Biology subjects

Hayes, M.

Publications and source records attributed to Hayes, M..

12 recordsLinked to original sources

bioRxiv2026

Hepatocyte UBE4A protects against MASLD/MASH by maintaining ER homeostasis via UBXN4 interaction

Molecular understanding of the regulation of endoplasmic reticulum (ER) functions in healthy and MASLD livers is limited. Here, we elucidate that Ube4A, a cytosolic E3 ubiquitin ligase, protects against MASLD development by maintaining ER homeostasis during nutritional stress. Hepatocyte-Ube4A deletion (HUKO) augments Gubra-Amylin-diet (GAN-D)-induced steatosis, inflammation, insulin resistance, ER stress and markers of steatohepatitis of the liver in both sexes of mice. Proteomic studies reveal that in addition to altered metabolic and fibrogenic pathways, levels of many ER proteins are also changed in HUKO livers. Impaired ER functions sensitize HUKO livers to nutrition- or chemical (tunicamycin)-induced ER stress. Moreover, HUKO primary hepatocytes exhibit increased ER stress. Furthermore, Ube4A maintains ER homeostasis by facilitating ER-associated protein degradation (ERAD). The lipogenic protein SCD1 is identified as one of the ERAD targets of Ube4A. SCD1 stability and triglyceride accumulation are amplified in HUKO primary hepatocytes. The liver Ube4A-interactome studies identified the ERAD mediator UBXN4 as a major Ube4A interacting protein. Alphafold3-based molecular modelling and interaction site mapping analyses pinpointed the Ube4A binding residues for UBXN4. ER-localized Ube4A-UBXN4 complex facilitates ERAD (e.g., SCD1) and UBXN4-binding deficient Ube4A mutants fail to enhance this process. Finally, Ube4A and UBXN4 are downregulated in the livers of human MASLD and MASH patients and this complex is diminished in GAN-D-fed mouse livers. In conclusion, Ube4A preserves ER homeostasis by maintaining ERAD via its interaction with UBXN4, which maintains liver health. Enhancing levels and/or preserving interaction of these proteins may offer new therapeutic strategies for MASLD treatment.

physiology↗

bioRxiv2026

Efficacy of RMC-6236 (Daraxonrasib) and novel combination strategies targeting resistance in RAS pathway-driven neuroblastoma

Metastatic neuroblastoma (NB), the most common pediatric extra-cranial solid tumor, has a cure rate of <50%. DNA-sequencing studies have demonstrated rare recurrent driver mutations at diagnosis, with the most common alterations detected in ALK-RAS-MAPK pathway. Activating ALK and RAS-MAPK mutations are associated with inferior outcome and are increased at relapse, and thus, represent therapeutic vulnerabilities in NB. Previously, we identified combinations of RAS/MAPK inhibitors, including SHP2 and MEK, with efficacy in resistant MAPK-altered tumor cells, including those with the most common NB-associated RAS mutation NRAS-Q61K. However, toxicities of SHP2 inhibitors and promising results using compounds that directly target RAS suggest there may be superior strategies to target RAS/MAPK pathway in NB. Here, we have assessed the efficacy of RAS/MAPK inhibitors, including tovorafenib (pan-RAF), RMC-6236/daraxonrasib (pan-active-RAS) and avutometinib (RAF/MEK) in NB in vitro and in vivo using NB models harboring differing genomic status of RAS/MAPK pathway effectors. We demonstrate selective efficacy of RMC-6236 and avutometinib via RAS-MAPK pathway inhibition in NB cells and xenografts harboring RAS, NF1 or ALK alterations. Importantly, we demonstrate that presence of the NRAS-Q61K mutation confers drug sensitivity. Using newly generated and previously established NB cell models of acquired resistance to RMC-6236 or the ALK inhibitor lorlatinib, we identified targeted combinations, including RMC-6236 plus avutometinib, that demonstrate re-sensitization in resistant NB cell and xenograft models. Finally, transcriptomic studies of RMC-6236-resistant cells detected upregulation of RAS/MAPK signatures, as well as TNF/NF{kappa}B and IL-6/JAK/STAT3 pathway enrichment, thus informing future combinations to enhance sensitivity to RAS inhibitors. STATEMENT OF SIGNIFICANCEOur work demonstrates that newly available RAS pathway inhibitors RMC-6236/daraxonrasib and avutometinib have efficacy in neuroblastoma tumors, which have frequent alterations in the RAS/MAPK pathway. These drugs with early efficacy results in adult RAS-driven tumors provide an important option for patients with relapsed neuroblastoma alone or in combination.

Cancer Biology↗

bioRxiv2026

Integrating Epstein-Barr virus (EBV) status into diffuse large B cell lymphoma (DLBCL) genetics

Diffuse large B-cell lymphoma (DLBCL), the most common aggressive lymphoma, encompasses histologically similar but genetically distinct cancers. Recent genetic studies have defined at least six molecular subtypes, yet none account for Epstein-Barr virus (EBV), despite 5-15% of DLBCLs being EBV-associated. By reanalyzing published whole-exome and RNA-sequencing data from 481 tumors, we identified 19 EBV-positive cases. These were significantly enriched in the BN2 subtype (6/19), while most (11/19) remained unclassified. In BN2 tumors, several subtype-defining mutations were reduced in frequency among EBV-positive cases, supporting the hypothesis that EBV oncogenes substitute for specific cellular alterations and may confound DLBCL classification algorithms. Extending our analysis to cell lines, we found that the widely used Val cell line harbors the B95-8 laboratory EBV strain; other EBV-positive lines appeared authentic but modeled only non-BN2 subtypes and expressed an atypical viral latency III program, whereas some DLBCL tumors expressed the atypical latency III program and others latency I or II. Together, these findings demonstrate that EBV-positive DLBCL, like DLBCL itself, is not a single disease, and that current in vitro models only partially capture its biological heterogeneity. Key pointsO_LIEBV-positive DLBCL is not a single disease and EBV status can impact genetic-based classifications. C_LIO_LICurrent EBV-positive DLBCL cell lines do not adequately capture tumor complexity; we determined that Val is a problematic cell line. C_LI

cancer biology↗

bioRxiv2023

Menstrual cycle-driven hormone concentrations co-fluctuate with white and grey matter architecture changes across the whole brain

Cyclic fluctuations in hypothalamic-pituitary-gonadal axis (HPG-axis) hormones exert powerful behavioral, structural, and functional effects through actions on the mammalian central nervous system. Yet, very little is known about how these fluctuations alter the structural nodes and information highways of the human brain. In a study of 30 naturally cycling women, we employed multidimensional diffusion and T1-weighted imaging during three estimated menstrual cycle phases (menses, ovulation, mid-luteal) to investigate whether HPG-axis hormone concentrations co-fluctuate with alterations in white matter (WM) microstructure, cortical thickness (CT), and brain volume. Across the whole brain, 17{beta}-estradiol and luteinizing hormone (LH) concentrations were directly proportional to diffusion anisotropy (FA), while follicle-stimulating hormone (FSH) was directly proportional to cortical thickness. Within several individual regions, FSH and progesterone demonstrated opposing associations with mean diffusivity and cortical thickness. These regions mainly reside within the temporal and occipital lobes, with functional implications for the limbic and visual systems. Lastly, progesterone was associated with increased tissue and decreased CSF volumes, with total brain volume remaining unchanged. These results are the first to report simultaneous brain-wide changes in human WM microstructure and cortical thickness coinciding with menstrual cycle-driven hormone rhythms. Strong brain-hormone interaction effects may not be limited to classically known HPG-axis receptor-dense regions.

neuroscience↗

bioRxiv2023

A transposase-derived gene required for human brain development

DNA transposable elements and transposase-derived genes are present in most living organisms, including vertebrates, but their function is largely unknown. PiggyBac Transposable Element Derived 5 (PGBD5) is an evolutionarily conserved vertebrate DNA transposase-derived gene with retained nuclease activity in human cells. Vertebrate brain development is known to be associated with prominent neuronal cell death and DNA breaks, but their causes and functions are not well understood. Here, we show that PGBD5 contributes to normal brain development in mice and humans, where its deficiency causes disorder of intellectual disability, movement, and seizures. In mice, Pgbd5 is required for the developmental induction of post-mitotic DNA breaks and recurrent somatic genome rearrangements. In the brain cortex, loss of Pgbd5 leads to aberrant differentiation and gene expression of distinct neuronal populations, including specific types of glutamatergic neurons, which explains the features of PGBD5 deficiency in humans. Thus, PGBD5 might be a transposase-derived enzyme required for brain development in mammals. One-Sentence SummaryPiggyBac Transposable Element Derived 5 (PGBD5) is required for brain development in humans and mice through genetic and epigenetic mechanisms.

neuroscience↗

bioRxiv2023

The Estrogen Receptor-Related Orphan Receptors (ERRs) Regulate Autophagy through TFEB

Autophagy is an essential self-degradative and recycling mechanism that maintains cellular homeostasis. Estrogen receptor-related orphan receptors (ERRs) play fundamental role in regulation of cardiac metabolism and function. Previously, we showed that ERR agonists improve cardiac function in models of heart failure and induce autophagy in cardiomyocytes. Here, we characterized a mechanism by which ERRs induce autophagy in cardiomyocytes. Transcription factor EB (TFEB) is a master regulator of the autophagy-lysosome pathway and has been shown to be important in cardiac autophagy. We discovered that TFEB is a direct ERR target gene whose expression is induced by ERR agonists. Activation of ERR results in increased TFEB expression in both neonatal rat ventricular myocytes and C2C12 myoblasts. ERR-dependent increases in TFEB expression results in increased expression of an array of TFEB target genes, which are critical for stimulation of autophagy. Pharmacologically targeting ERR is a promising potential method for treatment of many diseases where stimulation of autophagy may be therapeutic including heart failure.

cell biology↗

bioRxiv2022

A Synthetic ERRα Agonist Induces an Acute AerobicExercise Response and Enhances Exercise Capacity

Repetitive physical exercise induces physiological adaptations in skeletal muscle that improves exercise performance and is effective for the prevention and treatment of several diseases. Here we report the identification of a synthetic agonist for the orphan nuclear receptor ERR (estrogen receptor-related receptor ), SLU-PP-332, that activates an acute aerobic exercise genetic program in skeletal muscle in an ERR-dependent manner. SLU-PP-332 increases mitochondrial function and cellular respiration consistent with induction of this genetic program. When administered to mice, SLU-PP-332 increased the type IIa oxidative skeletal muscle fibers and enhanced exercise endurance. These data indicate the feasibility of targeting ERR for development of compounds that act as exercise mimetics that may be effective in treatment of numerous metabolic disorders and to improve muscle function in the aging.

pharmacology and toxicology↗

bioRxiv2022

Novel ERR pan-agonists ameliorate heart failure through boosting cardiac fatty acid metabolism and mitochondrial function

Cardiac metabolic dysfunction is a hallmark of heart failure. Estrogen related receptors ERR and ERR{gamma} are essential regulators for cardiac metabolism. Therefore, activation of ERR could be a potential therapeutic intervention for heart failure. However, no natural or synthetic ERR agonist is available to demonstrate their pharmacological effect in vivo. Using a structure-based design approach, we designed and synthesized two structurally distinct pan-ERR agonists, SLU-PP-332 (332) and SLU-PP-915 (915), which significantly improved ejection fraction and ameliorated fibrosis against pressure overload-induced heart failure without affecting cardiac hypertrophy. Mechanistically, a broad-spectrum of metabolic genes were transcriptionally activated by ERR agonists, particularly genes involved in fatty acid metabolism and mitochondrial function, which were mainly mediated by ERR{gamma}. Metabolomics analysis showed significant normalization of metabolic profiles in fatty acid/lipid and TCA/OXPHOS metabolites by 915 in the mouse heart with 6-week pressure overload. Autophagy was also induced by ERR agonists in cardiomycoyte. On the other hand, ERR agonism led to downregulation of cell cycle and development pathways, which was partially mediated by E2F1 in cardiomyocyte. In summary, ERR agonists maintain oxidative metabolism, which confers cardiac protection against pressure overload-induced heart failure in vivo. Our results provided direct pharmacological evidence supporting the further development of ERR agonists as novel heart failure therapeutics in vivo.

pharmacology and toxicology↗

bioRxiv2021

Experimental characterization and automatic identification of stridulatory sounds inside wood

The propagation of animal vocalizations in water and in air is a well-studied phenomenon, but sound produced by bark and wood boring insects, which feed and reproduce inside trees, is poorly understood. Often being confined to the dark and chemically-saturated habitat of wood, many bark- and woodborers have developed stridulatory mechanisms to communicate acoustically. Despite their ecological and economic importance and the unusual medium used for acoustic communication, very little is known about sound production in these insects, or their acoustic interactions inside trees. Here, we use bark beetles (Scolytinae) as a model system to study the effects of wooden tissue on the propagation of insect stridulations and propose algorithms for their automatic identification. We characterize distance-dependence of the spectral parameters of stridulatory sounds, propose data-based models for the power decay of the stridulations in both outer and inner bark, provide optimal spectral ranges for stridulation detectability, and develop automatic methods for their detection and identification. We also discuss the acoustic discernibility of species cohabitating the same log. The species tested can be acoustically identified with 99% of accuracy at distances up to 20 cm and detected to the greatest extent in the 2-6 kHz frequency band. Phloem was a better medium for sound transmission than bark.

biophysics↗

bioRxiv2021

Repeated administration of 2-hydroxypropyl-β-cyclodextrin (HPβCD) attenuates the chronic inflammatory response to experimental stroke

Globally, more than 67 million people are living with the effects of ischemic stroke. Importantly, many stroke survivors develop a chronic inflammatory response that may contribute to cognitive impairment, a common and debilitating sequela of stroke that is insufficiently studied and currently untreatable. 2-hydroxypropyl-{beta}-cyclodextrin (HP{beta}CD) is an FDA-approved cyclic oligosaccharide that can solubilize and entrap lipophilic substances. The goal of the present study was to determine whether the repeated administration of HP{beta}CD curtails the chronic inflammatory response to stroke by reducing lipid accumulation within stroke infarcts in a distal middle cerebral artery occlusion mouse model of stroke. To achieve this goal, we subcutaneously injected young adult and aged male mice with vehicle or HP{beta}CD three times per week, with treatment beginning one week after stroke. We evaluated mice at 7 weeks following stroke using immunostaining, RNA sequencing, lipidomics, and behavioral analyses. Chronic stroke infarct and peri-infarct regions of HP{beta}CD-treated mice were characterized by an upregulation of genes involved in lipid metabolism and a downregulation of genes involved in innate and adaptive immunity, reactive astrogliosis, and chemotaxis. Correspondingly, HP{beta}CD reduced the accumulation of lipid droplets, T lymphocytes, B lymphocytes, and plasma cells in stroke infarcts. Repeated administration of HP{beta}CD also preserved NeuN immunoreactivity in the striatum and thalamus and c-Fos immunoreactivity in hippocampal regions. Additionally, HP{beta}CD improved recovery through the protection of hippocampal-dependent spatial working memory and reduction of impulsivity. These results indicate that systemic HP{beta}CD treatment following stroke attenuates chronic inflammation and secondary neurodegeneration and prevents post-stroke cognitive decline. Significance StatementDementia is a common and debilitating sequela of stroke. Currently, there are no available treatments for post-stroke dementia. Our study shows that lipid metabolism is disrupted in chronic stroke infarcts, which causes an accumulation of uncleared lipid debris and correlates with a chronic inflammatory response. To our knowledge, these substantial changes in lipid homeostasis have not been previously recognized or investigated in the context of ischemic stroke. We also provide a proof of principle that solubilizing and entrapping lipophilic substances using HP{beta}CD could be an effective strategy for treating chronic inflammation after stroke and other CNS injuries. We propose that using HP{beta}CD for the prevention of post-stroke dementia could improve recovery and increase long-term quality of life in stroke sufferers.

neuroscience↗

bioRxiv2021

HolistiC: Leveraging Hi-C and Whole Genome Shotgun Sequencing for Double Minute Chromosome Discovery

Double minute chromosomes are acentric extrachromosomal DNA artifacts that are frequently observed in the cells of numerous cancers. They are highly amplified and contain oncogenes and drug resistance genes, making their presence a challenge for effective cancer treatment. Algorithmic discovery of double minutes (DM) can potentially improve bench-derived therapies for cancer treatment. A hindrance to this task is that DMs evolve, yielding circular chromatin that shares segments from progenitor double minutes. This creates double minutes with overlapping amplicon coordinates. Existing DM discovery algorithms use whole genome shotgun sequencing in isolation, which can potentially incorrectly classify DMs that share overlapping coordinates. In this study, we describe an algorithm called " HolistIC" that can predict double minutes in tumor genomes by integrating whole genome shotgun sequencing (WGS) and Hi-C sequencing data. The consolidation of these sources of information resolves ambiguity in double minute amplicon prediction that exists in DM prediction with WGS data used in isolation. We implemented and tested our algorithm on the tandem Hi-C and WGS datasets of three cancer datasets and a simulated dataset. Results on the cancer datasets demonstrated HolistICs ability to predict DMs from Hi-C and WGS data in tandem. The results on the simulated data showed the HolistIC can accurately distinguish double minutes that have overlapping amplicon coordinates, an advance over methods that predict extrachromosomal amplification using WGS data in isolation. AvailabilityOur software is available at http://www.github.com/mhayes20/HolistIC.

bioinformatics↗

bioRxiv2019

Membrane Protrusion Formation Mediated by Rho/ROCK Signalling and Modulation of Chloride Flux

Membrane protrusion is an important structural property associated with various cellular functions. The pentaspan membrane protein Prominin-1 (Prom1/CD133) is known to be localised to the protrusions and plays a pivotal role in migration and the determination of cellular morphology; however, the underlying mechanisms have been elusive. Here, we demonstrate that Prom1 is sufficient to trigger membrane protrusion formation. Overexpression of Prom1 in the RPE-1 cells triggers multiple long cholesterol-enriched protrusions, independently from actin and tubulin polymerisation. For this protrusion formation, the five amino acid stretch located at the carboxyl cytosolic region is essential. Moreover, the small GTPase Rho and its effector kinase ROCK are essential for this protrusion formation, and the intersection point of active Rho and Prom1 is where the protrusion formation initiates. Importantly, Prom1 causes the chloride ion efflux induced by calcium ion uptake, and protrusion formation is closely associated with the chloride efflux activity. Altogether, this study has elucidated that Prom1 plays critical roles for the membrane morphology and chloride ion flux.

cell biology↗