Biology subjects

Colmegna, I.

Publications and source records attributed to Colmegna, I..

4 recordsLinked to original sources

bioRxiv2026

Detecting DNA methylation patterns suggestive of variable escape from X-chromosome inactivation

The X chromosome is often excluded from studies analyzing associations between traits and DNA methylation. In females, one copy of most genes on the X is inactivated (X-chromosome inactivation; XCI) through DNA methylation of the gene promoter on the inactive X. This leads to challenges in analyzing and interpreting DNA methylation data patterns. Particularly for sex-biased diseases and traits, there may be many loci of interest on the X chromosome, which contains about 5% of the genome. To address the need for appropriate analysis of DNA methylation data on the X chromosome, we develop a statistical approach to infer locus-specific escape from XCI sensitive to phenotype or covariate values. Performance of this method is illustrated by analysis of data from two sex-biased traits: rheumatoid arthritis which is 3-fold more common in females, and recurrent venous thromboembolism which occurs 2.5 times more often in males. Analyses of these two datasets identify new trait-associated loci on the X chromosome, demonstrate the capabilities of the new method for both bisulfite sequencing data and Illumina EPIC data, suggest at least one locus where variable escape may explain a sex-specific disease association, and rule out variable escape as a potential explanation at other loci. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=176 HEIGHT=200 SRC="FIGDIR/small/732395v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@108c23aorg.highwire.dtl.DTLVardef@77dc0org.highwire.dtl.DTLVardef@1d105d0org.highwire.dtl.DTLVardef@1d4b543_HPS_FORMAT_FIGEXP M_FIG C_FIG Created with BioRender (bioRender.com)

genomics↗

bioRxiv2026

Increased Expression and Altered Functional Activities of Immune Receptors TREM1, PD-L1, and Others on Hematopoietic Progenitor Cells in a Mouse Model of Rheumatoid Arthritis

Hematopoietic stem and progenitor cells (HSPCs) sustain the production of hundreds of billions of new cells per day to maintain our blood and immune system. In this process, HSPCs regulate the hematopoietic output by sensing and integrating diverse physiological cues. Thus, HSPCs express many receptors traditionally studied for their functions in the immune system, and this allows HSPCs to directly detect microbial compounds, endogenous danger signals, cytokines, and other inflammatory mediators. However, how the expression levels of such receptors on HSPCs change under chronic inflammation and how such changes alter HSPC functions and immune cell production remains unexplored. Working in a murine model of rheumatoid arthritis, we demonstrate the induction of microbial sensors TLR2 and CD14, orphan inflammatory receptor TREM1, and checkpoint receptor PD-L1 on HSPCs and particularly the myeloid progenitor cells in the arthritis-afflicted mice. Furthermore, we demonstrate that the stimulation of HSPCs through these receptors in culture can significantly alter the dynamics of cell expansion and differentiation, with distinct responses from HSPCs of arthritis-afflicted versus healthy control mice. We hypothesize that the induction and stimulation of HSPCs through these immune receptors under chronic inflammation may impact the output and functional properties of their immune cell progeny, positing HSPCs as central players in the pathogenic inflammatory responses of rheumatoid arthritis and potentially other chronic inflammatory diseases. HIGHLIGHTSO_LIHematopoietic progenitor cells in murine models of rheumatoid arthritis show an upregulation of immune receptors TREM1, PD-L1, TLR2, and CD14. C_LIO_LIStimulation of murine hematopoietic stem and progenitor cells through these receptors in culture alters the dynamics of their expansion and differentiation. C_LIO_LIIn such cultures, hematopoietic stem and progenitor cells from mice afflicted with rheumatoid arthritis show altered responses to stimulation as compared to healthy controls. C_LI

immunology↗

bioRxiv2025

Trained Immunity Affecting Dendritic Cell Differentiation and Function in Rheumatoid Arthritis

Rheumatoid arthritis affects [~]0.5-1% of the adult population and results in joint inflammation, chronic pain, and many systemic comorbidities. Immune and inflammatory tissue damage is the main pathogenic mechanism in rheumatoid arthritis, and involves the hyperactivation of both innate and adaptive immune systems. Trained immunity has become well established as an important feature of the innate immune system that allows the host to mount functionally altered immune responses based on their previous history of immune exposures, independently of the classical adaptive immunological memory. However, the role of trained immunity in systemic autoimmune and inflammatory disorders remains poorly understood. In the current work, we demonstrate that emergency myelopoiesis is induced in chronic rheumatoid arthritis in murine models and acts not only to enhance innate immune cell numbers but also to produce functionally altered innate immune cells. Such effects are cell-intrinsic to hematopoietic stem and progenitor cells (HSPCs) and persist independently of the inflammatory disease milieu. Importantly, these trained immunity mechanisms impact not only macrophages but also dendritic cells, which are the major antigen presenting cells that bridge the innate and adaptive immune responses. Trained dendritic cells show changes in global gene expression profiles, and significantly altered responses to recall immune stimulation and capacity for T cell activation. This study therefore represents the first demonstration of dendritic cell trained immunity in rheumatoid arthritis.

immunology↗

bioRxiv2025

Low Dose Methotrexate has Divergent Effects on Cycling and Resting Human Hematopoietic Stem and Progenitor Cells

Low dose methotrexate (LD-MTX) remains the gold standard in rheumatoid arthritis (RA) therapy. Multiple mechanisms on a variety of immune cells contribute to the anti-inflammatory effects of LD-MTX. Inflammatory signaling is deeply implicated in hematopoiesis by regulating hematopoietic stem and progenitor cell (HSPC) fate decisions; raising the question of whether HSPC are also modulated by LD-MTX. This is the first study to characterize the effects of LD-MTX on HSPC. CD34+ HSPC were isolated from healthy donors non-mobilized peripheral blood. Resting and/or cycling HSPCs were treated with LD-MTX [dose equivalent to that used in RA patients]. Flow cytometry was performed to assess HSPC viability, cell cycle, surface abundance of reduced folate carrier 1 (RFC1), proliferation, reactive oxygen species (ROS) levels, DNA double-strand breaks, p38 activation, and CD34+ subpopulations. HSPC clonogenicity was tested in colony-forming cell assays. Our results indicate that in cycling HSPC, membrane RFC1 is upregulated and, following LD-MTX treatment, they accumulate more intracellular MTX than resting HSPC. In cycling HSPC, LD-MTX inhibits HSPC expansion by promoting S-phase cell-cycle arrest, increases intracellular HSPC ROS levels and DNA damage, and reduces HSPC viability. Those effects involve the activation of the p38 MAPK pathway and are rescued by folinic acid. The effects of LD-MTX are more evident in CD34+CD38High progenitors. In non-cycling HSPC, LD-MTX also reduces the proliferative response while preserving their clonogenicity. In summary, HSPC uptake LD-MTX differentially according to their cycling state. In turn, LD-MTX results in reduced proliferation and the preservation of HSPC clonogenicity. Study Highlight QuestionsO_ST_ABSWhat is the current knowledge on the topic?C_ST_ABSO_LILow dose-methotrexate (LD-MTX) regulates the function of key cells involved in rheumatoid arthritis (RA) pathogenesis (e.g. T cells, macrophages, neutrophils, endothelial cells and fibroblast-like synoviocytes) and through the activation of multiple pathways contribute to the suppression of inflammation in RA. C_LIO_LIInflammatory signaling impacts hematopoiesis by regulating hematopoietic stem and progenitor cells (i.e. HSPC, CD34+ cells). C_LI What question did this study address?O_LIDoes LD-MTX modulate key functional properties of HSPC subpopulations (i.e. resting and/or cycling HSPCs) C_LI What does this study add to our knowledge?O_LIHSPC uptake LD-MTX differentially according to their cycling state. C_LIO_LICycling HSPC upregulate membrane RFC1 and uptake more MTX than resting HSPC with activation of the p38 MAPK pathway. This leads to inhibition of HSPC expansion, increased intracellular ROS levels and DNA damage, and reduced HSPC viability. C_LIO_LILD-MTX preserves the clonogenicity of non-cycling HSPC. C_LI How might this change clinical pharmacology or translational science?O_LIWe describe a novel mechanism of action of LD-MTX that extends its therapeutic effects from mature immune cells to the modulation of hematopoiesis. C_LI

immunology↗