#METABOLOMICS WORKBENCH AnthonyDon_20250929_182902 DATATRACK_ID:6506 STUDY_ID:ST004262 ANALYSIS_ID:AN007092 PROJECT_ID:PR002689 VERSION 1 CREATED_ON October 5, 2025, 12:46 am #PROJECT PR:PROJECT_TITLE Histone methyltransferase PRDM9 promotes survival of drug-tolerant persister PR:PROJECT_TITLE cells in glioblastoma PR:PROJECT_SUMMARY Chemotherapy often kills a large fraction of cancer cells but leaves behind a PR:PROJECT_SUMMARY small population of drug tolerant persister cells. These persister cells survive PR:PROJECT_SUMMARY drug treatments through reversible, non-genetic mechanisms and cause tumour PR:PROJECT_SUMMARY recurrence upon cessation of therapy. Here, we report a drug tolerance mechanism PR:PROJECT_SUMMARY regulated by the germ-cell-specific H3K4 methyltransferase PRDM9. Through PR:PROJECT_SUMMARY histone proteomic, transcriptomic, lipidomic, and ChIP-sequencing studies PR:PROJECT_SUMMARY combined with CRISPR knockout and phenotypic drug screen, we identified that PR:PROJECT_SUMMARY chemotherapy-induced PRDM9 upregulation promotes metabolic rewiring in PR:PROJECT_SUMMARY glioblastoma stem cells, leading to chemotherapy tolerance. Mechanistically, PR:PROJECT_SUMMARY PRDM9-dependent H3K4me3 at cholesterol biosynthesis genes enhances cholesterol PR:PROJECT_SUMMARY biosynthesis, which persister cells rely on to maintain homeostasis under PR:PROJECT_SUMMARY chemotherapy induced oxidative stress and lipid peroxidation. PRDM9 inhibition, PR:PROJECT_SUMMARY combined with chemotherapy, resulted in strong anti-cancer efficacy in PR:PROJECT_SUMMARY preclinical glioblastoma models, significantly enhancing the magnitude and PR:PROJECT_SUMMARY duration of the antitumor response by eliminating persisters. These findings PR:PROJECT_SUMMARY demonstrate a previously unknown role of PRDM9 in promoting metabolic PR:PROJECT_SUMMARY reprogramming that enables the survival of drug-tolerant persister cells. PR:INSTITUTE The University of Sydney PR:DEPARTMENT School of Medical Sciences PR:LAST_NAME Don PR:FIRST_NAME Anthony PR:ADDRESS Office 3210, D17 Charles Perkins Centre, Camperdown, NSW, 2006, Australia PR:EMAIL anthony.don@sydney.edu.au PR:PHONE +612 8627 5578 PR:PUBLICATIONS Histone methyltransferase PRDM9 promotes survival of drug-tolerant persister PR:PUBLICATIONS cells in glioblastoma #STUDY ST:STUDY_TITLE The lipidome of drug-resistant glioblastoma persister cells. ST:STUDY_SUMMARY This study aimed to determine mechanisms through which glioblastoma stem cells ST:STUDY_SUMMARY acquire a drug-resistant phenotype. A small proportion of glioblastoma stem ST:STUDY_SUMMARY cells survive chemotherapy and radiotherapy, creating a drug-resistant persister ST:STUDY_SUMMARY cell population that resumes proliferation after the cessation of drug ST:STUDY_SUMMARY treatment. The specific experiment profiled the lipidome of glioblastoma stem ST:STUDY_SUMMARY cells that survive treatment with the anti-microtubule agent CMPD1. Glioblastoma ST:STUDY_SUMMARY stem cell line RKI1 was treated for 14 days with 25 micromolar CMPD1 to generate ST:STUDY_SUMMARY drug-resistant persister cells, replacing the cell culture medium every 3 days ST:STUDY_SUMMARY (n = 3). At day 14 of treatment, the CMPD1-treated cells were collected for ST:STUDY_SUMMARY lipid extraction and lipidomic analysis. The drug-resistant persister cells were ST:STUDY_SUMMARY compared to control cells grown in RKI1 growth medium and collected prior to ST:STUDY_SUMMARY drug-treatment (n = 3). The drug-resistant persister cells displayed ST:STUDY_SUMMARY significantly decreased levels of ceramide and cholesterol, and increased ST:STUDY_SUMMARY sphingomyelin and diacylgylcerol, indicative of membrane remodelling that may ST:STUDY_SUMMARY allow the cells to survive chemotherapy. Further investigation indicated that ST:STUDY_SUMMARY the reduced cholesterol content provides a point of metabolic vulnerability to ST:STUDY_SUMMARY eliminate the drug resistant persister cells. ST:INSTITUTE University of Sydney ST:DEPARTMENT School of Medical Sciences ST:LAST_NAME Don ST:FIRST_NAME Anthony ST:ADDRESS Office 3210, D17 Charles Perkins Centre, Camperdown, NSW, 2006 ST:EMAIL anthony.don@sydney.edu.au ST:PHONE +612 8627 5578 ST:NUM_GROUPS 2 ST:TOTAL_SUBJECTS 6 ST:STUDY_COMMENTS Control and drug-treated RKI1 glioblastoma cells ST:PUBLICATIONS Histone methyltransferase PRDM9 promotes survival of drug-tolerant persister ST:PUBLICATIONS cells in glioblastoma #SUBJECT SU:SUBJECT_TYPE Cultured cells SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 SU:CELL_BIOSOURCE_OR_SUPPLIER QIMR Berghofer Institute SU:CELL_STRAIN_DETAILS Patient-derived glioblastoma stem cell line RKI1 #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 - 4 Sample source:RKI1 cells | Factor:Control RAW_FILE_NAME(Raw file name)=4 SUBJECT_SAMPLE_FACTORS - 5 Sample source:RKI1 cells | Factor:Control RAW_FILE_NAME(Raw file name)=5 SUBJECT_SAMPLE_FACTORS - 3 Sample source:RKI1 cells | Factor:Control RAW_FILE_NAME(Raw file name)=3 SUBJECT_SAMPLE_FACTORS - 1 Sample source:RKI1 cells | Factor:Drug Treated RAW_FILE_NAME(Raw file name)=1 SUBJECT_SAMPLE_FACTORS - 6 Sample source:RKI1 cells | Factor:Drug Treated RAW_FILE_NAME(Raw file name)=6 SUBJECT_SAMPLE_FACTORS - 2 Sample source:RKI1 cells | Factor:Drug Treated RAW_FILE_NAME(Raw file name)=2 #COLLECTION CO:COLLECTION_SUMMARY Glioblastoma stem cell line RKI1 is a patient-derived line described in: CO:COLLECTION_SUMMARY Stringer BW, et al. A reference collection of patient-derived cell line and CO:COLLECTION_SUMMARY xenograft models of proneural, classical and mesenchymal glioblastoma. CO:COLLECTION_SUMMARY Scientific Reports 9, 4902 (2019). These cells are available at: CO:COLLECTION_SUMMARY https://www.qimrberghofer.edu.au/our-research/commercialisation/q-cell/. RKI1 CO:COLLECTION_SUMMARY cells are cultured in KnockOut DMEM/F-12 basal medium kit with neural CO:COLLECTION_SUMMARY supplement, EGF (20 ng/mL) and FGF-β (10 ng/mL) (ThermoFisher Scientific, Cat# CO:COLLECTION_SUMMARY 579 A1050901). GlutaMAX-ICTS (2 mM) (Thermofisher Scientific, Cat# A1286001) and CO:COLLECTION_SUMMARY Antibiotic- Antimycotic (Thermofisher Scientific, Cat# 15240112) were also CO:COLLECTION_SUMMARY added. Adherent cells were plated on flasks coated with 0.15% in PBS MatriGel CO:COLLECTION_SUMMARY Matrix (Corning Life Sciences, Cat# BDAA356237), incubated at 37 °C, 5% CO2. CO:COLLECTION_SUMMARY Specific treatment conditions are described under "treatment". CO:SAMPLE_TYPE Glioma cells #TREATMENT TR:TREATMENT_SUMMARY RKI1 cells (1.5 × 10^4 cells/cm2) were grown in 10 cm2 dishes and treated with TR:TREATMENT_SUMMARY CMPD1 (25 μM) for 14 days. Every 3 days, the media containing CMPD1 was TR:TREATMENT_SUMMARY replaced. At Day 14, three independent cultures of drug tolerant persister (DTP) TR:TREATMENT_SUMMARY cells were collected for lipidomic analysis. Control cells were RKI1 cells grown TR:TREATMENT_SUMMARY in culture medium without CMPD1 (1.5 x 10^5 cells in 10 cm2 dishes). Three TR:TREATMENT_SUMMARY independent cultures of the cells were used. RKI1 cells are cultured in KnockOut TR:TREATMENT_SUMMARY DMEM/F-12 basal medium kit with neural supplement, EGF (20 ng/mL) and FGF-β (10 TR:TREATMENT_SUMMARY ng/mL) (ThermoFisher Scientific, Cat# 579 A1050901). GlutaMAX-ICTS (2 mM) TR:TREATMENT_SUMMARY (Thermofisher Scientific, Cat# A1286001) and Antibiotic- Antimycotic TR:TREATMENT_SUMMARY (Thermofisher Scientific, Cat# 15240112) were also added. Adherent cells were TR:TREATMENT_SUMMARY plated on flasks coated with 0.15% in PBS MatriGel Matrix (Corning Life TR:TREATMENT_SUMMARY Sciences, Cat# BDAA356237), incubated at 37 °C, 5% CO2. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY RKI1 parent and CMPD1-derived drug-tolerant persister cells were collected, SP:SAMPLEPREP_SUMMARY homogenized in sample extraction buffer (50 mM Hepes pH 7.4, 25 mM KCl, Protease SP:SAMPLEPREP_SUMMARY Inhibitor Cocktail) by sonicating for 5 min (30 s on/30 s off) at 4ºC with a SP:SAMPLEPREP_SUMMARY Qsonica Q800R2 sonicating bath. Protein concentration was determined with the SP:SAMPLEPREP_SUMMARY BCA assay. Lipids were extracted from 200 µL lysate (~200 µg protein) using SP:SAMPLEPREP_SUMMARY the methyl-tert-butyl ether (MTBE)/methanol/water protocol. Cell homogenate was SP:SAMPLEPREP_SUMMARY combined with 250 µL methanol containing 0.01% SP:SAMPLEPREP_SUMMARY 3,5-di-tert-4-butylhydroxyltoluene (BHT), internal standards and 850 µL MTBE, SP:SAMPLEPREP_SUMMARY sonicated in a 4°C water bath for 30 min, and phase separation was induced by SP:SAMPLEPREP_SUMMARY centrifuging at 2000g for 5 min. The upper organic phase was transferred to a 5 SP:SAMPLEPREP_SUMMARY mL glass tube, and the aqueous phase was re-extracted with 500 µL MTBE and 150 SP:SAMPLEPREP_SUMMARY µL methanol. The organic phase from the second extraction was combined with the SP:SAMPLEPREP_SUMMARY first, after which the extracts were dried in a Savant SC210 SpeedVac dessicator SP:SAMPLEPREP_SUMMARY (ThermoFisher Scientific). Lipids were reconstituted in 400 µL of 80% (v/v) SP:SAMPLEPREP_SUMMARY methanol:20% water containing 0.01% BHT, 1 mM ammonium formate, and 0.1% formic SP:SAMPLEPREP_SUMMARY acid, and stored at -80 degrees C. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Thermo Vanquish CH:COLUMN_NAME Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um) CH:SOLVENT_A 10 mM ammonium formate, 0.1% formic acid, 60% acetonitrile and 40% water CH:SOLVENT_B 10 mM ammonium formate, 0.1% formic acid, 10% acetonitrile and 90% isopropanol CH:FLOW_GRADIENT 0-3 min, 20% B; 3-5.5 min, ramp to 45% B; 5.5-8 min, ramp to 65% B; 8-13 min, CH:FLOW_GRADIENT ramp to 85% B; 13-14 min, ramp to 100% B; 14-20 min, hold at 100% B; 20-25 min, CH:FLOW_GRADIENT decrease to 20% B and hold to 25 min CH:FLOW_RATE 0.28 ml/min CH:COLUMN_TEMPERATURE 45 #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo TSQ Altis MS:INSTRUMENT_TYPE Triple quadrupole MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS Acylcarnitine (AcCa), ceramide, sphingomyelin (SM), phosphatidylcholine (PC), MS:MS_COMMENTS lysophosphatidylcholine (LPC), and lysophosphatidylethanolamine (LPE) species MS:MS_COMMENTS were identified as the [M+H]+ precursor ion, with product ion m/z values of 85.0 MS:MS_COMMENTS for AcCa, 184.1 for PC, LPC and SM, 264.3 for ceramide and SM, and neutral loss MS:MS_COMMENTS of 141.0 for LPE. Diacylglycerol (DG) was detected as the [M+NH4]+ precursor MS:MS_COMMENTS ion, with product ions corresponding to neutral loss of 35.0 and RCOOH + NH3. PE MS:MS_COMMENTS was identified through neutral loss of the ethanolamine phosphate headgroup in MS:MS_COMMENTS positive ion mode (precursor m/z - 141) and a specific fatty acid product ion in MS:MS_COMMENTS negative ion mode. The PE species are listed under the negative ion mode data MS:MS_COMMENTS file. #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS pmoles/mg protein MS_METABOLITE_DATA_START Samples 4 5 3 1 6 2 Factors Sample source:RKI1 cells | Factor:Control Sample source:RKI1 cells | Factor:Control Sample source:RKI1 cells | Factor:Control Sample source:RKI1 cells | Factor:Drug Treated Sample source:RKI1 cells | Factor:Drug Treated Sample source:RKI1 cells | Factor:Drug Treated Cer(d18:1/14:0) 6.47 4.12 4.78 1.08 0.88 1.13 Cer(d18:1/16:0) 202.62 154.02 162.71 11.26 13.99 21.83 Cer(d18:1/18:0) 181.71 163.72 175.37 9.13 11.15 23.73 Cer(d18:1/20:0) 15.89 13.03 11.64 1.72 1.39 2.77 Cer(d18:1/22:0) 27.67 15.09 19.55 4.36 3.96 6.01 Cer(d18:1/22:1) 10.00 12.05 7.40 0.99 0.90 2.05 Cer(d18:1/24:0) 83.09 25.62 61.47 24.31 11.38 31.99 Cer(d18:1/24:1) 486.55 337.87 372.95 51.05 38.59 77.06 Cholesterol 73874.3 94071.3 64227.5 42719.8 23681.1 28878.3 DG(32:0) 52.24 61.73 20.16 82.06 94.49 105.00 DG(32:1) 85.35 59.99 46.51 87.60 112.42 107.55 DG(34:0) 42.87 31.68 15.05 25.37 79.16 94.78 DG(34:1) 888.36 794.57 627.10 1027.84 1317.20 1428.82 DG(34:2) 321.19 522.47 247.22 556.96 1067.39 988.72 DG(36:0) 105.42 92.16 87.88 228.16 200.49 217.83 DG(36:1) 893.33 938.43 650.24 1415.39 1584.13 1626.59 DG(36:2) 1829.30 1982.63 1418.08 4237.24 3741.00 4461.36 DG(36:3) 696.08 794.89 453.91 1815.11 1827.38 2326.79 DG(36:4) 157.60 131.80 128.38 344.37 492.42 501.76 DG(36:5) 10.99 12.50 7.81 25.98 51.68 72.06 DG(38:3) 877.06 448.92 560.81 1606.45 660.54 742.79 DG(38:4) 415.59 433.14 165.56 909.67 828.08 1006.18 DG(38:5) 225.02 136.28 156.61 244.52 217.60 334.54 DG(38:6) 19.22 27.61 16.69 53.83 58.44 89.49 DG(40:4) 202.33 152.59 186.84 440.27 218.77 276.66 DG(40:5) 121.80 124.01 156.28 243.55 147.97 324.98 DG(40:6) 109.34 104.54 65.66 167.01 297.62 290.67 LPC(16:0) 175.467 99.668 136.120 111.398 82.060 158.216 LPC(16:1) 18.000 11.729 14.868 8.528 7.870 16.106 LPC(18:0) 23.205 13.251 18.674 62.003 39.609 69.941 LPC(18:1) 189.722 157.553 158.099 213.844 243.030 313.857 LPC(18:2) 13.280 18.238 11.853 80.265 54.991 111.307 LPC(20:3) 6.181 4.067 5.169 15.900 10.127 19.309 LPC(20:4) 5.867 3.346 4.359 5.049 3.804 7.013 LPC(22:4) 1.397 0.686 1.246 1.702 2.061 1.663 LPC(22:5) 4.629 2.297 4.178 1.890 1.815 2.789 LPC(22:6) 3.238 1.448 2.652 1.049 0.550 1.801 LPE(16:0) 108.930 81.702 72.608 65.350 93.705 90.618 LPE(16:1) 5.647 3.499 3.331 3.819 3.877 5.638 LPE(18:0) 240.518 104.045 158.123 261.018 191.136 361.005 LPE(18:1) 351.463 304.772 249.312 381.333 259.492 381.023 LPE(18:2) 14.277 20.008 12.126 94.164 131.455 115.711 LPE(20:3) 33.112 27.164 23.241 86.237 120.134 104.015 LPE(20:4) 50.901 31.439 25.785 47.531 63.109 58.385 LPE(22:4) 31.242 21.293 20.000 53.258 114.217 58.619 LPE(22:5) 89.644 51.042 58.865 60.440 112.098 93.338 LPE(22:6) 61.568 33.783 41.816 30.636 26.664 42.881 PC(32:0) 24265.8 34024.8 15859.9 12787.8 56250.4 54360.7 PC(32:1) 63789.2 79844.5 43413.6 24128.0 79075.5 85357.4 PC(34:0) 9395.5 8126.1 6281.5 3773.1 8555.7 9216.4 PC(34:1) 114781.7 158931.5 84580.8 72091.7 247995.1 237232.3 PC(34:2) 37309.9 65927.3 30357.5 36920.7 163757.9 152929.0 PC(36:0) 783.2 884.9 564.5 625.5 1770.9 1547.5 PC(36:1) 35724.3 44539.5 25287.4 47369.8 97331.8 98023.3 PC(36:2) 42928.7 66978.4 32608.1 73395.1 249401.4 229539.8 PC(36:3) 25585.0 47548.4 19486.6 51604.0 162566.0 146591.8 PC(36:4) 8825.4 20321.3 5768.1 10963.0 32220.5 42654.1 PC(36:5) 449.5 1284.7 253.4 2084.8 5827.2 5295.8 PC(38:4) 9143.7 14163.9 7019.3 17852.6 57261.3 47869.9 PC(38:5) 581.6 6645.1 9118.5 12606.0 31710.1 29684.4 PC(40:7) 814.0 1219.6 726.8 906.4 2008.1 2118.2 SM(36:2) 149.7 218.2 154.2 10.4 13.3 19.6 SM(40:2) 125.3 169.5 137.3 25.8 9.5 26.4 SM(42:2) 5230.6 4518.9 4509.7 297.4 129.5 262.1 SM(d18:1/14:0) 157.1 129.4 193.5 12.1 6.3 12.2 SM(d18:1/16:0) 3266.6 3779.4 3475.2 185.7 155.2 284.5 SM(d18:1/18:0) 1800.1 2996.0 2602.0 46.3 68.8 100.5 SM(d18:1/20:0) 6506.5 7771.0 5392.4 9753.7 14712.5 14877.5 SM(d18:1/22:0) 5674.3 6067.9 4554.9 13595.7 16317.5 17114.6 SM(d18:1/24:0) 642.0 546.6 516.5 7190.9 4318.1 4627.6 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name Ion Precursor m/z Product m/z Cer(d18:1/14:0) [M+H] 510.5 264.3 Cer(d18:1/16:0) [M+H] 538.5 264.3 Cer(d18:1/18:0) [M+H] 566.6 264.3 Cer(d18:1/20:0) [M+H] 594.6 264.3 Cer(d18:1/22:0) [M+H] 622.6 264.3 Cer(d18:1/22:1) [M+H] 620.6 264.3 Cer(d18:1/24:0) [M+H] 650.6 264.3 Cer(d18:1/24:1) [M+H] 648.6 264.3 Cholesterol [M-H2O+H] 369.4 161.1 DG(32:0) [M+NH4] 586.5 551.5 DG(32:1) [M+NH4] 584.5 549.5 DG(34:0) [M+NH4] 614.6 579.5 DG(34:1) [M+NH4] 612.6 577.5 DG(34:2) [M+NH4] 610.5 575.5 DG(36:0) [M+NH4] 642.6 607.6 DG(36:1) [M+NH4] 640.6 605.6 DG(36:2) [M+NH4] 638.6 603.5 DG(36:3) [M+NH4] 636.6 601.5 DG(36:4) [M+NH4] 634.5 599.5 DG(36:5) [M+NH4] 632.5 597.5 DG(38:3) [M+NH4] 664.6 629.6 DG(38:4) [M+NH4] 662.6 627.5 DG(38:5) [M+NH4] 660.6 625.5 DG(38:6) [M+NH4] 658.5 623.5 DG(40:4) [M+NH4] 690.6 655.6 DG(40:5) [M+NH4] 688.6 653.6 DG(40:6) [M+NH4] 686.6 651.5 LPC(16:0) [M+H] 496.3 184.1 LPC(16:1) [M+H] 494.3 184.1 LPC(18:0) [M+H] 524.4 184.1 LPC(18:1) [M+H] 522.4 184.1 LPC(18:2) [M+H] 520.3 184.1 LPC(20:3) [M+H] 546.4 184.1 LPC(20:4) [M+H] 544.3 184.1 LPC(22:4) [M+H] 572.4 184.1 LPC(22:5) [M+H] 570.4 184.1 LPC(22:6) [M+H] 568.3 184.1 LPE(16:0) [M+H] 454.3 313.3 LPE(16:1) [M+H] 452.3 311.3 LPE(18:0) [M+H] 482.3 341.3 LPE(18:1) [M+H] 480.3 339.3 LPE(18:2) [M+H] 478.3 337.3 LPE(20:3) [M+H] 504.3 363.3 LPE(20:4) [M+H] 502.3 361.3 LPE(22:4) [M+H] 530.3 389.3 LPE(22:5) [M+H] 528.3 387.3 LPE(22:6) [M+H] 526.3 385.3 PC(32:0) [M+H] 734.6 184.1 PC(32:1) [M+H] 732.6 184.1 PC(34:0) [M+H] 762.6 184.1 PC(34:1) [M+H] 760.6 184.1 PC(34:2) [M+H] 758.6 184.1 PC(36:0) [M+H] 790.6 184.1 PC(36:1) [M+H] 788.6 184.1 PC(36:2) [M+H] 786.6 184.1 PC(36:3) [M+H] 784.6 184.1 PC(36:4) [M+H] 782.6 184.1 PC(36:5) [M+H] 780.6 184.1 PC(38:4) [M+H] 810.6 184.1 PC(38:5) [M+H] 808.6 184.1 PC(40:7) [M+H] 832.6 184.1 SM(36:2) [M+H] 729.6 184.1 SM(40:2) [M+H] 785.7 184.1 SM(42:2) [M+H] 813.7 184.1 SM(d18:1/14:0) [M+H] 675.6 184.1 SM(d18:1/16:0) [M+H] 703.6 184.1 SM(d18:1/18:0) [M+H] 731.6 184.1 SM(d18:1/20:0) [M+H] 759.6 184.1 SM(d18:1/22:0) [M+H] 787.7 184.1 SM(d18:1/24:0) [M+H] 815.7 184.1 METABOLITES_END #END