Biology subjects

Perkins, M.

Publications and source records attributed to Perkins, M..

8 recordsLinked to original sources

bioRxiv2025

Alternative splicing generates a Ribosomal Protein S24 isoform induced by neuroinflammation and neurodegeneration

Neuroinflammation, particularly that involving reactive microglia, the brains resident immune cells, is implicated in the pathogenesis of major neurodegenerative diseases. However, early markers of this process are in high demand. Multiple studies have reported changes in ribosomal protein (RP) expression during neurodegeneration, but the significance of these changes remains unclear. Ribosomes are evolutionarily conserved protein synthesizing machines, and although commonly viewed as invariant, accumulating evidence suggest functional ribosome specialization through variation in their protein composition. By analyzing cell type-specific translating mRNAs from mouse brains, we identify distinct RP expression patterns between neurons, astrocytes, and microglia, including neuron-specific RPs, Rpl13a and Rps10. We also observed complex expression relationships between RP paralogs and their canonical counterparts, suggesting regulated mechanisms for generating heterogeneous ribosomes. Analysis across brain regions revealed that Rplp0 and Rpl13a, commonly used normalization references, show heterogeneous expression, raising important methodological considerations for gene expression studies. Importantly, we show that Rps24, an essential ribosome component that undergoes alternative splicing to produce protein variants with different C-termini, exhibits striking cell type-specific isoform expression in brain. The Rps24c isoform is predominantly expressed in microglia and is increased by neuroinflammation caused by aging, neurodegeneration, or inflammatory chemicals. We verify increased expression of S24-PKE, the protein variant encoded by Rps24c, in brains with Alzheimers disease, Parkinsons disease, and Huntingtons disease, and relevant mouse models, using isoform-specific antibodies. These findings establish heterogeneous RP expression as a feature of brain cell types and identify Rps24c/S24-PKE as a novel marker for neuroinflammation and neurodegeneration.

neuroscience↗

bioRxiv2023

Tissue-specific vulnerability to apoptosis in Machado-Joseph disease

Machado-Joseph disease (MJD) is a dominant neurodegenerative disease caused by an expanded CAG repeat in the ATXN3 gene encoding the ataxin-3 protein. Several cellular processes, including transcription and apoptosis, are disrupted in MJD. To gain further insights into the extent of dysregulation of mitochondrial apoptosis in MJD, and to evaluate if expression alterations of specific apoptosis genes/proteins could be used as transcriptional biomarkers of disease, the levels of BCL2, BAX and TP53 and the BCL2/BAX ratio, an indicator of susceptibility to apoptosis, were assessed in blood and post-mortem brain samples from MJD subjects and MJD transgenic mice and controls. While patients show reduced levels of blood BCL2 transcripts, this measurement displays low accuracy to discriminate patients from matched controls. However, increased levels of blood BAX transcripts and decreased BCL2/BAX ratio are associated with earlier onset, indicating a possible association with MJD pathogenesis. Post-mortem MJD brains show increased BCL2/BAX transcript ratio in the dentate cerebellar nucleus (DCN) and increased BCL2/BAX insoluble protein ratio in the DCN and pons, suggesting that in these regions, severely affected by degeneration in MJD, cells show signs of apoptosis resistance. Interestingly, a follow-up study of 18 patients further shows that blood BCL2 and TP53 transcript levels increase over time in MJD patients. Furthermore, while the similar levels of blood BCL2, BAX, and TP53 transcripts observed in preclinical subjects and controls is mimicked by pre-symptomatic MJD mice, the expression profile of these genes in patient brains is partially replicated by symptomatic MJD mice. Globally, our findings indicate that there is tissue-specific vulnerability to apoptosis in MJD subjects and that this tissue dependent behavior is partially replicated in a MJD mouse model.

neuroscience↗

bioRxiv2022

Positional cues underlie cell fate specification during branching morphogenesis of the embryonic mammary epithelium

How cells coordinate morphogenetic cues and fate specification during development is a fundamental question at the basis of tissue formation. Lineage tracing studies have demonstrated that many stratified epithelia, including the mammary gland, first arise from multipotent stem cells, which are progressively replaced by distinct pools of unipotent progenitors that maintain tissue homeostasis postnatally. The lack of specific markers for early fate specification in the mammary gland has prevented the delineation of the features and spatial localization of lineage-committed progenitors that co-exist with multipotent stem cells (MaSCs) during tissue development. Here, using single-cell RNA-sequencing across 4 stages of embryonic development, we reconstructed the differentiation trajectories of multipotent mammary stem cells towards basal and luminal fate. Our data revealed that MaSCs can already be resolved into distinct populations exhibiting lineage commitment at the time coinciding with the first sprouting events of mammary branching morphogenesis (E15.5). By visualizing gene expression across our developmental atlas, we provide novel molecular markers for committed and multipotent MaSCs, and define their spatial distribution within the developing tissue. Furthermore, we show that the mammary embryonic mesenchyme is composed of two spatially-restricted cell populations, representing the sub-epithelial and dermal mesenchyme. Mechanistically, we explored the communication between different subsets of mesenchymal and epithelial cells, using time-lapse analysis of mammary embryonic explant cultures, and reveal that mesenchymal-produced FGF10 accelerates embryonic mammary branching morphogenesis without affecting cell proliferation. Altogether, our data elucidate the spatiotemporal signals underlying lineage specification of multipotent mammary stem cells and uncover the paracrine interactions between epithelial and mesenchymal cells that guide mammary branching morphogenesis.

developmental biology↗

bioRxiv2022

Control of contextual memory through interneuronal α5-GABAA receptors

{gamma}-aminobutyric acid type A receptors that incorporate 5 subunits (5-GABAARs) are highly enriched in the hippocampus and are strongly implicated in control of learning and memory. Receptors located on pyramidal neuron dendrites have long been considered responsible, but here we report that their selective knockout from either interneurons (5-i-KO) or pyramidal neurons (5-pyr-KO) interferes with the ability of the general anesthetic etomidate to suppress contextual conditioning. Using Ca2+ imaging of CA1 pyramidal neuron activity in freely exploring mice to assess hippocampal function directly, we found that etomidate blocked the development of place cells and spatial engrams in wild type (WT) and 5-pyr-KO mice, but not in 5-i-KO mice. In addition, 5-i-KO mice developed weaker spatial engrams than WT mice under control conditions. These findings show that interneuronal 5-GABAARs serve a physiological role in promoting spatial learning, and that they mediate the suppression of hippocampus-dependent memory by etomidate.

neuroscience↗

bioRxiv2021

GABAA α Subunit Control of Hyperactive Behavior in Developing Zebrafish

GABAA receptors mediate rapid responses to the neurotransmitter GABA and are robust regulators of the brain and spinal cord neural networks that control locomotor behaviors, such as walking and swimming. In developing zebrafish, gross pharmacological blockade of these receptors causes hyperactive swimming, which has been embraced as an epilepsy model. Although GABAA receptors are important to control locomotor behavior, the large number of subunits and homeostatic compensatory mechanisms have challenged efforts to determine subunit-selective roles. To address this issue, we mutated each of the eight zebrafish GABAA subunit genes individually and in pairs using a CRISPR-Cas9 somatic inactivation approach, then we examined the swimming behavior of the mutants at two developmental stages. We found that disrupting the expression of specific pairs of subunits resulted in different abnormalities in swimming behavior at the first development stage. Mutation of 4 and 5 selectively resulted in longer duration swimming episodes, mutations in 3 and 4 selectively caused excess, large-amplitude body flexions (C-bends), and mutation of 3 and 5 resulted in increases in both of these measures of hyperactivity. At the later stage of development, hyperactive phenotypes were nearly absent, suggesting that homeostatic compensation was able to overcome the disruption of even multiple subunits. Taken together, our results identify subunit-selective roles for GABAA 3, 4, and 5 in regulating locomotion. Given that these subunits exhibit spatially restricted expression patterns, these results provide a foundation to identify neurons and GABAergic networks that control discrete aspects of locomotor behavior.

neuroscience↗

bioRxiv2021

In vivo imaging of mammary epithelial cell dynamics in response to lineage-biased Wnt/Beta-catenin activation

Real-time, in vivo imaging provides an essential window into the spatiotemporal cellular and molecular events contributing to tissue development and pathology. By coupling longitudinal intravital imaging with genetic lineage tracing, here we captured the earliest cellular events underlying the impact of active Wnt/{beta}-catenin signaling on the organization and differentiation of the mammary epithelium. This enabled us to interrogate how Wnt/{beta}-catenin regulates the dynamics of distinct subpopulations of mammary epithelial cells in vivo and in real time. We show that {beta}-catenin stabilization, when targeted to either of the mammary luminal or basal epithelial lineages, invariably leads to cellular rearrangements that precipitate the formation of hyperplastic lesions that undergo squamous transdifferentiation. These results enhance our understanding of the earliest stages of hyperplastic lesion formation in vivo, and reveal that in mammary neoplastic development, {beta}-catenin activation dictates a hair-follicle/epidermal differentiation program independently of the targeted cell of origin.

cell biology↗

bioRxiv2020

Paracrine interactions between epithelial cells promote colon cancer growth

Tumours are complex ecosystems composed of different types of cells that communicate and influence each other. While the critical role of stromal cells in affecting tumour growth is well established, the impact of mutant cancer cells on healthy surrounding tissues remains poorly defined. Here, we uncovered a paracrine mechanism by which intestinal cancer cells reactivate foetal and regenerative Yap-associated transcriptional programs in neighbouring wildtype epithelial cells, rendering them adapted to thrive in the tumour context. We identified the glycoprotein Thrombospondin-1 (THBS1) as the essential factor that mediates non-cell autonomous morphological and transcriptional responses. Importantly, Thbs1 is associated with bad prognosis in several human cancers. This study reveals the THBS1-YAP axis as the mechanistic link mediating paracrine interactions between epithelial cells in intestinal tumours.

cancer biology↗

bioRxiv2020

Fluorescent Nanosensors Reveal Dynamic pH Gradients During Biofilm Formation

Understanding the dynamic environmental microniches of biofilms will permit us to detect, manage and exploit these communities. The components and architecture of biofilms have been interrogated in depth, however, little is known about the environmental microniches present. This is primarily because of the absence of tools with the required measurement sensitivity and resolution to detect these changes. We describe the application of ratiometric fluorescent pH-sensitive nanosensors, as a novel tool, to observe physiological pH changes in biofilms in real-time. Nanosensors comprised two pH-sensitive fluorophores covalently encapsulated with a reference pH-insensitive fluorophore in an inert polyacrylamide nanoparticle matrix. The nanosensors were used to analyse the real-time three-dimensional pH variation for two model biofilm formers: (i) opportunistic pathogen Pseudomonas aeruginosa, and (ii) oral pathogen Streptococcus mutans. The detection of sugar metabolism in real time by nanosensors provides a potential application to identify novel therapeutic solutions to improve oral health.

microbiology↗