#METABOLOMICS WORKBENCH Brodesser_20230816_054636 DATATRACK_ID:4224 STUDY_ID:ST003114 ANALYSIS_ID:AN005105 PROJECT_ID:PR001935 VERSION 1 CREATED_ON March 6, 2024, 10:51 am #PROJECT PR:PROJECT_TITLE Lipid unsaturation promotes BAX and BAK pore activity during apoptosis PR:PROJECT_SUMMARY BAX and BAK are proapoptotic members of the BCL2 family that directly mediate PR:PROJECT_SUMMARY mitochondrial outer membrane permeabilization (MOMP), a central step in PR:PROJECT_SUMMARY apoptosis execution. However, the molecular architecture of the mitochondrial PR:PROJECT_SUMMARY apoptotic pore remains a key open question and especially little is known about PR:PROJECT_SUMMARY the contribution of lipids to MOMP. By performing a comparative lipidomics PR:PROJECT_SUMMARY analysis of the proximal membrane environment of BAK isolated in lipid PR:PROJECT_SUMMARY nanodiscs, we find a significant enrichment of unsaturated species nearby BAK PR:PROJECT_SUMMARY and BAX in apoptotic conditions. We then demonstrate that unsaturated lipids PR:PROJECT_SUMMARY promote BAX pore activity in model membranes, isolated mitochondria and cellular PR:PROJECT_SUMMARY systems, which is further supported by molecular dynamics simulations. PR:PROJECT_SUMMARY Accordingly, the fatty acid desaturase FADS2 not only enhances apoptosis PR:PROJECT_SUMMARY sensitivity, but also the activation of the cGAS/STING pathway downstream mtDNA PR:PROJECT_SUMMARY release. The correlation of FADS2 levels with the sensitization to apoptosis of PR:PROJECT_SUMMARY different lung and kidney cancer cell lines by co-treatment with unsaturated PR:PROJECT_SUMMARY fatty acids supports the relevance of our findings. Altogether, our work PR:PROJECT_SUMMARY provides new insight on how local lipid environment affects BAX and BAK function PR:PROJECT_SUMMARY during apoptosis. PR:INSTITUTE University of Cologne PR:DEPARTMENT Institute for Genetics, Cluster of Excellence Cellular Stress Responses in PR:DEPARTMENT Aging-associated Diseases (CECAD) PR:LAST_NAME García-Sáez PR:FIRST_NAME Ana J. PR:ADDRESS Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany PR:EMAIL ana.garcia@uni-koeln.de PR:PHONE +49 221 478 84261 PR:CONTRIBUTORS Shashank Dadsena, Rodrigo Cuevas Arenas, Gonçalo Vieira, Susanne Brodesser, PR:CONTRIBUTORS Manuel N. Melo, Ana J. García-Sáez #STUDY ST:STUDY_TITLE Lipidomics analyses in model membranes, isolated mitochondria and cellular ST:STUDY_TITLE systems to study how the local lipid environment affects BAX and BAK function ST:STUDY_TITLE during apoptosis. ST:STUDY_SUMMARY To investigate how the local lipid environment affects BAX and BAK function ST:STUDY_SUMMARY during apoptosis, we performed quantitative analyses of different lipid classes ST:STUDY_SUMMARY (glycerophospholipids, fatty acids, ceramides and sphingomyelins) in cultured ST:STUDY_SUMMARY cells, isolated mitochondria and lipid nanodics formed by Styrene-Malic Acid ST:STUDY_SUMMARY (SMA) co-polymers. Ceramides, sphingomyelins, fatty acids and cardiolipins were ST:STUDY_SUMMARY analyzed by Liquid Chromatography coupled to Tandem Mass Spectrometry ST:STUDY_SUMMARY (LC-MS/MS). For glycerophospholipids (PC, PE, PI, PS, PG, PA) we applied direct ST:STUDY_SUMMARY infusion MS approaches (Shotgun Lipidomics). ST:INSTITUTE University of Cologne ST:DEPARTMENT Faculty of Medicine and University Hospital of Cologne, Cluster of Excellence ST:DEPARTMENT Cellular Stress Responses in Aging-associated Diseases (CECAD) ST:LABORATORY CECAD Lipidomics/Metabolomics Facility ST:LAST_NAME Brodesser ST:FIRST_NAME Susanne ST:ADDRESS Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany ST:EMAIL susanne.brodesser@uk-koeln.de ST:PHONE +49 221 478 84015 #SUBJECT SU:SUBJECT_TYPE Cultured cells SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 #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 - S01_mitos_control.SMA_1 Sample source:mitochondrial SMALPs | Genotype:WT | Condition:control RAW_FILE_NAME=GPL_S01_mitos_control.SMA_1.mzML; RAW_FILE_NAME=CerSM_S01_mitos_control.SMA_1.mzML; RAW_FILE_NAME=CL_S01_mitos_control.SMA_1.mzML; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S02_mitos_control.SMA_2 Sample source:mitochondrial SMALPs | Genotype:WT | Condition:control RAW_FILE_NAME=GPL_S02_mitos_control.SMA_2.mzML; RAW_FILE_NAME=CerSM_S02_mitos_control.SMA_2.mzML; RAW_FILE_NAME=CL_S02_mitos_control.SMA_2.mzML; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S03_mitos_control.SMA_3 Sample source:mitochondrial SMALPs | Genotype:WT | Condition:control RAW_FILE_NAME=-; RAW_FILE_NAME=CerSM_S03_mitos_control.SMA_3.mzML; RAW_FILE_NAME=CL_S03_mitos_control.SMA_3.mzML; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S04_mitos_control.SMA_4 Sample source:mitochondrial SMALPs | Genotype:WT | Condition:control RAW_FILE_NAME=GPL_S04_mitos_control.SMA_4.mzML; RAW_FILE_NAME=CerSM_S04_mitos_control.SMA_4.mzML; RAW_FILE_NAME=CL_S04_mitos_control.SMA_4.mzML; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S05_mitos_apoptosis.SMA_1 Sample source:mitochondrial SMALPs | Genotype:WT | Condition:apoptotic RAW_FILE_NAME=GPL_S05_mitos_apoptosis.SMA_1.mzML; RAW_FILE_NAME=CerSM_S05_mitos_apoptosis.SMA_1.mzML; RAW_FILE_NAME=CL_S05_mitos_apoptosis.SMA_1.mzML; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S06_mitos_apoptosis.SMA_2 Sample source:mitochondrial SMALPs | Genotype:WT | Condition:apoptotic RAW_FILE_NAME=GPL_S06_mitos_apoptosis.SMA_2.mzML; RAW_FILE_NAME=CerSM_S06_mitos_apoptosis.SMA_2.mzML; RAW_FILE_NAME=CL_S06_mitos_apoptosis.SMA_2.mzML; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S07_mitos_apoptosis.SMA_3 Sample source:mitochondrial SMALPs | Genotype:WT | Condition:apoptotic RAW_FILE_NAME=GPL_S07_mitos_apoptosis.SMA_3.mzML; RAW_FILE_NAME=CerSM_S07_mitos_apoptosis.SMA_3.mzML; RAW_FILE_NAME=CL_S07_mitos_apoptosis.SMA_3.mzML; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S08_mitos_apoptosis.SMA_4 Sample source:mitochondrial SMALPs | Genotype:WT | Condition:apoptotic RAW_FILE_NAME=-; RAW_FILE_NAME=CerSM_S08_mitos_apoptosis.SMA_4.mzML; RAW_FILE_NAME=CL_S08_mitos_apoptosis.SMA_4.mzML; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S09_mitos_control_1 Sample source:total mitochondria | Genotype:WT | Condition:control RAW_FILE_NAME=GPL_S09_mitos_control_1.mzML; RAW_FILE_NAME=CerSM_S09_mitos_control_1.mzML; RAW_FILE_NAME=CL_S09_mitos_control_1.mzML; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S10_mitos_control_2 Sample source:total mitochondria | Genotype:WT | Condition:control RAW_FILE_NAME=-; RAW_FILE_NAME=CerSM_S10_mitos_control_2.mzML; RAW_FILE_NAME=CL_S10_mitos_control_2.mzML; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S11_mitos_control_3 Sample source:total mitochondria | Genotype:WT | Condition:control RAW_FILE_NAME=GPL_S11_mitos_control_3.mzML; RAW_FILE_NAME=CerSM_S11_mitos_control_3.mzML; RAW_FILE_NAME=CL_S11_mitos_control_3.mzML; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S12_mitos_control_4 Sample source:total mitochondria | Genotype:WT | Condition:control RAW_FILE_NAME=GPL_S12_mitos_control_4.mzML; RAW_FILE_NAME=CerSM_S12_mitos_control_4.mzML; RAW_FILE_NAME=CL_S12_mitos_control_4.mzML; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S13_mitos_apoptosis_1 Sample source:total mitochondria | Genotype:WT | Condition:apoptotic RAW_FILE_NAME=GPL_S13_mitos_apoptosis_1.mzML; RAW_FILE_NAME=CerSM_S13_mitos_apoptosis_1.mzML; RAW_FILE_NAME=CL_S13_mitos_apoptosis_1.mzML; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S14_mitos_apoptosis_2 Sample source:total mitochondria | Genotype:WT | Condition:apoptotic RAW_FILE_NAME=-; RAW_FILE_NAME=CerSM_S14_mitos_apoptosis_2.mzML; RAW_FILE_NAME=CL_S14_mitos_apoptosis_2.mzML; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S15_mitos_apoptosis_3 Sample source:total mitochondria | Genotype:WT | Condition:apoptotic RAW_FILE_NAME=GPL_S15_mitos_apoptosis_3.mzML; RAW_FILE_NAME=CerSM_S15_mitos_apoptosis_3.mzML; RAW_FILE_NAME=CL_S15_mitos_apoptosis_3.mzML; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S16_mitos_apoptosis_4 Sample source:total mitochondria | Genotype:WT | Condition:apoptotic RAW_FILE_NAME=GPL_S16_mitos_apoptosis_4.mzML; RAW_FILE_NAME=CerSM_S16_mitos_apoptosis_4.mzML; RAW_FILE_NAME=CL_S16_mitos_apoptosis_4.mzML; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S02_pulldown_Control_22.08 Sample source:mitochondrial SMALPs | Genotype:mEGFP-BAK | Condition:control RAW_FILE_NAME=GPL_S02_pulldown_Control_22.08.mzML; RAW_FILE_NAME=CerSM_S02_pulldown_Control_22.08.mzML; RAW_FILE_NAME=-; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S03_pulldown_Control_01.09 Sample source:mitochondrial SMALPs | Genotype:mEGFP-BAK | Condition:control RAW_FILE_NAME=GPL_S03_pulldown_Control_01.09.mzML; RAW_FILE_NAME=CerSM_S03_pulldown_Control_01.09.mzML; RAW_FILE_NAME=-; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S04_pulldown_Control_04.09 Sample source:mitochondrial SMALPs | Genotype:mEGFP-BAK | Condition:control RAW_FILE_NAME=GPL_S04_pulldown_Control_04.09.mzML; RAW_FILE_NAME=CerSM_S04_pulldown_Control_04.09.mzML; RAW_FILE_NAME=-; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S05_pulldown_Control_31.09 Sample source:mitochondrial SMALPs | Genotype:mEGFP-BAK | Condition:control RAW_FILE_NAME=GPL_S05_pulldown_Control_31.09.mzML; RAW_FILE_NAME=CerSM_S05_pulldown_Control_31.09.mzML; RAW_FILE_NAME=-; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S06_pulldown_Apoptosis_22.08 Sample source:mitochondrial SMALPs | Genotype:mEGFP-BAK | Condition:apoptotic RAW_FILE_NAME=GPL_S06_pulldown_Apoptosis_22.08.mzML; RAW_FILE_NAME=CerSM_S06_pulldown_Apoptosis_22.08.mzML; RAW_FILE_NAME=-; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S07_pulldown_Apoptosis_01.09 Sample source:mitochondrial SMALPs | Genotype:mEGFP-BAK | Condition:apoptotic RAW_FILE_NAME=GPL_S07_pulldown_Apoptosis_01.09.mzML; RAW_FILE_NAME=CerSM_S07_pulldown_Apoptosis_01.09.mzML; RAW_FILE_NAME=-; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S08_pulldown_Apoptosis_04.09 Sample source:mitochondrial SMALPs | Genotype:mEGFP-BAK | Condition:apoptotic RAW_FILE_NAME=GPL_S08_pulldown_Apoptosis_04.09.mzML; RAW_FILE_NAME=CerSM_S08_pulldown_Apoptosis_04.09.mzML; RAW_FILE_NAME=-; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S09_pulldown_Apoptosis_31.09 Sample source:mitochondrial SMALPs | Genotype:mEGFP-BAK | Condition:apoptotic RAW_FILE_NAME=GPL_S09_pulldown_Apoptosis_31.09.mzML; RAW_FILE_NAME=CerSM_S09_pulldown_Apoptosis_31.09.mzML; RAW_FILE_NAME=-; RAW_FILE_NAME=- SUBJECT_SAMPLE_FACTORS - S01_mitos_no.treatment_WT_1 Sample source:total mitochondria | Genotype:WT | Condition:untreated RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=FA_S01_mitos_no.treatment_WT_1.mzML SUBJECT_SAMPLE_FACTORS - S02_mitos_no.treatment_WT_2 Sample source:total mitochondria | Genotype:WT | Condition:untreated RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=FA_S02_mitos_no.treatment_WT_2.mzML SUBJECT_SAMPLE_FACTORS - S03_mitos_no.treatment_WT_3 Sample source:total mitochondria | Genotype:WT | Condition:untreated RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=FA_S03_mitos_no.treatment_WT_3.mzML SUBJECT_SAMPLE_FACTORS - S04_mitos_no.treatment_WT_4 Sample source:total mitochondria | Genotype:WT | Condition:untreated RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=FA_S04_mitos_no.treatment_WT_4.mzML SUBJECT_SAMPLE_FACTORS - S05_mitos_linoleic.acid_WT_1 Sample source:total mitochondria | Genotype:WT | Condition:linoleic acid RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=FA_S05_mitos_linoleic.acid_WT_1.mzML SUBJECT_SAMPLE_FACTORS - S06_mitos_linoleic.acid_WT_2 Sample source:total mitochondria | Genotype:WT | Condition:linoleic acid RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=FA_S06_mitos_linoleic.acid_WT_2.mzML SUBJECT_SAMPLE_FACTORS - S07_mitos_linoleic.acid_WT_3 Sample source:total mitochondria | Genotype:WT | Condition:linoleic acid RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=FA_S07_mitos_linoleic.acid_WT_3.mzML SUBJECT_SAMPLE_FACTORS - S08_mitos_linoleic.acid_WT_4 Sample source:total mitochondria | Genotype:WT | Condition:linoleic acid RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=FA_S08_mitos_linoleic.acid_WT_4.mzML SUBJECT_SAMPLE_FACTORS - S09_smitos_no.treatment_KO_1 Sample source:total mitochondria | Genotype:FADS2 KO | Condition:untreated RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=FA_S09_mitos_no.treatment_KO_1.mzML SUBJECT_SAMPLE_FACTORS - S10_mitos_no.treatment_KO_2 Sample source:total mitochondria | Genotype:FADS2 KO | Condition:untreated RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=FA_S10_mitos_no.treatment_KO_2.mzML SUBJECT_SAMPLE_FACTORS - S11_mitos_no.treatment_KO_3 Sample source:total mitochondria | Genotype:FADS2 KO | Condition:untreated RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=FA_S11_mitos_no.treatment_KO_3.mzML SUBJECT_SAMPLE_FACTORS - S12_mitos_no.treatment_KO_4 Sample source:total mitochondria | Genotype:FADS2 KO | Condition:untreated RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=FA_S12_mitos_no.treatment_KO_4.mzML SUBJECT_SAMPLE_FACTORS - S13_mitos_linoleic.acid_KO_1 Sample source:total mitochondria | Genotype:FADS2 KO | Condition:linoleic acid RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=FA_S13_mitos_linoleic.acid_KO_1.mzML SUBJECT_SAMPLE_FACTORS - S14_mitos_linoleic.acid_KO_2 Sample source:total mitochondria | Genotype:FADS2 KO | Condition:linoleic acid RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=FA_S14_mitos_linoleic.acid_KO_2.mzML SUBJECT_SAMPLE_FACTORS - S15_mitos_linoleic.acid_KO_3 Sample source:total mitochondria | Genotype:FADS2 KO | Condition:linoleic acid RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=FA_S15_mitos_linoleic.acid_KO_3.mzML SUBJECT_SAMPLE_FACTORS - S16_mitos_linoleic.acid_KO_4 Sample source:total mitochondria | Genotype:FADS2 KO | Condition:linoleic acid RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=-; RAW_FILE_NAME=FA_S16_mitos_linoleic.acid_KO_4.mzML #COLLECTION CO:COLLECTION_SUMMARY Human osteosarcoma U2OS WT, U2OS BAK Ko expressing GFP BAK, and U2OS FADS2 KO CO:COLLECTION_SUMMARY cell lines were cultured at 37 °C and 5% CO2 in DMEM supplemented with 10% FBS CO:COLLECTION_SUMMARY and 1% penicillin/streptomycin (Invitrogen, Germany). For lipidomic experiments CO:COLLECTION_SUMMARY cells were incubated with 1 μM of ABT-737 and S63845 in the complete media and CO:COLLECTION_SUMMARY incubated for 50 min at 37°C and 5% CO2. FADS2 KO in U2OS cells was generated CO:COLLECTION_SUMMARY in the lab by the CRISPR/Cas9 method. Linoleic acid stock (50 mM) was prepared CO:COLLECTION_SUMMARY in ethanol and diluted into culture media before adding them to the cells. CO:COLLECTION_SUMMARY Mitochondria were isolated from cultured human osteosarcoma cells by mechanical CO:COLLECTION_SUMMARY disruption of cells followed by differential centrifugation: Cells were CO:COLLECTION_SUMMARY harvested by trypsinization, washed in PBS, and then resuspend in isolation CO:COLLECTION_SUMMARY buffer (IM;250 mM sucrose, 5 mM Tris, and 2 mM EDTA; pH 7.4 and protease CO:COLLECTION_SUMMARY inhibitor cocktail) and mechanically broken using glass homogenizer on ice CO:COLLECTION_SUMMARY (30-40 strokes on ice) and total cellular lysates were spin down first to remove CO:COLLECTION_SUMMARY nuclei and cell debris at 600 x g for 5 min and later at 10,800 x g for 10 min CO:COLLECTION_SUMMARY at 4°C to get the crude mitochondria. Mitochondrial pellet was washed 2-3 times CO:COLLECTION_SUMMARY with isolation buffer to remove other impurities from mitochondria. Isolated CO:COLLECTION_SUMMARY mitochondria were solubilized using SMA co-polymer. For this, mitochondria CO:COLLECTION_SUMMARY either from apoptotic or healthy cells were incubated with 0.5% SMA (2:1) for 45 CO:COLLECTION_SUMMARY min at room temperature with gentle rotation. Mitochondrial membrane was spun CO:COLLECTION_SUMMARY down at 100,000 x g for 40 min to separate solubilized SMALP from the CO:COLLECTION_SUMMARY insolubilized membrane. Next, the size of SMALP was analyzed by Dynamic Light CO:COLLECTION_SUMMARY Scattering (DLS). For DLS measurements, 15 μl of sample was added to a quartz CO:COLLECTION_SUMMARY cuvette which had been thoroughly cleaned with Milli-Q H2O. The cuvette was CO:COLLECTION_SUMMARY placed in DynaPro NanoStar (Wyatt Technology corporation, USA) and the sample CO:COLLECTION_SUMMARY was analyzed using 10 runs with 10 second acquisition time. This helps to CO:COLLECTION_SUMMARY determine the mass distribution of the sample as well as the estimated size of CO:COLLECTION_SUMMARY the particles. The distance distribution is shown on a log scale. The size of CO:COLLECTION_SUMMARY SMALP as well as the homogeneity with in the sample were also checked by CO:COLLECTION_SUMMARY Negative Transmission Electron Microscopy (TEM). For this the diluted SMALPs CO:COLLECTION_SUMMARY were placed onto a glow-discharged copper grid (Electron Microscopy Sciences) CO:COLLECTION_SUMMARY coated with a layer of thin carbon, washed twice with water, stained with 2% CO:COLLECTION_SUMMARY uranyl acetate for 5 min and then air-dried. The grids were imaged on a JEOL CO:COLLECTION_SUMMARY JEM2100PLUS electron microscope and recorded with a GATAN OneView camera (CECAD CO:COLLECTION_SUMMARY Imaging Facility). mEGFP-BAK-SMALPs were affinity purified from total CO:COLLECTION_SUMMARY solubilized mitochondrial membrane fraction (SMALP). For this total SMALP were CO:COLLECTION_SUMMARY incubated with 25 μl of GFP-trap MA beads for 90 min with slow rotation in cold CO:COLLECTION_SUMMARY room. Beads were washed 2 times with 100 μl of Tris buffer (50 mM Tris 150 mM CO:COLLECTION_SUMMARY NaCl pH 8), and finally resuspend in 100 ul of Tris buffer. Small aliquots of CO:COLLECTION_SUMMARY unbound and wash fractions were used to analyze the purification quality. CO:SAMPLE_TYPE Mitochondria #TREATMENT TR:TREATMENT_SUMMARY The samples were not subjected to any further treatment. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Glycerophospholipids: Lipids from isolated mitochondria treated with or without SP:SAMPLEPREP_SUMMARY SMA were extracted using a procedure previously described (Ejsing et al., 2009) SP:SAMPLEPREP_SUMMARY with some modifications: 30-100 µl of sample were brought to a volume of 200 SP:SAMPLEPREP_SUMMARY µl with 155 mM ammonium carbonate buffer. Lipids were extracted by adding 990 SP:SAMPLEPREP_SUMMARY µl of chloroform/methanol 17:1 (v/v) and internal standards (125 pmol PC SP:SAMPLEPREP_SUMMARY 17:0-20:4, 138 pmol PE 17:0-20:4, 118 pmol PI 17:0-20:4, 118 pmol PS 17:0-20:4, SP:SAMPLEPREP_SUMMARY 61 pmol PG 17:0/20:4, 72 pmol PA 17:0/20:4, 10 µl Cardiolipin Mix I; Avanti SP:SAMPLEPREP_SUMMARY Polar Lipids), followed by shaking at 900 rpm/min in a ThermoMixer (Eppendorf) SP:SAMPLEPREP_SUMMARY at 20 °C for 30 min. After centrifugation (12,000xg, 5 min, 4 °C), the lower SP:SAMPLEPREP_SUMMARY (organic) phase was transferred to a new tube, and the upper phase was extracted SP:SAMPLEPREP_SUMMARY again with 990 mL chloroform/methanol 2:1 (v/v). The combined organic phases SP:SAMPLEPREP_SUMMARY were dried under a stream of nitrogen. The residues were resolved in 200 µl of SP:SAMPLEPREP_SUMMARY methanol. Ceramides and sphingomyelins: For the analysis of ceramides and SP:SAMPLEPREP_SUMMARY sphingomyelins in isolated mitochondria without and after SMA treatment, lipids SP:SAMPLEPREP_SUMMARY were extracted as described above in the presence of 127 pmol ceramide 12:0 and SP:SAMPLEPREP_SUMMARY 124 pmol sphingomyelin 12:0 (internal standards, Avanti Polar Lipids). The dried SP:SAMPLEPREP_SUMMARY extracts were resolved in 100 µL of Milli-Q water and 750 µL of SP:SAMPLEPREP_SUMMARY chloroform/methanol 1:2 (v/v). Alkaline hydrolysis of glycerolipids was SP:SAMPLEPREP_SUMMARY conducted as previously published (Schwamb et al., 2012; Oteng et al., 2017). SP:SAMPLEPREP_SUMMARY Fatty acids: To 100 µl of a suspension of isolated mitochondria in PBS, 500 µl SP:SAMPLEPREP_SUMMARY of methanol, 250 µl of chloroform, and 0.5 µg palmitic-d31 acid SP:SAMPLEPREP_SUMMARY (Sigma-Aldrich) as internal standard were added. The mixture was sonicated for 5 SP:SAMPLEPREP_SUMMARY min, and lipids were extracted in a shaking bath at 48 °C for 1 h. SP:SAMPLEPREP_SUMMARY Glycerolipids were degraded by alkaline hydrolysis adding 75 µl of 1 M SP:SAMPLEPREP_SUMMARY potassium hydroxide in methanol. After 5 min of sonication, the extract was SP:SAMPLEPREP_SUMMARY incubated for 1.5 h at 37 °C, and then neutralized with 6 µl of glacial acetic SP:SAMPLEPREP_SUMMARY acid. 2 ml of chloroform and 4 ml of water were added to the extract which was SP:SAMPLEPREP_SUMMARY vortexed vigorously for 30 sec and then centrifuged (4,000 × g, 5 min, 4 °C) SP:SAMPLEPREP_SUMMARY to separate layers. The lower (organic) phase was transferred to a new tube, and SP:SAMPLEPREP_SUMMARY the upper phase extracted with additional 2 ml of chloroform. The combined SP:SAMPLEPREP_SUMMARY organic phases were dried under a stream of nitrogen. The residues were resolved SP:SAMPLEPREP_SUMMARY in 200 µl of acetonitrile/water 2:1 (v/v) and sonicated for 5 min. After SP:SAMPLEPREP_SUMMARY centrifugation (12,000 × g, 20 min, 4 °C), 40 µl of the clear supernatants SP:SAMPLEPREP_SUMMARY were transferred to autoinjector vials. References: Ejsing et al., Proc Natl SP:SAMPLEPREP_SUMMARY Acad Sci USA 2009, 106, 2136; Oteng et al., J Lipid Res 2017, 58, 1100; Schwamb SP:SAMPLEPREP_SUMMARY et al., Blood 2012, 120, 3978. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Shimadzu Nexera X2 CH:COLUMN_NAME Phenomenex Core-Shell Kinetex Biphenyl (100×3.0 mm, 2.6 μm, 100 Å) CH:SOLVENT_A 100% water; 0.012 % acetic acid; 5 mM ammonium acetate CH:SOLVENT_B 80% acetonitrile/20% isopropanol CH:FLOW_GRADIENT 0 min: 55% B, 4 min: 95% B, 7 min: 95% B, 7.1 min: 55% B, 10 min: 55% B CH:FLOW_RATE 0.7 ml/min CH:COLUMN_TEMPERATURE 40 #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME SCIEX QTRAP 6500 MS:INSTRUMENT_TYPE QTRAP MS:MS_TYPE ESI MS:ION_MODE NEGATIVE MS:MS_COMMENTS Fatty acid levels were determined by LC-ESI-MS/MS: Fatty acids were monitored in MS:MS_COMMENTS the negative ion mode using “pseudo” Multiple Reaction Monitoring (MRM) MS:MS_COMMENTS transitions (Hellmuth et al., Anal Chem 2012, 84, 1483). The instrument settings MS:MS_COMMENTS for nebulizer gas (Gas 1), turbo gas (Gas 2), curtain gas, and collision gas MS:MS_COMMENTS were 60 psi, 90 psi, 40 psi, and medium, respectively. The Turbo V ESI source MS:MS_COMMENTS temperature was 650 °C, and the ionspray voltage was -4 kV. The LC chromatogram MS:MS_COMMENTS peaks of the endogenous fatty acids and the internal standard palmitic-d31 acid MS:MS_COMMENTS were integrated using the MultiQuant 3.0.2 software (SCIEX). #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS counts per second (cps) MS_METABOLITE_DATA_START Samples S01_mitos_no.treatment_WT_1 S02_mitos_no.treatment_WT_2 S03_mitos_no.treatment_WT_3 S04_mitos_no.treatment_WT_4 S05_mitos_linoleic.acid_WT_1 S06_mitos_linoleic.acid_WT_2 S07_mitos_linoleic.acid_WT_3 S08_mitos_linoleic.acid_WT_4 S09_smitos_no.treatment_KO_1 S10_mitos_no.treatment_KO_2 S11_mitos_no.treatment_KO_3 S12_mitos_no.treatment_KO_4 S13_mitos_linoleic.acid_KO_1 S14_mitos_linoleic.acid_KO_2 S15_mitos_linoleic.acid_KO_3 S16_mitos_linoleic.acid_KO_4 Factors Sample source:total mitochondria | Genotype:WT | Condition:untreated Sample source:total mitochondria | Genotype:WT | Condition:untreated Sample source:total mitochondria | Genotype:WT | Condition:untreated Sample source:total mitochondria | Genotype:WT | Condition:untreated Sample source:total mitochondria | Genotype:WT | Condition:linoleic acid Sample source:total mitochondria | Genotype:WT | Condition:linoleic acid Sample source:total mitochondria | Genotype:WT | Condition:linoleic acid Sample source:total mitochondria | Genotype:WT | Condition:linoleic acid Sample source:total mitochondria | Genotype:FADS2 KO | Condition:untreated Sample source:total mitochondria | Genotype:FADS2 KO | Condition:untreated Sample source:total mitochondria | Genotype:FADS2 KO | Condition:untreated Sample source:total mitochondria | Genotype:FADS2 KO | Condition:untreated Sample source:total mitochondria | Genotype:FADS2 KO | Condition:linoleic acid Sample source:total mitochondria | Genotype:FADS2 KO | Condition:linoleic acid Sample source:total mitochondria | Genotype:FADS2 KO | Condition:linoleic acid Sample source:total mitochondria | Genotype:FADS2 KO | Condition:linoleic acid Palmitic acid-d31 (IS) 80585983 152271276 128426957 140482152 106544120 78615892 93275769 114741724 200014877 156921007 207400568 203326103 145157229 118024938 130704316 108732056 Myristic acid (14:0) 106821370 244677334 116764012 132615826 220350427 102707955 150567176 200451789 77541872 136571484 97412177 143373509 112732224 117896785 138868645 105025430 Tetradecenoic acid (14:1) 27199178 72131758 27435856 30558515 34138804 15029864 24131881 31265239 3614802 5932098 5205180 7224716 4393164 5583191 6017350 5487082 Palmitic acid (16:0) 24491134 37693196 28509507 29437283 32344318 23263138 27689886 30987833 24595534 24296073 28269110 28578433 24399895 26592246 24170518 25934787 Hexadecenoic acid (16:1) 90228905 172966565 95171389 104664650 112500184 59878382 81731668 105395926 51069089 76269327 74734373 70914975 52217357 67864507 71173406 61940172 Stearic acid (18:0) 76419479 132629534 92937391 100050129 124668216 76005966 95963121 115313639 67385704 60942398 85167923 82196163 75566653 87453070 76205240 80462974 Octadecenoic acid (18:1) 32147406 47563727 33440782 36835342 36020496 26120891 31707955 37288204 30910108 38687023 39492535 38060870 30146170 34473821 36929241 32645677 Octadecadienoic acid (18:2) 16789690 29055158 15123200 17084808 68332531 39406124 47448521 61365253 9393230 13971254 13114640 12505715 68206075 86964807 97064094 82978060 Octadecatrienoic acid (18:3) 36160015 86896917 32701389 40342702 334577957 139276139 199396744 300711902 6981400 10587814 11114985 10514718 9308828 13455099 13670712 11527654 Eicosenoic acid (20:1) 166124914 383320389 192277743 218536692 217235893 102730703 157512945 227346118 176182421 259935474 277151046 255389181 197798562 231816041 250292880 209968590 Eicosadienoic acid (20:2) 233514901 464157978 241044674 280555729 321728909 164563210 225508119 305840526 98395041 167111269 169201006 158807471 276962370 363995420 401509667 346055013 Eicosatrienoic acid (20:3) 410614961 683328458 415085720 470095757 659649897 455076940 545730342 638782448 71306944 103852926 105555583 103717508 168981875 214498836 227348393 193916867 Arachidonic acid (20:4) 389643000 631560227 422181091 470596776 746333384 520642388 608536516 729890832 275501273 365338558 375091363 355825148 296595005 334711375 370509099 305804067 Docosenoic acid (22:1) 78966085 246505457 94898371 108407405 138062974 53419373 79912824 147048231 102771429 131128251 151754367 142505304 105003251 129349914 148723961 112534448 Docosadienoic acid (22:2) 45668543 161116848 50377755 62157663 101681828 32331339 56402714 89983655 49169547 86727383 86187135 78292922 101327259 146036922 164120467 128564669 DHA (22:6) 229508492 423795788 246409595 276763750 203650120 129980947 169560130 220153677 126748952 190141217 193241652 184225188 106657972 133266520 146361018 118718201 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name Q1 Mass (Da) Q3 Mass (Da) RT (min) CE (volts) KEGG_ID Palmitic acid-d31 (IS) 286.1 286.1 2.19 -10 N/A Tetradecenoic acid (14:1) 225.0 225.0 1.62 -8 C08322 Myristic acid (14:0) 227.0 227.0 1.84 -25 C06424 Hexadecenoic acid (16:1) 253.0 253.0 2.01 -30 C21942/C08362 Palmitic acid (16:0) 255.0 255.0 2.25 -35 C00249 Octadecatrienoic acid (18:3) 277.1 277.1 2.00 -10 C06426/C08315/C08364/C06427 Octadecadienoic acid (18:2) 279.0 279.1 2.20 -32 C04056/C01595 Octadecenoic acid (18:1) 281.1 281.1 2.42 -37 C08363/C00712/C01712/C21944/C08367 Stearic acid (18:0) 283.1 283.1 2.67 -35 C01530 Arachidonic acid (20:4) 303.1 303.1 2.20 -10 C00219 Eicosatrienoic acid (20:3) 305.1 305.1 2.38 -8 C03242/C16522/C21938 Eicosadienoic acid (20:2) 307.1 307.2 2.59 -8 C16525/C21936 Eicosenoic acid (20:1) 309.1 309.1 2.81 -8 C16526/C21946 DHA (22:6) 327.1 327.0 2.18 -6 C06429 Docosadienoic acid (22:2) 335.1 335.1 2.99 -8 C16533 Docosenoic acid (22:1) 337.1 337.1 3.19 -8 C08316 METABOLITES_END #END