Biology subjects

Dupont, J.-B.

Publications and source records attributed to Dupont, J.-B..

7 recordsLinked to original sources

bioRxiv2026

Engineered muscle tissues with enhanced maturation enable the identification of clinically relevant rAAV capsids

Developing in vitro models that recapitulate both the structure and function of native human tissues is crucial for a better understanding of pathophysiology and for improving the reliability of preclinical studies. Here, we demonstrate that engineered muscle tissues derived from human pluripotent stem cells can serve as an in vitro platform for gene therapy. Recombinant vectors derived from the adeno-associated virus transduce engineered muscle tissues with high efficiency and in a dose-dependent manner, allowing long term assessment of transgene expression in a human cellular context. We next used this model to conduct a comparative analysis of 8 natural AAV capsids and showed that their relative efficiency depends on engineered muscle tissue maturation level. In more mature tissues subjected to uniaxial mechanical stretch, AAV9 performed better, which is reminiscent of its high clinical potential in patients with neuromuscular disorders. Finally, our model also confirmed the higher efficiency of artificial MyoAAV variants specifically developed to have an improved muscle transduction. Altogether, this work demonstrates the potential of human engineered muscle tissues in the preclinical testing of AAV vectors, paving the way for the development of personalized gene therapy platforms.

bioengineering↗

bioRxiv2025

Inference and validation of a dynamic gene regulatory network influencing cell fate during Duchenne muscular dystrophy initiation

The onset of gene regulatory disturbances leading to developmental disorders remains poorly understood, particularly when symptoms begin after birth. Using induced pluripotent stem cells, single-cell transcriptomics and computational modeling, we determined the gene expression waves guiding early myogenesis and how they are affected by a disease-causing mutation. We uncovered a dynamic gene regulatory network organized in two kernels that function as a toggle-switch controlling stochastic cell fate decisions. In cells derived from patients with Duchenne muscular dystrophy, these waves of regulation are less pronounced and the switch remains in the OFF state with a higher probability, resulting in convergence into a restricted cell fate. Experimental reactivation of the switch through RNA interference led to a rescued transcriptomic state and to a refined network topology. This work uncovers a dynamic regulatory mechanism underlying early cell fate divergence and provides a general framework to infer and validate dynamic gene regulatory networks involved in disease initiation.

bioinformatics↗

bioRxiv2025

Voluntary Running Sustains the Correction of Inflammation-Related Gene Expression Conferred by AAV Gene Therapy in Mdx Mice

Duchenne Muscular Dystrophy is a fatal disease characterized by persistent skeletal muscle degeneration, inflammation, and fibrosis. Gene therapy using an adeno-associated virus derived vector and a microdystrophin transgene is currently under investigation in patients but the impact of physical activity on long-term therapeutic outcome remains poorly understood. Recently, we reported 21-weeks of voluntary wheel running complemented the positive endurance and muscle function outcomes of gene therapy in mdx mice. In the present study, we performed a transcriptomic analysis of the gene expression changes associated with functional recovery in the diaphragm. RNA-Sequencing and bioinformatic analysis revealed 2881 dysregulated genes in untreated and unexercised mdx mice including inflammatory and fibrotic signaling pathways frequently affected in Duchenne Muscular Dystrophy patients. Among the dysregulated genes, 774 were rescued towards WT after adeno-associated virus microdystrophin injection. Importantly, 93% of the rescued genes were maintained by voluntary running, which indicates that physical exercise has no significant impact on the outcome of gene therapy in the mdx diaphragm. Our study provides vital information that could help guide DMD patient follow-up protocols after treatment with gene therapy.

pathology↗

bioRxiv2023

Dystrophin deficiency impairs cell junction formation during embryonic myogenesis

Mutations in the DMD gene lead to Duchenne muscular dystrophy, a severe X-linked neuromuscular disorder that manifests itself as young boys acquire motor functions. DMD is typically diagnosed at 2 to 4 years of age, but the absence of dystrophin negatively impacts muscle structure and function before overt symptoms appear in patients, which poses a serious challenge in the optimization of standards of care. In this report, we investigated the early consequences of dystrophin deficiency during skeletal muscle development. We used single-cell transcriptome profiling to characterize the myogenic trajectory of human pluripotent stem cells and showed that DMD cells bifurcate to an alternative branch when they reach the somite stage. Here, dystrophin deficiency was linked to marked dysregulations of cell junction protein families involved in the cell state transitions characteristic of embryonic somitogenesis. Altogether, this work demonstrates that in vitro, dystrophin deficiency has deleterious effects on cell-cell communication during myogenic development, which should be considered in future therapeutic strategies for DMD.

pathology↗

bioRxiv2022

High-throughput, real-time monitoring of engineered skeletal muscle function using magnetic sensing

Engineered muscle tissues represent powerful tools for examining tissue level contractile properties of skeletal muscle. However, limitations in the throughput associated with standard analysis methods limit their utility for longitudinal study, high throughput drug screens, and disease modeling. Here we present a method for integrating 3D engineered skeletal muscles with a magnetic sensing system to facilitate non-invasive, longitudinal analysis of developing contraction kinetics. Using this platform, we show that engineered skeletal muscle tissues derived from both induced pluripotent stem cell and primary sources undergo improvements in contractile output over time in culture. We demonstrate how magnetic sensing of contractility can be employed for simultaneous assessment of multiple tissues subjected to different doses of known skeletal muscle inotropes as well as the stratification of healthy versus diseased functional profiles in normal and dystrophic muscle cells. Based on these data, this combined culture system and magnet-based contractility platform greatly broadens the potential for 3D engineered skeletal muscle tissues to impact the translation of novel therapies from the lab to the clinic.

bioengineering↗

bioRxiv2019

Myogenesis modelled by human pluripotent stem cells uncovers Duchenne muscular dystrophy phenotypes prior to skeletal muscle commitment

Duchenne muscular dystrophy (DMD) causes severe disability of children and death of young men, with an incidence of approximately 1/5,000 male births. Symptoms appear in early childhood, with a diagnosis made around 4 years old, a time where the amount of muscle damage is already significant, preventing early therapeutic interventions that could be more efficient at halting disease progression. In the meantime, the precise moment at which disease phenotypes arise - even asymptomatically - is still unknown. Thus, there is a critical need to better define DMD onset as well as its first manifestations, which could help identify early disease biomarkers and novel therapeutic targets. In this study, we have used human induced pluripotent stem cells (hiPSCs) from DMD patients to model skeletal myogenesis, and compared their differentiation dynamics to that of healthy control cells by a comprehensive multi-omic analysis. Transcriptome and miRnome comparisons combined with protein analyses at 7 time points demonstrated that hiPSC differentiation 1) mimics described DMD phenotypes at the differentiation endpoint; and 2) homogeneously and robustly recapitulates key developmental steps - mesoderm, somite, skeletal muscle - which offers the possibility to explore dystrophin functions and find earlier disease biomarkers. Starting at the somite stage, mitochondrial gene dysregulations escalate during differentiation. We also describe fibrosis as an intrinsic feature of skeletal muscle cells that starts early during myogenesis. In sum, our data strongly argue for an early developmental manifestation of DMD whose onset is triggered before the entry into the skeletal muscle compartment, data leading to a necessary reconsideration of dystrophin functions during muscle development.

developmental biology↗

bioRxiv2018

AAV-mediated gene transfer restores a normal muscle transcriptome in a canine model of X-linked myotubular myopathy

Multiple clinical trials employing recombinant adeno-associated viral (rAAV) vectors have been initiated for neuromuscular disorders, including Duchenne and limb-girdle muscular dystrophies, spinal muscular atrophy, and recently X-linked myotubular myopathy (XLMTM). Previous work from our laboratory on a canine model of XLMTM showed that a single rAAV8-cMTM1 systemic infusion corrects structural abnormalities within the muscle and restores contractile function, with affected dogs surviving more than four years post injection. This exceptional therapeutic efficacy presents a unique opportunity to identify the downstream molecular drivers of XLMTM pathology, and to what extent the whole muscle transcriptome is restored to normal after gene transfer. Herein, RNA-sequencing was used to examine the transcriptomes of the Biceps femoris and Vastus lateralis in a previously-described canine cohort showing dose-dependent clinical improvements after rAAV8-cMTM1 gene transfer. Our analysis confirmed several dysregulated genes previously observed in XLMTM mice, but also identified new transcripts linked to XLMTM pathology. We demonstrated XLMTM transcriptome remodeling and dose-dependent normalization of gene expression after gene transfer and created new metrics to pinpoint potential biomarkers of disease progression and correction.

pathology↗