Biology subjects

Bouwman, P.

Publications and source records attributed to Bouwman, P..

4 recordsLinked to original sources

bioRxiv2026

Functional Mammary Gland Organoids From Human Induced Pluripotent Stem Cells

The human mammary gland arises through sequential lineage restrictions from surface ectoderm to hormone-responsive bilayered epithelium, yet a tractable in vitro model that captures these events has remained elusive. Here, we established a stepwise differentiation protocol that directs human induced pluripotent stem cells (hiPSCs) into mammary organoids (MGOs) by sequential induction of non-neural ectoderm, mammary placodes, and lineage maturation in a defined medium. The resulting MGOs reproducibly formed polarized basal (KRT14+, TP63+) and luminal (KRT8+, GATA3+) layers, with ~25% of luminal cells expressing oestrogen receptor (ER). MGOs accumulated lipids, expressed {beta}-casein upon prolactin stimulation, and retained lineage fidelity after serial passaging. Upon transplantation into cleared mouse mammary fat pads, MGOs generated branched mammary ductal networks. Single-cell transcriptomics confirmed the emergence of basal, luminal hormone-sensing, luminal secretory, and stromal populations, transcriptionally aligned with adult human breast epithelium and responsive to endocrine disruption. These findings demonstrate that hiPSCs can be reprogrammed into functional mammary epithelium, providing a platform to dissect development, endocrine signalling, and breast cancer pathogenesis.

cell biology↗

bioRxiv2025

Data-driven dynamic modelling identifies polyploidisation as key process in cell cycle progression upon DNA damage

Chemotherapeutic agents often cause DNA damage in order to kill fast-dividing cancer cells or disrupt their proliferation. Therefore, understanding the interplay between DNA damage and cell cycle progression is highly relevant for understanding cancer cell behaviour. An important regulator is transcription factor p53, primarily known for its function to maintain genomic stability, regulate transient and permanent cell cycle arrest and apoptosis. Activated p53 transcriptionally regulates the expression of many proteins, among which are MDM2, p21 and BTG2. MDM2 functions as a direct inhibitor of p53 by targeting it for ubiquitination. The proteins p21 and BTG2 are known for their regulatory function in G1 and G2 cell cycle arrest. Using HepG2-FUCCI cells, we showed that exposure to cisplatin or etoposide caused a temporary G2 arrest. To study the link between protein expression and cell cycle arrest, we developed a mathematical model in which we integrated a previously established model for the protein expression dynamics of p53, MDM2, p21 and BTG2 with a cell cycle model. This allowed us to determine the importance of p21 and BTG2 in their stimulation of G1 and G2 cell cycle arrest. We found that the protein dynamics could predict the G2 cell cycle arrest in exposed cells, but only in combination with endoreplication, i.e., the alternation of S and G phases without mitosis, resulting in polyploid cells. Our model predicted that the majority of cells endoreplicate upon exposure to high concentrations of cisplatin and most concentrations of etoposide, which we validated with additional time-lapse imaging data in which we could track individual cells. In conclusion, polyploidisation is a generic response of HepG2 cells after treatment with DNA-damaging compounds.

systems biology↗

bioRxiv2021

Transcriptomic mapping of the inter-individual variability of cellular stress response activation in primary human hepatocytes

Background & AimsOne of the early key events of drug-induced liver injury (DILI) is the activation of adaptive stress responses, a cellular mechanism to overcome stress. Given the diversity of DILI outcomes and lack in understanding of population variability, we mapped the inter-individual variability in stress response activation to improve DILI prediction. Approach & ResultsHigh-throughput transcriptome analysis of over 8,000 samples was performed in primary human hepatocytes of 50 individuals upon 8 to 24 h exposure to broad concentration ranges of stress inducers: tunicamycin to induce the unfolded protein response (UPR), diethyl maleate for the oxidative stress response, cisplatin for the DNA damage response and TNF for NF-{kappa}B signalling. This allowed investigation of the inter-individual variability in concentration-dependent stress response activation, where the average of benchmark concentrations (BMCs) had a maximum difference of 864, 13, 13 and 259-fold between different hepatocytes for UPR, oxidative stress, DNA damage and NF-{kappa}B signalling-related genes, respectively. Hepatocytes from patients with liver disease resulted in less stress response activation. Using a population mixed-effect framework, the distribution of BMCs and maximum fold change were modelled, allowing simulation of smaller or larger PHH panel sizes. Small panel sizes systematically under-estimated the variance and resulted in low probabilities in estimating the correct variance for the human population. Moreover, estimated toxicodynamic variability factors were up to 2-fold higher than the standard uncertainty factor of 101/2 to account for population variability during risk assessment, exemplifying the need of data-driven variability factors. ConclusionsOverall, by combining high-throughput transcriptome analysis and population modelling, improved understanding of variability in stress response activation across the human population could be established, thereby contributing towards improved prediction of DILI.

pharmacology and toxicology↗

bioRxiv2018

Radiosensitivity is an acquired vulnerability of PARPi-resistant BRCA1-deficient tumors

The homologous recombination (HR) defect in BRCA1-associated cancers can be therapeutically exploited by the treatment with DNA-damaging agents and poly (ADP-ribose) polymerase (PARP) inhibitors. We and others previously reported that BRCA1-deficient tumors are initially hypersensitive to the inhibition of topoisomerase I/II and PARP, but acquire drug resistance through restoration of HR activity by the loss of end-resection antagonists of the 53BP1/RIF1/REV7/Shieldin/CST pathway. Here, we identified radiotherapy as an acquired vulnerability of 53BP1;BRCA1-deficient cells in vitro and in vivo. In contrast to the radioresistance caused by HR restoration through BRCA1 reconstitution, HR restoration by 53BP1 pathway inactivation further increases radiosensitivity. This highlights the relevance of this pathway for the repair of radiotherapy-induced damage. Moreover, our data show that BRCA1-mutated tumors that acquired drug resistance due to BRCA1-independent HR restoration can be targeted by radiotherapy.\n\nSTATEMENT OF SIGNIFICANCEIn this study, we uncovered radiosensitivity as a novel therapeutically exploitable vulnerability of BRCA1-deficient mouse mammary cells that have acquired drug resistance due to the loss of the 53BP1 pathway.

cancer biology↗