Biology subjects

Chambers, D.

Publications and source records attributed to Chambers, D..

5 recordsLinked to original sources

bioRxiv2024

A comprehensive spatiotemporal map of dystrophin isoform expression in the developing and adult human brain

Mutations in the dystrophin gene (DMD) cause the severe muscle-wasting disease Duchenne Muscular Dystrophy (DMD). Additionally, there is a high incidence of intellectual disability and neurobehavioural comorbidities in individuals with DMD. Similar behavioural abnormalities are found in mdx dystrophic mouse models. Unlike muscle, several dystrophin isoforms are expressed in the human brain, but a detailed map of regional and cellular localisation of dystrophin isoforms is missing. This is crucial in understanding the neuropathology of DMD individuals, and for evaluating the translatability of pre-clinical findings in DMD mouse models receiving genetic therapy interventions. Here, we provide a comprehensive dystrophin expression profile in human brains from early development to adulthood. We reveal expression of dp427p2, dp427c, dp427m and dp40 isoforms in embryonic brains, not previously reported. Dp427p2 and dp140 were greatly downregulated in adult brains, although the latter continued to be expressed across several regions. Importantly, we demonstrate for the first-time expression of DMD transcripts in human motor neurons and co-expression of different dystrophin isoforms within single neurons in both developing and adult brains. Finally, we show localisation of DMD transcripts with GAD1+ GABAergic-associated transcripts in neurons including cerebellar Purkinje cells and interneurons, as well as in the majority of neocortical and hippocampal SLC17A7+ glutamatergic neurones, suggesting a role for dystrophin in signalling at the neuronal inhibitory and excitatory synapses. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=178 HEIGHT=200 SRC="FIGDIR/small/629620v1_ufig1.gif" ALT="Figure 1"> View larger version (70K): org.highwire.dtl.DTLVardef@1dda96corg.highwire.dtl.DTLVardef@19e133corg.highwire.dtl.DTLVardef@100e8c5org.highwire.dtl.DTLVardef@b1ef77_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

The integration of network biology and pharmacophore modeling suggests repurposing Clindamycin as an inhibitor of pyroptosis via Caspase-1 blockage in tumor-associated macrophages

BackgroundUveal melanoma (UM) is a highly malignant intraocular tumor with a poor prognosis and response to therapy, including immune checkpoint inhibitors (ICIs), after the onset of liver metastasis. The metastatic microenvironment contains high levels of tumor-associated macrophages (TAMs) that correlate positively with a worse patient prognosis. We hypothesized that one could increase the efficacy of ICIs in UM metastases by immunomodulating UM-associated macrophages. MethodsTo identify potential targets for the immunomodulation, we created a network-based representation of the biology of TAMs and employed (bulk and single-cell) differential gene expression analysis to obtain a regulatory core of UM macrophages-associated genes. We utilized selected targets for pharmacophore-based virtual screening against a library of FDA-approved chemical compounds, followed by refined flexible docking analysis. Finally, we ranked the interactions and selected one novel drug-target combination for in vitro validation. ResultsBased on the generated TAM-specific interaction network (3863 nodes, 9073 edges), we derived a UM macrophages-associated regulatory core (74 nodes, 286 edges). From the regulatory core genes, we selected eight potential targets for pharmacophore-based virtual screening (YBX1, GSTP1, NLRP3, ISG15, MYC, PTGS2, NFKB1, CASP1). Of 266 drug-target interactions screened, we identified the interaction between the antibiotic Clindamycin and Caspase-1 as a priority for experimental validation. Our in vitro validation experiments showed that Clindamycin specifically interferes with activated Caspase-1 and inhibits the secretion of IL-1{beta}, IL-18, and lactate dehydrogenase (LDH) in macrophages after stimulation. Our results suggest that repurposed Clindamycin could reduce pyroptosis in TAMs, a pro-inflammatory form of programmed immune cell death favouring tumor progression. ConclusionWe were able to predict a novel Clindamycin-Caspase-1 interaction that effectively blocks Caspase-1-mediated inflammasome activity and pyroptosis in vitro in macrophages. This interaction is a promising clinical immunomodulator of the tumor microenvironment for improving ICI responsivenss. This work demonstrates the power of combining network-based transcriptomic analysis with pharmacophore-guided screening for de novo drug-target repurposing. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/576201v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@310a9aorg.highwire.dtl.DTLVardef@1af0dcaorg.highwire.dtl.DTLVardef@1b272aborg.highwire.dtl.DTLVardef@86572b_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2023

The Effect of Synthetic Training Data on the Performance of a Deep Learning Based Markerless Biomechanics System

As markerless motion capture technologies develop and mature, there is an increasing demand from the biomechanics community to provide kinematic data with the same level of accuracy as current gold standard methods. The purpose of this study was to evaluate how adding synthetic data to the training dataset of a deep learning based markerless biomechanics system impacts the accuracy of kinematic measurements during two functional movements. Synchronized video from multiple camera views was captured along with marker-based data from 9 subjects who performed 3 repetitions of countermovement jumps and squats. Including synthetic data to the training reduced lower limb error on average by 65.1% and 70.1% for the countermovement jump and squat movements, respectively. These results demonstrate the promising utility of supplementing the training of a deep learning markerless motion capture system with synthetic data.

bioengineering↗

bioRxiv2022

Dynamical Systems Models for Plasma Dilution

Recent experiments provide evidence that diluting the blood plasma restores the plasma environment to a more youthful level at least partially restoring the health of organs and tissues throughout the body. We propose that a dynamical-systems model representing the plasma constituents could support the optimization process and help determine the appropriate dilution level, frequency and any simultaneous plasma infusions to achieve the most favorable outcome. We use a combination of a gradient descent, a simulated annealing and a genetic algorithm to find a population of models that fit illustrative data. We analyze this population and present distributions of the model parameters and include a collection of plots of the dilution process for illustrative models. We then consider modifications of the dilution in order to illustrate what predictions might be possible had we more data to disambiguate the model.

biophysics↗

bioRxiv2021

Transcription Profile And Pathway Analysis Of The Endocannabinoid Receptor Inverse Agonist AM630 In The Core And Infiltrative Boundary Of Human Glioblastoma Cells

BackgroundWe have previously reported that the endocannabinoid receptor inverse agonist AM630 is a potent inhibitor of isocitrade dehydrogenase-1 wild-type glioblastoma (GBM) core tumor cell proliferation. To uncover the mechanism behind the anti-tumour effects we have performed a transcriptional analysis of AM630 activity both in the tumour core cells (U87) and the invasive margin cells (GIN-8), the latter representing a better proxy of post-surgical residual disease. ResultsThe core and invasive margin cells exhibited markedly different gene expression profiles and only the core cells had high expression of a potential AM630 target, the CB1 receptor. Both cell types had moderate expression of the HTR2B serotonin receptor, a reported AM630 target. We found that the AM630 driven transcriptional response was substantially higher in the central cells than in the invasive margin cells, with the former driving the up regulation of immune response and the down regulation of cell cycle and metastatic pathways and correlating with transcriptional responses driven by established anti-neoplastics as well as serotonin receptor antagonists. ConclusionOur results highlight the different responsiveness of the core and invasive margin cells. Taken together, whilst our findings identify AM630 as an anti-neoplastic drug, showing a high correlation with known anti-proliferative drugs, we find distinct drug sensitivies of the infiltrative margin relative to contrast-enhanced core regions of GBM upon which failed molecular targeted therapies to date have been predicated.

cancer biology↗