Biology subjects

Gomez, A. M.

Publications and source records attributed to Gomez, A. M..

11 recordsLinked to original sources

bioRxiv2026

RyR2-Mediated Ca2+ Leak Drives Progressive Arrhythmogenic Cardiomyopathy

Background Abnormal sarcoplasmic reticulum (SR) Ca2+ release through ryanodine receptor 2 (RyR2) is a well-established mechanism of ventricular arrhythmias. Whether persistent RyR2 dysfunction can also initiate the structural remodeling characteristic of arrhythmogenic cardiomyopathy (ACM) remains unknown. We tested the hypothesis that chronic RyR2-mediated Ca2+ leak is sufficient to couple electrical instability to progressive cardiomyopathy. Methods We generated a rabbit carrying the severe gain-of-function RyR2-V2475F mutation and characterized disease progression using longitudinal cardiac phenotyping, continuous electrocardiographic monitoring, cellular electrophysiology and Ca2+ imaging, histopathology, biochemical analyses, and single-nucleus RNA sequencing (snRNA-seq). Therapeutic potential was evaluated by continuous treatment with the selective RyR2 inhibitor ent-verticilide for two months. Results RyR2-V2475F rabbits developed spontaneous ventricular tachyarrhythmias, sudden cardiac death, and progressive right ventricular (RV)-dominant fibrofatty cardiomyopathy recapitulating major features of human ACM. Malignant ventricular arrhythmias preceded overt structural remodeling and were associated at the cellular level with early spontaneous Ca2+ release and early afterdepolarizations. Early disease was characterized by remodeling of excitation-contraction coupling with preserved SR Ca2+ load and contractile function despite RyR2 dysfunction; upon disease progression, these compensatory changes were accompanied by SR Ca2+ depletion, impaired RV contractility and reduced left ventricular filling. Single-nucleus transcriptomics identified early fibroblast expansion and predicted cardiomyocyte-centered paracrine signaling before advanced fibrofatty infiltration. Cardiomyocytes also exhibited an altered lipid-metabolic transcriptome and intracellular lipid accumulation, accompanied by enhanced mitochondrial Ca2+ uptake. Selective RyR2 inhibition markedly reduced ventricular tachycardia burden and preserved RV contraction and LV filling during disease progression. Conclusions Severe RyR2 gain-of-function can lead to both malignant ventricular arrhythmias and progressive arrhythmogenic cardiomyopathy in a large-animal model, establishing persistent intracellular Ca2+ dysregulation as a mechanistic link between electrical and structural heart disease. The ability of selective RyR2 inhibition to suppress arrhythmias and preserve cardiac function identifies RyR2 as a potentially actionable therapeutic target in arrhythmogenic cardiomyopathy.

physiology↗

bioRxiv2025

CRISPR epi-editing reveals regulatory crosstalk between alternative promoters and splicing in Neurexin isoform expression

The use of alternative promoters and splicing increases molecular complexity and diversifies cellular functions. However, mechanisms of crosstalk between transcription and splicing remain poorly understood. Here, we utilize CRISPR epi-editing in neurons to manipulate isoforms of the synaptic organizer, Neurexin-1, and elucidate mechanisms underlying the co-regulation of alternative promoters and splicing. Surprisingly, silencing individual Neurexin-1 promoters altered downstream promoter activity via transcriptional interference and biased splicing decisions. Our data reveals transcriptional interference as key to shaping cell type-specific Neurexin-1 isoforms in the mouse hippocampus and demonstrates the power of epi-editing to uncover regulatory interactions between RNA processes in the brain.

molecular biology↗

bioRxiv2025

A multi-institutional investigation of psilocybin's effects on mouse behavior

Studies reporting novel therapeutic effects of psychedelic drugs are rapidly emerging. However, the reproducibility and reliability of these findings could remain uncertain for years. Here, we implemented a multi-institutional collaborative approach to define the robust and replicable effects of the psychedelic drug psilocybin on mouse behavior. Five laboratories performed the same experiments to test the acute and persistent effects of psilocybin (2 mg/kg, IP) on various behaviors that psychedelics have been proposed to affect, including anxiety-related approach-avoidance, exploration, sociability, depression-related behaviors, fear extinction, and social reward learning. Through this coordinated approach, we found that psilocybin had several robust and replicable acute effects on mouse behavior, including increased anxiety- and avoidance-related behaviors and decreased fear expression. Surprisingly, however, we found that psilocybin did not have replicable effects 24 hours post psilocybin administration on reducing anxiety- and depression-like behaviors or facilitating fear extinction learning. Additionally, we were unable to observe psilocybin-induced alterations in social preference or social reward learning. Overall, our comprehensive characterization of psilocybins acute and persistent behavioral effects using [~]200 total male and female mice per experiment spread across five independent labs demonstrates with unique certainty several acute drug effects and suggests that psilocybins persistent effects in mice may be more modest and inconsistent than previously suggested. We believe this unusual multi-laboratory, highly coordinated research effort serves as a model for facilitating the generation of replicable results and consequently will reduce efforts based on unreliable and spurious results.

neuroscience↗

bioRxiv2025

Animal-free recombinant nanobody rescues HCN4 channel deficit in sinus node dysfunction

Hyperpolarization-activated cyclic nucleotide-gated channels (HCN1-4) control cardiac and neuronal firing and their dysfunction leads to cardiac arrythmias (HCN4), epilepsy (HCN1) and chronic pain (HCN2). Prompted by the urgent need for HCN subtype-specific treatments, we screened a recombinant nanobody library in search of HCN4-specific binders. Here we show that nanobody 5 (NB5) binds to the extracellular side of HCN4 with high specificity and nanomolar affinity and activates the channel by a non-canonical electromechanical coupling path. In ex vivo and in vitro experiments, NB5 acts as an agonist of the pacemaker current If, increasing the firing rate of rabbit cardiac pacemaker myocytes and of human derived cardiomyocytes. Notably, NB5 rescued the effects of a LOF HCN4 mutation causing sinus node dysfunction in a patient. Our work illustrates that animal-free recombinant nanobodies have strong potential as next generation modulators for clinical application in symptomatic bradycardia.

biophysics↗

bioRxiv2025

Persistent large-scale changes in alternative splicing in prefrontal cortical neuron types following psychedelic exposure

Psychedelics engage the serotonergic system as potent neuromodulators, increasing neuroplasticity in humans and rodents. Persistent changes in cognitive flexibility, emotional regulation, and social cognition are thought to underlie the therapeutic effects of psychedelics. However, the underlying molecular and cellular basis of psychedelic-induced plasticity remains unclear. Here, we identify persistent, cell type-specific alternative splicing changes in the mouse medial prefrontal cortex (mPFC) induced by a single dose of psychedelics. Combining deep RiboTag sequencing and bioinformatics, we find that a single dose of psychedelics modestly alters gene expression while dramatically shifting patterns of alternative splicing lasting at least a month. We connect our functional enrichment and alternative splicing analysis with changes in the extracellular matrix, synaptic physiology, and intrinsic physiology in parvalbumin interneurons days to a week after psychedelic treatment. Our dataset is an essential resource for understanding the persistent, cell type-specific effects of psychedelics on cortical cell types and functions.

neuroscience↗

bioRxiv2024

The cytokine receptor Fn14 is a molecular brake on neuronal activity that mediates circadian function in vivo

To survive, organisms must adapt to a staggering diversity of environmental signals, ranging from sensory information to pathogenic infection, across the lifespan. At the same time, organisms intrinsically generate biological oscillations, such as circadian rhythms, without input from the environment. While the nervous system is well-suited to integrate extrinsic and intrinsic cues, how the brain balances these influences to shape biological function system-wide is not well understood at the molecular level. Here, we demonstrate that the cytokine receptor Fn14, previously identified as a mediator of sensory experience-dependent synaptic refinement during brain development, regulates neuronal activity and function in adult mice in a time-of-day-dependent manner. We show that a subset of excitatory pyramidal (PYR) neurons in the CA1 subregion of the hippocampus increase Fn14 expression when neuronal activity is heightened. Once expressed, Fn14 constrains the activity of these same PYR neurons, suggesting that Fn14 operates as a molecular brake on neuronal activity. Strikingly, differences in PYR neuron activity between mice lacking or expressing Fn14 were most robust at daily transitions between light and dark, and genetic ablation of Fn14 caused aberrations in circadian rhythms, sleep-wake states, and sensory-cued and spatial memory. At the cellular level, microglia contacted fewer, but larger, excitatory synapses in CA1 in the absence of Fn14, suggesting that these brain-resident immune cells may dampen neuronal activity by modifying synaptic inputs onto PYR neurons. Finally, mice lacking Fn14 exhibited heightened susceptibility to chemically induced seizures, implicating Fn14 in disorders characterized by hyperexcitation, such as epilepsy. Altogether, these findings reveal that cytokine receptors that mediates inflammation in the periphery, such as Fn14, can also play major roles in healthy neurological function in the adult brain downstream of both extrinsic and intrinsic cues. HighlightsO_LINeuronal activity induces Fn14 expression in pyramidal neurons of the hippocampus C_LIO_LIFn14 constrains neuronal activity near daily transitions between light and dark C_LIO_LILoss of Fn14 lengthens the endogenous circadian period and disrupts sleep-wake states and memory C_LIO_LIMicroglia contact excitatory synapses in an Fn14-dependent manner C_LI

neuroscience↗

bioRxiv2024

Circadian regulation of CaV1.2 expression by RORalpha in the mouse heart

BackgroundIn addition to show autonomous beating rhythmicity, the physiological functions of the heart present daily periodic oscillations. Notably the ventricular repolarization itself varies throughout the circadian cycle which was mainly related to the periodic expression of K+ channels. However, the involvement of the L-type Ca2+ channel (CaV1.2 encoded by Cacna1c gene) in these circadian variations remains elusive. MethodsWe used a transgenic mouse model (PCa-luc) that expresses the luciferase reporter under the control of the cardiac Cacna1c promoter and analyzed promoter activity by bioluminescent imaging, qPCR, immunoblot, Chromatin immunoprecipitation assay (ChIP) and CaV1.2 activity. ResultsUnder normal 12:12h light-dark cycle, we observed in vivo a biphasic diurnal variation of promoter activities peaking at 9 and 19.5 Zeitgeber time (ZT). This was associated with a periodicity of Cacna1c mRNA levels preceding 24-h oscillations of CaV1.2 protein levels in ventricle (with a 1.5 h phase shift) but not in atrial heart tissues. The periodicity of promoter activities and CaV1.2 proteins, which correlated with biphasic oscillations of L-type Ca2+ current conductance, persisted in isolated ventricular cardiomyocytes from PCa-Luc mice over the course of the 24-h cycle, suggesting an endogenous cardiac circadian regulation. Comparison of 24-h temporal patterns of clock gene expressions in ventricles and atrial tissues of the same mice revealed conserved circadian oscillations of the core clock genes except for the retinoid-related orphan receptor gene (ROR), which remained constant throughout the course of a day in atrial tissues. In vitro we found that ROR is recruited to two specific regions on the Cacna1c promoter and that incubation with specific ROR inhibitor disrupted 24-h oscillations of ventricular promoter activities and CaV1.2 protein levels. Similar results were observed for pore forming subunits of the K+ transient outward currents, KV4.2 and KV4.3. ConclusionsThese findings raise the possibility that the ROR-dependent rhythmic regulation of cardiac CaV1.2 and KV4.2/4.3 throughout the daily cycle may play an important role in physiopathology of heart function.

physiology↗

bioRxiv2023

Anti-citrullinated protein antibodies with diverse specificities ameliorate collagen antibody-induced arthritis in a time-dependent manner

Anti-citrullinated protein antibodies (ACPAs) are a hallmark of rheumatoid arthritis (RA) and have long been considered to contribute to pathogenesis. In this study, we sequenced the plasmablast antibody repertoires of RA patients and functionally characterized their encoded ACPAs. Recombinantly expressed monoclonal ACPAs bound citrullinated autoantigens, as well as autocitrullinated peptidylarginine deiminase 4 (PAD4). Using the collagen antibody induced arthritis (CAIA) mouse model, we demonstrated that the recombinant ACPAs significantly reduced paw thickness and arthritis severity as compared to isotype-matched control antibodies. Treatment with recombinant ACPAs also significantly reduced bone erosions, synovitis, and cartilage damage in histologic analysis of paws. This amelioration was observed for all the ACPAs tested and was independent of citrullinated antigen specificities. Furthermore, disease amelioration was more prominent when ACPAs were injected at earlier stages of CAIA than at later phases of the model, implying that ACPAs anti-inflammatory effects were more preventative than therapeutic. This study highlights a potential protective role for ACPAs in RA.

immunology↗

bioRxiv2022

Trans-cellular control of synapse properties by a cell type-specific splicing regulator

The recognition of synaptic partners and specification of synaptic properties are fundamental for the function of neuronal circuits. Terminal selector transcription factors coordinate the expression of terminal gene batteries that specify cell type-specific properties. Moreover, pan-neuronal alternative splicing regulators have been implicated in directing neuronal differentiation. However, the cellular logic of how splicing regulators instruct specific synaptic properties remains poorly understood. Here, we combine genome-wide mapping of mRNA targets and cell type-specific loss-of-function studies to uncover the contribution of the nuclear RNA binding protein SLM2 to hippocampal synapse specification. Focusing on hippocampal pyramidal cells and SST-positive GABAergic interneurons, we find that SLM2 preferentially binds and regulates alternative splicing of transcripts encoding synaptic proteins, thereby generating cell type-specific isoforms. In the absence of SLM2, cell type-specification, differentiation, and viability are unaltered and neuronal populations exhibit normal intrinsic properties. By contrast, cell type-specific loss of SLM2 results in highly selective, non-cell autonomous synaptic phenotypes, altered synaptic transmission, and associated defects in a hippocampus-dependent memory task. Thus, alternative splicing provides a critical layer of gene regulation that instructs specification of neuronal connectivity in a trans-synaptic manner.

neuroscience↗

bioRxiv2022

An Analysis of Protein Language Model Embeddings for Fold Prediction

The identification of the protein fold class is a challenging problem in structural biology. Recent computational methods for fold prediction leverage deep learning techniques to extract protein fold-representative embeddings mainly using evolutionary information in the form of multiple sequence alignment (MSA) as input source. In contrast, protein language models (LM) have reshaped the field thanks to their ability to learn efficient protein representations (protein-LM embeddings) from purely sequential information in a self-supervised manner. In this paper, we analyze a framework for protein fold prediction using pre-trained protein-LM embeddings as input to several fine-tuning neural network models which are supervisedly trained with fold labels. In particular, we compare the performance of six protein-LM embeddings: the LSTM-based UniRep and SeqVec, and the transformer-based ESM-1b, ESM-MSA, ProtBERT, and ProtT5; as well as three neural networks: Multi-Layer Perceptron (MLP), ResCNN-BGRU (RBG), and Light-Attention (LAT). We separately evaluated the pairwise fold recognition (PFR) and direct fold classification (DFC) tasks on well-known benchmark datasets. The results indicate that the combination of transformer-based embeddings, particularly those obtained at amino acid-level, with the RBG and LAT fine-tuning models performs remarkably well in both tasks. To further increase prediction accuracy, we propose several ensemble strategies for PFR and DFC, which provide a significant performance boost over the current state-of-the-art results. All this suggests that moving from traditional protein representations to protein-LM embeddings is a very promising approach to protein fold-related tasks.

bioinformatics↗

bioRxiv2020

Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function

MotivationProtein function prediction is a difficult bioinformatics problem. Many recent methods use deep neural networks to learn complex sequence representations and predict function from these. Deep supervised models require a lot of labeled training data which are not available for this task. However, a very large amount of protein sequences without functional labels is available. ResultsWe applied an existing deep sequence model that had been pre-trained in an unsupervised setting on the supervised task of protein function prediction. We found that this complex feature representation is effective for this task, outperforming hand-crafted features such as one-hot encoding of amino acids, k-mer counts, secondary structure and backbone angles. Also, it partly negates the need for deep prediction models, as a two-layer perceptron was enough to achieve state-of-the-art performance in the third Critical Assessment of Functional Annotation benchmark. We also show that combining this sequence representation with protein 3D structure information does not lead to performance improvement, hinting that three-dimensional structure is also potentially learned during the unsupervised pre-training. AvailabilityImplementations of all used models can be found at https://github.com/stamakro/GCN-for-Structure-and-Function. Contactameliavm@ugr.es Supplementary informationSupplementary data are available online.

bioinformatics↗