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MetabolomicsMetabolic Drug Response Phenotyping in Colorectal Cancer Organoids by LC-QTOF-MS
As metabolic rewiring is crucial for cancer cell proliferation, metabolic phenotyping of patient-derived organoids is desirable to identify drug-induced changes and trace metabolic vulnerabilities of tumor subtypes. We established a novel protocol for metabolomic and lipidomic profiling of colorecta...
2021-10-12 | MTBLS2130 | MetaboLights
ProteomicsCell-matrix adhesion contributes to permeability control in human colon organoids
Background and aims: Cell-cell adhesion structures (desmosomes and, especially, tight junctions) are known to play important roles in control of transepithelial permeability in the colon. The involvement of cell-matrix interactions in permeability control is less clear. The goals of the present stud...
ORGANISM(S): Homo sapiens (Human) 
2022-03-14 | PXD026923 | Pride
Colon organoids Basement membrane Gut barrier Colon Intestinal permeabilty 
TranscriptomicsRNA-seq of LGR5(+) and LGR5(-) cells isolated from human colon adenoma organoids and targeted DNA-seq of a colorectal biobank
This study has two components: (1) Human colon adenoma organoids (n=4 patients) were dissociated into single cells. Cells were incubated with a magnetic bead bound to an LGR5 antibody and run through a magnetic column. Magnet bound cells and flow through negative (FTN) cells were obtained. Magnet bo...
ORGANISM(S): Homo sapiens 
2020-04-30 | E-MTAB-4698 | biostudies-arrayexpress
TranscriptomicsLong-term in vitro expansion of epithelial organoids from human colon, adenoma, adenocarcinoma and Barrett's Esophagus
Background & Aims: We have recently established long-term culture conditions under which single crypts or stem cells derived from murine small intestine expand over long periods of time. Growing crypts undergo multiple crypt fission events, whilst simultaneously generating villus-like epithelial dom...
ORGANISM(S): Homo sapiens 
2011-12-07 | E-GEOD-28907 | biostudies-arrayexpress
ProteomicsProteomic Profile of Human Colon Organoids: Effects of a multi-mineral intervention alone and in the presence of pro-Inflammatory and anti-inflammatory treatments
Introduction: Aquamin, a multi-mineral product derived from fossilized red marine algae, has been shown to improve colon barrier structure and function. Mesalamine is commonly used as maintenance therapy for patients with mild-to-moderate ulcerative colitis (UC) or those in remission. Our long-term ...
ORGANISM(S): Homo sapiens (Human) 
2026-03-16 | PXD062086 | Pride
Ulcerative colitis Gut barrier Mesalamine Inflammation Aquamin Colon organoids 
TranscriptomicsAnalysis of human enteroids and colonoids (3D organoid models from small intestine and colon) exposed to chemotherapy agent 5-fluorouracil (5FU) in a dose-repeated exposure across three doses (10,100 and 1000uM) and sampled at three points (24, 48 and 72h) since initial exposure. Organoids were obtained from healthy human tissues.
ADRs (adverse drug reactions) are one of the main reasons for treatment discontinuation or alterations in dose regimens in clinical settings. Chemotherapy-induced ADRs are common, especially gastrointestinal-induced ones. Within TransQST (transqst.org), one of the main goal is to improve the in vitr...
ORGANISM(S): Homo sapiens 
2021-09-09 | E-MTAB-9134 | biostudies-arrayexpress
ProteomicsRed Algae-Derived Mineral Intervention to Counter Pro-inflammatory Activity in Human Colon Organoids
Human colon organoids were maintained in culture medium alone or exposed to lipopolysaccharide with a combination of three pro-inflammatory cytokines (tumor necrosis factor-a, interleukin-1b and interferon-g [LPS-cytokines]) to mimic the environment in the inflamed colon. Untreated organoids and tho...
ORGANISM(S): Homo sapiens (Human) 
2023-06-30 | PXD038941 | Pride
Lps Proteomics Inflammation Cytokines Gut barrier Multi-mineral Colon organoids 
ProteomicsPersonalized proteome profiles of healthy and tumor human colon organoids reveal both individual diversity and basic features of colorectal cancer.
We performed quantitative mass spectrometry based proteomic analysis and comparative transcriptomics analysis of 7 individual patient-derived human colorectal tumor and healthy organoids, the latter acquired from adjacent healthy tissue.
ORGANISM(S): Homo sapiens (Human) 
2017-01-16 | PXD004149 | Pride
Proteomics Organoids Colon cancer 
TranscriptomicsRNA-seq of BRAF-V600E_mutated and BRAF-V600E_corrected colon cancer organoids
We aimed to investigate transcriptional changes in human colon cancer organoids with the BRAF-V600E mutation and in human colon cancer organoids in which the BRAF-V600E mutation was corrected by means of CRISPR genome editing. RNAseq was performed at USEQ at the UMC Utrecht (The Netherlands).
ORGANISM(S): Homo sapiens 
2024-02-21 | E-MTAB-13806 | biostudies-arrayexpress
ProteomicsHuman colon organoids reveal distinct physiologic and oncogenic Wnt responses
Constitutive Wnt activation upon loss of Adenoma polyposis coli (APC) acts as main driver of colorectal cancers (CRC). Targeting Wnt signaling has proven difficult because the pathway is crucial for homeostasis and stem cell renewal. To distinguish oncogenic from physiologic Wnt activity, we have pe...
ORGANISM(S): Homo sapiens (Human) 
2019-02-28 | PXD012650 | Pride
Human colon Isogenic lines Organoids Label free quantification Crispr/cas9 Wnt signaling Apc mutation 
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