Biology subjects

Daniel, C.

Publications and source records attributed to Daniel, C..

15 recordsLinked to original sources

bioRxiv2026

MYC targeted de novo binders impair tumor growth

MYC is one of the most frequently dysregulated oncogenic drivers across many cancers, yet direct therapeutic targeting has remained difficult because its function is mediated by disordered regions and transient protein-protein interactions. Here we design proteins that bind epitopes within regions of MYC whose sequence is conserved between human and mouse, including intrinsically disordered motifs required for oncogenic activity. In vitro, the designs bind MYC with nanomolar affinity and in cells they engage MYC, disrupt interactions with MAX, and remodel MYC-associated protein complexes. Expression of the binders decreases cell proliferation across diverse MYC-dependent hematopoietic, liver, pancreatic, and patient-derived tumor models, and in an orthotopic pancreatic cancer model, binder-expressing tumor cells were selectively depleted. This work establishes de novo protein design as a generalizable strategy to therapeutically target intrinsically disordered transcription factors.

biochemistry↗

bioRxiv2026

Spatiotemporal Mapping of Glomerular Endothelial Regeneration Identifies Apold1 as an Intrinsic Regulator of Repair

Abstract Endothelial cell (EC) injury is central to the pathogenesis of various renal disorders, highlighting the critical importance of vascular repair for restoring organ health. However, due to limited access to human tissue during active regeneration, the exact reparative processes remain largely unknown. This study aimed to investigate regeneration mechanisms specifically within the glomerular microvasculature by utilizing a selective endothelial cell injury (ECI) model in mice.Lineage tracing identified the origin of regenerating ECs. To uncover the transcriptional dynamics driving these reparative changes, we combined single-cell RNA sequencing and Xenium spatial transcriptomics (ST), mapping distinct glomerular EC (gEC) subpopulations across different phases of injury and recovery. Apold1 emerged as a key regulatory candidate within this process. To functionally validate this gene's specific role during the regenerative phase, Apold1-deficient (Apold1-/-) mice underwent the ECI model. After showing that gECs regenerate primarily from local, pre-existing renal ECs, our transcriptomic analysis identified 10 distinct gEC subpopulations and revealed a complex temporal pattern of regeneration. This process begins with the expression of genes associated with inflammation, followed sequentially by endothelial cell (EC) migration, the activation of immediate early genes, vascular remodeling and cellular proliferation. Within this dynamic process, the EC-specific gene Apold1 was identified as a key regulatory candidate. Apold1-/- mice exhibited impaired endothelial regeneration, characterized by increased endothelial activation and greater immune cell infiltration seven days post-ECI. To our knowledge, this is the first study to elucidate the spatiotemporal mechanisms of glomerular endothelial cell regeneration. By identifying local gECs as the primary source of repair, and stablishing the change in their expression pattern during regeneration, as well as identifying Apold1 as an intrinsic regulator, we have laid the groundwork for future research on renal microvascular disorders.

molecular biology↗

bioRxiv2026

SATB1 is a targetable modulator of JAK-STAT signaling and cytokines in human Treg and Tconv cells

The chromatin organizer SATB1 is indispensable for thymic regulatory T cell (Treg cell) development and T helper cell induction. Several gene loci have been described to be SATB1-controlled, including the transcription factor GATA3 and the cytokine loci IL-4 and IL-17. However, the global effects of SATB1 on fully differentiated human CD4 conventional T cells (Tconv cells) and Treg cells, and thus SATB1s potential as a target for T cell engineering, are poorly understood. We describe SATB1-regulated gene signatures as largely subset-specific, with broader effects on Treg cells. Despite of the distinct gene-regulatory patterns, we observe overarching dysregulated cytokine and JAK-STAT signaling after SATB1 ablation. Functionally, SATB1 KO reduces human Treg cell suppressive capacities but boosts tumor clearance via CD4 CAR T cells in a preclinical, humanized mouse model. Together, Treg destabilization and simultaneous increased activation of CD4 CAR T cells by SATB1 modulation may be an interesting strategy to boost the efficiency of CAR T cell therapies.

immunology↗

bioRxiv2026

Convergent post-drought recovery of biomass and functional traits under constant and periodic warming in slow- and fast-growing plants

Extreme climate events such as droughts and heatwaves are intensifying under climate change, yet their combined effects on plant recovery remain unclear. In a two-year outdoor mesocosm experiment, we tested how grassland species with contrasting growth strategies recover from summer drought under four warming regimes: ambient, moderate warming (+2 {degrees}C), periodic heatwaves (+7 {degrees}C), and their combination. Experimental communities of native fast- and slow-growing species plus the invasive Solidago canadensis were assessed for above-ground biomass and leaf traits (SLA, LDMC, chlorophyll content, stomatal conductance) at one- and four-months post-drought. Biomass fully recovered within one month in both growth strategies, but leaf traits showed transient shifts, over-recovery in SLA and under-recovery in LDMC, likely reflecting production of new leaf tissues. These deviations generally returned to control levels by four months, regardless of warming treatments. Solidago canadensis exhibited high tolerance to heat and drought, with early biomass and trait recovery, indicating potential for dominance under climate extremes. Biomass recovery was similar across growth strategies, suggesting that growth-related differences play a minimal role in short-term recovery; however, early regrowth was characterised by contrasting trait shifts. Such lagged trait recovery, combined with rapid invasive recovery, suggests potential for longer-term shifts in grassland composition and function. We recommend that incorporating trait-based recovery dynamics is essential for predicting ecosystem stability under compound climate extremes.

ecology↗

bioRxiv2026

Glomerular Endothelial Cell-Derived Extracellular Vesicles Cross the Basement Membrane to Regulate Podocyte Function

BackgroundSmall extracellular vesicles (EVs) are nanosized, endosome-derived particles which transfer RNA, proteins, and bioactive molecules to mediate intercellular communication. While EV signaling has been observed in many organ systems, it remains unclear whether glomerular endothelial cell (GEC)-derived small EVs directly interact with podocytes in vivo or how they traverse the glomerular basement membrane (GBM). MethodsGEC-derived small EVs were characterized by nanoparticle tracking analysis, electron microscopy, RAMAN spectroscopy and flow cytometry. Cargo composition was analyzed by proteomics, and microRNA (miR) profiling. Functional and structural features were examined using protease, collagenase, adhesion, and multimodal imaging assays. GEC-derived small EV uptake and downstream transcriptional effects were studied in cultured podocytes, while in vivo trafficking was assessed by injection of labeled small EVs into transgenic zebrafish larvae under baseline conditions, puromycin-induced damage, and cd2ap-knockdown. ResultsGECs released bona fide exosome-like small EVs carrying a highly cell type-specific miR cargo. Small EV transfer to podocytes induced a defined transcriptional response consistent with miR-mediated repression of target genes involved in extracellular matrix organization, cell cycle regulation, and cellular stress responses. Proteomic analyses revealed enrichment of surface proteases and integrin-associated proteins that conferred sustained proteolytic activity and enabled GEC-derived small EV migration through extracellular matrix surrogates. In vivo, circulating small EVs traversed the GBM and localized selectively to podocytes in healthy glomeruli, whereas glomerular injury permitted small EV entry into the tubular compartment. ConclusionThese findings provide first in vivo evidence that GEC-derived small EVs can cross the GBM and impact on podocytes. By identifying integrin- and protease-dependent mechanisms which facilitate vesicle passage, this study redefines the GBM as a dynamic interface of heterocellular, vesicle-mediated communication.

physiology↗

bioRxiv2025

Extracellular vesicles as indicators of environmental stress response in Lactiplantibacillus plantarum: a multi-platform study

Extracellular vesicles (EVs) are key mediators of bacterial communication and adaptation to environmental stress. Their size, cargo, and surface charge are influenced by several factors, including environmental conditions, bacterial physiology, and isolation methods, and are highly strain-specific. Herein, we investigated how exposure to bile, a physiological component of the gut environment, affects the production and properties of EVs released by the probiotic strain Lactiplantibacillus plantarum NCIMB 8826. Through ultracentrifugation followed by size-exclusion chromatography (SEC), we isolated highly purified L. plantarum EVs (LpEVs) and characterized them according to the Minimal Information for Studies of Extracellular Vesicles guidelines. SEC purification significantly reduced the contents of contaminating proteins and peptidoglycans, improving the compositional purity of the isolated EVs. Compared with the parent bacteria, purified LpEVs exhibited distinct surface lipid profiles and zeta potential as well as remarkable stability across varying pH levels, elevated NaCl concentrations, and increasing detergent challenges. Under bile stress, the bacteria released larger LpEVs enriched in bile metabolism-related proteins, suggesting vesicle-mediated adaptation. Fourier-transform infrared spectroscopy further revealed bile-induced molecular alterations in LpEVs that differed from those in the parent bacteria. These findings highlight bacterial EVs as dynamic environmental communicators that respond to stress and may modulate host-microbe interactions before detectable changes occur in the bacterial cells.

microbiology↗

bioRxiv2025

Stably coexisting communities deliver higher ecosystem multifunctionality

Linking the processes determining species coexistence and effects of biodiversity on ecosystem functioning is important for a mechanistic understanding of how species loss impacts ecosystems1. There are good theoretical reasons to expect stably coexisting communities to deliver higher ecosystem functioning, as niche differences should promote coexistence and complementarity2, however, there is still little empirical evidence to demonstrate this relationship3. We present a novel experimental approach to tackle this question, in which we first measured interaction coefficients and intrinsic growth rates for 12 grassland species4 and used population models to estimate coexistence5. We then assembled 48 three-species communities, predicted to differ in their degree of coexistence and measured seven above and belowground functions. Here we extend findings demonstrating that biodiversity increases multifunctionality6,7 to show that amongst communities with the same initial diversity, multifunctionality is higher when all the species are predicted to coexist. Decomposing coexistence into the influence of niche and fitness differences showed that multifunctionality was high in niche differentiated communities but also in those with a single highly competitive species. We further examined the effect of indirect interactions, which provide an alternative mechanism of coexistence in multispecies communities, and found that they also provided an alternative route to high multifunctionality. Our results point the way to a unification of coexistence and biodiversity theory and to a more mechanistic understanding of the functional effects of biodiversity change.

ecology↗

bioRxiv2025

PIN1 Drives Cellular Plasticity and Immune Modulation in Chronic Pancreatitis

Background and AimsChronic pancreatitis (CP) is characterized by inflammation, fibrosis, and acinar-to-ductal metaplasia (ADM). PIN1, known to drive oncogenic signaling and cellular plasticity in cancer, has an unexplored role in CP. This study investigates PIN1s expression and function in CP pathogenesis using human tissues and mouse models. MethodsPIN1 expression was assessed in human CP tissue microarrays (TMAs) via immunohistochemistry (IHC) and cyclic immunofluorescence (CyCIF). Acute and chronic pancreatitis were induced in wild-type (WT) and PIN1 knockout (PIN1KO) mice using caerulein. Disease progression was monitored histologically, and immune profiling was conducted using flow cytometry. Pharmacological inhibition was performed using a small molecule PIN1 inhibitor-Sulfopin, and effects were evaluated by histology, qPCR, and cytokine analysis. Single-cell RNA sequencing (scRNA-seq) was performed on pancreatic tissues to perform pathway analysis and intercellular communication. ResultsPIN1 expression was elevated in human CP tissues, correlating with disease severity and ADM. In mice, both acute and chronic pancreatitis increased PIN1 expression, but only in our chronic PIN1KO mice displayed reduced pancreatic injury, fibrosis, ADM, and modulated immune infiltration. Pharmacological PIN1 inhibition mimicked the protective effects of genetic knockout, dampening inflammatory pathways. scRNA-seq revealed that PIN1 inhibition altered the intercellular communication networks between epithelial, immune, and stromal cells. ConclusionPIN1 drives cellular plasticity, immune modulation, and disease progression in CP. Targeting PIN1 may offer a therapeutic strategy to mitigate CP. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=184 HEIGHT=200 SRC="FIGDIR/small/653850v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@67f9fcorg.highwire.dtl.DTLVardef@4d4c1forg.highwire.dtl.DTLVardef@c099d7org.highwire.dtl.DTLVardef@b41aa5_HPS_FORMAT_FIGEXP M_FIG C_FIG Created in BioRender. Shah, V. (2025) https://BioRender.com/undefined

cell biology↗

bioRxiv2025

MYC Serine 62 phosphorylation promotes its binding to DNA double strand breaks to facilitate repair and cell survival under genotoxic stress.

Genomic instability is a hallmark of cancer, driving oncogenic mutations that enhance tumor aggressiveness and drug resistance. MYC, a master transcription factor that is deregulated in nearly all human tumors, paradoxically induces replication stress and associated DNA damage while also increasing expression of DNA repair factors and mediating resistance to DNA-damaging therapies. Emerging evidence supports a non-transcriptional role for MYC in preserving genomic integrity at sites of active transcription and protecting stalled replication forks under stress. Understanding how MYCs genotoxic and genoprotective functions diverge may reveal new therapeutic strategies for MYC-driven cancers. Here, we identify a non-canonical role of MYC in DNA damage response (DDR) through its direct association with DNA breaks. We show that phosphorylation at serine 62 (pS62-MYC) is crucial for the efficient recruitment of MYC to damage sites, its interaction with repair factors BRCA1 and RAD51, and effective DNA repair to support cell survival under stress. Mass spectrometry analysis with MYC-BioID2 during replication stress reveals a shift in MYCs interactome, maintaining DDR associations while losing transcriptional regulators. These findings establish pS62-MYC as a key regulator of genomic stability and a potential therapeutic target in cancers.

cancer biology↗

bioRxiv2025

Gut-on-Chip Methodology Based on 3D-Printed Molds: A Cost-Effective and Accessible Approach

1Gut-on-chips (GoC) represent a disruptive technology with great potential to understand the underlying mechanisms of gut health and pathology. Researchers who want to implement this approach, can either use expensive commercial microfluidic chips or build them from scratch in their lab. However, the design of such devices demands specific technical skills and expertise in computer assisted design (CAD). Additionally, the fabrication of the master molds for the chip production is very costly, time consuming and requires dedicated microfabrication facilities. Thus, the diffusion of these models in biology and health research laboratories remains limited due to this technological complexity and lack of affordability. In order to break these two bottlenecks, we present here the 3DP-{micro}Gut with open access designs and a simple fabrication approach based on a commercial 3D printer intended for general users. To ensure a good reproducibility with a sufficient number of available replicates for biological experiments, the method has been optimized to allow the production of multiple GoC per batch. The chips were also improved for confocal live imaging microscopy analyses. The chips are designed to be compatible with different types of microfluidics pumps, from stand-alone to completely integrated instrumentation. As a proof of concept, Caco-2 cells were seeded inside the fabricated GoC to validate their biocompatibility and functionality. After 7 days of maturation, cells self-differentiated in a 3D epithelium resembling in vivo expected structures. In summary we proposed a low-cost and open access GoC design and fabrication method with medium throughput. These results demonstrate the advantage of using 3D SLA printing to accelerate GoC implementation for gut physiopathology research.

bioengineering↗

bioRxiv2024

The food grade bacterium Lactobacillus helveticus VEL12193 promotes autophagy by releasing membrane vesicles

Autophagy-related processes, including canonical macroautophagy, are crucial for maintaining cellular homeostasis in eukaryotic organisms. Alterations or reduced activity of these processes have been strongly linked to a broad range of human diseases including inflammatory bowel disease (IBD) and age-related diseases such as age-related macular degeneration - a disease that affect the central area of the retina. In contrast, long-term autophagy stimulation appears to be safe and to extend lifespan in model organisms such as mice. Thus, enhancing autophagy represents a promising strategy for promoting healthy aging. Several studies indicate that the gut microbiota can influence host autophagy at the gut mucosa but also in peripheral organs, and some microbial metabolites have been identified as autophagy modulators. In this study, we studied the capacity of bacterial species commonly used in food fermentation (ferments) or health (probiotics) to modulate host autophagy by in vitro and in vivo approaches. In vitro screening of a library of 11 bacterial strains revealed a strain-dependent ability of lactobacilli and bifidobacteria to stimulate autophagy in human epithelial cells. The Lactobacillus helveticus strain VEL12193, isolated from cheese, emerged as the most effective inducer of autophagy. In vivo experiment using mice showed that long-term dietary supplementation with L. helveticus VEL12193 was associated with stimulation of autophagy in the gut mucosa and retina. We identified L. helveticus-derived membrane vesicles (MVs) as a bacterial component involved in bacterial-induced autophagy in epithelial and immune cells. Moreover, in vitro, we demonstrated that L. helveticus VEL12193 possesses immunomodulatory properties in macrophages, as well as in the gut mucosa of a preclinical mouse model of IBD. With this study we provide robust proof of concept that ferments/probiotics can stimulate autophagy at the organism scale and that this phenotype involved MVs. In addition, we identify L. helveticus VEL12193 as a candidate strain of interest for the design of healthy-aging strategies.

microbiology↗

bioRxiv2023

Fast-slow traits predict competition network structure and its response to resources and enemies.

Plants interact in complex networks but how their structure depends on resources, natural enemies and species resource-use strategy remains poorly understood. Here, we quantified competition networks among 18 plants varying in fast-slow strategy, by testing how increased nutrient availability and reduced foliar pathogens affected intra- and inter-specific interactions. Our results show that nitrogen and pathogens altered several aspects of network structure, often in unexpected ways due to fast and slow growing species responding differently. Nitrogen addition increased competition asymmetry in slow growing networks, as expected, but decreased it in fast growing networks. Pathogen reduction made networks more even and less skewed because pathogens targeted weaker competitors. Surprisingly, pathogens and nitrogen dampened each others effect. Our results show that plant growth strategy is key to understand how competition respond to resources and enemies, a prediction from classic theories which has rarely been tested by linking functional traits to competition networks.

ecology↗

bioRxiv2023

KRAS-mediated upregulation of CIP2A promotes suppression of PP2A-B56α to initiate pancreatic cancer development

Oncogenic mutations in KRAS are present in approximately 95% of patients diagnosed with pancreatic ductal adenocarcinoma (PDAC) and are considered the initiating event of pancreatic intraepithelial neoplasia (PanIN) precursor lesions. While it is well established that KRAS mutations drive the activation of oncogenic kinase cascades during pancreatic oncogenesis, the effects of oncogenic KRAS signaling on regulation of phosphatases during this process is not fully appreciated. Protein Phosphatase 2A (PP2A) has been implicated in suppressing KRAS-driven cellular transformation. However, low PP2A activity is observed in PDAC cells compared to non-transformed cells, suggesting that suppression of PP2A activity is an important step in the overall development of PDAC. In the current study, we demonstrate that KRASG12D induces the expression of both an endogenous inhibitor of PP2A activity, Cancerous Inhibitor of PP2A (CIP2A), and the PP2A substrate, c-MYC. Consistent with these findings, KRASG12D sequestered the specific PP2A subunit responsible for c-MYC degradation, B56, away from the active PP2A holoenzyme in a CIP2A-dependent manner. During PDAC initiation in vivo, knockout of B56 promoted KRASG12D tumorigenesis by accelerating acinar-to-ductal metaplasia (ADM) and the formation of PanIN lesions. The process of ADM was attenuated ex vivo in response to pharmacological re-activation of PP2A utilizing direct small molecule activators of PP2A (SMAPs). Together, our results suggest that suppression of PP2A-B56 through KRAS signaling can promote the MYC-driven initiation of pancreatic tumorigenesis.

cancer biology↗

bioRxiv2022

Macrophages inhibit Coxiella burnetii by the ACOD1-itaconate pathway for containment of Q fever

Infection with the intracellular bacterium Coxiella (C.) burnetii can cause chronic Q fever with severe complications and limited treatment options. Here, we identify the enzyme cis- aconitate decarboxylase 1 (ACOD1 or IRG1) and its product itaconate as protective host immune pathway in Q fever. Infection of mice with C. burnetii induced expression of several anti-microbial candidate genes, including Acod1. In macrophages, Acod1 was essential for restricting C. burnetii replication, while other antimicrobial pathways were dispensable. Intratracheal or intraperitoneal infection of Acod1-/- mice caused increased C. burnetii burden, significant weight loss and stronger inflammatory gene expression. Exogenously added itaconate restored pathogen control in Acod1-/- mouse macrophages and blocked replication in human macrophages. In axenic cultures, itaconate directly inhibited growth of C. burnetii. Finally, treatment of infected Acod1-/-mice with itaconate efficiently reduced the tissue pathogen load. Thus, ACOD1-derived itaconate is a key factor in the macrophage-mediated defense against C. burnetii and may be exploited for novel therapeutic approaches in chronic Q fever.

immunology↗

bioRxiv2021

Super-resolved local recruitment of CLDN5 to filtration slits implicates a direct relationship with podocyte foot process effacement

Under healthy conditions, foot processes of neighboring podocytes are interdigitating and connected by an electron-dense slit diaphragm. Beside slit diaphragm proteins, typical adherens junction proteins are also found to be expressed at this cell-cell junction. It is therefore considered as a highly specialized type of adherens junction. During podocyte injury, podocyte foot processes lose their characteristic 3D structure and the filtration slits typical meandering structure gets linearized. It is still under debate how this change of structure leads to the phenomenon of proteinuria. Using super-resolution 3D structured illumination microscopy, we observed a spatially restricted up-regulation of the tight junction protein claudin 5 (CLDN5) in areas where podocyte processes of patients suffering from minimal change disease (MCD), focal and segmental glomerulosclerosis (FSGS) as well as in murine nephrotoxic serum (NTS) nephritis and uninephrectomy DOCA-salt hypertension models, were locally injured. CLDN5/nephrin ratios in human glomerulopathies and NTS-treated mice were significantly higher compared to controls. In patients, the CLDN5/nephrin ratio is significantly correlated with the filtration slit density as a foot process effacement marker, confirming a direct association of local CLDN5 up-regulation in injured foot processes. Moreover, CLDN5 up-regulation was observed in some areas of high filtration slit density, suggesting that CLND5 up-regulation preceded the changes of foot processes. Therefore, CLDN5 could serve as a biomarker predicting early foot process effacement. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/429338v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1d05e3aorg.highwire.dtl.DTLVardef@da61f4org.highwire.dtl.DTLVardef@154e7f1org.highwire.dtl.DTLVardef@147bc6b_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗