Biology subjects

Joosten, R.

Publications and source records attributed to Joosten, R..

11 recordsLinked to original sources

bioRxiv2026

Inflammation-driven reprogramming of goblet cells underlies the onset of serrated adenomas in colon cancer

In the context of inflammation, fully committed and post-mitotic cell lineages can initiate intestinal tumorigenesis in the mouse through dedifferentiation and acquisition of revival stem cell (RSC) features1,2. Likewise, by means of machine-learning analysis of whole-genome mutation spectra, the secretory goblet cell was predicted as the most frequent cell-of-origin (COO) of colon cancer in inflammatory bowel disease (IBD) patients2. Of note, even among sporadic (non-IBD) colon cancer patients, goblet cells were predicted as the most common differentiated COO of cancer in the colonic epithelium2, suggestive of the main role played by diet-induced inflammation in the onset of a large proportion of malignancies of the large bowel. However, how goblet cells respond to inflammation and reprogram their identity to become potential tumor-initiating cells remains unclear. Here, by taking advantage of publicly available single-cell RNAseq data from colonic tissues of ulcerative colitis (UC) patients3, we have characterized the inflammation-driven reprogramming of goblet cells. By means of an RNA velocity-based computational approach, we show that the mucus-producing goblet cells acquire an aberrant proliferative state earmarked by MUC5AC+ expression. Trajectory analysis of serrated adenoma cells4 reveal aberrant goblet cells as an intermediate state in the transition to revival stem cells, notably more common in BRAF-mutant cases. In support of these findings, COO predictions using whole-genome mutation spectra from a cohort of sporadic colon cancers5 connect tumors with a predicted goblet origin to BRAF mutations and reveal transcriptional remnants of the aberrant goblet cell state.

Cancer Biology↗

bioRxiv2026

Western diet suppresses canonical intestinal stem cells and reprograms c-Kit+ reserve stem cells via proinflammatory dysbiosis

While colorectal cancer (CRC) is thought to originate primarily from resident stem cells, diet heavily influences intestinal stem cell homeostasis and disease onset. In this study, we demonstrate that a Western-style diet (WSD) alters intestinal homeostasis by uncoupling canonical stemness from tumorigenesis. WSD exposure suppresses canonical Lgr5 stem cells while activating an alternative pool of facultative c-Kit secretory cells. Although these reprogrammed stem-like cells exhibit genotoxic stress, they remain proliferative under prolonged dietary exposure, suggesting increased susceptibility to tumor-initiating mutations. We identify diet-induced microbial shifts and the expansion of enterotoxigenic Bacteroides fragilis (ETBF) as the upstream driver. ETBF and its toxin fragilysin autonomously trigger multipotency in c-Kit+ cells through Wnt/{beta}-catenin and YAP signaling. Importantly, these alterations are fully reversible upon dietary intervention. Together, our results highlight a targetable dietary-microbial axis that shapes epithelial stemness and underscores the role of facultative stem cells in diet-induced CRC onset.

cell biology↗

bioRxiv2024

Reconstructing Biological Molecules with Help from Video Gamers

Foldit is a citizen science video game in which players tackle a variety of complex biochemistry puzzles. Here, we describe a new series of puzzles in which Foldit players improve the accuracy of the public repository of experimental protein structure models, the Protein Data Bank (PDB). Analyzing the results of these puzzles showed that the Foldit players were able to considerably improve the deposited structures and thus, in most cases, improved the output of the automated PDB-REDO refinement pipeline. These improved structures are now being hosted at PDB-REDO. These efforts highlight the continued need for the engagement of the lay population in science.

biophysics↗

bioRxiv2024

A tug-of-war between the NuRD and SWI/SNF chromatin remodelers regulates the coordinated activation of Epithelial-Mesenchymal Transition and inflammation in oral cancer.

Phenotypic plasticity and inflammation, two well-established hallmarks of cancer, play key roles in local invasion and distant metastasis by enabling rapid adaptation of tumor cells to dynamic micro- environmental changes. Here, we show that in oral squamous carcinoma cell carcinoma (OSCC), the competition between the NuRD and SWI/SNF chromatin remodeling complexes plays a pivotal role in regulating both epithelial-mesenchymal plasticity (EMP) and inflammation. By perturbing these complexes, we demonstrate their opposing downstream effects on inflammatory pathways and EMP regulation. In particular, downregulation of the BRG1-specific SWI/SNF complex deregulates key inflammatory genes such as TNF- and IL6 in opposite ways when compared with loss of CDK2AP1, a key member of the NuRD complex. We show that CDK2AP1 genetic ablation triggers a pro-inflammatory secretome encompassing several chemo- and cytokines thus promoting the recruitment of monocytes into the tumor microenvironment (TME). Furthermore, CDK2AP1 deletion stimulates their differentiation into M2-like macrophages, as also validated on tumor microarrays from OSCC patient- derived tumor samples. Further analysis of the inverse correlation between CDK2AP1 expression and TME immune infiltration revealed specific downstream effects on CD68+ macrophage abundance and localization. Our study sheds light on the role of chromatin remodeling complexes in OSCC locoregional invasion and points at the potential of CDK2AP1 and other members of the NuRD and SWI/SNF chromatin remodeling complexes as prognostic markers and therapeutic targets.

cancer biology↗

bioRxiv2023

The origin of intestinal cancer in the context of inflammation

According to conventional views, colon cancer originates from stem cells. However, inflammation, a key risk factor for colon cancer, was shown to suppress intestinal stemness. Here, we employed Paneth cells (PCs) as a model to assess the capacity of differentiated lineages to trigger tumorigenesis in the context of inflammation. Upon inflammation, PC-specific Apc mutations led to intestinal tumors reminiscent not only of those arising in inflammatory bowel disease (IBD) patients but also of a larger fraction of sporadic colon cancers. The latter is likely due to the inflammatory consequences of Western-style dietary habits, the major colon cancer risk factor. Computational methods designed to predict the cell-of-origin of cancer confirmed that, in a substantial fraction of sporadic colon cancers the cells-of-origin are secretory lineages and not stem cells. One-Sentence SummarySecretory cell lineages trigger tumor formation in the context of the major etiologic colon cancer risk factors.

cancer biology↗

bioRxiv2023

Distant sequence regions of JBP1 contribute to J-DNA binding

Base-J ({beta}-D-Glucopyranosyloxymethyluracil) is a modified DNA nucleotide that replaces 1% of thymine in kinetoplastid flagellates. The biosynthesis and maintenance of base-J depends on the base-J Binding Protein 1 (JBP1), that has a thymidine hydroxylase domain (THD) and a J-DNA binding domain (JDBD). How the THD synergizes with the JDBD to hydroxylate thymine in specific genomic sites, maintaining base-J during semi-conservative DNA replication, remains unclear. Here we present a crystal structure of the JDBD including a previously disordered DNA-contacting loop and use it as starting point for Molecular Dynamics (MD) simulations and computational docking studies to propose recognition models for JDBD binding to J-DNA. These models guided mutagenesis experiments, providing additional data for docking, which reveals a binding mode for JDBD onto J-DNA. This model, together with the crystallographic structure of the TET2 JBP1-homologue in complex with DNA and the AlphaFold model of full-length JBP1, allowed us to hypothesize that the flexible JBP1 N-terminus contributes to DNA-binding, which we confirmed experimentally. A high-resolution JBP1:J-DNA complex, which must involve conformational changes, would however need to be determined experimentally to further understand this unique underlying molecular mechanism that ensures replication of epigenetic information.

biochemistry↗

bioRxiv2022

3D-Beacons: Decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

While scientists can often infer the biological function of proteins from their 3-dimensional quaternary structures, the gap between the number of known protein sequences and their experimentally determined structures keeps increasing. A potential solution to this problem is presented by ever more sophisticated computational protein modelling approaches. While often powerful on their own, most methods have strengths and weaknesses. Therefore, it benefits researchers to examine models from various model providers and perform comparative analysis to identify what models can best address their specific use cases. To make data from a large array of model providers more easily accessible to the broader scientific community, we established 3D-Beacons, a collaborative initiative to create a federated network with unified data access mechanisms. The 3D-Beacons Network allows researchers to collate coordinate files and metadata for experimentally determined and theoretical protein models from state-of-the-art and specialist model providers and also from the Protein Data Bank.

bioinformatics↗

bioRxiv2020

Phenotypic plasticity and partial EMT underlie local invasion and distant metastasis in colon cancer

Phenotypic plasticity represents the most relevant hallmark of the carcinoma cell as it bestows it with the capacity of transiently altering its morphologic and functional features while en route to the metastatic site. However, the study of phenotypic plasticity is hindered by the rarity of these events within primary lesions and by the lack of experimental models. Here, we identified a subpopulation of phenotypic plastic colon cancer cells: EpCAMlo cells are motile, invasive, chemo-resistant, and highly metastatic. EpCAMlo bulk and single-cell RNAseq analysis indicated 1. enhanced Wnt/{beta}-catenin signaling, 2. a broad spectrum of degrees of EMT activation including hybrid E/M states (partial EMT) with highly plastic features, and 3. high correlation with the CMS4 subtype, accounting for colon cancer cases with poor prognosis and a pronounced stromal component. Of note, a signature of genes specifically expressed in EpCAMlo cancer cells is highly predictive of overall survival in tumors other than CMS4, thus highlighting the relevance of quasi-mesenchymal tumor cells across the spectrum of colon cancers. Enhanced Wnt and the downstream EMT activation represent key events in eliciting phenotypic plasticity along the invasive front of primary colon carcinomas. Distinct sets of epithelial and mesenchymal genes define transcriptional trajectories through which state transitions arise. pEMT cells, often earmarked by the extracellular matrix glycoprotein SPARC together with nuclear ZEB1 and {beta}-catenin along the invasive front of primary colon carcinomas, are predicted to represent the origin of these (de)differentiation routes through biologically-distinct cellular states, and to underlie the phenotypic plasticity of colon cancer cells.

cancer biology↗

bioRxiv2018

Characterisation and structure determination of a llama-derived nanobody targeting the J-base binding protein 1

The J-base Binding Protein 1 (JBP1) contributes to biosynthesis and maintenance of base J ({beta}-D-glucosyl-hydroxymethyluracil), a modification of thymidine confined to some protozoa. Camelid (llama) single domain antibody fragments (nanobodies) targeting JBP1 were produced for use as crystallization chaperones. Surface plasmon resonance (SPR) screening identified Nb6 as a strong binder, recognising JBP1 with a 1:1 stoichiometry and high affinity (kD=30nM). Crystallisation trials of JBP1 in complex with Nb6, yielded crystals diffracting to 1.47[A] resolution.\n\nHowever, the asymmetric unit dimensions and molecular replacement with a nanobody structure, clearly showed that the crystals of the expected complex with JBP1 were of the nanobody alone. Nb6 crystallizes in spacegroup P31 with two molecules in the asymmetric unit; its crystal structure was refined to a final resolution of 1.64[A]. Ensemble refinement suggests that on the ligand-free state one of the complementarity determining regions (CDRs) is flexible while the other two adopt well-defined conformations.\n\nSynopsisA camelid single domain antibody fragment (nanobody) is shown to have high affinity towards its recognition target, the J-base binding protein 1 (JBP1). The serendipitous crystallisation of this nanobody alone, and its crystal structure solution and refinement to 1.64[A] resolution are described. Ensemble refinement suggests that on the ligand-free state one of the complementarity determining regions (CDRs) is flexible while the other two adopt well-defined conformations.

biochemistry↗

bioRxiv2018

Homology-based loop modelling yields more complete crystallographic protein structures

Inherent protein flexibility, poor or low-resolution diffraction data, or poor electron density maps, often inhibit building complete structural models during X-ray structure determination. However, advances in crystallographic refinement and model building nowadays often allow to complete previously missing parts. Here, we present algorithms that identify regions missing in a certain model but present in homologous structures in the Protein Data Bank (PDB), and \"graft\" these regions of interest. These new regions are refined and validated in a fully automated procedure. Including these developments in our PDB-REDO pipeline, allowed to build 24,962 missing loops in the PDB. The models and the automated procedures are publically available through the PDB-REDO databank and web server (https://pdb-redo.eu). More complete protein structure models enable a higher quality public archive, but also a better understanding of protein function, better comparison between homologous structures, and more complete data mining in structural bioinformatics projects.\n\nSynopsisThousands of missing regions in existing protein structure models are completed using new methods based on homology.

bioinformatics↗

bioRxiv2017

Understanding inhibitor resistance in Mps1 kinase through novel biophysical assays and structures

Monopolar spindle 1 (Mps1/TTK) is a protein kinase essential in mitotic checkpoint signalling, preventing anaphase until all chromosomes are properly attached to spindle microtubules. Mps1 has emerged as a potential target for cancer therapy, and a variety of compounds have been developed to inhibit its kinase activity. Mutations in the catalytic domain of Mps1 that give rise to inhibitor resistance, but retain catalytic activity and do not display cross-resistance to other Mps1 inhibitors, have been described. Here we characterize the interactions of two such mutants, Mps1 C604Y and C604W, which raise resistance to two closely related compounds, NMS-P715 and its derivative Cpd-5, but not to the well-characterised Mps1 inhibitor, reversine. We show that estimates of the IC50 (employing a novel specific and efficient assay that utilizes a fluorescently labelled substrate) and of the binding affinity (KD) indicate that in both mutants, Cpd-5 should be better tolerated than the closely related NMS-P715. To gain further insight, we determined the crystal structure of the Mps1 kinase mutants bound to Cpd-5 and NMS-P715, and compare the binding modes of Cpd-5, NMS-P715 and reversine. The difference in steric hindrance between Tyr/Trp604 and the trifluoromethoxy moiety of NMS-P715, the methoxy moiety of Cpd-5, and complete absence of such a group in reversine, account for differences we observe in vitro. Our analysis enforces the notion that inhibitors targeting Mps1 drug-resistant mutations can emerge as a feasible intervention strategy based on existing scaffolds, if the clinical need arises.\n\nSummary statementThe inhibition of specific Mps1 kinase inhibitors towards the wild-type protein and inhibitor-resistant mutants is explained by a novel specific activity assay, biophysical characterisation, and X-ray structures.\n\nAbbreviations

biochemistry↗