#METABOLOMICS WORKBENCH xin_hu_emory_20210506_153418 DATATRACK_ID:2627 STUDY_ID:ST001802 ANALYSIS_ID:AN002924 VERSION 1 CREATED_ON 02-08-2024 #PROJECT PR:PROJECT_TITLE A scalable workflow for the human exposome PR:PROJECT_TYPE Untargeted GC-MS quantitative analysis PR:PROJECT_SUMMARY Complementing the genome with an understanding of the human exposome is an PR:PROJECT_SUMMARY important challenge for contemporary science and technology. Tens of thousands PR:PROJECT_SUMMARY of chemicals are used in commerce, yet cost for targeted environmental chemical PR:PROJECT_SUMMARY analysis limits surveillance to a few hundred known hazards. To overcome PR:PROJECT_SUMMARY limitations which prevent scaling to thousands of chemicals, we developed a PR:PROJECT_SUMMARY single-step express liquid extraction (XLE), gas chromatography high-resolution PR:PROJECT_SUMMARY mass spectrometry (GC-HRMS) analysis and computational pipeline to PR:PROJECT_SUMMARY operationalize the human exposome. We show that the workflow supports PR:PROJECT_SUMMARY quantification of environmental chemicals in human plasma (200 µL) and tissue PR:PROJECT_SUMMARY (≤ 100 mg) samples. The method also provides high resolution, sensitivity and PR:PROJECT_SUMMARY selectivity for exposome epidemiology of mass spectral features without a priori PR:PROJECT_SUMMARY knowledge of chemical identity. The simplicity of the method can facilitate PR:PROJECT_SUMMARY harmonization of environmental biomonitoring between laboratories and enable PR:PROJECT_SUMMARY population level human exposome research with limited sample volume. PR:INSTITUTE Emory University PR:DEPARTMENT Medicine, Pulmonary PR:LABORATORY Dean Jones PR:LAST_NAME Hu PR:FIRST_NAME Xin PR:ADDRESS Emory University Whitehead building (Rm 225), 615 Michael Street, Atlanta, PR:ADDRESS Georgia, 30322, USA PR:EMAIL xin.hu2@emory.edu PR:PHONE 4047275091 PR:FUNDING_SOURCE This study was supported by the NIEHS, U2C ES030163 (DPJ), U2C ES030859 (DIW) PR:FUNDING_SOURCE and P30 ES019776 (CJM), NIDDK RC2 DK118619 (KNL), NHLBI R01 HL086773 (DPJ), US PR:FUNDING_SOURCE Department of Defense W81XWH2010103 (DPJ), and the Chris M. Carlos and Catharine PR:FUNDING_SOURCE Nicole Jockisch Carlos Endowment Fund in Primary Sclerosing Cholangitis (PSC) PR:FUNDING_SOURCE (KNL). PR:DOI http://dx.doi.org/10.21228/M8VQ4D PR:CONTRIBUTORS Xin Hu, Douglas I. Walker, Yongliang Liang, M. Ryan Smith, Michael L. Orr, Brian PR:CONTRIBUTORS D. Juran, Chunyu Ma, Karan Uppal, Michael Koval, Greg S. Martin, David C. PR:CONTRIBUTORS Neujahr, Carmen J. Marsit, Young-Mi Go, Kurt Pennell, Gary W. Miller, PR:CONTRIBUTORS Konstantinos N. Lazaridis, Dean P. Jones #STUDY ST:STUDY_TITLE Human lung exposomics analysis ST:STUDY_TYPE Untargeted MS anlaysis ST:STUDY_SUMMARY We tested the general utility of XLE in a variety of human biological samples by ST:STUDY_SUMMARY analyzing human lung and thyroid tissues and stool samples. We quantified 32 ST:STUDY_SUMMARY environmental chemicals in 11 human lungs, with HCB, PCB-28 and PCB-18 being ST:STUDY_SUMMARY most frequently detected (10 out of 11). The commonly detected chemicals in ST:STUDY_SUMMARY human plasma were detected less frequently in the lung. For the 11 lungs, ST:STUDY_SUMMARY p,p’-DDE was detected in eight, PCB-153 in five, PBDE-47 and PCB-138 in four ST:STUDY_SUMMARY and PCB-180 in three. Although the plasma samples were from non-diseased ST:STUDY_SUMMARY individuals and the lungs were both diseased and non-diseased individuals, HCA ST:STUDY_SUMMARY results suggest that environmental chemical profiles in human lung may be very ST:STUDY_SUMMARY different from plasma. ST:INSTITUTE Emory University ST:DEPARTMENT Medicine/Pulmonary ST:LABORATORY Dean Jones ST:LAST_NAME Hu ST:FIRST_NAME Xin ST:ADDRESS Emory University Whitehead building (Rm 225), 615 Michael Street ST:EMAIL xin.hu2@emory.edu ST:PHONE 4047275091 ST:SUBMIT_DATE 2021-05-06 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - ExSTD5 type:external std RAW_FILE_NAME=ExSTD5.mzXML; gender=-; age=-; smoking_status=-; lung_disease=- SUBJECT_SAMPLE_FACTORS - T18-1 type:lung RAW_FILE_NAME=T18-1.mzXML; gender=M; age=59; smoking_status=YES; lung_disease=COPD SUBJECT_SAMPLE_FACTORS - T18-2 type:lung RAW_FILE_NAME=T18-2.mzXML; gender=M; age=59; smoking_status=YES; lung_disease=COPD SUBJECT_SAMPLE_FACTORS - T19-1 type:lung RAW_FILE_NAME=T19-1.mzXML; gender=F; age=59; smoking_status=YES; lung_disease=COPD/PH SUBJECT_SAMPLE_FACTORS - T19-2 type:lung RAW_FILE_NAME=T19-2.mzXML; gender=F; age=59; smoking_status=YES; lung_disease=COPD/PH SUBJECT_SAMPLE_FACTORS - T21-1 type:lung RAW_FILE_NAME=T21-1.mzXML; gender=F; age=30; smoking_status=YES; lung_disease=CF SUBJECT_SAMPLE_FACTORS - T21-2 type:lung RAW_FILE_NAME=T21-2.mzXML; gender=F; age=30; smoking_status=YES; lung_disease=CF SUBJECT_SAMPLE_FACTORS - T25-1 type:lung RAW_FILE_NAME=T25-1.mzXML; gender=F; age=45; smoking_status=YES; lung_disease=NONE SUBJECT_SAMPLE_FACTORS - T25-2 type:lung RAW_FILE_NAME=T25-2.mzXML; gender=F; age=45; smoking_status=YES; lung_disease=NONE SUBJECT_SAMPLE_FACTORS - T26-1 type:lung RAW_FILE_NAME=T26-1.mzXML; gender=M; age=57; smoking_status=NO; lung_disease=NONE SUBJECT_SAMPLE_FACTORS - T26-2 type:lung RAW_FILE_NAME=T26-2.mzXML; gender=M; age=57; smoking_status=NO; lung_disease=NONE SUBJECT_SAMPLE_FACTORS - T27-1 type:lung RAW_FILE_NAME=T27-1.mzXML; gender=F; age=72; smoking_status=NO; lung_disease=NONE SUBJECT_SAMPLE_FACTORS - T27-2 type:lung RAW_FILE_NAME=T27-2.mzXML; gender=F; age=72; smoking_status=NO; lung_disease=NONE SUBJECT_SAMPLE_FACTORS - T28-1 type:lung RAW_FILE_NAME=T28-1.mzXML; gender=M; age=18; smoking_status=YES; lung_disease=NONE SUBJECT_SAMPLE_FACTORS - T28-2 type:lung RAW_FILE_NAME=T28-2.mzXML; gender=M; age=18; smoking_status=YES; lung_disease=NONE SUBJECT_SAMPLE_FACTORS - T29-1 type:lung RAW_FILE_NAME=T29-1.mzXML; gender=M; age=51; smoking_status=YES; lung_disease=NONE SUBJECT_SAMPLE_FACTORS - T29-2 type:lung RAW_FILE_NAME=T29-2.mzXML; gender=M; age=51; smoking_status=YES; lung_disease=NONE SUBJECT_SAMPLE_FACTORS - T30-1 type:lung RAW_FILE_NAME=T30-1.mzXML; gender=M; age=0.75; smoking_status=NO; lung_disease=NONE SUBJECT_SAMPLE_FACTORS - T30-2 type:lung RAW_FILE_NAME=T30-2.mzXML; gender=M; age=0.75; smoking_status=NO; lung_disease=NONE SUBJECT_SAMPLE_FACTORS - T31-1 type:lung RAW_FILE_NAME=T31-1.mzXML; gender=F; age=25; smoking_status=NO; lung_disease=CF SUBJECT_SAMPLE_FACTORS - T31-2 type:lung RAW_FILE_NAME=T31-2.mzXML; gender=F; age=25; smoking_status=NO; lung_disease=CF SUBJECT_SAMPLE_FACTORS - T33-1 type:lung RAW_FILE_NAME=T33-1.mzXML; gender=F; age=54; smoking_status=-; lung_disease=COPD SUBJECT_SAMPLE_FACTORS - T33-2 type:lung RAW_FILE_NAME=T33-2.mzXML; gender=F; age=54; smoking_status=-; lung_disease=COPD SUBJECT_SAMPLE_FACTORS - NIST1958_1-1 type:SRM1958 RAW_FILE_NAME=NIST1958_1-1.mzXML; gender=-; age=-; smoking_status=-; lung_disease=- SUBJECT_SAMPLE_FACTORS - NIST1958_1-2 type:SRM1958 RAW_FILE_NAME=NIST1958_1-2.mzXML; gender=-; age=-; smoking_status=-; lung_disease=- SUBJECT_SAMPLE_FACTORS - NIST1958_2-1 type:SRM1958 RAW_FILE_NAME=NIST1958_2-1.mzXML; gender=-; age=-; smoking_status=-; lung_disease=- SUBJECT_SAMPLE_FACTORS - NIST1958_2-2 type:SRM1958 RAW_FILE_NAME=NIST1958_2-2.mzXML; gender=-; age=-; smoking_status=-; lung_disease=- #COLLECTION CO:COLLECTION_SUMMARY Whole human lungs were from eleven individuals; 4 were end-stage diseased lungs CO:COLLECTION_SUMMARY acquired from the Emory Transplant Center (IRB approval No. 00006248), one was CO:COLLECTION_SUMMARY from Cystic Fibrosis Biospecimen Registry at Emory University (IRB approval No. CO:COLLECTION_SUMMARY 00095116) and 6 non-diseased post-mortem lungs were obtained through the CO:COLLECTION_SUMMARY International Institute for the Advancement of Medicine (IIAM, Edison, NJ) or CO:COLLECTION_SUMMARY Novabiosis (Morrisville, NC). CO:SAMPLE_TYPE Lung #TREATMENT TR:TREATMENT_SUMMARY Tissue materials were processed similarly with a consistent ratio of 1:5 (sample TR:TREATMENT_SUMMARY to hexane-ethyl acetate mixture), i.e., 100 mg lung was homogenized in 300 µL TR:TREATMENT_SUMMARY water and extracted with 150 µL formic acid and 400 µL hexane-ethyl acetate TR:TREATMENT_SUMMARY mixture, while 40 mg thyroid was homogenized in 250 µL water and extracted with TR:TREATMENT_SUMMARY 50 µL formic acid and 200 µL hexane-ethyl acetate mixture. Stool samples (100 TR:TREATMENT_SUMMARY mg) were homogenized and extracted directly in 50 µL formic acid and 500 µL TR:TREATMENT_SUMMARY hexane-ethyl acetate mixture and then processed as plasma samples. The variation TR:TREATMENT_SUMMARY of 1:4 from 1:5 in lung extraction was arbitrary in consideration of the lower TR:TREATMENT_SUMMARY density of lung as an organ. The internal standards were spiked at final TR:TREATMENT_SUMMARY concentration: 1 ng/mL. The sample mixture was shaken vigorously on ice using TR:TREATMENT_SUMMARY multi-tube vortexer (VWR VX-2500) for 1 h and centrifuged at 1000 g, 4 °C for TR:TREATMENT_SUMMARY 10 min. The sample mixture was chilled during entire extraction procedure. The TR:TREATMENT_SUMMARY organic supernatant was transferred to a new tube with 25 mg MgSO4 (≥99.99% TR:TREATMENT_SUMMARY pure, Sigma-Aldrich) for testing of QuEChERS based procedure, and vortexed TR:TREATMENT_SUMMARY vigorously to remove water. After 10 min centrifugation at 1000 g, 80 µL of the TR:TREATMENT_SUMMARY final supernatant was spiked with instrumental internal standards (final TR:TREATMENT_SUMMARY concentration: 1 ng/mL) for analysis. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Same as treatment #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Samples were analyzed with three injections using GC-HRMS with a Thermo CH:CHROMATOGRAPHY_SUMMARY Scientific Q Exactive GC hybrid quadrupole Orbitrap mass spectrometer with 2 µL CH:CHROMATOGRAPHY_SUMMARY per injection. A capillary DB-5MS column (15 m × 0.25 mm × 0.25 µm film CH:CHROMATOGRAPHY_SUMMARY thickness) was used with the following temperature program: hold 75 °C for 1 CH:CHROMATOGRAPHY_SUMMARY min, 25 °C/min to 180 °C, 6 °C/min to 250 °C, 20 °C/min to 350 °C and hold CH:CHROMATOGRAPHY_SUMMARY for 5 min. The flow rate of the helium carrier gas was 1 mL/min. Ion source and CH:CHROMATOGRAPHY_SUMMARY transfer line temperatures were 250°C and 280°C, respectively. Data were CH:CHROMATOGRAPHY_SUMMARY collected from 3 to 24.37 min with positive electron ionization (EI) mode (+70 CH:CHROMATOGRAPHY_SUMMARY eV), scanning from m/z 85.0000 to 850.0000 with a resolution of 60,000. CH:INSTRUMENT_NAME Thermo Trace 1310 CH:COLUMN_NAME Agilent DB5-MS (15m x 0.25mm,0.25um) CH:CHROMATOGRAPHY_TYPE GC #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE EI MS:MS_COMMENTS Data were collected from 3 to 24.37 min with positive electron ionization (EI) MS:MS_COMMENTS mode (+70 eV), scanning from m/z 85.0000 to 850.0000 with a resolution of MS:MS_COMMENTS 60,000. Raw data were examined by checking signal-to-noise ratio, peak shape and MS:MS_COMMENTS spectral information for surrogate and internal standards using a 5 ppm m/z MS:MS_COMMENTS tolerance and 30 s retention time window in xCalibur Qualbrowser software. Data MS:MS_COMMENTS extraction was performed by XCMS to generate about 40,000 chemical features MS:MS_COMMENTS identified by spectral m/z and retention time. MS:ION_MODE POSITIVE MS:MS_RESULTS_FILE ST001802_AN002924_Results.txt UNITS:raw intensity Has m/z:Yes Has RT:Yes RT units:Seconds #END