#METABOLOMICS WORKBENCH silviaradenkovic_20230814_141643 DATATRACK_ID:4220 STUDY_ID:ST002812 ANALYSIS_ID:AN004579 PROJECT_ID:PR001759 VERSION 1 CREATED_ON August 15, 2023, 5:13 pm #PROJECT PR:PROJECT_TITLE Metabolomic profiling of PMM2-CDG brain organoids PR:PROJECT_SUMMARY PMM2-CDG is a rare inborn error of metabolism caused by deficiency of the PMM PR:PROJECT_SUMMARY enzyme, which leads to impaired protein glycosylation. While the disorder has PR:PROJECT_SUMMARY primarily neurological presentation, there is limited knowledge about the PR:PROJECT_SUMMARY specific brain-related changes that result from PMM deficiency. Utilizing 3D PR:PROJECT_SUMMARY brain organoids derived from individuals with PMM2-CDG, we identified abnormal PR:PROJECT_SUMMARY glucose metabolism in PMM2-CDG organoids, indicating disturbances in metabolic PR:PROJECT_SUMMARY utilization. PR:INSTITUTE Mayo Clinic PR:LAST_NAME Radenkovic PR:FIRST_NAME Silvia PR:ADDRESS 200 2nd Ave SW Rochester MN PR:EMAIL radenkovic.silvia@mayo.edu PR:PHONE 507(77) 6-6107 PR:FUNDING_SOURCE NIH, KU Leuven #STUDY ST:STUDY_TITLE Metabolomic profiling of PMM2-CDG brain organoids - Part 1 ST:STUDY_SUMMARY PMM2-CDG is a rare inborn error of metabolism caused by deficiency of the PMM ST:STUDY_SUMMARY enzyme, which leads to impaired protein glycosylation. While the disorder has ST:STUDY_SUMMARY primarily neurological presentation, there is limited knowledge about the ST:STUDY_SUMMARY specific brain-related changes that result from PMM deficiency. Utilizing 3D ST:STUDY_SUMMARY brain organoids derived from individuals with PMM2-CDG, we identified abnormal ST:STUDY_SUMMARY glucose metabolism in PMM2-CDG organoids, indicating disturbances in metabolic ST:STUDY_SUMMARY utilization. In this experiment, day 160 organoids were used. ST:INSTITUTE Mayo Clinic ST:LAST_NAME Radenkovic ST:FIRST_NAME Silvia ST:ADDRESS 200 2nd Ave SW Rochester MN, USA ST:EMAIL radenkovic.silvia@mayo.edu ST:PHONE 507(77) 6-6107 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 SU:GENOTYPE_STRAIN WT/PMM2-CDG SU:AGE_OR_AGE_RANGE 5-7 SU:GENDER Male and female #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 1363 S01 (1) Genotype:CTR Cell type=Brain organoids; RAW_FILE_NAME=S01 (1); DAYS IN VITRO=160; Weight in mg=4.4 SUBJECT_SAMPLE_FACTORS 1363 S01 (2) Genotype:CTR Cell type=Brain organoids; RAW_FILE_NAME=S01 (2); DAYS IN VITRO=160; Weight in mg=4.5 SUBJECT_SAMPLE_FACTORS 8858 S01 (3) Genotype:CTR Cell type=Brain organoids; RAW_FILE_NAME=S01 (3); DAYS IN VITRO=160; Weight in mg=3.4 SUBJECT_SAMPLE_FACTORS 8858 S01 (4) Genotype:CTR Cell type=Brain organoids; RAW_FILE_NAME=S01 (4); DAYS IN VITRO=160; Weight in mg=4.8 SUBJECT_SAMPLE_FACTORS 8858 S01 (5) Genotype:CTR Cell type=Brain organoids; RAW_FILE_NAME=S01 (5); DAYS IN VITRO=160; Weight in mg=4.1 SUBJECT_SAMPLE_FACTORS P2 S01 (6) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S01 (6); DAYS IN VITRO=160; Weight in mg=5.6 SUBJECT_SAMPLE_FACTORS P2 S01 (7) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S01 (7); DAYS IN VITRO=160; Weight in mg=5.3 SUBJECT_SAMPLE_FACTORS P2 S01 (8) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S01 (8); DAYS IN VITRO=160; Weight in mg=11.4 SUBJECT_SAMPLE_FACTORS P2 S01 (9) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S01 (9); DAYS IN VITRO=160; Weight in mg=9.6 SUBJECT_SAMPLE_FACTORS P1 S01 (10) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S01 (10); DAYS IN VITRO=160; Weight in mg=6.1 SUBJECT_SAMPLE_FACTORS P1 S01 (11) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S01 (11); DAYS IN VITRO=160; Weight in mg=9.5 SUBJECT_SAMPLE_FACTORS P1 S01 (12) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S01 (12); DAYS IN VITRO=160; Weight in mg=7.5 SUBJECT_SAMPLE_FACTORS P1 S01 (13) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S01 (13); DAYS IN VITRO=160; Weight in mg=13.2 SUBJECT_SAMPLE_FACTORS P3 S01 (14) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S01 (14); DAYS IN VITRO=160; Weight in mg=6.6 SUBJECT_SAMPLE_FACTORS P3 S01 (15) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S01 (15); DAYS IN VITRO=160; Weight in mg=4.4 SUBJECT_SAMPLE_FACTORS P3 S01 (16) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S01 (16); DAYS IN VITRO=160; Weight in mg=6.3 SUBJECT_SAMPLE_FACTORS P3 S01 (17) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S01 (17); DAYS IN VITRO=160; Weight in mg=7.5 #COLLECTION CO:COLLECTION_SUMMARY Brain were collected at day in vitro 160. Briefly, 5 organoids per cell line CO:COLLECTION_SUMMARY were collected and washed three times in DPBS (Gibco). The DPBS was then CO:COLLECTION_SUMMARY removed, the organoids flash frozen and kept in -80 °C prior to metabolomics CO:COLLECTION_SUMMARY experiments. The metabolites were extracted using two phase extraction protocol. CO:COLLECTION_SUMMARY First, the organoids were transferred to lysing matrix tube and 350 µL of CO:COLLECTION_SUMMARY ice-cold extraction buffer (80 % MeOH, IS) was added to the sample. Next, the CO:COLLECTION_SUMMARY organoids were lyzed with ribolyzer, the lysate transferred to 1.5 mL Eppendorf CO:COLLECTION_SUMMARY tube and placed overnight at -80 °C. Further, the samples were centrifuged at CO:COLLECTION_SUMMARY 15,000 rpm, 4 °C, 20 min. 100 µL of supernatant was transferred to a fresh CO:COLLECTION_SUMMARY Eppendorf tube and 35 µL of ddH20 was added, followed by 800 µL 100% CO:COLLECTION_SUMMARY chloroform. The samples were then vortexed and stored at 4 °C overnight. Next, CO:COLLECTION_SUMMARY the polar phase was the used for Liquid Chromatography/Mass Spectrometry (LC/MS) CO:SAMPLE_TYPE Brain organoids CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY NA #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Briefly, 5 organoids per cell line were collected and washed three times in SP:SAMPLEPREP_SUMMARY DPBS. The DPBS was then removed, the organoids flash frozen and kept in -80 °C SP:SAMPLEPREP_SUMMARY prior to metabolomics experiments. The metabolites were extracted using two SP:SAMPLEPREP_SUMMARY phase extraction protocol. First, the organoids were transferred to lysing SP:SAMPLEPREP_SUMMARY matrix tube and 350 µL of ice-cold extraction buffer (80 % MeOH, IS) was added SP:SAMPLEPREP_SUMMARY to the sample. Next, the organoids were lyzed with ribolyzer, the lysate SP:SAMPLEPREP_SUMMARY transferred to 1.5 mL Eppendorf tube and placed overnight at -80 °C. Further, SP:SAMPLEPREP_SUMMARY the samples were centrifuged at 15,000 rpm, 4 °C, 20 min. 100 µL of SP:SAMPLEPREP_SUMMARY supernatant was transferred to a fresh Eppendorf tube and 35 µL of ddH20 was SP:SAMPLEPREP_SUMMARY added, followed by 800 µL 100% chloroform. The samples were then vortexed and SP:SAMPLEPREP_SUMMARY stored at 4 °C overnight. Next, the polar phase was the used for Liquid SP:SAMPLEPREP_SUMMARY Chromatography/Mass Spectrometry (LC/MS) SP:PROCESSING_STORAGE_CONDITIONS -80℃ SP:EXTRACT_STORAGE -80℃ #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY C18 iP REVERSE PHASE CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Waters Acquity CH:COLUMN_NAME Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um) CH:SOLVENT_A 100% water; 10mM tributylamine; 15mM acetic acid CH:SOLVENT_B 100% methanol CH:FLOW_GRADIENT The gradient started with 5% of solvent B and 95% solvent A and remained at 5% B CH:FLOW_GRADIENT until 2 min post injection. A linear gradient to 37% B was carried out until 7 CH:FLOW_GRADIENT min and increased to 41% until 14 min. Between 14 and 26 minutes the gradient CH:FLOW_GRADIENT increased to 95% of B and remained at 95% B for 4 minutes. At 30 min the CH:FLOW_GRADIENT gradient returned to 5% B. The chromatography was stopped at 40 min CH:FLOW_RATE 0.25 ml/min CH:COLUMN_TEMPERATURE 40 #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE NEGATIVE MS:MS_COMMENTS El-Maven polly, ThermoFisher Xcalibur, Metabolites were annotated based on the MS:MS_COMMENTS in-house metabolite library- elution time and m/z values #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS AUC MS_METABOLITE_DATA_START Samples S01 (1) S01 (2) S01 (3) S01 (4) S01 (5) S01 (6) S01 (7) S01 (8) S01 (9) S01 (10) S01 (11) S01 (12) S01 (13) S01 (14) S01 (15) S01 (16) S01 (17) Factors Genotype:CTR Genotype:CTR Genotype:CTR Genotype:CTR Genotype:CTR Genotype:PMM2-CDG Genotype:PMM2-CDG Genotype:PMM2-CDG Genotype:PMM2-CDG Genotype:PMM2-CDG Genotype:PMM2-CDG Genotype:PMM2-CDG Genotype:PMM2-CDG Genotype:PMM2-CDG Genotype:PMM2-CDG Genotype:PMM2-CDG Genotype:PMM2-CDG 13C5-D5-15N Glutamic acid 3.20E+08 2.36E+08 4.24E+08 3.10E+08 1.32E+08 3.82E+08 7.91E+07 4.46E+08 4.51E+08 4.79E+08 4.81E+08 4.76E+08 4.69E+08 4.62E+08 4.06E+08 4.48E+08 4.53E+08 GDP-mannose 1.18E+06 6.80E+05 9.26E+05 4.36E+05 3.03E+04 4.20E+06 3.52E+05 4.06E+06 1.16E+06 4.42E+06 2.35E+06 2.77E+06 5.54E+06 2.07E+06 5.29E+06 3.72E+06 7.37E+06 Glucose 1.73E+08 1.88E+08 7.25E+07 1.27E+08 9.22E+07 1.50E+08 5.35E+07 1.06E+08 8.39E+07 3.68E+08 3.63E+08 5.19E+08 2.91E+08 1.73E+08 2.96E+08 2.13E+08 2.95E+08 Glucose-6-P 8.22E+06 5.43E+06 1.56E+07 9.63E+06 5.35E+06 4.87E+08 3.48E+06 5.53E+07 1.70E+08 1.30E+09 4.61E+08 5.94E+08 1.10E+09 2.12E+08 2.30E+08 1.79E+07 5.70E+08 Lactate 2.69E+09 3.14E+09 2.77E+09 2.26E+09 1.79E+09 3.98E+09 2.16E+09 5.42E+09 2.91E+09 3.84E+09 3.02E+09 3.36E+09 3.64E+09 3.15E+09 3.52E+09 4.77E+09 1.09E+10 Sorbitol 8.41E+07 1.00E+08 7.80E+07 1.81E+08 7.80E+07 1.12E+08 2.90E+07 1.08E+08 1.26E+08 6.48E+07 7.70E+07 6.53E+07 1.26E+08 1.05E+08 8.44E+07 7.72E+07 5.13E+07 Pyruvate 7.32E+08 7.59E+08 6.74E+08 6.64E+08 6.74E+08 7.51E+08 8.47E+08 7.77E+08 7.11E+08 8.86E+08 9.22E+08 9.68E+08 9.39E+08 8.95E+08 8.76E+08 9.41E+08 1.02E+09 Taurine 6.23E+08 4.49E+08 3.77E+08 4.15E+08 2.85E+08 2.11E+08 8.53E+07 1.93E+08 1.34E+08 8.39E+08 8.65E+08 8.99E+08 7.26E+08 5.11E+08 5.51E+08 6.58E+08 6.33E+08 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name parent formula M/Z HMDB ID 13C5-D5-15N Glutamic acid HOO13C13CD213CD213CD(15NH2)13COOH 157.09107 329766021 GDP-mannose C16H25N5O16P2 604.06988 HMDB01163 Glucose C6H12O6 179.05611 HMDB00122 Glucose-6-P C6H13O9P 259.02244 HMDB01401 Lactate C3H6O3 89.02442 HMDB00190 Sorbitol C6H14O6 181.07164 HMDB00247 Pyruvate C3H4O3 87.00877 HMDB00243 Taurine C2H7NO3S 124.00739 HMDB00251 METABOLITES_END #END