Using a hybrid approach to model central carbon metabolism across - PowerPoint PPT Presentation

Using a hybrid approach to model central carbon metabolism across the cell cycle Cécile Moulin 1 , 2 , Laurent Tournier 2 and Sabine Peres 1 , 2 1 LRI, Université Paris-Sud, CNRS, Université Paris-Saclay, France 2 MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France 6th April 2019 - HSB 2019

Metabolism is a production system Glucose Oxygen Metabolism CO 2 Lipids ATP Nucleotides Cécile Moulin Hybrid model of metabolism and cell cycle 2 / 21

Metabolism is a reaction network Glucose Oxygen CO 2 Lipids ATP Nucleotides Cécile Moulin Hybrid model of metabolism and cell cycle 2 / 21

Metabolism is a huge network Recon3D:13 543 metabolic reactions, 4 140 unique metabolites (Brunk et al., 2018). Kegg Map (metabolism global view): Cécile Moulin Hybrid model of metabolism and cell cycle 3 / 21

Solution: Metabolic Pathways Glycolysis Pentose Phosphate Pathway Glucose Over fl ow Nucleotides TCA Cycle Glutaminolysis Lactate Lipids AKG Glutamine Cécile Moulin Hybrid model of metabolism and cell cycle 4 / 21

Metabolic pathways are coupled by currency metabolites Glycolysis Pentose Phosphate NADP NADPH Pathway Glucose Over fl ow ADP NAD Nucleotides TCA ATP Cycle ATP NADH Glutaminolysis NADPH NADP Lactate Lipids NAD NADH ATP AKG NADH ADP NADPH NAD ATP NADP ADP Glutamine Cécile Moulin Hybrid model of metabolism and cell cycle 4 / 21

Eukaryotic cell cycle: From one mother cell to two daughter cells G0 G1 I n t s e i M s r o p S t h i M a s e G2 Cell Cycle Cécile Moulin Hybrid model of metabolism and cell cycle 5 / 21

Eukaryotic cell cycle: Divided into 4 phases G0 Growth Proteins G1 Duplication of DNA M S Cell Division G2 Growth Membrane Cécile Moulin Hybrid model of metabolism and cell cycle 5 / 21

Eukaryotic cell cycle: Linked to the metabolism G0 Energy Amino Acids Growth Nucleotides Proteins G1 Duplication of DNA Energy not M known S Nucle- otides Cell Division G2 Growth Lipids Membrane (da Veiga Moreira et al. , Theoretical Biology and Medical Modelling, 2015) Cécile Moulin Hybrid model of metabolism and cell cycle 5 / 21

Goal: Create a model coupling metabolism and cell cycle G0 Energy Glucose Amino Acids Growth Oxygen Nucleotides Proteins G1 Duplication How do metabolism of DNA and cell cycle Energy not M known communicate? S Nucle- otides CO 2 Lipids ATP Cell Division Nucleotides G2 Growth Lipids Membrane Cécile Moulin Hybrid model of metabolism and cell cycle 6 / 21

Goal: Create a model coupling metabolism and cell cycle G0 Energy Glucose Amino Acids Growth Oxygen Nucleotides Proteins G1 Duplication How do metabolism of DNA and cell cycle Energy not M known communicate? S Nucle- otides CO 2 Lipids ATP Cell Division Nucleotides G2 Growth Lipids Membrane Challenges: Different time scales Which level of knowledge? Cécile Moulin Hybrid model of metabolism and cell cycle 6 / 21

“Wherever continuous and discrete dynamics interact, hybrid systems arise.” (Heemels et al. , Handbook of Hybrid Systems Control , 2009) G1 ? Energy S ? Nucleotides ? G2 Lipids Cécile Moulin Hybrid model of metabolism and cell cycle 7 / 21

Outline The metabolic model 1 Introduction of the model Test the model with cell cycle inputs The hybrid model 2 Parameters selection Behavior of the hybrid model Cécile Moulin Hybrid model of metabolism and cell cycle 8 / 21

Extended mammalian Central Carbon Metabolism model The original models: Robitaille et al. , PLOS ONE, 2015 da Veiga Moreira et al. , Scientific Reports, 2019 (CHO) (mice) Cécile Moulin Hybrid model of metabolism and cell cycle 9 / 21

Extended mammalian Central Carbon Metabolism model The original models: Robitaille et al. , PLOS ONE, 2015 da Veiga Moreira et al. , Scientific Reports, 2019 (CHO) (mice)   x I ( t ) 16 x ( t ) = x II ( t ) 7   x biomass ( t ) 1 � S I � ∈ Q 23 × 30 S = S II θ ∈ R ∼ 100 +  x I ˙ = S I ν θ ( x ( t )) − µ θ ( x ( t )) x I ( t ) ,  x II ˙ = S II ν θ ( x ( t )) , ˙ = µ θ ( x ( t )) x biomass ( t ) . x biomass  ATP + G 6 P + R 5 P + PALM → X + ADP Cécile Moulin Hybrid model of metabolism and cell cycle 9 / 21

Example: production/consumption of fructose 6-phosphate (F6P) 2 2 dF 6 P = ν pgi _ f ( t ) − ν pgi _ b ( t ) − ν pfk ( t ) + 2 ν tkt ( t ) − µ ( t ) F 6 P ( t ) . dt (Robitaille et al. , PLOS ONE, 2015) Cécile Moulin Hybrid model of metabolism and cell cycle 10 / 21

Example: production/consumption of fructose 6-phosphate (F6P) 2 2 dF 6 P = ν pgi _ f ( t ) − ν pgi _ b ( t ) − ν pfk ( t ) + 2 ν tkt ( t ) − µ ( t ) F 6 P ( t ) . dt (Robitaille et al. , PLOS ONE, 2015) Cécile Moulin Hybrid model of metabolism and cell cycle 10 / 21

Example: production/consumption of fructose 6-phosphate (F6P) 1 Michaelis-Menten ν max = k cat [ E ] F 6 P ν pfk = ν max K m 1 + F 6 P (Robitaille et al. , PLOS ONE, 2015) (Ghorbaniaghdam et al. , Bioprocess and Biosystems Engineering, 2013) (Segel, Enzyme kinetics , 1993) Cécile Moulin Hybrid model of metabolism and cell cycle 11 / 21

Example: production/consumption of fructose 6-phosphate (F6P) 1 Michaelis-Menten ν max = k cat [ E ] 2 Currency Metabolites ATP F 6 P ADP ν pfk = ν max K m 1 + F 6 P K m 2 + ATP ADP (Robitaille et al. , PLOS ONE, 2015) (Ghorbaniaghdam et al. , Bioprocess and Biosystems Engineering, 2013) (Segel, Enzyme kinetics , 1993) Cécile Moulin Hybrid model of metabolism and cell cycle 11 / 21

Example: production/consumption of fructose 6-phosphate (F6P) 1 Michaelis-Menten ν max = k cat [ E ] 2 Currency Metabolites 3 Non-competitive inhibition ATP F 6 P K i ADP ν pfk = ν max K m 1 + F 6 P K m 2 + ATP K i + CIT ADP (Robitaille et al. , PLOS ONE, 2015) (Ghorbaniaghdam et al. , Bioprocess and Biosystems Engineering, 2013) (Segel, Enzyme kinetics , 1993) Cécile Moulin Hybrid model of metabolism and cell cycle 11 / 21

Example: production/consumption of fructose 6-phosphate (F6P) 1 Michaelis-Menten ν max = k cat [ E ] 2 Currency Metabolites 3 Non-competitive inhibition 4 Non-essential activation � � β AMP F 6 P 1 + ATP K i α K ATP ADP ν pfk = ν max � 1 + 1 AMP � � 1 AMP � K m 2 + ATP K i + CIT + F 6 P 1 + K m 1 K ATP α K ATP ADP (Robitaille et al. , PLOS ONE, 2015) (Ghorbaniaghdam et al. , Bioprocess and Biosystems Engineering, 2013) (Segel, Enzyme kinetics , 1993) Cécile Moulin Hybrid model of metabolism and cell cycle 11 / 21

The model reaches a stationary regime θ ∈ R ∼ 100 + Cécile Moulin Hybrid model of metabolism and cell cycle 12 / 21

The model responds correctly to G1 inputs (Diaz-Moralli et al. 2013) [...] the accumulation of PFK/FB3 leads to the activation of glycolysis and an increase in lactate production. [...] Moreover cyclin D1 is able to downregulate the expression of lipogenic enzymes [...] preventing pyruvate consumption in lipogenesis and contributing to lactate formation. (Diaz-Moralli et al. Pharmacology & Therapeutics, 2013) Cécile Moulin Hybrid model of metabolism and cell cycle 13 / 21

The model responds correctly to G1 inputs (Diaz-Moralli et al. 2013) [...] the accumulation of PFK/FB3 leads to the activation of glycolysis and an increase in lactate production. [...] Moreover cyclin D1 is able to downregulate the expression of lipogenic enzymes [...] preventing pyruvate consumption in lipogenesis and contributing to lactate formation. (Diaz-Moralli et al. Pharmacology & Therapeutics, 2013) Cécile Moulin Hybrid model of metabolism and cell cycle 13 / 21

The model responds correctly to S inputs (Diaz-Moralli et al. 2013) [...] proliferating cells increase G6PD activity during late G1- and S-phases [...]. Moreover, during S-phase the activation of the SCF ubiquitin ligase [...] allows [the proteasome degradation of ] PFKFB3 . [...] Through these mechanisms cells redirect the glucose flux from the direct glycolytic pathway to the PPP [...] (Diaz-Moralli et al. Pharmacology & Therapeutics, 2013) Cécile Moulin Hybrid model of metabolism and cell cycle 14 / 21

The model responds correctly to G2 inputs (Diaz-Moralli et al. 2013) [...] transketolase activity showed an acute increase in late S. This shift allows [...] recycling the excess of R5P back to glycolysis in late S- and G2-phases, when lipid synthesis [... is highly demanded]. Moreover, [...] the activation of transcription of lipogenic enzymes [contributes] to this process [...]. (Diaz-Moralli et al. Pharmacology & Therapeutics, 2013) Cécile Moulin Hybrid model of metabolism and cell cycle 15 / 21

Creation of the three sub-models: G1, S, G2 G1 ր PFK: ր glycolysis S ր G6PDH: ր PPP G1 S G2 PFK + - - G1 ց VPALM: ր LAC G2 ր TKT: ր end of PPP G6PDH - + + S ց PFK: ր PPP G2 ր VPALM: ր PALM TKT - - + VPALM - - + Cécile Moulin Hybrid model of metabolism and cell cycle 16 / 21

Validation of the sub-models G1: High Glycolysis activity and Lactate production S: High beginning of Pentose Phosphate Pathway activity G2: High Pentose Phosphate Pathway activity and Lipids production Cécile Moulin Hybrid model of metabolism and cell cycle 17 / 21

Hybrid model: transition between phases G1 ? Energy S ? Nucleotides ? G2 Lipids Cécile Moulin Hybrid model of metabolism and cell cycle 18 / 21