Biology subjects

Jacob, J.

Publications and source records attributed to Jacob, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Resource Mismatch in Phototrophic Subaerial Biofilms and Resulting Phototroph/Heterotroph Ratios

Photosynthesis-driven microbial communities are frequently observed on air-exposed stone such as, for example, marble surfaces. These environments are stark, subject to varying water, temperature, UV and other stresses. As a consequence, resident microbes likely have significant maintenance requirements. Those microbes however, have access to plentiful energy when conditions are favorable for photosynthesis. High rates of photosynthesis for purposes of energy generation may also generate excess organic carbon which can be released as extracellular overflow, becoming available for heterotrophic organisms. Here we propose a simple model to explore possible consequences of this hypothesized resource mismatch. The model predicts that heterotrophs can invade purely phototrophic communities, with the resulting mixed community eventually approaching a phototroph/heterotroph ratio at steady state as a consequence of stoichiometric balance. Results from field observations at three geographically separated sites (Lincoln Memorial, Washington D.C., Merchants' Exchange, Philadelphia PA, and the Federal Hall National Memorial, New York NY), analyzed using two independent methods, are seen to match model predictions, demonstrating both cyanobacterial dominated communities as well as, mostly, mixed communities with a heterotrophs-to-cyanobacteria biovolume ratio of approximately 0.4.

microbiology↗

bioRxiv2026

Characterization of artificial riboswitches for Coxsackievirus B3 detection using machine learning

With the increase of recycled water to offset water demand, the potential possibility to spread contagious RNA viruses, such as Coxsackievirus B3, increases. However, detection of viral particles remains challenging because of low viral concentrations in wastewater and high mutation rates of the RNA virus. Robust monitoring is needed with low cost and low infrastructure technologies to increase accessibility of monitoring technologies worldwide. Novel viral detection methods have been developed, based on synthetic riboswitches that bind to the target virus and trigger a reporter gene, thus amplifying the detection signals. Such monitoring technologies can leverage machine learning to optimize the candidate nucleic acid sequences used for detection. To support the design of effective riboswitches, we present a machine learning model for classifying riboswitch performance, integrating RNA sequence data with secondary structural features based on free energy calculations and parameters that represent single strandedness. This model uses a sparsely gated Mixture of Experts (MoE) architecture to route sequence and thermodynamic features to specialized experts, achieving strong generalization performance across cross-validation and held-out testing. When evaluated against baseline Decision Tree, Random Forest, Gaussian Naive Bayes, and Dense Neural Network classifiers, the MoE model demonstrated near-zero classification errors. Furthermore, post-hoc feature importance and k-mer analyzes reveal that near-perfect predictive performance in silico is strongly driven by sequence constructs in addition to generalizable folding mechanics. An ablation study of numerical feature and sequence inputs showed that while the Dense Neural Network also achieved high accuracy across all ablation conditions, the MoE architecture was retained as the primary model because its specialized subnetworks do not require all model parameters to be activated offering a potential computational advantage.

bioinformatics↗

bioRxiv2026

Detection and characterisation of alpha- and betacoronaviruses in rodents and bats from Germany, France, Belgium and Ireland

Recent zoonotic coronavirus outbreaks have sparked an interest in understanding coronaviruses circulating in animal reservoirs. While bats are recognised as major reservoirs for these viruses, coronaviruses have also been detected in a wide range of terrestrial small mammals, particularly rodents. However, coronavirus diversity in these mammals, specifically in Europe, is still poorly characterised. In this study, we detected and characterised coronaviruses in terrestrial small mammals and bats from Belgium, France, Germany, and Ireland. We screened tissue samples from rodents and shrews and environmental bat guano using pan-coronavirus real-time and conventional PCRs, with positive results confirmed by sanger sequencing. Among 2667 bat and 1152 terrestrial mammal samples, we detected 59 positive samples, 36 from bats and 23 from rodents, from which we recovered 60 coronavirus sequences, spanning both Alphacoronavirus and Betacoronavirus lineages. Through next generation sequencing we identified one Pipistrellus pygmaeus bat guano sample carrying two distinct alphacoronaviruses, representing Nyctacovirus and Pedacovirus subgenera. Among rodents, most coronavirus-positive samples originated from a zoo in Belgium, where several CoV lineages co-circulated. The identified rodent coronaviruses clustered among previously described rodent-associated lineages, some of which also include human and other mammal-derived coronavirus sequences. Consistent with previous studies, we found sarbecoviruses in horseshoe bats (particularly Rhinolophus ferrumequinum and R. hipposideros) and merbecoviruses in Plecotus auritus bats, and these viruses are distantly related to the human coronaviruses of the respective families. Similar to bat coronaviruses, some rodent coronaviruses strains seemed to be association with specific rodent species. In conclusion, our study enhances the understanding of coronaviruses in rodents and bats, revealing potential hotspots for these viruses and their implication for human and animal health. These findings underscore the necessity for continued surveillance of coronaviruses in wildlife reservoirs to mitigate future zoonotic spillover risks.

microbiology↗

bioRxiv2026

BigHeart: Mapping connectivity in the adult human heart at the micron scale

The human heart depends on coordinated muscular, electrical, vascular, lymphatic, and neural systems, but their three-dimensional relationships remain unresolved at microscopic resolution across an intact adult organ. Using hierarchical phase-contrast tomography, we generated a continuous three-dimensional structural reference of a whole adult human heart at 8.01 micrometer isotropic voxel size, without sectioning or staining. Organ-wide imaging revealed hierarchical myocardial architecture, and quantitative orientation analysis identified regional differences in myocardial cell aggregate organization. The atrioventricular conduction axis was traced into a distinct subendocardial Purkinje network interfacing with working myocardium. Integrated segmentation showed that coronary vessels, lymphatic collectors, and autonomic nerves occupy shared epicardial corridors. This publicly accessible dataset integrates cardiac systems within a common spatial framework for anatomy, computational modeling, and future molecular atlases.

physiology↗

bioRxiv2026

Multi-omics reveals a monocyte-macrophage-fibroblast axis in post-COVID-19 fibroinflammatory lung remodelling

Post-COVID-19 residual lung abnormalities (RLA) are associated with persistent respiratory symptoms and radiological changes, yet the underlying mechanisms remain unclear. We performed integrated multi-omic profiling of paired bronchoalveolar lavage and blood samples from patients with post-COVID-19 RLA and healthy controls, combining single-cell RNA sequencing, CITE-seq, single-cell T cell receptor sequencing, bronchoalveolar lavage fluid proteomics and functional fibroblast assays. In post-COVID-19 RLA lungs, we identified an increased abundance of profibrotic SPP1hi monocyte-derived alveolar macrophages, arising from an expanded circulating HLA-DRlowCD163+PDE4Dhi classical monocyte progenitor population, supporting a blood-lung myeloid axis. Cell-cell communication modelling positioned macrophages as central hubs of immune-stromal crosstalk, promoting monocyte recruitment with profibrotic priming, and fibroblast activation. Proteomic analysis of bronchoalveolar lavage fluid from post-COVID-19 RLA and idiopathic pulmonary fibrosis, compared with healthy controls, revealed shared and distinct signatures. These alveolar proteins in post-COVID-19 RLA were predominantly attributed to myeloid cells and predicted to engage fibroblast receptors. Bronchoalveolar lavage fluid induced fibroblast proliferation, differentiation and collagen deposition in vitro, with proliferation attenuated by the antifibrotic drug nintedanib. We also identified compartment-specific lymphoid dysregulation, including depletion of mucosal-associated invariant T (MAIT) cells in both the lung and blood, decreased natural killer (NK) cells with oligoclonal T cell expansion in the lung, and expansion of regulatory and cytotoxic T cells in the blood. These findings support a persistent monocyte-macrophage-fibroblast axis linking immune dysregulation to fibroproliferative remodelling after COVID-19 and highlights candidate therapeutic targets for post-viral lung fibrosis. We provide a publicly available atlas (on publication).

systems biology↗

bioRxiv2026

Alpha-2-Macroglobulin/LRP1 signaling promotes mitochondrial clearance and autophagic extracellular vesicle release in erythroid cells

Despite advances in the understanding of the cellular and molecular mechanisms involved in erythropoiesis, there are still unanswered questions regarding the coordination between autophagy, vesicular trafficking, and endocytic signaling during this process. The complexity of these events suggests the existence of regulatory mechanisms capable of integrating these pathways. In this context, low-density lipoprotein receptor-related protein 1 (LRP1) emerges as a potential modulator given its function as a multifunctional endocytic receptor and its involvement in the regulation of degradation and signaling processes in various cellular models. However, its role in modulating mitophagy, a particular type of autophagy, and its link to vesicular trafficking associated with multivesicular bodies (MVBs) and the release of exosomes during erythroid maturation has been poorly explored. In this regard, alpha-2-Macroglobulin (2M), the main physiological ligand of LRP1, has been identified in extracellular vesicles (EVs) in various pathophysiological contexts, suggesting that it may be involved in vesicular dynamics and cellular clearance. In this study, we demonstrate that activated 2M (2M*), induces autophagy and particularly mitophagy, in K562 cells, and that LRP1 is directly responsible for this activation. Furthermore, we observed that 2M* stimulates the interaction of autophagosomes with MVBs/amphisomes and that EVs from K562 cells are positive for LC3, supporting a close relationship between the endocytic pathway and the autophagic pathway mediated by the 2M-LRP1 interaction. Taken together, these findings expand our understanding of erythroid biology and provide a conceptual foundation for exploring altered mechanisms in erythropoietic diseases and for the development of diagnostic and therapeutic strategies.

Molecular Biology↗

bioRxiv2026

Neuroanatomy of the clitoris

The clitoris is one of the least studied organs of the human body. The detailed anatomy of the clitoris is challenging to address through a gross dissection, as most of its parts are embedded internally, surrounded by pubic bone and several pelvic organs. While clinical imaging methods such as magnetic resonance imaging can capture the gross 3D morphology, they lack the spatial resolution required to resolve the detailed structures. In this study, we generated micron-scale computed tomography images of the female pelvises, leveraging a synchrotron radiation X-ray source. This unique data revealed the complex trajectory of the dorsal nerve of the clitoris, the main sensory nerve of the clitoris. Notably, the nerve trunks within the clitoral glans were revealed, with the maximum diameter ranging from 0.2 to 0.7 mm. They showed a tree-like branching pattern projecting towards the surface of the glans. We also revealed that some branches of the dorsal nerve of the clitoris ramify to innervate the clitoral hood and mons pubis. Finally, the posterior labial nerve, a branch of the perineal nerves, was shown to innervate the surroundings of the clitoris and the labial structures. These findings have an immediate impact on operations performed around the vulva area, such as gender-affirmation surgery and reconstruction surgery after genital mutilation.

neuroscience↗

bioRxiv2026

Comparison of Biofilm quantification in strains of Candida auris and Candida albicans evaluated by means of Crystal violet, MTT, ATP and NBTZ/BCIP Assays.

The study presented here shows Biofilm quantification in microtiter plates in strains of Candida auris and Candida albicans evaluated by means of Crystal violet, MTT, ATP-Luminescence and NBTZ/BCIP assays. The results showed significant differences in biofilm formation between Candida auris and Candida albicans but also within Candida auris outbreak strains in contrast to Candida auris DSM 21092 reference strain.

microbiology↗

bioRxiv2026

From Stress to Survival: Trophoblast-Derived Extracellular Vesicle Proteome Captures Aspirin-Driven Cellular Reprogramming in a Preeclampsia Model.

BackgroundLow-dose aspirin (LDA) reduces preeclampsia (PE) risk by up to 40%, yet its molecular effects on chorion trophoblast cells (CTCs) a fetal membrane lineage at the feto-maternal interface remain obscure. CTCs form a structural and immunoregulatory barrier whose dysfunction drives inflammation-associated membrane pathology in PE. Extracellular vesicles (EVs) released by CTCs may encode cellular stress and adaptation states, offering a molecular window into aspirins timing-dependent effects on PE risk modification. MethodsHuman CTCs were challenged with cigarette smoke extract (CSE) to model oxidative stress-driven PE pathology. Two paradigms were tested: (1) prophylactic aspirin (4 and 40 {micro}g/ml) before and/or flanking CSE, and (2) therapeutic aspirin after CSE challenge. EVs were isolated via ultracentrifugation and size exclusion chromatography, characterized by nanoparticle tracking and immunoblotting, and profiled by quantitative mass spectrometry. Network pathway analysis and machine-learning biomarker selection defined EV-encoded molecular states. ResultsCTC-derived EVs from CSE-exposed cells carried a PE-like proteomic signature marked by suppressed VEGF/ECM remodeling, activated TNF-p53 apoptotic signaling, and heightened inflammation. Prophylactic low-dose aspirin shifted EV cargo toward preserved angiogenic capacity (VEGFA, COL1A1, MMP14) with attenuated apoptotic and NF-{kappa}B signatures. High-dose aspirin produced broad transcriptional suppression without vascular benefit in EVs. Therapeutic aspirin partially rescued injury-associated EV cargo but failed to restore angiogenic signatures. Machine-learning analysis of EV proteomes identified a prophylactic biomarker panel anchored by HSPA8, SERPINF2, COL4A1, and PLOD1, linked to angiogenic recovery and redox balance. ConclusionsCTC-derived EV proteomic signatures capture dose-and timing-dependent aspirin effects, positioning the chorion as a pharmacological "secondary responder" favoring cellular resilience over classical anti-inflammatory suppression. EV-based molecular profiling might offer a framework for stratifying aspirin responders from non-responders toward personalized PE prevention.

cell biology↗

bioRxiv2026

Hierarchical Phase-Contrast Tomography Imaging: Applicability in biomedical research

ObjectivesHierarchical Phase-Contrast Tomography (HiP-CT) enables non-destructive, multi-scale imaging of whole human organs. We describe how HiP-CT is utilized for biomedical research within the Human Organ Atlas Hub through three case studies: mapping the enteric nervous system (ENS) of the human colon, analysing myocardial and AV conduction architecture in Tetralogy of Fallot (TOF), and characterizing ductal organization in breast carcinoma. The challenges we faced with this novel biomedical data are discussed. MethodsWhole-organ and region-of-interest scans of three types of human organs were acquired at the European Synchrotron Radiation Facility (ESRF) with isotropic voxel sizes ranging from 20 {micro}m to 0.8 {micro}m. For the colon, voxel binning and RootPainter were employed to tackle data size to segment the ENS. For the heart, voxel-wise myocyte orientation mapping was calculated in terabyte-scale datasets with a high-performance computational framework (Cardiotensor). Breast carcinoma samples were correlated with histopathology for structure validation. ResultsHiP-CT revealed the large-scale organization of the ENS in the colon, enabling visualisation of the 3D structures of the ENS across the colon In TOF hearts, analysis uncovered abnormal myocardial structure and heterogeneous conduction system morphology. In breast carcinoma, HiP-CT resolved the full hierarchy of ductal structures and vascular relationships within tumour and peritumoral regions. ConclusionsHiP-CT provides unprecedented, hierarchical insight into intact human organ structure, bridging the gap between histology and radiology. Advances in knowledgeHiP-CT establishes a new ex vivo radiological modality capable of linking microscale pathology to whole-organ context, advancing translational research in neurogastroenterology, cardiology, and oncology

biophysics↗

bioRxiv2025

The Human Organ Atlas

We present the Human Organ Atlas (HOA), an open data repository making accessible multiscale 3D imaging of human organs. The repository also provides software tools and training resources enabling worldwide access, sharing, and analysis of these datasets, facilitating further research and the continued expansion of the HOA. The images are generated using a synchrotron imaging technique - Hierarchical Phase-Contrast Tomography (HiP-CT) that uses the ESRFs Extremely Brilliant Source, spanning whole organ imaging at around 20 m/voxel with local volumes of interest within the intact organs imaged down to [~] 1 m/voxel. This offers a comprehensive exploration of human anatomy, providing unparalleled insights into intricate structures and spatial relationships. The Human Organ Atlas offers researchers, clinicians, and educators a valuable resource for anatomical study, image analysis, medical education, and large-scale data mining.

bioinformatics↗

bioRxiv2025

The pleuroparenchymal fibroelastosis atlas reveals aberrant cell states and their zonation as an alternate roadmap to lung fibrosis

BackgroundPleuroparenchymal fibroelastosis (PPFE) is a progressive interstitial lung disease with higher prevalence in females, histologically characterized by intra-alveolar fibrosis with septal elastosis (AFE). Effective treatments are lacking, highlighting the need to dissect its pathogenesis at single-cell resolution. MethodsWe performed single-nucleus RNA sequencing (snRNAseq) on explanted lungs from a German (n=23) and a French cohort (n=17) of PPFE patients, and controls (n=16). Identified cell populations were localized by immunofluorescence and multiplex RNA in-situ hybridization. Hierarchical phase-contrast computed tomography (HiP-CT) and micro-CT provided 3D spatial context. Reanalyzed snRNAseq data from a Belgian IPF cohort (n=9) served as disease comparator. FindingsWe present the first snRNAseq atlas of PPFEs cellular and structural landscape based on a European multinational cohort. 24 PPFE patients were female (60.0%), while 34 were non-smokers (85.0%). 519,920 nuclear transcriptomes from PPFE and IPF patients, and controls were profiled. We identified PPFE-specific accumulations of MFAP5+PI16+SFRP2+ adventitial and LEPR+ITGA8+SFRP2+DIO2+ elastofibrotic fibroblasts as main drivers of elastotic remodeling in PPFE. Multiple PPFE fibroblast subsets acquire an inflammatory activation state as highlighted by the expression of CXCL12 and CXCL14. This is accompanied by a marked increase in lymphocytes and the formation of tertiary lymphoid structures (TLS) in a disease that was previously considered to be purely elastofibrotic. We identified CTHRC1+ fibrotic fibroblasts and Aberrant Basaloid cells in PPFE as well, forming the "Usual Fibrotic Niche". 3D reconstruction of the pronounced COL15A1+ vascular conglomerate at the border of the elastofibrotic and subpleural fibrosis indicates communication with interlobar veins. Last, we observed a zonation of the PPFE lesion, constructed by the above-mentioned PPFE-associated cell types. InterpretationOur unprecedented cellular and molecular survey uncovers previously unobserved PPFE-specific inflammatory and elastogenic fibroblast populations, as well as the presence of CTHRC1+ fibroblasts and Aberrant Basaloid cells common to other fibrotic ILDs. These findings provide the foundation for including PPFE patients in current antifibrotic trials, as well as development of PPFE-specific therapies. FundingSupported mainly by the Else Kroner-Fresenius Foundation, the German Center for Lung Research and the Fondation du Souffle.

cell biology↗

bioRxiv2024

Drivers of host-pathogen community assemblies in European forests and urban green spaces

Major advances in the understanding of infectious diseases have been achieved in the last decades. However, the persistence and re-emergence of pathogens continue to raise public and veterinary health concerns, of which the recent COVID-19 pandemic may be one of the most dramatic examples. Understanding the impact of habitat alterations and concomitant biodiversity loss on pathogen transmission and emergence from wildlife remains challenging. Here, we aim to elucidate the interlinkages between biodiversity and rodent-borne diseases at local and European scales. We present recently collected host-pathogen data from 21 temperate forest sites and eight urban green spaces throughout five European countries, environments where rodents are abundant and human/domestic animals - wildlife interactions are likely to occur. 3766 specimens were analyzed during the period from 2020 to 2022 comprising 15 different small mammal species. Different organ tissues of each specimen were screened for bacteria by either 16S rRNA amplicon sequencing or specific PCR. The presence of antibodies to different families of viruses was screened using immunofluorescent assays. A multitude of pathogens of zoonotic potential from several genera including Bartonella, Borrelia, Mycoplasma, Anaplasma, Neoehrlichia, Leptospira, Orthohantavirus and Orthopoxvirus were detected at non-negligible prevalence in 11 different terrestrial mammal species. A shift in host community composition was observed along the anthropization gradient with more urban adapters in more anthropized sites. Pathogen richness increased with an increase in host species diversity, following the "host-diversity begets parasite-diversity" hypothesis. The absence of some vector-transmitted parasites in urban areas suggests a shift in pathogen community along the anthropization gradient. Host species and host intrinsic factors were dominant explanatory variables for endoparasitic Mycoplasma species and Sarcocystidae, while extrinsic environmental and climatic factors where influential in explaining variations in occurrences of several vector-transmitted pathogens. Apodemus sylvaticus and Clethrionomys glareolus were important connector host species in respectively urban green spaces and temperate forests. Increased host diversity, but not anthropization, correlated with a richer pathogen community. These results ultimately lead to an increased understanding of the complex host-pathogen system at the local landscape that can aid future management decisions and support the public health sector.

ecology↗

bioRxiv2024

Tube2FEM: a general-purpose highly-automated pipeline for flow related processes in (embedded) tubular objects

This paper presents a comprehensive and highly-automated open-source pipeline for simulating flow and flow-related processes in (embedded) tubular structures. Addressing a critical gap in computational fluid dynamics (CFD) and simulation sciences, it facilitates the transition from raw three-dimensional imaging, graph networks, or CAD models of tubular objects to refined, simulation-ready meshes. This transition, traditionally labor-intensive and challenging, is streamlined and highly-automated through a series of innovative steps that include surface mesh processing, centre-line construction, anisotropic mesh generation, and volumetric meshing, leading to Finite Element Method (FEM) simulations. The pipeline leverages a range of open-source software and libraries, notably GIBBON, FEniCS, and Paraview, to provide flexibility and broad applicability across different simulation scenarios, ranging from biomedical to industrial applications. We demonstrate the versatility of our approach through five distinct applications, including the mesh generation for soil-root systems, lung airways, microcirculation networks, and portal vein networks, each originating from a different data source. Moreover, for several of these cases, we incorporate Computational Fluid Dynamics (CFD) simulations and strategies for 3D-1D coupling between the embedding domain and the embedded structures. Finally, we outline some future perspectives aimed at enhancing accuracy, reducing computational time, and incorporating advanced modeling and boundary condition strategies to further refine the frameworks capabilities.

bioengineering↗

bioRxiv2024

Flexible Cell Modeling Using Frequency Modulation

Computational models of the cell can be used to study the impact of drugs and assess pathological risks. Typically, computational models are computationally demanding or difficult to implement in dedicated hardware for real-time emulation. A new Frequency Modulation (FM) model is proposed to address these limitations. This new model utilizes a single sine generator with constant amplitude, but phase/frequency is modulated to emulate an action potential (AP). The crucial element of this model is the identification of the modulating signal. Focusing on FPGA implementation, we have utilized a piecewise linear polynomial with a fixed number of breakpoints to serve as a modulating signal. The ability to adapt this modulating signal permits the emulation of dynamic properties and coupling of cells. We have introduced a state controller that handles both of these requirements. The building blocks of the FM model have direct integer equivalents and are amenable to implementation on digital platforms like Field Programming Gate Arrays (FPGA). We have demonstrated wavefront propagation of our model in 1-D and 2-D models of a tissue. Various parameters were used to quantify the wavefront propagation in 2-D tissues. We also emulate some cellular dysfunctions. The FM model can replicate any detailed cell model and emulate its corresponding tissue model. Overall, the results depict that the FM model has the potency for real-time cell and tissue emulation on an FPGA.

bioengineering↗

bioRxiv2024

Sonic hedgehog medulloblastoma cells in co-culture with cerebellar organoids converge towards in vivo malignant cell states

BackgroundIn the malignant brain tumour sonic hedgehog medulloblastoma (SHH-MB) the properties of cancer cells are influenced by their microenvironment, but the nature of those effects and the phenotypic consequences for the tumour are poorly understood. The aim of this study was to identify phenotypic properties of SHH-MB cells that were driven by the non-malignant tumour microenvironment. MethodsHuman induced pluripotent cells (iPSC) were differentiated to cerebellar organoids to simulate the non-malignant tumour microenvironment. Tumour spheroids were generated from two distinct, long-established SHH-MB cell lines which were co-cultured with cerebellar organoids. We profiled the cellular transcriptomes of malignant and non-malignant cells by performing droplet-based single-cell RNA-sequencing (scRNA-seq). The transcriptional profiles of tumour cells in co-culture were compared with those of malignant cells cultured in isolation and with public SHH-MB datasets of patient tumours and patient-derived xenograft (PDX) models. ResultsSHH-MB cell lines in organoid co-culture adopted patient tumour-associated phenotypes and showed increased heterogeneity compared to monocultures. Sub-populations of co-cultured SHH-MB cells activated a key marker of differentiating granule cells, NEUROD1 that was not observed in tumour monocultures. Other sub-populations expressed transcriptional determinants consistent with a cancer stem cell (CSC)-like state that resembled cell states identified in vivo. ConclusionFor SHH-MB cell lines in co-culture, there was a convergence of malignant cell states towards patterns of heterogeneity in patient tumours and PDX models implying these states were non-cell autonomously induced by the microenvironment. Therefore, we have generated an advanced, novel in vitro model of SHH-MB with potential translational applications.

cancer biology↗

bioRxiv2024

Antibody-drug conjugates targeting EGFR ligand Epiregulin inhibit colorectal tumor growth irrespective of RAS mutational status

As colorectal cancer (CRC) remains a leading cause of cancer-related death, identifying therapeutic targets and approaches is essential to improve patient outcomes. The EGFR ligand epiregulin (EREG) is highly expressed in RAS wildtype and mutant CRC with minimal expression in normal tissues, making it an attractive target for antibody-drug conjugate (ADC) development. In this study, we produced and purified an EREG monoclonal antibody (mAb), H231, that had high specificity and affinity for human and mouse EREG. H231 also internalized to lysosomes, which is important for ADC payload release. ImmunoPET and ex vivo biodistribution studies showed significant tumor uptake of 89Zr-labeled H231 with minimal uptake in normal tissues. H231 was conjugated to either cleavable dipeptide or tripeptide chemical linkers attached to the DNA-alkylating payload duocarmycin DM, and cytotoxicity of EREG ADCs was assessed in a panel of CRC cell lines. EREG ADCs incorporating tripeptide linkers demonstrated the highest potency in EREG-expressing CRC cells irrespective of RAS mutations. Preclinical safety and efficacy studies showed EREG ADCs were well-tolerated, neutralized EGFR pathway activity, caused significant tumor growth inhibition or regression, and increased survival in CRC cell line and patient-derived xenograft models. These data suggest EREG is a promising target for the development of ADCs for treating CRC and other cancer types that express high levels of EREG. While the efficacy of clinically approved anti-EGFR mAbs are largely limited by RAS mutational status, EREG ADCs may show promise for both RAS mutant and wildtype patients, thus improving existing treatment options. Significance: EREG-targeting antibody-drug conjugates demonstrate acceptable safety and robust therapeutic efficacy in RAS mutant and wildtype colorectal cancer, suggesting their potential as an alternative to EGFR-targeted therapy to benefit a broader patient population.

cancer biology↗

bioRxiv2024

On the ecology of Acinetobacter baumannii - jet stream rider and opportunist by nature

The natural reservoirs of the nosocomial pathogen Acinetobacter baumannii are not well defined. We previously identified white storks as a model system to study the ecology of A. baumannii. Having screened more than 1,300 white stork nestlings over a period of six years across different regions of Poland and Germany (overall isolation rate of [~]29.5%), including food chain analyses and environmental samplings, we come up with a detailed picture of the dynamics and diversity of A. baumannii in their natural habitats. Adult storks, rather than being stably colonized with strains of A. baumannii which are successively transferred to their offspring, instead initially encounter these bacteria while foraging. Among their common food sources, consisting of earthworms, small mammals, and insects, we identified earthworms as a potential source of A. baumannii, but more so the associated soil as well as plant roots. Through this, hotspot soil and compost habitats were identified which enable population dynamics to be studied over the course of the year. We demonstrate that sterilized plant material is rapidly colonized by airborne A. baumannii suggesting they patrol to search for novel habitats, being opportunist by nature. The prevalence of A. baumannii exhibited a strong seasonality and peaked during summer. The strains we collected in Poland and Germany represent more than 50% of the worldwide known diversity in terms of the intrinsic OXA-51-like {beta}-lactamase. A set of [~]400 genomes was determined and compared to a diverse set of publicly available genomes. Our pan-genome estimate of the species ([~]51,000 unique genes) more than doubles the amount proposed by previous studies. Core-genome based phylogenetic analyses illustrated numerous links between wildlife isolates and hospital strains, including ancient as well as recent intercontinental transfer. Our data further suggest massive radiation within the species early after its emergence, matching with human activity during the Neolithic. Deforestation in particular seemed to set the stage for this bloom as we found that forests do not provide conducive conditions for the proliferation of A. baumannii. In contrast, wet and nutrient-rich soil alongside rivers sampled during the summer can yield an isolation rate of [~]30%. Linking published work on the interaction between A. baumannii and fungi and on aspergillosis as a major cause of mortality in white stork nestlings to our findings, we hypothesized that fungi and A. baumannii share a long history of coevolution. Interaction studies revealed the capability of A. baumannii to adhere to fungal spores and to suppress spore germination. Taken together, the intrinsic resistance endowment and potential to acquire antibiotic resistance can be explained by coevolution with antibiotic-producing fungi and other microorganisms within soil, and resistance to desiccation stress and radiation can be interpreted in the light of intercontinental hitchhiking through fungal spores. Originality - SignificanceThe ecology of the nosocomial pathogen Acinetobacter baumannii remains poorly understood outside the hospital. Here, we present the most comprehensive study on its environmental biology to date, after having collected more than 1,450 independent isolates of which around 400 were whole genome-sequenced. This study more than doubles the size of the pan-genome of the species, illustrating both the diversity of our collection and the bias of previous work, but also the bottleneck for the establishment of lineages within the hospital environment. We reached isolation rates of about 30% both in white stork (Ciconia ciconia) nestlings and in soil samples when considering for sampling all preferences of A. baumannii we uncovered. Thus, it is now possible to study the ecology and evolution of A. baumannii in nature at an unprecedented temporal and spatial resolution. We describe the worldwide spread of A. baumannii lineages in nature as an ancient phenomenon that even surpasses that of human-associated bacteria in magnitude. This is likely due to airborne spread, putatively facilitated by association with fungal spores. We propose that A. baumannii is an opportunist by nature, using airborne patrolling to rapidly enter new suitable habitats consisting of organic matter in early stages of decomposition. Our collective data suggest that A. baumannii, early after its speciation, went through massive radiation during the Neolithic, likely due to deforestation, settlement and farming producing numerous favorable habitats. Their natural lifestyle, which requires rapid adaptability to various habitats as well as tolerance to desiccation, radiation and antibiotic stress, perfectly predispose these opportunistic pathogens to establish within the hospital setting. Comparison of genomes from environmental and clinical isolates will now enable studies of the adaptive evolution of environmental bacteria towards multidrug-resistant opportunistic pathogens.

microbiology↗