Biology subjects

Soucy, J. R.

Publications and source records attributed to Soucy, J. R..

6 recordsLinked to original sources

bioRxiv2025

Optimizing Tissue Clearing Methods for Improved Imaging of Whole-Mount Retinas

Gene and cell therapies are promising approaches for restoring vision in hereditary and advanced optic neuropathies. However, these therapeutic approaches must be accurately evaluated through a combination of methods, including advanced imaging, to reach the clinic. We present a whole-mount tissue-clearing methodology to improve imaging of donor neuron integration in the retina following cell transplantation in mice. Mouse retinas were processed using five different clearing methods, comparing tissue transparency, pigmentation, and immunohistochemical clarity. Among the tested methods, ScaleS consistently outperformed its peers, demonstrating a 46% increase in tissue transparency and an 89% increase in immunohistochemical clarity compared to controls. We developed a modified version of ScaleS, termed ScaleH, by adding polyvinyl alcohol to reduce fluorescence decay and enhance sample stability. ScaleH maintained fluorescence stability over extended periods (32% less decay) and proved compatible with immunolabeling and endogenous fluorescent reporters, enabling improved visualization of transplanted human stem cell-derived retinal neurons in the mouse retina. Moreover, ScaleH also improved optic nerve imaging, demonstrating the potential for broader neurobiological applications. Our clearing workflow supports robust, high-resolution imaging for evaluating the integration of transplanted cells in regenerative studies.

bioengineering↗

bioRxiv2024

Unraveling the developmental heterogeneity within the human retina to reconstruct the continuity of retinal ganglion cell maturation and stage-specific intrinsic and extrinsic factors

Tissue development is a complex spatiotemporal process with multiple interdependent components. Anatomical, histological, sequencing, and evolutional strategies can be used to profile and explain tissue development from different perspectives. The introduction of scRNAseq methods and the computational tools allows to deconvolute developmental heterogeneity and draw a decomposed uniform map. In this manuscript, we decomposed the development of a human retina with a focus on the retinal ganglion cells (RGC). To increase the temporal resolution of retinal cell classes maturation state we assumed the working hypothesis that that maturation of retinal ganglion cells is a continuous, non-discrete process. We have assembled the scRNAseq atlas of human fetal retina from fetal week 8 to week 27 and applied the computational methods to unravel maturation heterogeneity into a uniform maturation track. We align RGC transcriptomes in pseudotime to map RGC developmental fate trajectories against the broader timeline of retinal development. Through this analysis, we identified the continuous maturation track of RGC and described the cell-intrinsic (DEGs, maturation gene profiles, regulons, transcriptional motifs) and -extrinsic profiles (neurotrophic receptors across maturation, cell-cell interactions) of different RGC maturation states. We described the genes involved in the retina and RGC maturation, including de novo RGC maturation drivers. We demonstrate the application of the human fetal retina atlas as a reference tool, allowing automated annotation and universal embedding of scRNAseq data. Altogether, our findings deepen the current knowledge of the retina and RGC maturation by bringing in the maturation dimension for the cell class vs. state analysis. We show how the pseudotime application contributes to developmental-oriented analyses, allowing to order the cells by their maturation state. This approach not only improves the downstream computational analysis but also provides a true maturation track transcriptomics profile.

bioinformatics↗

bioRxiv2024

Sustained neurotrophic factor cotreatment enhances donor and host retinal ganglion cell survival in mice

Retinal ganglion cells (RGCs) lack regenerative capacity in mammals, and their degeneration in glaucoma leads to irreversible blindness. Autologous and allogeneic RGC replacement with stem cell-derived neurons has been established as a promising strategy for vision restoration, but it has been limited by relatively low (<1%) survival rates of donor cells in the hostile microenvironment of a diseased retina and optic nerve. Brain-derived neurotrophic factor (BDNF) and glial-derived neurotrophic factor (GDNF) are known to support the survival of neurons, including RGCs in. vitro and in vivo. Here, we aim to improve donor RGC survival by supplementing our in vitro cultures and in transplants with a slow-release formulation of these neuroprotective agents. We show that slow-release BDNF/GDNF significantly enhances RGC differentiation, survival, and function in vitro. Furthermore, we demonstrated that BDNF/GDNF co-treatment improved mouse and human stem cell-derived donor RGC transplantation outcomes by 2.7- and 15-fold in mice, respectively. Lastly, we show that slow-release BDNF/GDNF provides neuroprotective effects on host RGCs, preserving retinal function in a model of optic neuropathy. Altogether, this approach of engineering the retinal microenvironment with slow-release neurotrophic factors significantly enhances both donor and host neuron survival, representing a promising approach for treating glaucoma and other optic neuropathies. Table of Contents Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/583961v3_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@62d2eorg.highwire.dtl.DTLVardef@1805635org.highwire.dtl.DTLVardef@9bbea7org.highwire.dtl.DTLVardef@101e2f9_HPS_FORMAT_FIGEXP M_FIG C_FIG Engineering the retinal environment with neurotrophic factors to mimic development improves donor and host neuron survival, outgrowth, and function in an optic neuropathy mouse model.

bioengineering↗

bioRxiv2022

Introduced chemokine gradients guide transplanted and regenerated retinal neurons toward their natural position in the retina

Ongoing cell replacement studies and clinical trials have demonstrated the need to control donor and newborn cell behavior within their target tissue. Here we present a methodology to guide stem cell-derived and endogenously regenerated neurons by engineering the microenvironment. Being an "approachable part of the brain," the eye provides a unique opportunity to study donor neuron fate, migration, and integration within the central nervous system. Glaucoma and other optic neuropathies lead to the permanent loss of retinal ganglion cells (RGCs) - the neurons in the retina that transfer all visual information from the eye to the brain. Cell transplantation and transdifferentiation strategies have been proposed to restore RGCs, and one of the significant barriers to successful RGC integration into the existing retinal circuitry is cell migration towards their natural position in the retina. Here we describe a framework for identifying, selecting, and applying chemokines to direct cell migration in vivo within the retina. We have performed an in silico analysis of the single-cell transcriptome of the developing human retina and identified six receptor-ligand candidates to guide stem cell-derived or newborn neurons. The lead candidates were then tested in functional in vitro assays for their ability to guide stem cell-derived RGCs. For the in vivo studies, donor and newborn neurons were differentiated in human and mouse retinal organoids or endogenously reprogrammed with proneuronal transcription factors, respectively. An exogenous stromal cell-derived factor-1 (SDF1) gradient led to a 2.7-fold increase in donor RGC migration into the ganglion cell layer and a 3.3-fold increase in the displacement of newborn RGCs out of the inner nuclear layer. Furthermore, by altering the migratory profile of donor RGCs toward multipolar migration, overall migration was improved in mature retinal tissues. Together, these results highlight the ability and importance of engineering the tissue microenvironment and the individual cells for research and clinical applications in gene and cell therapies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC="FIGDIR/small/510158v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@1856140org.highwire.dtl.DTLVardef@1b3ca26org.highwire.dtl.DTLVardef@9c9b34org.highwire.dtl.DTLVardef@19187c0_HPS_FORMAT_FIGEXP M_FIG C_FIG In brief, the "in silico - in vitro - in vivo" funnel holds significant potential for identifying targets to control cellular processes in research and clinical applications. In this report, Soucy et al. describes a framework for identifying, selecting, and applying chemokines to direct retinal ganglion cell migration in vivo within the adult mouse retina.

bioengineering↗

bioRxiv2020

Innervated adrenomedullary microphysiological system to model prenatal nicotine and opioid exposure

The transition to extrauterine life results in a critical surge of catecholamines necessary for increased cardiovascular, respiratory, and metabolic activity. The mechanisms mediating adrenomedullary catecholamine release are poorly understood, given the sympathetic adrenomedullary control systems functional immaturity. Important mechanistic insight is provided by newborns delivered by cesarean section or subjected to prenatal nicotine or opioid exposure, demonstrating the impaired release of adrenomedullary catecholamines. To investigate mechanisms regulating adrenomedullary innervation, we developed compartmentalized 3D microphysiological systems (MPS) by exploiting the meniscus pinning effect via GelPins, capillary pressure barriers between cell-laden hydrogels. The MPS comprises discrete 3D cultures of adrenal chromaffin cells and preganglionic sympathetic neurons within a contiguous bioengineered microtissue. Using this model, we demonstrate that adrenal chromaffin innervation plays a critical role in hypoxia-medicated catecholamine release. Furthermore, opioids and nicotine were shown to affect adrenal chromaffin cell response to a reduced oxygen environment, but neurogenic control mechanisms remained intact. GelPin containing MPS represent an inexpensive and highly adaptable approach to study innervated organ systems and improve drug screening platforms by providing innervated microenvironments.

bioengineering↗

bioRxiv2018

Glial cells in the heart? Replicating the diversity of the myocardium with low-cost 3D models

Excitation-contraction (EC) coupling in the heart has, until recently, been solely accredited to cardiomyocytes. The inherent complexities of the heart make it difficult to examine nonmuscle contributions to contraction in vivo, and conventional in vitro models fail to capture multiple features and cellular heterogeneity of the myocardium. Here, we report on the development of a 3D cardiac Tissue towards recapitulating the architecture and composition of native myocardium in vitro. Cells are encapsulated within micropatterned gelatin-based hydrogels formed via visible light photocrosslinking. This system enables spatial control of cardiac microarchitecture, perturbation of the cellular composition, and functional measures of EC coupling via video microscopy and a custom algorithm to quantify beat frequency and degree of coordination. To demonstrate the robustness of these tools and evaluate the impact of altered cell population densities on cardiac Tissues, contractility and cell morphology were assessed with the inclusion of exogenous non-myelinating Schwann cells (SCs). Results demonstrate that the addition of exogenous SCs alter cardiomyocyte EC, profoundly inhibiting the response to electrical pacing. Computational modeling of connexin-mediated coupling suggests that SCs impact cardiomyocyte resting potential and rectification following depolarization. Cardiac Tissues hold potential for examining the role of cellular heterogeneity in heart health, pathologies, and cellular therapies.

bioengineering↗