#METABOLOMICS WORKBENCH lai_yunjia_20210716_173915 DATATRACK_ID:2750 STUDY_ID:ST001871 ANALYSIS_ID:AN003033 PROJECT_ID:PR001181
VERSION             	1
CREATED_ON             	July 19, 2021, 7:05 pm
#PROJECT
PR:PROJECT_TITLE                 	Effects of Acute 2,3,7,8-Tetrachlorodibenzo-p-dioxin Exposure on the Circulating
PR:PROJECT_TITLE                 	and Cecal Metabolome Profile
PR:PROJECT_TYPE                  	Untargeted metabolomics
PR:PROJECT_SUMMARY               	2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is a polyhalogenated planar
PR:PROJECT_SUMMARY               	hydrocarbon belonging to a group of highly toxic and persistent environmental
PR:PROJECT_SUMMARY               	contaminants known as “dioxins”. TCDD is an animal teratogen and carcinogen
PR:PROJECT_SUMMARY               	that is well characterized for causing immunosuppression through activation of
PR:PROJECT_SUMMARY               	Aryl Hydrocarbon Receptor (AHR). In the current study, we investigated the
PR:PROJECT_SUMMARY               	effect of exposure of mice to an acute dose of TCDD on the metabolic profile
PR:PROJECT_SUMMARY               	within the serum and cecal contents to better define the effects of TCDD on host
PR:PROJECT_SUMMARY               	physiology. Our findings demonstrated that within the circulating metabolome
PR:PROJECT_SUMMARY               	following acute TCDD, there was significant dysregulation in the metabolism of
PR:PROJECT_SUMMARY               	bioactive lipids, amino acids, and carbohydrates when compared to the VEH
PR:PROJECT_SUMMARY               	treated mice. These wide-spread changes in metabolite abundance were identified
PR:PROJECT_SUMMARY               	to regulate host immunity via modulating Nuclear Factor-Kappa B (NF-κB) and
PR:PROJECT_SUMMARY               	Extracellular Signal‑Regulated Protein Kinase (ERK1/2) activity, and work as
PR:PROJECT_SUMMARY               	biomarkers for a variety of organ injuries and dysfunctions that follow TCDD
PR:PROJECT_SUMMARY               	exposure. Within the cecal content, of mice exposed to TCDD, we were able to
PR:PROJECT_SUMMARY               	detect changes in inflammatory markers that regulate NF-κB, markers of
PR:PROJECT_SUMMARY               	injury-related inflammation, and changes in lysine degradation, nicotinamide
PR:PROJECT_SUMMARY               	metabolism, and butanoate metabolism, which suggested an immediate suppression
PR:PROJECT_SUMMARY               	microbial metabolism. Collectively, these results demonstrate that acute TCDD
PR:PROJECT_SUMMARY               	exposure results in immediate irregularities in the circulating and intestinal
PR:PROJECT_SUMMARY               	metabolome which likely contributes to TCDD toxicity and can be used as
PR:PROJECT_SUMMARY               	biomarkers for the early detection of individual exposure.
PR:INSTITUTE                     	University of South Carolina School of Medicine
PR:DEPARTMENT                    	Department of Pathology
PR:LABORATORY                    	On behalf of Dr. Mitzi Nagarkatti Lab
PR:LAST_NAME                     	Lai
PR:FIRST_NAME                    	Yunjia
PR:ADDRESS                       	1104 MHRC, 135 Dauer Dr., Chapel Hill, NC, 27599, USA
PR:EMAIL                         	yunjia.lai@outlook.com
PR:PHONE                         	9194805489
PR:FUNDING_SOURCE                	National Institute of Health: P01AT003961, P20GM103641, R01ES030144, R01AI129788
PR:FUNDING_SOURCE                	and R01AI123947
PR:PROJECT_COMMENTS              	This is supporting metabolomics data for the publication in Chemosphere.
PR:PUBLICATIONS                  	Chemosphere
#STUDY
ST:STUDY_TITLE                   	Untargeted LC-MS metabolomics analysis of cecal content of mice treated with
ST:STUDY_TITLE                   	TCDD vs. vehicle control (part I)
ST:STUDY_SUMMARY                 	Six-week-old female wildtype (WT) C57BL/6 mice were administered a single 100µl
ST:STUDY_SUMMARY                 	intraperitoneal injection containing sterile corn oil (VEH group) or an
ST:STUDY_SUMMARY                 	intraperitoneal injection of 10µg/kg TCDD suspended within sterile corn oil
ST:STUDY_SUMMARY                 	(TCDD group). At the 72h time point following TCDD or VEH exposure, the mice
ST:STUDY_SUMMARY                 	were humanely euthanized by an overdose of inhaled isoflurane. During necropsy,
ST:STUDY_SUMMARY                 	cecal content and blood serum samples were collected for untargeted metabolomics
ST:STUDY_SUMMARY                 	profiling.
ST:INSTITUTE                     	University of South Carolina School of Medicine
ST:DEPARTMENT                    	Department of Pathology
ST:LABORATORY                    	(On behalf of) Mitzi Nagarkatti Lab
ST:LAST_NAME                     	Lai
ST:FIRST_NAME                    	Yunjia
ST:ADDRESS                       	135 Dauer Drive, Chapel Hill, NC 27599
ST:EMAIL                         	yunjia.lai@outlook.com
ST:NUM_GROUPS                    	2
ST:TOTAL_SUBJECTS                	20
ST:NUM_FEMALES                   	20
ST:PUBLICATIONS                  	Chemosphere
ST:STUDY_TYPE                    	Untargeted metabolomics
ST:PHONE                         	919-480-5489
#SUBJECT
SU:SUBJECT_TYPE                  	Mammal
SU:SUBJECT_SPECIES               	Mus musculus
SU:TAXONOMY_ID                   	10090
SU:GENOTYPE_STRAIN               	C57BL/6 mice (Wild-type)
SU:AGE_OR_AGE_RANGE              	six weeks old
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           	-	CV1	Experimental factor:Vehicle	Mouse_strain=C57BL/6; Gender=Female; RAW_FILE_NAME=CV1.raw
SUBJECT_SAMPLE_FACTORS           	-	CV2	Experimental factor:Vehicle	Mouse_strain=C57BL/6; Gender=Female; RAW_FILE_NAME=CV2.raw
SUBJECT_SAMPLE_FACTORS           	-	CV3	Experimental factor:Vehicle	Mouse_strain=C57BL/6; Gender=Female; RAW_FILE_NAME=CV3.raw
SUBJECT_SAMPLE_FACTORS           	-	CV4	Experimental factor:Vehicle	Mouse_strain=C57BL/6; Gender=Female; RAW_FILE_NAME=CV4.raw
SUBJECT_SAMPLE_FACTORS           	-	CV5	Experimental factor:Vehicle	Mouse_strain=C57BL/6; Gender=Female; RAW_FILE_NAME=CV5.raw
SUBJECT_SAMPLE_FACTORS           	-	CV6	Experimental factor:Vehicle	Mouse_strain=C57BL/6; Gender=Female; RAW_FILE_NAME=CV6.raw
SUBJECT_SAMPLE_FACTORS           	-	CV7	Experimental factor:Vehicle	Mouse_strain=C57BL/6; Gender=Female; RAW_FILE_NAME=CV7.raw
SUBJECT_SAMPLE_FACTORS           	-	CV8	Experimental factor:Vehicle	Mouse_strain=C57BL/6; Gender=Female; RAW_FILE_NAME=CV8.raw
SUBJECT_SAMPLE_FACTORS           	-	CV9	Experimental factor:Vehicle	Mouse_strain=C57BL/6; Gender=Female; RAW_FILE_NAME=CV9.raw
SUBJECT_SAMPLE_FACTORS           	-	CV10	Experimental factor:Vehicle	Mouse_strain=C57BL/6; Gender=Female; RAW_FILE_NAME=CV10.raw
SUBJECT_SAMPLE_FACTORS           	-	CT1	Experimental factor:TCDD	Mouse_strain=C57BL/6; Gender=Female; RAW_FILE_NAME=CT1.raw
SUBJECT_SAMPLE_FACTORS           	-	CT2	Experimental factor:TCDD	Mouse_strain=C57BL/6; Gender=Female; RAW_FILE_NAME=CT2.raw
SUBJECT_SAMPLE_FACTORS           	-	CT3	Experimental factor:TCDD	Mouse_strain=C57BL/6; Gender=Female; RAW_FILE_NAME=CT3.raw
SUBJECT_SAMPLE_FACTORS           	-	CT4	Experimental factor:TCDD	Mouse_strain=C57BL/6; Gender=Female; RAW_FILE_NAME=CT4.raw
SUBJECT_SAMPLE_FACTORS           	-	CT5	Experimental factor:TCDD	Mouse_strain=C57BL/6; Gender=Female; RAW_FILE_NAME=CT5.raw
SUBJECT_SAMPLE_FACTORS           	-	CT6	Experimental factor:TCDD	Mouse_strain=C57BL/6; Gender=Female; RAW_FILE_NAME=CT6.raw
SUBJECT_SAMPLE_FACTORS           	-	CT7	Experimental factor:TCDD	Mouse_strain=C57BL/6; Gender=Female; RAW_FILE_NAME=CT7.raw
SUBJECT_SAMPLE_FACTORS           	-	CT8	Experimental factor:TCDD	Mouse_strain=C57BL/6; Gender=Female; RAW_FILE_NAME=CT8.raw
SUBJECT_SAMPLE_FACTORS           	-	CT9	Experimental factor:TCDD	Mouse_strain=C57BL/6; Gender=Female; RAW_FILE_NAME=CT9.raw
SUBJECT_SAMPLE_FACTORS           	-	CT10	Experimental factor:TCDD	Mouse_strain=C57BL/6; Gender=Female; RAW_FILE_NAME=CT10.raw
#COLLECTION
CO:COLLECTION_SUMMARY            	Six-week-old female wildtype (WT) C57BL/6 mice acquired from Jackson
CO:COLLECTION_SUMMARY            	Laboratories (Bar Harbor, ME) were housed in an AAALAC-accredited
CO:COLLECTION_SUMMARY            	specific-pathogen-free animal facility located at the grounds of the University
CO:COLLECTION_SUMMARY            	of South Carolina School of Medicine for the entirety of all experiments. Mice
CO:COLLECTION_SUMMARY            	within the facility were housed within polycarbonate cages containing cellulose
CO:COLLECTION_SUMMARY            	fiber chips as bedding in a temperature and humidity-controlled environment.
CO:COLLECTION_SUMMARY            	After a 2-week acclimatization period, the mice were divided randomly into two
CO:COLLECTION_SUMMARY            	groups that would be administered a single 100µl intraperitoneal injection
CO:COLLECTION_SUMMARY            	containing sterile corn oil (VEH group) or an intraperitoneal injection of
CO:COLLECTION_SUMMARY            	10µg/kg TCDD suspended within sterile corn oil (TCDD group). At the 72h time
CO:COLLECTION_SUMMARY            	point following TCDD or VEH exposure, the mice were humanely euthanized by an
CO:COLLECTION_SUMMARY            	overdose of inhaled isoflurane. Cecal content and blood sera were collected at
CO:COLLECTION_SUMMARY            	the time of necropsy.
CO:SAMPLE_TYPE                   	Cecal content
#TREATMENT
TR:TREATMENT_SUMMARY             	Six-week-old female wildtype (WT) C57BL/6 mice acquired from Jackson
TR:TREATMENT_SUMMARY             	Laboratories (Bar Harbor, ME) were housed in an AAALAC-accredited
TR:TREATMENT_SUMMARY             	specific-pathogen-free animal facility located at the grounds of the University
TR:TREATMENT_SUMMARY             	of South Carolina School of Medicine for the entirety of all experiments. Mice
TR:TREATMENT_SUMMARY             	within the facility were housed within polycarbonate cages containing cellulose
TR:TREATMENT_SUMMARY             	fiber chips as bedding in a temperature and humidity-controlled environment.
TR:TREATMENT_SUMMARY             	After a 2-week acclimatization period, the mice were divided randomly into two
TR:TREATMENT_SUMMARY             	groups that would be administered a single 100µl intraperitoneal injection
TR:TREATMENT_SUMMARY             	containing sterile corn oil (VEH group) or an intraperitoneal injection of
TR:TREATMENT_SUMMARY             	10µg/kg TCDD suspended within sterile corn oil (TCDD group). At the 72h time
TR:TREATMENT_SUMMARY             	point following TCDD or VEH exposure, the mice were humanely euthanized by an
TR:TREATMENT_SUMMARY             	overdose of inhaled isoflurane. Cecal content and blood sera were collected at
TR:TREATMENT_SUMMARY             	the time of necropsy.
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Cecal content and serum samples were processed according to previously described
SP:SAMPLEPREP_SUMMARY            	methods for the metabolomic profiling using liquid chromatography-mass
SP:SAMPLEPREP_SUMMARY            	spectrometry (LC-MS) with slight modifications. For cecal content, ~25 mg was
SP:SAMPLEPREP_SUMMARY            	aliquoted into 1.5-mL Eppendorf tubes (Hamburg, Germany) containing ~20 mg acid
SP:SAMPLEPREP_SUMMARY            	washed glass beads (Sigma-Aldrich, St. Louis, MO), extracted into ice-cold
SP:SAMPLEPREP_SUMMARY            	MeOH:water (1:1, v/v) on a Qiagen TissueLyzer at 50 Hz for 10 min (Hilden,
SP:SAMPLEPREP_SUMMARY            	Germany), and centrifuged at 12,000 rpm for 10 min. For blood sera, 20 µL
SP:SAMPLEPREP_SUMMARY            	aliquots were extracted by adding 180 µL cold MeOH, briefly vortexed, and
SP:SAMPLEPREP_SUMMARY            	incubated at -20ºC for 30 min for protein precipitation. The supernatants of
SP:SAMPLEPREP_SUMMARY            	both matrices were dried in a CentriVap vacuum concentrator (Labconco, MO) and
SP:SAMPLEPREP_SUMMARY            	resuspended in ACN:water (2:98, v/v) upon analysis.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Thermo Vanquish
CH:COLUMN_NAME                   	Waters Acquity BEH HSS T3 (100 x 2.1mm, 1.8um)
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Thermo Q Exactive Orbitrap
MS:INSTRUMENT_TYPE               	Orbitrap
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	POSITIVE
MS:MS_COMMENTS                   	fullscan *.raw data acquired by Thermo XCalibur software
MS:MS_RESULTS_FILE               	ST001871_AN003033_Results.txt	UNITS:m/z	Has m/z:Yes	Has RT:Yes	RT units:Minutes
#END