Comment[ArrayExpressAccession]	E-GEOD-42612
MAGE-TAB Version	1.1										
Public Release Date	2012-11-30
Investigation Title	Quiescent Fibroblasts Exhibit High Metabolic Activity										
Comment[Submitted Name]	Quiescent Fibroblasts Exhibit High Metabolic Activity
Experiment Description	Many cells in mammals exist in the state of quiescence, which is characterized by reversible exit from the cell cycle. Quiescent cells are widely reported to exhibit reduced size, nucleotide synthesis, and metabolic activity. Much lower glycolytic rates have been reported in quiescent compared with proliferating lymphocytes. In contrast, we show here that primary human fibroblasts continue to exhibit high metabolic rates when induced into quiescence via contact inhibition. By monitoring isotope labeling through metabolic pathways and quantitatively identifying fluxes from the data, we show that contact-inhibited fibroblasts utilize glucose in all branches of central carbon metabolism at rates similar to those of proliferating cells, with greater overflow flux from the pentose phosphate pathway back to glycolysis. Inhibition of the pentose phosphate pathway resulted in apoptosis preferentially in quiescent fibroblasts. By feeding the cells labeled glutamine, we also detected a “backwards” flux in the tricarboxylic acid cycle from α-ketoglutarate to citrate that was enhanced in contact-inhibited fibroblasts; this flux likely contributes to shuttling of NADPH from the mitochondrion to cytosol for redox defense or fatty acid synthesis. The high metabolic activity of the fibroblasts was directed in part toward breakdown and resynthesis of protein and lipid, and in part toward excretion of extracellular matrix proteins. Thus, reduced metabolic activity is not a hallmark of the quiescent state. Quiescent fibroblasts, relieved of the biosynthetic requirements associated with generating progeny, direct their metabolic activity to preservation of self integrity and alternative functions beneficial to the organism as a whole. mRNAs were analyzed by two color microarray from two separate human neonatal dermal fibroblasts cell lines in proliferating, 7 days contact inhibition, or 14 days contact inhibition. Contact inhibited samples were co-hybridized to proliferating samples as a control, while an additional array co-hybridized the two proliferating samples to analyze reproducibility.										
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl									
Person Last Name	Suh	Lemons	Feng	Bennet	Legesse-Miller	Johnson	Raitman	Pollina	Rabitz	Rabinowitz	Coller
Person First Name	Eric	Johanna	Xiao-Jiang	Bryson	Aster	Elizabeth	Irene	Elizabeth	Herschel	Joshua	Hilary
Person Mid Initials	Jungwoo	M		D		L		A	A	D	A
Person Email	geo@ncbi.nlm.nih.gov										
Person Affiliation	Princeton University										
Person Address	Molecular Biology, Princeton University, 14 Washington Rd, Princeton, NJ, USA										
Person Roles	submitter										
Protocol Name	P-GSE42612-1	P-GSE42612-6	P-GSE42612-5	P-GSE42612-2	P-GSE42612-3	P-GSE42612-4	P-GSE42612-7				
Protocol Description	ID_REF =  VALUE = log2 transformed ratio of Cy5 to Cy3 signal.	Scanned using Agilent G2505B array scanner according to manufacturer's protocol.	Labeled cRNA were hybridized to arrays according to Agilent's manufacturer's protocol	Fibroblasts were maintained in asynchronously proliferating culture, 7 days of contact inhibition, or 14 days of contact inhibition	Total RNA isolated from fibroblasts 48 hours post-transfection using mirVana total RNA isolation kit and procedure.	Total RNA extracts were cRNA labeled using the Agilent Low RNA Input Fluorescent Labeling Kit according to the manufacturer's protocol	Probes were filtered to eliminate those flagged by Feature Extractor for saturation or no signal above background in any array Replicated signals from identical sequence-probes were averaged. For each array, the ratio of Cy5 to Cy3 (red to green) was log2 transformed and zero-centered.				
Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	specified_biomaterial_action	nucleic_acid_extraction	labeling	feature_extraction				
Publication Title	Quiescent fibroblasts exhibit high metabolic activity.										
Publication Author List	Lemons JM, Feng XJ, Bennett BD, Legesse-Miller A, Johnson EL, Raitman I, Pollina EA, Rabitz HA, Rabinowitz JD, Coller HA										
PubMed ID	21049082										
Publication DOI	10.1371/journal.pbio.1000514										
Comment[SecondaryAccession]	GSE42612										
Comment[GEOReleaseDate]	2012-11-30										
Comment[ArrayExpressSubmissionDate]	2012-11-29										
Comment[GEOLastUpdateDate]	2013-01-04										
Comment[AEExperimentType]	transcription profiling by array										
SDRF File	E-GEOD-42612.sdrf.txt