#METABOLOMICS WORKBENCH alexchao_20220422_055158 DATATRACK_ID:3214 STUDY_ID:ST002151 ANALYSIS_ID:AN003522 PROJECT_ID:PR001364 VERSION 1 CREATED_ON April 22, 2022, 7:26 am #PROJECT PR:PROJECT_TITLE Placenta NTA studies PR:PROJECT_SUMMARY Multi-omics study on placental samples to characterize xenobiotics and PR:PROJECT_SUMMARY epigenomic/transcriptomic changes associated with preeclampsia PR:INSTITUTE U.S. EPA PR:LAST_NAME Chao PR:FIRST_NAME Alex PR:ADDRESS 109 TW Alexander Dr, Durham, NC 27709, USA PR:EMAIL chao.alex@epa.gov PR:PHONE 9195414261 #STUDY ST:STUDY_TITLE Integrative Exposomic, Transcriptomic, Epigenomic Analyses of Human Placental ST:STUDY_TITLE Samples Links Understudied Chemicals to Preeclampsia ST:STUDY_SUMMARY Background Environmental health research has recently undergone a dramatic ST:STUDY_SUMMARY shift, with ongoing technological advancements allowing for broader coverage of ST:STUDY_SUMMARY exposure and molecular biology signatures. Approaches to integrate such measures ST:STUDY_SUMMARY are still needed to increase understanding between systems-level exposure and ST:STUDY_SUMMARY biology. Objectives We address this gap by evaluating placental tissues to ST:STUDY_SUMMARY identify novel chemical-biological interactions associated with preeclampsia. ST:STUDY_SUMMARY This study tests the hypothesis that understudied chemicals are present in the ST:STUDY_SUMMARY human placenta and associated with preeclampsia-relevant disruptions, including ST:STUDY_SUMMARY overall case status (preeclamptic vs. normotensive patients) and underlying ST:STUDY_SUMMARY transcriptomic/epigenomic signatures. Methods A non-targeted analysis based on ST:STUDY_SUMMARY high-resolution mass spectrometry was used to analyze placental tissues from a ST:STUDY_SUMMARY cohort of 35 patients with preeclampsia (n = 18) and normotensive (n = 17) ST:STUDY_SUMMARY pregnancies. Molecular feature data were queried against chemicals within the ST:STUDY_SUMMARY U.S. Environmental Protection Agency’s DSSTox database, and prioritized for ST:STUDY_SUMMARY confirmation based on association with preeclampsia case status and confidence ST:STUDY_SUMMARY of chemical identification. All molecular features were evaluated for ST:STUDY_SUMMARY relationships to mRNA, microRNA, and CpG methylation (i.e., multi-omic) ST:STUDY_SUMMARY signature alterations involved in preeclampsia. Results A total of 183 molecular ST:STUDY_SUMMARY features were identified with significantly differentiated abundance in ST:STUDY_SUMMARY placental extracts of preeclamptic patients; these features clustered into ST:STUDY_SUMMARY distinct chemical groupings using unsupervised methods. Of these features, 53 ST:STUDY_SUMMARY were identified (mapping to 40 distinct chemicals) using chemical standards, ST:STUDY_SUMMARY fragmentation spectra, and chemical metadata. In general, human metabolites had ST:STUDY_SUMMARY the largest feature intensities and strongest associations with ST:STUDY_SUMMARY preeclampsia-relevant multi-omic changes. Exogenous drugs were second most ST:STUDY_SUMMARY abundant and had fewer associations with multi-omic changes. Other exogenous ST:STUDY_SUMMARY chemicals (non-drugs) were least abundant and had the fewest associations with ST:STUDY_SUMMARY multi-omic changes. Conclusions These global data trends suggest that human ST:STUDY_SUMMARY metabolites are heavily intertwined with biological processes involved in ST:STUDY_SUMMARY preeclampsia etiology, while exogenous chemicals may still impact select ST:STUDY_SUMMARY transcriptomic/epigenomic processes. This study serves as a demonstration of ST:STUDY_SUMMARY merging systems exposures with systems biology to better understand ST:STUDY_SUMMARY chemical-disease relationships. 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Q19_Negative_MSMS Treatment:preeclampsia RAW_FILE_NAME=Q19_Negative_MS_Placenta_MSMS.mgf SUBJECT_SAMPLE_FACTORS - Q20_Negative_MSMS Treatment:preeclampsia RAW_FILE_NAME=Q20_Negative_MS_Placenta_MSMS.mgf SUBJECT_SAMPLE_FACTORS - Blank_Positive_MS_UNC_1 Treatment:blank RAW_FILE_NAME=Blank_Positive_MS_UNC_1.mzdata SUBJECT_SAMPLE_FACTORS - Blank_Positive_MS_UNC_2 Treatment:blank RAW_FILE_NAME=Blank_Positive_MS_UNC_2.mzdata SUBJECT_SAMPLE_FACTORS - Blank_Positive_MS_UNC_3 Treatment:blank RAW_FILE_NAME=Blank_Positive_MS_UNC_3.mzdata SUBJECT_SAMPLE_FACTORS - QC_Positive_MS_Pool_1 Treatment:QC RAW_FILE_NAME=QC_Positive_MS_Pool_1.mzdata SUBJECT_SAMPLE_FACTORS - QC_Positive_MS_Pool_2 Treatment:QC RAW_FILE_NAME=QC_Positive_MS_Pool_2.mzdata SUBJECT_SAMPLE_FACTORS - QC_Positive_MS_Pool_3 Treatment:QC RAW_FILE_NAME=QC_Positive_MS_Pool_3.mzdata SUBJECT_SAMPLE_FACTORS - QC_Positive_MS_Pool_Front1 Treatment:QC RAW_FILE_NAME=QC_Positive_MS_Pool_Front1.mzdata SUBJECT_SAMPLE_FACTORS - QC_Positive_MS_Pool_Front2 Treatment:QC RAW_FILE_NAME=QC_Positive_MS_Pool_Front2.mzdata SUBJECT_SAMPLE_FACTORS - QC_Positive_MS_Pool_Front3 Treatment:QC RAW_FILE_NAME=QC_Positive_MS_Pool_Front3.mzdata SUBJECT_SAMPLE_FACTORS - QC_Positive_MS_Pool_Front4 Treatment:QC RAW_FILE_NAME=QC_Positive_MS_Pool_Front4.mzdata SUBJECT_SAMPLE_FACTORS - QC_Positive_MS_Pool_Front5 Treatment:QC RAW_FILE_NAME=QC_Positive_MS_Pool_Front5.mzdata SUBJECT_SAMPLE_FACTORS - QC_Positive_MS_Pool_Mid1 Treatment:QC RAW_FILE_NAME=QC_Positive_MS_Pool_Mid1.mzdata SUBJECT_SAMPLE_FACTORS - QC_Positive_MS_Pool_Mid2 Treatment:QC RAW_FILE_NAME=QC_Positive_MS_Pool_Mid2.mzdata SUBJECT_SAMPLE_FACTORS - QC_Positive_MS_Pool_Mid3 Treatment:QC RAW_FILE_NAME=QC_Positive_MS_Pool_Mid3.mzdata SUBJECT_SAMPLE_FACTORS - Blank_Negative_MS_UNC_1 Treatment:blank RAW_FILE_NAME=Blank_Negative_MS_UNC_1.mzdata SUBJECT_SAMPLE_FACTORS - Blank_Negative_MS_UNC_2 Treatment:blank RAW_FILE_NAME=Blank_Negative_MS_UNC_2.mzdata SUBJECT_SAMPLE_FACTORS - Blank_Negative_MS_UNC_3 Treatment:blank RAW_FILE_NAME=Blank_Negative_MS_UNC_3.mzdata SUBJECT_SAMPLE_FACTORS - QC_Negative_MS_Pool_1 Treatment:QC RAW_FILE_NAME=QC_Negative_MS_Pool_1.mzdata SUBJECT_SAMPLE_FACTORS - QC_Negative_MS_Pool_2 Treatment:QC RAW_FILE_NAME=QC_Negative_MS_Pool_2.mzdata SUBJECT_SAMPLE_FACTORS - QC_Negative_MS_Pool_3 Treatment:QC RAW_FILE_NAME=QC_Negative_MS_Pool_3.mzdata SUBJECT_SAMPLE_FACTORS - QC_Negative_MS_Pool_Front1 Treatment:QC RAW_FILE_NAME=QC_Negative_MS_Pool_Front1.mzdata SUBJECT_SAMPLE_FACTORS - QC_Negative_MS_Pool_Front2 Treatment:QC RAW_FILE_NAME=QC_Negative_MS_Pool_Front2.mzdata SUBJECT_SAMPLE_FACTORS - QC_Negative_MS_Pool_Front3 Treatment:QC RAW_FILE_NAME=QC_Negative_MS_Pool_Front3.mzdata SUBJECT_SAMPLE_FACTORS - QC_Negative_MS_Pool_Front4 Treatment:QC RAW_FILE_NAME=QC_Negative_MS_Pool_Front4.mzdata SUBJECT_SAMPLE_FACTORS - QC_Negative_MS_Pool_Front5 Treatment:QC RAW_FILE_NAME=QC_Negative_MS_Pool_Front5.mzdata SUBJECT_SAMPLE_FACTORS - QC_Negative_MS_Pool_Mid1 Treatment:QC RAW_FILE_NAME=QC_Negative_MS_Pool_Mid1.mzdata SUBJECT_SAMPLE_FACTORS - QC_Negative_MS_Pool_Mid2 Treatment:QC RAW_FILE_NAME=QC_Negative_MS_Pool_Mid2.mzdata SUBJECT_SAMPLE_FACTORS - QC_Negative_MS_Pool_Mid3 Treatment:QC RAW_FILE_NAME=QC_Negative_MS_Pool_Mid3.mzdata #COLLECTION CO:COLLECTION_SUMMARY Placentas were first processed by collecting samples ~4-6 inches in length and CO:COLLECTION_SUMMARY ½ inch in diameter via cross-section punch biopsy, with blinded identifiers to CO:COLLECTION_SUMMARY ensure unbiased collection. These samples were stored at -80°C, until further CO:COLLECTION_SUMMARY processing on dry ice into individual samples for chemical analyses. Here, CO:COLLECTION_SUMMARY sterile scalpels were used to cut samples in half and a ¼ inch slice was CO:COLLECTION_SUMMARY removed from the middle and weighed, yielding isolated samples ranging in weight CO:COLLECTION_SUMMARY between 0.4 and 0.6 g. CO:SAMPLE_TYPE Placenta #TREATMENT TR:TREATMENT_SUMMARY Placentas were first processed by collecting samples ~4-6 inches in length and TR:TREATMENT_SUMMARY ½ inch in diameter via cross-section punch biopsy, with blinded identifiers to TR:TREATMENT_SUMMARY ensure unbiased collection. These samples were stored at -80°C, until further TR:TREATMENT_SUMMARY processing on dry ice into individual samples for chemical analyses. Here, TR:TREATMENT_SUMMARY sterile scalpels were used to cut samples in half and a ¼ inch slice was TR:TREATMENT_SUMMARY removed from the middle and weighed, yielding isolated samples ranging in weight TR:TREATMENT_SUMMARY between 0.4 and 0.6 g. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY One sample per tissue was used in chemical analyses. Chemicals were separated SP:SAMPLEPREP_SUMMARY from tissue via solid-liquid extraction by adding 2 mL of room temperature SP:SAMPLEPREP_SUMMARY water:acetonitrile (1:1) per sample. Placenta samples were disrupted and SP:SAMPLEPREP_SUMMARY homogenized using a TissueRuptor (Qiagen), vortexed for 5 min, and placed in a SP:SAMPLEPREP_SUMMARY centrifuge at 4000 rpm for 5 min. The resulting supernatant was collected, and a SP:SAMPLEPREP_SUMMARY second round of solid-liquid extraction was performed using 8 mL acetonitrile SP:SAMPLEPREP_SUMMARY with 2% formic acid. Samples were vortexed and centrifuged again, and both SP:SAMPLEPREP_SUMMARY supernatants combined yielding a final total volume of 10 mL. Of the 10 mL SP:SAMPLEPREP_SUMMARY combined supernatant sample, 3 mL were then run through solid filtration with a SP:SAMPLEPREP_SUMMARY Captiva EMR-lipid column (Agilent Technologies). Resulting eluates were placed SP:SAMPLEPREP_SUMMARY into liquid chromatography mass spectrometry (LCMS) vials in 1.0 mL aliquots. SP:SAMPLEPREP_SUMMARY Remaining supernatant volumes were banked at -80°C. Method blanks were SP:SAMPLEPREP_SUMMARY collected in parallel using the same steps without adding tissues. For SP:SAMPLEPREP_SUMMARY non-targeted chemical analysis, 20 µL of 1.25 µg/mL tracer solution was added SP:SAMPLEPREP_SUMMARY to each 1.0 mL aliquot of post-filtration eluate (for study samples, blanks, and SP:SAMPLEPREP_SUMMARY controls) yielding a final concentration of 25 ng/mL per sample. In addition, SP:SAMPLEPREP_SUMMARY tracers were added to a single sample in duplicate prior to extraction to SP:SAMPLEPREP_SUMMARY evaluate extraction recovery and reproducibility. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Agilent 1290 Infinity II CH:COLUMN_NAME Agilent Zorbax Eclipse Plus C8 (2.1 x 100 mm, 1.8 µm) UHPLC column #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Agilent 6545 QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE UNSPECIFIED MS:MS_COMMENTS See Acquisition_Methods.docx for more comprehensive acquisition parameters MS:MS_RESULTS_FILE ST002151_AN003522_Results.txt UNITS:amu Has m/z:No Has RT:No RT units:No RT data #END