Biology subjects

Gorelik, J.

Publications and source records attributed to Gorelik, J..

12 recordsLinked to original sources

bioRxiv2026

Submembrane geography dictates GPCR signalling compartmentation and physiological function

G-protein-coupled receptors (GPCRs) are key mediators of intercellular signalling and targets for the vast majority of current therapeutics. Numerous biochemical and biophysical studies have uncovered that individual GPCRs activated at different subcellular locations can mediate distinct functional effects due to compartmentalization of the downstream second messengers in subcellular nanodomains. However, the reasons why a single receptor subtype activated at the same subcellular compartment such as plasma membrane leads to various functional responses have remained poorly understood. Here, we used beta1-adrenergic receptor and cardiomyocytes as classical examples of a therapeutically relevant GPCR and highly compartmentalized cell, to study communication between membrane receptors and subcellular cAMP nanodomains based on a combination of nanoscale scanning ion conductance microscopy assisted local receptor activation with Foerster resonance energy transfer based live cell imaging of the cAMP pathway. Unexpectedly, this approach revealed that beta1-adrenoceptors located in cardiomyocyte T-tubular membrane are strongly coupled to the regulation of cardiac contractility, whereas receptors residing in the outer non-tubular membrane preferentially engage nuclear nanodomains linked to hypertrophy. This unique mechanism of spatially segregated signalling was maintained in failing rodent and human hearts, indicating that it is conserved across species and preserved in disease. Finally, we explored potential therapeutic targeting of this mechanism by generating submembrane-specific beta-blockers acting exclusively at the outer non-tubular membrane. These improved compounds could ameliorate hypertrophy and cardiac remodeling without reducing contractility in vitro and in vivo. Together, these findings uncover an unexpected level of spatial organization of GPCR signaling within the same subcellular compartment and show that not only its identity but also its submembrane location determines cellular signaling and functional response engaged by the same GPCR.

pharmacology and toxicology↗

bioRxiv2026

Long-PDE4D degradation attenuates left ventricular cardiomyocyte hypertrophic remodelling

Spatial compartmentalisation enables cyclic AMP (cAMP) to regulate distinct cellular functions, yet selectively targeting disease-associated signalling remains challenging. Phosphodiesterases constrain local cAMP responses, but conventional inhibitors offer limited isoform selectivity. Here we investigate whether targeted degradation of long phosphodiesterase-4D (PDE4D) isoforms can suppress pathological growth while preserving contractile function. Using adult rat and human ventricular cardiomyocytes and human myocardial slices, we show that the proteolysis-targeting chimera KTX-184 enhances compartmentalised cAMP signalling and attenuates hypertrophic remodelling. In rat cardiomyocytes, KTX-184 increases {beta}-adrenergic cAMP responses in the cytosol and at the plasma membrane, including T-tubule and crest regions, and enhances nuclear protein kinase A activity. In contrast, phospholamban- and ryanodine receptor-associated cAMP nanodomains, calcium transients and sarcomere shortening remain unchanged. KTX-184 prevents angiotensin II-induced hypertrophic remodelling, preserves T-tubule organisation and normalises hypertrophic marker expression. In human cardiomyocytes, it increases cytosolic cAMP responses and prevents overload-induced hypertrophy in myocardial slices. These findings identify long PDE4D isoforms as targets for spatially selective modulation of cAMP signalling and support targeted degradation as an approach to suppress cardiac hypertrophy without increasing contractility.

pharmacology and toxicology↗

bioRxiv2026

Nucleoli as drivers of nuclear remodelling in cardiomyocytes during Heart Failure

Cardiomyocyte mechanotransduction has traditionally focused on the sarcomere and cytoskeleton, yet emerging evidence highlights the nucleus as an active mechanical responder. To adapt to the dynamic mechanical environment, the nucleus forms nuclear invaginations (NIs), double-membrane folds that provide structural support to chromatin and incorporate nuclear pore complexes to facilitate nucleo-cytoplasmic transport, including Ca2+ transport. However, how these structures are formed is not yet understood. We leveraged advances in high-resolution microscopy, mechanical stimulation, rat models and human samples, to study the formation, function and remodelling of cardiac NIs in Heart Failure (HF). Here, we demonstrate that the formation of NI in cardiomyocytes is regulated by both, cytoskeleton such as actin and detyrosinated microtubules as well as intranuclear nucleolar interactions with NI disruption resulting in elevated baseline nuclear Ca2+. In a 16-week post-Myocardial Infarction (MI) end-stage HF rat model, as well as in human Dilated Cardiomyopathy samples, a marked reduction in NIs was observed. Importantly, NI loss was already evident at 8 weeks post-MI, preceding detectable cytoskeletal stiffening. At this stage, we observed increased DNA damage in the peri-nucleolar region, accompanied by nucleolar remodelling and a shift in nucleolar biomechanical properties. In conclusion, preserving nucleolar integrity emerges as a potential target for intervention.

cell biology↗

bioRxiv2026

Multimodal mechano-SICM and FRET with stretch for probing cardiomyocyte function.

Cardiac function is dependent upon the ability of cardiomyocytes to adapt their contractions to meet the demands of the body. Increased preload lengthens the sarcomere, altering the efficiency of contraction. The surface topography of cardiomyocytes is distinct from other cell types. T-tubules are key membrane structures which protrude into the cell body, aligned with the edges of the sarcomere. These are key signalling domains which ensure efficient and adaptable excitation-contraction coupling. It has been shown that T-tubules are dynamic structures which deform during the contraction cycle however, how the T-tubule structure adapts to increased preload has not been realised. Here we demonstrate a methodology for the measurement of the surface topography and sub-cellular signalling of isolated adult cardiomyocytes under diastolic stretch. We track individual T-tubule openings, showing that increased load causes them to shift, increase diameter and become stiffer. Future applications of this system include experimental modelling of preload-reducing therapies, for the treatment of acute and chronic heart failure.

physiology↗

bioRxiv2025

Targeting Troponin I Phosphorylation for Precision Treatment of Diastolic Dysfunction

BackgroundDefective cardiac relaxation (diastolic dysfunction) is prevalent in heart failure, particularly in the context of diabetes, obesity, hypertension, and ageing, and is associated with increased mortality. Yet there is no available treatment that directly targets this abnormal relaxation. Phosphorylation of troponin I by cAMP-dependent protein kinase A (PKA) promotes relaxation, but global PKA activation has widespread, undesirable effects. Here we investigated whether selectively enhancing troponin I phosphorylation could improve relaxation without engaging the broader PKA signalling network. MethodsTo resolve cAMP signalling at subcellular scales, we combined real-time cAMP measurements with FRET-based genetically encoded reporters targeted to defined nanodomains, alongside biochemical and genetic approaches. Protein-protein interaction surfaces were mapped using peptide-array technology, which guided the design of a disruptor peptide to displace specific interactions. The peptides effects on cardiomyocyte function were assessed in vitro using rodent and human cardiomyocytes with biochemical assays, real-time imaging, and work-loop analysis. In vivo effects were evaluated through echocardiography and haemodynamic measurements. ResultsWe identified a previously unrecognized regulatory mechanism in which the cAMP-hydrolyzing enzyme PDE4D9 interacts with troponin I and restricts local cAMP levels within a nanometre-scale domain, thereby selectively controlling troponin I phosphorylation. We found that PDE4D9-troponin I association is markedly increased in cardiac disease in both rodents and humans. A peptide that displaces PDE4D9 from troponin I in a mouse model of heart failure selectively enhances troponin I phosphorylation, accelerates cardiomyocyte relaxation, and prevents diastolic dysfunction, without compromising systolic contractility. ConclusionsThese findings reveal a highly specific regulatory nanodomain governing troponin I phosphorylation and points to a first-in-class, mechanism-based therapeutic strategy with the potential to address a major unmet contributor to heart failure. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABSO_LIWe identify a previously unrecognized, nanometre-scale regulatory mechanism in which PDE4D9 binds troponin I to locally suppress cAMP, limit troponin I phosphorylation and attenuate relaxation. C_LIO_LIWe demonstrate that this mechanism becomes maladaptive in disease: PDE4D9-troponin I interaction is markedly upregulated in failing hearts in both rodents and humans, which can mechanistically explain the impaired cardiac relaxation. C_LIO_LIWe show that this interaction is druggable: a rationally designed peptide can selectively displace PDE4D9, restore localized cAMP-PKA signalling, and normalize myocardial relaxation without global cAMP perturbation. C_LIO_LIDisplacement of PDE4D9 from TPNI improves relaxation with no impact on the calcium transient amplitude and without adversely affecting systolic output and cardiac reserve. C_LI What Are the Clinical Implications?O_LIDiastolic dysfunction, a major cause of heart failure with no targeted treatments, may be amenable to therapies that modulate cAMP signalling with subcellular precision rather than global pathway modulation. C_LIO_LISelective disruption of PDE4D9-troponin I binding offers a mechanism-based approach with potential to restore diastolic function while minimizing off-target effects typical of GPCR-directed therapies. C_LIO_LIBy enhancing relaxation while preserving systolic function and cardiac reserve, this approach may overcome limitations of myofilament-targeted therapies currently under evaluation for diastolic dysfunction that exhibit negative inotropic effects. C_LIO_LIMore broadly, this work establishes a platform for targeting localized signalling domains, a concept that may extend beyond cardiovascular disease to other pathological conditions in which dysregulated cAMP contributes to dysfunction. C_LI

cell biology↗

bioRxiv2025

Different data analysis models for detecting miRNAs using nanopores

Nanopore sensors offer exceptional sensitivity for detecting single molecules, making them ideal for early disease diagnostics. In this study, we present a multiplexed nanopore-based assay that combines DNA-barcoded probes with advanced computational analysis to detect microRNAs (miRNAs) with high specificity and quantitative accuracy. Each probe binds selectively to its target biomarker and generates a characteristic delay in the ionic current signal upon translocation through the nanopore, enabling label-free detection. We evaluated three analytical strategies for classifying delayed versus non-delayed events: (1) moving standard deviation (MSD), (2) spectral entropy (SE), and (3) a convolutional neural network (CNN). While MSD and SE rely on manually defined thresholds and exhibit limited sensitivity, the CNN model, trained on image representations of raw current traces, achieved near-perfect classification performance across all metrics. Grad-CAM visualisation confirmed that the CNN focused on biophysically relevant signal regions, enhancing interpretability and generalisability. All methods produced sigmoidal concentration-response curves consistent with expected binding kinetics, and nanopore-derived delay metrics closely matched RT-qPCR validation data. All three methods were capable of distinguishing between signal classes; however, the CNN model demonstrated superior sensitivity and robustness. This work highlights the importance of data interpretation in nanopore sensing and presents a comparative framework for binary event classification. The findings pave the way for the development of machine learning-driven nanopore diagnostics capable of detecting diverse biomarker types at the single-molecule level.

biophysics↗

bioRxiv2025

Multiparametric Correlative Topographical and Volumetric Fluorescence Microscopy

Live-cell imaging of cell surface topography and intracellular architecture is essential for understanding cellular function. However, conventional approaches often involve trade-offs between resolution, invasiveness, and volumetric coverage. Here, we present an integrated Scanning Ion Conductance Microscope and single-objective Oblique Plane Microscope (SICM-OPM) system that enables simultaneous non-contact topographical imaging and volumetric fluorescence imaging within the same live cell. Beyond correlative live imaging, the platform supports nanomechanical mapping with tens-of-nanometres resolution, fluorescence-guided localised molecular delivery via the SICM, and benefits from reduced photobleaching due to light-sheet excitation. We demonstrate this platforms capabilities by visualising imipramine-induced T-tubule remodelling in live cardiomyocytes, revealing subsurface detubulation while surface morphology remains preserved. Additionally, we show precision delivery of fluorescent cargos--including dextrans and -synuclein--into diatom and mammalian cells, alongside localised stiffness mapping to evaluate mechanical responses. We believe this technique opens new avenues for correlative structural, functional, and biophysical studies in live cells, with broad relevance to cell biology, neurodegeneration, and mechanobiology.

biophysics↗

bioRxiv2024

Depleting trafficking regulator CASK promotes intercalated disc organization and ventricular function

BackgroundThe intercalated disc (ID) electromechanically couples adjacent cardiomyocytes. Alteration of this structure plays a central role in cardiac arrhythmias, notably arrhythmogenic cardiomyopathy (ACM), an inherited genetic disorder of desmosomes. Calcium/Calmodulin-Dependent Serine Protein Kinase (CASK), a costameric component of the lateral membrane, regulates cardiomyocyte protein trafficking. Here, we investigated CASK regulation of the organization of ID components in normal and pathological contexts. Here, we investigated CASK regulation of the organization of ID components in normal and pathological contexts. MethodsWe studied the outcomes of CASK depletion in neonatal rat hearts using a cardiac-specific adeno-associated virus strategy. We used conventional and strain echocardiography, hemodynamics, electrocardiography, histology, and gene and protein expression studies to characterize adult rat hearts. We also studied the effects of CASK depletion in neonatal rat ventricular cardiomyocytes (NRVM), and control and ACM (PKP2+/-) IPS cell-derived CM (hIPS-CM) using proteomics, electron microscopy, high-resolution imaging, mechano-scanning ion conductance microscopy (mechano-SICM), and stress resistance tests. We studied cardiac CASK expression and localization in human ACM and non-transplantable control hearts. ResultsDepletion of CASK in our multiple experimental models revealed that CASK regulates cardiomyocyte IDs. In rats, CASK depletion improved contractile reserve and compliance. In cultured rat cardiomyocytes, CASK knockdown increased localization of connexin 43 (Cx43) and PKP2 at IDs, resulting in increased contact stiffness. In PKP2+/- hIPS-CMs, CASK expression was increased. CASK depletion in these cells promoted PKP2 accumulation at cell contacts, formation of desmosome-like structures, and stress resistance. In the right ventricles of ACM patients, CASK protein level was also increased and CASK abnormally localized at the ID. ConclusionCASK functions as a repressor of ID organization and tissue cohesion, suggesting novel mechanisms for regulating ID structure and function. These observations, along with CASK upregulation and mislocalization in ACM, open up new perspectives on understanding the pathophysiology of ACM and suggest innovative strategies for its treatment.

physiology↗

bioRxiv2023

Development and Characterization of the Mode-of-Action of Inhibitory and Agonist Peptides Targeting the Voltage-Gated Sodium Channel SCN1B/β1 Subunit

Treatment of cardiac arrhythmias by targeting ion channels is challenging, with safe and effective therapies remaining an unmet clinical need. Modeling and experimental studies have shown that a voltage-gated sodium channel (VGSC)-rich nanodomain at edge of the gap junction (GJ) called the perinexus could provide new mechanistic insights into normal and abnormal conduction of action potentials in the heart. We have reported that a 19 amino acid SCN1B ({beta}1/{beta}1B) mimetic peptide derived from the immunoglobulin domain of the VGSC subunit called {beta}adp1 acutely disrupts {beta}1-mediated adhesive interactions at cardiac perinexii, prompting arrhythmogenic changes during time courses of up to an hour. In the present study, we sought to gain further insight on {beta}adp1 mode-of-action, as well as identifying new SCN1B ({beta}1/{beta}1B) mimetic peptides, with potential for inhibiting and/or promoting {beta}1-mediated adhesion. This included studies of the effect of {beta}adp1 and related peptides on SCN1B ({beta}1/{beta}1B) Regulated Intramembrane Proteolysis (RIP) - a signaling pathway that has been shown to effect gene transcription, including that of VGSC subunits. Using patch clamp to assay cell-cell contact-associated VGSC activity in cardiomyocytes, and electric cell substrate impedance sensing (ECIS) to assess intercellular adhesion in cells heterologously expressing {beta}1, we find that inhibitory effects of {beta}adp1 can persist for up to 5 hours. However, this acute inhibition is not sustained, with {beta}adp1 effects on {beta}1-mediated adhesion lost after 24 hours. We also determined that a short peptide (LQLEED) near the carboxyl-terminal portion of {beta}adp1 inhibited adhesion in {beta}1-expressing cells in a manner similar to {beta}adp1. Paradoxically, dimeric peptides incorporating a repeat of the LQLEED sequence promoted intercellular adhesion at all time points studied over a 2-day time course. Inhibitory and agonistic peptides were found to effect {beta}1 RIP, with {beta}adp1increasing RIP continuously over 48 hours, whilst dimeric agonists acutely increased RIP at 6 hours post-treatment, but not thereafter. In the presence of DAPT, an inhibitor of RIP, the effects of {beta}adp1 on ECIS-measured intercellular adhesion were lost, suggesting a relationship between RIP and inhibitory effects of the peptide. In sum, we identify novel SCN1B ({beta}1/{beta}1B) mimetic peptides with potential to inhibit and promote intercellular {beta}1-mediated adhesion, possibly including by effects on {beta}1 RIP, suggesting paths to development of anti-arrhythmic drugs targeting the perinexus.

cell biology↗

bioRxiv2023

Interleukin 11-induced microRNAs as functional mediators and circulating biomarkers of cardiac fibrosis

BackgroundCardiac fibrosis can be triggered by several pathologies, including ischemic heart disease and aortic stenosis (AS). Cardiac fibrosis is brought about by uncontrolled extracellular matrix (ECM) deposition by myofibroblasts. Interleukin-11 (IL-11) has been firmly demonstrated to be a major trigger of multi-organ fibrosis. However, the molecular mechanisms underpinning IL-11-induced fibrosis requires further characterisation. Recent studies indicate that microRNA (miRNA) dysregulation contributes to the pathogenesis of cardiac fibrosis and can be targeted therapeutically. In this study, we explored the hypothesis that miRNAs act as downstream effectors of IL-11-induced cardiac fibrosis. Moreover, we investigated the translational potential of IL-11-regulated miRNAs as circulating biomarkers of cardiac fibrosis in AS patients. Methods and ResultsUsing computational approaches, we identified miRNA-497-5p and miRNA-27b-5p as potential new downstream profibrotic effectors of IL-11 in fibroblasts. We next confirmed that both miRNAs increased in healthy rat CF stimulated with IL-11 and in CF derived from post-infarction failing hearts. At the functional level, miRNA-497-5p and miRNA-27b-5p inhibition indirectly reduced the mRNA expression of collagen 1 (Col1a1). Conversely, transfection of CFs with mimics for each of the two miRNAs promoted fibroblast-to-myofibroblast transition and increased Col1a1 levels. We provided evidences that miRNA-27b-5p and miRNA-497-5p converge to promote hypoxia-inducible factor 1 signalling, by targeting its regulator EGLN (PHD) family members. The clinical relevance of our findings was confirmed using left ventricle (LV) specimens obtained from surgical patients with AS. The miRNA-27b-5p and miRNA-497-5p measured in the LV, peripheral plasma and plasma extracellular vesicles correlated with the severity of LV fibrosis, indicating these miRNAs potential as new circulating biomarkers of cardiac fibrosis. ConclusionsIn this study, we have newly identified the potential value of miRNA-27b-5p and miRNA-497-5p as actionable biomarkers of the profibrotic response to IL-11 in the heart. Future studies should validate the translational potential of the miRNAs as new clinical biomarkers and therapeutic targets.

molecular biology↗

bioRxiv2022

Highly multiplexed detection of microRNAs, proteins and small molecules using barcoded molecular probes and nanopore sequencing

Currently, most blood tests in a clinical setting only investigate a handful of markers. A low-cost, rapid, and highly multiplexed platform for the quantitative detection of blood biomarkers has the potential to advance clinical diagnostics beyond the single biomarker paradigm. In this study, we perform nanopore sequencing of barcoded molecular probes that have been engineered to recognise a panel of biological targets (miRNAs, proteins, and small molecules such as neurotransmitters), allowing for highly multiplexed simultaneous detection. Our workflow is rapid, from sample preparation to results in 1 hour. We also demonstrate that the strategy can be used to detect biomarkers directly from human serum without extraction or amplification. The established method is easily adaptable, as the number and type of targets detected can be greatly expanded depending on the application required.

biophysics↗

bioRxiv2019

Persistent anti-heart autoimmunity causes cardiomyocyte damage in chronic heart failure.

Although clinicians and researchers have long appreciated the detrimental effects of excessive acute inflammation after myocardial infarction (MI), less is known about the role of the adaptive immune system in MI complications including heart failure. Yet, abundant cardiac self-antigens released from necrotic cardiomyocytes in a highly inflammatory environment are likely to overwhelm peripheral mechanisms of immunological self-tolerance and adaptive auto-reactivity against the heart may cause ongoing tissue destruction and exacerbate progression to chronic heart failure (CHF). Here, we confirm that the adaptive immune system is indeed persistently active in CHF due to ischemic heart disease triggered by MI in rats. Heart draining mediastinal lymph nodes contain active secondary follicles with mature class-switched IgG2a positive cells, and mature anti-heart auto-antibodies binding to cardiac epitopes are still present in serum as late as 16 weeks after MI. When applied to healthy cardiomyocytes in vitro, humoral factors present in CHF serum promoted apoptosis, cytotoxicity and signs of hypertrophy. These findings directly implicate post-MI autoimmunity as an integral feature of CHF progression, constituting a roadblock to effective regeneration and a promising target for therapeutic intervention.

immunology↗