#METABOLOMICS WORKBENCH STUDY_ID:ST000276 ANALYSIS_ID:AN000441 PROJECT_ID:PR000154 VERSION 1 CREATED_ON 01-15-2019 #PROJECT PR:PROJECT_TITLE Isocitrate dehydrogenase-1 and Glioma Studies PR:PROJECT_SUMMARY Dr. Stegh will define the role of a novel glioma oncoprotein, termed isocitrate PR:PROJECT_SUMMARY dehydrogenase-1 (IDH1), in driving progression and therapy resistance of PR:PROJECT_SUMMARY glioblastoma (GBM). Understanding the molecular basis of the therapy PR:PROJECT_SUMMARY refractoriness of GBM is one of the most important areas of glioma research. PR:PROJECT_SUMMARY IDH1 is a critical enzyme of the citric acid cycle (CAC) and is a master PR:PROJECT_SUMMARY regulator of metabolism. Building on his preliminary studies, Dr. Stegh will PR:PROJECT_SUMMARY molecularly characterize the precise mechanism, by which IDH1 protects glioma PR:PROJECT_SUMMARY cells from therapy-induced cell death using glioma cell and mouse models. To PR:PROJECT_SUMMARY target IDH1 signaling in GBM, he will leverage these model systems and PR:PROJECT_SUMMARY mechanistical knowledge to develop and preclinically characterize RNA PR:PROJECT_SUMMARY interference RNAi-based nanomaterials. He will generate RNAi-functionalized PR:PROJECT_SUMMARY spherical nucleic acids (SNAs) that neutralize IDH1 expression in established PR:PROJECT_SUMMARY gliomas. Due to the negative charge of the RNA backbone, however, siRNA PR:PROJECT_SUMMARY oligonucleotides have many downsides, such as they trigger auto-immune PR:PROJECT_SUMMARY responses, and cannot cross the blood-brain-barrier (BBB). In contrast, SNAs are PR:PROJECT_SUMMARY able to transverse cellular membranes, do not require the use of toxic auxiliary PR:PROJECT_SUMMARY reagents, and accumulate in cells and intracranial tumors very effectively. They PR:PROJECT_SUMMARY also exhibit extraordinary stability in physiological environments, cross the PR:PROJECT_SUMMARY BBB, are highly resistant to nuclease degradation, and thus, can move through PR:PROJECT_SUMMARY biological fluids and avoid being destroyed as “foreign materials.” Dr. PR:PROJECT_SUMMARY Stegh proposes to preclinically evaluate these IDH1-targeting nanoconjugates to PR:PROJECT_SUMMARY provide a fundamentally novel treatment option of patients diagnosed with GBM, PR:PROJECT_SUMMARY and will aid in successfully implementing RNAi-based therapies into PR:PROJECT_SUMMARY neuro-oncological practice. PR:INSTITUTE Northwestern University PR:DEPARTMENT Neurology PR:LABORATORY Stegh Lab PR:LAST_NAME Stegh PR:FIRST_NAME Alexander PR:ADDRESS Evanston, IL PR:EMAIL a-stegh@northwestern.edu PR:PHONE 312-503-2879 PR:DOI http://dx.doi.org/10.21228/M8688J #STUDY ST:STUDY_TITLE IDH1 and Glioma knockdown idh1 ST:STUDY_SUMMARY This study is a part of series performed for the same researcher through ST:STUDY_SUMMARY pilot/feasibility grant program, so the publication is relevant reference for ST:STUDY_SUMMARY other studies (ST000199)This specific experiment is a pilot study to compare the ST:STUDY_SUMMARY metabolism of cells transformed using empty vector against cells transformed ST:STUDY_SUMMARY with vector carrying short hairpin RNA (shRNA) targeted to silence isocitrate ST:STUDY_SUMMARY dehydrogenase-1 (IDH1) gene. ST:INSTITUTE University of Michigan ST:DEPARTMENT Neurology ST:LABORATORY Stegh Lab (Northwestern University) ST:LAST_NAME Calvert ST:FIRST_NAME Andrea ST:ADDRESS Evanston, IL ST:EMAIL a-calvert@u.northwestern.edu ST:PHONE 312-503-3134 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 SU:SPECIES_GROUP Human #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - S00014999 IDH1 Knockdown:No SUBJECT_SAMPLE_FACTORS - S00015000 IDH1 Knockdown:No SUBJECT_SAMPLE_FACTORS - S00015001 IDH1 Knockdown:No SUBJECT_SAMPLE_FACTORS - S00015002 IDH1 Knockdown:No SUBJECT_SAMPLE_FACTORS - S00015003 IDH1 Knockdown:No SUBJECT_SAMPLE_FACTORS - S00015004 IDH1 Knockdown:yes SUBJECT_SAMPLE_FACTORS - S00015005 IDH1 Knockdown:yes SUBJECT_SAMPLE_FACTORS - S00015006 IDH1 Knockdown:yes SUBJECT_SAMPLE_FACTORS - S00015007 IDH1 Knockdown:yes SUBJECT_SAMPLE_FACTORS - S00015008 IDH1 Knockdown:yes #COLLECTION CO:SAMPLE_TYPE Cells, Cultured CO:COLLECTION_SUMMARY - #TREATMENT TR:TREATMENT_SUMMARY - #SAMPLEPREP SP:SAMPLEPREP_PROTOCOL_FILENAME Gly-TCA-nucleotides_analysis_protocol-2015-03-09.docx SP:SAMPLEPREP_SUMMARY - #CHROMATOGRAPHY CH:METHODS_ID AQM011 CH:METHODS_FILENAME ALPHA_KETO_ACIDS-FULL.M.zip CH:INSTRUMENT_NAME Agilent 7890A CH:COLUMN_NAME Agilent DB5-MS (30m × 0.25mm, 0.25um) CH:CHROMATOGRAPHY_TYPE GC #ANALYSIS AN:LABORATORY_NAME MRC2 (University of Michigan) AN:ANALYSIS_TYPE MS AN:ACQUISITION_PARAMETERS_FILE ALPHA_KETO_ACIDS-FULL.M AN:PROCESSING_PARAMETERS_FILE EX00317-MassHunterQuant-GlyTCA-DataAnalysis-GCMS-Method.m #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Agilent 5975C MS:INSTRUMENT_TYPE Single quadrupole MS:MS_TYPE EI MS:ION_MODE POSITIVE #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS pmol/µg protein MS_METABOLITE_DATA_START Samples S00014999 S00015000 S00015001 S00015002 S00015003 S00015004 S00015005 S00015006 S00015007 S00015008 Factors IDH1 Knockdown:No IDH1 Knockdown:No IDH1 Knockdown:No IDH1 Knockdown:No IDH1 Knockdown:No IDH1 Knockdown:yes IDH1 Knockdown:yes IDH1 Knockdown:yes IDH1 Knockdown:yes IDH1 Knockdown:yes Alanine 996.2817 910.7413 1281.7169 698.7935 844.0850 1041.1305 647.4352 946.3281 1024.3858 867.1329 alpha-Ketoglutarate 16.4588 22.3602 23.5513 12.7843 16.7499 21.2418 14.1643 22.3870 15.7013 16.7397 Aspartate 356.2586 276.7119 578.6748 312.8998 191.0696 702.4607 502.8527 628.2349 574.3030 566.6498 fumarate 14.7099 11.9777 17.9796 11.6283 8.9059 13.2667 8.3125 11.3369 11.5190 11.8588 Glutamate 166.5818 120.7442 184.1360 121.4537 85.6198 227.2815 154.6118 246.7419 168.0500 157.7775 glutamine 2409.2674 2039.1899 2390.0722 1695.1824 1966.8836 1442.3682 1002.0822 1743.0489 1836.5683 1482.1244 Lactate 4859.4627 5828.3572 7505.5884 3540.7433 6401.0627 3732.3973 2521.0120 3340.4079 3761.1185 3620.8429 Oxaloacetate pyruvate 53.1017 59.6396 61.5282 24.5963 64.7677 33.9041 31.0891 34.9901 35.0506 41.2705 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name pubchem_id inchi_key kegg_id other_id other_id_type ri ri_type moverz_quant Alanine 5950 C00041 ALA UM_Target_ID alpha-Ketoglutarate 51 C00026 AKG UM_Target_ID Aspartate 5960 C00049 ASP UM_Target_ID fumarate 444972 C00122 FUM UM_Target_ID Glutamate 611 GLU UM_Target_ID glutamine 5961 C00064 GLN UM_Target_ID Lactate 107689 C00186 LAC UM_Target_ID Oxaloacetate 970 C00036 OAA UM_Target_ID pyruvate 1060 C00022 PYR UM_Target_ID METABOLITES_END #END