Biology subjects

Jayasinghe, I.

Publications and source records attributed to Jayasinghe, I..

11 recordsLinked to original sources

bioRxiv2026

Structural and functional heterogeneity in cardiac RyR signalling nanodomains revealed with quantitative single molecule mapping toolkit

The nanoscale organisation of ryanodine receptor type 2 (RyR2) channels and junctophilin-2 (JPH2) shapes cardiac Ca{superscript 2} release, but how this relationship is remodelled in right ventricular failure remains unclear. We developed an integrated analysis pipeline building on multiplexed DNA-PAINT data to quantify RyR2 and JPH2 abundance, stoichiometry of co-clustering, and spatial organisation within individual subsarcolemmal Ca{superscript 2}-release nanodomains. Applied to cardiomyocytes from control rats with pulmonary hypertension-induced right ventricular failure, the approach revealed reduced co-localisation between RyR2 and JPH2 within peripheral junctions and greater variability in their co-clustering stoichiometry across the cell. A sub-variogram analysis further showed divergent remodelling of JPH2 expression patterns across subcellular length scales, indicating that disease alters both local molecular composition and cell-wide spatial heterogeneity. Experimentally derived RyR2/JPH2 maps were then used to model as two-dimensional templates for stochastic reaction-diffusion of Ca{superscript 2} release. Simulations of spontaneous Ca{superscript 2} waves from failing cells showed up to 25% wave propagation. Maps from failing cells supported faster transverse and longitudinal Ca{superscript 2} dependent release, consistent with the emergence, that support the likelihood of heterogeneous modulation and coupling of RyR resulting from the RyR redistribution and heterogeneous JPH2 expression in the failing cell. Together, these findings identify spatially heterogeneous RyR2-JPH2 remodelling as a potential substrate for dysregulated Ca{superscript 2} signalling in right ventricular failure and establish a transferable toolkit for linking molecular nanostructure to cellular function.

cell biology↗

bioRxiv2025

Mapping EGFR1 sorting domains in endosomes with a calibrated 3D expansion microscopy toolkit

Endosomes are nanoscale intracellular compartments that sort and recycle cell surface receptors such as epidermal growth factor receptor 1 (EGFR1). Nanometre-scale interactions and co-clustering of signalling proteins, cargo, and the membrane are critical to this process. Direct visualisation of these interactions has been hindered by the limited 3D resolution achievable with conventional and super-resolution microscopies. Here, we present the adaptation of expansion microscopy (ExM) to visualise, and quantify nanoclusters of endosomal proteins of human retinal pigment epithelial (RPE-1) cells. A 3D distortion analysis was developed leveraging the Farneback optical flow principle for detecting anisotropies in the hydrogel expansion. Analysis of pre- and post- ExM image volumes for 3D anisotropies revealed under-expansion of cytoplasmic regions within ExM hydrogels, often leading to over-estimation of size and distance measurements of small compartments such as endosomes. A self-assembling protein nanocage that reports the true local and nanoscale expansion factor was genetically introduced into the cells to calibrate ExM images of cytoplasmic regions containing endosomes. To stimulate and visualise the internalisation and sorting of EGFR1 in mammalian cells, a pulse-chase protocol was carried out with fluorescently-tagged EGF. The cells were subsequently fixed at 15- and 30- minute time points and subjected to 10-fold ExM and multiplexed 3D Airyscan microscopy to map cargo and EGFR1 vs other endosomal proteins. A volume tracing pipeline was developed to visualise the changes in the labelled EGF and EGFR1 densities at the limiting membrane of the endosomes. With multiplexed 3D ExM image volumes, we observed the enrichment of both EGF and EGFR1 in the endosomal interior and the accumulation of endosomal protein Rab5a near the limiting membrane during this early maturation of the endosomes. Taken together, the multiplexed 3D ExM toolkit offers a quantitative framework for visualising and measuring the intrinsic biology of small sub-cellular organelles like endosomes at true molecular-scale resolution.

biophysics↗

bioRxiv2023

Differential labelling of human sub-cellular compartments with fluorescent dye esters and expansion microscopy

Amine-reactive esters of aromatic fluorescent dyes are emerging as imaging probes for nondescript staining of cellular and tissue architectures. We characterised the differential staining patterns of 14 fluorescent dye ester species with varying physical and spectral properties in the broadly studied human cell line - HeLa. When combined with expansion microscopy (ExM), these stains reveal nanoscale features such as the nuclear proteome, membrane-bound compartments and vesicles. Among N-Hydroxysuccinimide (NHS) esters, we observe differential compartment specificity and weighting of labelling density which correlates with the hydrophobicity of the dye ester. We also observe changes in both staining density and compartment specificity for a given dye ester depending on the presence of a second dye ester species and on the timepoint of application in the ExM protocol. Our findings confirm these dye esters as a useful addition to the repertoire of biomedical stains of the cellular proteome, either on their own, or as counterstains to immunofluorescence.

cell biology↗

bioRxiv2023

Geometry-preserving Expansion Microscopy microplates enable high fidelity nanoscale distortion mapping

Expansion microscopy (ExM) is a versatile super-resolution microscopy pipeline, leveraging nanoscale biomolecular cross- linking and osmotically driven swelling of hydrogels. In its current implementation, ExM remains a laborious and skill-intensive technique, involving manual handling of the hydrogels that can compromise the integrity of the gel matrix and diminish reproducibility. The lack of protocols to constrain the gel orientation during this process lends to challenges in tracking gel isotropy during or after the swelling. We have developed a bespoke microplate system capable of carrying out the entire ExM workflow within each well. The microplates enable in situ image acquisition and eliminate the need for direct physical handling of the hydrogels. The preservation of the gel geometry and orientation by the design of the microplate wells also enables convenient tracking of gel expansion, pre- and post-ExM image acquisition, and distortion mapping of every cell or region of interest. We demonstrate the utility of this approach with both single-colour and multiplexed ExM of HeLa cells cultured within the microplate wells to reveal nuclear and sub-plasmalemmal regions as distortion-prone structures.

biophysics↗

bioRxiv2023

Correlative super-resolution analysis of cardiac calcium sparks and their molecular origins in health and disease

Rapid release of calcium from internal stores via ryanodine receptors (RyRs) is one of the fastest types of cytoplasmic second messenger signalling in excitable cells. In the heart, rapid summation of the elementary events of calcium release, calcium sparks, determine the contraction of the myocardium. Recent advances in super-resolution microscopy methods have revealed complex clustering patterns of RyRs at single-channel resolution. Here, we have experimentally correlated sub-sarcolemmal spontaneous calcium sparks in rat right ventricular myocytes with the underlying nanoscale sub-sarcolemmal RyR patterns resolved with super-resolution DNA-PAINT microscopy. Local functional groupings and clustering patterns of RyR were sampled by the location and the two-dimensional area of each calcium spark to reveal a steep dependence of the integral of a calcium spark on the sum of the local RyRs. Visualisation of recurring spark sites showed evidence of repeated and triggered saltatory activation of multiple local RyR clusters. In similar myocytes taken from rats with induced right ventricular failure, RyR clusters themselves showed a dissipated morphology and fragmented (smaller) clusters. The failing myocytes featured greater heterogeneity in both the spark properties and the relationship between the integral of the calcium spark and the local ensemble of RyRs. Whilst fragmented (smaller) RyR clusters were rarely observed to directly underlying the larger sparks or the recurring spark sites, local interrogation of the channel-to-channel distances confirmed a clear link between the positions of each calcium spark and the tight non-random clustering of the local RyRs in both healthy and failing ventricles.

biophysics↗

bioRxiv2022

Cysteine post-translational modifications regulate protein interactions of caveolin-3

Caveolae are small flask-shaped invaginations of the surface membrane which are proposed to recruit and co-localise signalling molecules. The distinctive caveolar shape is achieved by the oligomeric structural protein caveolin, of which three isoforms exist. Aside from the finding that caveolin-3 is specifically expressed in muscle, functional differences between the caveolin isoforms have not been rigorously investigated. Caveolin-3 is relatively cysteine-rich compared to caveolins 1 and 2, so we investigated its cysteine post-translational modifications. We find that caveolin-3 is palmitoylated at 6 cysteines and becomes glutathiolated following redox stress. We map the caveolin-3 palmitoylation sites to a cluster of cysteines in its C terminal membrane domain, and the glutathiolation site to an N terminal cysteine close to the region of caveolin-3 proposed to engage in protein interactions. Glutathiolation abolishes caveolin-3 interaction with heterotrimeric G protein alpha subunits. Our results indicate that a caveolin-3 oligomer contains up to 66 palmitates, compared to up to 33 for caveolin-1. The additional palmitoylation sites in caveolin-3 therefore provide a mechanistic basis by which caveolae in smooth and striated muscle can possess unique phospholipid and protein cargoes. These unique adaptations of the muscle-specific caveolin isoform have important implications for caveolar assembly and signalling.

cell biology↗

bioRxiv2022

Expansion microscopy reveals subdomains in C. elegans germ granules

Many membraneless organelles (MLOs) have been shown to form via liquid-liquid phase separation (LLPS). Light and electron microscopy techniques have been indispensable in the identification and characterization of LLPS MLOs. However, for complex MLOs such as the perinuclear germ granule in C. elegans, our understanding of how the organelle as a whole is regulated is hampered by 1) the technical limitations in confocal fluorescence imaging in which only a few granule protein markers can be examined at a time and 2) the inaccessibility of electron microscopy. In this study, we take advantage of the newly developed super-resolution method of expansion microscopy (ExM) and in-situ staining of the whole proteome to examine the C. elegans germ granule, the P granule. We show that in small RNA pathway mutants, the P granule is smaller compared with wild type animals. Furthermore, we investigate the relationship between the P granule and two other germ granules, mutator foci and Z granule, and show that they are located within the same protein-dense regions while occupying distinct subdomains within this ultrastructure. The experimental workflow developed here will serve as an important tool in our understanding of germ granule biology as well as the biological role of LLPS.

cell biology↗

bioRxiv2021

3D visualisation of the cardiac ryanodine receptor clusters and the molecular-scale fraying of dyads

Clusters of ryanodine receptor calcium channels (RyRs) form the primary molecular machinery in cardiomyocytes. Various adaptations of super-resolution microscopy have revealed intricate details of the structure, molecular composition and locations of these couplons. However, most optical super-resolution techniques lack the capacity for three-dimensional (3D) visualisation. Enhanced Expansion Microscopy (EExM) offers resolution (in-plane and axially) sufficient to spatially resolve individual proteins within peripheral couplons and within dyads located in the interior. We have combined immunocytochemistry and immunohistochemistry variations of EExM with 3D visualisation to examine the complex topologies, geometries and molecular sub-domains within RyR clusters. We observed that peripheral couplons exhibit variable co-clustering ratios and patterns between RyR and the structural protein, junctophilin-2 (JPH2). Dyads possessed sub-domains of JPH2 which occupied the central regions of the RyR cluster, whilst the poles were typically devoid of JPH2 and broader, and likely specialise in turnover and remodelling of the cluster. In right ventricular myocytes from rats with monocrotaline-induced right ventricular failure, we observed hallmarks of RyR cluster fragmentation accompanied by similar fragmentations of the JPH2 sub-domains. We hypothesise that the frayed morphology of RyRs in close proximity to fragmented JPH2 structural sub-domains may form the primordial foci of RyR mobilisation and dyad remodelling.

biophysics↗

bioRxiv2020

A super-resolution protocol to correlate structural underpinnings of fast second-messenger signalling in primary cell types

Nanometre-scale cellular information obtained through super-resolution microscopies are often unaccompanied by functional information, particularly transient and diffusible signals through which life is orchestrated in the nano-micrometre spatial scale. We describe a correlative imaging protocol which allows the ubiquitous intracellular second messenger, calcium (Ca2+), to be directly visualised against nanoscale patterns of the ryanodine receptor (RyR) Ca2+ channels which give rise to these Ca2+ signals in wildtype primary cells. This was achieved by combining total internal reflection fluorescence (TIRF) imaging of the elementary Ca2+ signals, with the subsequent DNA-PAINT imaging of the RyRs. We report a straightforward image analysis protocol of feature extraction and image alignment between correlative datasets and demonstrate how such data can be used to visually identify the ensembles of Ca2+ channels that are locally activated during the genesis of cytoplasmic Ca2+ signals.

biophysics↗

bioRxiv2020

Peptide ligands of the cardiac ryanodine receptor as super-resolution imaging probes

To study the structural basis of pathological remodelling and altered calcium channel functional states in the heart, we sought to re-purpose high-affinity ligands of the cardiac calcium channel, the ryanodine receptor (RyR2), into super-resolution imaging probes. Imperacalcin (IpCa), a scorpion toxin peptide which induces channel sub-conduction states, and DPc10, a synthetic peptide corresponding to a sequence of the RyR2, which replicates arrhythmogenic CPVT functional changes, were used in fluorescent imaging experiments. Isolated adult rat ventricular cardiomyocytes were saponin-permeabilised and incubated with each peptide. IpCa-A546 became sequestered into the mitochondria. This was prevented by treatment of the permeabilised cells with the ionophore FCCP, revealing a striated staining pattern in confocal imaging which had weak colocalisation with RyR2 clusters. Poor specificity (as an RyR2 imaging probe) was confirmed at higher resolution with expansion microscopy (proExM) (~70 nm). DPc10-FITC labelled a striated pattern, which had moderate colocalisation with RyR2 cluster labelling in confocal and proExM. There was also widespread non-target labelling of the Z-discs, intercalated discs, and nuclei, which was unaffected by incubation times or 10 mM caffeine. The inactive peptide mut-DPc10-FITC (which causes no functional effects) displayed a similar labelling pattern. Significant labelling of structures unrelated to RyR2 by both peptide conjugates makes their use as highly specific imaging probes of RyR2 in living isolated cardiomyocytes highly challenging. We investigated the native DPc10 sequence within the RyR2 structure to understand the domain interactions and proposed mechanism of peptide binding. The native DPc10 sequence does not directly interact with another domain, and but is downstream of one such domain interface. The rabbit Arg2475 (equivalent to human Arg2474, mutated in CPVT) in the native sequence is the most accessible portion and most likely location for peptide disturbance, suggesting FITC placement does not impact peptide binding.

cell biology↗

bioRxiv2020

Self-activated photoblinking of nitrogen vacancy centers in nanodiamonds (sandSTORM): A method for rapid single molecule localization microscopy with unlimited observation time

Stochastic optical reconstruction microscopy (STORM) is one of the most commonly used super-resolution microscopy techniques. Popular implementations of STORM utilize aromatic fluorophores and consist of a number of intrinsic limitations such the finite photostability of the dyes, the reliance upon non-physiological redox buffers and speed which is ultimately limited by the off-rates of the photoblinking. Self-activated nanodiamond-based STORM (sandSTORM) has been developed as an accelerated STORM protocol which harvests the rapid, high quantum-yield and sustained photoblinking of nanodiamonds (ND). Photoluminescence emanating from the stochastic charge-state interconversion of Nitrogen Vacancy (NV) centers between NV0and NV- is localized using conventional STORM-optimized hardware and image processing protocols over an unlimited duration of imaging. This produces super-resolution images of matching resolution at [~] 3-times the speed and [~] 100 times less light exposure to the sample compared to traditional STORM. The enabling NDs have been used to map arrays of ryanodine receptor in skeletal muscle tissues via immunolabelling and directly visualize the internal spaces of living neurons via endocytosis of NDs. This paper details the physical basis of sandSTORM, factors which optimize its performance, and key characteristics which make it a powerful STORM protocol suitable for imaging nanoscale sub-cellular structures.

biophysics↗