Biology subjects

Clark, M. J.

Publications and source records attributed to Clark, M. J..

8 recordsLinked to original sources

bioRxiv2025

Microglial MyD88-dependent signaling influences extracellular matrix development and interneuron maturation in the hippocampus

Parvalbumin interneurons (PVIs) are disrupted across diverse neurodevelopmental disorders, highlighting their vulnerability to developmental perturbations. Inflammation can perturb PVI development and function, and inflammatory mechanisms are often propagated within the brain by microglia. Yet the microglial mechanisms linking inflammatory signals to interneuron development are unclear. To test the role of microglial innate immune signaling in PVI development, we used mice lacking toll-like receptor adaptor MyD88 specifically in microglia. MyD88-deficient microglia showed reduced inflammatory responses but increased early-life phagocytosis of inhibitory synaptic material. In adulthood, males without microglial MyD88 exhibited increased hippocampal PVI density, increased extracellular matrix (ECM) deposition, increased inhibitory signaling, and impaired discrimination behaviors. We determined the cytokine interleukin (IL)-33, which normally drives adult microglial remodeling of the ECM, is developmentally regulated in the hippocampus. MyD88-deficient microglia fail to respond to IL-33, leading to reduced remodeling of the ECM component aggrecan. These results reveal microglial immune signaling via MyD88 regulates hippocampal inhibitory circuit development in a sex-specific manner.

neuroscience↗

bioRxiv2022

Social deficits induced by pervasive environmental stressors are prevented by microbial or dopaminergic modulation

Environmental toxicant exposure, including air pollution, is increasing worldwide. However, toxicant exposures are not equitably distributed. Rather, low-income and minority communities bear the greatest burden, along with higher levels of psychosocial stress. Both air pollution and maternal stress during pregnancy have been linked to neurodevelopmental disorders such as autism, but biological mechanisms and targets for therapeutic intervention remain poorly understood. We demonstrate that combined prenatal exposure to air pollution (diesel exhaust particles, DEP) and maternal stress (MS) in mice induces social behavior deficits only in male offspring, in line with the male bias in autism. These behavioral deficits are accompanied by changes in microglia and dopaminergic circuits in the brain, along with changes in the structure of the gut epithelium and microbiome. Importantly, DEP/MS-induced social deficits in males are prevented by shifting the gut microbiome by cross-fostering at birth and reversed by chemogenetic activation of the dopamine system.

neuroscience↗

bioRxiv2021

Prenatal opioid exposure inhibits microglial sculpting of the dopamine system during adolescence

The current opioid epidemic has dramatically increased the number of children who are prenatally exposed to opioids, including oxycodone. A number of social and cognitive abnormalities have been documented in these children as they reach young adulthood. However, little is known about the mechanisms underlying developmental effects of prenatal opioid exposure. Microglia, the resident immune cells of the brain, respond to acute opioid exposure in adulthood. Moreover, microglia are known to sculpt neural circuits during healthy development. Indeed, we recently found that microglial phagocytosis of dopamine D1 receptors (D1R) in the nucleus accumbens (NAc) is required for the natural developmental decline in NAc-D1R that occurs between adolescence and adulthood in rats. This microglial pruning occurs only in males, and is required for the normal developmental trajectory of social play behavior. However, virtually nothing is known as to whether this developmental program is altered by prenatal exposure to opioids. Here, we show in rats that maternal oxycodone self-administration during pregnancy leads to reduced adolescent microglial phagocytosis of D1R and subsequently higher D1R density within the NAc in adult male, but not female, offspring. Finally, we show that prenatal opioid exposure abolishes the extinction of oxycodone-conditioned place preference in these male offspring. This work demonstrates for the first time that microglia play a key role in translating prenatal opioid exposure to long-term changes in neural systems and behavior. HighlightsO_LIPrenatal opioid exposure decreases offspring viability and body weight in males and females C_LIO_LIPrenatal opioid exposure decreases microglial phagocytosis of D1R in the nucleus accumbens in males only C_LIO_LIPrenatal opioid exposure increases nucleus accumbens dopamine D1 receptor expression in males but not females C_LIO_LIAdult males fail to extinguish oxycodone-conditioned place preference following prenatal oxycodone exposure C_LI

neuroscience↗

bioRxiv2020

Leveraging non-structural data to predict structures of protein-ligand complexes

Over the past fifty years, tremendous effort has been devoted to computational methods for predicting properties of ligands that bind macromolecular targets, a problem critical to rational drug design. Such methods generally fall into two categories: physics-based methods, which directly model ligand interactions with the target given the targets three-dimensional (3D) structure, and ligand-based methods, which predict ligand properties given experimental measurements for similar ligands. Here we present a rigorous statistical framework to combine these two sources of information. We develop a method to predict a ligands pose--the 3D structure of the ligand bound to its protein target--that leverages a widely available source of information: a list of other ligands that are known to bind the same target but for which no 3D structure is available. This combination of physics-based and ligand-based modeling improves upon state-of-the-art pose prediction accuracy across all major families of drug targets. As an illustrative application, we predict binding poses of antipsychotics and validate the results experimentally. Our statistical framework and results suggest broad opportunities to predict diverse ligand properties using machine learning methods that draw on physical modeling and ligand data simultaneously.

biophysics↗

bioRxiv2019

Genome-wide association and functional analyses identify CASC20 and KIF26B as target loci in heterotopic ossification

Heterotopic ossification (HO) is bone formation that occurs after trauma within tissues that do not normally have the property of ossification, resulting in pain and disability. The genetic architecture of HO remains unclear. In the first genome-wide association studies of this disease, we identify the human-only long non-coding RNA-encoding gene CASC20 as a robust, replicating susceptibility locus for HO and KIF26B as a potential severity locus. We find that both CASC20 and KIF26B are expressed in human bone. Both CASC20 and KIF26B expression is upregulated upon BMP2 induced osteogenic differentiation in primary human mesenchymal stem cells, followed by RUNX2 and OSTERIX upregulation and mineralised nodule formation. A CRISPR-Cas9 mediated knockout of Kif26b inhibits BMP2-induced Runx2, Sp7/Osterix, Col1A1, Alp, and Bglap/Osteocalcin expression in a murine myocyte model of osteogenic trans-differentiation, and prevents mineralised nodule formation. These studies provide the first insights into the heritable biology of common, complex HO.

genetics↗

bioRxiv2019

Decoding the genomic basis of osteoarthritis

Osteoarthritis causes pain and functional disability for a quarter of a billion people worldwide, with no disease-stratifying tools nor modifying therapy. Here, we use primary cartilage and synovium from osteoarthritis patients to construct a molecular quantitative trait locus map of gene expression and protein abundance. By integrating data across omics levels, we identify likely effector genes for osteoarthritis-associated genetic signals. We detect pronounced molecular differences between macroscopically intact and highly degenerated cartilage. We identify molecularly-defined patient subgroups that correlate with clinical characteristics, stratifying patients on the basis of their molecular profile. We construct and validate a 7-gene classifier that reproducibly distinguishes between these disease subtypes, and identify potentially actionable compounds for disease modification and drug repurposing.

genomics↗

bioRxiv2018

Tissue flow induces cell shape changes during organogenesis

In embryonic development, cell shape changes are essential for building functional organs, but in many cases the mechanisms that precisely regulate these changes remain unknown. We propose that fluid-like drag forces generated by the motion of an organ through surrounding tissue could generate changes to its structure that are important for its function. To test this hypothesis, we study the zebrafish left-right organizer, Kupffers vesicle (KV), using experiments and mathematical modeling. During development, monociliated cells that comprise the KV undergo region-specific shape changes along the anterior-posterior axis that are critical for KV function: anterior cells become long and thin, while posterior cells become short and squat. Here, we develop a mathematical vertex-like model for cell shapes, which incorporates both tissue rheology and cell motility, and constrain the model parameters using previously published rheological data for the zebrafish tailbud [Serwane et al.] as well as our own measurements of the KV speed. We find that drag forces due to dynamics of cells surrounding the KV could be sufficient to drive KV cell shape changes during KV development. More broadly, these results suggest that cell shape changes could be driven by dynamic forces not typically considered in models or experiments.

biophysics↗

bioRxiv2018

An unconventional myosin, myosin 1d regulates Kupffer’s vesicle morphogenesis and laterality

INTRODUCTION INTRODUCTION RESULTS MATERIALS AND METHODS AUTHOR CONTRIBUTIONS REFERENCES Establishing left-right (LR) asymmetry is a fundamental process essential for arrangement of visceral organs during development. In vertebrates, motile cilia driven fluid flow in the left-right organizer (LRO) is essential for initiating symmetry breaking event1-3. Without a definite LRO structure in invertebrates, LR asymmetry is initiated at a cellular level by actin-myosin driven chirality4, 5. In Drosophila, myosin1D drives tissue-specific chirality in hind-gut looping6, 7. Here, we show that myosin 1d (myo1d) is essential for establishing LR asymmetry in zebrafish. Using super-r ...

developmental biology↗