Biology subjects

Reddy, A. B.

Publications and source records attributed to Reddy, A. B..

15 recordsLinked to original sources

bioRxiv2026

AMPK Signalling Rewires WWP1 mediated RUNX1 Ubiquitination in CML Progression

Despite the remarkable success of BCR:ABL1-targeted tyrosine kinase inhibitors, disease progression and therapeutic resistance remain major challenges in chronic myeloid leukemia (CML), highlighting the need to identify additional molecular mechanisms that sustain leukemic survival. In this study, we identify the HECT-type E3 ubiquitin ligase WWP1 as a previously unrecognized regulator of RUNX1 and define a signaling network linking ubiquitination to AMP-activated protein kinase (AMPK)-dependent phosphorylation in CML. We demonstrate that WWP1 directly associates with the PPxY motif of RUNX1 and catalyzes its K63-linked polyubiquitination, thereby enhancing protein stability and promoting leukemic cell growth. Disruption of WWP1, either by genetic silencing or pharmacological inhibition, diminished RUNX1 ubiquitination, impaired proliferation, induced G2/M cell-cycle arrest, and triggered apoptosis. Mechanistic investigations further revealed that WWP1 is a direct substrate of AMPK. Phosphorylation of WWP1 at Thr692 by AMPK promoted its lysosomal degradation, thereby limiting WWP1-dependent ubiquitination of RUNX1. In parallel, AMPK-mediated phosphorylation of RUNX1 reduced its leukemogenic activity, collectively shifting the signaling balance toward growth suppression. Activation of AMPK with metformin reproduced these molecular effects in leukemia cell lines, primary CML patient-derived cells, and xenograft tumors, supporting the physiological relevance of this pathway. Together, our findings establish an AMPK-WWP1-RUNX1 signaling axis that integrates phosphorylation and non-proteolytic ubiquitination to regulate RUNX1 function and CML progression. These results identify WWP1 as a potential therapeutic vulnerability and provide a mechanistic rationale for targeting the AMPK-WWP1 pathway in CML.

cancer biology↗

bioRxiv2026

Sleep regulates hepatic neutrophil trafficking by modulating uric acid metabolism via sympathetic nervous system activity

Sleep is essential for survival and serves as a key regulator of metabolic and immune function. Sleep loss is strongly associated with metabolic stress and liver inflammation. The mechanisms linking sleep disruption to hepatic metabolic inflammation (metaflammation) remain poorly defined. Here, we show that sleep loss triggers metaflammation through a sympathetic-metabolic-immune axis. Acute sleep deprivation (SD) activates hepatic sympathetic signaling, leading to increased uric acid (UA) synthesis driven by enhanced expression and activity of xanthine dehydrogenase/xanthine oxidase (XDH/XO) in the liver. Elevated UA, acting as an immune-stimulatory metabolic signal, promotes hepatic neutrophil recruitment and pro-inflammatory cytokine production, a response that is rapidly reversed upon sleep recovery. Our findings identify sleep-dependent sympathetic control of hepatic UA metabolism as a driver of acute liver inflammation and reveal how acute sleep loss reprograms liver immune-metabolic homeostasis.

neuroscience↗

bioRxiv2026

HSF1-mediated Proteostasis Decline Links Aging and Sleep Disruption

Sleep disruption increases with age and is associated with adverse age-related outcomes, yet the molecular mechanisms linking these phenomena remain unclear. Here, through integrative analysis of human and mouse transcriptomic and proteomic datasets, we identify proteostasis-related pathways whose aging trajectories align with transcriptional responses to chronic sleep disruption across tissues and cell types. In the human prefrontal cortex, gene expression exhibits coherent age-associated directional shifts. Across human peripheral blood following sleep restriction and multiple aging mouse tissues and cell types, proteostasis pathways exhibit concordant downregulation. Among these, heat shock response pathways emerge as the most persistent and cross-modal signatures, with components of the heat shock factor 1 (HSF1)-mediated proteostasis network displaying diminished inducibility with age and chronic sleep insufficiency, in contrast to transient activation following short-term sleep deprivation. This attenuation is particularly pronounced in neurons, where age-associated suppression of HSF1 target programs indicates selective vulnerability of neuronal proteostasis. Spatial and single-cell analyses map this vulnerability to hippocampal circuits during aging and to superficial cortical layers and glutamatergic neurons in Alzheimers disease. These findings support a model in which repeated sleep disruption progressively reduces the inducible capacity of proteostatic stress responses, shifting from adaptive activation to progressive attenuation and accelerating age-related decline in proteome maintenance. Consistent with emerging functional evidence, this identifies HSF1-mediated proteostasis as an integrative axis linking sleep stability and molecular aging, suggesting a self-reinforcing relationship in which sleep disruption and proteostasis decline reciprocally exacerbate one another. These results connect transient molecular responses to sleep perturbations with long-term aging trajectories, revealing a systems-level mechanism through which cumulative sleep disruption may increase vulnerability during aging.

neuroscience↗

bioRxiv2026

Optogenetic Modeling of Wake-Like Transcriptional Progression in Human SH-SY5Y Neuronal Cells

Sleep deprivation induces extensive transcriptional remodeling in the brain, yet it remains unclear how much of this response arises directly from sustained neuronal excitation versus systemic and behavioral confounds. Here we establish a reductionist human neuronal cell model to isolate the cell-autonomous consequences of prolonged depolarization. Controlled optogenetic stimulation of human SH-SY5Y neuronal cells elicited scalable calcium influx and robust induction of canonical activity-dependent genes, enabling precise manipulation of excitation history independent of receptor-specific pleiotropy. Time-resolved RNA sequencing revealed that sustained excitation does not produce a uniform transcriptional shift. Instead, responses partitioned into a small set of reproducible temporal modules including early-, mid-, and late-peaking induction, sustained induction, biphasic responses, and suppression, each associated with distinct functional and regulatory signatures. At the systems level, pathway activities evolved through three sequential transcriptional states, each defined by a distinct mixture of these temporal gene modules within individual programs. State transitions were directional and asymmetric across stimulation and recovery, consistent with cumulative excitation-history-dependent reorganization rather than simple reversal after stimulus offset. Cross-dataset mapping with in vivo mouse sleep datasets showed selective concordance between defined temporal modules and independent sleep-deprivation signatures. Together, these findings show that sustained neuronal excitation alone is sufficient to generate staged, wake-like transcriptional progression, linking gene-level temporal structure to higher-order regulatory states shaped by excitation history.

neuroscience↗

bioRxiv2026

Intrinsic Circadian Organization of the Spinal Cord and Dorsal Root Ganglia

Circadian rhythms coordinate daily fluctuations in physiology and behavior, yet their organization within primary sensory pathways remains poorly defined. Although somatosensory responsiveness varies across the day-night cycle, it is unclear whether peripheral sensory circuits possess molecular mechanisms for temporal regulation. Here, we demonstrate that the spinal-peripheral sensory axis harbors robust, tissue-autonomous circadian clocks. Using real-time bioluminescence imaging, we observed sustained oscillations of the core clock protein PER2 in the spinal dorsal horn and dorsal root ganglia (DRGs), indicating autonomous circadian timing within these tissues. To define the molecular scope of this regulation, we performed RNA sequencing across a 52-hour circadian time course in DRGs. Circadian analysis identified 626 rhythmic transcripts, representing 3.6% of expressed genes. These genes exhibited non-uniform phase distributions and segregated into discrete temporal clusters. Functional annotation revealed phase-specific enrichment of biological processes related to transport, neuronal structure, and proteostasis, suggesting coordinated temporal deployment of distinct molecular programs rather than uniform oscillations across the circadian cycle. Cross-referencing circadian genes with neuropathic pain-associated gene sets revealed limited overlap; however, overlapping genes aligned to specific baseline phase windows enriched for regenerative annotations. Potassium channel-related signaling components implicated in neuropathic pain also showed baseline circadian modulation. Together, these findings establish the spinal dorsal horn and DRGs as intrinsically circadian tissues and reveal a temporally structured molecular landscape in primary sensory neurons, providing a framework for understanding how peripheral sensory processing, plasticity, and homeostatic regulation are coordinated across the day-night cycle.

neuroscience↗

bioRxiv2025

Asymmetric Cross-Reactivity of Nuclear Receptors Reveals an Evolutionary Buffer Between Estrogen and Androgen Signaling

A comprehensive all-by-all receptor ligand affinity screen using Boltz-2, a deep learning framework for protein-ligand interaction prediction, reveals a previously unrecognized asymmetry in steroid hormone receptor binding. Using systematic in silico affinity prediction, we show that estradiol binds the androgen receptor with higher predicted affinity than testosterone and also displays strong affinity for multiple related steroid hormone receptors, whereas the reciprocal interaction - binding of non-aromatized steroids to estrogen receptors - is not observed. Structural modeling demonstrates that estradiol and testosterone occupy the same canonical ligand-binding pocket within the androgen receptor, indicating a conserved steroid-recognition architecture rather than a specialized binding mode. Analysis of a clinically relevant androgen receptor mutation shows modest and broadly distributed stabilization of ligand engagement, consistent with tuning of a pre-existing estradiol-compatible interaction rather than generation of a novel binding mechanism. Reconstruction of ancestral steroid receptors indicates that estradiol maintains high predicted affinity across both ancestral and modern receptors, while other steroids progressively diversify in their receptor preferences following lineage expansion. Together, these results support an evolutionary model in which estradiol represents an early steroid ligand, with younger receptors retaining ancestral estrogen compatibility while evolving specificity for upstream steroid hormones. Functionally, this asymmetric architecture provides a mechanism by which estradiol may modulate androgen receptor signaling under physiological conditions and may contribute to altered receptor activation in pathological contexts such as advanced prostate cancer. These findings define a coherent biochemical and evolutionary framework for estradiol cross-reactivity and highlight the estradiol-androgen receptor interface as a potential therapeutic target.

cell biology↗

bioRxiv2025

Chronic sleep curtailment expediates brain aging by activating the complement and coagulation cascades in mice

Chronic sleep insufficiency is prevalent in modern society and has been associated with age-related neurodegenerative diseases. Loss of sleep accelerates the progression of neurodegeneration in animal models of neurological diseases. Here, we study whether chronic sleep curtailment leads to brain aging in wild-type animals without a genetic predisposition. We used a wild-type mouse model to simulate modern-day conditions of restricted sleep and compared the brain (cortex) proteome of young sleep-restricted animals with different aged control groups. We report the alteration of 149 proteins related to sleep and 1269 related to age with 96 proteins common between them. Through pathway analysis of proteins common to sleep restriction and aging, we discovered that the complement and coagulation cascade pathways were enriched by alterations of complement component 3 (C3), alpha-2-macroglobulin (A2M), fibrinogen alfa and beta chain (FGA and FGB). This is the first study indicating the possible role of the complement and coagulation pathways in brain aging and by chronic sleep restriction (CSR) in mice.

neuroscience↗

bioRxiv2024

Heat Shock Factor 1 Governs Sleep-Wake Cycles Across Species

Heat Shock Factor 1 (HSF1) is a critical transcription factor for cellular proteostasis, but its role in sleep regulation remains unexplored. We demonstrate that nuclear HSF1 levels in the mouse brain fluctuate with sleep-wake cycles, increasing during extended wakefulness and decreasing during sleep. Using CUT&RUN and RNA-seq, we identified HSF1-regulated transcriptional changes involved in synaptic organization, expanding its known functions beyond traditional heat shock responses. Both systemic and brain-specific Hsf1 knockout mice exhibit altered sleep homeostasis, including increased delta power after sleep deprivation and upregulation of sleep-related genes. However, these knockouts struggle to maintain sleep due to disrupted synaptic organization. In Drosophila, knockout of HSF1s ortholog results in fragmented sleep patterns, suggesting a conserved role for HSF1 in sleep regulation across species. Our findings reveal a novel molecular mechanism underlying sleep regulation and offer potential therapeutic targets for sleep disturbances.

neuroscience↗

bioRxiv2024

An integrative analysis of cell-specific transcriptomics and nuclear proteomics of sleep-deprived mouse cerebral cortex

Sleep regulation follows a homeostatic pattern. The mammalian cerebral cortex is the repository of homeostatic sleep drive and neurons and astrocytes of the cortex are principal responders of sleep need. The molecular mechanisms by which these two cell types respond to sleep loss are not yet clearly understood. By combining cell-type specific transcriptomics and nuclear proteomics we investigated how sleep loss affects the cellular composition and molecular profiles of these two cell types in a focused approach. The results indicate that sleep deprivation regulates gene expression and nuclear protein abundance in a cell-type-specific manner. Our integrated multi-omics analysis suggests that this distinction arises because neurons and astrocytes employ different gene regulatory strategies under accumulated sleep pressure. These findings provide a comprehensive view of the effects of sleep deprivation on gene regulation in neurons and astrocytes.

neuroscience↗

bioRxiv2023

SlumberNet: Deep learning classification of sleep stages using residual neural networks

Sleep research is fundamental to understanding health and well-being, as proper sleep is essential for maintaining optimal physiological function. Here we present SlumberNet, a novel deep learning model based on residual network (ResNet) architecture, designed to classify sleep states in mice using electroencephalogram (EEG) and electromyogram (EMG) signals. Our model was trained and tested on data from mice undergoing baseline sleep, sleep deprivation, and recovery sleep, enabling it to handle a wide range of sleep conditions. Employing k-fold cross-validation and data augmentation techniques, SlumberNet achieved high levels of accuracy ([~]98%) in predicting sleep stages and showed robust performance even with a small and diverse training dataset. Comparison of SlumberNets performance to manual sleep stage classification revealed a significant reduction in analysis time ([~]50x faster), without sacrificing accuracy. Our study showcases the potential of deep learning to facilitate sleep research by providing a more efficient, accurate, and scalable method for sleep stage classification. Our work with SlumberNet demonstrates the power of deep learning in sleep research, and looking forward, SlumberNet could be adapted to human EEG analysis and sleep stage classification. Thus, SlumberNet could be a valuable tool in understanding both sleep physiology and disorders in mammals.

neuroscience↗

bioRxiv2021

Circadian regulation of lung repair and regeneration

Optimal lung repair and regeneration is essential for recovery from viral infections such as that induced by influenza A virus (IAV). We have previously demonstrated that lung inflammation induced by IAV is under circadian control. However, it is not known if the circadian clock exerts its influence on lung repair and regenerative processes independent of acute inflammation from IAV. Here, we demonstrate for the first time that lung organoids have a functional clock as they mature and that the absence of an intact circadian clock impairs regenerative capacity. Using several models of circadian disruption, we show that with the absence of an intact clock lung proliferation is disrupted. Further, we find that the circadian clock acts through direct control of the Wnt/{beta}-catenin pathway. We speculate, that adding the circadian dimension to the critical process of lung repair and regeneration will lead to novel therapies and improve outcomes. Finally, we use data from UK Biobank to demonstrate at the population level, the role of poor circadian rhythms in mediating negative outcomes following lung infection.

cell biology↗

bioRxiv2021

Clock gene-independent daily regulation of haemoglobin oxidation in red blood cells

Cellular circadian rhythms confer temporal organisation upon physiology that is fundamental to human health. Rhythms are present in red blood cells (RBCs), the most abundant cell type in the body, but their physiological function is poorly understood. Here, we present a novel biochemical assay for haemoglobin (Hb) oxidation status which relies on a redox-sensitive covalent haem-Hb linkage that forms during SDS-mediated cell lysis. Formation of this linkage is lowest when ferrous Hb is oxidised, in the form of ferric metHb. Daily haemoglobin oxidation rhythms are observed in RBCs cultured in vitro or taken from freely behaving mice or humans exhibit and are unaffected by mutations that affect circadian rhythms in nucleated cells. These rhythms correlate with daily rhythms in core body temperature, with temperature lowest when metHb levels are highest. Raising metHb levels with dietary sodium nitrite can further decrease daytime core body temperature in mice via NO signaling. These results extend our molecular understanding of RBC circadian rhythms and suggest they contribute to the regulation of body temperature.

cell biology↗

bioRxiv2020

Single-cell transcriptomics and cell-specific proteomics reveals molecular signatures of sleep

Every day, we sleep for a third of the day. Sleep is important for cognition, brain waste clearance, metabolism, and immune responses. The molecular mechanisms governing sleep are largely unknown. Here, we used a combination of single cell RNA sequencing and cell-type specific proteomics to interrogate the molecular underpinnings of sleep. Different cell types in three important brain regions for sleep (brainstem, cortex, and hypothalamus) exhibited diverse transcriptional responses to sleep need. Sleep restriction modulates astrocyte-neuron crosstalk and sleep need enhances expression of specific sets of transcription factors in different brain regions. In cortex, we also interrogated the proteome of two major cell types: astrocytes and neurons. Sleep deprivation differentially alters the expression of proteins in astrocytes and neurons. Similarly, phosphoproteomics revealed large shifts in cell-type specific protein phosphorylation. Our results indicate that sleep need regulates transcriptional, translational, and post-translational responses in a cell-specific manner.

neuroscience↗

bioRxiv2018

Thrombospondins 1 and 2 affect lysyl oxidase protein and collagen matrix maturation in cortical bone of growing male and female mice via non-redundant pathways

Thrombospondin-2-deficiency is associated with impaired matrix maturation in osteoblasts and cortical bone of growing mice. Here we addressed the possibility that lysyl oxidase (LOX) contributes to this phenotype. After overnight serum starvation, pro-LOX levels were elevated compared to wild-type in marrow-derived osteoblasts from male and female TSP2-/- mice. The liberated LOX pro-peptide (LOPP) was faintly visible in serum-starved cultures. When serum was maintained, pro-LOX content was not affected by TSP2 status, but relative LOPP levels were elevated in cultures from female TSP2-/- mice. Two isoforms of pro-LOX at 75 kDa and 50 kDa were detected in detergent soluble protein extracts of diaphyseal tissue from growing mice. In female mice, TSP2 status did not affect detergent soluble pro-LOX content or the relative contribution of each band to the total signal. Instead, levels of the 50 kDa band were reduced in female TSP1-/- samples. In male diaphyseal tissue, total pro-LOX content and the contribution each isoform made to the total signal was not affected by TSP1 or TSP2 status. We did not detect 32 kDa mature LOX in detergent soluble preparations of cells or whole bone tissue. Detergent insoluble hydroxyproline content was reduced in diaphyseal tissue obtained from female TSP1-/- and TSP2-/- mice. In male diaphyseal cortical samples, TSP2 but not TSP1 deficiency was associated with reduced insoluble hydroxyproline content. Our data suggest that the trimeric thrombospondins contribute to bone matrix quality via non-redundant mechanisms that are dependent on the unique tissue milieu of the male and female skeleton.

cell biology↗

bioRxiv2017

Non-canonical circadian oscillations in Drosophila S2 cells drive gene-expression cycles coupled to metabolic oscillations

Circadian rhythms are cell-autonomous biological oscillations with a period of about 24 hours. Current models propose that transcriptional feedback loops are the principal mechanism for the generation of circadian oscillations. In these models, Drosophila S2 cells are generally regarded as non-rhythmic cells, as they do not express several canonical circadian components. Using an unbiased multi-omics approach, we made the surprising discovery that Drosophila S2 cells do in fact display widespread daily rhythms. Transcriptomics and proteomics analyses revealed that hundreds of genes and their products are rhythmically expressed in a 24-hour cycle. Metabolomics analyses extended these findings and illustrated that central carbon metabolism and amino acid metabolism are the main pathways regulated in a rhythmic fashion. We thus demonstrate that daily genome-wide oscillations, coupled to metabolic cycles, take place in eukaryotic cells without the contribution of known circadian regulators.

systems biology↗