jingchen-biomodel/cent-ploidy-evo: Code for tetraploid evolution model, sensitivity analysis, and data fitting

Oxidative stress and serum deprivation influence the evolution of newly formed tetraploid cells during tumorigenesis

Megan L. Sweet, Mathew Bloomfield , Nicholas Keen, Nazia Bano, Xiang Pan, Nicolaas C. Baudoin, Barath Udayasuryan, Raffae N. Ahmad, Eva Riddervold, Erica Klaiber, Scott S. Verbridge, Eva M. Schmelz, Jing Chen, and Daniela Cimini

PNAS, 2026

Abstract:

We recently found that newly formed tetraploid (4N) cells in culture quickly lose extra centrosomes after whole genome doubling (WGD). This is inconsistent with the high incidence of centrosome number abnormalities in human cancers and with the observation that 4N cells from mouse tumors carry extra centrosomes, suggesting that centrosome numbers could be affected by certain conditions in the tumor microenvironment (TME). To determine the effect of the TME on the evolution of newly formed 4N cells, we induced WGD in DLD1 colorectal cancer cells and analyzed centrosome and chromosome numbers in mouse xenograft samples. We found that the 4N cells displayed a proliferation defect in vivo, that they could enhance the recruitment of stromal cells to the tumor site, and that they were more likely to harbor extra centrosomes compared to 4N cell populations evolved in vitro. Combining a mathematical model that tracks the coevolution of ploidy and centrosome numbers in different cell populations with Bayesian inference, we identified centrosome overduplication as the mechanism underlying the supernumerary centrosome phenotype. Finally, through in vitro evolution experiments, we found that deprivation of growth factors and oxidative stress could explain, respectively, the proliferation defect and the supernumerary centrosomes identified in our in vivo experiments. Overall, our work shows that oxidative stress plays a major role in centrosome overduplication, particularly in 4N cells, suggesting that supernumerary centrosomes and WGD may coexist in certain tumors. Moreover, our findings suggest that the oncogenic effects of WGD could be due, in part, to stromal cell recruitment.

Full Changelog: https://github.com/jingchen-biomodel/cent-ploidy-evo/commits/cent-ploidy-evo_2026