#METABOLOMICS WORKBENCH Tingting_Zhao_20230530_105302 DATATRACK_ID:4055 STUDY_ID:ST002722 ANALYSIS_ID:AN004413 PROJECT_ID:PR001688 VERSION 1 CREATED_ON June 2, 2023, 11:37 am #PROJECT PR:PROJECT_TITLE Gut genomic and metabolic signature predicts hepatic decompensation and PR:PROJECT_TITLE mortality in NAFLD-related cirrhosis PR:PROJECT_SUMMARY There are limited data on the diagnostic accuracy of gut microbial signatures PR:PROJECT_SUMMARY for predicting hepatic decompensation in patients with cirrhosis. The aim of PR:PROJECT_SUMMARY this study is to determine whether a stool genomic and metabolic signature PR:PROJECT_SUMMARY accurately detects hepatic decompensation and mortality risk in cirrhosis PR:PROJECT_SUMMARY secondary to nonalcoholic fatty liver disease (NAFLD). Based on the severity of PR:PROJECT_SUMMARY cirrhosis, cirrhosis patients can be categorized as compensated or PR:PROJECT_SUMMARY decompensated. Shotgun metagenomic sequencing was performed on fecal samples PR:PROJECT_SUMMARY collected from a prospective cohort of adults with NAFLD-related cirrhosis. The PR:PROJECT_SUMMARY signatures were further validated with a metabolomic study on fecal and serum PR:PROJECT_SUMMARY samples. Finally, we developed a Random Forest machine learning algorithm to PR:PROJECT_SUMMARY make predictions on hepatic decompensation and mortality in NAFLD-related PR:PROJECT_SUMMARY cirrhosis. Here we uploaded the metabolomics study data of serum samples in PR:PROJECT_SUMMARY LC-MS/MS analysis. PR:INSTITUTE University of British Columbia PR:DEPARTMENT Chemistry PR:LAST_NAME Zhao PR:FIRST_NAME Tingting PR:ADDRESS 2036 Main Mall, Vancouver, V6T 1Z1 PR:EMAIL tingzhao@chem.ubc.ca PR:PHONE 6048221253 PR:PUBLICATIONS Gut metagenome-derived signature predicts hepatic decompensation and mortality PR:PUBLICATIONS in NAFLD-related cirrhosis. Aliment Pharmacol Ther. 2022;56:1475–1485. DOI: PR:PUBLICATIONS 10.1111/apt.17236 #STUDY ST:STUDY_TITLE Cirrhosis-related metabolomics study ST:STUDY_SUMMARY There are limited data on the diagnostic accuracy of gut microbial signatures ST:STUDY_SUMMARY for predicting hepatic decompensation in patients with cirrhosis. The aim of ST:STUDY_SUMMARY this study is to determine whether a stool genomic and metabolic signature ST:STUDY_SUMMARY accurately detects hepatic decompensation and mortality risk in cirrhosis ST:STUDY_SUMMARY secondary to nonalcoholic fatty liver disease (NAFLD). Shotgun metagenomic ST:STUDY_SUMMARY sequencing was performed on fecal samples collected from a prospective cohort of ST:STUDY_SUMMARY adults with NAFLD-related cirrhosis. The signatures were further validated with ST:STUDY_SUMMARY a metabolomic study on serum samples. Finally, we developed a Random Forest ST:STUDY_SUMMARY machine learning algorithm to make predictions on hepatic decompensation and ST:STUDY_SUMMARY mortality in NAFLD-related cirrhosis. Here we uploaded the metabolomics study ST:STUDY_SUMMARY data from LC-MS/MS. ST:INSTITUTE University of British Columbia ST:LAST_NAME Zhao ST:FIRST_NAME Tingting ST:ADDRESS 2036 Main Mall, V6T 1Z1 ST:EMAIL tingzhao@chem.ubc.ca ST:PHONE 6048221253 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 SU:GENDER Not applicable #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 - CIR5 Phenotype:compensated RAW_FILE_NAME=CIR5.mzXML SUBJECT_SAMPLE_FACTORS - CIR6 Phenotype:compensated RAW_FILE_NAME=CIR6.mzXML SUBJECT_SAMPLE_FACTORS - CIR7 Phenotype:compensated RAW_FILE_NAME=CIR7.mzXML SUBJECT_SAMPLE_FACTORS - CIR16 Phenotype:compensated RAW_FILE_NAME=CIR16.mzXML SUBJECT_SAMPLE_FACTORS - CIR18 Phenotype:compensated RAW_FILE_NAME=CIR18.mzXML SUBJECT_SAMPLE_FACTORS - CIR19 Phenotype:compensated RAW_FILE_NAME=CIR19.mzXML SUBJECT_SAMPLE_FACTORS - CIR20 Phenotype:decompensated RAW_FILE_NAME=CIR20.mzXML SUBJECT_SAMPLE_FACTORS - CIR21 Phenotype:compensated RAW_FILE_NAME=CIR21_hilic_pos.mzXML SUBJECT_SAMPLE_FACTORS - CIR22 Phenotype:compensated RAW_FILE_NAME=CIR22_hilic_pos.mzXML SUBJECT_SAMPLE_FACTORS - CIR23 Phenotype:compensated RAW_FILE_NAME=CIR23_hilic_pos.mzXML SUBJECT_SAMPLE_FACTORS - CIR32 Phenotype:decompensated RAW_FILE_NAME=CIR32_hilic_pos.mzXML SUBJECT_SAMPLE_FACTORS - CIR41 Phenotype:compensated RAW_FILE_NAME=CIR41_hilic_pos.mzXML SUBJECT_SAMPLE_FACTORS - CIR51 Phenotype:compensated RAW_FILE_NAME=CIR51_hilic_pos.mzXML SUBJECT_SAMPLE_FACTORS - CIR52 Phenotype:compensated RAW_FILE_NAME=CIR52_hilic_pos.mzXML SUBJECT_SAMPLE_FACTORS - CIR53 Phenotype:decompensated RAW_FILE_NAME=CIR53_hilic_pos.mzXML SUBJECT_SAMPLE_FACTORS - CIR55 Phenotype:compensated RAW_FILE_NAME=CIR55_hilic_pos.mzXML SUBJECT_SAMPLE_FACTORS - CIR57 Phenotype:decompensated RAW_FILE_NAME=CIR57.mzXML SUBJECT_SAMPLE_FACTORS - CIR58 Phenotype:decompensated RAW_FILE_NAME=CIR58.mzXML SUBJECT_SAMPLE_FACTORS - CIR59 Phenotype:compensated RAW_FILE_NAME=CIR59.mzXML SUBJECT_SAMPLE_FACTORS - CIR60 Phenotype:compensated RAW_FILE_NAME=CIR60.mzXML SUBJECT_SAMPLE_FACTORS - CIR61 Phenotype:decompensated RAW_FILE_NAME=CIR61.mzXML SUBJECT_SAMPLE_FACTORS - CIR63 Phenotype:compensated RAW_FILE_NAME=CIR63.mzXML #COLLECTION CO:COLLECTION_SUMMARY Participants with non-alcohol fatty liverdisease (NAFLD)-related cirrhosis were CO:COLLECTION_SUMMARY recruited in the outpatient setting between August 2014 and November 2017 at the CO:COLLECTION_SUMMARY University of California San Diego (UCSD) NAFLD Research Center. The participant CO:COLLECTION_SUMMARY met the criteria for NAFLD related cirrhosis if they had NAFLD and biopsy-proven CO:COLLECTION_SUMMARY cirrhosis or a diagnosis of cirrhosis from a board-certified gastroenterologist CO:COLLECTION_SUMMARY based on imaging and clinical parameters. All participants underwent a baseline CO:COLLECTION_SUMMARY standardized clinical research visit that included a detailed medical history CO:COLLECTION_SUMMARY and physical examination. The severity of cirrhosis at the baseline research CO:COLLECTION_SUMMARY visit was categorized as compensated or decompensated. Decompensation was CO:COLLECTION_SUMMARY defined by any of the following: ascites requiring intervention (diuretics, CO:COLLECTION_SUMMARY paracentesis and/or transjugular intrahepatic portosystemic shunt), upper CO:COLLECTION_SUMMARY gastrointestinal haemorrhage secondary to gastroesophageal varices or hepatic CO:COLLECTION_SUMMARY encephalopathy (grade ≥ 2 based on West Haven Criteria10). Serum samples were CO:COLLECTION_SUMMARY also collected from participants at baseline. CO:SAMPLE_TYPE serum CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY N/A The severity of cirrhosis at the baseline research visit was categorised as TR:TREATMENT_SUMMARY compensated or decompensated. Thus, the participants were divided into TR:TREATMENT_SUMMARY compensated and decompensated group. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Dual extraction procedures of serum metabolome were as follows: A 50 μl serum SP:SAMPLEPREP_SUMMARY sample was mixed with 300 μl ice-cold methanol in a 1.5 ml Eppendorf vial and SP:SAMPLEPREP_SUMMARY vortex for 2 min. The solution was kept at −20°C for 4 h to precipitate SP:SAMPLEPREP_SUMMARY proteins. After that, 1000 μl methyl tert-butyl ether was added to extract SP:SAMPLEPREP_SUMMARY lipids. After 5 min shake, 350 μl H2O was added to induce the phase separation. SP:SAMPLEPREP_SUMMARY The solution was vortex for 10 s and rested at room temperature for 10 min, SP:SAMPLEPREP_SUMMARY followed by centrifugation at 14,000 rpm at 4°C for 15 min, for complete phase SP:SAMPLEPREP_SUMMARY separation. The clear lower layer was separated into a new vial and dried in SP:SAMPLEPREP_SUMMARY SpeedVac at 20°C for 4 h. The dried extract was then reconstituted in 150 μl SP:SAMPLEPREP_SUMMARY acetonitrile and water (1:1, v:v) mixed solvent for LC–MS metabolomics SP:SAMPLEPREP_SUMMARY analysis. The method blank was also prepared following the same protocol but SP:SAMPLEPREP_SUMMARY without adding serum. A 5 μl aliquot from each individual sample was pooled SP:SAMPLEPREP_SUMMARY together to make a quality control sample. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY SeQuant ZIC-pHILIC Column (5 μm, 2.1 mm × 150 mm) CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME 1290 Infinity II UHPLC system (Agilent Technologies) CH:COLUMN_NAME SeQuant ZIC-pHILIC Column CH:SOLVENT_A 10 mM ammonium acetate at pH 4.8 CH:SOLVENT_B pure ACN CH:FLOW_GRADIENT 0 min, 95% B; 20 min, 5% B; 25 min, 5% B; 25.01 min, 95% B; 30 min, 95% B; 35 CH:FLOW_GRADIENT min, 95% B. CH:FLOW_RATE 0.15 ml/min CH:COLUMN_TEMPERATURE 30°C #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Bruker Impact II QqTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS MS acquistion Comments: capillary voltage, 4.5 kV; nebulizer gas, 1.6 bar; dry MS:MS_COMMENTS gas, 7 L/min; dry gas temperature, 220 °C; mass scan range, 70–1000 (m/z); MS:MS_COMMENTS spectra rate, 8.00 Hz; and cycle time, 3.0 s; data-dependent acquisition (one MS:MS_COMMENTS MS1 scan is followed by multiple MS2 scan for the top-N abundant precursors) MS:MS_COMMENTS Data processing Comments: xcmsSet()function in XCMS R package. MS:COLLISION_ENERGY 16~30 eV MS:COLLISION_GAS Nitrogen MS:DRY_GAS_TEMP 220 °C MS:FRAGMENTATION_METHOD Collision induced dissociation MS:IONIZATION ESI MS:IONIZATION_POTENTIAL 4.5 kV MS:MS_RESULTS_FILE ST002722_AN004413_Results.txt UNITS:Height Has m/z:Yes Has RT:Yes RT units:Seconds #END