Biology subjects

Daniel, L.

Publications and source records attributed to Daniel, L..

8 recordsLinked to original sources

bioRxiv2026

Constitutive ATR Signaling Enforces Domain-Wide Origin Synchrony

Eukaryotic DNA replication relies on organized spatial-temporal domains, yet how neighboring origins are coordinated at the single-molecule level remains unresolved. Combining single-molecule DNA combing with super-resolution microscopy, we demonstrate that during unperturbed early S-phase, adjacent replication origins across diverse vertebrate species fire synchronously as a coordinated unit. This domain-wide temporal harmony is continuously enforced by a baseline, constitutive ATR CHK1 signaling axis that restrains local CDK2 and CDC7 kinase activities. Strikingly, replication stress dismantles this coordination, shifting origin activation toward an asynchronous, replicon-autonomous mode. Mechanistically, stress-induced phosphorylation of the cohesin subunit SMC1A promotes an SMC1A ATR complex that sequesters ATR at stalled replication forks. This localized sequestration creates a regional ATR loss-of-function phenotype, relieving CDK2/CDC7 suppression and driving premature, uncoordinated origin firing. Super-resolution imaging shows that ATR sequestration structurally reorganizes replication foci, converting coordinated clustered foci into fragmented, lower-density clusters. Together, our findings uncover a baseline role for constitutive ATR signaling in enforcing domain synchrony and reveal a molecular switch that dynamically decouples origin activation during genomic stress to safeguard chromosome duplication.

molecular biology↗

bioRxiv2026

Type 1 and type 2 dendritic cell subsets cooperate to maintain intestinal immune tolerance via integrin αvβ8-mediated TGF-β activation

The gastrointestinal tract is a unique immunological environment where the host must balance tolerance to commensal microbes with defense against pathogens. A critical mechanism for maintaining this balance is the peripheral conversion of naive T cells into regulatory T cells (pTregs), a process that depends on the TGF-{beta} cytokine, which is produced in a latent form and must be activated. While the activation of latent TGF-{beta} relies on the membrane-bound v{beta}8 integrin, the precise cellular subset(s) responsible for this essential process have yet to be clearly defined. Conventional dendritic cells (cDCs), which migrate from the intestinal lamina propria to the gut-draining mesenteric lymph nodes (MLN), have long been considered the primary antigen-presenting cells (APCs) responsible for v{beta}8-mediated TGF-{beta} activation and pTreg induction. However, recent studies have challenged this paradigm by highlighting a new family of rare ROR{gamma}t-expressing APCs, able to induce pTreg via v integrins, raising questions about the in vivo role of cDCs in the maintenance of mucosal immune homeostasis. Using a {beta}8 integrin gene reporter mouse model (Itgb8-IRES-tdTomato) combined with single-cell profiling, we comprehensively mapped Itgb8-expressing APCs in the MLN. We show that cDCs, in particular migratory type 1 (cDC1) and type 2 (cDC2), constitute the predominant Itgb8TdTomato+ cells, both in neonatal and adult mice. Through cDC subset-specific {beta}8 knockout models, we demonstrate that both cDC1 and cDC2 are required for optimal pTreg generation. Loss of {beta}8 integrin in either subset led to a partial reduction in pTreg, while combined deletion resulted in profound pTreg loss and spontaneous colitis. Importantly, these effects were independent of ROR{gamma}t APC populations, including ILC3s and Thetis cells. These findings resolve longstanding questions about the identity of key APCs driving pTreg induction in the MLNs. They demonstrate that cDC1 and cDC2 are non-redundant, essential mediators of pTreg induction and intestinal immune tolerance. Although different populations of ROR{gamma}t APCs may contribute in specific contexts, such as early development, infection, or in the prevention of allergic disease, cDCs remain one of the primary guardians of intestinal immune homeostasis in response to microbiota.

immunology↗

bioRxiv2025

Cellular adaptation of mitochondrial metabolism and biogenesis in response to partial ATP synthase uncoupling

Cellular energy metabolism relies on tight regulation of mitochondrial biogenesis and turnover to maintain bioenergetic homeostasis. Understanding the signaling pathways that modulate mitochondrial content in response to changing energetic demands is therefore essential. This work examines how partial mitochondrial uncoupling reshapes mitochondrial content and metabolism in yeast and how such adaptations mirror features of pathological or age-associated states. Using a Saccharomyces cerevisiae ATP synthase mutant lacking the epsilon subunit ({Delta}{varepsilon}) and carrying a compensatory mutation that allows survival under uncoupling ({Delta}{varepsilon}+c-L57F), mitochondrial abundance, organization, and function were compared with those of wild-type and rescue strains (mutant re-expressing the epsilon subunit of the ATP synthase). Analyses included respiration assays, mitochondrial DNA quantification, {beta}-galactosidase reporters, fluorescence microscopy of the mitochondrial network, and 2D-DiGE proteomics. Uncoupling in the mutant led to a strong increase in mitochondrial mass per cell, higher respiratory capacity, elevated cytochrome levels, and increased mtDNA copy number, together with augmented transcriptional activity consistent with activation of HAP-dependent mitochondrial biogenesis. Despite a fragmented network, mitochondria retained typical ultrastructural features, while proteomic profiling indicated a shift toward ATP production via substrate-level phosphorylation. Overall, partial uncoupling promotes reversible mitochondrial biogenesis and metabolic remodeling that depend on a preserved proton-motive force, highlighting mitochondrial signaling as a key regulator of cellular energy homeostasis and offer new perspectives for studying metabolic disorders and mitochondrial pathologies. GRAPHICAL ABSTRACTS O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=179 SRC="FIGDIR/small/695256v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@19b1eceorg.highwire.dtl.DTLVardef@103a6ceorg.highwire.dtl.DTLVardef@bc48f6org.highwire.dtl.DTLVardef@15a191c_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIMitochondrial uncoupling triggers a marked increase in mitochondrial biogenesis in yeast. C_LIO_LIUncoupling leads to fragmentation of the mitochondrial network, while preserving mitochondrial ultrastructure. C_LIO_LIUncoupling induces metabolic remodeling that favors ATP production through substrate-level phosphorylation. C_LIO_LIThese cellular adaptations are reversible upon re-establishment of mitochondrial coupling. C_LIO_LIThe proton motive force serves as a key signal sensed by the cell. C_LI

molecular biology↗

bioRxiv2025

Discovery of two structurally distinct classes of inhibitors targeting the nuclease MUS81 and enhancing efficacy of chemotherapy in cancer cells

Nucleases are emerging as promising pharmacological targets due to their essential role in maintaining genomic stability, which is crucial for cellular viability and can be exploited in the prevention and treatment of various diseases, including cancer. The conserved structure-specific endonuclease MUS81 is required for resolving branched DNA intermediates during replication, repair, and recombination. Aberrant activity of MUS81 leads to DNA damage, chromosomal abnormalities and genome instability, and contributes to oncogenesis. Pharmacological targeting of MUS81 thus represents an attractive underexplored therapeutic approach. Here we describe the discovery of two chemically distinct classes of small-molecule inhibitors of MUS81, exemplified by the compounds MU262 and MU876. Both compounds can effectively inhibit MUS81 in vitro and in the cell-based context and sensitize cancer cells to DNA-damaging agents through impairing their ability to repair DNA lesions. These compounds can be also used as chemical biology tools for further exploration of MUS81 function, and as leads in the process of drug discovery focused on development of new therapies that exploit DNA repair vulnerabilities in the treatment of cancer.

molecular biology↗

bioRxiv2025

Efficient elastic tissue motions indicate general motor skill

Insights into the general nature of motor skill could fundamentally change how we develop movement abilities, with implications for musculoskeletal well-being and injury. Here, we sought to identify indicators of general motor skill-those shared by experts across disciplines (e.g., squash, ballet, volleyball) during non-specialized movements (e.g., reaching for water). Identifying such general indicators of motor skill has remained elusive. Using ultrasound imaging with deep learning and optical flow analysis, we tracked elastic tissues (muscles and associated connective tissues) during a simple reaching task performed similarly by world-class athletes and regional-level athletes drawn from diverse disciplines, as well as untrained non-experts. We analyzed previously unexamined inefficiencies: transverse elastic tissue motions orthogonal to muscle fiber direction and physiological tremors, which are oscillations that do not contribute to the net work done by muscles. We discovered that world-class experts minimize both these inefficient motions compared to regional level athletes and non-experts. While regional- level athletes surprisingly showed similar inefficiencies to non-experts, they used elastic tissues more effectively, achieving equivalent movements with smaller actuation-related tissue motions. We establish elastic tissue motion as a key indicator of general motor skill, expanding our understanding of elastic mechanisms and their role in general aspects of motor skill.

animal behavior and cognition↗

bioRxiv2020

TCR affinity controls the dynamics but not the functional specification of the Th1 response to mycobacteria

The quality of T cell responses depends on the lymphocytes ability to undergo clonal expansion, acquire effector functions and traffic to the site of infection. Although TCR signal strength is thought to dominantly shape the T cell response, by using TCR transgenic CD4+ T cells with different pMHC binding affinity, we reveal that TCR affinity does not control Th1 effector function acquisition nor the functional output of individual effectors following mycobacterial infection. Rather, TCR affinity calibrates the rate of cell division to synchronize the distinct processes of T cell proliferation, differentiation and trafficking. By timing cell division-dependent IL-12R expression, TCR affinity controls when T cells become receptive to Th1-imprinting IL-12 signals, determining the emergence and magnitude of the Th1 effector pool. These findings reveal a distinct yet cooperative role for IL-12 and TCR signalling in Th1 differentiation and suggests that the temporal activation of clones with different TCR affinity is a major strategy to coordinate immune surveillance against persistent pathogens.

immunology↗

bioRxiv2019

β-Actin and Nuclear Myosin I are responsible for nucleolar reorganization during DNA Repair.

During DNA Repair, ribosomal DNA and RNA polymerase I (rDNA/RNAP1) are reorganized within the nucleolus. Until now, the proteins and the molecular mechanism governing this reorganisation remained unknown.\n\nHere we show that Nuclear Myosin I (NMI) and Nuclear Beta Actin (ACT{beta}) are essential for the proper reorganisation of the nucleolus, after completion of the DNA Repair reaction.\n\nIn NMI and ACT{beta} depleted cells, the rDNA/RNAP1 complex can be displaced at the periphery of the nucleolus after DNA damage but cannot re-enter within the nucleolus after completion of the DNA Repair. Both proteins act concertedly in this process. NMI binds the damaged rDNA at the periphery of the nucleolus, while ACT{beta} brings the rDNA back within the nucleolus after DNA repair completion. Our results reveal a previously unidentified function for NMI and ACT{beta} and disclose how these two proteins work in coordination to re-establish the proper rDNA position after DNA repair.

molecular biology↗

bioRxiv2018

Serum GlycA level is a candidate biomarker for disease activity in systemic lupus erythematosus and for proliferative status of lupus nephritis, independent of renal function impairment.

ObjectiveGlycoprotein acetylation (GlycA) is a novel biomarker for chronic inflammation, associated to cardiovascular risk. Serum GlycA levels are increased in several inflammatory diseases, including systemic lupus erythematosus (SLE). We investigated the relevance of serum GlycA measurement in SLE and lupus nephritis (LN).\n\nMethodsGlycA was measured by NMR in 194 serum samples from patients and controls. Comparisons were performed between groups. Clinical and biological parameters were tested for correlation with GlycA levels. The predictive value of GlycA to differentiate proliferative from non-proliferative LN was determined using logistic regression models.\n\nResultsGlycA was correlated to C-reactive protein (CRP), neutrophil count, proteinuria and the SLE disease activity index (SLEDAI), and inversely with serum albumin. GlycA was higher in active (n=105) than in quiescent (n=39) SLE patients, in healthy controls (n=29), and in patients with non-lupus nephritis (n=21), despite a more altered renal function in the latter. In patients with biopsy-proven active LN, GlycA was higher in proliferative (n=32) than non-proliferative (n=11) LN, independent of renal function and proteinuria level. Logistic regression models showed that, in univariate models, GlycA outperforms traditional biomarkers. A bivariate model using GlycA and BMI better predicted the proliferative status of LN than a model comprising CRP, renal function (eGFR), serum albumin, proteinuria, C3 consumption and the presence of anti-dsDNA antibodies.\n\nConclusionSerum GlycA is elevated in SLE, and correlates with disease activity and LN. Serum GlycA, which summarizes different inflammatory processes, could be a valuable biomarker to discriminate proliferative from non-proliferative LN and should be tested in large, prospective cohorts.

immunology↗