Biology subjects

Dabrowska, K.

Publications and source records attributed to Dabrowska, K..

12 recordsLinked to original sources

bioRxiv2026

A synthetic phageome reveals widespread and diverse human antibody responses to bacteriophages

Bacteriophages colonize humans, yet their recognition by humoral immunity remains unclear. We developed PhageScan, a PhIP- Seq platform comprising 277,051 phage and 49,630 human viral oligopeptides. Profiling sera from 192 healthy donors without prior phage therapy characterized anti-phage response specificity and revealed widespread, strong IgG reactivity to phages, comparable in prevalence and magnitude to that against human viruses. Recognition patterns were however highly individualized. Among phage sequences, 12,576 peptides were significantly enriched in at least two individuals. Strongly immunogenic epitopes preferentially originated from phages infecting pathogenic bacteria, whereas widely shared ''public'' epitopes were enriched among phages of environmental and food-associated bacteria. ImmE, a lactococcal phage endolysin recognized in 59.9% of individuals, showed reduced antibacterial activity in the presence of sera identified as ImmE-reactive by PhageScan, demonstrating functional relevance. These findings establish phage-directed antibodies as a widespread component of human immunity and PhageScan as a scalable platform for defining phage--antibody interactions.

immunology↗

bioRxiv2026

Subcellular spatial proteomics of the heterotrophic nanoflagellate, Cafeteria roenbergensis

Cafeteria roenbergensis is the best-studied free-living heterotrophic nanoflagellate, an abundant marine bacterivore and the host of the giant virus CroV, yet almost nothing is known about how its cell is organized. To provide broad insight into the localization of its proteome, we used subcellular spatial proteomics (SSP), based on a label-free version of LOPIT-DC (Localisation of Organelle Proteins by Isotope Tagging after Differential ultraCentrifugation), in which organelles are separated by differential centrifugation and each protein is assigned to a compartment from its abundance profile across fractions. We detected 5,948 proteins (5,889 protein groups), corresponding to 69.7% of the predicted C. roenbergensis proteome, and assigned high-confidence localizations to 2,945 proteins across 14 subcellular compartments, including basal body/cilia, cytosol, ER, Golgi, lysosome, membrane-trafficking, mitochondria, nucleoplasm, nucleus, peroxisome, plasma membrane, proteasome, ribosome, and spliceosome. This study serves as a proteomic dataset to resolve protein compartmentalization in a free-living heterotrophic stramenopile, enabling evolutionary, biological and functional insight and analysis. Investigators interested in using these data prior to publication are encouraged to contact us to avoid overlap and to facilitate coordinated and collaborative use of this resource.

cell biology↗

bioRxiv2026

Subcellular spatial proteomics of the close animal relative, Capsaspora owczarzaki

Capsaspora owczarzaki is one of the closest relatives of animals and an increasingly tractable model for investigating the evolution of multicellularity. However, very little cell biological work has been done on the sister linages to animals. Subcellular spatial proteomics (SSP) is a technique that can localize thousands of proteins to subcellular compartments in a single experiment by combining cell fractionation with sensitive mass spectrometry. To provide broad insight into the localization of the Capsaspora proteome, we performed SSP based on a label-free version of LOPIT-DC (Localisation of Organelle Proteins by Isotope Tagging after Differential ultraCentrifugation). We detected 6,466 proteins, corresponding to 68.4% of the predicted Capsaspora proteome, and assigned high-confidence localizations to 3,106 of them across 13 subcellular compartments. This study serves as a proteomic dataset to resolve cellular compartmentalization in a close relative of animals, enabling downstream evolutionary, biological, and functional analyses. Investigators interested in using these data prior to publication are encouraged to contact us to avoid overlap and to facilitate coordinated and collaborative use of this resource.

cell biology↗

bioRxiv2026

Precision Targeting of Heparan Sulfate Proteoglycans Broadly Dysregulates Survival Signaling and Metabolic Adaptation in Pancreatic Cancer

Treatments for pancreatic ductal adenocarcinoma (PDAC) often fail because of the cancer's ability to adapt its signaling and metabolic pathways to circumvent treatment mechanisms. PDAC hallmarks that promote treatment resistance (increased fatty acid metabolism, survival signaling, desmoplasia, and macropinocytosis) are extensively regulated by heparan sulfate proteoglycans (HSPGs) and their binding partners. The pro-tumor functions of HSPGs are controlled by site-specific cleavage of their heparan sulfate chains by mammalian heparanase; however, cleavage by bacterial heparinase III (HepIII) represses these functions and prevents downstream, pro-tumor signaling. Using tumor-targeting, attenuated Salmonella typhimurium (strain YS1646), we have limited HepIII transgene expression to tumor tissue. Degradation of tumor cell heparan sulfates by HepIII resulted in decreased macropinocytosis, reduced survival signaling, lipid storage depletion, and decreased expression of translational machinery. This tumor-targeting treatment has the potential to improve the efficacy of several approved pancreatic cancer therapies, which is predicted to increase patient survival.

cancer biology↗

bioRxiv2026

Global mapping of protein localization in vegetative Dictyostelium discoideum by subcellular spatial proteomics

Dictyostelium discoideum is a genetically tractable amoebozoan model organism widely used to study conserved eukaryotic cellular processes, yet a comprehensive map of its subcellular proteome has been lacking. Here, we combined subcellular fractionation with label-free mass spectrometry to resolve a global protein localization map for D. discoideum. We detected 6,337 proteins (~50% of the predicted proteome) and generated protein abundance profiles across 10 subcellular fractions. Using a curated marker set and a support vector machine classifier with a median cutoff, we assigned high-confidence localizations to 3,169 proteins across 17 subcellular compartments. Independent validation using sequence-based targeting predictions strongly supported the compartment assignments. Together, this study provides the first global subcellular localization map of the Dictyostelium proteome, establishing a foundational resource for functional, cell biological, and evolutionary analyses. We are currently preparing manuscripts that further analyze (i) the membrane trafficking system of Dictyostelium, including detailed investigation of the contractile vacuole, Jotnarlogs, and patchy proteins, and (ii) the composition of the Dictyostelium peroxisome, with a focus on the subcellular localization of sterol biosynthesis enzymes. Investigators interested in using these data are encouraged to contact us prior to publication to avoid overlap and to facilitate coordinated and collaborative use of this resource.

cell biology↗

bioRxiv2026

Viral Burden: New insights into Estimating IgG Recognition Across Human Populations

Assessment of viral burden in populations is essential for understanding virus epidemiology and herd immunity potential. While serological profiling is straightforward at the individual level, it remains challenging at scale. We propose analysis advancing in serological technologies for broader population-level analysis and comparison. We used an epitope library in Phage Display ImmunoPrecipitation (PhIP) technology (VirScan type library) to assess IgG recognition of 49,630 representative viral oligopeptides in 134 serum samples from two populations (Poland and the US). Only 5.9% of oligopeptides were immunogenic, yet IgG recognition of viruses was consistent across populations - over 90% of virus species, 99% of genera, and 97% of families were detected. Shannon Diversity Index analysis supported these findings. Among immunogenic peptides, 9.1% were significantly more frequently recognized, though not correlated with recognition strength. We further proposed a normalization method to account for differences in viral proteome representation when assessing immune burden: the burden score. Finally, we demonstrated how this approach facilitates serological comparisons between populations. These observations show that while people are exposed to similar viruses, they produce antibodies against different viral epitopes. This individual variability, combined with broad virus recognition, likely strengthens population-level protection. Epitope recognition frequency seems to be shaped more by population exposure than by magnitude of response that an epitope can induce. Accurately measuring viral burden can inform healthcare planning, and antiviral technologies development.

immunology↗

bioRxiv2024

Triadic Dynamics of Gastric Bacterial Microbiome, Phageome, and Host Genotype, with Implications for Disease Associations

The microbiota plays a key role for human health, and microbiome composition has been linked to specific health disorders many times. Different fractions of the microbiome enter dynamic interactions, particularly bacteria and bacteriophages (phages) - viruses preying on bacteria. Since the microbiome exists inside the human body, the body strongly affects the microbes, although not in a uniform way, but shaped by the extreme diversity of human genetic variants. These triadic dynamics of the bacterial microbiome, phageome, and human host genotype remain poorly understood; hence our goal in this study was to comprehend them as a holistic and interdependent system. Gastric biopsies were the source of the stomach microbiome (bacteria and phages). Genotyping of patients was conducted on blood samples. They were analyzed by next generation sequencing followed by multiway statistical comparisons of identified bacterial and phage taxa, human genetic variants, and medical data from the patients, including gastric disorder diagnostics. Commonly expected associations between presence of bacteriophages and their specific hosts were not found to be a universal principle. With comparable SNP correlations, the strongest associations between Staphylococcus and some staphylococcal phages or Enterobacteria and some enterobacteria phages were discovered. However, many more phage groups were not found to be clearly associated with their bacterial hosts, though often associated with SNPs, particularly those linked to immunological functions and body responses to bacteria and viruses. Thus, in addition to the expected effect on phage communities by shaping the communities of their bacterial hosts, the human body seems to affect phages directly, selecting for phages that survive its specific selective pressure, which can be defined by detection of particular genetic variants.

molecular biology↗

bioRxiv2024

Phageome transfer from gut to circulation and its regulation by human immunity

Bacteriophages dominate the human gut virome, yet their presence in the bloodstream remains orders of magnitude lower, suggesting that systemic dissemination is tightly regulated. How gut phages cross the intestinal barrier and which factors govern their persistence in circulation remain poorly understood, largely because prior studies characterized gut and blood viromes independently rather than in matched samples from the same individuals. Here we investigated phage translocation by shotgun metagenomics of matched colon mucosal biopsies and sera from 37 individuals with phage specific IgG profiling using a pan-phage proteome-derived phage display epitope library, complemented by an oral T4 model in mice. We found that phage abundance decreased by approximately 98% from intestinal mucosa to serum. The mucosal virome was dominated by Microviridae, which also accounted for most of the translocated phages. In the mouse model, phage titers dropped stepwise by [~]106 fold from gut content to blood, with the sharpest reduction occurring at the mucosal-lymphatic interface. Among translocated viral operational taxonomic units 93.1% lacked taxonomic assignment, yet network analysis revealed reproducible co-enrichement with annotated families including Herelleviridae and Straboviridae, which showed significantly higher gut abundance among translocated observations (FDR <0.01). IgG reactivity against a specific phage in 90% of investigated individuals was associated with the absence of that phage in the patients virome; at the collective population analysis, IgG reactivity showed a weak negative association with serum phage abundance. These observations suggest antibody-mediated clearance that limits systemic persistence. Together, these findings suggest that rare epithelial passage, lymphatic trafficking, and IgG-mediated neutralization act as sequential filters that limit which gut phages reach and persist in the circulation, with implications for phage therapy delivery and for the dissemination of accessory genetic elements beyond the intestine.

microbiology↗

bioRxiv2024

Super-resolution going viral: T4 virus particles as perfect nature-designed 3D-Bio-NanoRulers

In the burgeoning field of super-resolution fluorescence microscopy, significant efforts are being dedicated to expanding its applications into the three-dimensional domain. Various methodologies have been developed that enable isotropic resolution at the nanometer scale, facilitating the visualization of three-dimensional subcellular structures with unprecedented clarity. Central to this progress is the need for reliable 3D structures that are biologically compatible for validating resolution capabilities. Choosing the optimal standard poses a considerable challenge, necessitating, among other attributes, precisely defined geometry and the capability for specific labeling at sub-diffraction-limit distances. In this context, we introduce the use of the non-human-infecting virus, bacteriophage T4, as an effective and straightforward bio-ruler for three-dimensional super-resolution imaging. Employing DNA point accumulation for imaging in nanoscale topography (DNA-PAINT) along with the technique of astigmatic imaging, we uncover the icosahedral capsid of the bacteriophage T4, measuring 120 nm in length and 86 nm in width, and its hollow viral tail. This level of detail in light microscopy represents a significant advancement. We further outline a simple protocol for the production and preparation of samples. Moreover, we explore the extensive potential of bacteriophage T4 as a multi-faceted 3D bio-ruler, proposing its application as a novel benchmark for three-dimensional super-resolution imaging in biological studies.

biophysics↗

bioRxiv2023

Identification of cross-reacting IgG hotspots to prevent immune evasion of SARS-CoV-2 variants

The major factor that shapes the global perspective for increase or diminution of successive pandemic waves of COVID-19 is the immunological protection. The SARS-CoV-2 virus constantly develops new variants, and capability of immune evasion is among the major factors that promote variant spreading in the human population. After two years of the pandemic and virus evolution, it is almost impossible to explain effects of all possible combinations different viral strains, a few types of vaccinations or new variants infecting an individual patient. Instead of variant-to-variant comparisons, identification of key protein regions linked to immune evasion could be efficient. Here we report an approach for experimental identification of SARS-CoV-2 protein regions that (i) have characteristics of cross-reacting IgG hot-spots, and (ii) are highly immunogenic. Cross-reacting IgG hot spots are regions of protein frequently recognized in many variants by cross-reacting antibodies. Immunogenic regions efficiently induce specific IgG production in SARS-CoV-2 infected patients. We determined four regions that demonstrate both significant immunogenicity and the activity of a cross-reacting IgG hot-spot in protein S, and two such regions in protein N. Their distribution within the proteins suggests that they may be useful in vaccine design and in serological diagnostics of COVID-19.

immunology↗

bioRxiv2022

Escaping antibody responses to bacteriolytic enzymes Pal and Cpl-1 by epitope scanning and engineering

Bacteriolytic enzymes are promising antibacterial agents, but they can cause a typical immune response in vivo. In this study, we used a targeted modification of two antibacterial endolysins, Pal and Cpl-1. We identified the key immunogenic amino-acids, and designed and tested new, bacteriolytic variants with altered immunogenicity. One new variant of Pal (257-259 MKS [->] TFG) demonstrated decreased immunogenicity while a similar mutant (257-259 MKS [->] TFK) demonstrated increased immunogenicity. A third variant (280-282 DKP [->] GGA) demonstrated significantly increased antibacterial activity and it was not cross-neutralized by antibodies induced by the wild-type enzyme. We propose this variant as a new engineered endolysin with increased antibacterial activity that is capable of escaping cross-neutralization by antibodies induced by wild-type Pal. We show that efficient antibacterial enzymes that avoid cross-neutralization by IgG can be developed by epitope scanning, in silico modelling, and substitutions of identified key amino acids with a high rate of success. Importantly, this universal approach can be applied to many proteins beyond endolysins and has the potential for design of numerous biological drugs.

bioengineering↗

bioRxiv2021

Heterotypic Assembly Mechanism Regulates CHIP E3 Ligase Activity

The E3 ubiquitin ligases CHIP/CHN-1 and UFD-2 team up to accelerate ubiquitin chain formation. However, it remained largely unclear how the high processivity of this E3 set is achieved. Here we studied the molecular mechanism and function of the CHN-1/UFD-2 complex in Caenorhabditis elegans. Our data show that UFD-2 binding promotes the cooperation between CHN-1 and ubiquitin-conjugating E2 enzymes by stabilizing the CHN-1 U-box dimer. The HSP-1 chaperone outcompetes UFD-2 for CHN-1 binding and promotes the auto-inhibited CHN-1 state by acting on the conserved position of the U-box domain. The interaction with UFD-2 enables CHN-1 to efficiently ubiquitinate S-Adenosylhomocysteinase (AHCY-1), an enzyme crucial for lipid metabolism. Our results define the molecular mechanism underlying the synergistic cooperation of CHN-1 and UFD-2 in substrate ubiquitylation. HIGHLIGHTSO_LIE3 ligase UFD-2 stimulates ubiquitylation activity of CHIP/CHN-1 C_LIO_LIUFD-2 binding promotes dimerization of CHIP/CHN-1 U-box domains and utilization of E2 enzymes C_LIO_LIHSP70/HSP-1 by latching the U-box and TPR domains stabilizes the autoinhibitory state of CHIP/CHN-1, limiting interactions with E2s and UFD-2 C_LIO_LIAssembly with UFD-2 enables CHIP/CHN-1 to regulate lipid metabolism by ubiquitylation of S-Adenosylhomocysteinase C_LI

molecular biology↗