MetaboLights

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5_Sample_No_10_RPPOS.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/RP/NEG/20220915_Sample_No_6_RPNEG.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/HILIC/NEG/20220915_Sample_No_9_HILICNEG.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/RP/NEG/20220915_Sample_No_33_RPNEG.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/HILIC/POS/20220915_Pool-QC_2A_HILICPOS.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/RP/POS/20220915_Sample_No_24_RPPOS.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/HILIC/POS/20220915_Sample_No_11_HILICPOS.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/HILIC/NEG/20220915_Sample_No_1_HILICNEG.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/HILIC/NEG/20220915_Sample_No_16_HILICNEG.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/RP/POS/20220915_Sample_No_32_RPPOS.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/HILIC/POS/20220915_Sample_No_2_HILICPOS.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/HILIC/POS/20220915_Sample_No_31_HILICPOS.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/HILIC/POS/20220915_Sample_No_27_HILICPOS.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/RP/NEG/20220915_Sample_No_17_RPNEG.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/HILIC/NEG/20220915_Sample_No_12_HILICNEG.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/RP/NEG/20220915_Pool-QC_3A_RPNEG.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/RP/POS/20220915_Sample_No_16_RPPOS.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/RP/NEG/20220915_Sample_No_10_RPNEG.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/RP/NEG/20220915_Sample_No_5_RPNEG.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/HILIC/NEG/20220915_Sample_No_20_HILICNEG.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/RP/POS/20220915_Blank_3_RPPOS.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/HILIC/POS/20220915_Sample_No_23_HILICPOS.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/RP/NEG/20220915_Sample_No_32_RPNEG.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671/FILES/RAW_FILES/HILIC/NEG/20220915_Sample_No_28_HILICNEG.rawprimaryOK200ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS11671Compound annotations were made using mzcloudTM, mzVault and ChemSpider databases within the Compound Discoverer Software (version 3.3). The annotations were manually re-checked afterwards.MetaboLightsPublicLiquid Chromatography MS - negative - reverse phaseLiquid Chromatography MS - positive - hilicLiquid Chromatography MS - positive - reverse phaseLiquid Chromatography MS - negative - hilicAll analyses were conducted using a Dionex Ultimate 3000 chromatography system coupled with a Q Exactive Focus mass spectrometer, both from Thermo Fisher Scientific, Dreieich, Germany. The instrument was equipped with a heated electrospray ionization (HESI) source and was operated via TraceFinder 4.1 software. Each sample underwent analysis in both RP and HILIC, with data collected in both positive and negative polarization. QC samples consisting of pooled aliquots from all samples were injected every five samples to allow correcting for instrument variations. For RP, the system utilized an Acquity UPLC BEH C18 column measuring 1.7 µm in particle size and 2.1 x 100 mm in dimensions, along with a 2.1 x 5 mm guard column to extend the column's lifespan. The RP eluent system consisted of water with 0.1% formic acid as mobile phase A, and methanol with 0.1% formic acid as mobile phase B. Chromatographic separation was achieved using a gradient program starting with 10% B, increased linearly to 98% B over 9 min. This concentration was maintained until 11 min, followed by a return to 10% B from 11.1 to 15 min for re-equilibration.For HILIC analysis, an Acquity UPLC BEH Amide column of the same dimensions (1.7 µm, 2.1 x 100 mm) was used, also with a 2.1 x 5 mm guard column. The HILIC eluent system comprised mobile phase A, a solution of 10 mM ammonium formate with 0.1% formic acid, and mobile phase B, 10 mM ammonium formate with 5% water, 95% acetonitrile, and 0.1% formic acid. The HILIC gradient program startet with 100% B for the first 2 min, gradually decreasing to 30% B by the 14th min, and then reverting to the starting conditions by 16.5 min.For both chromatographic methods, the column temperature was consistently maintained at 40°C, the flow rate was set at 0.35 mL/ min and the injection volume was 2 µL.Targeting PI3K inhibitor resistance in breast cancer with metabolic drugs. 10.1038/s41392-025-02180-4. PMID:40113784Core Facility for Metabolomics, Philipps University of MarburgR. Verena Taudtesolventbreast cancer cellmass spectrometry assay The extracts were centrifuged (16000 rpm, 4°C, 5 min) and the supernatant aliquoted into HPLC vials (2 x 350 uL) and one aliquot used to create a pooled aliquot (250 uL). The extracts were dried overnight in a speed vac and then reconstituted in 200 uL of eluent (for HILIC and RP respectively).blankHomo sapienshttps://www.ebi.ac.uk/metabolights/MTBLS11671Niklas Gremke. Philipps University of Marburg. Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University, Marburg, Germany. gremken@staff.uni-marburg.de.Thorsten Stiewe. Philipps University of Marburg. Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University, Marburg, Germany. stiewe@uni-marburg.de.For data analysis, Compound Discoverer 3.3 was used (Thermo Fisher Scientific, Dreieich, Germany). Retention time tolerance for alignment and mass tolerance for annotation were set to 0.2 min and 5 ppm respectively. Compound annotations were made using mzcloudTM, mzVault and ChemSpider databases. After pre-processing, peaks were manually filtered by re-checking individual chromatograms and spectral matching with the above-mentioned libraries. Peak areas of the individual compounds were normalized according to cell count and underwent further QC correction. The peak list of the individual modi i.e., HILIC negative, HILIC positive, RP negative, and RP positive were merged, whereby for compounds detected in multiple modi, the entry with the highest abundance was used. TreatmentGenotypeCell countTimepointmetabolomics@uni-marburg.deCells (parental, ATG 7 ko and PI3KI res) were cultured on 6 well plates and treated with metformin for 2 or 5 days. After these times, cells were harvested following this protocol:At first, cells were washed with PBS (37°C) three times, then PBS was removed and 2 x 500 uL 80% MeOH (ice cold, -20°C) added and the cells scratched. The lysates were transferred in 1.5 mL Eppendorf tubes. The extracts were centrifuged (16000 rpm, 4°C, 5 min) and the supernatant aliquoted into HPLC vials (2 x 350 uL) and one aliquot used to create a pooled aliquot (250 uL). The extracts were dried overnight in a speed vac and then reconstituted in 200 uL of eluent (for HILIC and RP respectively).Metabolomicspooled quality control sampleautophagyblankuntargeted analysissolvent blankbreast cancermetforminHomo sapiensThermo Scientific Dionex Ultimate 3000 HPLC systemresistanceexperimental sampleuntargeted metabolitessolventThermo Scientific Q Exactive FocusPhosphatidylinositide 3-Kinase Inhibitorbreast cancer cellpooled quality control sampleautophagyblankuntargeted analysissolvent blankbreast cancermetforminHomo sapiensThermo Scientific Dionex Ultimate 3000 HPLC systemresistanceexperimental sampleuntargeted metabolitessolventThermo Scientific Q Exactive FocusPhosphatidylinositide 3-Kinase Inhibitorbreast cancer cellThe Q Exactive Focus mass spectrometer was operated with a capillary voltage of 3.5 kV in positive mode and -3 kV in negative mode. The capillary temperature was set to 380°C, while the auxiliary gas temperature was 400°C. The sheath gas pressure, auxiliary gas pressure and sweep gas flow rate were set to 60, 20, and 0 arbitrary units, respectively. Nitrogen 5.0 was used for these gases. The scanning range was set from 66.7 to 1000 m/z. For full scan (MS1) analysis, the mass resolution was set to 70,000, with the automatic gain control (AGC) target set at 1e6 and the maximum injection time set to auto mode. In data-dependent MS2 (ddMS2) mode, the resolution was reduced to 35,000, with an AGC target of 5e4 and the maximum injection time also set to auto.Activating PIK3CA mutations, present in up to 40% of hormone receptor-positive (HR+), human epidermal growth factor receptor 2-negative (Her2-) breast cancer (BC) patients, can be effectively targeted with the alpha isoform-specific PI3K inhibitor Alpelisib. This treatment significantly improves outcomes for HR+, Her2-, and PIK3CA-mutated metastatic BC patients. However, acquired resistance, often due to aberrant activation of the mTOR complex 1 (mTORC1) pathway, remains a significant clinical challenge. Our study, using in vitro and orthotopic xenograft mouse models, demonstrates that constitutively active mTORC1 signaling renders PI3K inhibitor-resistant BC exquisitely sensitive to various drugs targeting cancer metabolism. Mechanistically, mTORC1 suppresses the induction of autophagy during metabolic perturbation, leading to energy stress, a critical depletion of aspartate, and ultimately cell death. Supporting this mechanism, BC cells with CRISPR/Cas9-engineered knockouts of canonical autophagy genes showed similar vulnerability to metabolically active drugs. In BC patients, high mTORC1 activity, indicated by 4E-BP1T37/46 phosphorylation, correlated with p62 accumulation, a sign of impaired autophagy. Together, these markers predicted poor overall survival in multiple BC subgroups. Our findings reveal that aberrant mTORC1 signaling, a common cause of PI3K inhibitor resistance in BC, creates a druggable metabolic vulnerability by suppressing autophagy. Additionally, the combination of 4E-BP1T37/46 phosphorylation and p62 accumulation serves as a biomarker for poor overall survival, suggesting their potential utility in identifying BC patients who may benefit from metabolic therapies.Targeting PI3K inhibitor resistance in breast cancer with metabolic drugs.Gremke Niklas N, Besong Isabelle I, Stroh Alina A, von Wichert Luise L, Witt Marie M, Elmshäuser Sabrina S, Wanzel Michael M, Fromm Martin F MF, Taudte R Verena RV, Schmatloch Sabine S, Karn Thomas T, Reinisch Mattea M, Hirmas Nader N, Loibl Sibylle S, Wündisch Thomas T, Litmeyer Anne-Sophie AS, Jank Paul P, Denkert Carsten C, Griewing Sebastian S, Wagner Uwe U, Stiewe Thorsten TfalseTargeting PI3K inhibitor resistance in breast cancer with metabolic drugsActivating PIK3CA mutations, present in up to 40% of hormone receptor-positive (HR+), human epidermal growth factor receptor 2-negative (Her2-) breast cancer (BC) patients, can be effectively targeted with the alpha isoform-specific PI3K inhibitor Alpelisib. This treatment significantly improves outcomes for HR+, Her2-, and PIK3CA-mutated metastatic BC patients. However, acquired resistance, often due to aberrant activation of the mTOR complex 1 (mTORC1) pathway, remains a significant clinical challenge.Our study demonstrates that constitutively active mTORC1 signaling renders PI3K inhibitor-resistant BC exquisitely sensitive to various inhibitors of cancer metabolism. Mechanistically, mTORC1 inhibits the induction of autophagy during metabolic perturbation, leading to energy stress and cell death, both in vitro and orthotopic xenograft mouse models. Supporting this, BC cells with CRISPR/Cas9-engineered knockouts of canonical autophagy genes showed similar vulnerability to metabolically active drugs. In BC patients, high mTORC1 activity, indicated by 4E-BP1T37/46 phosphorylation, correlated with p62 accumulation, a sign of impaired autophagy. Together, these markers predicted poor overall survival in multiple BC subgroups. Our findings reveal that aberrant mTORC1 signaling, a common cause of PI3K inhibitor resistance in BC, creates a druggable metabolic vulnerability by suppressing autophagy. Additionally, the combination of 4E-BP1T37/46 phosphorylation and p62 accumulation serves as a biomarker for poor overall survival, suggesting their potential utility in identifying BC patients who may benefit from metabolic therapies.2026-08-212026-07-31MTBLS1167140113784