#METABOLOMICS WORKBENCH spinelli_lab_20251112_110517 DATATRACK_ID:6667 STUDY_ID:ST004390 ANALYSIS_ID:AN007335 PROJECT_ID:PR002783 VERSION 1 CREATED_ON November 20, 2025, 4:30 pm #PROJECT PR:PROJECT_TITLE Metabolic Reprogramming during Human Neuron Differentiation Indicates PR:PROJECT_TITLE Glutaminase as a Key Determinant in Fragile X Syndrome PR:PROJECT_SUMMARY Metabolic homeostasis gone awry is a contributor to, if not an underlying cause PR:PROJECT_SUMMARY of, several neurologic disorders. Fragile X syndrome (FXS) is a PR:PROJECT_SUMMARY neurodevelopmental disorder caused by a trinucleotide repeat expansion in FMR1 PR:PROJECT_SUMMARY and consequent loss of the encoded protein FMRP, which results in downstream PR:PROJECT_SUMMARY molecular, neurologic, and mitochondrial deficits that are linked to cognitive PR:PROJECT_SUMMARY impairment. In human postmortem brain, many metabolites and solute carrier PR:PROJECT_SUMMARY proteins are coordinately dysregulated, which also occurs during differentiation PR:PROJECT_SUMMARY of human iPSCs into excitatory neurons. Metabolic tracing in FXS neurons PR:PROJECT_SUMMARY demonstrates a dearth of glutamine deamidation to glutamate, which reduces PR:PROJECT_SUMMARY anaplerosis into the TCA cycle, potentially hindering bioenergetic and PR:PROJECT_SUMMARY biosynthetic functions of mitochondria. Mechanistically, aberrant expression of PR:PROJECT_SUMMARY glutaminase isoforms in FXS is responsible for reduced glutaminolysis, thereby PR:PROJECT_SUMMARY altering glutamate levels which may contribute to FXS. PR:INSTITUTE UMass Chan Medical School PR:LAST_NAME UMass Chan PR:FIRST_NAME Richter Lab PR:ADDRESS 55 Lake Avenue North, Worcester, Massachusetts, 01605, USA PR:EMAIL spinellilab@gmail.com PR:PHONE (508) 856-8989 ext. 68148 #STUDY ST:STUDY_TITLE Human Fragile X Syndrome cortex compared to typically developing ST:STUDY_SUMMARY Polar metabolic profiling of human cortex with and without Fragile X Syndrome. ST:INSTITUTE UMass Chan Medical School ST:LAST_NAME UMass Chan ST:FIRST_NAME Richter Lab ST:ADDRESS 55 Lake Avenue North, Worcester, Massachusetts, 01605, USA ST:EMAIL spinellilab@gmail.com ST:PHONE (508) 856-8989 ext. 68148 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 #FACTORS #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 - TD01 Sample source:Homo Sapien Male Cortex | Genotype:TD RAW_FILE_NAME(Raw_file_name)=20230214_RichterLab_SS_17.raw SUBJECT_SAMPLE_FACTORS - TD02 Sample source:Homo Sapien Male Cortex | Genotype:TD RAW_FILE_NAME(Raw_file_name)=20230214_RichterLab_SS_18.raw SUBJECT_SAMPLE_FACTORS - TD03 Sample source:Homo Sapien Male Cortex | Genotype:TD RAW_FILE_NAME(Raw_file_name)=20230214_RichterLab_SS_19.raw SUBJECT_SAMPLE_FACTORS - TD04 Sample source:Homo Sapien Male Cortex | Genotype:TD RAW_FILE_NAME(Raw_file_name)=20230214_RichterLab_SS_20.raw SUBJECT_SAMPLE_FACTORS - TD05 Sample source:Homo Sapien Male Cortex | Genotype:TD RAW_FILE_NAME(Raw_file_name)=20230214_RichterLab_SS_21.raw SUBJECT_SAMPLE_FACTORS - TD06 Sample source:Homo Sapien Male Cortex | Genotype:TD RAW_FILE_NAME(Raw_file_name)=20230214_RichterLab_SS_22.raw SUBJECT_SAMPLE_FACTORS - FXS01 Sample source:Homo Sapien Male Cortex | Genotype:FXS RAW_FILE_NAME(Raw_file_name)=20230214_RichterLab_SS_23.raw SUBJECT_SAMPLE_FACTORS - FXS02 Sample source:Homo Sapien Male Cortex | Genotype:FXS RAW_FILE_NAME(Raw_file_name)=20230214_RichterLab_SS_24.raw SUBJECT_SAMPLE_FACTORS - FXS03 Sample source:Homo Sapien Male Cortex | Genotype:FXS RAW_FILE_NAME(Raw_file_name)=20230214_RichterLab_SS_25.raw SUBJECT_SAMPLE_FACTORS - FXS04 Sample source:Homo Sapien Male Cortex | Genotype:FXS RAW_FILE_NAME(Raw_file_name)=20230214_RichterLab_SS_26.raw SUBJECT_SAMPLE_FACTORS - FXS05 Sample source:Homo Sapien Male Cortex | Genotype:FXS RAW_FILE_NAME(Raw_file_name)=20230214_RichterLab_SS_27.raw SUBJECT_SAMPLE_FACTORS - FXS06 Sample source:Homo Sapien Male Cortex | Genotype:FXS RAW_FILE_NAME(Raw_file_name)=20230214_RichterLab_SS_28.raw #COLLECTION CO:COLLECTION_SUMMARY The post-mortem brain tissues were powdered under liquid nitrogen and samples CO:COLLECTION_SUMMARY were normalized based on tissue weight. The metabolites were extracted using 80% CO:COLLECTION_SUMMARY methanol. CO:SAMPLE_TYPE Brain cortex #TREATMENT TR:TREATMENT_SUMMARY Frozen post-mortem cortex and cerebellum tissues were obtained from University TR:TREATMENT_SUMMARY of California, Davis Brain Repository for Typically Developing (TD) males and TR:TREATMENT_SUMMARY age-matched FXS males (n=6 each genotype). #SAMPLEPREP SP:SAMPLEPREP_SUMMARY The metabolites were extracted using 80% methanol. The extracts were spun down SP:SAMPLEPREP_SUMMARY and the supernatant was vacuum dried before resuspending in LC/MS grade water. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Thermo Vanquish CH:COLUMN_NAME Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) CH:SOLVENT_A 100% water; 0.1% ammonium hydroxide; 20mM ammonium carbonate CH:SOLVENT_B 100% acetonitrile CH:FLOW_GRADIENT 20 min, 80% - 20% B; 0.5 min, 20% - 80% B; 7.5min, 80% B CH:FLOW_RATE 0.15ml/min CH:COLUMN_TEMPERATURE 25 #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive Plus Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS The mass spectrometer was set to full scan (70-1000 m/z), with the spray voltage MS:MS_COMMENTS set to 4.0 kV, heated capillary to 350°C, and the HESI probe at 30 °C. The MS:MS_COMMENTS sheath gas flow was set at 10 units, auxiliary gas at 1 units, and sweep gas MS:MS_COMMENTS flow at 1 unit. The resolution of scan was set to 70,000, AGC target to 1x106, MS:MS_COMMENTS and maximum injection time at 20 msec. Data acquired by Thermo Fisher's Xcalibur MS:MS_COMMENTS software and analyzed by their Tracefinder software. The raw files provided MS:MS_COMMENTS contain data from both positive and negative ion mode. #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS Peak Area MS_METABOLITE_DATA_START Samples TD01 TD02 TD03 TD04 TD05 TD06 FXS01 FXS02 FXS03 FXS04 FXS05 FXS06 Factors Sample source:Homo Sapien Male Cortex | Genotype:TD Sample source:Homo Sapien Male Cortex | Genotype:TD Sample source:Homo Sapien Male Cortex | Genotype:TD Sample source:Homo Sapien Male Cortex | Genotype:TD Sample source:Homo Sapien Male Cortex | Genotype:TD Sample source:Homo Sapien Male Cortex | Genotype:TD Sample source:Homo Sapien Male Cortex | Genotype:FXS Sample source:Homo Sapien Male Cortex | Genotype:FXS Sample source:Homo Sapien Male Cortex | Genotype:FXS Sample source:Homo Sapien Male Cortex | Genotype:FXS Sample source:Homo Sapien Male Cortex | Genotype:FXS Sample source:Homo Sapien Male Cortex | Genotype:FXS Anserine 8473768.419 4128746.783 12303625.84 11159343.81 13061453.08 6557587.051 12088066.75 20511639.03 10195213.23 10438188.28 11842208.69 0 Arginine 2668562550 4713237634 2628317820 2298335362 2535690384 2248049430 2029759211 1805207172 2236694219 1417889626 1644813129 1952110731 Asparagine 25291409.32 66664123.59 25695532.91 46477823.18 29411353.23 27134402.91 17597138.18 17540122.26 16396153 12044087.26 15138920.36 38107368.71 NAD+ 12474253.97 18316799.44 8142277.331 5400621.26 4791260.694 6228976.731 1908523.624 4567996.026 2231797.561 1344717.238 34424497.21 2792327.377 Carnosine 16489331.79 6040690.502 35919524.37 59842563.04 65228045.98 20942867.04 27415455.49 7684556.781 10071003.87 11508015.8 11072140.84 61617310.11 Choline 1117768635 673646627.2 447820886.8 864726105.1 998487988.9 429955715.4 707991066.9 418372212.3 723675303.2 319384316.6 269005139 1039923322 Creatine 48462784039 47628795041 38685875244 41917392054 43212062254 41816773509 47710698150 43959838296 47174271018 41233895121 46223889546 42685468235 Cystathionine 400991904 154296241.2 153238166.9 129449555.6 331873033.2 142726070.6 547552795.1 292439933.9 197927835.9 202203980.7 339578188.1 115655071.9 Cystine 33984574.93 52660288.04 74048886.55 82741685.96 76421769.82 42100589 21337050.26 16901322.99 34449998.48 18817722.11 23091663.01 72049811.3 Cytidine 102666450.1 20323050.16 4972644.131 5002744.345 17795565.04 14405394.54 66733745.11 68330978.48 49985171.71 13672981.37 37241283.67 19194415.19 Cytosine 359059608.3 58251207.91 14951055.52 14234601.91 65936107.93 44756949.86 239854512.7 217843247.4 162210224.7 40414802.3 104224025.7 74282294.47 Alanine 1067923226 1079508179 916969409.7 973931130.6 981276537.2 945776274 1052049284 978017877.4 1048547967 922417922.9 1007188550 971262040.8 D-Ornithine 51324320.16 58656298.64 76505454.44 206917867.7 157637497.3 56843187.24 28991875.47 39403181.65 33252920.71 18911353.43 34203878.04 196056747.8 FAD 1983015.083 3176574.711 1728698.202 1687070.899 2290443.196 1741307 2757305.828 1236157.406 2561728.219 1744165.313 2897357.516 1477542.459 Glutamine 2312879709 2928195782 4289977646 2284364328 4132855028 2385858561 2589754826 3326525269 3812204096 2873804918 3585816688 2536957882 Glutathione 817016685.6 464512881 154322126.6 161651976.3 246704574.1 306570754.1 500346691.8 428418187.8 374932233.9 202499705.6 629872393.1 162855320.2 Glycine 10522381.98 11640976.37 10968697.68 9941618.844 10634315.64 6608891.9 6974845.538 5131153.78 7042224.495 4471966.392 5626755.552 8958072.505 Oxidized glutathione 16866484.8 13427448.13 6114707.874 15761292.96 9231525.113 15708616.97 33137735.88 22584077.48 26797309.67 41439790.36 70297832.8 12162423.09 Guanine 40105732.27 73030653.43 30214352.49 43331396.39 40044810.06 29986643.04 23294447.02 16631657.68 22545697.88 13985489.17 17919227.31 36772708.77 Homocysteine 3944107.993 883715.4619 318045.257 818535.7173 733727.8968 870356.1652 1212385.082 886565.0629 625602.5895 998916.831 1814024.124 545448.045 Homoserine 116502777.6 188140458 279672693.3 209839457.8 248825879.4 134663097.3 109501922.4 61352997.81 98460862.29 82326210.63 79719602.27 178357353.7 Hypotaurine 340785.9304 624687.1797 2064114.236 3644393.199 3532418.318 555853.9705 361595.2462 1094769.307 653728.04 107480.4291 783917.6718 1158462.268 Hypoxanthine 14914575399 11077178156 8801612087 11374891017 13371582773 10724510325 14538962806 7540088035 11078503180 7014332895 8242202358 12951265132 Inosine 224136143.5 184377229 44929950.85 44669710.09 80108340.99 248977099.9 246727957.8 171524320.1 186851418.3 262599106.2 311775504.9 94451368.04 Isoleucine 874475760.9 1372362545 556953231.9 828442892.5 867255783.7 552315713.2 425044590.2 279359473.4 434112776 193093071.3 257562751.3 690661925.5 Kynurenine 9634002.523 9741366.634 40644310.69 17728130.03 25799162.86 6148870.37 4310201.545 9637351.103 26764228.68 12598930.96 17146671.01 3948756.243 Carnitine 4988388815 4503060611 9501789853 5659170576 5348838344 2383117905 2508449945 4268790313 2760845591 2919143737 2435500021 2190961293 Leucine 1302426674 2702579428 1525336051 1763161630 1593036799 1210126326 821378795.4 547361122.5 760376767.3 415244532.5 537471709.7 1347739318 Lysine 751640677.1 1253840411 828075917.6 887691194.4 917601567.2 567060588.3 433280534.8 337734733.1 483224888.4 271478020.6 355732354.8 653866934.3 Methionine 934538578.6 1627782928 702902381.7 977017924.5 916395394.3 655846435.6 532516819.7 360631889 525470561.9 321008445.2 409029139.6 842441298.7 NADP+ 1018450.214 368372.8684 141430.504 372991.5725 553509.9024 452054.4814 107425.9698 570166.7434 84391.93319 225998.9394 1975304.428 0 NADPH 469052.5972 226594.9049 373810.1692 177845.5582 348380.8893 50954.75523 299010.4783 69015.22103 69828.67237 97069.33555 434534.6487 0 Niacinamide 6234143024 6113357293 2689730615 3746752576 4575507273 4528792172 6378917443 5024633123 6023441871 5401341236 4531046348 4921447117 Phenylalanine 1232377405 3073400077 2077269786 1945862125 1695814706 1202718945 715931131.5 870897152.3 972355445.4 613906893.2 940922512.9 1226431567 Proline 4838873747 7487714432 6683553903 6364864085 6741457381 3913557914 3208153991 2662643385 3871144076 1948313464 2524205651 5173449402 S-Adenosylhomocysteine 59963973.03 139988371.5 53634732.75 57832734.49 68780224.23 77975930.71 122498151.1 80698176.01 105804029 80998904.5 126313256 32185937.86 S-Adenosylmethionine 12087525.89 39481264.21 36233197.98 32221205.69 15488696.42 33883145.67 24633860.6 40308005.8 33488827.24 48691798.37 94866657.39 14921226.15 Serine 62442148.38 93825757.01 94855636.99 78238286.7 80071669.3 44633181.47 47106710.04 37226563.7 46730590.49 31527405.41 32451052.48 63482995.89 Taurine 387164499.4 302219622.5 135810238.4 263111743.5 264008293 161247534.8 244457243.1 231425128.5 160264889.7 120040949.1 163210705.3 175274773.5 Threonine 116487506.1 186366095.9 276943219.1 207491335.8 248566299.9 134663097.3 109487300.5 61195453.99 98237992.02 82132200.58 79719602.27 177507622.5 Tryptophan 217140867 481220192.2 221363550.4 300989193.7 314622704.4 165929069.7 111679335.8 110292116.3 201072652.2 90248775.96 164336619.5 181978982.3 Tyrosine 417057400.2 804999036.2 410327519.7 481746176.2 584258455.4 346567268 290800008.4 260028912.5 398588163.3 214974403.5 346825758.5 364644676.8 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name Retention Index Quantified m/z PubChem ID KEGG ID Anserine 7.4 241.1295 112072 C01262 Arginine 13 175.119 6322 C00062 Asparagine 8.26 133.0608 6267 C00152 NAD+ 8 664.1164 5893 C00003 Carnosine 8.4 227.1139 439224 C00386 Choline 9.75 105.1148 305 C00114 Creatine 8 132.0768 586 C00300 Cystathionine 9.5 223.0747 439258 C02291 Cystine 9.3 241.0311 67678 C00491 Cytidine 6.13 244.0928 6253 C00475 Cytosine 6 112.0505 597 C00380 Alanine 7.9 90.055 5950 C00041 D-Ornithine 11.5 133.0972 71082 C00515 FAD 6.3 786.1644 643975 C00016 Glutamine 8.1 147.0764 5961 C00064 Glutathione 8.5 308.0911 124886 C00051 Glycine 8.5 76.0393 750 C00037 Oxidized glutathione 10.5 613.1592 65359 C00127 Guanine 5.7 152.0567 135398634 C00242 Homocysteine 9.38 136.0427 91552 C00155 Homoserine 7.7 120.0655 12647 C00263 Hypotaurine 8.15 110.027 107812 C00519 Hypoxanthine 5.21 137.0458 135398638 C00262 Inosine 5.59 269.0881 135398641 C00294 Isoleucine 5.5 132.1019 6306 C00407 Kynurenine 5.4 209.0921 161166 C00328 Carnitine 7 162.1125 10917 C00318 Leucine 5.3 132.1019 6106 C00123 Lysine 12.6 147.1128 5962 C00047 Methionine 5.7 150.0583 6137 C00073 NADP+ 10 744.0827 5886 C00006 NADPH 10 746.0984 5884 C00005 Niacinamide 3.33 123.0553 936 C00153 Phenylalanine 4.87 166.0863 6140 C00079 Proline 6.76 116.0706 145742 C00148 S-Adenosylhomocysteine 7 385.1289 439155 C00021 S-Adenosylmethionine 8.7 400.1523 34756 C00019 Serine 8.5 106.0499 5951 C00716 Taurine 8.1 126.0219 1123 C00245 Threonine 7.8 120.0655 6288 C00188 Tryptophan 5.9 205.0972 6305 C00078 Tyrosine 6.65 182.0812 6057 C00082 METABOLITES_END #END