#METABOLOMICS WORKBENCH silviaradenkovic_20230418_123415 DATATRACK_ID:3869 STUDY_ID:ST002565 ANALYSIS_ID:AN004226 PROJECT_ID:PR001653
VERSION             	1
CREATED_ON             	April 18, 2023, 5:08 pm
#PROJECT
PR:PROJECT_TITLE                 	Metabolomic profiling of PMM2-CDG after fructose tracer experiments
PR:PROJECT_SUMMARY               	Abnormal polyol metabolism has been predominantly associated with diabetes,
PR:PROJECT_SUMMARY               	where excess glucose is converted to sorbitol by aldose reductase (AR).
PR:PROJECT_SUMMARY               	Recently, abnormal polyol metabolism has also been implicated in
PR:PROJECT_SUMMARY               	phosphomannomutase 2-congenital disorder of glycosylation (PMM2-CDG), and
PR:PROJECT_SUMMARY               	epalrestat, an AR inhibitor, proposed as a potential therapy for this disorder.
PR:PROJECT_SUMMARY               	Given that the PMM enzyme is not closely connected to polyol metabolism, and,
PR:PROJECT_SUMMARY               	unlike in diabetes, PMM2-CDG does not present with hyperglycemia in blood, the
PR:PROJECT_SUMMARY               	increased polyol production, and the therapeutic mechanism of epalrestat in
PR:PROJECT_SUMMARY               	PMM2-CDG remained largely elusive. PMM2-CDG is caused by deficiency of the PMM
PR:PROJECT_SUMMARY               	enzyme and results in a depletion of mannose-1-P and guanosine diphosphate
PR:PROJECT_SUMMARY               	mannose (GDP-mannose), which is essential for glycosylation. Here, we show that
PR:PROJECT_SUMMARY               	apart from glycosylation abnormalities, PMM2 deficiency also leads to changes in
PR:PROJECT_SUMMARY               	intracellular glucose flux, which results in an increase in intracellular
PR:PROJECT_SUMMARY               	polyols. To investigate the influence of fructose on polyol abundance, and
PR:PROJECT_SUMMARY               	glucose flux we performed 13C6 glucose and fructose study in patient and healthy
PR:PROJECT_SUMMARY               	control fibroblasts.
PR:INSTITUTE                     	Mayo Clinic
PR:LAST_NAME                     	Radenkovic
PR:FIRST_NAME                    	Silvia
PR:ADDRESS                       	200 2nd Ave SW Rochester MN
PR:EMAIL                         	radenkovic.silvia@mayo.edu
PR:PHONE                         	507(77) 6-6107
PR:FUNDING_SOURCE                	NIH, KU Leuven
#STUDY
ST:STUDY_TITLE                   	Metabolomic profiling of PMM2-CDG after siRNA mediated KD of AKR1b1 - 13C6
ST:STUDY_TITLE                   	glucose and fructose study
ST:STUDY_SUMMARY                 	Abnormal polyol metabolism has been predominantly associated with diabetes,
ST:STUDY_SUMMARY                 	where excess glucose is converted to sorbitol by aldose reductase (AR).
ST:STUDY_SUMMARY                 	Recently, abnormal polyol metabolism has also been implicated in
ST:STUDY_SUMMARY                 	phosphomannomutase 2-congenital disorder of glycosylation (PMM2-CDG), and
ST:STUDY_SUMMARY                 	epalrestat, an AR inhibitor, proposed as a potential therapy for this disorder.
ST:STUDY_SUMMARY                 	Given that the PMM enzyme is not closely connected to polyol metabolism, and,
ST:STUDY_SUMMARY                 	unlike in diabetes, PMM2-CDG does not present with hyperglycemia in blood, the
ST:STUDY_SUMMARY                 	increased polyol production, and the therapeutic mechanism of epalrestat in
ST:STUDY_SUMMARY                 	PMM2-CDG remained largely elusive. PMM2-CDG is caused by deficiency of the PMM
ST:STUDY_SUMMARY                 	enzyme and results in a depletion of mannose-1-P and guanosine diphosphate
ST:STUDY_SUMMARY                 	mannose (GDP-mannose), which is essential for glycosylation. Here, we show that
ST:STUDY_SUMMARY                 	apart from glycosylation abnormalities, PMM2 deficiency also leads to changes in
ST:STUDY_SUMMARY                 	intracellular glucose flux, which results in an increase in intracellular
ST:STUDY_SUMMARY                 	polyols. Ssing tracer glucose studies, we demonstrate that AR inhibition diverts
ST:STUDY_SUMMARY                 	glucose flux away from polyol production towards the synthesis of sugar
ST:STUDY_SUMMARY                 	nucleotides.
ST:INSTITUTE                     	Mayo Clinic
ST:LAST_NAME                     	Radenkovic
ST:FIRST_NAME                    	Silvia
ST:ADDRESS                       	200 2nd Ave SW Rochester MN, USA
ST:EMAIL                         	radenkovic.silvia@mayo.edu
ST:PHONE                         	507(77) 6-6107
#SUBJECT
SU:SUBJECT_TYPE                  	Cultured cells
SU:SUBJECT_SPECIES               	Homo sapiens
SU:TAXONOMY_ID                   	9606
SU:GENOTYPE_STRAIN               	WT/PMM2-CDG
SU:AGE_OR_AGE_RANGE              	40-45
SU:GENDER                        	Female
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data
SUBJECT_SAMPLE_FACTORS           	P2	SR01	Genotype:PMM2-CDG | Treatment:13C glu + 12C fructose	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR01
SUBJECT_SAMPLE_FACTORS           	P2	SR02	Genotype:PMM2-CDG | Treatment:13C glu + 12C fructose	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR02
SUBJECT_SAMPLE_FACTORS           	P2	SR03	Genotype:PMM2-CDG | Treatment:12C fructose + 12C glucose	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR03
SUBJECT_SAMPLE_FACTORS           	P2	SR04	Genotype:PMM2-CDG | Treatment:12C fructose + 12C glucose	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR04
SUBJECT_SAMPLE_FACTORS           	P2	SR05	Genotype:PMM2-CDG | Treatment:12C fructose+13C fructose	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR05
SUBJECT_SAMPLE_FACTORS           	P2	SR06	Genotype:PMM2-CDG | Treatment:12C fructose+13C fructose	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR06
SUBJECT_SAMPLE_FACTORS           	P2	SR07	Genotype:PMM2-CDG | Treatment:12C fructose + 12C glucose	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR07
SUBJECT_SAMPLE_FACTORS           	P2	SR08	Genotype:PMM2-CDG | Treatment:12C fructose + 12C glucose	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR08
SUBJECT_SAMPLE_FACTORS           	P2	SR09	Genotype:PMM2-CDG | Treatment:5.5mM 13C glucose	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR09
SUBJECT_SAMPLE_FACTORS           	P2	SR10	Genotype:PMM2-CDG | Treatment:5.5mM 13C glucose	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR10
SUBJECT_SAMPLE_FACTORS           	P2	SR11	Genotype:PMM2-CDG | Treatment:5.5mM glucose +	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR11
SUBJECT_SAMPLE_FACTORS           	P2	SR12	Genotype:PMM2-CDG | Treatment:5.5mM glucose +	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR12
SUBJECT_SAMPLE_FACTORS           	C3	SR13	Genotype:WT | Treatment:13C glu + 12C fructose	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR13
SUBJECT_SAMPLE_FACTORS           	C3	SR14	Genotype:WT | Treatment:13C glu + 12C fructose	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR14
SUBJECT_SAMPLE_FACTORS           	C3	SR15	Genotype:WT | Treatment:12C fructose + 12C glucose	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR15
SUBJECT_SAMPLE_FACTORS           	C3	SR16	Genotype:WT | Treatment:12C fructose + 12C glucose	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR16
SUBJECT_SAMPLE_FACTORS           	C3	SR17	Genotype:WT | Treatment:12C fructose+13C fructose	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR17
SUBJECT_SAMPLE_FACTORS           	C3	SR18	Genotype:WT | Treatment:12C fructose+13C fructose	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR18
SUBJECT_SAMPLE_FACTORS           	C3	SR19	Genotype:WT | Treatment:12C fructose + 12C glucose	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR19
SUBJECT_SAMPLE_FACTORS           	C3	SR20	Genotype:WT | Treatment:12C fructose + 12C glucose	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR20
SUBJECT_SAMPLE_FACTORS           	C3	SR21	Genotype:WT | Treatment:5.5mM glucose +	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR21
SUBJECT_SAMPLE_FACTORS           	C3	SR22	Genotype:WT | Treatment:5.5mM glucose +	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR22
SUBJECT_SAMPLE_FACTORS           	C3	SR23	Genotype:WT | Treatment:5.5mM 13C glucose	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR23
SUBJECT_SAMPLE_FACTORS           	C3	SR24	Genotype:WT | Treatment:5.5mM 13C glucose	Organism=Homo sapiens; Tissue type=Fibroblasts; RAW_FILE_NAME=SR24
#COLLECTION
CO:COLLECTION_SUMMARY            	Cells were washed with PBS, cells were incubated with extraction buffer for 2min
CO:COLLECTION_SUMMARY            	before scraping and transferring to a fresh eppendorf. Samples were precipitated
CO:COLLECTION_SUMMARY            	overnight at -80, then they were centrifuged at max rpm, 20min, 4 degrees C and
CO:COLLECTION_SUMMARY            	supernatant transferred to an M/S vial.
CO:SAMPLE_TYPE                   	Fibroblasts
CO:STORAGE_CONDITIONS            	-80℃
#TREATMENT
TR:TREATMENT_SUMMARY             	Cells were treated with 12C/13C glucose +/- 12C/13C fructose
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Metabolites were extracted with 80% Methanol and IS (d27 myristic acid)
SP:PROCESSING_STORAGE_CONDITIONS 	-80℃
SP:EXTRACT_STORAGE               	-80℃
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	C18 iP REVERSE PHASE
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Waters Acquity
CH:COLUMN_NAME                   	Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
CH:SOLVENT_A                     	100% water; 10mM tributylamine; 15mM acetic acid
CH:SOLVENT_B                     	100% methanol
CH:FLOW_GRADIENT                 	The gradient started with 5% of solvent B and 95% solvent A and remained at 5% B
CH:FLOW_GRADIENT                 	until 2 min post injection. A linear gradient to 37% B was carried out until 7
CH:FLOW_GRADIENT                 	min and increased to 41% until 14 min. Between 14 and 26 minutes the gradient
CH:FLOW_GRADIENT                 	increased to 95% of B and remained at 95% B for 4 minutes. At 30 min the
CH:FLOW_GRADIENT                 	gradient returned to 5% B. The chromatography was stopped at 40 min.
CH:FLOW_RATE                     	0.25 mL/min
CH:COLUMN_TEMPERATURE            	40
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Thermo Q Exactive Orbitrap
MS:INSTRUMENT_TYPE               	Orbitrap
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	NEGATIVE
MS:MS_COMMENTS                   	El-Maven polly, ThermoFisher Xcalibur; Metabolites were annotated using the
MS:MS_COMMENTS                   	inhouse standard metabolite library- elution time and m/z values.
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	AUC
MS_METABOLITE_DATA_START
Samples	SR01	SR02	SR03	SR04	SR05	SR06	SR07	SR08	SR09	SR10	SR11	SR12	SR13	SR14	SR15	SR16	SR17	SR18	SR19	SR20	SR21	SR22	SR23	SR24
Factors	Genotype:PMM2-CDG | Treatment:13C glu + 12C fructose	Genotype:PMM2-CDG | Treatment:13C glu + 12C fructose	Genotype:PMM2-CDG | Treatment:12C fructose + 12C glucose	Genotype:PMM2-CDG | Treatment:12C fructose + 12C glucose	Genotype:PMM2-CDG | Treatment:12C fructose+13C fructose	Genotype:PMM2-CDG | Treatment:12C fructose+13C fructose	Genotype:PMM2-CDG | Treatment:12C fructose + 12C glucose	Genotype:PMM2-CDG | Treatment:12C fructose + 12C glucose	Genotype:PMM2-CDG | Treatment:5.5mM 13C glucose	Genotype:PMM2-CDG | Treatment:5.5mM 13C glucose	Genotype:PMM2-CDG | Treatment:5.5mM glucose +	Genotype:PMM2-CDG | Treatment:5.5mM glucose +	Genotype:WT | Treatment:13C glu + 12C fructose	Genotype:WT | Treatment:13C glu + 12C fructose	Genotype:WT | Treatment:12C fructose + 12C glucose	Genotype:WT | Treatment:12C fructose + 12C glucose	Genotype:WT | Treatment:12C fructose+13C fructose	Genotype:WT | Treatment:12C fructose+13C fructose	Genotype:WT | Treatment:12C fructose + 12C glucose	Genotype:WT | Treatment:12C fructose + 12C glucose	Genotype:WT | Treatment:5.5mM glucose +	Genotype:WT | Treatment:5.5mM glucose +	Genotype:WT | Treatment:5.5mM 13C glucose	Genotype:WT | Treatment:5.5mM 13C glucose
Sorbitol	9.11E+06	6.44E+06	1.53E+07	1.26E+07	9.77E+06	9.28E+06	1.62E+07	1.50E+07	1.12E+07	1.02E+07	1.03E+07	9.66E+06	6.51E+06	6.59E+06	9.50E+06	9.70E+06	8.00E+06	6.70E+06	7.77E+06	6.93E+06	9.42E+06	9.56E+06	7.11E+06	6.48E+06
D-Glucose	9.32E+08	1.10E+09	1.34E+09	1.49E+09	8.00E+08	9.57E+08	1.40E+09	1.23E+09	9.30E+08	8.82E+08	1.08E+09	1.26E+09	8.12E+08	8.71E+08	1.01E+09	1.00E+09	9.78E+08	9.53E+08	1.36E+09	1.19E+09	9.87E+08	1.09E+09	9.68E+08	1.16E+09
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	parent formula	M/Z	HMDB ID	isotopeLabel	isotope count
Sorbitol	C6H14O6	181.07164	HMDB00247	C12 PARENT	m0-6
D-Glucose	C6H12O6	179.056061	HMDB00122	C12 PARENT	m0-6
METABOLITES_END
#END