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Q UANTIFYING METABOLIC FLUXES IN CANCER AND STEM CELLS An integrative approach monitoring metabolic reprogramming Christin Zasada Kempa Lab - Integrative Proteomics & Metabolomics

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Genome-regulatory code 2 Genomics three billion DNA base pairs 20000 - 25000 protein-coding genes Transcriptomics 2 % of the genome Proteomics ~ 5 000 Metabolomics

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Reprogramming of metabolism 3 Warburg effect regulation CCM enzymes hypoxia nutrient availability carbon re-routing oncogenic regulation mitochondrial activity www.kegg.org

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Quantitative information turns functional 4 Proteomics pulsed stable isotope resolved metabolomics (pSIRM) LC-MS/MS label-free, SILAC quantification ~ 3500 proteins GC-MS approach identification ~ 100 metabolites absolute quantification ~ 40 metabolites application of stable isotopes > time-resolved > position-specific > indirect measurement of flux

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Non-stationary metabolic flux analysis 5 Model parameter 168 labeling data point 5 measured rates 14 measured pool sizes in cooperation with Katharina Nh and Sebastian Niedenfhr Forschungszentrum Jlich GmBH Niedenfhr S, Nh K, Wiechert W Current Opinion in Biotechnology 2015, 34:8290 Flux information InputOutput Pathways coverage Glycolysis TCA-Cycle Pentose-Phosphate Pathway Glutaminolysis Amino acid synthesis Biosynthesis Time courses for: Glucose Glutamine metabolic steady & isotopic non-stationary

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6 GC-MS fragment mapping to molecule level

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Monitoring metabolic reprogramming - experimental setup 7 13 C-Glucose 13 C-Glutamine 13 C-Pyruvate Proteomics hESC-DFhESC MDA-MB231 DFiPSC HFF1 NFH2 BJ1 in cooperation with R. Bucowiecki and A. Prigione (MDC, Berlin, Germany)

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Re-arrangement of carbon fate 8

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Routing of 13 C-Pyruvic acid 9 LFQ Int

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Summary 10

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Acknowledgments 11 Alessandro Prigione Raul Bukowiecki MDC Berlin-Buch, Germany Katharina Nh Sebastian Niedenfhr Forschungszentrum Jlich Germany thank you for your attention