Biology subjects

Zomer, A.

Publications and source records attributed to Zomer, A..

8 recordsLinked to original sources

bioRxiv2026

Cancer-myeloid cell invasive program in pediatric-type diffuse high-grade glioma

Pediatric-type diffuse high-grade gliomas (pHGGs) are aggressive, heterogeneous brain tumors shaped by intricate cancer-microenvironment cell-cell interactions. Here, we present an integrative multimodal pHGGmap, encompassing over 800,000 cells from 136 patients profiled across transcriptomic, epigenomic, and spatial modalities. Its analysis delineated robust cancer-myeloid cell programs that structured the tumor ecosystem and identified ten distinct cancer cell states, including previously unrecognized developmental and context-responsive programs. Among these, radial glial-like (RG-like) cells exhibited dual stress-adapted and infiltrative phenotypes. Tumor-associated monocyte-derived macrophages and resident microglia engaged in four distinct immunomodulatory programs aligned with specific cancer states. Three conserved multicellular communities were maintained across treatment, including a stable, spatially and transcriptionally linked RG-like/complement-macrophage niche, indicative of cellular co-option and adaptation to support invasion. Longitudinal profiling of a metastatic diffuse midline glioma case showed that RG-like cells predominate during dissemination and remain associated with complement-enriched macrophages, whose reprogramming restores immune activation. pHGGmap establishes a landmark resource for translational discovery. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=183 SRC="FIGDIR/small/701142v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@7ae699org.highwire.dtl.DTLVardef@b95b92org.highwire.dtl.DTLVardef@12adcf9org.highwire.dtl.DTLVardef@1118703_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Single-cell spatial analysis of pediatric high-grade glioma reveals a novel population of SPP1+/GPNMB+ myeloid cells with immunosuppressive and tumor-promoting capabilities

BackgroundPediatric-type diffuse high-grade gliomas (pHGG) are a leading cause of pediatric cancer-related mortality. Although immunotherapy offers a promising treatment avenue, clinical responses in pHGG patients remain limited. A detailed understanding of the tumor immune microenvironment (TIME) is essential for advancing immunotherapeutic strategies. MethodsWe performed single-cell spatial analysis integrating cyclical immunofluorescence imaging and Spatial Molecular Imaging to interrogate the proteomic and transcriptomic landscape of pHGG. A tissue microarray comprising 32 diagnostic patient-derived pHGG samples was utilized to map the spatial distribution of immune and tumor cells. ResultsOur analyses reveal that the pHGG TIME is predominantly composed of myeloid cells, including brain-resident microglia and monocyte-derived macrophages, with only few T cells. A significant subset of these myeloid cells express mesenchymal-like genes and are positive for SPP1 and GPNMB. Spatial mapping further demonstrated that SPP1+/GPNMB+ myeloid cells localize in close proximity to mesenchymal-like tumor cells, and negatively correlate with the location and presence of CD8+ T cells. These cells also express genes related to immunosuppression and epithelial-to-mesenchymal transition, indicating their potential role in establishing an immunosuppressive niche. ConclusionsOur findings reveal a distinct immune landscape in pHGG characterized by SPP1+/GPNMB+ myeloid cells which may contribute to the exclusion of CD8+ T cells. This spatially resolved insight identifies these myeloid cells as promising therapeutic targets and provides a rationale for developing novel immunotherapeutic strategies to improve outcomes in pediatric high-grade gliomas.

cancer biology↗

bioRxiv2024

BEHAV3D Tumor Profiler to map heterogeneous cancer cell behavior in the tumor microenvironment

Intravital microscopy (IVM) enables live imaging of animals at single-cell level, offering essential insights into cancer progression. This technique allows for the observation of single-cell behaviors within their natural 3D tissue environments, shedding light on how genetic and microenvironmental changes influence the complex dynamics of tumors. IVM generates highly complex datasets that often exceed the analytical capacity of traditional uni-parametric approaches, which can neglect single-cell heterogeneous in vivo behavior and limit insights into microenvironmental influences on cellular behavior. To overcome these limitations, we present BEHAV3D Tumor Profiler (BEHAV3D-TP), a computational framework that enables unbiased single-cell classification based on a range of morphological, environmental and dynamic single cell features. BEHAV3D-TP integrates with widely used 2D and 3D image processing pipelines, enabling researchers without advanced computational expertise to profile cancer and healthy cell dynamics in IVM data. Here, we apply BEHAV3D-TP to study diffuse midline glioma (DMG), a highly aggressive pediatric brain tumor characterized by invasive progression. By extending BEHAV3D-TP to incorporate tumor microenvironment (TME) data from IVM or fixed correlative imaging, we demonstrate that distinct migratory behaviors of DMG cells are associated with specific TME components, including tumor-associated macrophages and vasculature. BEHAV3D-TP enhances the accessibility of computational tools for analyzing the complex behaviors of cancer cells and their interactions with the TME in IVM data.

cancer biology↗

bioRxiv2024

Prevotella timonensis degrades the vaginal epithelial glycocalyx through high fucosidase and sialidase activities

Bacterial vaginosis (BV) is a polymicrobial infection of the female reproductive tract (FRT). BV is characterized by replacement of health-associated Lactobacillus species by diverse anaerobic bacteria, including the well-known Gardnerella vaginalis. Prevotella timonensis and Prevotella bivia are anaerobes that are found in a significant percentage of BV patients, but their pathogenic properties are yet to be determined. Defining characteristics of anaerobic overgrowth in BV are adherence to the mucosal surface and the increased activity of mucin-degrading enzymes such as sialidases in vaginal secretions. Here, we demonstrate that P. timonensis but not P. bivia strongly adhered to vaginal and endocervical cells to a similar level as G. vaginalis but did not elicit a comparable pro-inflammatory response. The P. timonensis genome uniquely encodes a large set of mucus-degrading enzymes including 4 putative fucosidases and 2 putative sialidases, PtNanH1 and PtNanH2. Enzyme assays demonstrated that fucosidase and sialidase activity in P. timonensis cell-bound and secreted fractions was significantly higher than for other vaginal anaerobes. Infection assays revealed that P. timonensis fucosidases and sialidases efficiently removed fucose and 2,3- and 2,6-linked sialic acid moieties from the epithelial glycocalyx. Recombinantly expressed P. timonensis NanH1 and NanH2 efficiently removed 2,3 and 2,6-linked sialic acids from the epithelial surface and sialic acid removal by P. timonensis could be blocked using inhibitors. This study demonstrates that P. timonensis has distinct virulence properties that include initial adhesion and a high capacity for mucin degradation at the vaginal epithelial mucosal surface. Our results underline the importance of understanding the role of different anaerobic bacteria in BV. Significance statement (Layman)Bacterial vaginosis (BV) is a common vaginal infection that affects a high percentage of women and is associated with reduced fertility and increased risk of secondary infections. Gardnerella vaginalis is the most well-known BV-associated bacterium, but Prevotella species including P. timonensis and P. bivia may also play an important role. We showed that, similar to G. vaginalis, P. timonensis adhered well to the vaginal epithelium, suggesting that both bacteria could be important in the first stage of infection. Compared to the other bacteria, P. timonensis was unique in efficiently removing the protective mucin sugars that cover the vaginal epithelium. These results underscore that vaginal bacteria play different roles in the initiation and development of BV.

microbiology↗

bioRxiv2023

Graphite: painting genomes using a colored De Bruijn graph

The recent growth of microbial sequence data allows comparisons at unprecedented scales, enabling tracking of strains, mobile genetic elements, or genes. Querying a genome against a large reference database can easily yield thousands of matches that are tedious to interpret and pose computational challenges. We developed Graphite that uses a colored De Bruijn graph (cDBG) to paint query genomes, selecting the local best matches along the full query length. By focusing on the closest genomic match of each query region, Graphite reduces the number of matches while providing promising leads for genomic forensics. When applied to hundreds of Campylobacter genomes we found extensive gene sharing, including a previously undetected C. coli plasmid that matched a C. jejuni chromosome. Together, genome painting using cDBGs as enabled by Graphite, can reveal new biological phenomena by mitigating computational hurdles. Graphite is implemented in Julia, available at https://github.com/MGXlab/Graphite.

bioinformatics↗

bioRxiv2021

Comparative analysis of L-fucose utilization and its impact on growth and survival of Campylobacter isolates

Campylobacter jejuni and Campylobacter coli were previously considered asaccharolytic, but are now known to possess specific saccharides metabolization pathways, including L-fucose. To investigate the influence of the L-fucose utilization cluster on Campylobacter growth, survival and metabolism, we performed comparative genotyping and phenotyping of the C. jejuni reference isolate NCTC11168 (human isolate), C. jejuni Ca1352 (chicken meat isolate), C. jejuni Ca2426 (sheep isolate), and C. coli Ca0121 (pig manure isolate), that all possess the L-fucose utilization cluster. All isolates showed enhanced survival and prolonged spiral cell morphology in aging cultures up to day seven in L-fucose-enriched MEM medium (MEMF) compared to MEM. HPLC analysis indicated L-fucose utilization linked to acetate, lactate, pyruvate and succinate production, confirming the activation of the L-fucose pathway in these isolates. Highest consumption of L-fucose by C. coli Ca0121, is conceivably linked to its enhanced growth performance up to day 7, reaching 9.3 log CFU/ml compared to approximately 8.3 log CFU/ml for the C. jejuni isolates. Genetic analysis of their respective L-fucose clusters revealed several differences, including a 1 bp deletion in the Cj0489 gene of C. jejuni NCTC11168, causing a frameshift in this isolate resulting in two separate genes, Cj0489 and Cj0490, while no apparent phenotype could be linked to the presumed frameshift in the NCTC11168 isolate. Additionally, we found that the L-fucose cluster of C. coli Ca0121 was most distant from C. jejuni NCTC11168, but confirmation of links to L-fucose metabolism associated phenotypic traits in C. coli versus C. jejuni isolates requires further studies. ImportanceCampylobacter is the leading cause of gastroenteritis in humans worldwide, with increasing incidence and prevalence in recent years. The most prevalent species are Campylobacter jejuni and C. coli with 83% and 10% of all Campylobacter cases, respectively. Previously it was found that the majority of Campylobacter isolates are able to metabolize L-fucose (fuc+ isolates), a sugar that is widely present in the human gut. Putative roles for L-fucose in fuc+ C. jejuni isolates were found in growth, biofilm formation and virulence. Despite this, relatively little is known about L-fucose metabolism and the impact on growth and survival in fuc+ Campylobacter isolates. The results from our comparative genotyping and phenotyping study demonstrate that L-fucose, in both C. jejuni and C. coli fuc+ isolates, is involved in enhanced survival, prolonged spiral cell morphology and changes in the general metabolism. Possible links between phenotypes and differences in respective L-fucose gene clusters are discussed.

microbiology↗

bioRxiv2019

Whole genome sequencing of dog specific assemblages C and D of Giardia duodenalis from single and pooled cysts indicates host associated genes

Giardia duodenalis (Syn. G. intestinalis or G. lamblia) infects over 280 million people each year and numerous animals. G. duodenalis can be subdivided into 8 assemblages with different host specificity. Unculturable assemblages have so far resisted genome sequencing efforts. In this study we isolated single and pooled cysts of assemblage C and D from dog faeces by FACS and sequenced them using multiple displacement amplification and Illumina paired end sequencing. The genomes of assemblages C and D were compared with genomes of assemblages A and B from humans and assemblage E from ruminants and pigs. The genomes obtained from the pooled cysts and from the single cysts were considered complete (>99% marker genes observed) and the allelic sequence heterozygosity (ASH) of assemblage C and D was 0.89% and 0.74%, respectively. Higher than for assemblage B (> 0.43%) and much higher than for assemblages A and E (<0.01%). The flavohemoglobin and 4Fe-4S binding domain family gene involved in O2 and NO detoxification were only present in assemblages A, B and E. Cathepsin-B orthologs were found in all genomes. Six clades of cathepsin-B orthologs contained one gene of each genome, while in three clades not all assemblages were represented. We conclude that whole genome sequencing from a single Giardia cyst results in complete draft genomes making the genomes of unculturable Giardia assemblages accessible. Observed differences between the genomes of assemblage C and D on one hand and the assemblages A, B and E on the other hand are possibly associated with host specificity.

molecular biology↗

bioRxiv2016

Genome-Wide Fitness Analyses of the Foodborne Pathogen Campylobacter jejuni in In Vitro and In Vivo Models

Infection by Campylobacter is recognised as the most common cause of foodborne bacterial illness worldwide. Faecal contamination of meat, especially chicken, during processing represents a key route of transmission to humans. There is currently no licenced vaccine and no Campylobacter-resistant chickens. In addition, preventative measures aimed at reducing environmental contamination and exposure of chickens to Campylobacter jejuni (biosecurity) have been ineffective. There is much interest in the factors/mechanisms that drive C. jejuni colonisation and infection of animals, and survival in the environment. It is anticipated that understanding these mechanisms will guide the development of effective intervention strategies to reduce the burden of C. jejuni infection. Here we present a comprehensive analysis of C. jejuni fitness during growth and survival within and outside hosts. A comparative analysis of transposon (Tn) gene inactivation libraries in three C. jejuni strains by Tn-seq demonstrated that a large proportion, 331 genes, of the C. jejuni genome is dedicated to (in vitro) growth. An extensive Tn library in C. jejuni M1cam (~10,000 mutants) was screened for the colonisation of commercial broiler chickens, survival in houseflies and under nutrient-rich and-poor conditions at low temperature, and infection of human gut epithelial cells. We report C. jejuni factors essential throughout its life cycle and we have identified genes that fulfil important roles across multiple conditions, including maf3, fliW, fliD, pflB and capM, as well as novel genes uniquely implicated in survival outside hosts. Taking a comprehensive screening approach has confirmed previous studies, that the flagella are central to the ability of C. jejuni to interact with its hosts. Future efforts should focus on how to exploit this knowledge to effectively control infections caused by C. jejuni.\n\nAuthor SummaryCampylobacter jejuni is the leading bacterial cause of human diarrhoeal disease. C. jejuni encounters and has to overcome a wide range of \"stress\" conditions whilst passing through the gastrointestinal tract of humans and other animals, during processing of food products, on/in food and in the environment. We have taken a comprehensive approach to understand the basis of C. jejuni growth and within/outside host survival, with the aim to inform future development of intervention strategies. Using a genome-wide transposon gene inactivation approach we identified genes core to the growth of C. jejuni. We also determined genes that were required during the colonisation of chickens, survival in the housefly and under nutrient-rich and -poor conditions at low temperature, and during interaction with human gut epithelial tissue culture cells. This study provides a comprehensive dataset linking C. jejuni genes to growth and survival in models relevant to its life cycle. Genes important across multiple models were identified as well as genes only required under specific conditions. We identified that a large proportion of the C. jejuni genome is dedicated to growth and that the flagella fulfil a prominent role in the interaction with hosts. Our data will aid development of effective control strategies.

microbiology↗