Biology subjects

Dombrowicz, D.

Publications and source records attributed to Dombrowicz, D..

8 recordsLinked to original sources

bioRxiv2026

Rev-erbα inhibits vascular calcification by repressing osteogenic reprogramming in atherosclerosis

Background: Atherosclerotic plaque rupture is the most deleterious atherogenic event, responsible for the majority of fatal acute atherothrombotic and myocardial infarctions. Intimal microcalcification is a major cause of atherosclerotic plaque instability. Yet, a thorough characterization of the mechanisms controlling intimal calcification is needed to develop innovative therapeutic strategies to treat high risk patients. The nuclear receptor Rev-erb regulates lipoprotein metabolism and exerts anti-inflammatory activities. Here, we hypothesized that Rev-erb modulates atherogenesis by regulating arterial calcification processes. Methods: We used a multi-omics approach in the ANGIOSAFE and the ATHEROPORTAL human cohort to identify pathways and factors associated with vascular calcification in diabetic patients. We then compared REV-ERB expression between calcified and non-calcified areas of human endarterectomies using laser capture microdissection assays (n=11-22/group). We assessed the role of Rev-erb on calcium deposition and expression of osteoblast markers in aortic roots of 18-month-old Ldlr-/-Rev-erb-/- and Ldlr-/-Rev-erb+/+ mice (n=10/group). Rev-erb-dependent molecular pathways that drive calcification were identified using gene expression profiling in aortic plaques from Ldlr-/-Rev-erb-/- and Ldlr-/-Rev-erb+/+ mice (n=8-10/group). We then confirmed omics data using primary aortic smooth muscle cells (SMCs) (n=3-6) in vitro assessing inflammation-driven calcification process as well as Rev-erb-dependent transcriptional mechanisms. Results: REV-ERB expression is significantly lower in circulating anti-inflammatory classical CD14+CD16- monocytes from diabetic patients with low coronary artery calcium (CAC) compared to those exhibiting high CAC scores while its expression is lower in highly calcified plaques from patients with diabetes mellitus compared to those with no diabetes or no calcification. Consistently, REV-ERB is markedly downregulated in calcified areas of human endarterectomy samples, while remaining higher in non-calcified regions. Rev-erb deficient Ldlr-/- mice exhibit accelerated atherogenesis and vascular calcification, and aortic smooth muscle cells (SMCs) exhibit a reprogramming toward an osteochondroblastic phenotype. Functional in vitro studies show that Rev-erb maintains SMC identity by preventing their IL-1{beta}-driven transdifferentiation into osteochondroblast-like cells, notably through the repression of key osteogenic regulators. Finally, while hyaluronic acid degradation is known to promote intimal calcification, we demonstrate that Rev-erb represses the hyaluronidase Cemip expression during SMC transdifferentiation. Conclusions: Rev-erb is identified as an important brake on SMC-driven vascular calcification, suppressing both osteogenic reprogramming and matrix-remodeling pathways. Thus, this study opens new avenues for developing novel therapeutic tools targeting Rev-erb to reduce vascular calcification and associated cardiovascular risk in high-risk patients.

pathology↗

bioRxiv2026

A multimodal framework for immune cell annotation across blood and tissue single-cell data

AbstractAccurate cell annotation remains a central challenge in single-cell analysis, particularly when datasets contain rare populations, transitional states, and tissue-adapted phenotypes. We previously developed scODIN as an expert-guided framework for immune cell annotation in single-cell RNA-sequencing data. Here, we present pyODIN, a major extension of this framework for Python. pyODIN supports multimodal annotation using RNA, antibody-derived tag (ADT), or combined RNA-ADT information. It also substantially expands the annotation database from a CD4 T-cell-centred framework to a broader cell-type reference resource spanning major and minor peripheral blood cell populations as well as tissue-associated subsets. We benchmarked pyODIN against CellTypist, MMoCHi and HiCAT using independently curated immune reference datasets. pyODIN demonstrated the highest overall classification accuracy, and at the top-lineage level, pyODIN reduced cross-lineage errors relative to the benchmark methods. At finer resolution, pyODIN preserved substantially greater CD4 T-cell subtype structure than CellTypist and HiCAT, resolving regulatory, follicular, helper, memory, and cytotoxic states that were collapsed into broader categories by the comparator methods. In a controlled marker-ablation experiment, pyODIN outperformed MMoCHi when key lineage-defining RNA markers were removed from the expression feature set, and the addition of ADT information restored NK and CD8 T-cell annotation, demonstrating the value of multimodal annotation when transcript-level evidence is incomplete. Finally, application to liver fine-needle aspirate data showed that the expanded framework supports annotation beyond PBMC datasets. Together, pyODIN provides an expert-guided, adaptable cell annotation framework for Python, designed for multimodal cell phenotyping across blood and tissue single-cell datasets. pyODIN is freely available at https://github.com/SondergaardLab/pyODIN.

immunology↗

bioRxiv2025

CSF1R regulates monocyte subset differentiation and intracellular metabolism.

Monocytes are key circulating effectors of vascular homeostasis, innate immunity and inflammation. Following their generation in mouse bone marrow, classical (Ly6Chigh) monocytes are mobilized into the blood circulation where they mature into non-classical (Ly6Clow) patrolling monocytes or are recruited into peripheral tissues where they differentiate into tissue resident or inflammatory macrophages. Monocytes and macrophages express CSF1R (CD115), the receptor for lineage-specific growth factors CSF1 and IL34. Here, we report that acute CSF1R blockade or genetic deletion negatively interferes with monocyte intracellular metabolism and reduces blood Ly6Clow monocytes in part by blunting differentiation of Ly6Chigh monocytes. Based upon lineage-specific deletion of GFPT1 (Glutamine-Fructose-6-Phosphate Transaminase 1), the hexosamine biosynthetic pathway (HBP) is identified as a novel regulator of CSF1R expression and monocyte subset diversity. Our findings provide new insights into the link between CSF1R signaling, metabolic regulation, and monocyte survival and differentiation.

immunology↗

bioRxiv2025

PI3Kδ Bridges Microbial Surveillance with Antigen Presentation to Reinforce Intestinal Immunity

Phosphoinositide 3-kinase delta (PI3K{delta}) is essential for immune cell functions, preventing immunodeficiency and inflammation; however, its role in dendritic cell (DC)-mediated immune regulation remains unknown. Here, we report a key role for DC-intrinsic PI3K{delta} in linking microbial recognition with antigen presentation for effective T-cell priming. Using genetic and functional assays, we demonstrate that PI3K{delta} deficiency in DCs leads to broad dysregulation of intestinal CD4 T-cell immunity, characterized by impaired regulatory T-cell expansion and increased susceptibility to colitis. DC-based studies show that PI3K{delta} links pattern-recognition-receptor signaling to MHC class I- and II-restricted presentation of phagosome-associated antigens by facilitating NOX2-dependent oxidative burst through RAC2, while mitigating inflammasome activation. In contrast, PI3K{delta} deficiency disrupts phagosomal pH balance, leading to accelerated acidification and proteolysis of antigens, impairing T-cell activation. Our study identifies PI3K{delta} as a key coordinator of phagosome dynamics, important for DC adaptive programming that shapes T-cell responses and supports intestinal immune homeostasis.

immunology↗

bioRxiv2024

CD226+ adipose tissue macrophages arise from MDP-derived monocytes and regulate lipid metabolism.

Macrophages are innate immune cells present in all tissues, in which they participate in immune responses and maintenance of tissue homeostasis. They develop either from embryonic precursors or from circulating monocytes, and their origin impacts their functions. We previously observed robust recruitment of monocytes to brown adipose tissue in which they could differentiation into two distinct macrophage subsets identifiable by CD206 or CD226 expression. In the present study, we investigated monocyte differentiation pathways in brown adipose tissue and the function of monocyte-derived macrophages. Fate mapping analysis revealed a low contribution of GMP- and a high contribution of MDP-derived monocytes to the CD226high macrophage subset. Importantly, adoptive transfer experiments demonstrate that MDP- but not GMP-derived monocytes are pre-conditioned to give rise to CD226high macrophages. We found that MDP-derived CD226high macrophages were also present in other tissues including peritoneal cavity, adrenal glands and all adipose depots. CD226high macrophages were regulated by both GM-CSF and CSF1R. Genetic depletion of CD226high macrophages caused increased BAT and plasma triglyceride content. We thus identify CD226high MDP-derived macrophages as a new myeloid cell type conserved across tissues and tied to lipid metabolism homeostasis.

immunology↗

bioRxiv2024

CytoBatchNorm: an R package with graphical interface for batch effects correction of cytometry data

Innovation in cytometry propelled it to an almost "omic" dimension technique during the last decade. The application fields concomitantly enlarged, resulting in generation of high-dimensional high-content data sets which have to be adequately designed, handled and analyzed. Experimental solutions and detailed data processing pipelines were developed to reduce both the staining conditions variability between samples and the number of tubes to handle. However, an unavoidable variability appears between samples, barcodes, series and instruments (in multicenter studies) contributing to "batch effects" that must be properly controlled. Computer aid to this aim is necessary, and several methods have been published so far, but configuring and carrying out batch normalization remains unintuitive for scientists with "pure" academic backgrounds in biology. To address this challenge, we developed an R package called CytoBatchNorm that offers an intuitive and user-friendly graphical interface. Although the processing is based on the script by Schuyler et al., the graphical interface revolutionizes its use. CytoBatchNorm enables users to define a specific correction for each marker in a single run. It provides a graph that guides you through quickly setting the correction for each marker. It allows corrections to be previewed and inter-marker effects to be checked as the settings are made. CytoBatchNorm will help the cytometry community to adequately scale data between batches, reliably reducing batch effects and improving subsequent dimension reduction and clustering. VISUAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/596492v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@600a1eorg.highwire.dtl.DTLVardef@13860cborg.highwire.dtl.DTLVardef@5ad915org.highwire.dtl.DTLVardef@6218dc_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2023

A time- and space-resolved nuclear receptor atlas in mouse liver

The unique functional versatility of the liver is paramount for organismal homeostasis. Both liver development and adult functions are controlled by tightly regulated transcription factor networks, within which nuclear receptors regulate essential functions of parenchymal and non-parenchymal cells. Acting as transcription factors sensitive to extracellular cues such as steroidal hormones, lipid metabolites, xenobiotics... and modulated by intracellular signaling pathways, nuclear receptors orchestrate many aspects of hepatic physiology. While liver functional zonation and adaptability to fluctuating conditions are known to rely on a sophisticated cellular architecture, a comprehensive knowledge of nuclear receptor functions in the different liver cell types is still lacking. As a first step toward the accurate mapping of nuclear receptor functions in mouse liver, we characterized their levels of expression in whole liver as a function of time and diet, and explored nuclear receptor isoform expression in hepatocytes, cholangiocytes, Kupffer cells, hepatic stellate cells and liver sinusoidal cells. In addition, we leveraged liver single cell RNAseq studies to provide here an up-to-date compendium of nuclear receptor expression in mouse liver in space and time.

molecular biology↗

bioRxiv2022

The HDAC inhibitor trichostatin A impairs pancreatic β-cell function through an epigenome-wide reprogramming

ObjectiveThe pancreatic islets of Langerhans contain distinct cell subtypes including insulin-producing {beta} cells. Although their cell-specific gene expression pattern defines their identity, the underlying molecular network driving this transcriptional specificity is not fully understood. Among the numerous transcriptional regulators, histone deacetylases (HDAC) enzymes are potent chromatin modifiers which directly regulate gene expression through deacetylation of lysine residues within specific histone proteins. The precise molecular mechanisms underlying HDAC effects on cellular plasticity and {beta}-cell identity are currently unknown. MethodsThe pharmacological inhibition of HDAC activity by trichostatin A (TSA) was studied in the mouse Min6 and human EndocBH1 cell lines, as well as primary mouse sorted {beta} cells and human pancreatic islets. The molecular and functional effects of treating these complementary {beta}-cell models with TSA was explored at the epigenomic and transcriptomic level through next-generation sequencing of chromatin immunoprecipitation (ChIP) assays (ChIP-seq) and RNA sequencing (RNA-seq) experiments, respectively. ResultsWe showed that TSA alters insulin secretion associated with {beta}-cell specific transcriptome programming in both mouse and human {beta}-cell lines, as well as on human pancreatic islets. We also demonstrated that this alternative {beta}-cell transcriptional program in response to HDAC inhibition is related to an epigenome-wide remodeling at both promoters and enhancers. ConclusionsTaken together, our data indicate that full HDAC activity is required to safeguard the epigenome, to protect against loss of {beta}-cell identity with unsuitable expression of genes associated with alternative cell fates.

genomics↗