# Computational insights in cell physiology

**Authors:** Geneviève Dupont, Didier Gonze

PMC · DOI: 10.3389/fsysb.2024.1335885 · Frontiers in Systems Biology · 2024-03-13

## TL;DR

The paper discusses how computational models help understand complex cellular processes and their regulation.

## Contribution

The paper presents selected examples showing how modeling addresses complex questions in cellular physiology.

## Key findings

- Modeling aids in understanding rhythmic phenomena and signaling in cells.
- Computational approaches reveal insights into cell differentiation and metabolic regulation.
- Examples include chronopharmacology and calcium dynamics.

## Abstract

Physiological processes are governed by intricate networks of transcriptional and post-translational regulations. Inter-cellular interactions and signaling pathways further modulate the response of the cells to environmental conditions. Understanding the dynamics of these systems in healthy conditions and their alterations in pathologic situations requires a “systems” approach. Computational models allow to formalize and to simulate the dynamics of complex networks. Here, we briefly illustrate, through a few selected examples, how modeling helps to answer non-trivial questions regarding rhythmic phenomena, signaling and decision-making in cellular systems. These examples relate to cell differentiation, metabolic regulation, chronopharmacology and calcium dynamics.

## Full-text entities

- **Genes:** Hspg2 (perlecan (heparan sulfate proteoglycan 2)) [NCBI Gene 15530] {aka HSPG, Pcn, Plc, per}, stm (stumpy) [NCBI Gene 20882], Nanog (Nanog homeobox) [NCBI Gene 71950] {aka 2410002E02Rik, ENK, Stm1, ecat4}, Gata6 (GATA binding protein 6) [NCBI Gene 14465] {aka GATA-6}, FGF4 (fibroblast growth factor 4) [NCBI Gene 2249] {aka FGF-4, HBGF-4, HST, HST-1, HSTF-1, HSTF1}, Pcna (proliferating cell nuclear antigen) [NCBI Gene 18538], Orai1 (ORAI calcium release-activated calcium modulator 1) [NCBI Gene 109305] {aka D730049H07Rik, Tmem142a, orai-1}, Duox2 (dual oxidase 2) [NCBI Gene 214593] {aka A430065P05Rik, LNOX2, NOXEF2, P138-TOX, THOX2}, MAPK1 (mitogen-activated protein kinase 1) [NCBI Gene 5594] {aka ERK, ERK-2, ERK2, ERT1, MAPK2, NS13}, GATA6 (GATA binding protein 6) [NCBI Gene 2627], Bmal1 (basic helix-loop-helix ARNT like 1) [NCBI Gene 11865] {aka Arnt3, Arntl, BMAL1b, MOP3, bHLHe5, bmal1b'}, Ryr1 (ryanodine receptor 1, skeletal muscle) [NCBI Gene 20190] {aka RYR-1, Ryr, skrr}, Grn (granulin) [NCBI Gene 14824] {aka GP88, PCDGF, PEPI, Pgrn, epithelin}, NANOG (Nanog homeobox) [NCBI Gene 79923], Fgf4 (fibroblast growth factor 4) [NCBI Gene 14175] {aka Fgf-4, Fgf7a, Fgfk, HBGF-4, Hst1, Hstf-1}, Stim1 (stromal interaction molecule 1) [NCBI Gene 20866] {aka SIM}, Trav6-3 (T cell receptor alpha variable 6-3) [NCBI Gene 328483] {aka Gm13948, Gm193, Gm4, TCR}, Cd247 (CD247 antigen) [NCBI Gene 12503] {aka 4930549J05Rik, A430104F18Rik, Cd3, Cd3-eta, Cd3-zeta, Cd3h}, Stim2 (stromal interaction molecule 2) [NCBI Gene 116873], Mapk1 (mitogen-activated protein kinase 1) [NCBI Gene 26413] {aka 9030612K14Rik, ERK, Erk2, MAPK2, PRKM2, Prkm1}, Ptk2 (PTK2 protein tyrosine kinase 2) [NCBI Gene 14083] {aka FADK 1, FAK, FRNK, Fadk, p125FAK}, Nr1d1 (nuclear receptor subfamily 1, group D, member 1) [NCBI Gene 217166] {aka A530070C09Rik}
- **Diseases:** insulin resistance (MESH:D007333), cancer (MESH:D009369), metabolic disorders (MESH:D008659), diabetes (MESH:D003920), toxicity (MESH:D064420), hyperglycemia (MESH:D006943)
- **Chemicals:** NAADP (MESH:C024376), calcium (MESH:D002118), Ca2+ (-), Glucose (MESH:D005947), Dex (MESH:D003907), blood glucose (MESH:D001786), IP3 (MESH:D015544)
- **Species:** Mus musculus (house mouse, species) [taxon 10090]
- **Cell lines:** T — Homo sapiens (Human), Esophageal squamous cell carcinoma, Cancer cell line (CVCL_3174)

## Full text

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## Figures

2 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12341975/full.md

## References

48 references — full list in the complete paper: https://tomesphere.com/paper/PMC12341975/full.md

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Source: https://tomesphere.com/paper/PMC12341975