Geodesic
Modeling compartmentalization within intracellular signaling pathway
Claire Alamichel1 ; Juan Calvo2 ; Erwan Hingant3 ; Saoussen Latrach4 ; Nathan Quiblier5 ; Romain Yvinec6
1 Université Paris-Saclay, CNRS UMR 8071, Univ Evry, Laboratoire de Mathématiques et Modélisation d’Evry, 91037, Evry-Courcouronnes, France & Department of Mathematical Sciences, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino, 10129, Italy
2 Universidad de Granada, Avda. Hospicio s/n, 18071, Granada, Spain & Research Unit “Modeling Nature” (MNat)
3 Université de Picardie Jules Verne, LAMFA, CNRS UMR 7352, 33 rue Saint-Leu, 80039, Amiens, France
4 Laboratoire Analyse, Géométrie et Application, Université Sorbonne Paris Nord
5 AIstroSight, Inria, Université Claude Bernard Lyon 1, Hospices Civils de Lyon & Liris, UMR 5205 CNRS, INSA Lyon, Université Claude Bernard Lyon 1
6 Université Paris-Saclay, Inria, Inria Saclay-Île-de-France, 91120, Palaiseau, France
ESAIM. Proceedings, Tome 77 (2024), pp. 100-122.

Voir la notice de l'article provenant de la source EDP Sciences

We present a novel approach to modeling receptor-activated signaling pathways that take into account the compartmentalization of receptors and their effectors, both on the cell surface and in dynamic intracellular vesicles called endosomes. The first building block of the model concerns compartment dynamics. It takes into account creation of de novo endosomes, i.e. endocytosis, and further recycling of endosomes to the cell surface or degradation, as well as fusion of endosomes via coagulation dynamics. The second building block concerns biochemical reactions on the cell surface and within intra-cellular compartments. Both building blocks are coupled by the transfer of molecules that occurs at each event that modifies the compartments.The model is formulated as a integro-partial differential equation, with transport and coagulation operators, and source terms, coupled to an integro-differential equation. In this work, we prove sufficient conditions to obtain exponential ergodicity for the size distribution of intracellular compartments. We further design a finite volume scheme to simulate our model. Finally, we show two application cases that show qualitative agreement with recently published data, proving that our model can help capture the spatio-temporal complexity of receptor-activated signaling pathway.
DOI : 10.1051/proc/202477100

Claire Alamichel 1 ; Juan Calvo 2 ; Erwan Hingant 3 ; Saoussen Latrach 4 ; Nathan Quiblier 5 ; Romain Yvinec 6

1 Université Paris-Saclay, CNRS UMR 8071, Univ Evry, Laboratoire de Mathématiques et Modélisation d’Evry, 91037, Evry-Courcouronnes, France & Department of Mathematical Sciences, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino, 10129, Italy
2 Universidad de Granada, Avda. Hospicio s/n, 18071, Granada, Spain & Research Unit “Modeling Nature” (MNat)
3 Université de Picardie Jules Verne, LAMFA, CNRS UMR 7352, 33 rue Saint-Leu, 80039, Amiens, France
4 Laboratoire Analyse, Géométrie et Application, Université Sorbonne Paris Nord
5 AIstroSight, Inria, Université Claude Bernard Lyon 1, Hospices Civils de Lyon & Liris, UMR 5205 CNRS, INSA Lyon, Université Claude Bernard Lyon 1
6 Université Paris-Saclay, Inria, Inria Saclay-Île-de-France, 91120, Palaiseau, France 
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     author = {Claire Alamichel and Juan Calvo and Erwan Hingant and Saoussen Latrach and Nathan Quiblier and Romain Yvinec},
     title = {Modeling compartmentalization within intracellular signaling pathway},
     journal = {ESAIM. Proceedings},
     pages = {100--122},
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     volume = {77},
     year = {2024},
     doi = {10.1051/proc/202477100},
     language = {en},
     url = {https://geodesic-test.mathdoc.fr/articles/10.1051/proc/202477100/}
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Claire Alamichel; Juan Calvo; Erwan Hingant; Saoussen Latrach; Nathan Quiblier; Romain Yvinec. Modeling compartmentalization within intracellular signaling pathway. ESAIM. Proceedings, Tome 77 (2024), pp. 100-122. doi : 10.1051/proc/202477100. https://geodesic-test.mathdoc.fr/articles/10.1051/proc/202477100/

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