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Biology subjects

Kirby, J.

Publications and source records attributed to Kirby, J..

4 recordsLinked to original sources

Astrocyte dysfunction distinguishes monozygotic twin C9orf72 expansion carriers discordant for amyotrophic lateral sclerosis.

Hexanucleotide repeat expansions in C9orf72 are the most common genetic cause of amyotrophic lateral sclerosis, yet many carriers remain asymptomatic for decades or never develop disease. This incomplete penetrance suggests that phenoconversion from genetic susceptibility to symptomatic disease onset is governed by epigenetic, environmental and cell-intrinsic modifiers. Astrocytes are key mediators of non-cell-autonomous neurodegeneration in ALS, but whether they undergo disease-associated phenoconversion in C9orf72 expansion carriers remains unclear. We investigated astrocyte-associated mechanisms of phenoconversion using a unique C9orf72 pedigree comprising monozygotic twins discordant for ALS and their asymptomatic father. This enabled analysis across a continuum from non-penetrance to late-stage neurodegeneration while controlling for inherited genetic background. Notably, the unaffected twin exhibited hypermethylation of the expanded C9orf72 allele, identifying an epigenetic correlate of non-penetrance. To define symptomatic and asymptomatic-associated astrocyte states, fibroblasts from this pedigree were directly reprogrammed into astrocytes and subjected to molecular, functional, electrophysiological and translatome analyses. Astrocytes derived from symptomatic ALS individuals were found to exhibit astrocyte-mediated toxicity towards motor neurons, canonical C9orf72 molecular pathology and connexin-related membrane dysfunction. Specifically, RNA foci and dipeptide repeat protein burden peaked in astrocytes obtained early in disease in the symptomatic twin and declined in astrocytes derived from samples obtained at advanced disease stages, whereas motor neuron toxicity increased progressively, demonstrating a dissociation between aggregate burden and functional neurotoxicity. In contrast, connexin-mediated electrophysiological dysfunction emerged with symptomatic disease and closely tracked with maximal toxicity. Translatome profiling revealed early global translational repression and impaired proteostasis in symptomatic astrocytes, whereas unaffected and non-penetrant C9-carriers retained enrichment of protein homeostasis pathways. These findings define distinct astrocyte states associated with asymptomatic, early symptomatic and late-stage disease. Notably, the affected twin reported substantially higher lifetime strenuous physical activity compared to the unaffected twin, consistent with a potential role for sustained exercise-related stress in accelerating disease onset in genetically susceptible individuals. Experimentally modelling increased stress induced aberrant upregulation of connexin-mediated currents in C9orf72 astrocytes, including in asymptomatic carriers, indicating that physiological stress can unmask latent astrocyte-intrinsic vulnerability and precipitate dysfunction in cellular homeostasis. Together, these findings redefine phenoconversion in C9orf72-associated amyotrophic lateral sclerosis to be associated with a significant upregulation of astrocyte toxicity, failure of resilience and demonstrate that the astrocyte disease state can be potentially induced by external stressors.

neuroscience↗

Characterization of the cellular and subcellular distribution of fms-like tyrosine kinase 3 (FLT3) and other neuronal proteins using an alkaline phosphatase (AP) immunolabeling method

Precisely localizing the spatial distribution of proteins within various cell types in the brain, and in sub-cellular compartments such as the synapses, is critical for generating and testing hypothesis to elucidating the function of target proteins in the brain. The fms-like tyrosine kinase-3 (FLT3) has been studied extensively in the context of blood cell development and leukemia pathogenesis, but little is known about its role in the brain. Previous work characterizing FLT3 protein expression in the brain have not yielded convincing results, mainly limited by the low expression level of FLT3 and poor sensitivity of standard immunolabeling method using fluorescent secondary antibody. In this study, we report the systematic characterization of FLT3 protein localization during brain development using a highly sensitive immunolabeling methodology based on alkaline phosphatase (AP) polymer biochemistry. Our results reveal a previously unknown neuron-selective FLT3 expression pattern in both mouse and human cerebellum tissue samples, and demonstrate a gradual increase in the total FLT3 protein level and a cytosolic-to-dendritic change in subcellular FLT3 distribution during mouse cerebellum development. Through combining the AP immunolabeling of FLT3 with standard immunostaining of various cell type markers to achieve hybrid co-labeling of multiple antigens in tissue sections, we demonstrate that the main cell type that express FLT3 in the cerebellum is PV+, Calbindin+ Purkinje cells. To expand the use case of AP immunolabeling method in labeling neuronal proteins, we show robust labeling of Kir2.1, a potassium channel protein that is expressed at low level in neurons, in brain tissue sections collected from mouse, pig, and human brains. We further established that the AP immunolabeling method can be used in human stem cell-derived neurons to detect postsynaptic density scaffold protein PSD95 within fine subcellular structures such as dendritic spines and synapses, in cultured primary mouse cortical neurons and human stem cell-derived neurons. To our knowledge, our work represents the first report of applying AP immunolabeling to detect neuronal protein expression in brain tissue and cell samples. Moreover, our work reveals a previously unknown neuron-specific pattern of FLT3 expression in the brain, providing the foundation for further mechanistic studies to uncover its role in brain development and functioning.

neuroscience↗

A toolset of constitutive promoters for metabolic engineering of Rhodosporidium toruloides

BackgroundRhodosporidium toruloides is a promising host for the production of bioproducts from lignocellulosic biomass. A key prerequisite for efficient pathway engineering is the availability of robust genetic tools and resources. However, there is a lack of characterized promoters to drive expression of heterologous genes for strain engineering in R. toruloides.\n\nResultsOur data describes a set of native R. toruloides promoters, characterized over time in four different media commonly used for cultivation of this yeast. The promoter sequences were selected using transcriptional analysis and several of them were found to drive expression bidirectionally. We measured promoter expression strength by flow cytometry using a dual fluorescent reporter system. From these analyses, we found a total of 20 constitutive promoters (12 monodirectional and 8 bidirectional) of potential value for genetic engineering of R. toruloides.\n\nConclusionsWe present a list of robust and constitutive, native promoters to facilitate genetic engineering of R. toruloides. This set of thoroughly characterized promoters significantly expands the range of engineering tools available for this yeast and can be applied in future metabolic engineering studies.

synthetic biology↗

Rhodosporidium toruloides: A new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts

BackgroundEconomical conversion of lignocellulosic biomass into biofuels and bioproducts is central to the establishment of a robust bioeconomy. This requires a conversion host that is able to both efficiently assimilate the major lignocellulose-derived carbon sources and divert their metabolites toward specific bioproducts.\n\nResultsIn this study, the carotenogenic yeast Rhodosporidium toruloides was examined for its ability to convert lignocellulose into two non-native sesquiterpenes with biofuel (bisabolene) and pharmaceutical (amorphadiene) applications. We found that R. toruloides can efficiently convert a mixture of glucose and xylose from hydrolyzed lignocellulose into these bioproducts, and unlike many conventional production hosts, its growth and productivity were enhanced in lignocellulosic hydrolysates relative to purified substrates. This organism was demonstrated to have superior growth in corn stover hydrolysates prepared by two different pretreatment methods, one using a novel biocompatible ionic liquid (IL) choline -ketoglutarate, which produced 261 mg/L of bisabolene at bench-scale, and the other using an alkaline pretreatment, which produced 680 mg/L of bisabolene in a high gravity fed-batch bioreactor. Interestingly, R. toruloides was also observed to assimilate p-coumaric acid liberated from acylated grass lignin in the IL hydrolysate, a finding we verified with purified substrates. R. toruloides was also able to consume several additional compounds with aromatic motifs similar to lignin monomers, suggesting that this organism may have the metabolic potential to convert depolymerized lignin streams alongside lignocellulosic sugars.\n\nConclusionsThis study highlights the natural compatibility of R. toruloides with bioprocess conditions relevant to lignocellulosic biorefineries and demonstrates its ability to produce non-native terpenes.

bioengineering↗