{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002151","ANALYSIS_ID":"AN003522","VERSION":"1","CREATED_ON":"April 22, 2022, 7:26 am"},

"PROJECT":{"PROJECT_TITLE":"Placenta NTA studies","PROJECT_SUMMARY":"Multi-omics study on placental samples to characterize xenobiotics and epigenomic/transcriptomic changes associated with preeclampsia","INSTITUTE":"U.S. EPA","LAST_NAME":"Chao","FIRST_NAME":"Alex","ADDRESS":"109 TW Alexander Dr, Durham, NC 27709, USA","EMAIL":"chao.alex@epa.gov","PHONE":"9195414261"},

"STUDY":{"STUDY_TITLE":"Integrative Exposomic, Transcriptomic, Epigenomic Analyses of Human Placental Samples Links Understudied Chemicals to Preeclampsia","STUDY_SUMMARY":"Background Environmental health research has recently undergone a dramatic shift, with ongoing technological advancements allowing for broader coverage of exposure and molecular biology signatures. Approaches to integrate such measures are still needed to increase understanding between systems-level exposure and biology. Objectives We address this gap by evaluating placental tissues to identify novel chemical-biological interactions associated with preeclampsia. This study tests the hypothesis that understudied chemicals are present in the human placenta and associated with preeclampsia-relevant disruptions, including overall case status (preeclamptic vs. normotensive patients) and underlying transcriptomic/epigenomic signatures. Methods A non-targeted analysis based on high-resolution mass spectrometry was used to analyze placental tissues from a cohort of 35 patients with preeclampsia (n = 18) and normotensive (n = 17) pregnancies. Molecular feature data were queried against chemicals within the U.S. Environmental Protection Agency’s DSSTox database, and prioritized for confirmation based on association with preeclampsia case status and confidence of chemical identification. All molecular features were evaluated for relationships to mRNA, microRNA, and CpG methylation (i.e., multi-omic) signature alterations involved in preeclampsia. Results A total of 183 molecular features were identified with significantly differentiated abundance in placental extracts of preeclamptic patients; these features clustered into distinct chemical groupings using unsupervised methods. Of these features, 53 were identified (mapping to 40 distinct chemicals) using chemical standards, fragmentation spectra, and chemical metadata. In general, human metabolites had the largest feature intensities and strongest associations with preeclampsia-relevant multi-omic changes. Exogenous drugs were second most abundant and had fewer associations with multi-omic changes. Other exogenous chemicals (non-drugs) were least abundant and had the fewest associations with multi-omic changes. Conclusions These global data trends suggest that human metabolites are heavily intertwined with biological processes involved in preeclampsia etiology, while exogenous chemicals may still impact select transcriptomic/epigenomic processes. This study serves as a demonstration of merging systems exposures with systems biology to better understand chemical-disease relationships.","INSTITUTE":"EPA","LAST_NAME":"Chao","FIRST_NAME":"Alex","ADDRESS":"109 TW Alexander Drive, Durham, NC 27709, USA","EMAIL":"chao.alex@epa.gov","PHONE":"9195414261"},

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"Additional sample data":{"RAW_FILE_NAME":"Blank_Positive_MS_EPA_2.mzdata"}
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"Sample ID":"P17_Positive_3",
"Factors":{"Treatment":"Control"},
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"Sample ID":"P18_Positive_2",
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"Sample ID":"P19_Positive_1",
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"Sample ID":"P19_Positive_2",
"Factors":{"Treatment":"Control"},
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"Subject ID":"-",
"Sample ID":"P20_Positive_1",
"Factors":{"Treatment":"Control"},
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"Sample ID":"P20_Positive_2",
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"Factors":{"Treatment":"Control"},
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"Subject ID":"-",
"Sample ID":"Q1_Positive_1",
"Factors":{"Treatment":"preeclampsia"},
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"Subject ID":"-",
"Sample ID":"Q1_Positive_2",
"Factors":{"Treatment":"preeclampsia"},
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"Sample ID":"Q1_Positive_3",
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"Subject ID":"-",
"Sample ID":"Q3_Positive_1",
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"Subject ID":"-",
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"Subject ID":"-",
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"Subject ID":"-",
"Sample ID":"Q4_Positive_2",
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"Subject ID":"-",
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"Subject ID":"-",
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"Subject ID":"-",
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"Subject ID":"-",
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"Additional sample data":{"RAW_FILE_NAME":"Q5_Positive_MS_Placenta_3.mzdata"}
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"Subject ID":"-",
"Sample ID":"Q6_Positive_1",
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{
"Subject ID":"-",
"Sample ID":"Q6_Positive_2",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q6_Positive_MS_Placenta_2.mzdata"}
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{
"Subject ID":"-",
"Sample ID":"Q6_Positive_3",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q6_Positive_MS_Placenta_3.mzdata"}
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{
"Subject ID":"-",
"Sample ID":"Q7_Positive_1",
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"Subject ID":"-",
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"Factors":{"Treatment":"preeclampsia"},
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"Subject ID":"-",
"Sample ID":"Q7_Positive_3",
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"Additional sample data":{"RAW_FILE_NAME":"Q7_Positive_MS_Placenta_3.mzdata"}
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"Subject ID":"-",
"Sample ID":"Q9_Positive_2",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q9_Positive_MS_Placenta_2.mzdata"}
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{
"Subject ID":"-",
"Sample ID":"Q9_Positive_3",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q9_Positive_MS_Placenta_3.mzdata"}
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{
"Subject ID":"-",
"Sample ID":"Q10_Positive_1",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q10_Positive_MS_Placenta_1.mzdata"}
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{
"Subject ID":"-",
"Sample ID":"Q10_Positive_2",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q10_Positive_MS_Placenta_2.mzdata"}
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{
"Subject ID":"-",
"Sample ID":"Q10_Positive_3",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q10_Positive_MS_Placenta_3.mzdata"}
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"Factors":{"Treatment":"preeclampsia"},
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{
"Subject ID":"-",
"Sample ID":"Q11_Positive_2",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q11_Positive_MS_Placenta_2.mzdata"}
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{
"Subject ID":"-",
"Sample ID":"Q11_Positive_3",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q11_Positive_MS_Placenta_3.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"Q12_Positive_1",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q12_Positive_MS_Placenta_1.mzdata"}
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{
"Subject ID":"-",
"Sample ID":"Q12_Positive_2",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q12_Positive_MS_Placenta_2.mzdata"}
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{
"Subject ID":"-",
"Sample ID":"Q12_Positive_3",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q12_Positive_MS_Placenta_3.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"Q13_Positive_PostspikeA_Positive_1",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q13_Positive_MS_Placenta_PostspikeA_1.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"Q13_Positive_PostspikeA_Positive_2",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q13_Positive_MS_Placenta_PostspikeA_2.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"Q13_Positive_PostspikeA_Positive_3",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q13_Positive_MS_Placenta_PostspikeA_3.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"Q13_Positive_PostspikeB_Positive_1",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q13_Positive_MS_Placenta_PostspikeB_1.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"Q13_Positive_PostspikeB_Positive_2",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q13_Positive_MS_Placenta_PostspikeB_2.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"Q13_Positive_PostspikeB_Positive_3",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q13_Positive_MS_Placenta_PostspikeB_3.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"Q13_Positive_PrespikeA_Positive_1",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q13_Positive_MS_Placenta_PrespikeA_1.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"Q13_Positive_PrespikeA_Positive_2",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q13_Positive_MS_Placenta_PrespikeA_2.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"Q13_Positive_PrespikeA_Positive_3",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q13_Positive_MS_Placenta_PrespikeA_3.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"Q13_Positive_PrespikeB_Positive_1",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q13_Positive_MS_Placenta_PrespikeB_1.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"Q13_Positive_PrespikeB_Positive_2",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q13_Positive_MS_Placenta_PrespikeB_2.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"Q13_Positive_PrespikeB_Positive_3",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q13_Positive_MS_Placenta_PrespikeB_3.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"Q14_Positive_1",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q14_Positive_MS_Placenta_1.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"Q14_Positive_2",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q14_Positive_MS_Placenta_2.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"Q14_Positive_3",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q14_Positive_MS_Placenta_3.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"Q15_Positive_1",
"Factors":{"Treatment":"preeclampsia"},
"Additional sample data":{"RAW_FILE_NAME":"Q15_Positive_MS_Placenta_1.mzdata"}
},
{
"Subject ID":"-",
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{
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"Additional sample data":{"RAW_FILE_NAME":"QC_Negative_MS_Pool_Front4.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"QC_Negative_MS_Pool_Front5",
"Factors":{"Treatment":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC_Negative_MS_Pool_Front5.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"QC_Negative_MS_Pool_Mid1",
"Factors":{"Treatment":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC_Negative_MS_Pool_Mid1.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"QC_Negative_MS_Pool_Mid2",
"Factors":{"Treatment":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC_Negative_MS_Pool_Mid2.mzdata"}
},
{
"Subject ID":"-",
"Sample ID":"QC_Negative_MS_Pool_Mid3",
"Factors":{"Treatment":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC_Negative_MS_Pool_Mid3.mzdata"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Placentas were first processed by collecting samples ~4-6 inches in length and ½ inch in diameter via cross-section punch biopsy, with blinded identifiers to ensure unbiased collection. These samples were stored at -80°C, until further processing on dry ice into individual samples for chemical analyses. Here, sterile scalpels were used to cut samples in half and a ¼ inch slice was removed from the middle and weighed, yielding isolated samples ranging in weight between 0.4 and 0.6 g.","SAMPLE_TYPE":"Placenta"},

"TREATMENT":{"TREATMENT_SUMMARY":"Placentas were first processed by collecting samples ~4-6 inches in length and ½ inch in diameter via cross-section punch biopsy, with blinded identifiers to ensure unbiased collection. These samples were stored at -80°C, until further processing on dry ice into individual samples for chemical analyses. Here, sterile scalpels were used to cut samples in half and a ¼ inch slice was removed from the middle and weighed, yielding isolated samples ranging in weight between 0.4 and 0.6 g."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"One sample per tissue was used in chemical analyses. Chemicals were separated from tissue via solid-liquid extraction by adding 2 mL of room temperature water:acetonitrile (1:1) per sample. Placenta samples were disrupted and homogenized using a TissueRuptor (Qiagen), vortexed for 5 min, and placed in a centrifuge at 4000 rpm for 5 min. The resulting supernatant was collected, and a second round of solid-liquid extraction was performed using 8 mL acetonitrile with 2% formic acid. Samples were vortexed and centrifuged again, and both supernatants combined yielding a final total volume of 10 mL. Of the 10 mL combined supernatant sample, 3 mL were then run through solid filtration with a Captiva EMR-lipid column (Agilent Technologies). Resulting eluates were placed into liquid chromatography mass spectrometry (LCMS) vials in 1.0 mL aliquots. Remaining supernatant volumes were banked at -80°C. Method blanks were collected in parallel using the same steps without adding tissues. For non-targeted chemical analysis, 20 µL of 1.25 µg/mL tracer solution was added to each 1.0 mL aliquot of post-filtration eluate (for study samples, blanks, and controls) yielding a final concentration of 25 ng/mL per sample. In addition, tracers were added to a single sample in duplicate prior to extraction to evaluate extraction recovery and reproducibility."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 1290 Infinity II","COLUMN_NAME":"Agilent Zorbax Eclipse Plus C8 (2.1 x 100 mm, 1.8 µm) UHPLC column"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Agilent 6545 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"UNSPECIFIED","MS_COMMENTS":"See Acquisition_Methods.docx for more comprehensive acquisition parameters","MS_RESULTS_FILE":"ST002151_AN003522_Results.txt UNITS:amu Has m/z:No Has RT:No RT units:No RT data"}

}