Summary of Study ST003598

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002226. The data can be accessed directly via it's Project DOI: 10.21228/M8WG15 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

Study ID	ST003598
Study Title	Nuclear Factor I A (NFIA) Regulates Articular Chondrocyte Fatty Acid Metabolism and Joint Homeostasis
Study Summary	Osteoarthritis (OA) has recently been recognized as a joint disease with an etiology partially rooted in metabolic dysfunction, yet the underlying mechanism(s) in this context are not determined, limiting opportunities to develop therapeutic treatments. In this study, we utilized a multi-omics approach combining RNA-seq, ATAC-seq, MRE-seq, and metabolomics to reveal that OA articular chondrocytes induced by imbalanced Transforming Growth Factor β 1/Bone Morphogenetic Protein 2 (TGF-β/BMP) signaling, possess increased fatty acid synthesis and oxidation processes regulated by Nuclear Factor I A (NFIA) upregulation
Institute	Washington University in St. Louis
Department	Orthopaedic Surgery, Chemistry, Medicine
Laboratory	Shen Laboratory and Patti Laboratory
Last Name	Cho
First Name	Kevin
Address	1 Brookings Drive
Email	kevin.cho@wustl.edu
Phone	314-935-8813
Submit Date	2024-11-26
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2025-07-21
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002226
Project DOI:	doi: 10.21228/M8WG15
Project Title:	Nuclear Factor I A (NFIA) regulates articular chondrocyte fatty acid metabolism and joint homeostasis
Project Summary:	Osteoarthritis (OA) has recently been recognized as a joint disease with an etiology partially rooted in metabolic dysfunction, yet the underlying mechanism(s) in this context are not determined, limiting opportunities to develop therapeutic treatments. In this study, we utilized a multi-omics approach combining RNA-seq, ATAC-seq, MRE-seq, and metabolomics to reveal that OA articular chondrocytes induced by imbalanced Transforming Growth Factor β 1/Bone Morphogenetic Protein 2 (TGF-β/BMP) signaling, possess increased fatty acid synthesis and oxidation processes regulated by Nuclear Factor I A (NFIA) upregulation
Institute:	Washington University in St. Louis
Department:	Orthopaedic Surgery, Chemistry, Medicine
Laboratory:	Shen Laboratory and Patti Laboratory
Last Name:	Cho
First Name:	Kevin
Address:	1 Brookings Drive
Email:	kevin.cho@wustl.edu
Phone:	314-935-8813

Subject:

Subject ID:	SU003727
Subject Type:	Mammal
Subject Species:	Mus musculus; Homo sapiens
Taxonomy ID:	10090; 9606
Species Group:	Mammals

Factors:

Subject type: Mammal; Subject species: Mus musculus; Homo sapiens (Factor headings shown in green)

mb_sample_id	local_sample_id	Sample source	Genotype	Treatment
SA392359	H_Healthy_Gln_1	Human Chondrocytes	Healthy	N/A
SA392360	H_Healthy_OA_3	Human Chondrocytes	Healthy	N/A
SA392361	H_Healthy_OA_2	Human Chondrocytes	Healthy	N/A
SA392362	H_Healthy_OA_1	Human Chondrocytes	Healthy	N/A
SA392363	H_Healthy_PA_3	Human Chondrocytes	Healthy	N/A
SA392364	H_Healthy_PA_2	Human Chondrocytes	Healthy	N/A
SA392365	H_Healthy_Gln_3	Human Chondrocytes	Healthy	N/A
SA392366	H_Healthy_Gln_2	Human Chondrocytes	Healthy	N/A
SA392367	H_Healthy_PA_1	Human Chondrocytes	Healthy	N/A
SA392368	H_Ctrl_Gln_2	Human Chondrocytes	OA	Lenti-GFP
SA392369	H_Ctrl_PA_3	Human Chondrocytes	OA	Lenti-GFP
SA392370	H_Ctrl_PA_2	Human Chondrocytes	OA	Lenti-GFP
SA392371	H_Ctrl_PA_1	Human Chondrocytes	OA	Lenti-GFP
SA392372	H_Ctrl_Gln_1	Human Chondrocytes	OA	Lenti-GFP
SA392373	H_Ctrl_Gln_3	Human Chondrocytes	OA	Lenti-GFP
SA392374	H_Lenti_Gln_1	Human Chondrocytes	OA	Lenti-shNFIA
SA392375	H_Lenti_PA_3	Human Chondrocytes	OA	Lenti-shNFIA
SA392376	H_Lenti_PA_2	Human Chondrocytes	OA	Lenti-shNFIA
SA392377	H_Lenti_PA_1	Human Chondrocytes	OA	Lenti-shNFIA
SA392378	H_Lenti_Gln_3	Human Chondrocytes	OA	Lenti-shNFIA
SA392379	H_Lenti_Gln_2	Human Chondrocytes	OA	Lenti-shNFIA
SA392380	H_OA_OA_3	Human Chondrocytes	OA	N/A
SA392381	H_OA_PA_2	Human Chondrocytes	OA	N/A
SA392382	H_OA_PA_1	Human Chondrocytes	OA	N/A
SA392383	H_OA_PA_3	Human Chondrocytes	OA	N/A
SA392384	H_OA_Gln_3	Human Chondrocytes	OA	N/A
SA392385	H_OA_Gln_2	Human Chondrocytes	OA	N/A
SA392386	H_OA_Gln_1	Human Chondrocytes	OA	N/A
SA392387	H_OA_OA_1	Human Chondrocytes	OA	N/A
SA392388	H_OA_OA_2	Human Chondrocytes	OA	N/A
SA392389	M_BMP_PA_2	Mice Chondrocytes	WT	BMP2
SA392390	M_BMP_OA_1	Mice Chondrocytes	WT	BMP2
SA392391	M_BMP_Gln_2	Mice Chondrocytes	WT	BMP2
SA392392	M_BMP_PA_3	Mice Chondrocytes	WT	BMP2
SA392393	M_BMP_Gln_3	Mice Chondrocytes	WT	BMP2
SA392394	M_BMP_Gln_1	Mice Chondrocytes	WT	BMP2
SA392395	M_BMP_PA_1	Mice Chondrocytes	WT	BMP2
SA392396	M_BMP_OA_3	Mice Chondrocytes	WT	BMP2
SA392397	M_BMP_OA_2	Mice Chondrocytes	WT	BMP2
SA392398	M_TGFb_Gln_3	Mice Chondrocytes	WT	TGFb1
SA392399	M_TGFb_OA_1	Mice Chondrocytes	WT	TGFb1
SA392400	M_TGFb_OA_2	Mice Chondrocytes	WT	TGFb1
SA392401	M_TGFb_OA_3	Mice Chondrocytes	WT	TGFb1
SA392402	M_TGFb_PA_3	Mice Chondrocytes	WT	TGFb1
SA392403	M_TGFb_PA_2	Mice Chondrocytes	WT	TGFb1
SA392404	M_TGFb_Gln_2	Mice Chondrocytes	WT	TGFb1
SA392405	M_TGFb_PA_1	Mice Chondrocytes	WT	TGFb1
SA392406	M_TGFb_Gln_1	Mice Chondrocytes	WT	TGFb1

Showing results 1 to 48 of 48

Showing results 1 to 48 of 48

Collection:

Collection ID:	CO003720
Collection Summary:	Human articular chondrocytes were isolated from the femoral condyle and tibia plateau specimens obtained from healthy donors and OA patients. Following with 90 minutes digestion at 37 °C by 0.4% pronase and 14 hours digestion by 0.035% collagenase P, human articular chondrocytes were filtered through the 70 μm cell strainer and seeded at the density of 105 cells/cm2 for experiments. Murine articular chondrocytes were isolated from femoral heads of 3-week-old wildtype (C57BL/6J) pups. Following with 6 hours digestion at 37°C by 0.05% collagenase P, murine chondrocytes were harvested and plated at the density of 105 cells/cm2 for experiments. Both human and murine articular chondrocytes were cultured in the Dulbecco’s modified Eagle’s medium supplemented with 25 mM Glucose, 2 mM L-Glutamine, 10% fetal bovine serum, and 1% penicillin/streptomycin. The chondrocytes were treated with vehicle, TGF-β1 (5 ng/ml) and BMP2 (100 ng/ml) for 24-72 hours to examine the alterations of gene expression and metabolites. For NFIA/Nfia knockdown experiments, the chondrocytes were transfected with lentivirus expressing shRNA against NFIA and Nfia gene at a multiplicity of 10 in the presence of polybrene (10 μg/ml) in viral infection media (DMEM medium supplemented with 25 mM Glucose, 2 mM L-Glutamine and 2% FBS) for 24 hours. Lentivirus expressing shRNA against scramble sequences was used as control. For Nfia overexpression, the primary murine articular chondrocytes were transfected with lentivirus expressing murine Nfia gene at a multiplicity of 5 in the presence of polybrene for 48 hours. Lentivirus expression Gfp gene was used as control.
Sample Type:	Chondrocytes

Treatment:

Treatment ID:	TR003736
Treatment Summary:	The chondrocytes were treated with vehicle, TGF-β1 (5 ng/ml) and BMP2 (100 ng/ml). For isotope labeling, Articular chondrocytes were cultured in DMEM containing stable isotopically nutrient to assess the lipid metabolism in vitro. To assess lipids synthesis, articular chondrocytes were cultured in glutamine free DMEM supplemented with 10% dialyzed FBS, and 4 mM U-13C glutamine for 72 hours or cells were cultured in glucose free DMEM supplemented with 10% dialyzed FBS, and 25 mM U-13C glucose for 72 hours. To assess lipids oxidation, articular chondrocytes were cultured with 100 mM U-13C palmitic acid conjugated to BSA for 24 hours or 400 uM U-13C oleic acid.

Treatment ID:

TR003736

Treatment Summary:

The chondrocytes were treated with vehicle, TGF-β1 (5 ng/ml) and BMP2 (100 ng/ml). For isotope labeling, Articular chondrocytes were cultured in DMEM containing stable isotopically nutrient to assess the lipid metabolism in vitro. To assess lipids synthesis, articular chondrocytes were cultured in glutamine free DMEM supplemented with 10% dialyzed FBS, and 4 mM U-13C glutamine for 72 hours or cells were cultured in glucose free DMEM supplemented with 10% dialyzed FBS, and 25 mM U-13C glucose for 72 hours. To assess lipids oxidation, articular chondrocytes were cultured with 100 mM U-13C palmitic acid conjugated to BSA for 24 hours or 400 uM U-13C oleic acid.

Sample Preparation:

Sampleprep ID:	SP003734
Sampleprep Summary:	Cell pellets were treated with a methanol/acetonitrile/water (2:2:1) solution and reconstituted in 40 μL acetonitrile/water (1:1) per milligram dry weight.

Chromatography:

Chromatography ID:	CH004487
Instrument Name:	Agilent 1260
Column Name:	Phenomenex Luna NH2 (150 x 2mm,3um)
Column Temperature:	40
Flow Gradient:	100% to 0% B from 0–45 min and 0% B from 45–50 min
Flow Rate:	50 uL/min
Solvent A:	95% water/5% acetonitrile; 10 mM ammonium hydroxide; 10 mM ammonium acetate
Solvent B:	95% acetonitrile/5% water
Chromatography Type:	HILIC

Chromatography ID:	CH004488
Instrument Name:	Thermo Dionex Ultimate 3000 RS
Column Name:	Merck SeQuant ZIC-pHILIC (100 x 2.1mm,5um)
Column Temperature:	40
Flow Gradient:	90% B from 0-1 min and 90% to 25% B from 1–15 min
Flow Rate:	250 uL/min
Solvent A:	95% water/5% acetonitrile; 10 mM ammonium bicarbonate; 0.1% ammonium hydroxide; 2.5 mM medronic acid
Solvent B:	95% acetonitrile/5% water; 2.5 uM medronic acid
Chromatography Type:	HILIC

Chromatography ID:	CH004489
Instrument Name:	Thermo Vanquish
Column Name:	HILICON iHILIC-(P)-Classic (100 x 2.1mm,5um)
Column Temperature:	45
Flow Gradient:	0-1 min, 90% B; 12 min, 35% B; 12.5-14.5 min, 25% B; 15 min, back to 90% B
Flow Rate:	250 uL/min
Solvent A:	95% water/5% acetonitrile; 20 mM ammonium bicarbonate; 2.5 uM medronic acid; 0.1% ammonium hydroxide
Solvent B:	95% acetonitrile/5% water
Chromatography Type:	HILIC

Chromatography ID:	CH004490
Instrument Name:	Agilent 1290 Infinity
Column Name:	Phenomenex Kinetex C18 (150 x 2.1mm,2.6um)
Column Temperature:	40
Flow Gradient:	30% B from 0-3 min, 30% B to 95% B from 3–30 min and 95% B from 30–40 min
Flow Rate:	200 uL/min
Solvent A:	100% water; 0.1% formic acid
Solvent B:	100% acetonitrile; 0.1% formic acid
Chromatography Type:	Reversed phase

Analysis:

Analysis ID:	AN005910
Analysis Type:	MS
Chromatography ID:	CH004487
Num Factors:	6
Num Metabolites:	9
Units:	peak area

Analysis ID:	AN005911
Analysis Type:	MS
Chromatography ID:	CH004488
Num Factors:	6
Num Metabolites:	9
Units:	peak area

Analysis ID:	AN005912
Analysis Type:	MS
Chromatography ID:	CH004489
Num Factors:	6
Num Metabolites:	9
Units:	peak area

Analysis ID:	AN005913
Analysis Type:	MS
Chromatography ID:	CH004490
Num Factors:	6
Num Metabolites:	10
Units:	peak area