, opening the way for the generation of metabolic hypotheses that will certainly contribute to the understanding of tissue metabolism, tissue-tissue interactions and metabolic responses to the most varied interventions. Moreover, it brings the potential to determine novel pathways and accurately identify biomarkers in cancer and other diseases. The metabolites indicated in our study have a close relationship with the tumor microenvironment in accordance with the literature review.</p>
2023-12-12 | MTBLS5375 | MetaboLights
Project description:Commonly used monolayer cell cultures lack the capacity to provide a physiologically relevant environment for cell culture in terms of cell-cell architecture, extracellular matrix composition, and spatiotemporal delivery of key growth factors and small molecules, such as oxygen. Here, we describe a three-dimensional (3D) approach to cell culture in vitro, utilizing a bioreactor system designed to control oxygenation of 3D cancer cell cultures, in order to better mimic tumor microenvironments observed in vivo. We found transcriptomic differences in breast and ovarian cancer cell cultures grown in traditional monolayer cultures as compared to cultures grown in a Matrigel three-dimensional matrix. We also investigated the transcriptomes of 3D cultures grown in 21% O2, 3% O2, and a gradient of 3% O2 to 0% O2 using our bioreactor system. By controlling oxygen delivery, we observed differences in cell growth morphology and transcriptome regulation under the three conditions.
2019-04-02 | GSE129111 | GEO
Project description:Organoid culture has been extensively exploited for normal tissue reconstruction and disease modeling, however, it is still challenging to establish physiologically relevant architecture, size and functions in homeostasis. Here, we describe the development of a long-term adult stem cell derived mammary mini-gland culture system that supports robust 3D outgrowths recapitulating the morphology, cellular context, transcriptional heterogeneity of the normal mammary gland. The self-organization ability of stem cells and the stability of the outgrowths were determined by a coordinated combination of extracellular matrix, environmental signalings and dynamic physiological cycles. These mini glands are hormone responsive and reproduce the entire postnatal mammary development including puberty, estrous cycle, lactation and involution. Most intriguingly, these mini glands maintained the mammary stem cells and represented the fate transition from embryonic bipotency to postnatal unipotency in lineage tracing assays. In addition, induced oncogene expression in the mini glands drove the clinically relevant cancer initiation that can be monitored chronologically. Together, this study provides an experimental system fostering a dynamic organ miniature that can be studied chronologically and spatially for physiologically relevant biological processes with complexity.
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Project description:The liver is the most common site for colorectal cancer (CRC) metastasis and new tissue culture models are needed to study hepatic metastasis from CRC as none of the current models mimic the biological, biochemical and structural characteristics of the metastatic microenvironment. Decellularization provides a novel approach for the study of cancer extracellular matrix (ECM) as decellularized scaffolds retained their tissue-specific features and biological properties. In the present study we created a 3D model of CRC and matched CRC liver metastasis (CRLM) using patient-derived decellularized ECM scaffolds seeded with HT-29 CRC cell line. Here we show increased HT-29 cell proliferation and migration capability when cultured in cancer-derived scaffolds compared to same-patient healthy colon and liver tissues. CRLM scaffolds also induced activation of epithelial-mesenchymal transition (EMT) with cancer cells showing loss of E-cadherin expression and increased Vimentin expression. EMT was confirmed by gene expression profiling, with the most represented biological processes in CRLM-seeded scaffolds involving demethylation, deacethylation, cellular response to stress metabolic processes, response to oxygen level and to starvation. The complex 3D culture environment reduced the HT-29 cell response to anti-CRC drug 5-FU when used at standard IC50 determined in 2D cultures. In conclusion, our 3D culture system with patient-derived tissue-specific decellularized ECM better recapitulates the metastatic microenvironment compared to conventional 2D culture conditions and represents a relevant approach for the study of liver CRC metastasis formation and progression. Transcriptomic analysis was performed comparing the global gene expression profiles of HT29 cells grown on CRLM and HL scaffolds. The transcriptomic profile of each 3D subtype was compared with HT29 cells grown in plastic. Hierarchical clustering analysis revealed that the gene expression signature of recellularized CRLM scaffolds was more comparable to recellularized HL scaffolds, than to HT29 cells grown in 2D. Gene set enrichment analysis (GSEA) of the differently expressed genes (DEG) up-regulated in recellularized CRLM scaffolds compared to HT29 grown in 2D revealed that genes involved in demethylation, deacethylation and metabolic process belong to the most enriched biological pathways in repopulated-CRLM scaffolds. Comparing the DEG between recellularized CRLM scaffolds vs HT29 grown in 2D with a series of a-priori defined gene-set, called Hallmark, we obtained concordant results with the “HYPOXIA” and “EPITHELIAL_MESENCHYMAL_TRANSITION” pathway, enriched in recellularized CRLM, supporting the idea that 3D culture models are the ability to re-create a complex environment in terms of oxygen tension, nutrients, and metabolic gradient, similarly to the in vivo environment.
2019-11-30 | GSE125404 | GEO