Biology subjects

Anderson, A.

Publications and source records attributed to Anderson, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Adipocyte sphingosine kinase 1 regulates histone modifiers to disrupt circadian function

Circadian rhythms align biological functions with the 24-hour day-night cycle, but modern artificial light disrupts these patterns, contributing to health issues like obesity and cardiovascular disease. The circadian clock operates through a transcriptional-translational feedback loop involving core components such as BMAL1 and CLOCK. Recent research has shown circadian variations in sphingolipid metabolism, specifically sphingosine-1-phosphate (S1P), which plays crucial signaling roles. This study investigates the sphingolipid enzyme, sphingosine kinase 1 (SphK1), which converts sphingosine to S1P, as a circadian-regulated gene in adipocytes. We find that SphK1 expression and activity follow a circadian rhythm, regulated by BMAL1 and CLOCK binding to its promoter. Adipocyte-specific SphK1 knockout mice exhibit disrupted circadian rhythms, and impaired adipocyte function. Additionally, SphK1 deficiency leads to reduced histone acetylation and altered histone deacetylase (HDAC) localization, affecting gene regulation. These results highlight the critical role of SphK1 in linking lipid metabolism with circadian biology.

biochemistry↗

bioRxiv2024

Sphingosine kinase 1 is induced by glucocorticoids in adipose derived stem cells and enhances glucocorticoid mediated signaling in adipose expansion.

Sphingosine kinase 1 (SphK1) plays a crucial role in regulating metabolic pathways within adipocytes and is elevated in the adipose tissue of obese mice. While previous studies have reported both pro- and inhibitory effects of SphK1 and its product, sphingosine-1-phosphate (S1P), on adipogenesis, the precise mechanisms remain unclear. This study explores the timing and downstream effects of SphK1/S1P expression and activation during in vitro adipogenesis. We demonstrate that the synthetic glucocorticoid dexamethasone robustly induces SphK1 expression, suggesting its involvement in glucocorticoid-dependent signaling during adipogenesis. Notably, the activation of C/EBP{delta}, a key gene in early adipogenesis and a target of glucocorticoids, is diminished in SphK1-/- adipose-derived stem cells (ADSCs). Furthermore, glucocorticoid administration promotes adipose tissue expansion via SphK1 in a depot-specific manner. Although adipose expansion still occurs in SphK1-/- mice, it is significantly reduced. These findings indicate that while SphK1 is not essential for adipogenesis, it enhances early gene activation, thereby facilitating adipose tissue expansion.

biochemistry↗

bioRxiv2024

Cell identity revealed by precise cell cycle state mapping links data modalities

Several methods for cell cycle inference from sequencing data exist and are widely adopted. In contrast, methods for classification of cell cycle state from imaging data are scarce. We have for the first time integrated sequencing and imaging derived cell cycle pseudo-times for assigning 449 imaged cells to 693 sequenced cells at an average resolution of 3.4 and 2.4 cells for sequencing and imaging data respectively. Data integration revealed thousands of pathways and organelle features that are correlated with each other, including several previously known interactions and novel associations. The ability to assign the transcriptome state of a profiled cell to its closest living relative, which is still actively growing and expanding opens the door for genotype-phenotype mapping at single cell resolution forward in time.

bioinformatics↗

bioRxiv2024

Attentional priority and limbic activity favor gains over losses

Prospect theory has suggested that decisions reflect a bias toward avoidance of loss compared to equivalent gains. In our study we examine whether a similar bias is found in decisions regarding whether a loss associated stimulus or a gain associated stimulus is given priority in perception. We find that for most people, gains are given priority over loss in the decision of which of the two stimuli occurs first. We also ask whether gains are reflected in greater activity in limbic systems related to emotion. In an fMRI study, we find that most people show greater emotional response to gains, not losses. We consider how these findings might be related to risk aversion in studies of decision making.

neuroscience↗

bioRxiv2024

Physiological Processing of Aversiveness in the Mind's Ear: Comparing Audiovisual, Auditory and Imagined Auditory Affective Stimuli

Understanding the somatovisceral responses to auditory affective imagery has important implications in disorders like misophonia. The current study compared physiological responses to aversive and nonaversive states across three modalities: audiovisual, auditory, and auditory imagery. Electromyographic activity over corrugator supercilii (EMGc) and zygomaticus major (EMGz), electrodermal activity (EDA), heart rate (HR), and finger skin temperature (SKT) were measured. There was significant differentiation in EMGc, EDA, and HR deceleration between aversive and nonaversive audiovisual stimuli. EMGc potentiation was the only physiological measure showing consistent differentiation across the three modalities. Cross-modal aversiveness classification results revealed a similar physiological response pattern between audiovisual and auditory modalities. The physiological response pattern during auditory affective imagery was useful for predicting the aversiveness in audiovisual modality but not the other way around. Vividness in auditory imagery correlated with subjective hedonic valence ratings, but not physiological responses. Taken together, the current data suggest that the aversiveness of auditory imagery is differentiable in subjective affective experience and facial muscle potentiation. These results of the physiological responses to imagined aversive sounds in nonclinical population would serve as a comparison baseline for the study of misophonia.

physiology↗

bioRxiv2024

Invariant sets for switched systems to tackle bacterial resistance

The limited availability of antibiotics and the need for prompt decision-making present significant challenges for healthcare practitioners. When faced with this situation, practitioners must prioritize their approach based on several key factors. By leveraging the emergent understanding of collateral sensitivity among antibiotic-exposed pathogens, we demonstrate the utility of control invariant sets to predict treatment failure when antibiotic cycling is applied as a therapeutic strategy aiming to eradicate or prevent emergence of multi-drug resistant pathogens. Our results here pave the way for point-of-care diagnostic technologies to identify infections and select appropriate treatments quickly, reducing unnecessary antibiotic use.

bioinformatics↗

bioRxiv2024

The collective application of shorebird tracking data to conservation

Addressing urgent conservation issues, like the drastic declines of North American migratory birds, requires creative, evidence-based, efficient, and collaborative approaches. Over 50% of monitored North American shorebird populations have lost over 50% of their abundance since 1980. To address these declines, we developed a partnership of scientists and practitioners called the Shorebird Science and Conservation Collective (hereinafter "the Collective"). Here, we present this successful case study as an example for others engaged in translational science. The Collective acts as an intermediary whereby dedicated staff collate and analyze data contributions from scientists to support knowledge requests from conservation practitioners. Data contributions from 74 organizations include over 6.7 million shorebird locations forming movement paths of 3,345 individuals representing 36 species tracked across the Americas. We describe the founding and structure of the Collective and conservation activities we supported in our first two years. As the volume of scientific data on animal movements continues to grow, groups like the Collective can be vital liaisons to rapidly integrate and interpret research to support conservation action.

ecology↗

bioRxiv2024

Experimental variables that impact outcomes in Caenorhabditis elegans aging stress response

Cellular stress is a fundamental component of age-associated disease. Cells encounter various forms of stress - oxidative stress, protein misfolding, DNA damage, etc. - and respond by activating specific, well-defined stress response pathways. As we age, the burden of stress and resulting damage increases while our cells ability to deal with the consequences becomes diminished due to dysregulation of cellular stress response pathways. Many interventions that extend lifespan activate one or more stress response pathways or allow cells to maintain normal stress response later in life. The nematode Caenorhabditis elegans is a commonly used model for both aging and stress response research. As such, stress response experiments are regularly conducted as part of studies focused on mechanisms of aging in C. elegans. However, experimental design across experiments in the field are highly variable, including stressor dose, age at exposure, culture type (liquid vs. solid), bacterial strain used as a food source, and environmental temperature. These differences can result in different experimental outcomes, making comparison of results between studies challenging. Here we evaluate several experimental variables that are variable in the published literature and find that each can meaningfully alter experimental outcomes for multiple stressors. Our goal is to raise awareness of the issue of experimental variability within the field and suggest a standardized experimental design to serve as a set of guidelines for future experiments. By adopting these guidelines as a starting point, and explicitly noting differences in specific experiments, we aim to promote rigor and reproducibility, ultimately fostering more interpretable and translatable outcomes in geroscience research.

molecular biology↗

bioRxiv2023

Organelle phenotyping and multi-dimensional microscopy identify C1q as a novel regulator of microglial function.

Microglia, the immune cells of the central nervous system (CNS), are incredibly dynamic and heterogenous cells. While single cell RNA sequencing has become the conventional methodology for evaluating microglial state, transcriptomics do not provide insight into functional changes. Here, we propose a novel organelle phenotyping approach where we treat live human induced pluripotent stem cell-derived microglia (iMGL) with organelle dyes (mitochondria, lipids, lysosomes) and acquire data by live-cell spectral microscopy. Dimensionality reduction techniques and unbiased cluster identification allow for recognition of microglial subpopulations based in organelle function. We validate this methodology using lipopolysaccharide (LPS) and IL-10 treatment to polarize iMGL to an inflammatory" and "anti-inflammatory state, respectively, and then apply it to identify a novel regulator of iMGL function, complement protein C1q. C1q is traditionally known as the initiator of the complement cascade, but here we use organelle phenotyping to identify a role for C1q in regulating iMGL fatty acid storage and mitochondria membrane potential. Follow up evaluation of microglia with more traditional read outs of activation state confirm that C1q drives an increase in microglia pro-inflammatory cytokine production and migration, while suppressing microglial proliferation. These data together validate the use of a novel organelle phenotyping approach and enable better mechanism investigation of molecular regulators of microglial state, such as C1q.

neuroscience↗

bioRxiv2023

Interferon-α promotes neo-antigen formation andpreferential HLA-B-restricted antigen presentation in pancreatic β-cells

Interferon (IFN)- is the earliest cytokine signature observed in individuals at risk for type 1 diabetes (T1D), but its effect on the repertoire of HLA Class I (HLA-I)-bound peptides presented by pancreatic {beta}-cells is unknown. Using immunopeptidomics, we characterized the peptide/HLA-I presentation in in-vitro resting and IFN--exposed {beta}-cells. IFN- increased HLA-I expression and peptide presentation, including neo-sequences derived from alternative mRNA splicing, post-translational modifications - notably glutathionylation - and protein cis-splicing. This antigenic landscape relied on processing by both the constitutive and immune proteasome. The resting {beta}-cell immunopeptidome was dominated by HLA-A-restricted ligands. However, IFN- only marginally upregulated HLA-A and largely favored HLA-B, translating into a major increase in HLA-B-restricted peptides and into an increased activation of HLA-B-restricted vs. HLA-A-restricted CD8+ T-cells. A preferential HLA-B hyper-expression was also observed in the islets of T1D vs. non-diabetic donors, and we identified islet-infiltrating CD8+ T-cells from T1D donors reactive to HLA-B-restricted granule peptides. Thus, the inflammatory milieu of insulitis may skew the autoimmune response toward epitopes presented by HLA-B, hence recruiting a distinct T-cell repertoire that may be relevant to T1D pathogenesis.

immunology↗

bioRxiv2023

Substrate-Specific Function of PNPLA3 Facilitates Hepatic VLDL-Triglyceride Secretion During Stimulated Lipogenesis

The I148M variant of PNPLA3 is strongly linked to hepatic steatosis. Evidence suggests a gain-of-function role for the I148M mutant as an ATGL inhibitor, leaving the physiological relevance of wild-type PNPLA3 undefined. Here we show that PNPLA3 selectively degrades triglycerides (TGs) enriched in polyunsaturated fatty acids (PUFAs) independently of ATGL in cultured cells and mice. Lipidomics and metabolite tracing analyses demonstrated that PNPLA3 mobilizes PUFAs from intracellular TGs for phospholipid desaturation, supporting hepatic secretion of TG-rich lipoproteins. Consequently, mice with liver-specific knockout or acute knockdown of PNPLA3 both exhibited aggravated liver steatosis and concomitant decreases in plasma VLDL-TG, phenotypes that manifest only under lipogenic conditions. I148M-knockin mice similarly displayed impaired hepatic TG secretion during lipogenic stimulation. Our results highlight a specific context whereby PNPLA3 facilitates the balance between hepatic TG storage and secretion and suggest the potential contributions of I148M variant loss-of-function to the development of hepatic steatosis in humans. Summary StatementWe define the physiological role of wild type PNPLA3 in maintaining hepatic VLDL-TG secretion.

physiology↗

bioRxiv2023

Quantitative image analysis pipeline for detecting circulating hybrid cells in immunofluorescence images with human-level accuracy

Circulating hybrid cells (CHCs) are a newly discovered, tumor-derived cell population identified in the peripheral blood of cancer patients and are thought to contribute to tumor metastasis. However, identifying CHCs by immunofluorescence (IF) imaging of patient peripheral blood mononuclear cells (PBMCs) is a time-consuming and subjective process that currently relies on manual annotation by laboratory technicians. Additionally, while IF is relatively easy to apply to tissue sections, its application on PBMC smears presents challenges due to the presence of biological and technical artifacts. To address these challenges, we present a robust image analysis pipeline to automate the detection and analyses of CHCs in IF images. The pipeline incorporates quality control to optimize specimen preparation protocols and remove unwanted artifacts, leverages a {beta}-variational autoencoder (VAE) to learn meaningful latent representations of single-cell images and employs a support vector machine (SVM) classifier to achieve human-level CHC detection. We created a rigorously labeled IF CHC dataset including 9 patients and 2 disease sites with the assistance of 10 annotators to evaluate the pipeline. We examined annotator variation and bias in CHC detection and then provided guidelines to optimize the accuracy of CHC annotation. We found that all annotators agreed on CHC identification for only 65% of the cells in the dataset and had a tendency to underestimate CHC counts for regions of interest (ROI) containing relatively large amounts of cells (>50,000) when using conventional enumeration methods. On the other hand, our proposed approach is unbiased to ROI size. The SVM classifier trained on the {beta}-VAE encodings achieved an F1 score of 0.80, matching the average performance of annotators. Our pipeline enables researchers to explore the role of CHCs in cancer progression and assess their potential as a clinical biomarker for metastasis. Further, we demonstrate that the pipeline can identify discrete cellular phenotypes among PBMCs, highlighting its utility beyond CHCs.

bioinformatics↗

bioRxiv2023

Learning to Adapt - Deep Reinforcement Learning in Treatment-Resistant Prostate Cancer

Standard-of-care treatment regimes have long been designed to for maximal cell kill, yet these strategies often fail when applied to treatment-resistant tumors, resulting in patient relapse. Adaptive treatment strategies have been developed as an alternative approach, harnessing intra-tumoral competition to suppress the growth of treatment resistant populations, to delay or even prevent tumor progression. Following recent clinical implementations of adaptive therapy, it is of significant interest to optimise adaptive treatment protocols. We propose the application of deep reinforcement learning models to provide generalised solutions within adaptive drug scheduling, and demonstrate this framework can outperform the current adaptive protocols, extending time to progression by up to a quarter. This strategy is robust to varying model parameterisations, and the underlying tumor model. We demonstrate the deep learning framework can produce interpretable, adaptive strategies based on a single tumor burden threshold, replicating and informing a novel, analytically-derived optimal treatment strategy with no knowledge of the underlying mathematical tumor model. This approach is highly relevant beyond the simple, analytically-tractable tumor model considered here, demonstrating the capability of deep learning frameworks to help inform and develop treatment strategies in complex settings. Finally, we propose a pathway to integrate mechanistic modelling with DRL to tailor generalist treatment strategies to individual patients in the clinic, generating personalised treatment schedules that consistently outperform clinical standard-of-care protocols.

cancer biology↗

bioRxiv2023

Reconstructing colonization dynamics to establish how human activities transformed island biodiversity

AimThe drivers and dynamics of initial human migrations across individual islands and archipelagos are poorly understood, affecting assessments of human-modification of island biodiversity. Here, we describe and test a process-explicit approach for reconstructing human arrival and expansion on islands, which combines archaeological and climate records with high-resolution spatial population models. Using Polynesian colonisation of New Zealand as an example, we show that our new method can generate information crucial for assessing how humans affected biodiversity on islands. InnovationThe transition of islands from prehuman to human dominated ecosystems has typically been assessed by comparing biodiversity before and after time of first arrival, without considering the potential importance of the spatiotemporal dynamics of the human expansion event. Our new approach, which uses pattern-oriented modelling methods to combine inferences of human colonisation dynamics from dated archaeological material with spatially explicit population models, produces validated reconstructions of the pattern and pace of human migration across islands at high spatiotemporal resolutions. From these reconstructions, demographic and environmental drivers of human colonization can be identified, and the role that people had on biodiversity established. Using this technique, we show that closely reconciling inferences of Polynesian colonisation of New Zealand requires there to have been a single founding population of approximately 500 people, arriving between 1233 and 1257 AD, settling multiple areas, and expanding quickly over both North and South islands. The resultant maps of M[a]ori colonisation dynamics provide new opportunities to better determine how human activities transformed biodiversity of New Zealand in space and time. Main conclusionsProcess-explicit models can reconstruct human migration across large islands, producing validated, high resolution spatiotemporal projections of human occupancy and abundance that account for dispersal and population dynamics. This modelling framework should prove effective across any islands and archipelagos where climate and archaeological records are available.

ecology↗

bioRxiv2022

METTL3 maintains epithelial homeostasis through m6A-dependent regulation of chromatin modifiers

The balance between epithelial stemness and differentiation requires the precise regulation of gene expression programs. Epitranscriptomic RNA modifications have been implicated in both epithelial development as well as cancers. However, the underlying mechanisms are poorly understood. Here, we show that deletion of the m6A methyltransferase, METTL3, impairs the m6A-mediated degradation of numerous mRNA transcripts encoding critical chromatin modifying enzymes, resulting in widespread gene expression abnormalities as well as both aberrant cutaneous and oral epithelial phenotypes in vivo. Collectively, these results offer new insights into a new layer of gene regulation within epithelial surface tissues and will inform future epitranscriptomic studies within epithelial cancer and developmental biology.

molecular biology↗

bioRxiv2022

H3K36M provokes cellular plasticity to drive aberrant glandular formation and squamous carcinogenesis

Epigenetic dysregulation is pervasive in cancer, frequently impairing normal tissue development and differentiation1. Beyond alterations in histone modifying enzymes, "oncohistone" mutations have been described across a variety of cancers2-4, although the in vivo effects and underlying mechanisms behind these observations have not been well- studied and remain unclear. Here, by inducing the in vivo expression of histone H3.3 carrying a lysine to methionine (K to M) mutation at position 36 (H3K36M) in self- renewing stratifying epithelial tissues, we show that the H3K36M oncohistone dramatically disrupts normal epithelial differentiation, leading to extensive tissue dysplasia characterized by a significant increase in mitotic, proliferative basal stem cells. Furthermore, this differentiation blockade promotes increased cellular plasticity and enrichment of alternate cell fates, and in particular the aberrant generation of excessive glandular tissue including both hypertrophic salivary, sebaceous, and meibomian glands. Upon carcinogen stress, H3K36M mice display markedly enhanced squamous tumorigenesis. These aberrant phenotypic and gene expression manifestations are associated with global loss of H3K36me2 and concomitant gain of H3K27me3. Collectively, these results have revealed a previously unknown critical role for H3K36 methylation in both the in vivo maintenance of proper epithelial cell fate decisions and the prevention of squamous carcinogenesis. Additionally, they suggest that H3K36 methylation modulation may offer new avenues for the regulation of numerous common disorders driven by over- or under-active glandular function.

cancer biology↗

bioRxiv2022

Integration of single-cell RNA and protein data identifies novel clinically-relevant lymphocyte phenotypes in breast cancers

Immune cells are critical determinants of solid tumour aetiology, but the diverse phenotypes of intra-tumoural immune cells remain incompletely characterised. We applied integrated single cell RNA sequencing (scRNA-Seq) and highly multiplexed protein epitope analysis to a cohort of breast cancer samples to resolve cell states within the tumour microenvironment. We reveal novel protein markers for resting and activated tumour infiltrating lymphocytes, and show that high expression of CD103 primarily marks exhausted CD8 rather than tissue resident CD8 T-cells in human breast cancers. We identify two distinct states of activated CD4+ T follicular helper (Tfh) cells. A population resembling conventional Tfh (cTfh) cells were localised primarily to lymphoid aggregates by spatial transcriptomics. In contrast, cancer associated Tfh (caTfh) cells expressing markers of tissue residency and exhaustion co-localized with cancer foci and signalled to macrophages. Importantly, increased caTfh : cTfh ratio associated with improved disease outcome and response to checkpoint immunotherapy.

immunology↗

bioRxiv2022

Disease-modifying effects of sodium selenate in a model of drug-resistant, temporal lobe epilepsy.

There are no pharmacological disease-modifying treatments that can mitigate the seizures and comorbidities associated with established chronic temporal lobe epilepsy (TLE). This study evaluated the effect of sodium selenate in the post-status epilepticus (SE) rat model of chronic drug resistant TLE. Wistar rats underwent kainic acid-induced SE or sham. Ten-weeks post-SE, rats were randomly assigned to receive either sodium selenate, levetiracetam, or vehicle treatments continuously for 4 weeks. To evaluate the effects of the treatments, 1 week of continuous video-EEG was acquired before, during, and 4, 8 weeks post-treatment, followed by behavioral tests. Targeted and untargeted proteomics and metabolomics were performed on post-mortem brain tissue to identify potential pathways associated with modified disease outcomes. Telomere length was investigated as a novel surrogate marker of disease severity. Sodium selenate treatment was able to mitigate disease severity, reducing the number of spontaneous seizures (p< 0.05), cognitive dysfunction (p< 0.05 in both novel object placement and recognition tasks), and sensorimotor deficits (p< 0.01) 8 weeks post-treatment cessation. Moreover, increased protein phosphatase 2A (PP2A) expression, reduced hyperphosphorylated tau, and reversed telomere length shortening caused by SE (p< 0.05). Network medicine integration of multi-omics/ pre-clinical outcomes identified protein-metabolite modules positively correlated with the TLE phenotype. Our results provide evidence that treatment with sodium selenate results in a sustained disease modifying effect in chronically epileptic rats in the post-KA SE model of TLE, including improved comorbid learning and memory deficits.

neuroscience↗