#METABOLOMICS WORKBENCH silviaradenkovic_20230814_142459 DATATRACK_ID:4221 STUDY_ID:ST002816 ANALYSIS_ID:AN004583 PROJECT_ID:PR001759 VERSION 1 CREATED_ON August 17, 2023, 1:19 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 2 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 40 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 8858 S (1) Genotype:CTR Cell type=Brain organoids; RAW_FILE_NAME=S (1); DAYS IN VITRO=40; Weight in mg=12 SUBJECT_SAMPLE_FACTORS 8858 S (2) Genotype:CTR Cell type=Brain organoids; RAW_FILE_NAME=S (2); DAYS IN VITRO=40; Weight in mg=12 SUBJECT_SAMPLE_FACTORS 8858 S (3) Genotype:CTR Cell type=Brain organoids; RAW_FILE_NAME=S (3); DAYS IN VITRO=40; Weight in mg=12 SUBJECT_SAMPLE_FACTORS 8858 S (4) Genotype:CTR Cell type=Brain organoids; RAW_FILE_NAME=S (4); DAYS IN VITRO=40; Weight in mg=9.9 SUBJECT_SAMPLE_FACTORS 8858 S (5) Genotype:CTR Cell type=Brain organoids; RAW_FILE_NAME=S (5); DAYS IN VITRO=40; Weight in mg=6.5 SUBJECT_SAMPLE_FACTORS 1363 S (6) Genotype:CTR Cell type=Brain organoids; RAW_FILE_NAME=S (6); DAYS IN VITRO=40; Weight in mg=22 SUBJECT_SAMPLE_FACTORS 1363 S (7) Genotype:CTR Cell type=Brain organoids; RAW_FILE_NAME=S (7); DAYS IN VITRO=40; Weight in mg=22 SUBJECT_SAMPLE_FACTORS 1363 S (8) Genotype:CTR Cell type=Brain organoids; RAW_FILE_NAME=S (8); DAYS IN VITRO=40; Weight in mg=22 SUBJECT_SAMPLE_FACTORS 1363 S (9) Genotype:CTR Cell type=Brain organoids; RAW_FILE_NAME=S (9); DAYS IN VITRO=40; Weight in mg=10.1 SUBJECT_SAMPLE_FACTORS 1363 S (10) Genotype:CTR Cell type=Brain organoids; RAW_FILE_NAME=S (10); DAYS IN VITRO=40; Weight in mg=13.7 SUBJECT_SAMPLE_FACTORS P1 S (11) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S (11); DAYS IN VITRO=40; Weight in mg=15 SUBJECT_SAMPLE_FACTORS P1 S (12) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S (12); DAYS IN VITRO=40; Weight in mg=15 SUBJECT_SAMPLE_FACTORS P1 S (13) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S (13); DAYS IN VITRO=40; Weight in mg=15 SUBJECT_SAMPLE_FACTORS P1 S (14) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S (14); DAYS IN VITRO=40; Weight in mg=14.5 SUBJECT_SAMPLE_FACTORS P1 S (15) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S (15); DAYS IN VITRO=40; Weight in mg=15.7 SUBJECT_SAMPLE_FACTORS P2 S (16) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S (16); DAYS IN VITRO=40; Weight in mg=28 SUBJECT_SAMPLE_FACTORS P2 S (17) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S (17); DAYS IN VITRO=40; Weight in mg=28 SUBJECT_SAMPLE_FACTORS P2 S (18) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S (18); DAYS IN VITRO=40; Weight in mg=28 SUBJECT_SAMPLE_FACTORS P3 S (19) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S (19); DAYS IN VITRO=40; Weight in mg=29.4 SUBJECT_SAMPLE_FACTORS P3 S (20) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S (20); DAYS IN VITRO=40; Weight in mg=29.4 SUBJECT_SAMPLE_FACTORS P3 S (21) Genotype:PMM2-CDG Cell type=Brain organoids; RAW_FILE_NAME=S (21); DAYS IN VITRO=40; Weight in mg=29.4 #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 S (1) S (2) S (3) S (4) S (5) S (6) S (7) S (8) S (9) S (10) S (11) S (12) S (13) S (14) S (15) S (16) S (17) S (18) S (19) S (20) S (21) Factors Genotype:CTR Genotype:CTR Genotype:CTR Genotype:CTR Genotype:CTR 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 13C5-D5-15N Glutamic acid 173146528 180944384 181920528 9.77E+07 5.95E+07 173586048 169469952 173499040 7.04E+07 8.66E+07 153715424 154236992 153976352 1.16E+08 1.16E+08 157056400 156501760 153445328 158393792 156283600 162014768 GDP-mannose 1.73E+07 1.74E+07 1.73E+07 1.77E+06 8.58E+05 4.76E+07 4.95E+07 4.87E+07 7.34E+05 1.61E+06 5.63E+06 5.39E+06 5.97E+06 1.52E+06 1.96E+06 2.87E+07 2.73E+07 2.74E+07 4.53E+07 4.43E+07 4.19E+07 Glucose 3.04E+08 3.32E+08 3.16E+08 3.37E+08 2.96E+08 4.43E+08 4.47E+08 4.51E+08 4.80E+08 5.14E+08 1.63E+08 1.61E+08 1.64E+08 2.10E+08 1.73E+08 3.31E+08 3.23E+08 3.23E+08 3.06E+08 3.15E+08 3.19E+08 Glucose-6-P 7.19E+07 7.68E+07 7.58E+07 2.90E+06 9.00E+06 3.06E+08 3.17E+08 3.24E+08 9.20E+05 5.61E+06 3.70E+07 3.77E+07 3.83E+07 3.10E+07 9.30E+07 4.69E+08 4.79E+08 4.84E+08 5.34E+08 5.49E+08 5.44E+08 Lactate 9.44E+09 9.78E+09 9.83E+09 3.63E+09 2.16E+09 1.44E+10 1.47E+10 1.44E+10 3.42E+09 3.75E+09 1.11E+10 1.13E+10 1.14E+10 4.08E+09 5.24E+09 1.58E+10 1.59E+10 1.60E+10 1.39E+10 1.43E+10 1.41E+10 Sorbitol 4.37E+07 4.38E+07 4.47E+07 9.83E+06 9.29E+06 4.14E+07 4.31E+07 4.46E+07 1.26E+07 1.28E+07 2.28E+07 2.33E+07 2.34E+07 1.20E+07 1.05E+07 2.94E+07 3.12E+07 3.01E+07 2.65E+07 2.71E+07 2.84E+07 Pyruvate 4.71E+08 4.74E+08 4.73E+08 1.55E+07 7.02E+06 1.60E+09 1.56E+09 1.54E+09 3.68E+07 3.19E+07 6.01E+08 5.96E+08 5.93E+08 3.28E+07 4.53E+07 1.35E+09 1.33E+09 1.33E+09 1.20E+09 1.19E+09 1.17E+09 Taurine 4.99E+08 5.12E+08 5.21E+08 1.00E+08 9.51E+07 6.97E+08 7.70E+08 7.63E+08 1.10E+08 1.03E+08 2.02E+08 2.11E+08 2.21E+08 2.40E+08 2.72E+08 6.17E+08 6.43E+08 6.42E+08 6.23E+08 6.17E+08 6.15E+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