Biology subjects

Bakker, P. L.

Publications and source records attributed to Bakker, P. L..

7 recordsLinked to original sources

bioRxiv2026

p53 activity links chromosomal instability to pro-migratory extracellular vesicles

Chromosomal instability (CIN) promotes tumor evolution and metastasis while imposing cellular stress that can limit cell proliferation via activation of p53 and its downstream effector p21. However, how cells recover from this p53-mediated proliferation block while adopting a more malignant fate remains poorly understood. Here, using a p21-RFP reporter in p53-proficient NIH/3T3 cells, we show that acute CIN gives rise to two phenotypically distinct p21 cell populations with divergent recovery trajectories. p21-RFPLOW cells re-enter the cell cycle following a short cell-cycle arrest, while p21-RFPHIGH cells display a more persistent arrest that coincides with a senescence-like state. Longitudinal transcriptomic and extracellular vesicle (EV) proteomic analyses reveal that extracellular-matrix (ECM)- and adhesion-associated programs are initially suppressed following CIN but specifically reactivated in p21-RFPHIGH cells. The content of late-stage p21-RFPHIGH-derived EVs is enriched for ECM-, adhesion-, and cytoskeleton-associated proteins compared with that of p21-RFPLOW-derived EVs. Consequently, EVs derived from p21-RFPHIGH cells confer increased migration. Together, these findings reveal that CIN can yield distinct p21-expressing cell populations that display different cell-cycle recovery trajectories, EV makeup, and migration-associated paracrine activity.

cancer biology↗

bioRxiv2025

Increased activity of PRMT5-MEP50 complex improves survival of chromosomally unstable cancer cells by increasing tolerance to protein aggregation and proteotoxicity

Most cancers display chromosomal instability (CIN), a condition that leads to increased rates of chromosome missegregation and thus yields aneuploidy. CIN and aneuploidy are detrimental to healthy cells and therefore, aneuploid cells rely on aneuploidy-tolerating mechanisms to adopt a malignant fate. We previously found PRMT5 to be frequently amplified in a mouse model for aneuploid T cell lymphoblastic lymphoma. In this study, we investigated a possible role of PRMT5 as an aneuploidy tolerating gene. We report that PRMT5 is prone to aggregation when expressed at supra-stoichiometric levels compared to its obligate partner protein MEP50 (methylosome protein 50, WDR77). Intriguingly, we also find that protein aggregation, induced by CIN, is mitigated by jointly increased expression of PRMT5 and MEP50. Accordingly, concomitant PRMT5:MEP50 expression renders cancer cells less sensitive to proteasome inhibitors and CIN while inhibition sensitizes cells to CIN. Our findings provide a possible explanation for why PRMT5 and MEP50 display increased expression, particularly in aneuploid cancers and might reveal a targetable vulnerability of aneuploid cancer.

cancer biology↗

bioRxiv2022

IFNγ protects motor neurons from oxidative stress via enhanced global protein synthesis in FUS-associated Amyotrophic Lateral Sclerosis

Amyotrophic lateral sclerosis type 6 (ALS6) is a familial subtype of ALS linked to Fused in Sarcoma (FUS) gene mutation. FUS mutations lead to decreased global protein synthesis, but the mechanism that drives this has not been established. Here, we used ALS6 patient-derived induced pluripotent stem cells (hIPSCs) to study the effect of the ALS6 FUSR521H mutation on the translation machinery in motor neurons (MNs). We find, in agreement with findings of others, that protein synthesis is decreased in ALS6 MNs. Furthermore, ALS6 MNs are more sensitive to oxidative stress and display reduced expression of TGF-{beta} and mTORC gene pathways when stressed. Finally, we show that IFN{gamma} treatment reduces apoptosis of ALS6 MNs exposed to oxidative stress and partially restores the translation rates in ALS6 MNs. Overall, these findings suggest that a functional IFN{gamma} response is important for FUS-mediated protein synthesis, possibly by FUS nuclear translocation in ALS6. Highlights and eTOC blurbO_LIALS6 patient-derived motor neurons show decreased viability and reduced production of innate immune cytokines following oxidative stress C_LIO_LIFUS cytoplasmic localization coincides with decreased protein synthesis rates C_LIO_LIIFN{gamma} treatment of ALS6 patient-derived motor neurons reduces apoptosis and ameliorates translation rates resulting from oxidative stress C_LI

neuroscience↗

bioRxiv2021

Cancer tolerance to chromosomal instability is driven by Stat1 inactivation in vivo

Chromosomal instability is a hallmark of cancer, but also an instigator of aneuploidy-induced stress, reducing cellular fitness. To better understand how cells with CIN adjust to aneuploidy and adopt a malignant fate in vivo, we performed a genome-wide mutagenesis screen in mice. We find that specifically aneuploid tumors inactivate Stat1 signaling in combination with increased Myc activity. By contrast, loss of p53 is common, but not enriched in CIN tumors. Validation in another tissue type confirmed that CIN promotes immune cell infiltration, which is alleviated by Stat1 loss combined with Myc activation, but not with p53 inactivation, or Myc activation alone. Importantly, we find that this mechanism is preserved in human aneuploid cancers. We conclude that aneuploid cancers inactivate Stat1 signaling to circumvent immune surveillance.

cancer biology↗

bioRxiv2021

A synthetic lethal screen identifies HDAC4 as a potential target in MELK overexpressing cancers

Maternal embryonic leucine zipper kinase (MELK) is frequently overexpressed in cancer, but the role of MELK in cancer is still poorly understood. MELK was shown to have roles in many cancer-associated processes including tumor growth, chemotherapy resistance, and tumor recurrence. To determine whether the frequent overexpression of MELK can be exploited in therapy, we performed a high-throughput screen using a library of Saccharomyces cerevisiae mutants to identify genes whose functions become essential when MELK is overexpressed. We identified two such genes: LAG2 and HDA3. LAG2 encodes an inhibitor of the SCF ubiquitin-ligase complex, while HDA3 encodes a subunit of the HDA1 histone deacetylase complex. We find that one of these synthetic lethal interactions is conserved in mammalian cells, as inhibition of a human homolog of HDA3 (HDAC4) is synthetically toxic in MELK overexpression cells. Altogether, our work might provide a new angle of how to exploit MELK overexpression in cancers and might thus lead to novel intervention strategies.

genetics↗

bioRxiv2020

Acute systemic loss of Mad2 leads to intestinal atrophy in adult mice

Chromosomal instability (CIN) is a hallmark of cancer, leading to aneuploid cells. To study the role that CIN plays in tumor evolution, several mouse models have been engineered over the last two decades. These studies have unequivocally shown that systemic high-grade CIN is embryonic lethal. We and others have previously shown that embryonic lethality can be circumvented by provoking CIN in a tissue-specific fashion. In this study, we provoke systemic high-grade CIN in adult mice as an alternative to circumvent embryonic lethality. For this, we disrupt the spindle assembly checkpoint (SAC) by alleviating Mad2 or truncating Mps1, both essential genes for SAC functioning, with or without p53 inactivation. We find that disruption of the SAC leads to rapid villous atrophy, atypia and apoptosis of intestinal epithelia, substantial weight loss, and death within 10 days after the start of the CIN insult. Despite this severe intestinal phenotype, most other tissues are unaffected, except for minor abnormalities in spleen, presumably due to the low proliferation rate in these tissues. We conclude that high-grade CIN in vivo in adult mice is most toxic to intestinal epithelia, presumably due to the high cell turnover in this tissue.

cancer biology↗

bioRxiv2018

Single cell DNA sequencing reveals distinct molecular types of basal cell carcinoma with unique transcriptome features

Background: Aneuploidy, a hallmark of cancer, is the result of chromosomal instability (CIN) during mitosis. While some aneuploid cancers display stable karyotypes, other tumours display cell-to-cell karyotype variability indicative of CIN. CIN cancers are typically associated with poor clinical outcome, as they are endowed with the potential to adjust their genomes to changing conditions including therapy. To further explore this, we assessed the degree of aneuploidy and CIN in basal cell carcinoma (BCC) and investigated whether the karyotypic makeup of tumours was associated with distinct transcriptional responses. Patients and Methods: Samples from 11 BCC patients were processed for single-cell whole genome sequencing (scWGS) to measure aneuploidy and karyotype heterogeneity. In parallel, samples were processed for transcriptome analysis. Results: scWGS revealed different grades of aneuploidy between BCCs, ranging from euploidy to tumours with up to 7 aneusomic chromosomes. Importantly, a subset of BCCs displayed intratumour karyotype heterogeneity, indicating that CIN can play a role in BCC. Samples were clustered into three groups based on the level of aneuploidy and intratumour karyotype heterogeneity. Karyotype-driven group classification was also reflected by the tumour transcriptomes and revealed distinct gene expression signatures related to metabolism for aneuploid BCCs and a DNA damage signature for CIN BCCs. Conclusions: While BCCs are typically classified based on histopathological features, we find that BCCs can be stratified based on karyotypic landscape. Importantly, this classification is linked to distinct molecular features and could thus be the starting point of a molecular classification system for BCC including a readout for CIN. Importantly, the approach that we have developed is broadly applicable and could therefore also improve the diagnosis and treatment of other cancer types.

cancer biology↗