Biology subjects

Cox, B.

Publications and source records attributed to Cox, B..

10 recordsLinked to original sources

bioRxiv2025

Early intervention with a PACAP lactoside following repetitive mild traumatic brain injury prevents persistent LHb hyperactivity and motivational deficits in male mice

Mild traumatic brain injury (mTBI) often leads to long-lasting mood disorders and motivational deficits, significantly decreasing quality of life. The neuropeptide pituitary adenylate cyclase-activating polypeptide (PACAP) has known neuroprotective effects and is often deficient in neurological conditions, but its role in preventing mTBI's long-term effects on mood circuits remains unclear. Our previous studies of repetitive closed-head mTBI in murine models found that the lateral habenula (LHb) is a key area for post-injury impairments. These impairments are characterized by mTBI-induced LHb hyperactivity and mood-related behavioral deficits. Here we investigated if a novel PACAP type I receptor (PAC1R) agonist, TES2320, could prevent or treat these long-term mTBI effects. The drug is based on a truncated glycoside analogue of PACAP that is stable and brain penetrant. Using RNAscope, we first found that mTBI caused a persistent and widespread reduction in PACAP mRNA within the LHb, suggesting a possible mTBI-related PACAP signaling deficiency in LHb circuits. We then used two intervention strategies in young adult male mice: an early intervention administered immediately after injury and a late intervention given as a single injection one-month post-injury. One month after injury, we measured LHb activity and self-care grooming motivation. Both early and late PAC1 agonist interventions almost completely normalized the mTBI-induced increases in LHb spontaneous tonic activity and hyperexcitability. However, only the early intervention improved the delayed initiation of grooming seen in mTBI mice. Unfortunately, a single late PAC1R agonist injection not only failed to reverse the grooming delay, but also significantly reduced total grooming behavior 24 hours after treatment. This finding points to a potential behavioral side effect of late PAC1R agonist administration on grooming. Overall, our findings confirm that an early PAC1R agonist intervention effectively prevents mTBI-induced LHb hyperactivity and associated motivational deficits, likely by restoring the persistent PACAP signaling deficiency in the LHb and its related circuits. This preclinical study provides strong evidence that novel PAC1R agonists could be a valuable preventive therapy for mTBI-related depression and anti-reward circuit dysfunction.

neuroscience↗

bioRxiv2025

Extracellular matrix remodeling supports Hydra vulgaris head regeneration and stem cell invasion

The small freshwater cnidarian Hydra vulgaris is a classic model for investigating the genetic regulation of whole-body regeneration, but the underlying cell biology is comparatively underexplored. Hydra has a simple body plan consisting of two epithelial monolayers separated by an extracellular matrix (ECM). This ECM contains conserved components such as collagen and laminin, making Hydra well suited for dissecting ECM function during regeneration. Following head amputation and wound closure, we observe a retraction of ECM proteins from the wound site, creating a region of low ECM protein accumulation that persists for several days during head regeneration. Several matrix metalloproteinase (MMP) genes are expressed during this process, and MMP inhibition reduces the size of the ECM gap and results in a regenerative outcome with gross morphological defects. We further find that interstitial stem cells (ISCs), which originate in the ectoderm, localize in the regenerating head endoderm near regions of reduced ECM. This suggests that the ECM gap facilitates stem cell invasion to populate the new head with neurons and gland cells. However, inhibition of collagen cross-linking reveals that collagen synthesis is also required for regeneration, indicating that Hydra must balance ECM degradation and synthesis to complete regeneration. Together, these findings highlight ECM remodeling as a critical and conserved feature of regeneration. Summary statementThis study uses Hydra vulgaris, a highly regenerative freshwater cnidarian, to study remodeling of extracellular matrix proteins and stem cell invasion during tissue regeneration.

developmental biology↗

bioRxiv2023

Identification of anti-pathogenic activity among in silico predicted small molecule inhibitors of Pseudomonas aeruginosa LasR or Nitric Oxide Reductase (NOR)

Antibiotic resistant Pseudomonas aeruginosa strains cause considerable morbidity and mortality. Identification of novel targets in this notorious pathogen is urgently warranted to facilitate discovery of new anti-pathogenic agents acting against it. Attacking non-essential targets is believed to be a potential anti-virulence strategy. This study attempted to identify small molecule inhibitors of two important proteins LasR and nitric oxide reductase (NOR) in P. aeruginosa. This bacterial pathogen possesses multiple quorum sensing (QS) systems to regulate expression of many of its genes including those associated with virulence. Among these QS systems, Las system can be said to be the master regulator, whose receptor protein is LasR. Similarly, NOR plays crucial role in detoxification of reactive nitrogen species. This study attempted in silico identification of potential LasR or NOR inhibitors through a virtual screen employing AtomNet(R), a proprietary deep learning neural network. Following virtual screening of a large number of compounds for their affinity to LasR or NOR, a final subset of <100 compounds was created by clustering and filtering the top scoring compounds. These compounds were evaluated for their in vivo anti-pathogenic activity by challenging the model host Caenorhabditis elegans with P. aeruginosa in presence or absence of test compounds. Survival of the worm population in 24-well assay plates was monitored over a period of 5 days microscopically. Of the 96 predicted LasR inhibitors, 11 exhibited anti-Pseudomonas activity (23-96% inhibition of bacterial virulence as per third-day end point) at 25-50 {micro}g/ml. Of the 85 predicted NOR inhibitors, 8 exhibited anti-Pseudomonas activity (40-85% inhibition of bacterial virulence as per second-day end point) at 25-50 {micro}g/ml. Further investigation on molecular mode of action of active compounds is warranted.

microbiology↗

bioRxiv2023

Local, Quantitative Morphometry of Fibroproliferative Lung Injury using Laminin.

Investigations into the mechanisms of injury and repair in pulmonary fibrosis require consideration of the spatial heterogeneity inherent in the disease. Most scoring of fibrotic remodeling in preclinical animal models rely on the modified Ashcroft score, which is a semi-quantitative scoring rubric of macroscopic resolution. The obvious limitations inherent in manual pathohistological grading have generated an unmet need for unbiased, repeatable scoring of fibroproliferative burden in tissue. Using computer vision approaches on immunofluorescent imaging of the extracellular matrix (ECM) component laminin, we generate a robust and repeatable quantitative remodeling scorer (QRS). In the bleomycin lung injury model, QRS shows significant agreement with modified Ashcroft scoring with a significant Spearman coefficient r=0.768. This antibody-based approach is easily integrated into larger multiplex immunofluorescent experiments, which we demonstrate by testing the spatial apposition of tertiary lymphoid structures (TLS) to fibroproliferative tissue. The tool reported in this manuscript is available as a standalone application which is usable without programming knowledge.

pathology↗

bioRxiv2022

Leishmania mexicana Promotes Pain-reducing Metabolomic Reprogramming In Cutaneous Lesions

Cutaneous leishmaniasis (CL) is characterized by extensive skin lesions associated with an aggressive inflammatory reaction. Despite the extensive inflammation, CL lesions are usually painless, indicating that Leishmania infection may trigger anti-nociceptive activities in the infected tissues. To this date, the molecular mechanisms responsible for this clinical phenomenon have not been identified. Through an untargeted metabolomic analysis by mass spectrometry, we found enriched anti-nociceptive metabolic pathways in mice infected with Leishmania (L.) mexicana. In particular, endogenous purines were elevated at the lesion site during chronic infection, as well as in vitro in infected macrophages, compared to non-infected mice. These purines have known anti-inflammatory and analgesic properties by acting through adenosine receptors and inhibiting transient receptor potential channels of the vanilloid subtype 1 (TRPV1). Additionally, purine metabolites can promote interleukin (IL)-10 production, with a subsequent decrease in inflammation and pain sensitivity. We also found arachidonic acid metabolism enriched in the ear lesions compared to the non-infected controls. Arachidonic acid is a metabolite of anandamide (AEA) and 2-arachidonoylglycerol (2-AG). These endocannabinoids act on cannabinoid receptors 1 and 2 and TRPV1 channels to exert anti-inflammatory and analgesic effects. Our study provides the first evidence of metabolic pathways upregulated during L. mexicana infection that may mediate anti-nociceptive effects experienced by CL patients and identifies macrophages as a source of these metabolites. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=170 SRC="FIGDIR/small/503319v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@576ef2org.highwire.dtl.DTLVardef@34d939org.highwire.dtl.DTLVardef@1a13478org.highwire.dtl.DTLVardef@7bcab6_HPS_FORMAT_FIGEXP M_FIG L. mexicana infection promotes the production of purines, as well as endocannabinoid mediators, which could act on different channels of dorsal root ganglia neuron to inhibit nociception. C_FIG

microbiology↗

bioRxiv2022

Decoding the activated stem cell phenotype of the vividly maturing neonatal pituitary

The pituitary represents the endocrine master regulator. In mouse, the gland undergoes vivid maturation immediately after birth. Here, we in detail portrayed the stem cell compartment of neonatal pituitary. Single-cell RNA-sequencing pictured an active gland, revealing proliferative stem as well as hormonal (progenitor) cell populations. The stem cell pool displayed a hybrid epithelial/mesenchymal phenotype, characteristic of development-involved tissue stem cells. Organoid culturing recapitulated the stem cells phenotype, interestingly also reproducing their paracrine activity. The pituitary stem cell-activating interleukin-6 (IL-6) advanced organoid growth, although the neonatal stem cell compartment was not visibly affected in IL-6-/- mice, likely due to cytokine family redundancy. Further transcriptomic analysis exposed a pronounced WNT pathway in the neonatal gland, shown to be involved in stem cell activation and to overlap with the (fetal) human pituitary transcriptome. Following local damage, the neonatal gland efficiently regenerates, despite absence of additional stem cell proliferation, or upregulated IL-6 or WNT expression, all in line with the already high stem cell activation status, thereby exposing striking differences with adult pituitary. Together, our study decodes the stem cell compartment of neonatal pituitary, exposing an activated state in the vividly maturing gland. Understanding stem cell activation is key to potential pituitary regenerative prospects.

developmental biology↗

bioRxiv2020

Early life stress dysregulates kappa opioid receptor signaling within the lateral habenula

The lateral habenula (LHb) is an epithalamic brain region associated with value-based decision making and stress evasion through its modulation of dopamine (DA)-mediated reward circuitry. Specifically, increased activity of the LHb is associated with drug addiction, schizophrenia and stress-related disorders such as depression, anxiety and posttraumatic stress disorder. Dynorphin (Dyn)/Kappa opioid receptor (KOR) signaling is a mediator of stress response in reward circuitry. Previously, we have shown that maternal deprivation (MD), a severe early life stress, increases LHb intrinsic excitability while blunting the response of LHb neurons to extra hypothalamic corticotropin-releasing factor (CRF) signaling, another stress mediator. CRF pathways also interact with Dyn/KOR signaling. Surprisingly, there has been little study of direct KOR regulation of the LHb despite its distinct role in stress, reward and aversion processing. To test the functional role of Dyn-KOR signaling in the LHb, we utilized ex-vivo electrophysiology combined with pharmacological tools in rat LHb slices. We show that activation of KORs by a KOR agonist (U50,488) exerts differential effects on the excitability of two distinct subpopulations of LHb neurons that differ in their expression of hyperpolarization-activated cation currents (HCN, Ih). Specifically, KOR stimulation increases neuronal excitability in LHb neurons with large Ih currents (Ih+) while decreases neuronal excitability in small/negative Ih (Ih-) neurons. Additionally, we found that an intact fast-synaptic transmission is required for the effects of U50,488 on the excitability of both Ih- and Ih+ LHb neuronal subpopulations. Consistently, KOR activation also altered both glutamatergic and GABAergic synaptic transmission. While stimulation of presynaptic KORs uniformly suppressed glutamate release onto LHb neurons, we found that U50, 488 either increased or decreased GABA release. We also found that MD significantly increased immunolabeled Dyn (the endogenous KOR agonist) labeling in neuronal fibers in LHb while significantly decreased mRNA levels of KORs in LHb tissues compared to those from non-maternally deprived (non-MD) control rats. While total p38 MAPK (a downstream signaling pathway driven by KOR activation) expression was elevated in the LHb of MD rats compared to non-MD controls, we found that application of KOR-specific agonist, U50,488, onto LHb slices was still able to alter phosphorylated p38 MAPK (ph-p38) expression in MD rats similar to non-MD controls. Moreover, we found that the U50,488-mediated increase in LHb neuronal firing observed in non-MD rats was absent following MD. Altogether, this is the first demonstration of the existence of the functional Dyn/KOR signaling in the LHb that can be modulated in response to severe early life stressors such as MD.

neuroscience↗

bioRxiv2020

Mechanism of action of HBV capsid assembly modulators predicted from binding to early assembly intermediates

Interfering with the self-assembly of virus nucleocapsids is a promising approach for the development of novel antiviral agents. Applied to hepatitis B virus (HBV), this approach has led to several classes of capsid assembly modulators (CAMs) that target the virus by either accelerating nucleocapsid assembly or misdirecting it into non-capsid-like particles. Here, we have assessed the structures of early nucleocapsid assembly intermediates, with and without bound CAMs, using molecular dynamics simulations. We find that distinct conformations of the intermediates are induced depending on whether the bound CAM accelerates or misdirects assembly; these structures are predictive of the final assembly. We also selected non-capsid-like structures from our simulations for virtual screening, resulting in the discovery of several compounds with moderate anti-viral activity and low toxicity. Cryo-electron microscopy and capsid melting experiments suggest that our compounds possess a novel mechanism for assembly modulation, potentially opening new avenues for HBV inhibition.

molecular biology↗

bioRxiv2019

Accurate ethnicity prediction from placental DNA methylation data

BackgroundThe influence of genetics on variation in DNA methylation (DNAme) is well documented. Yet confounding from population stratification is often unaccounted for in DNAme association studies. Existing approaches to address confounding by population stratification using DNAme data may not generalize to populations or tissues outside those in which they were developed. To aid future placental DNAme studies in assessing population stratification, we developed an ethnicity classifier, PlaNET (Placental DNAme Elastic Net Ethnicity Tool), using five cohorts with Infinium Human Methylation 450k BeadChip array (HM450k) data from placental samples that is also compatible with the newer EPIC platform.\n\nResultsData from 509 placental samples was used to develop PlaNET and show that it accurately predicts (accuracy = 0.938, kappa = 0.823) major classes of self-reported ethnicity/race (African: n = 58, Asian: n = 53, Caucasian: n = 389), and produces ethnicity probabilities that are highly correlated with genetic ancestry inferred from genome-wide SNP arrays (>2.5 million SNP) and ancestry informative markers (n = 50 SNPs). PlaNETs ethnicity classification relies on 1860 HM450K microarray sites, and over half of these were linked to nearby genetic polymorphisms (n = 955). Our placental-optimized method outperforms existing approaches in assessing population stratification in placental samples from individuals of Asian, African, and Caucasian ethnicities.\n\nConclusionPlaNET provides an improved approach to address population stratification in placental DNAme association studies. The method can be applied to predict ethnicity as a discrete or continuous variable and will be especially useful when self-reported ethnicity information is missing and genotyping markers are unavailable. PlaNET is available as an R package at (https://github.com/wvictor14/planet).

genomics↗

bioRxiv2017

The value of DNA methylation profiling in characterizing preeclampsia and intrauterine growth restriction

Placental health is a key component to healthy pregnancy. Placental insufficiency (PI), inadequate nutrient delivery to the fetus, is associated with preeclampsia (PE), a maternal hypertensive disorder, and intrauterine growth restriction (IUGR), pathologically poor fetal growth. PI is more common in early-onset PE (EOPE) than late-onset PE (LOPE). However, the relationship between these disorders remains unclear. While DNA methylation (DNAm) alterations have been identified in PE and IUGR, these entities can overlap and few studies have analyzed these separately. This study aims to identify altered DNAm in EOPE, LOPE, and normotensive IUGR, validate these alterations, and use them to better understand the relationships between these related disorders.\n\nPlacental samples from a discovery cohort (43 controls, 22 EOPE, 18 LOPE, 11 IUGR) and validation cohort (15 controls, 22 EOPE, 11 LOPE) were evaluated using the Illumina HumanMethylation450 array. To minimize gestational age (GA) effects, EOPE samples were compared to pre-term controls (GA <37 weeks), while LOPE and IUGR were compared to term controls (GA >37 weeks). There were 1703 differentially methylated (DM) sites (FDR<0.05, {Delta}{beta}>0.1) in EOPE, 5 in LOPE, and 0 in IUGR. Of the 1703 EOPE sites, 599 were validated in the second cohort. These sites cluster samples from both cohorts into 3 distinct methylation clusters. Interestingly, LOPE samples diagnosed between 34-36 weeks with co-occurring IUGR clustered with the EOPE methylation cluster. DNAm profiling may provide an independent tool to refine clinical diagnoses into subgroups with more uniform pathology. The challenges in reproducing genome-wide DNAm studies are also discussed.

genomics↗