Biology subjects

Sachs, D.

Publications and source records attributed to Sachs, D..

6 recordsLinked to original sources

bioRxiv2025

Regulation of Muscle Stem Cell Dynamics and Quiescence by Netrin-1 Cytoskeletal Signaling

The hallmark property of muscle stem cells (MuSCs) at homeostasis is quiescence. However, MuSCs have cellular protrusions that are heterogeneous, complex, and tipped with filopodia, all signs of motile structures. Such protrusions may serve as sensors of the MuSC niche. Through development of a novel ex vivo live imaging assay for MuSC protrusion dynamics, we report here the identification of a regulatory pathway in this process. The axon guidance cue Netrin-1 promotes MuSC protrusion outgrowth ex vivo in a manner dependent on its receptors Dcc and Neogenin, the small GTPase Rac1, and the actin-branching factor Arp2/3; this pathway is also required for Netrin-dependent axonal growth cone motility. Adult MuSC-specific genetic removal of Netrin-1 receptors, Rac1, and Arp2/3 each result in failure to maintain homeostatic protrusion lengths, spontaneous quiescence exit, and MuSC attrition in uninjured mice. These findings reveal an unanticipated level of morphological dynamism by a quiescent stem cell at homeostasis and link this phenomenon to preservation of the quiescent state.

cell biology↗

bioRxiv2025

Development and validation of HIV SMRTcap for the characterization of HIV-1 reservoirs across tissues and subtypes

Human Immunodeficiency Virus type 1 (HIV-1) is responsible for the global HIV/AIDS epidemic and the establishment of an integrated HIV-1 reservoir remains the primary obstacle to cure. Upon therapy interruption, reactivation of the persistent HIV-1 reservoir propagates viral rebound and mediates continued immunological decline. While furthering understanding of the HIV-1 reservoir is essential for HIV-1 cure, commonly used sequencing strategies are often limited by the reliance on short-read sequencing across separate assays to determine integration sites and proviral integrity - something that does not always adequately resolve complex human genomic repeats or low complexity regions. Simultaneous identification of proviral integration sites and proviral integrity at the single molecule level would enable HIV-1 reservoir characterization with minimal imputation or bioinformatic reconstruction. Here we present HIV Single Molecule Real Time Capture (HIV SMRTcap), a novel molecular and computational pipeline that directly and simultaneously identifies HIV-1 integration sites, defines proviral integrity, and characterizes clonal expansion of HIV-1 provirus-containing cells with single molecule resolution. In combination with long-read, single-molecule, real-time (SMRT) sequencing and custom analytic pipelines, HIV SMRTcap enables a highly comprehensive characterization of HIV-1 reservoirs. Moreover, we demonstrate here that HIV SMRTcap performs robustly across the major global subtypes (HIV-1 subtype A, B, C, D and A/D recombinant viruses), and can use both cell- and tissue-derived inputs, including samples from antiretroviral therapy (ART) treated individuals with undetectable viral loads. Our results demonstrate that HIV SMRTcap serves as a comprehensive, robust method for unbiased HIV-1 reservoir characterization. Used alone, or in combination with single-cell based methods, HIV SMRTcap will enable novel exploration of viral reservoirs across subtypes and in tissue-specific compartments, providing critical information needed to inform HIV-1 cure.

genomics↗

bioRxiv2024

Finite element model of the non-keratinized buccal tissue under the impact of negative pressure

The buccal mucosa is a highly interesting site for non-invasive drug delivery due to its relatively permeable epithelium and good accessibility. Recently, device-based systems have enabled the delivery of macromolecular drugs by leveraging mechanical stretching forces on the tissue to assist drug diffusion. Despite the successful exploitation of the buccal route with such systems, the biomechanics of buccal tissue are still poorly characterized and understood due to a lack of adequate characterization methods. Therefore, we propose a combination of physiological tissue modeling with simple suction experiments as a tool for characterizing and understanding the buccal tissue under the impact of negative pressure. Here, we present an initial step towards a multiphasic and poroelastic model specifically designed for the non-keratinized buccal tissue under the impact of negative pressure. A validated finite element model (FEM) for human skin was adapted to represent the histological structure of porcine buccal tissue. We performed suction experiments using the NIMBLE device, specifically developed for measuring skin stiffness, to characterize its mechanical behavior and train the FEM model. The resulting simulation tracks essential physiological parameters and allows the prediction of measurable changes in the tissue, such as the thinning of the epithelium and single-cell stretching. The FEM simulation was validated through histochemically stained tissue sections at the NIMBLE application site. A good correlation was demonstrated between predicted and experimentally observed changes. This work serves as a first step towards a computational representation of buccal tissue under the impact of negative pressure.

bioengineering↗

bioRxiv2021

PPARdelta signaling activation improves metabolic and contractile maturation of human pluripotent stem cell-derived cardiomyocytes.

Pluripotent stem cell-derived cardiomyocytes (PSC-CMs) provide an unprecedented opportunity to study human heart development and disease. A major caveat however is that they remain functionally and structurally immature in culture, limiting their potential for disease modeling and regenerative approaches. Here, we address the question of how different metabolic pathways can be modulated in order to induce efficient hPSC-CM maturation. We show that PPAR signaling acts in an isoform-specific manner to balance glycolysis and fatty acid oxidation (FAO). PPARD activation or inhibition results in efficient respective up- or down-regulation of the gene regulatory networks underlying FAO in hPSC-CMs. PPARD induction further increases mitochondrial and peroxisome content, enhances mitochondrial cristae formation and augments FAO flux. Lastly PPARD activation results in enhanced myofibril organization and improved contractility. Transient lactate exposure, commonly used in hPSC-CM purification protocols, induces an independent program of cardiac maturation, but when combined with PPARD activation equally results in a metabolic switch to FAO. In summary, we identify multiple axes of metabolic modifications of hPSC-CMs and a role for PPARD signaling in inducing the metabolic switch to FAO in hPSC-CMs. Our findings provide new and easily implemented opportunities to generate mature hPSC-CMs for disease modeling and regenerative therapy.

cell biology↗

bioRxiv2020

Genome-wide transposon mutagenesis of paramyxoviruses reveals constraints on genomic plasticity: implications for vaccine and gene therapy

The antigenic and genomic stability of paramyxoviruses remains a mystery. Here, we evaluate the genetic plasticity of Sendai virus (SeV) and mumps virus (MuV), sialic acid-using paramyxoviruses that infect mammals from two Paramyxoviridae subfamilies (Orthoparamyxovirinae and Rubulavirinae). We performed saturating whole-genome transposon insertional mutagenesis, and identified important commonalities: disordered regions in the N and P genes near the 3 genomic end were more tolerant to insertional disruptions; but the envelope glycoproteins were not, highlighting structural constraints that contribute to the restricted antigenic drift in paramyxoviruses. Nonetheless, when we applied our strategy to a fusion-defective Newcastle disease virus (Avulavirinae subfamily), we could select for F-revertants and other insertants in the 5 end of the genome. Our genome-wide interrogation of representative paramyxovirus genomes from all three Paramyxoviridae subfamilies provides a family-wide context in which to explore specific variations within and among paramyxovirus genera and species.

microbiology↗

bioRxiv2020

SARS-CoV-2 launches a unique transcriptional signature from in vitro, ex vivo, and in vivo systems

One of the greatest threats to humanity is the emergence of a pandemic virus. Among those with the greatest potential for such an event include influenza viruses and coronaviruses. In the last century alone, we have observed four major influenza A virus pandemics as well as the emergence of three highly pathogenic coronaviruses including SARS-CoV-2, the causative agent of the ongoing COVID-19 pandemic. As no effective antiviral treatments or vaccines are presently available against SARS-CoV-2, it is important to understand the host response to this virus as this may guide the efforts in development towards novel therapeutics. Here, we offer the first in-depth characterization of the host transcriptional response to SARS-CoV-2 and other respiratory infections through in vitro, ex vivo, and in vivo model systems. Our data demonstrate the each virus elicits both core antiviral components as well as unique transcriptional footprints. Compared to the response to influenza A virus and respiratory syncytial virus, SARS-CoV-2 elicits a muted response that lacks robust induction of a subset of cytokines including the Type I and Type III interferons as well as a numerous chemokines. Taken together, these data suggest that the unique transcriptional signature of this virus may be responsible for the development of COVID-19.

microbiology↗