Biology subjects

Kok, R. N. U.

Publications and source records attributed to Kok, R. N. U..

7 recordsLinked to original sources

bioRxiv2026

NuclearIDTracker resolves intestinal cell identity and lineage dynamics through nuclear phenotypic signatures

Organoid models have transformed our understanding of intestinal renewal. Fluorescent imaging has been extensively used to identify key cell types and their differentiation pathways, but immunofluorescence provides only static readouts, whereas live imaging requires fluorescent-reporter engineering and is constrained by limited multiplexing and spectral overlap. Here, we introduce NuclearIDTracker, an explainable machine-learning framework that infers cell identity directly from 3D nuclear segmentations. Using a single nuclear marker, NuclearIDTracker accurately classifies intestinal cell types and integrates with single-cell tracking to resolve lineages and reconstruct dynamic state transitions during organoid development. We show that TA-like cells, rather than stem cells, drive early crypt formation and generate enterocyte and Paneth lineages, as well as the stem-cell population, which emerges only later and subsequently replenishes the TA-like compartment. Following stem-cell ablation, crypt regeneration was not driven by a single discrete cell type. Instead, multiple epithelial populations converged on a proliferative regenerative state with a nuclear phenotypic signature that resembled, but remained distinct from, that of homeostatic TA-like cells, and a YAP/TAZ-associated fetal-like transcriptional signature. Thus, nuclear phenotypic signatures resolve cell identity and reveal coordinated epithelial plasticity during crypt regeneration. NuclearIDTracker establishes a non-perturbative tool to quantify cell identity and state dynamics at single-cell resolution, revealing previously inaccessible biological dynamics and expanding the toolkit for studying epithelial homeostasis, regeneration, and disease.

cell biology↗

bioRxiv2026

Mechanical strain of the intestinal epithelium directs absorptive lineage maturation

The intestinal epithelium is continuously subjected to a variety of mechanical forces, including extrinsic peristaltic contractions and intrinsic tensile forces generated by epithelial cell migration. Yet, how these mechanical cues influence the cellular processes underlying intestinal homeostasis remains poorly understood. In this study, we examine the impact of mechanical forces on intestinal cell dynamics by applying controlled external stretch to intestinal organoids, combined with high-throughput single-cell transcriptomic profiling. Our analyses reveal that prolonged cyclic mechanical strain alters the composition of differentiated intestinal cell populations. Specifically, we identify a strain-induced shift in the absorptive lineage towards a less mature state, with expansion of the population of early-stage enterocytes at the crypt-villus interface. This shift is associated with downregulation of transcriptional programs controlling enterocyte maturation within absorptive precursor populations. Our findings indicate that mechanical strain directs the maturation of the intestinal absorptive lineage, and highlight a role for mechanical forces in shaping intestinal epithelial composition and function.

cell biology↗

bioRxiv2026

Hydrogen Peroxide induces resistance to DNA damage in a localization and p53 dependent manner.

Organisms need to be able to adapt to a changing environment in order to survive. The adaptive response invoked by a low dose of a stressor resulting in resistance to high levels of that stressor is known as hormesis and can even lead to lifespan extension of organisms. The exact mechanisms underlying stress-induced hormesis are unknown, although multiple studies pose mitochondria-derived Reactive Oxygen Species (ROS, e.g. H2O2) as an important contributor. Here we used chemo-genetic H2O2 production as a model to study ROS-dependent adaptive responses in a localization-dependent manner. We found that brief, sublethal H2O2 production at the nucleosomes provides p53-dependent resistance to a subsequent high dose of H2O2, whereas mitochondrial H2O2 production, surprisingly, does not. A multi-omics approach revealed that p53-induced hormesis is accompanied by metabolic rewiring that boosts reductive capacity, and that the increased stress resistance can mostly be attributed to its downstream target p21. Importantly, brief p53 stabilization also mounted protection against chemotherapy-induced DNA damage, suggesting that p53-dependent hormesis could be exploited to selectively protect healthy, p53-wildtype tissue from chemotherapy in the treatment of patients with p53 mutant tumors.

cancer biology↗

bioRxiv2024

WNT7B drives a program for pancreatic cancer subtype switching and progression

Hyperactivation of WNT signaling is a well-established hallmark of cancer. Various epithelial cancers express high levels of WNT7B and WNT10A that are not commonly expressed during tissue homeostasis, but rather associate with tissue development and regeneration. Although increased WNT7B/10A expression correlates with aggressive disease and lower patient survival rates, the mechanism by which these WNTs influence cancer progression remains unknown. Here, we use patient-derived organoids to show that tumor-intrinsic expression of WNT7B/10A drives survival and growth of advanced pancreatic ductal adenocarcinoma (PDAC). Bulk and single-cell profiling reveal that WNT7B drives proliferation and promotes expression of a poor prognosis basal-like state by preventing expression of a more differentiated, classical PDAC signature. By generating WNT7B reporter organoids, we show that heterogeneously distributed WNT-high PDAC cells are shifted towards a more basal-like phenotype and stably co-exist with WNT-low/negative lineages. Furthermore, hybrid co-cultures of WNT7B-proficient and -knockout PDAC organoids demonstrate that WNT-sending cells drive survival and proliferation of neighboring WNT-negative cells within the cancer epithelium via short range, cell contact-dependent signaling. In summary, our work uncovers a prominent role of WNT7B/10A in driving PDAC subtype heterogeneity and argues that WNT inhibition may be applied to force a class switch to a more differentiated, less aggressive cancer subtype that correlates with improved therapeutical response.

cancer biology↗

bioRxiv2022

Mother cells control daughter cell proliferation in intestinal organoids to minimize proliferation fluctuations

During renewal of the intestine, cells are continuously generated by proliferation. Proliferation and differentiation must be tightly balanced, as any bias towards proliferation results in uncontrolled exponential growth. Yet, the inherently stochastic nature of cells raises the question how such fluctuations are limited. We used time-lapse microscopy to track all cells in crypts of growing mouse intestinal organoids for multiple generations, allowing full reconstruction of the underlying lineage dynamics in space and time. Proliferative behavior was highly symmetric between sister cells, with both sisters either jointly ceasing or continuing proliferation. Simulations revealed that such symmetric proliferative behavior minimizes cell number fluctuations, explaining our observation that proliferating cell number remained constant even as crypts increased in size considerably. Proliferative symmetry did not reflect positional symmetry, but rather lineage control through the mother cell. Our results indicate a concrete mechanism to balance proliferation and differentiation with minimal fluctuations, that may be broadly relevant for other tissues.

cell biology↗

bioRxiv2022

Minimizing cell number fluctuations in self-renewing tissues with a stem cell niche

Self-renewing tissues require that a constant number of proliferating cells is maintained over time. This maintenance can be ensured at the single-cell level or the population level. Maintenance at the population level leads to fluctuations in the number of proliferating cells over time. Often, it is assumed that those fluctuations can be reduced by increasing the number of asymmetric divisions, i.e. divisions where only one of the daughter cells remains proliferative. Here, we study a model of cell proliferation that incorporates a stem cell niche of fixed size, and explicitly model the cells inside and outside the niche. We find that in this model fluctuations are minimized when the difference in growth rate between the niche and the rest of the tissue is maximized and all divisions are symmetric divisions, producing either two proliferating or two non-proliferating daughters. We show that this optimal state leaves visible signatures in clone size distributions and could thus be detected experimentally.

cell biology↗

bioRxiv2020

OrganoidTracker: efficient cell tracking using machine learning and manual error correction

Time-lapse microscopy is routinely used to follow cells within organoids, allowing direct study of division and differentiation patterns. There is an increasing interest in cell tracking in organoids, which makes it possible to study their growth and homeostasis at the single-cell level. As tracking these cells by hand is prohibitively time consuming, automation using a computer program is required. Unfortunately, organoids have a high cell density and fast cell movement, which makes automated cell tracking difficult. In this work, a semi-automated cell tracker has been developed. To detect the nuclei, we use a machine learning approach based on a convolutional neural network. To form cell trajectories, we link detections at different time points together using a min-cost flow solver. The tracker raises warnings for situations with likely errors. Rapid changes in nucleus volume and position are reported for manual review, as well as cases where nuclei divide, appear and disappear. When the warning system is adjusted such that virtually error-free lineage trees can be obtained, still less than 2% of all detected nuclei positions are marked for manual analysis. This provides an enormous speed boost over manual cell tracking, while still providing tracking data of the same quality as manual tracking.

bioinformatics↗