Biology subjects

Parent, C.

Publications and source records attributed to Parent, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Fatty acids in the tumor microenvironment reprogram neutrophils to induce immunosuppression via adenosine

As solid tumors progress, the tumor microenvironment (TME) becomes increasingly immunosuppressive, impairing cytotoxic T-cell activity and limiting the efficacy of the immune checkpoint blockade. However, the mechanistic drivers of this immunosuppression remain poorly understood. Here, we identify a tumor-derived lipid-neutrophil-adenosine axis as a critical regulator of immune suppression in advanced colorectal cancer (CRC). We show that fatty acids enriched in tumor interstitial fluid reprogram neutrophils to generate adenosine via PPAR activation, leading to T-cell suppression. Using AB928, a dual A2aR/A2bR adenosine receptor antagonist currently in clinical trials, we restored T-cell proliferation, effector function, and tumor-killing capacity in vitro and in vivo. Importantly, AB928 synergized with anti-PD-1 therapy to enhance survival in an autochthonous model of metastatic CRC. Our findings define a metabolic immune evasion mechanism in the TME and provide a rationale for targeting neutrophil-derived adenosine signaling to improve immunotherapy responses in CRC and other solid tumors.

cancer biology↗

bioRxiv2026

Spatially Distinct Myosin II Architectures Regulate Protrusion Dynamics and Directional Persistence during Immune Cell Migration

Directional persistence is essential for efficient immune cell migration in tissues, yet how cytoskeletal systems stabilize migration in complex three-dimensional environments remains unclear. Using intravital subcellular microscopy and quantitative analysis of membrane dynamics, we identify two spatially distinct architectures of non-muscle myosin II (NMII) that coordinate protrusion dynamics during neutrophil migration. In vivo and in collagen matrices, NMII assembles at the leading edge into lattice-like structures that are structurally and functionally distinct from rear contractile actomyosin bundles. Protrusion-resolved analyses reveal that directional persistence correlates strongly with protrusion lifetime and sustained NMII engagement, with rear NMII load showing the strongest association with protrusion persistence. Strikingly, directional migration is not determined by the abundance of favorable protrusions but by their temporal organization during migration. Pharmacological perturbations that redistribute NMII activity disrupt this temporal organization and alter migration trajectories. Together, these findings reveal that spatially distinct NMII architectures coordinate protrusion dynamics across time to stabilize directional migration in complex environments. HighlightsO_LIMigrating neutrophils assemble spatially distinct myosin II architectures at the leading edge and rear C_LIO_LIProtrusion dynamics and directional persistence are linked to sustained myosin II engagement C_LIO_LIDirectional migration emerges from the temporal organization of protrusion states rather than their abundance C_LI

cell biology↗

bioRxiv2026

AN OPTIMIZED METHOD TO DIFFERENTIATE HL60 CELLS INTO NEUTROPHIL-LIKE CELLS

The HL60 promyelocytic leukemia cell line is widely used to investigate neutrophil biology due to its genetic tractability and accessibility. HL60 cells can be differentiated into neutrophil-like cells using all-trans retinoic acid (ATRA) or dimethyl sulfoxide (DMSO) treatment. However, these approaches produce cells that lack critical features of mature granulocytes, such as robust chemotaxis with ATRA treatment or multilobed nuclear morphology with DMSO treatment. To overcome these limitations, we developed a sequential differentiation protocol - ATRA for one day followed by DMSO for four days (A1D4) - which yields neutrophil-like cells that more faithfully recapitulate the morphology and functionality of mature human neutrophils. A1D4-differentiated HL60 cells display segmented nuclei with low lamin A/C expression and demonstrate strong chemotactic, oxidative burst, and phagocytic activity. This protocol combines the advantages of individual compounds, producing cells that closely mimic primary neutrophils in both phenotype and function. SUMMARY SENTENCEThe authors provide an improved method to differentiate HL60 cells into neutrophil-like cells that faithfully recapitulates the morphology and functionality of mature human neutrophils.

immunology↗

bioRxiv2025

Tracking community change via network coherence

Understanding how ecological communities respond to environmental change remains a key challenge for biodiversity monitoring. To characterize such responses, we need tools that capture how coherently species respond across a community, and to predict their consequences, we must account for ecological interactions. We first introduce the Ecological Coherence (EC) framework, which describes how species co-responses are structured within a community. Building on this foundation, we extend it to Ecological Network Coherence (ENC), which embeds co-responses within the network of interactions by restricting them to interacting species. Both are expressed through two complementary representations: a response correlation matrix and the distribution of its values. The first can reveal aspects such as coherent or incoherent modules and the roles species play in shaping coherence, whereas the second provides a profile whose shape may serve as an early-warning indicator of instability. These can be applied to both intrinsic responses (environmental performance) and realized responses (abundance dynamics), derived from currently available monitoring data. We illustrate this approach in two empirical systems: a tropical pollination network, where interacting mutualists were more coherent in their temperature responses than the broader community, and a marine food web, where coherence in abundance trends shifted during collapse. Using a Lotka-Volterra model, we further show that ENC distributions with higher variance--reflecting stronger positive and negative co-responses--increase the risk of instability or amplification in dynamics. We also find that species influential in both the correlation matrix and the interaction matrix are key drivers of major dynamic shifts. These results point to the importance of further exploring ENC distributions as potential early-warning indicators of ecological disruption.

ecology↗

bioRxiv2025

Shell-bound archives: uncovering nematode encapsulations in the Galapagos' largest radiation

How macroevolution interacts with ecological networks remains a major question in eco-evolutionary science. We investigate this interplay in the Naesiotus snail radiation of the Galapagos Islands, which encapsulates parasitic nematodes within the shell--a recently discovered gastropod defense. Using a natural history collection, we examined dry shells from 47 species across 12 islands, quantified encapsulations, and sequenced nematode DNA to reconstruct a host-parasite network. Encapsulations were widespread and revealed high nematode diversity, including in snail hosts presumed extinct. Nematode diversity was shaped by habitat, while encapsulation load was better explained by host species identity, suggesting species-specific defenses. Neither trait showed phylogenetic signal, and shell brightness was unrelated to nematode interactions. Similarly, host diversification rate did not predict network position, suggesting that macroevolution may leave a weak or obscured imprint on this host-parasite network. This snail-nematode system in islands readily enables integration of ecological networks, phylogeny, functional traits, and biogeography.

ecology↗

bioRxiv2025

Phylogenetic signal dynamics during niche filling in food webs

Understanding how phylogenetic signal in ecological networks--the tendency for closely related species to resemble one another in ecological roles--emerges and persists remains a central challenge in community ecology. Here, we simulate food web evolution to track how the correspondence between phylogeny and trophic structure changes as communities assemble and niche space fills. By simulating trait evolution coupled with trait-matching for ecological interactions, we quantify how phylogenetic signal in trophic structure changes through time and examine how species network positions relate to their phylogenetic distinctiveness and diversification dynamics. We find that the signal declines over time, driven by emergent feedbacks between node extinction, link reorganization, and trait divergence. Species with high phylogenetic distinctiveness tend to be more specialized and occupy peripheral network positions, particularly in late-stage communities. Centrality consistently constrains diversification in intermediate consumers, emerges as a limiting factor for top predators after niche saturation, and shows nonlinear effects in basal species diversification. Applying our framework to empirical food webs from the Galapagos Islands, we find partial support for these predictions: phylogenetic signal in foraging and vulnerability roles declines with island age, but shows contrasting trends with island area and elevation. We also detect discrepancies between distance-based and clustering-based measures of phylogenetic signal, highlighting the need for robust methods to compare phylogenetic and network structures. Together, our results reveal how trophic interactions mediate the erosion of phylogenetic structure during community assembly and offer testable predictions for systems at different stages of diversification.

ecology↗

bioRxiv2025

Trapped in the web: network architectures spread coevolution and shape adaptation

Adaptation is critical for biodiversity to persist under global change. Within ecological communities, species often face trade-offs between adapting to shifting abiotic conditions and navigating the complex selective pressures imposed by interaction networks. We hypothesize that network architectures characterized by high interaction diversity and overlap constrain coevolutionary dynamics, with asymmetric outcomes for exploiters and victims. Specifically, we predict that exploiters, subject to spread and conflicting selection imposed by their victims, will evolve more slowly and show reduced capacity to track victims evolutionary responses, with these constraints strongest for generalist exploiters. In contrast, victims will show more variable dynamics depending on the coherence of selection (i.e., whether pressures from different exploiters push the victims trait in the same vs. different directions). To test this, we simulated trait evolution in coevolving communities of exploiters and victims across 91 empirical networks, and in artificial networks designed to isolate specific structural effects. Our results show that higher connectance, species richness, nestedness, and centrality homogenize biotic effects and increase fluctuations in trait matching, ultimately weakening coevolutionary coupling. Under these conditions, exploiters face conflicting selection that slows evolution, whereas victims either benefit from aligned selection that accelerates evolution or are constrained by multiple pressures. Together, our findings suggest that network architecture plays a fundamental role in shaping coevolution and adaptation, and raises broader questions about its influence on eco-evolutionary processes in more complex and environmentally variable systems.

ecology↗

bioRxiv2025

Ecological coherence in abundance dynamics across terrestrial and marine assemblages

Understanding how communities respond to environmental change requires assessing not just overall variability but also the structure of co-variation among taxa. We frame this idea under the Ecological Coherence (EC) framework, which generalizes previous notions such as community synchrony or coherence. EC captures the structure of co-responses among taxa within assemblages and can be expressed through two complementary objects: (1) the co-response matrix C, which contains all pairwise correlations between taxa and can be used to identify clusters of taxa with coherent responses as well as the contributions of individual species to community-wide coherence; and (2) the EC distribution, which summarizes the overall profile of co-responses by capturing their shape, spread, and central tendency across the community. By combining these two views, EC moves beyond single summary metrics and provides a richer picture of how coherence is organized within communities. Analyzing the EC distribution across 341 terrestrial and 105 marine assemblages worldwide, we found a general prevalence of weak correlations and a few strong, directional correlations. We also found that it varies with community composition, sampling effort, and biogeographic region. Moreover, the C matrix consistently identified a small subset of taxa with strong correlations to many others, suggesting a promising path to detecting those that may play central roles in amplifying or buffering community responses to environmental change. Our findings on EC pave the way for deeper investigations into what drives the diversity of ecological responses to environmental changes and how it shapes community dynamics, while also underscoring the need for strategically distributing ecological monitoring across trophic guilds and functional roles.

ecology↗

bioRxiv2025

GPR97/ADGRG3 is activated by its tethered peptide agonist and not by steroids to induce neutrophil polarization and migration

Most adhesion G protein coupled receptors (AGPCRs) are activated by intramolecular binding of a tethered-peptide agonist (TA). Shear force-induced dissociation of the AGPCR N-terminal fragment (NTF) and C-terminal fragment (CTF) exposes the TA. The decrypted TA binds rapidly to its orthosteric site within the CTF to stabilize the active state of the AGPCR. Corticosteroids were previously proposed to be agonists for GPR97/ADGRG3. Later, other steroids and androgens were purported to be selective agonists of additional AGPCRs. Here, we demonstrate that GPR97/ADGRG3 is activated by dissociation of its NTF/CTF and follows the TA mechanism. TA peptidomimetics and the ADGRG subfamily partial agonist 3-acetoxydihydrodeoxygeduin (3--DOG), but not corticoids, stimulated GPR97/ADGRG3 in cell-based luciferase reporter assays and receptor/G protein reconstitution assays. GPR97 was defined as a promiscuous AGPCR that couples to G13, Gs and Gi, but not Gq. GPR97 is highly expressed in human polymorphonuclear neutrophils (hPMNs). Neutrophils undergo actin polymerization-induced cell shape changes and polarization and migrate upon activation. We found that GPR97 activation via TA peptidomimetics or 3--DOG robustly stimulated hPMN and mouse bone-marrow neutrophil (mBMN) polarization. Furthermore, GPR97 TA peptidomimetics and 3--DOG, but not beclomethasone, induced hPMN and mBMN chemotaxis. Together, our results demonstrate that GPR97/ADGRG3 utilizes a tethered agonist mechanism to activate G protein signaling and induce neutrophil polarization and migration. One Sentence SummaryGPR97/ADGRG3 tethered agonism regulates G protein signaling in neutrophils.

pharmacology and toxicology↗

bioRxiv2025

Insulin modulates mPFC gene expression and emotional behavior in a sex-specific manner following fetal growth restriction

Exposure to prenatal adversity (e.g., stress, malnutrition) is a major risk factor for lifelong vulnerability to neuropsychiatric and metabolic disorders, and alterations in the function of peripheral hormones in the brain are suggested as a possible and unexplored mechanism. Although insulin is well known for its peripheral metabolic functions, it also influences brain development and emotional regulation, particularly within the medial prefrontal cortex (mPFC). Here, we identify insulin signaling as a key mechanistic link between prenatal stress and long-term alterations in brain function and behavior. Using a validated rat model of prenatal adversity (prenatal food restriction, FR), we found that insulin administration selectively modulates gene expression in FR animals at P0, P21 and P90, affecting pathways involved in neurodevelopment and stress regulation, such as Wnt/{beta}-catenin signaling. Targeted insulin infusion into the mPFC of adult animals reversed behavioral phenotypes induced by FR in a sex- and context-dependent manner, decreasing emotional reactivity to environmental cues. These findings offer novel insight into the neurodevelopmental role of insulin and suggest that insulin signaling may serve as a therapeutic target to mitigate the long-term brain and behavioral consequences of prenatal adversity.

genomics↗

bioRxiv2025

cPLA2α Targeting to Exosomes Connects Nuclear Deformation to LTB4-Signaling During Neutrophil Chemotaxis

Efficient neutrophil chemotaxis requires the integration of mechanical forces and lipid-mediated signaling. While the signaling lipid leukotriene B4 (LTB4) reinforces cellular polarity, how mechanical cues regulate its production remains unclear. We now show that cytosolic phospholipase A2 (cPLA2), which is essential for the synthesis of LTB4, functions as a nuclear curvosensor. cPLA2 responds to nuclear constrictions by localizing to ceramide-rich inner nuclear membrane microdomains and incorporating onto the exofacial surface of nuclear envelope-derived exosomes. This unique topology enables localized LTB4 synthesis, which promotes myosin light chain II phosphorylation, and sustains polarity and directional persistence after constriction. In neutrophils squeezing through small constrictions, loss of cPLA2 impairs nuclear curvature sensing, exosomal LTB4 production, and post-constriction motility. These findings uncover a cPLA2-dependent mechano-chemical axis linking nuclear architecture to chemotactic efficiency and offering new strategies to modulate inflammatory responses.

cell biology↗

bioRxiv2025

Perivascular matrix densification dysregulates angiogenesis and activates pro-inflammatory endothelial cells

Fibrosis is central to numerous fatal conditions including solid cancers, pulmonary fibrosis, cirrhosis and post-infarct cardiac fibrosis amongst many others, thereby collectively contributing to 45% of all deaths in developed nations. The potential for fibrosis across most organ systems may stem from its connections to wound healing and the ubiquitous presence of vascular endothelium. Endothelial cells (ECs) and angiogenesis, cells and associated biological program central to wound healing, have been heavily implicated in many organ-specific fibroses, but the relationship between angiogenesis and fibrogenesis remains debated and little has been established in terms of how the EC phenotype governs tissue healing vs. fibrosis. Here, we examine a murine lung injury model enabling EC lineage tracing and observe the invasion of aberrant ECs from the bronchial microvasculature following lung injury along with concurrent densification of matrix fibers surrounding these vessels. To investigate the underlying mechanisms governing their appearance, we established a microphysiological system (MPS) of arteriole/venule-scale microvessels embedded within a tunable stromal mimetic matrix and find that heightened extracellular matrix fiber density activates ECs, drives endothelial to mesenchymal transition, and promotes aberrant tip EC (ATEC) invasion into the matrix. ATECs remain adherent to fibrotic matrix and possess a pro-inflammatory phenotype that secretes TGF-{beta}2. Notably, our studies establish that the formation of ATECs is gated by destabilization of endothelial adherens junction upon EC adhesion to fibrous matrix, and associated regulation of TGF-{beta} signaling that is mediated by a novel VE-cadherin - TGF-{beta}R2 axis. The current lack of effective anti-fibrotic therapies suggests potential critical involvement of other cell types such as ECs, and our findings suggest new contributions of ECs to fibrotic progression that may better inform future targets for novel anti-fibrotic therapeutics.

bioengineering↗

bioRxiv2025

Label-free Machine Learning Prediction of Chemotherapy on Tumor Spheroids using a Microfluidics Droplet Platform

To rapidly evaluate the effects of anticancer treatments in 3D models, an integrated approach is proposed, combining a droplet-based microfluidic platform for spheroid formation and single-spheroid chemotherapy application, label-free morphological analysis, and machine learning to assess treatment response. Morphological features of spheroids, such as size and color intensity, are extracted and selected using the Multivariate Information-based Inductive Causation (MIIC) algorithm, and used to train a neural network for spheroid classification into viability classes, derived from metabolic assays performed within the same platform as a benchmark. The model was tested on Ewing sarcoma cell line and patient-derived xenograft (PDX) cells, demonstrating robust performance across datasets. It accurately predicts spheroid viability, used to generate dose-response curves and to determine half-maximal inhibitory concentration (IC50) values comparable to traditional biochemical assays. Notably, a model trained on cell line spheroids successfully classifies PDX spheroids, highlighting its adaptability. Compared to convolutional neural network-based approaches, this method works with smaller training datasets and provides greater interpretability by identifying key morphological features. The droplet platform further reduces cell requirements, while single spheroid confinement enhances classification quality. Overall, this label-free experimental and analytical platform is confirmed as a scalable, efficient, and dynamic tool for drug screening.

bioengineering↗

bioRxiv2024

Keratin 16 spatially inhibits type I interferon responses in stressed skin

The stress-induced keratin 16 is broadly used as a biomarker in inflammatory skin disorders while pathogenic variants in KRT16 cause pachyonychia congenita (PC), a condition in which differentiation and homeostasis are disrupted in palmoplantar epidermis and epithelial appendages. How K16 impacts these disorders at a molecular level is poorly understood. Here we report that K16 spatially restricts type I interferon (IFN) signaling and innate immunity in palmoplantar keratoderma (PPK) lesions in PC patients, imiquimod- and phorbol ester-induced models of sterile inflammation in mouse skin, and poly(I:C)-treated human keratinocytes ex vivo. Mechanistically, K16 interacts with effectors of the RIG-I-like receptor (RLR) pathway, including 14-3-3{varepsilon}, and inhibits the 14-3-3{varepsilon}:RIG-I interaction upstream of IFN activation. Topical application of the JAK inhibitor Ruxolitinib reduces the severity of PC-PPK-like lesions in Krt16 null mice. These findings uncover a new paradigm for keratin-dependent regulation of innate immunity and suggest a new approach to PC treatment. One sentence summaryKRT16 negatively regulates type I interferon signaling and innate immune responses in the skin, offering insight into the pathophysiology of inflammatory skin diseases including pachyonychia congenita, psoriasis and others.

immunology↗

bioRxiv2024

TGFβ1-TNFα regulated secretion of neutrophil chemokines is independent of epithelial-mesenchymal transitions in breast tumor cells

Neutrophils have tumor-promoting roles in breast cancer and are detected in higher numbers in aggressive breast tumors. How aggressive breast tumors recruit neutrophils remains undefined. Here, we investigated the roles of TGF-{beta}1 and TNF- in the regulation of neutrophil recruitment by breast cancer cells. TGF-{beta}1 and TNF- are pro-inflammatory factors upregulated in breast tumors and induce epithelial to mesenchymal transitions (EMT), a process linked to cancer cell aggressiveness. We report that, as expected, dual treatment with TGF-{beta}1 and TNF- induces EMT signatures in premalignant M2 cells, which are part of the MCF10A breast cancer progression model. Conditioned media (CM) harvested from M2 cells treated with TGF-{beta}1/TNF- gives rise to amplified neutrophil chemotaxis compared to CM from control M2 cells. This response correlates with higher levels of the neutrophil chemokines CXCL1, CXCL2, and CXCL8 and is significantly attenuated in the presence of a CXCL8-neutralizing antibody. Furthermore, we found that secretion of CXCL1 and CXCL8 from treated M2 cells depends on p38MAPK activity. By combining gene editing, immunological and biochemical approaches, we show that the regulation of neutrophil recruitment and EMT signatures are not mechanistically linked in treated M2 cells. Finally, analysis of publicly available cancer cell line transcriptomic databases revealed a significant correlation between CXCL8 and TGF-{beta}1/TNF--regulated or effector genes in breast cancer. Together, our findings establish a novel role for the TGF-{beta}1/TNF-/p38 MAPK signaling axis in regulating neutrophil recruitment in breast cancer, independent of TGF-{beta}1/TNF- regulated EMT.

cancer biology↗

bioRxiv2024

Resting-state fMRI reveals altered functional connectivity associated with resilience and susceptibility to chronic social defeat stress in mouse brain

Chronic stress is a causal antecedent condition for major depressive disorder and associates with altered patterns of neural connectivity. There are nevertheless important individual differences in susceptibility to chronic stress. How stress-induced alterations in functional connectivity amongst depression-related brain regions associates with resilience and susceptibility to chronic stress is largely unknown. We used resting-state functional magnetic resonance imaging (rs-fMRI) to examine functional connectivity between established depression-related regions in susceptible (SUS) and resilient (RES) adult mice following chronic social defeat stress (CSDS). Seed-seed FC analysis revealed that the ventral dentate gyrus (vDG) exhibited the greatest number of group differences in functional connectivity with targeted brain regions. SUS mice showed greater functional connectivity between the vDG and subcortical regions compared to both control (CON) or RES groups. Whole brain vDG seed-voxel analysis supported seed-seed findings in SUS mice and indicated significantly decreased connectivity between the vDG and anterior cingulate area compared to CON mice. Interestingly, RES mice exhibited enhanced connectivity between the vDG and anterior cingulate area compared to SUS mice. Moreover, RES mice showed greater connectivity between the infralimbic prefrontal cortex and the nucleus accumbens shell. These findings indicate unique differences in functional connectivity patterns in SUS and RES mice that could represent a neurobiological basis for vulnerability for stress-induced depression.

neuroscience↗

bioRxiv2023

TGF-β1 activates neutrophil signaling and gene expression but not migration

Tumor-associated neutrophils are found in many types of cancer and are often reported to contribute to negative outcomes. The presence of transforming growth factor-beta (TGF-{beta}) in the tumor microenvironment reportedly contributes to the skewing of neutrophils to a more pro-tumor phenotype. The effects of TGF-{beta} on neutrophil signaling and migration are, however, unclear. We sought to characterize TGF-{beta} signaling in both primary human neutrophils and the neutrophil-like cell line HL-60 and determine whether it directly induces neutrophil migration. We found that TGF-{beta}1 does not induce neutrophil chemotaxis in transwell or underagarose migration assays. TGF-{beta}1 does activate canonical signaling through SMAD3 and noncanonical signaling through ERK1/2 in neutrophils in a time-and dose-dependent manner. Additionally, TGF-{beta}1 present in the tumor-conditioned media (TCM) of invasive breast cancer cells results in SMAD3 activation. We discovered that TCM induces neutrophils to secrete leukotriene B4 (LTB4), which is a lipid mediator important for amplifying the range of neutrophil recruitment. However, TGF-{beta}1 alone does not induce secretion of LTB4. RNA-sequencing revealed that TGF-{beta}1 and TCM alter gene expression in HL-60 cells, including the mRNA levels of the pro-tumor oncostatin M (OSM) and vascular endothelial growth factor A (VEGFA). These new insights into the role and impact of TGF-{beta}1 on neutrophil signaling, migration, and gene expression have significant implications in the understanding of the changes in neutrophils that occur in the tumor microenvironment.

immunology↗

bioRxiv2023

Simple droplet microfluidics platform for drug screening on cancer spheroids

3D in vitro biological systems are progressively replacing 2D systems to increase the physiological relevance of cellular studies. Microfluidics-based approaches can be powerful tools towards such biomimetic systems, but often require high-end complicated and expensive processes and equipments for microfabrication. Herein, a drug screening platform is proposed, minimizing technicality and manufacturing steps. It provides an alternate way of spheroid generation in droplets in tubes. Droplets microfluidics then elicit multiple droplets merging events at programmable times, to submit sequentially the spheroids to chemotherapy and to reagents for cytotoxicity screening. After a comprehensive study of tumorigenesis within the droplets, the system is validated for drug screening (IC50) with chemotherapies in cancer cell lines as well as cells from patient-derived-xenografts (PDX). As compared to microtiter plates methods, our sytem reduces the initial amout of cell up to 10 times and opens new avenues towards primary tumors drug screening approaches.

cancer biology↗