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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
ProteomicsHighly contractile 3D tissue engineered skeletal muscles from human iPSCs reveal similarities with primary myoblast-derived tissues
Skeletal muscle research is transitioning towards 3D tissue engineered in vitro models reproducing muscle’s native architecture and supporting measurement of functionality. Human induced pluripotent stem cells (hiPSCs) offer high yields of cells for differentiation. It has been difficult to differen...
ORGANISM(S): Homo sapiens (Human) 
2023-10-02 | PXD045145 | Pride
Myongeic differentiation Hipsc 3d tissue 
MetabolomicsCross-modal Integration of Metabolomics and Cardiac Functionality Captures Dynamic Metabotoxic Effects of Doxorubicin in Engineered Heart Tissues

Functional stem cell-derived heart models offer new avenues for preclinical, animal-free physiological assessment of drug cardiotoxicity. Yet, comprehensive molecular profiling in these models remains limited, leaving key metabolic drivers of cardiotoxicity unexplored.

Here, we leveraged an...

2025-12-07 | MTBLS13225 | MetaboLights
ProteomicsiTRAQ-Based Quantitative Proteomic Comparison of 2D and 3D Adipocyte Cell Models Co-cultured with Macrophages Using Online 2D-nanoLC-ESI-MS/MS
The demand for novel three-dimensional (3D) cell culture models of adipose tissue has been increasing, and proteomic investigations are important for determining the underlying causes of obesity, type II diabetes, and metabolic disorders. In this study, we performed global quantitative proteomic pro...
ORGANISM(S): Mus musculus (Mouse) 
2020-05-26 | PXD014437 | Pride
3d-culture Macrophages Adipocytes Proteomic quantification Itraq 
MetabolomicsSpatial metabolomics of in situ, host-microbe interactions (On-tissue MALDI imaging MS/MS assay)
Spatial metabolomics describes the location and chemistry of small molecules involved in metabolic phenotypes, defense molecules and chemical interactions in natural communities. Most current techniques are unable to spatially link the genotype and metabolic phenotype of microorganisms in situ at a ...
2019-11-15 | MTBLS805 | MetaboLights
ProteomicsExtracellular vesicles secreted by 3D tumor organoids are enriched for immune regulatory signaling biomolecules compared to conventional 2D glioblastoma cell systems
Background: Newer 3D culturing approaches are a promising way to better mimic the in vivo tumor microenvironment and to study the interactions between the heterogeneous cell populations of glioblastoma multiforme. Like many other tumors, glioblastoma uses extracellular vesicles as an intercellular c...
ORGANISM(S): Homo sapiens (Human) 
2024-04-09 | PXD047328 | Pride
Ev Extracellular vesicle Proteomics Microrna 3d organoid model Brain cancer Glioblastoma multiforme 
ProteomicsBioprinted 3D vascularized human placenta models recapitulate early and late stages of pregnancy
The placenta is a highly dynamic organ that supports the growth and development of the fetus throughout the different stages of pregnancy. Malfunction of the placenta causes disorders of the pregnancy, including preeclampsia and pre-term birth. The study of the pathophysiology of the placenta at dif...
ORGANISM(S): Homo sapiens (Human) 
2026-09-07 | PXD072837 | Pride
Lc-msms Human Placenta 3d model 
TranscriptomicsTranscription profiling by array of human stromal cells cultured with or without 3D BPH-1 prostate epithelial cells
BPH-1 prostate epithelial cells when cultured in Matrigel form 3D acini which closely recapitulate the tissue architecture of the prostate. The presence of primary stroma increases epithelial adhesions and causes changes in morphology. To identify the stromal signals which control actin/cadherin dy...
ORGANISM(S): Homo sapiens 
2010-06-09 | E-MEXP-2657 | biostudies-arrayexpress
ProteomicsA comparison of human skeletal muscle cell maturation in 2D versus 3D culture: A quantitative proteomic study C4PR_LIV
Background Three-dimensional (3D) bioengineered models of human skeletal muscle are a promising approach for studying muscle development, function and disease in vitro. These models more closely resemble the complexity of native muscle tissue than two-dimensional (2D) monolayer culture and allow for...
ORGANISM(S): Homo sapiens (Human) 
2025-06-23 | PXD061227 | Pride
Bioengineering In vitro models Skeletal muscle Maturation Proteomics 3d culture Hydrogel 
ProteomicsAssessing inter-line reproducibility of a novel iPSC-derived 3D brain tissue model (3BTM) and comparison to 2D co-cultures
Stem-cell-based in vitro models offer promising potential to elucidate human brain cell functions and interactions under healthy conditions and in disease states. However, harnessing this potential is currently impaired by low reproducibility, maturity, and cell-type diversity of models. Therefore, ...
ORGANISM(S): Homo sapiens (Human) 
2026-02-23 | PXD069984 | Pride
3d brain tissue model 3btm Brain Ipsc 
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