Biology subjects

Wroblewska, A.

Publications and source records attributed to Wroblewska, A..

5 recordsLinked to original sources

bioRxiv2026

Common Ground in Chaos: Diversified Photodynamic Treatments Converge on a Unified Stress Architecture in Escherichia coli

The rise of antimicrobial resistance has intensified interest in antimicrobial photodynamic inactivation (aPDI) and antimicrobial blue light (aBL) as alternatives or adjuvants to conventional antibiotics. However, whether chemically distinct photodynamic treatments elicit a shared bacterial response remains unclear. Here, we integrated transcriptomic profiles of Escherichia coli BW25113 exposed to five short-term, sub-lethal photodynamic treatments: antimicrobial blue light (aBL), aBL combined with 5-aminolevulinic acid (aBL+ALA), rose bengal (RB), new methylene blue (NMB), and the cationic porphyrin TMPyP. Intersection analysis identified 891 conserved core genes differentially expressed across all treatments, of which approximately 98% changed in a consistent direction despite differences in photosensitizer chemistry and activating wavelength. Random-effects meta-analysis and robust rank aggregation prioritized 88 high-confidence genes, revealing induction of envelope stress and cytoplasmic protein quality control pathways alongside repression of acid resistance, hydrogen metabolism, molybdate transport, and biofilm formation. Regulon enrichment indicated that heat-shock sigma factor {sigma}32/RpoH and the envelope-stress regulators CpxR, BaeR, {sigma}24/RpoE, and PspF were enriched among induced genes, whereas GadW/GadX/GadE, Fur, and {sigma}38/RpoS were enriched among repressed genes. Functional validation using selected single-gene Keio knockouts confirmed that deletion of conserved-core genes sensitized E. coli to photodynamic treatment and delayed post-treatment recovery in a modality-dependent manner. Moreover, RT-qPCR analysis of selected transcriptional responses confirmed the direction and overall pattern of RNA-seq-derived expression changes. Together, these findings define a unified conserved early survival program in E. coli after chemically distinct photodynamic treatments and identify stress-response modules that may serve as targets for potentiating aPDI. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/744726v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@dbbadaorg.highwire.dtl.DTLVardef@1c85538org.highwire.dtl.DTLVardef@152d699org.highwire.dtl.DTLVardef@18705a6_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

A ML-framework for the discovery of next-generation IBD targets using a harmonized single-cell atlas of patient tissue

Target discovery for IBD has traditionally relied on genetic associations, which lack the cellular resolution needed to identify novel, actionable, cell type-specific disease pathways. Here, we describe an integrated analytical and experimental framework that leverages harmonized single-cell data to systematically discover novel therapeutic strategies for IBD. We used AMICA DBTM, Immunais harmonized database of single-cell RNA datasets to construct a harmonized 1 million single-cell atlas of the human intestine. We applied a machine learning framework (Immune Patient Representation, IPR) to identify disease-associated transcriptional programs and cell type-specific gene targets. Candidate targets were prioritized using atlas-derived metrics, refined using custom criteria emphasizing translational actionability, and validated across independent clinical cohorts. Select candidates were evaluated in human primary-cell models reflecting the targets cell-type context. The IPR framework identified 85 disease-associated transcriptional programs and ranked 400 cell type-specific target genes across immune and stromal lineages. Disease-associated programs were interpreted using a structured AI-assisted reasoning framework for structured biological reasoning, linking them to IBD-relevant pathways and guiding the identification of novel, promising gene targets. Functional validation of two cell-type-specific candidates, PTGIR in myeloid cells and IL6ST in fibroblasts, confirmed the reduction of inflammatory and fibrotic pathways linked to IBD pathology. Multi-omic profiling and projection of in vitro phenotypes to patient datasets demonstrated the reversal of disease-associated programs via mechanisms distinct from those of existing biologics. Our single-cell anchored, machine-learning framework integrates in silico discovery with experimental validation, revealing new cell type-specific therapeutic opportunities and supporting a scalable approach for precision target discovery in IBD and other immune-mediated diseases.

bioinformatics↗

bioRxiv2025

Evolutionarily conserved transcriptional regulators control monoaminergic neuron development

To what extent conserved developmental programs specify homologous cell types is a central question in biology. Here, we address this by focusing on reconstructing monoaminergic neuron development in Drosophila melanogaster embryo using time- resolved single-cell genomics, spatial transcript mapping with hybridisation chain reaction, and targeted metabolomics. We uncover a regulatory landscape in which specific transcription factors are activated before biosynthetic enzymes, establishing a prospective temporal architecture for monoaminergic fate specification. Comparative analyses of developmental single-cell atlases from zebrafish and sea urchin indicate that components of this machinery are conserved across [~]550 million years of bilaterian evolution with orthologous transcription factors showing similar temporal dynamics. Together, these findings point to a putatively conserved regulatory core that interfaces with other context-dependent transcription factors; this interplay accommodates monoaminergic multifunction and subtype diversity across distinct neuroanatomies.

evolutionary biology↗

bioRxiv2021

Perturb-map enables CRISPR genomics with spatial resolution and identifies regulators of tumor immune composition

The cellular architecture of a tumor, particularly immune composition, has a major impact on cancer outcome, and thus there is an interest in identifying genes that control the tumor microenvironment (TME). While CRISPR screens are helping uncover genes regulating many cell-intrinsic processes, existing approaches are suboptimal for identifying gene functions operating extracellularly or within a tissue context. To address this, we developed an approach for spatial functional genomics called Perturb-map, which utilizes protein barcodes (Pro-Code) to enable spatial detection of barcoded cells within tissue. We show >120 Pro-Codes can be imaged within a tumor, facilitating spatial mapping of 100s of cancer clones. We applied Perturb-map to knockout dozens of genes in parallel in a mouse model of lung cancer and simultaneously assessed how each knockout influenced tumor growth, histopathology, and immune composition. Additionally, we paired Perturb-map and spatial transcriptomics for unbiased molecular analysis of Pro-Code/CRISPR lesions. Our studies found in Tgfbr2 knockout lesions, the TME was converted to a mucinous state and T-cells excluded, which was concomitant with increased TGF{beta} expression and pathway activation, suggesting Tgfbr2 loss on lung cancer cells enhanced suppressive effects of TGF{beta} on the TME. These studies establish Perturb-map for functional genomics within a tissue at single cell-resolution with spatial architecture preserved.

immunology↗

bioRxiv2019

Disruption of the CSF-1-CSF-1R axis alters cerebellar microglia and is associated with motor and social interaction defects

Microglia, the brain resident macrophages, critically shape forebrain neuronal circuits. However, their precise function in the cerebellum is unknown. Here we show that human and mouse cerebellar microglia express a unique molecular program distinct from forebrain microglia. Cerebellar microglial identity was driven by the CSF-1R ligand CSF-1, independently of the alternate CSF-1R ligand, IL-34. Accordingly, CSF-1 depletion from Nestin+ cells led to severe depletion and transcriptional alterations of cerebellar microglia, while microglia in the forebrain remained intact. Strikingly, CSF-1 deficiency and alteration of cerebellar microglia were associated with reduced Purkinje cells, altered neuronal function, and defects in motor learning and social novelty interactions. These findings reveal a novel CSF-1-CSF-1R signaling-mediated mechanism that contributes to motor function and social behavior.\n\nSummaryMicroglia are a heterogeneous population whose identity and function are dictated by signals from their microenvironment. Kana et al. show that CSF-1 signaling is critical for maintaining cerebellar microglial transcriptional identity and homeostasis, and that altering the CSF-1 - CSF-1R axis leads to motor and behavioral defects.

neuroscience↗