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MetabolomicsComparative non-targeted LC-MS metabolomic profiling of murine bone marrow-derived macrophages cultured in 2D versus 3D

Macrophages are key drivers of inflammatory and fibrotic diseases and their activation is shaped by interactions in their tissue microenvironment. However, dissecting the processes that drive immunopathology has proved challenging as traditional 2D culture methods fail to capture the complex mole...

2026-06-08 | MTBLS12917 | MetaboLights
MetabolomicsLiquid chromatography coupled to high-resolution mass spectrometry metabolomics: A useful tool for investigating tumor secretome based on a three-dimensional co-culture model

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 int...

2023-12-12 | MTBLS5375 | MetaboLights
MetabolomicsOrganotypic microfluidic breast cancer model reveals starvation-induced spatial-temporal metabolic adaptations
BACKGROUND: Ductal carcinoma in situ (DCIS) is the earliest stage of breast cancer. During DCIS, tumor cells remain inside the mammary duct, growing under a microenvironment characterized by hypoxia, nutrient starvation, and waste product accumulation; this harsh microenvironment promotes genomic in...
2019-02-08 | MTBLS669 | MetaboLights
MetabolomicsEffects of hypoxic preconditioning on neuroblastoma tumour oxygenation and metabolic signature in a chick embryo model
Hypoxia episodes and areas in tumours have been associated with metastatic dissemination and poor prognosis. Given the link between tumour tissue oxygen levels and cellular metabolic activity, we hypothesised that the metabolic profile between metastatic and non-metastatic tumours would reveal poten...
2018-08-13 | MTBLS541 | MetaboLights
ProteomicsDevelopment of a 3D in vitro model of Dupuytren’s disease as a platform for drug screening
Background: Dupuytren’s disease (DD) is a common fibrotic disorder of the hand, characterized by progressive thickening and contracture of the palmar and digital fascia. Surgical excision remains the primary treatment; however, there are currently no therapies to prevent disease progression or recur...
ORGANISM(S): Homo sapiens (Human) 
2026-04-06 | PXD072354 | Pride
Myofibroblasts Proteomics Dupuytren’s disease 3d in vitro model Fibrosis Minoxidil Collagen type i Decellularization 
ProteomicsXenografted Tumor decellularization provides cell-specific in vitro 3D environment
In vitro cell culture studies are common in cancer research field, and reliable biomimetic 3D models are needed to ensure physiological relevance. In this manuscript, we hypothesized that decellularized xenograft tumors can serve as an optimal 3D substrate to generate a top-down approach for in vitr...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2022-09-12 | PXD034597 | Pride
Tumor xenograft  decellularization  in vitro 3d model  breast cancer 
Transcriptomics21T series cell lines show distinct stage-specific gene expression alterations
Pathologic and epidemiologic evidence has led to a histologic model of breast cancer progression that involves advancement through specific morphologic stages including atypical ductal hyperplasia (ADH), ductal carcinoma in situ (DCIS) and invasive mammary carcinoma (IMC), although not necessarily a...
ORGANISM(S): Homo sapiens 
2010-04-06 | E-GEOD-18370 | biostudies-arrayexpress
ProteomicsMolecular characterization of hematopoietic stem cells after in vitro amplification on biomimetic 3D PDMS cell culture scaffoldsMolecular characterization of hematopoietic stem cells after in vitro amplification on biomimetic 3D PDMS cell culture scaffolds
Hematopoietic stem cell transplantation (HSCT) is successfully applied since the late 1950s, however, its efficacy still needs to be improved. A promising strategy is to transplant high numbers of pluripotent hematopoietic stem cells (HSCs). Therefore, an advanced ex vivo culture system is needed th...
ORGANISM(S): Homo sapiens (Human) 
2021-11-10 | PXD025849 | Pride
Hematopoietic stem cell transplantation (hsct) Proteomics Foxo Cholesterol Human hematopoietic stem cell (hsc) Srebp Biomimetic In vitro amplification 3d cell cultivation system Mtor Cell metabolism 
Proteomicsin vivo-like scaffold-free 3D in vitro Models of Muscular Dystrophies: The Case for Anchored Cell Sheet Engineering in Personalized Medicine
The study of muscle dystrophies, including Duchenne and Myotonic dystrophies, has faced significant challenges due to the lack of physiologically relevant in vitro models. This research introduces a novel, scaffold- and biomaterial-free platform based on cell sheet engineering to create in vitro mod...
ORGANISM(S): Homo sapiens (Human) 
2024-12-24 | PXD052728 | Pride
Drug treatment In vitro model Cell sheet engineering Scaffold-free Proteomics Dystrophy Skeletal muscle 
TranscriptomicsGenome-Wide Dynamics of Replication Timing Revealed by In Vitro Models of Mouse Embryogenesis
This SuperSeries is composed of the following subset Series: GSE17980: Genome-Wide Dynamics of Replication Timing Revealed by In Vitro Models of Mouse Embryogenesis (Expression) GSE17983: Genome-Wide Dynamics of Replication Timing Revealed by In Vitro Models of Mouse Embryogenesis (WG_CGH; Replicati...
ORGANISM(S): Mus musculus 
2010-05-19 | E-GEOD-18019 | biostudies-arrayexpress
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