Biology subjects

Blais, A.

Publications and source records attributed to Blais, A..

10 recordsLinked to original sources

bioRxiv2026

LOSS OF PARKIN DISRUPTS NUCLEAR AND MITOCHONDRIAL PROGRAMS REQUIRED FOR MUSCLE REGENERATION

Skeletal muscle stem cells (MuSCs) rely on precisely coordinated metabolic and nuclear transitions to exit quiescence, enter the cell cycle, and regenerate tissue. How these processes are coupled remains poorly defined. Here, we identify PARKIN as a critical integrator of mitochondrial quality control and nuclear RNA processing programs that together enable balanced MuSC lineage progression. Using a MuSC-specific, inducible Park2 knockout model, we show that PARKIN supports mitophagy in quiescent MuSCs, and its loss triggers premature mitochondrial polarization and fragmentation -- hallmarks of metabolic activation -- that compromise appropriate self-renewal and fate specification. Unexpectedly, MuSCs harbor a constitutive nuclear pool of PARKIN that rises rapidly upon activation and localizes to interchromatin regions, with focal association with nuclear speckles. Park2-deficient MuSCs exhibit transcriptomic signatures consistent with widespread RNA isoform switching and intron retention, particularly affecting splicing machinery components, accompanied by altered nuclear speckle organization and impaired cell cycle progression. These findings reveal that PARKIN safeguards both mitochondrial homeostasis and the RNA processing architecture essential for activation, thereby coordinating metabolic and nuclear reprogramming during early MuSC state transitions. Our work positions PARKIN as a dual compartment regulator required for robust skeletal muscle regeneration.

cell biology↗

bioRxiv2026

SynAPSeg: A novel dataset and image analysis framework for deep learning-based synapse detection and quantification

Synapses are the fundamental units of neural computation, yet quantifying their organization across circuit-level scales remains a critical bottleneck in neuroscience. While advances in fluorescent labeling and imaging can generate vast datasets, analysis is often the limiting factor. Several deep learning-based tools have been proposed to ameliorate these issues. However, existing applications primarily focus on dendritic spines and lack robust solutions for segmenting synaptic puncta in dense tissue preparations. To address this, we introduce SynAPSeg, which encompasses an open-source framework for deep learning-based analysis and, to the best of our knowledge, the first large-scale, publicly available instance segmentation dataset specifically curated for synaptic puncta. We use this dataset to train deep learning models that reach the performance of human experts across a unique benchmark dataset. SynAPSeg integrates these models into an interactive interface, with support for multi-dimensional data, enabling fully automated segmentation and quantification pipelines alongside an annotation module for refinement and validation. We demonstrate the frameworks scalability by performing the first comprehensive mapping of nearly 4 million excitatory postsynaptic PSD95 puncta within inhibitory interneurons across the dorsal hippocampus, revealing regional differences in synapse properties. Finally, we show SynAPSegs utility for 3D quantification by applying these models to study aging-associated synaptic changes in CA1 parvalbumin (PV)-positive inhibitory neurons. Through this approach, we uncover a reduction in PSD95 density along PV dendrites in the aged CA1, indicating reduced glutamatergic recruitment of PV neurons which could contribute to age-related cognitive decline. Collectively, these results demonstrate that SynAPSeg provides a scalable solution for comprehensively studying synaptic architecture in health and disease.

neuroscience↗

bioRxiv2025

Acute PFOS exposure consistently dysregulates glucose-stimulated insulin secretion across model systems

Aims/hypothesisPoly- and perfluoroalkyl substances (PFAS) are fluorinated chemicals widely used in consumer and industrial products. Serum PFAS concentrations have been linked to increased type 2 diabetes risk, but whether this is caused by direct effects of PFAS on the endocrine pancreas remains unclear. This study expands on previous biodistribution data to better characterize PFAS accumulation in human pancreas. We also assessed the effects of perfluorooctane sulfonic acid (PFOS) on pancreatic beta cell function using various model systems. MethodsWe measured concentrations of three legacy PFAS (PFOS, PFOA, PFHxS) in plasma and pancreas from 88 human donors. We also modeled PFOS and PFOA exposure in mice to confirm our human biodistribution data. We next exposed immortalized INS-1 cells, primary human donor islets, and primary mouse islets to DMSO (vehicle) or PFOS (1, 10 or 100 M) either acutely during a glucose-stimulated insulin secretion (GSIS) assay or for 48h (prolonged) and GSIS was subsequently measured. We also assessed whether the acute effects of PFOS on GSIS in mouse islets were mediated by G-protein coupled receptor-40 (GPR40) and/or glucagon-like peptide-1 receptor (GLP-1R). Lastly, we exposed female mice to DMSO or 10 mg/kg PFOS with or without a 2 g/kg glucose bolus to assess the acute effects of PFOS on glucose homeostasis in vivo. ResultsPFOS was detected at higher concentrations in both plasma and pancreas compared to PFOA and PFHxS in our human donor population. Similarly, PFOS accumulated in pancreas at concentrations 2x higher than PFOA in our mouse model. We provide compelling evidence that PFOS exposure dysregulates insulin secretion in various model systems. Prolonged PFOS exposure suppressed GSIS in INS-1 832/3 cells and mouse islets, whereas acute PFOS exposure stimulated GSIS in mouse islets and in a subset of our human donor islets. We also show that the acute effects of PFOS on GSIS in mouse islets were partly mediated by GLP-1R. Importantly, acute PFOS exposure increased plasma insulin levels in female mice in vivo, but only when PFOS exposure was concurrent with a glucose bolus. ConclusionsLegacy PFAS chemicals are consistently detected in human pancreas tissue. We clearly show that PFOS exposure dysregulates insulin secretion in various model systems, although effects varied based on the model and duration of exposure. Collectively, our findings support emerging evidence that PFOS contribute to beta cell dysfunction and points to the importance of model selection when assessing toxicological effects of PFAS on islet function.

molecular biology↗

bioRxiv2023

The glucocorticoid receptor is a critical regulator of muscle satellite cell quiescence.

Glucocorticoids are powerful anti-inflammatory medications that are associated with muscle atrophy. The effect of glucocorticoids in myofibers is well-studied, yet the role of the glucocorticoid receptor (GR), the primary mediator of glucocorticoid transcriptional responses, and the impact of glucocorticoid signalling in muscle stem cells (MuSCs), the adult progenitors responsible for regeneration, remain unknown. We developed a conditional null mouse model to knock out glucocorticoid receptor (GR) expression in MuSCs (GRMuSC-/-) and established that while GR is dispensable for muscle regeneration, it is a critical regulator of MuSC homeostasis. Loss of GR significantly increased cycling MuSCs as compared to controls in injury-naive mice and on single EDL myofiber cultures, and as such, loss of GR in MuSCs leads to precocious activation and subsequent proliferation as compared to controls. Bulk RNA-sequencing from in situ fixed MuSCs from injury-naive GRMuSC-/- muscle identified a gene signature consistent with cells that have exited quiescence and undergone activation, with evidence of sexual dimorphism. Using ATAC-seq and footprinting we identify putative GR targets that promote quiescence. Thus, we advance the GR as a previously unrecognized crucial transcriptional regulator of gene expression in MuSCs whose activity is highest in quiescent cells and is essential to maintain that state.

cell biology↗

bioRxiv2023

BCL7 proteins, metazoan-specific subunits of the mammalian SWI/SNF complex, bind the nucleosome core particle

BCL7 proteins are among the most recently identified subunits of the mammalian SWI/SNF (mSWI/SNF) chromatin remodeling complex and are absent from the unicellular version of the complex. Mutations in BCL7 proteins are associated with different kind of cancers including blood malignancies. The information on the molecular function and on the structure of BCL7 proteins is to date very limited. Here we report that BCL7 proteins directly bind the nucleosome core particle (NCP) and free DNA with high affinity. We demonstrate that BCL7 proteins form defined complexes with the NCP and we identify the conserved N-terminal part of BCL7 proteins as sufficient to nucleosome binding. We further characterize the impact of BCL7 protein mutations reported in cancer patients on NCP binding and show that the R11S driver mutation reduces the affinity for the nucleosome. Our findings clarify the molecular function of BCL7 proteins and help rationalize the impact of cancer-associated mutations.

biochemistry↗

bioRxiv2022

Transcriptome and chromatin accessibility mapping reveals a type I interferon response triggered by Mycobacterium tuberculosis infection

Tuberculosis, a deadly infectious lung disease caused by Mycobacterium tuberculosis (Mtb), remains the leading cause of bacterial disease-related deaths worldwide. The success of Mtb as a human pathogen depends on its ability to manipulate host immune response pathways, many of which are regulated by epigenetic mechanisms that control the accessibility of chromatin to the transcriptional machinery. Recent reports suggest that host phosphatases, such as PPM1A, may play a role in the regulation of chromatin accessibility during bacterial infections. However, changes in genome-wide chromatin accessibility during Mtb infection and whether PPM1A plays a role in this process remains unknown. Using combinatorial chromatin accessibility (ATAC-seq) and transcriptomics (RNA-seq) profiling of wild-type (WT), PPM1A knockout ({Delta}PPM1A) and PPM1A overexpressing (PPM1A+) macrophages, we demonstrate that Mtb infection induces global chromatin remodeling consistent with changes in gene expression signatures. The strongest concordant chromatin accessibility and gene expression signature triggered by Mtb infection was enriched for genes involved in the type I interferon (IFN) signaling pathways. Modulation of PPM1A expression results in altered chromatin accessibility signatures during Mtb infection that are reflected in the total number, chromosome location and directionality of change. Transcription factor motif analysis revealed an enrichment for transcription factors involved in the type I IFN pathway during Mtb infection, including IRF4, MEF2A, and JDP2. In contrast, both deletion and overexpression of PPM1A produced unique transcription factor enrichment signatures linked to the genomic regions with altered chromatin accessibility. Our study demonstrates that altered type I IFN responses in Mtb-infected macrophages occurs as a result of genome-wide changes in chromatin accessibility, and that PPM1A likely plays a role in a subset of these signatures.

genomics↗

bioRxiv2022

Improved sensitivity and resolution of ATAC-seq differential DNA accessibility analysis

Eukaryotic genomes are packaged into chromatin, and the extent of its compaction must be modulated to allow several biological processes such as gene transcription. The regulatory elements of expressed genes are typically in relatively accessible chromatin, and several studies have revealed a reliable correlation between the abundance of mRNA transcripts and the degree of DNA accessibility at the regulatory elements of their coding genes. In consequence, the genome-wide profiling of DNA accessibility by methods such as ATAC-seq can help in the study of gene regulatory networks by serving as a proxy for gene expression and by helping identify important gene cis-regulatory elements and the trans-acting factors that bind them. The predominant approach used to identify differentially accessible genomic loci from ATAC-seq data obtained in two conditions of interest is comparable to that employed in RNA-seq gene expression profiling studies: accessible regions are identified through peak calling and treated like "genes", then sequenced DNA fragments (originating from two neighboring transposase insertion events) that overlap them are counted and subjected to abundance modeling, which then allows to identify those that have a significant difference between the two conditions. We reasoned that this approach could be improved in terms of sensitivity and resolution by introducing two changes: bypassing peak calling, using instead a genome-wide sliding window quantification approach, and counting transposase insertion sites, instead of fragments originating from two neighboring insertion sites. We present the development of this approach, which we term "widaR", for Window- and Insertion-based Differential Accessibility in R, using a murine skeletal myoblast differentiation dataset. Reproducible R code is provided.

genomics↗

bioRxiv2021

Six1 Promotes Skeletal Muscle Thyroid Hormone Response through Regulation of the MCT10 Transporter

The Six1 transcription factor is implicated in controlling the development of several tissue types, notably skeletal muscle. Six1 also contributes to muscle metabolism and its activity is associated with the fast-twitch, glycolytic phenotype. Six1 regulates the expression of certain genes of the fast muscle program by directly stimulating their transcription or indirectly acting through a long non-coding RNA. Under the hypothesis that additional mechanisms of action might be at play, a combined analysis of gene expression profiling and genome-wide location analysis data was performed. The Slc16a10 gene, encoding the thyroid hormone transmembrane transporter MCT10, was identified as a gene with a transcriptional enhancer directly bound by Six1 and requiring Six1 activity for full expression in adult mouse tibialis anterior, a predominantly fast-twitch muscle. Of the various thyroid hormone transporters, MCT10 mRNA was found to be the most abundant in skeletal muscle, and to have a stronger expression in fast-twitch compared to slow-twitch muscle groups. Loss-of-function of MCT10 in the tibialis anterior recapitulated the effect of Six1 on the expression of fast-twitch muscle genes and led to lower activity of a thyroid hormone receptor-dependent reporter gene. These results shed light on the molecular mechanisms controlling the tissue expression profile of MCT10 and identify modulation of the thyroid hormone signaling pathway as an additional mechanism by which Six1 influences skeletal muscle metabolism.

molecular biology↗

bioRxiv2020

GREM1 is epigenetically reprogrammed in muscle cells after exercise training and controls myogenesis and metabolism

Exercise training improves skeletal muscle function, notably through tissue regeneration by muscle stem cells. Here, we hypothesized that exercise training reprograms the epigenome of muscle cell, which could account for better muscle function. Genome-wide DNA methylation of myotube cultures established from middle-aged obese men before and after endurance exercise training identified a differentially methylated region (DMR) located downstream of Gremlin 1 (GREM1), which was associated with increased GREM1 expression. GREM1 expression was lower in muscle satellite cells from obese, compared to lean mice, and exercise training restored GREM1 levels to those of control animals. We show that GREM1 regulates muscle differentiation through the negative control of satellite cell self-renewal, and that GREM1 controls muscle lineage commitment and lipid oxidation through the AMPK pathway. Our study identifies novel functions of GREM1 and reveals an epigenetic mechanism by which exercise training reprograms muscle stem cells to improve skeletal muscle function.

cell biology↗

bioRxiv2018

TCF7L1 and TCF7 differentially regulate specific mouse ES cell genes in response to GSK-3 inhibition

The genome-wide chromatin occupancy of the TCF/LEF factors and its modulation by Wnt pathway activation remain poorly defined. Here, we describe mouse ES cell (mESC) lines expressing a single copy knock-in of the 3xFLAG epitope at the N-terminus of TCF7L1 and TCF7, the two most-highly expressed TCF/LEF factors in mESCs. TCF7L1 protein levels, detected by immunoblotting with a FLAG antibody, were much higher than TCF7 in mESCs maintained in standard serum- and LIF-supplemented medium, even in the presence of the GSK-3 inhibitor, CHIR99021 (CHIR). We used FLAG antibody-mediated ChIP-seq to determine TCF7 and TCF7L1 chromatin occupancy in mESCs cultured in standard medium with or without CHIR for 14 hours. TCF7 and TCF7L1 displayed very few overlapping ChIP peaks across the genome, with TCF7L1 binding significantly more genes than TCF7 in both culture conditions. Despite a reduction in total TCF7L1 protein after CHIR treatment, the TCF7L1 ChIP peak profiles were not uniformly attenuated. Our data demonstrate that TCF7L1 chromatin occupancy upon short-term CHIR treatment is modulated in a target-specific manner. Our findings also suggest that Wnt target genes in mESCs are not regulated by TCF/LEF switching, and TCF7L1, although often called a constitutive repressor, may serve as a transcriptional activator of certain target genes in CHIR-treated mESCs.\n\nHighlightsO_LIChIP and cytometry data suggest that TCF7L1 does not directly regulate mESC Nanog expression.\nC_LIO_LITCF7L1 remains associated with {beta}-catenin in the presence of CHIR99021.\nC_LIO_LITCF7 and TCF7L1 display different chromatin occupancies in mESCs.\nC_LIO_LITCF7L1 binding at specific genomic sites is variably altered by CHIR99021.\nC_LI

cell biology↗