Biology subjects

Moses, E.

Publications and source records attributed to Moses, E..

13 recordsLinked to original sources

bioRxiv2024

The cGAS-STING pathway is an in vivo modifier of genomic instability syndromes

Mutations in genes involved in DNA damage repair (DDR) often lead to premature aging syndromes. While recent evidence suggests that inflammation, alongside mutation accumulation and cell death, may drive disease phenotypes, its precise contribution to in vivo pathophysiology remains unclear. Here, by modeling Ataxia Telangiectasia (A-T) and Bloom Syndrome in the African turquoise killifish (N. furzeri), we replicate key phenotypes of DDR syndromes, including infertility, cytoplasmic DNA fragments, and reduced lifespan. The link between DDR defects and inflammation is attributed to the activation of the cGAS-STING pathway and interferon signaling by cytoplasmic DNA. Accordingly, mutating cGAS partially rescues germline defects and senescence in A-T fish. Double mutants also display reversal of telomere abnormalities and suppression of transposable elements, underscoring cGASs non-canonical role as a DDR inhibitor. Our findings emphasize the role of interferon signaling in A-T pathology and identify the cGAS-STING pathway as a potential therapeutic target for genomic instability syndromes.

genetics↗

bioRxiv2024

Effective excitability captures network dynamics across development and phenotypes

Neuronal cultures in vitro are a versatile system for studying the fundamental properties of individual neurons and neuronal networks. Recently, this approach has gained attention as a precision medicine tool. Mature neuronal cultures in vitro exhibit synchronized collective dynamics called network bursting. If analyzed appropriately, this activity could offer insights into the networks properties, such as its composition, topology, and developmental and pathological processes. A promising method for investigating the collective dynamics of neuronal networks is to map them onto simplified dynamical systems. This approach allows the study of dynamical regimes and the characteristics of the parameters that lead to data-consistent activity. We designed a simple biophysically inspired dynamical system and used Bayesian inference to fit it to a large number of recordings of in vitro population activity. Even with a small number of parameters, the model showed strong inter-parameter dependencies leading to invariant bursting dynamics for many parameter combinations. We further validated this observation in our analytical solution. We found that in vitro bursting can be well characterized by each of three dynamical regimes: oscillatory, bistable, and excitable. The probability of finding a data-consistent match in a particular regime changes with network composition and development. The more informative way to describe the in vitro network bursting is the effective excitability, which we analytically show to be related to the parameter-invariance of the models dynamics. We establish that the effective excitability can be estimated directly from the experimentally recorded data. Finally, we demonstrate that effective excitability reliably detects the differences between cultures of cortical, hippocampal, and human pluripotent stem cell-derived neurons, allowing us to map their developmental trajectories. Our results open a new avenue for the model-based description of in vitro network phenotypes emerging across different experimental conditions.

neuroscience↗

bioRxiv2023

The germline regulates longevity and somatic repair in a sex-specific manner

Classical evolutionary theories propose tradeoffs between reproduction, damage repair, and lifespan. However, the specific role of the germline in shaping vertebrate aging remains largely unknown. Here, we use the turquoise killifish (N. furzeri) to genetically arrest germline development at discrete stages, and examine how different modes of infertility impact life-history. We first construct a comprehensive single-cell gonadal atlas, providing cell-type-specific markers for downstream phenotypic analysis. Next, we show that germline depletion - but not arresting germline differentiation - enhances damage repair in female killifish. Conversely, germline-depleted males instead showed an extension in lifespan and rejuvenated metabolic functions. Through further transcriptomic analysis, we highlight enrichment of pro-longevity pathways and genes in germline-depleted male killifish and demonstrate functional conservation of how these factors may regulate longevity in germline-depleted C. elegans. Our results therefore demonstrate that different germline manipulation paradigms can yield pronounced sexually dimorphic phenotypes, implying alternative responses to classical evolutionary tradeoffs.

genetics↗

bioRxiv2023

Exploring life-long tissue homeostasis through lineage tracing and cell transplantation

The antagonistic pleiotropy theory of aging predicts functional trade-offs between early-life and late-life fitness. However, empirical evidence for these trade-offs in vertebrates remains scarce, particularly in the context of ecologically relevant life histories. Here, we identify vestigial-like 3 (vgll3), a transcription cofactor previously linked with age at maturity in humans and Atlantic salmon through GWAS studies, as an antagonistically pleiotropic gene in turquoise killifish (Nothobranchius furzeri). By disrupting two conserved vgll3 isoforms, we show that reduction of vgll3, in an isoform- or dose-dependent manner, accelerated male growth and reproductive development. This indicates that vgll3 regulates sexual maturity. However, early-life benefits come at a late-life cost, as older mutant males with a disrupted long isoform develop melanoma-like tumors, validated via transplantation into immunodeficient rag2 models, and exhibit increased age-related mortality rate. These findings highlight vgll3 as a key regulator of vertebrate life-history trade-offs, balancing early-life fitness with late-life disease risks.

genetics↗

bioRxiv2023

Broad sialic acid usage amongst species D human adenovirus.

Human adenoviruses (HAdV) are widespread pathogens causing infections of the respiratory and gastrointestinal tracts, genitourinary system and the eye. Species D (HAdV-D) are the most diverse species and cause both gastrointestinal tract infections and epidemic keratoconjunctivitis (EKC). Despite being significant pathogens, HAdV-D are understudied and knowledge around basic mechanisms of cell infection is lacking. Sialic acid (SA) usage has been proposed as a major mechanism of cell infection for EKC causing HAdV-D. Here, we provide apo state crystal structures for fiber knob proteins of 7 previously undetermined HAdV-D, and provide crystal structures of HAdV-D25, HAdV-D29 and HAdV-D53 knob proteins bound to SA. Biologically, we demonstrate that removal of cell surface SA reduced infectivity of HAdV-C5 vectors pseudotyped with HAdV-D fiber knob proteins, whilst engagement of the classical HAdV receptor, CAR was variable. Together, these data indicate an important role for SA engagement in the tropism of many HAdV-D and may facilitate the development of suitable antivirals to control EKC outbreaks.

microbiology↗

bioRxiv2023

A scalable platform for functional interrogation of peptide hormones in fish

Fish display a remarkable diversity of life-history traits, including body size, age at maturity, and longevity. Although pituitary hormones are conserved mediators of life-history transitions, regulatory networks are less understood in fish. However, the relatively long life-cycles and germline-dependent maturation of classical fish models are less compatible with rapid exploration of adult physiology, particularly in females. Here, we describe a high-throughput platform that combines, for the first time, loss- and gain-of-function of peptide hormones in a naturally short-lived fish. As a proof-of-principle, we first manipulate growth by mutating growth hormone (gh1) in the turquoise killifish (N. furzeri). Next, to rescue growth defects, we designed a vector in which hormones are tagged by a self-cleavable fluorescent reporter, and are ectopically expressed using intramuscular electroporation. A single injection of a gh1-T2A-GFP plasmid was sufficient to produce a stable expression of tag-free hormone and rescue growth phenotypes. This, in contrast to current practice for which multiple injections of recombinant hormones are required. We demonstrate the versatility of our platform by rescuing female sterility, which is induced by manipulating the follicle stimulating hormone (fshb). As killifish maturation is germline-independent, both sexes can be explored in genetic models with germline defects. Finally, we describe a doxycycline-inducible system for tunable expression control. Together, this platform significantly advances the state-of-the-art by allowing high-throughput functional dissection of distinct life-history strategies in fish. This method could be multiplexed to facilitate various applications, including optimizing commercially valuable traits in aquaculture, or screening pro-longevity hormonal interventions in aging.

genetics↗

bioRxiv2022

Identification of protein aggregates in the aging vertebrate brain with prion-like andphase separation properties

Protein aggregation, which can sometimes spread in a prion-like manner, is a hallmark of neurodegenerative diseases. However, whether prion-like aggregates form during normal brain aging remains unknown. Here we use quantitative proteomics in the African turquoise killifish to identify protein aggregates that accumulate in old vertebrate brains. These aggregates are enriched for prion-like RNA binding proteins, notably the ATP-dependent RNA helicase DDX5. We validate that DDX5 forms mislocalized cytoplasmic aggregates in the brains of old killifish and mice. Interestingly, DDX5s prion-like domain allows these aggregates to propagate across many generations in yeast. In vitro, DDX5 phase separates into condensates. Mutations that abolish DDX5 prion propagation also impair the proteins ability to phase separate. DDX5 condensates exhibit enhanced enzymatic activity, but they can mature into inactive, solid aggregates. Our findings suggest that protein aggregates with prion-like properties form during normal brain aging, which could have implications for the age-dependency of cognitive decline.

neuroscience↗

bioRxiv2022

Tissue-specific landscape of protein aggregation and quality control in an aging vertebrate

Protein aggregation is a hallmark of age-related neurodegeneration. Yet, aggregation during normal aging and in tissues other than the brain is poorly understood. Here we leverage the African turquoise killifish to systematically profile protein aggregates in seven tissues of an aging vertebrate. Age-dependent aggregation is strikingly tissue-specific, and not simply driven by protein expression differences. Experimental interrogation, combined with machine learning, indicates that this specificity is linked to both protein-autonomous biophysical features and tissue-selective alterations in protein quality control. Co-aggregation of protein quality control machinery during aging may further reduce proteostasis capacity, exacerbating aggregate burden. A segmental progeria model with accelerated aging in specific tissues exhibits selectively increased aggregation in these same tissues. Intriguingly, many age-related protein aggregates arise in wild-type proteins that, when mutated, drive human diseases. Our data chart a comprehensive landscape of protein aggregation during aging and reveal strong, tissue-specific associations with dysfunction and disease. HIGHLIGHTSO_LITissue-specific protein aggregation is prevalent during vertebrate aging C_LIO_LIBoth protein biophysical properties and tissue-specific protein homeostasis patterns impact aggregation C_LIO_LIA segmental progeria model with accelerated aging exhibits selectively increased protein aggregation in affected tissues C_LIO_LIMany aggregates that accumulate during physiological aging are linked to disease C_LI

systems biology↗

bioRxiv2020

The fiber knob protein of human adenovirus type 49 mediates highly efficient and promiscuous infection of cancer cell lines using a novel cell entry mechanism

The human adenovirus (HAdV) phylogenetic tree is diverse, divided across seven species and comprising over 100 individual types. Species D HAdV are rarely isolated with low rates of pre-existing immunity, making them appealing for therapeutic applications. Several species D vectors have been developed as vaccines against infectious diseases where they induce robust immunity in pre-clinical models and early phase clinical trials. However, many aspects of the basic virology of species D HAdV, including their basic receptor usage and means of cell entry, remain understudied. Here, we investigated HAdV-D49, which previously has been studied for vaccine and vascular gene transfer applications. We generated a pseudotyped HAdV-C5 presenting the HAdV-D49 fiber knob protein (HAdV-C5/D49K). This pseudotyped vector was efficient at infecting cells devoid of all known HAdV receptors, indicating HAdV-D49 uses an unidentified cellular receptor. Conversely, a pseudotyped vector presenting the fiber knob protein of the closely related HAdV-D30 (HAdV-C5/D30K), differing in four amino acids to HAdV-D49, failed to demonstrate the same tropism. These four amino acid changes resulted in a change in isoelectric point of the knob protein, with HAdV-D49K possessing a basic apical region compared to a more acidic region in HAdV-D30K. Structurally and biologically we demonstrate that HAdV-D49 knob protein is unable to engage CD46, whilst potential interaction with CAR is extremely limited by extension of the DG loop. HAdV-C5/49K efficiently transduced cancer cell lines of pancreatic, breast, lung, oesophageal and ovarian origin, indicating it may have potential for oncolytic virotherapy applications, especially for difficult to transduce tumour types. ImportanceAdenoviruses are powerful tools experimentally and clinically. To maximise efficacy, the development of serotypes with low pre-existing levels of immunity in the population is desirable. Consequently, attention has focussed on those derived from species D, which have proven robust vaccine platforms. This widespread usage is despite limited knowledge in their basic biology and cellular tropism. We investigated the tropism of HAdV-D49, demonstrating it uses a novel cell entry mechanism that bypasses all known HAdV receptors. We demonstrate, biologically, that a pseudotyped HAdV-C5/D49K vector efficiently transduces a wide range of cell lines, including those presenting no known adenovirus receptor. Structural investigation suggests that this broad tropism is the result of a highly basic electrostatic surface potential, since a homologous pseudotyped vector with a more acidic surface potential, HAdV-C5/D30K, does not display a similar pan-tropism. Therefore, HAdV-C5/D49K may form a powerful vector for therapeutic applications capable of infecting difficult to transduce cells.

microbiology↗

bioRxiv2020

Variability of dynamic patterns of cortical excitability in schizophrenia: A test-retest TMS-EEG study

BackgroundAltered stimuli processing is a key feature of schizophrenia. Application of concurrent transcranial magnetic stimulation (TMS) with electroencephalography (TMS-EEG) is an effective stimulus which allows direct measurement of the cortical response within a millisecond time resolution. Test-retest TMS-EEG studies present evidence of high reproducibility in healthy controls (HC), however, this stability of response has not been examined in schizophrenia. ObjectiveThe current study maps TMS-evoked patterns of cortical excitability in schizophrenia and examine whether these cortical patterns are amenable to change as symptoms of schizophrenia improve. MethodsOne hundred single-pulse TMS and 100 sham pulses were applied to frontal regions of 19 schizophrenia in-patients and 26 HC while electroencephalography data were simultaneously acquired. Medication and schizophrenia symptoms were reported. This protocol was repeated across three sessions (1 week apart) for each participant. The TMS-evoked cortical response of each participant was averaged and compared between groups. ResultsSchizophrenia patients showed reduced cortical excitability at early time-windows and increased excitability at later time-windows. Increased excitability at later windows was associated with heightened symptom severity. Schizophrenia patients showed an increased variability in cortical response over sessions relative to HC. Increased change in cortical response from session 1 to session 3 correlated with symptom improvement. ConclusionsSchizophrenia patients presented with abnormal patterns of cortical excitability when processing TMS stimuli. These dynamic patterns of cortical response were amenable to change as symptoms of schizophrenia improved. Further research into electrophysiological biomarkers of symptom improvement is hoped to improve current diagnosis and treatment models of schizophrenia.

neuroscience↗

bioRxiv2019

Phase-amplitude markers of synchrony and noise: A resting-state and TMS-EEG study of schizophrenia

The electroencephalogram (EEG) of schizophrenia patients is known to exhibit a reduction of signal-to-noise ratio and of phase locking, as well as a facilitation of excitability, in response to a variety of external stimuli. Here we demonstrate these effects in transcranial magnetic stimulation (TMS)-evoked potentials and in the resting-state EEG. To ensure veracity we used three weekly sessions and analyzed both resting state and TMS-EEG data. For the TMS responses our analysis verifies known results. For the resting state we introduce the methodology of mean-normalized variation to the EEG analysis (quartile-based coefficient of variation), which allows for a comparison of narrow-band EEG amplitude fluctuations to narrow-band Gaussian noise. This reveals that amplitude fluctuations in the delta, alpha and beta bands of healthy controls are different from those in schizophrenia patients, on time scales of tens of seconds. We conclude that the EEG-measured cortical activity patterns of schizophrenia patients are more similar to noise, both in alpha and beta resting state and in TMS responses. Our results suggest that the ability of neuronal populations to form stable, locally and temporally correlated activity is reduced in schizophrenia, a conclusion that is in accord with previous experiments on TMS-EEG and on resting-state EEG.

neuroscience↗

bioRxiv2018

Potassium channel regulators are differentially expressed in hippocampi of Ts65Dn and Tc1 Down syndrome mouse models

BackgroundDown syndrome remains the main genetic cause of intellectual disability, with an incidence rate of about 1 in 700 live births. The Ts65Dn mouse strain, with an extra murine chromosome that includes genes from chromosomes 10, 16 and 17 of the mouse and the Tc1 strain with an extra human chromosome 21, are currently accepted as informative and well-studied models for Down Syndrome. Using whole cell patch clamp we recently showed changes in several types of transmembrane currents in hippocampal neuronal cultures of Ts65Dn and Tc1 embryos. The associated genetic changes responsible for these changes in physiology were yet to be studied.\n\nMethodsWe used qPCR to measure RNA expression level of a few of the channel genes that we suspect are implicated in the previously reported changes of measured currents, and performed statistical analysis using Matlab procedures for the standard t-test and ANOVA and for calculating correlations between the RNA expression levels of several channel genes.\n\nResultsWe present differential gene expression levels measured using qPCR of the potassium channel regulators KCNE1 and KCNE2 in both Ts65Dn and Tc1 embryos and pups compared to controls. In Tc1, the human genes KCNJ6 and KCNJ15 are expressed in addition to a statistically insignificant increase of expression in the mouse genes KCNJ6 and KCNJ15. All channel genes that we have measured with large replication, have the same up-regulation or down-regulation in both mouse models, indicating that the transcription mechanism acts similarly in these two mouse models. The large dataset furthermore allows us to observe correlations between different channel genes. We find that, despite the significant changes in expression levels, channels that are known to interact have a high and significant correlation in expression both in controls and in the Down syndrome mouse model.\n\nConclusionsWe suggest the differential expression of KCNE1 and KCNE2 as a possible cause for our previously reported changes in potassium currents. We report a KCNJ6 and KCNJ15 overexpression, which plays a role in the increased input conductance and the reduced cell excitability that we previously reported in the Tc1 mouse model. The large and significant positive (KCNQ2-KCNQ3, KCNE1-KCNE2, KCNQ3-KCNE1, KCNQ2-KCNE1, KCNQ2-KCNE2, KCNQ3-KCNE2) and negative correlations (KCNE1-KCNJ15, KCNE2-KCNJ15) that we find between channel genes indicate that these genes probably work in a cooperative or in a mutually exclusive manner.

neuroscience↗

bioRxiv2018

Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques

The need to reduce per sample cost of RNA-seq profiling for scalable data generation has led to the emergence of highly multiplexed RNA-seq. These technologies utilize barcoding of cDNA sequences in order to combine samples into single sequencing lane to be separated during data processing. In this study, we report the performance of one such technique denoted as sparse full length sequencing (SFL), a ribosomal RNA depletion-based RNA sequencing approach that allows for the simultaneous sequencing of 96 samples and higher. We offer comparisons to well established single-sample techniques, including: full coverage Poly-A capture RNA-seq and microarray, as well as another low-cost highly multiplexed technique known as 3 digital gene expression (3DGE). Data was generated for a set of exposure experiments on immortalized human lung epithelial (AALE) cells in a two-by-two study design, in which samples received both genetic and chemical perturbations of known oncogenes/tumor suppressors and lung carcinogens. SFL demonstrated improved performance over 3DGE in terms of coverage, power to detect differential gene expression, and biological recapitulation of patterns of differential gene expression from in vivo lung cancer mutation signatures.

bioinformatics↗