Multicellular model of neuroblastoma proposes unconventional therapy based on multiple roles of p53

Wertheim, Kenneth Y.; Chisholm, Robert; Richmond, Paul; Walker, Dawn

Abstract

Neuroblastoma is the most common extra-cranial solid tumour in children. Over half of all high-risk cases are expected to succumb to the disease even after chemotherapy, surgery, and immunotherapy. Although the importance of MYCN amplification in this disease is indisputable, the mechanistic details remain enigmatic. Here, we present a multicellular model of neuroblastoma comprising a continuous automaton, discrete cell agents, and a centre-based mechanical model, as well as the simulation results we obtained with it. The continuous automaton represents the tumour microenvironment as a grid-like structure, where each voxel is associated with continuous variables such as the oxygen level therein. Each discrete cell agent is defined by several attributes, including its cell cycle position, mutations, gene expression pattern, and more with behaviours such as cell cycling and cell death being stochastically dependent on these attributes. The centre-based mechanical model represents the properties of these agents as physical objects, describing how they repel each other as soft spheres. By implementing a stochastic simulation algorithm on modern GPUs, we simulated the dynamics of over one million neuroblastoma cells over a period of months. Specifically, we set up 1200 heterogeneous tumours and tracked the MYCN-amplified clone’s dynamics in each, revealed the conditions that favour its growth, and tested its responses to 5000 drug combinations. Our results are in agreement with those reported in the literature and add new insights into how the MYCN-amplified clone’s reproductive advantage in a tumour, its gene expression profile, the tumour’s other clones (with different mutations), and the tumour’s microenvironment are inter-related. Based on the results, we formulated a hypothesis, which argues that there are two distinct populations of neuroblastoma cells in the tumour; the p53 protein is pro-survival in one and pro-apoptosis in the other. It follows that alternating between inhibiting MDM2 to restore p53 activity and inhibiting ARF to attenuate p53 activity is a promising, if unorthodox, therapeutic strategy. The multicellular model has the advantages of modularity, high resolution, and scalability, making it a potential foundation for creating digital twins of neuroblastoma patients.

Citation

Wertheim, K. Y., Chisholm, R., Richmond, P., & Walker, D. (2024). Multicellular model of neuroblastoma proposes unconventional therapy based on multiple roles of p53. PLoS Computational Biology, 20(12), Article e1012648. https://doi.org/10.1371/journal.pcbi.1012648

• Journal Article Type: Article
• Acceptance Date: Nov 18, 2024
• Online Publication Date: Dec 23, 2024
• Publication Date: Dec 1, 2024
• Deposit Date: Jan 3, 2025
• Publicly Available Date: Jan 13, 2025
• Journal: PLOS Computational Biology
• Print ISSN: 1553-734X
• Publisher: Public Library of Science
• Peer Reviewed: Peer Reviewed
• Volume: 20
• Issue: 12
• Article Number: e1012648
• DOI: https://doi.org/10.1371/journal.pcbi.1012648
• Public URL: https://hull-repository.worktribe.com/output/5001193