Biology subjects

Gagnon, A.

Publications and source records attributed to Gagnon, A..

7 recordsLinked to original sources

bioRxiv2026

sf-pediatric: A robust and age-adaptable end-to-end pipeline for pediatric diffusion MRI

Diffusion MRI (dMRI) provides a powerful, non-invasive window into white matter (WM) development. Yet, most existing processing pipelines are not well-suited to the rapidly evolving neurophysiology of the pediatric brain. Here, we introduce sf-pediatric, a scalable, end-to-end, age-adaptable dMRI pipeline that integrates normative models of brain diffusivities to enable optimal subject-specific analysis from birth through 18 years old. Leveraging normative trajectories derived from nearly 2,000 participants from six cohorts, sf-pediatric dynamically calibrates diffusion priors, template selection, segmentation, and WM atlases based on the subjects age. By incorporating automatic quality control into a portable, tested, containerized, open-access, and press-button framework across computing environments, sf-pediatric provides a robust pipeline for large-scale pediatric dMRI studies. We validated this approach by showing improved local modeling and cortical fanning while preserving reproducibility and the ability to derive brain-behavior relationships. Additionally, we demonstrated robust recovery of known developmental trajectories of WM microstructure and connectome-derived network organization.

neuroscience↗

bioRxiv2025

Regional brain age deviations reveal divergent developmental pathways in youth

BackgroundNormative modeling of brain development has gained traction for quantifying individual deviations in maturation. The brain age gap (BAG), the difference between predicted age from MRI features and chronological age, offers a potential individualized normative metric of neurodevelopment. However, consistent patterns across psychiatric disorders remain elusive, and no studies have examined whether BAG can predict developmental trajectories within an inclusive continuous model of youths cognition and behavior. MethodsUsing longitudinal data from the Adolescent Brain Cognitive Development Study (ages 9-15, n=9,074), we built 8 region-specific brain age models using volumes, thicknesses, and surface areas of parcels from the Brainnetome adolescent atlas. We derived psychiatric diagnoses from a parental questionnaire. Multivariate linear regression was used to assess case-control differences and cross-sectional continuous cognitive/behavioral profiles. We modeled cognitive/behavioral trajectories using a multivariate joint latent-class mixed model and assessed the relationship with BAG values using multinomial logistic regression. ResultsChildren with ADHD showed delayed maturation across multiple regions (Cohens d: - 0.12 to -0.08), while subcortical BAG emerged as a transdiagnostic indicator of delayed development (d: -0.07, pfdr = 0.024). Accelerated maturation characterized the high cognition and low symptom profile, while the inverse was found for the low cognition profile. Three developmental trajectories were identified: stable, towards externalizing behaviors, or internalizing behaviors. Widespread accelerated maturation predicted evolution towards internalizing behaviors but was protective against the externalizing trajectory. ConclusionsIntegrating BAG with continuous cognitive and behavioral profiles yielded a plausible framework for early identification of atypical trajectories, potentially contributing to personalized medicine in psychiatry.

neuroscience↗

bioRxiv2025

Chronic exposure to PFAS triggers systems-level cellular reprogramming independent of their bioaccumulation

Per- and polyfluoroalkyl substances (PFAS), or "forever chemicals," are linked to metabolic, immune, and neurotoxic disorders, yet their long-term cellular effects remain unclear. Using a 24-week chronic exposure model with non-transformed human epithelial cells, we examined responses to low, environmentally relevant concentrations of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS). Integrated transcriptomic and lipidomic analyses revealed that cellular accumulation was minimal, and molecular changes instead emerged around week 17, marked by activation of oxidative stress responses, cell survival pathways, and lipid metabolism. Our data support a multi-faceted model in which PFAS-induced oxidative stress, mediated by SESN2 and SOD3, alongside increased lipid biosynthesis via SREBP axis and compound-specific disruptions of membrane lipids. These findings highlight the importance of multi-omic, time-resolved approaches in uncovering mechanisms of chronic low-dose chemical exposure and provide a foundation for future in vivo studies.

pharmacology and toxicology↗

bioRxiv2025

A novel in vitro 3D cancer model based on modular tissue engineering approach

An emerging tool to better recapitulate the complexity of tumor biology in vitro is 3D culture models. Here, we describe a free-floating collagen-based hydrogel system with embedded cancer cells, called microtissues. The microtissues are based on the well-established modular tissue engineering method. They mimic the natural development of the tumor microenvironment, with features such as hypoxia and treatment resistance. To demonstrate the utility of microtissues as a 3D tumor model system, triple negative breast cancer cells were cultured using this method and were shown to maintain cell viability and proliferation with minimal cell death, along with mimicking natural emergence of tumor properties such as, a hypoxic core. Furthermore, by screening the model with commonly used anti-breast cancer chemotherapeutics, we observed drug resistance to concentrations which are largely in accordance with the used doses in the clinics. Therefore, our model offers the opportunity to naturally reproduce fundamental features of a tumor in vitro, leading to emergence of a similar cell reprogramming which is responsible for clinical drug resistance.

cancer biology↗

bioRxiv2023

Pathogenic IgE-fated B cell memory retains functional plasticity

Long-lived immunoglobulin (Ig) E responses against innocuous environmental and dietary antigens (Ags) are maintained by an IgG1-dominant memory B cell (MBC) compartment primed for IL-4 responsiveness. The plasticity of the MBC compartment destined for IgE class switch recombination (CSR), however, remains poorly understood. In this work, we report a critical IL-4/IL-13 dependency for the pathogenic IgE fate of type 2-polarized MBCs. Initiating a recall response in the absence of IL-4/IL-13 signaling diminished the type 2 MBC phenotype in mice and humans and, in mice, permitted the emergence of long-lived Ag-specific IgG2c+ MBCs. The divergence to a type 1-like response was dependent on IFN-{gamma} signaling and arose from both unswitched and class-switched Ag-specific B cells in vivo. This reprogrammed fate was sustained even beyond therapeutic intervention, revealing fundamental insight into the plasticity of the allergen-specific MBC response. One Sentence SummaryB cell responses to allergens can be reprogrammed away from a pathogenic fate through IL-4/IL-13 signaling blockade.

immunology↗

bioRxiv2023

Environmental effects on reproductive performance in preindustrial women

Early life environments can have long-lasting effects on adult reproductive performance, but disentangling the influence of early and adult life environments on fitness is challenging, especially for long-lived species. Using a detailed dataset spanning over two centuries, we studied how early and adult life environments impact reproductive performance in preindustrial women. We assessed the effect of environmental conditions associated with the parish of birth and the parish where the women had their offspring. We considered resource availability differences between rural, urban, northern, and southern parishes by comparing women who switched environments during their lifetime with those who did not. We found that urban-born women had an earlier age at first reproduction and lower offspring survival to adulthood than rural-born women, while South Quebec women had more offspring born than North Quebec women. Moreover, switching from urban to rural led to higher offspring survival, while the reverse had the opposite effect. In addition, moving from South to North resulted in fewer offspring born and surviving, whereas moving from North to South had the inverse effect. Finally, women who changed from rural to urban and from South to North had their first child at an older age compared to those who stayed in the same urbanity type. Our study underscores the complex and interactive effects of early and adult life environments on reproductive traits, highlighting the need to consider both when studying environmental effects on reproductive outcomes.

ecology↗

bioRxiv2021

Activation of the Zinc-sensing receptor GPR39 promotes T cell reconstitution after hematopoietic stem cell transplant

Prolonged lymphopenia represents a major clinical problem after cytoreductive therapies such as chemotherapy and the conditioning required for hematopoietic stem cell transplant (HCT), contributing toward the risk of infections and malignant relapse. Restoration of T cell immunity is dependent on tissue regeneration in the thymus, the primary site of T cell development; although the capacity of the thymus to repair itself diminishes over lifespan. However, although boosting thymic function and T cell reconstitution is of considerable clinical importance, there are currently no approved therapies for treating lymphopenia. Here we found that Zinc (Zn), is critically important for both normal T cell development as well as repair after acute damage. Accumulated Zn in thymocytes during development was released into the extracellular milieu after HCT conditioning, where it triggered regeneration by stimulating endothelial cell-production of BMP4 via the cell surface receptor GPR39. Dietary supplementation of Zn was sufficient to promote thymic function in a mouse model of allogeneic HCT, including enhancing the number of recent thymic emigrants in circulation; although direct targeting of GPR39 with a small molecule agonist enhanced thymic function without the need for prior Zn accumulation in thymocytes. Together, these findings not only define an important pathway underlying tissue regeneration, but also offer an innovative preclinical approach to treat lymphopenia in HCT recipients. KEY POINTSO_LIThymocytes release zinc after HCT conditioning is sensed by GPR39 and promotes epithelial repair C_LIO_LIPharmacologic stimulation of GPR39 promotes T cell reconstitution after HCT C_LI

immunology↗