Biology subjects

De Vos, W.

Publications and source records attributed to De Vos, W..

7 recordsLinked to original sources

bioRxiv2024

PAC-MAP: Proximity Adjusted Centroid Mapping for Accurate Detection of Nuclei in Dense 3D Cell Systems

MotivationIn the past decade, deep learning algorithms have surpassed the performance of many conventional image segmentation pipelines. Powerful models are now available for segmenting cells and nuclei in diverse 2D image types, but segmentation in 3D cell systems remains challenging due to the high cell density, the heterogenous resolution and contrast across the image volume, and the difficulty in generating reliable and sufficient ground truth data for model training. Reasoning that most image processing applications rely on nuclear segmentation but do not necessarily require an accurate delineation of their shapes, we implemented PAC-MAP, a 3D U-net based method that predicts the position of nuclei centroids and their proximity to other nuclei. ResultsWe show that our model outperforms existing methods, predominantly by boosting recall, especially in conditions of high cell density. When trained from scratch PAC-MAP attained an average F1 score of 0.793 in dense spheroids. When pretraining using weakly supervised bulk data input and finetuning with few expert annotations the average F1 score could be significantly improved up to 0.817. We demonstrate the utility of our method for quantifying the cell content of spheroids and mapping the degree of glioblastoma multiforme infiltration in cerebral organoids. Availability and implementationThe code is available on GitHub, at https://github.com/DeVosLab/PAC-MAP. ContactWinnok H. De Vos (winnok.devos@uantwerpen.be)

bioinformatics↗

bioRxiv2024

The Aggregated Gut Viral Catalogue (AVrC): A Unified Resource for Exploring the Viral Diversity of the Human Gut

Despite the growing interest in the role of the gut virome in human health and disease, identifying viral sequences from human gut metagenomes remains computationally challenging due to underrepresentation of viral genomes in reference databases. Several recent large-scale efforts have mined human gut metagenomes to establish viral sequence catalogues, using varied computational tools and quality control criteria. However, there has been no consistent comparison of these catalogues quality, diversity, and completeness, nor unification into a comprehensive resource. Here, we systematically surveyed nine previously published human gut viral catalogues, assessing their quality and the overlap of the viral sequences retrieved. While these catalogues collectively screened >40,000 human fecal metagenomes, 82% of the recovered 345,613 viral sequences were unique to one catalogue, highlighting limited redundancy. We further expanded representation by mining 7,867 infant gut metagenomes, retrieving 1,205,739 additional putative viral sequences. From these datasets, we constructed the Aggregated Gut Viral Catalogue (AVrC), a unified modular resource containing 1,018,941 dereplicated viral sequences (449,859 species-level vOTUs). Detailed annotations were generated for sequence quality, taxonomy, predicted lifestyle, and putative host. The AVrC reveals the gut viromes substantial unexplored diversity, providing a pivotal resource for viral discovery. The AVrC is accessible as a relational database and through a web interface allowing customized querying and subset retrieval, enabling streamlined utilization by the research community and future expansions as novel data becomes available. Author summaryThe human gut is home to a vast array of viruses, collectively known as the gut virome, which play a crucial role in human health and disease. Recently, several research groups aiming at providing an overview of the Human gut viral diversity, have created catalogues of viral sequences found in the human gut by analyzing a large number of fecal samples from different individuals. In this study, we compared nine of these existing catalogues and found that there was surprisingly little overlap between them, with 82% of the viral sequences being unique to a single catalogue. To further expand the available data, we analyzed nearly 8,000 additional fecal samples from infants. By combining all this ressources, we created a unified resource called the Aggregated Gut Viral Catalogue (AVrC), which contains more than a million distinct viral sequences, representing nearly 450,000 different viral species. This catalogue, which is easily accessible to the scientific community through a user-friendly web interface, provides a valuable tool for exploring the vast diversity of the human gut virome and its potential implications for human health.

microbiology↗

bioRxiv2024

Unbiased identification of cell identity in dense mixed neural cultures

Induced pluripotent stem cell (iPSC) technology is revolutionizing cell biology. However, the variability between individual iPSC lines and the lack of efficient technology to comprehensively characterize iPSC-derived cell types hinder its adoption in routine preclinical screening settings. To facilitate the validation of iPSC-derived cell culture composition, we have implemented an imaging assay based on cell painting and convolutional neural networks to recognize cell types in dense and mixed cultures with high fidelity. We have benchmarked our approach using pure and mixed cultures of neuroblastoma and astrocytoma cell lines and attained a classification accuracy above 96%. Through iterative data erosion we found that inputs containing the nuclear region of interest and its close environment, allow achieving equally high classification accuracy as inputs containing the whole cell for semi-confluent cultures and preserved prediction accuracy even in very dense cultures. We then applied this regionally restricted cell profiling approach to evaluate the differentiation status of iPSC-derived neural cultures, by determining the ratio of postmitotic neurons and neural progenitors. We found that the cell-based prediction significantly outperformed an approach in which the time in culture was used as classification criterion (96% vs. 86%, resp.). In mixed iPSC-derived neuronal cultures, microglia could be unequivocally discriminated from neurons, regardless of their reactivity state. A tiered strategy, allowed for discriminating microglial cell states as well, albeit with lower accuracy. Thus, morphological single cell profiling provides a means to quantify cell composition in complex mixed neural cultures and holds promise for use in quality control of iPSC-derived cell culture models.

cell biology↗

bioRxiv2023

Resource-efficient nitrogen removal from source separated urine with partial nitritation/anammox in a membrane aerated biofilm reactor

Source separation and decentralized urine treatment can cut costs in centralized wastewater treatment by diverting 80% of the nitrogen load in sewage. One promising approach for nitrogen removal in this context is partial nitritation/anammox (PN/A), reducing the aeration demand by 67% and organics dosage by 100% compared to nitrification/denitrification. Whilst previous studies with suspended biomass have encountered stability issues during PN/A treatment of urine, a PN/A biofilm was hypothesized to be more resilient. Its use for urine treatment was pioneered here for maximum rates and efficiencies in the energy efficient membrane-aerated biofilm reactor (MABR). Nitrogen removal rates of 1.0 g N L-1 d-1 and removal efficiencies of 80-95% were achieved during a 335-day stable operation at 28{degrees}C on stabilized (pH>11), diluted urine (10%). A balance between N2 and NO3 - formation was observed whilst optimizing the supply of O2 and was rate limiting for the conversion towards N2. Short-term operation on less- and undiluted urine yielded N removal rates of 0.6-0.8 g N L-1 d-1 and removal efficiencies of 93% on 66% urine and 85% on undiluted urine. Metataxonomic analysis and fluorescence in-situ hybridization confirmed the presence of biofilms consisting of nitrifiers (Nitrosomonas, Nitrospira) at the membrane side and anammox bacteria ("Candidatus Brocadia") at the anoxic bulk side. The findings suggest that a biofilm approach to PN/A treatment of urine overcomes stability issues, and a PN/A-MABR has significant potential for resource efficient decentralized treatment. In human long-duration deep-space missions, this gravity-independent technology could produce N2 to compensate artificial atmosphere losses whilst facilitating water recovery from urine. [GRAPHICAL ABSTRACT, COLOR] O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/572732v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1680b0corg.highwire.dtl.DTLVardef@1ad822dorg.highwire.dtl.DTLVardef@3d5c4borg.highwire.dtl.DTLVardef@764841_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2023

S100A8-enriched microglia populate the brain of tau-seeded and accelerated aging mice

Long considered to fluctuate between pro- and anti-inflammatory states, it has now become evident that microglia occupy a variegated phenotypic landscape with relevance to aging and neurodegeneration. However, whether specific microglial subsets converge in or contribute to both processes that eventually affect brain function is less clear. To investigate this, we analyzed microglial heterogeneity in a tauopathy mouse model (K18-seeded P301L) and an accelerated aging model (senescence accelerated mouse prone 8, SAMP8) using cellular indexing of transcriptomes and epitopes by sequencing. We found that widespread tau pathology in K18-seeded P301L mice caused a significant change in the number and morphology of microglia, but only a mild overrepresentation of disease-associated microglia. At the cell population-level, we observed a marked upregulation of the calprotectin-encoding genes S100a8 and S100a9. In 9-months-old SAMP8 mice, we identified a unique microglial subpopulation that showed partial similarity with the disease-associated microglia phenotype and was additionally characterized by a high expression of the same calprotectin gene set. Immunostaining for S100A8 revealed that this population was enriched in the hippocampus, correlating with the cognitive impairment observed in this model. However, incomplete colocalization between their residence and markers of neuronal loss suggests regional specificity. Importantly, S100A8-positive microglia were also retrieved in brain biopsies of human AD and tauopathy patients as well as in a biopsy of an aged individual without reported pathology. Thus, the emergence of S100A8-positive microglia portrays a conspicuous commonality between accelerated aging and tauopathy progression, which may have relevance for ensuing brain dysfunction. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=162 SRC="FIGDIR/small/566543v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@d1e4e1org.highwire.dtl.DTLVardef@98adeorg.highwire.dtl.DTLVardef@7c15aaorg.highwire.dtl.DTLVardef@7265ca_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2022

Enteric glia adopt an activated pro-inflammatory state in response to human and bacterial amyloids

Mounting evidence suggests a role for the microbiome-gut-brain axis in amyloid-associated neurodegeneration, but the pathogenic changes induced by amyloids in the gastro-intestinal tract remain elusive. To scrutinize the early response to amyloids of human and bacterial origin, we challenged primary murine myenteric networks with A{beta}1-42 (vs a scrambled version of A{beta}1-42) and curli (vs culture medium), respectively, and performed shotgun RNA sequencing. Both amyloid types induced a transcriptional signature of DNA damage and cell cycle dysregulation. Using in vitro neurosphere-derived cultures and in vivo amyloid injections we found that enteric glia and smooth muscle cells were the most responsive cell types, showing increased proliferation, {gamma}H2AX burden and SOD2 levels after amyloid challenge. Consistent with this activated state, we identified a pro-inflammatory hub in the transcriptional profile of amyloid-stimulated myenteric networks. Enteric glia were the principal source of the associated cytokines, and in vivo, this was accompanied by an influx of immune cells. Together, these results shed new light on the intrinsic vulnerability of ENS cells to both amyloid species and position enteric glial cell activation as an early driver of neurodegenerative disease progression. Significance statementThe increasing socio-economic impact of Alzheimers disease (AD), long sub-clinical disease progression window, and failure of drug candidates demand mechanistic insight into the early stages of disease development. Epidemiological associations and experimental studies in rodents suggest that the gut may be vulnerable to amyloids and mediate their transfer to the brain. However, whether and how amyloids induce local pathology in the gastro-intestinal wall is not known. We identified a pathogenic program that becomes activated in the gastro-intestinal tract after exposure to amyloid {beta} and curli (the main bacterial amyloid), and show that enteric glia are responsible for creating an amyloid-induced pro-inflammatory environment. This insight of an early response in a distant, more accessible organ than the brain, may have important implications for both disease diagnosis and therapy.

neuroscience↗

bioRxiv2021

Prediction of biological age by morphological staging of sarcopenia in Caenorhabditis elegans

Sarcopenia encompasses a progressive decline in allover muscle quantity and quality. Given its close association with aging, it may represent a valuable healthspan marker. Given the strong commonalities with human muscle structure and the facile visualization possibilities, C. elegans represents an attractive model for studying the relationship between sarcopenia and healthspan. However, classical assessment relies on visual scoring of muscle architecture, which is subjective and inaccurate. To resolve this, we have developed an automated image analysis pipeline for the detailed quantification and classification of muscle integrity in confocal microscopy images from a cohort of aging myosin::GFP reporter strains. We then extracted a variety of morphological descriptors and found a subset to scale linearly with age. This allowed us to establish a general linear model that predicts biological age from a morphological muscle signature. To validate the model, we evaluated muscle architecture in long-lived worms that are known to experience delayed sarcopenia by targeted RNAi-mediated knockdown of the daf-2 gene. We conclude that quantitative microscopy allows for staging sarcopenia in C. elegans and will be of use for systematic screening for pharmacological or genetic modulators that mitigate age-related muscle frailty and thus improve healthspan in C. elegans.

bioinformatics↗