#METABOLOMICS WORKBENCH dagaul_20220106_071715 DATATRACK_ID:3023 STUDY_ID:ST002052 ANALYSIS_ID:AN003339 PROJECT_ID:PR001298 VERSION 1 CREATED_ON January 6, 2022, 12:26 pm #PROJECT PR:PROJECT_TITLE Multi-omic attributes and unbiased computational modeling for the prediction of PR:PROJECT_TITLE immunomodulatory potency of mesenchymal stromal cells PR:PROJECT_SUMMARY Mesenchymal stromal cells (MSCs) are “living medicines” that continue to be PR:PROJECT_SUMMARY evaluated in clinical trials to treat various clinical indications, yet remain PR:PROJECT_SUMMARY unapproved. Because these cell therapies can be harvested from different tissue PR:PROJECT_SUMMARY sources, are manufactured ex vivo, and are composed of highly responsive cells PR:PROJECT_SUMMARY from donors of varying demographics, significant complexities limit the current PR:PROJECT_SUMMARY understanding and advancements to clinical practice. However, we propose a model PR:PROJECT_SUMMARY workflow used to overcome challenges by identifying multi-omic features that can PR:PROJECT_SUMMARY serve as predictive therapeutic outcomes of MSCs. Here, features were identified PR:PROJECT_SUMMARY using unbiased symbolic regression and machine learning models that correlated PR:PROJECT_SUMMARY multi-omic datasets to results from in vitro functional assays based on putative PR:PROJECT_SUMMARY mechanisms of action of MSCs. Together, this study provides a compelling PR:PROJECT_SUMMARY framework for achieving the identification of candidate CQAs specific to MSCs PR:PROJECT_SUMMARY that may help overcome current challenges, advancing MSCs to broad clinical use. PR:PROJECT_SUMMARY This upload contains the metabolomic dataset which were correlated with quality PR:PROJECT_SUMMARY metrics, such as potency. PR:INSTITUTE Georgia Institute of Technology PR:LAST_NAME Gaul PR:FIRST_NAME David PR:ADDRESS 311 Ferst Drive Atlanta, GA 30332 PR:EMAIL david.gaul@chemistry.gatech.edu PR:PHONE 4048943870 #STUDY ST:STUDY_TITLE Multi-omic Attributes and Unbiased Computational Modeling for the Prediction of ST:STUDY_TITLE Immunomodulatory Potency of Mesenchymal Stromal Cells ST:STUDY_SUMMARY Mesenchymal stromal cells (MSCs) are “living medicines” that continue to be ST:STUDY_SUMMARY evaluated in clinical trials to treat various clinical indications, yet remain ST:STUDY_SUMMARY unapproved. Because these cell therapies can be harvested from different tissue ST:STUDY_SUMMARY sources, are manufactured ex vivo, and are composed of highly responsive cells ST:STUDY_SUMMARY from donors of varying demographics, significant complexities limit the current ST:STUDY_SUMMARY understanding and advancements to clinical practice. However, we propose a model ST:STUDY_SUMMARY workflow used to overcome challenges by identifying multi-omic features that can ST:STUDY_SUMMARY serve as predictive therapeutic outcomes of MSCs. Here, features were identified ST:STUDY_SUMMARY using unbiased symbolic regression and machine learning models that correlated ST:STUDY_SUMMARY multi-omic datasets to results from in vitro functional assays based on putative ST:STUDY_SUMMARY mechanisms of action of MSCs. Together, this study provides a compelling ST:STUDY_SUMMARY framework for achieving the identification of candidate CQAs specific to MSCs ST:STUDY_SUMMARY that may help overcome current challenges, advancing MSCs to broad clinical use. ST:STUDY_SUMMARY This upload contain the metabolomic datasets, which were correlated with quality ST:STUDY_SUMMARY metrics, such as potency. ST:INSTITUTE Georgia Institute of Technology ST:LABORATORY System Mass Spectrometry Core ST:LAST_NAME Gaul ST:FIRST_NAME David ST:ADDRESS 311 Ferst Drive Atlanta, GA 30332 ST:EMAIL david.gaul@chemistry.gatech.edu ST:PHONE 4048943870 #SUBJECT SU:SUBJECT_TYPE Cultured cells SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 #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 - Blank01 Factor:NA sample_type=QC_Blank; RAW_FILE_NAME=Blank01 SUBJECT_SAMPLE_FACTORS - Blank02 Factor:NA sample_type=QC_Blank; RAW_FILE_NAME=Blank02 SUBJECT_SAMPLE_FACTORS - Blank04 Factor:NA sample_type=QC_Blank; RAW_FILE_NAME=Blank04 SUBJECT_SAMPLE_FACTORS - Blank05 Factor:NA sample_type=QC_Blank; RAW_FILE_NAME=Blank05 SUBJECT_SAMPLE_FACTORS - QC01 Factor:NA sample_type=QC_Pooled; RAW_FILE_NAME=QC01 SUBJECT_SAMPLE_FACTORS - QC02 Factor:NA sample_type=QC_Pooled; RAW_FILE_NAME=QC02 SUBJECT_SAMPLE_FACTORS - QC03 Factor:NA sample_type=QC_Pooled; RAW_FILE_NAME=QC03 SUBJECT_SAMPLE_FACTORS - QC04 Factor:NA sample_type=QC_Pooled; RAW_FILE_NAME=QC04 SUBJECT_SAMPLE_FACTORS - QC05 Factor:NA sample_type=QC_Pooled; RAW_FILE_NAME=QC05 SUBJECT_SAMPLE_FACTORS - QC06 Factor:NA sample_type=QC_Pooled; RAW_FILE_NAME=QC06 SUBJECT_SAMPLE_FACTORS - QC07 Factor:NA sample_type=QC_Pooled; RAW_FILE_NAME=QC07 SUBJECT_SAMPLE_FACTORS - BM1_1 Factor:MSC_BoneMarrow sample_type=Sample; RAW_FILE_NAME=Sample01_RB139_OOT SUBJECT_SAMPLE_FACTORS - BM1_2 Factor:MSC_BoneMarrow sample_type=Sample; RAW_FILE_NAME=Sample02_RB139_OOT SUBJECT_SAMPLE_FACTORS - BM2_1 Factor:MSC_BoneMarrow sample_type=Sample; RAW_FILE_NAME=Sample03_RB168 SUBJECT_SAMPLE_FACTORS - BM2_2 Factor:MSC_BoneMarrow sample_type=Sample; RAW_FILE_NAME=Sample04_RB168 SUBJECT_SAMPLE_FACTORS - BM2_3 Factor:MSC_BoneMarrow sample_type=Sample; RAW_FILE_NAME=Sample05_RB168 SUBJECT_SAMPLE_FACTORS - BM3_1 Factor:MSC_BoneMarrow sample_type=Sample; RAW_FILE_NAME=Sample06_RB171 SUBJECT_SAMPLE_FACTORS - BM3_2 Factor:MSC_BoneMarrow sample_type=Sample; RAW_FILE_NAME=Sample07_RB171 SUBJECT_SAMPLE_FACTORS - BM3_3 Factor:MSC_BoneMarrow sample_type=Sample; RAW_FILE_NAME=Sample08_RB171 SUBJECT_SAMPLE_FACTORS - BM4_1 Factor:MSC_BoneMarrow sample_type=Sample; RAW_FILE_NAME=Sample09_RB174 SUBJECT_SAMPLE_FACTORS - BM4_2 Factor:MSC_BoneMarrow sample_type=Sample; RAW_FILE_NAME=Sample10_RB174 SUBJECT_SAMPLE_FACTORS - BM4_3 Factor:MSC_BoneMarrow sample_type=Sample; RAW_FILE_NAME=Sample11_RB174 SUBJECT_SAMPLE_FACTORS - BM5_1 Factor:MSC_BoneMarrow sample_type=Sample; RAW_FILE_NAME=Sample12_RB177 SUBJECT_SAMPLE_FACTORS - BM5_2 Factor:MSC_BoneMarrow sample_type=Sample; RAW_FILE_NAME=Sample13_RB177 SUBJECT_SAMPLE_FACTORS - BM5_3 Factor:MSC_BoneMarrow sample_type=Sample; RAW_FILE_NAME=Sample14_RB177 SUBJECT_SAMPLE_FACTORS - BM6_1 Factor:MSC_BoneMarrow sample_type=Sample; RAW_FILE_NAME=Sample15_RB179 SUBJECT_SAMPLE_FACTORS - BM6_2 Factor:MSC_BoneMarrow sample_type=Sample; RAW_FILE_NAME=Sample16_RB179 SUBJECT_SAMPLE_FACTORS - BM6_3 Factor:MSC_BoneMarrow sample_type=Sample; RAW_FILE_NAME=Sample17_RB179 SUBJECT_SAMPLE_FACTORS - BM7_1 Factor:MSC_BoneMarrow sample_type=Sample; RAW_FILE_NAME=Sample18_RB183 SUBJECT_SAMPLE_FACTORS - BM7_2 Factor:MSC_BoneMarrow sample_type=Sample; RAW_FILE_NAME=Sample19_RB183 SUBJECT_SAMPLE_FACTORS - BM7_3 Factor:MSC_BoneMarrow sample_type=Sample; RAW_FILE_NAME=Sample20_RB183 SUBJECT_SAMPLE_FACTORS - CT1 Factor:MSC_CordTissue sample_type=Sample; RAW_FILE_NAME=Sample26_GMP075EXP SUBJECT_SAMPLE_FACTORS - CT2 Factor:MSC_CordTissue sample_type=Sample; RAW_FILE_NAME=Sample27_GMP088EXP SUBJECT_SAMPLE_FACTORS - CT3 Factor:MSC_CordTissue sample_type=Sample; RAW_FILE_NAME=Sample28_GMP087EXP #COLLECTION CO:COLLECTION_SUMMARY Bone Marrow derived Mesenchymal Stromal Cells were purchased from RoosterBio, CO:COLLECTION_SUMMARY and the cord tissue derived Mesenchymal Stromal Cells were from Duke University CO:COLLECTION_SUMMARY School of Medicine. CO:SAMPLE_TYPE Stem cells #TREATMENT TR:TREATMENT_SUMMARY BM-MSCs were expanded in either regular media or xeno-free media, while the TR:TREATMENT_SUMMARY CT-MSCs were expanded in xeno-free media. Harvested cells were resuspended in TR:TREATMENT_SUMMARY CryoStor CS5. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Metabolites were extracted using a modified bligh-Dyer on 1 million MSC pellet SP:SAMPLEPREP_SUMMARY with bead homogenization.The Aqueous layer was dried, reconstituted with 80% SP:SAMPLEPREP_SUMMARY MeOH with internal standards prior to analysis. the organic layer was also SP:SAMPLEPREP_SUMMARY dried, reconstituted with IPA with internal standards prior to analysis #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Thermo Vanquish CH:COLUMN_NAME Thermo Accucore C30 (150 x 2.1 mm, 2.6um) #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive HF hybrid Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS Compound Discoverer used to process MS:MS_RESULTS_FILE ST002052_AN003339_Results.txt UNITS:peak area Has m/z:Neutral masses Has RT:Yes RT units:Minutes #END