Biology subjects

Padmanabhan, P.

Publications and source records attributed to Padmanabhan, P..

14 recordsLinked to original sources

bioRxiv2025

Tau controls NMDA receptor trafficking during homeostatic synaptic plasticity

Homeostatic synaptic plasticity is essential for maintaining stable neural circuit function by preventing excessive neuronal excitation or inhibition. Chronic perturbation of neuronal activity triggers a compensatory modulation of the number of -amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) and N-methyl-D-aspartate (NMDA) glutamate receptors at the excitatory synapses. Previous research has primarily focused on AMPA receptors, yet the molecular mechanisms regulating the trafficking of NMDA receptors during homeostatic synaptic scaling remain unclear. Here we identify the microtubule-associated protein Tau as an essential molecule that mediates the synaptic upscaling of GluN2B-containing NMDA receptors during prolonged synaptic inactivity. Chronic activity blockade increases Tau phosphorylation at Ser-235 by cyclin-dependent kinase 5 (Cdk5), enhancing its interaction with and retention of active Fyn tyrosine kinase in the postsynaptic compartment. This promotes the phosphorylation of GluN2B at Tyr-1472, subsequently stabilising the expression of NMDA receptors on the neuronal plasma membrane. Finally, we showed that Tau pathology and disease-associated mutations in Tau and the GluN2B carboxyl-terminal tail disrupt the homeostatic synaptic upscaling of NMDA receptors following chronic neuronal silencing. Together, our findings identify a physiological role for Tau in homeostatic synaptic plasticity, the perturbation of which can lead to neuronal hyperexcitation, seizures and excitotoxic cell death.

neuroscience↗

bioRxiv2025

Variants in glycine decarboxylase activate mechanisms of mitochondrial energy metabolism in the brain.

Brain energy metabolism is produced from glucose by mitochondrial oxidative phosphorylation. Variants in the mitochondrial enzyme glycine decarboxylase (GLDC) cause a rare neurological disease, non-ketotic hyperglycinemia (NKH), with expected hallmarks of brain glycine elevation and responsiveness to folate deficiency that are equivalent to the severity of Gldc mutations. We remarkably find that brains of young- attenuated mutant mice with a 1.5-fold increase in glycine are reduced > 5-fold in GLDC, show a decline in both the mitochondrial lipoyl-transfer protein GCSH and lipoylation of the pyruvate dehydrogenase (PDH) complex, as well as concomitant rise in signatures of astrocyte mitochondrial {beta}-oxidation of fatty acids and activation of neuronal PDH. Our findings suggest a novel GLDC mechanism of remodeling mitochondrial energy systems throughout the brain, established early in and sustained throughout post-natal NKH disease.

neuroscience↗

bioRxiv2025

High-resolution imaging reveals a cascade of interconnected cellular bioeffects differentiating the long-term fates of sonoporated cells

Low-intensity ultrasound combined with microbubbles is a promising, non-invasive treatment strategy for enhancing vascular permeability and targeted intracellular drug or gene delivery. After ultrasound insonification, cells can undergo reversible sonoporation, involving adaptation and recovery, or irreversible sonoporation, marked by a loss of cell viability. To design effective sonoporation-based therapeutic delivery strategies, it is therefore critical to identify the biological responses that determine these distinct cell fates. Here, we developed a custom-built high-resolution multicolour imaging device and applied a single pulse of ultrasound (267 kHz frequency, 20 s duration, and [~]110 kPa peak-negative pressure) to trigger targeted microbubble-mediated reversible and irreversible sonoporation events within a confluent monolayer of cultured Madin-Darby canine kidney (MDCK) II cells. We found that intracellular calcium levels rose rapidly and peaked within 10 s in both types of sonoporated cells, although the levels declined differently. In reversibly sonoporated cells, these levels gradually returned to baseline, whereas in irreversibly sonoporated cells, they dropped rapidly, falling well below baseline within 7.9 {+/-} 3.0 min (mean {+/-} s.d.). Using single-vesicle imaging, we further found that vesicles containing the tight junction protein claudin-5 remained mobile with subtly reduced movement in reversibly sonoporated cells, whereas they almost stalled in irreversibly sonoporated cells. The underlying microtubule network was partially disrupted in the reversibly sonoporated cells, recovering fully within 3.2 {+/-} 2.9 min (mean {+/-} s.d.). In contrast, in irreversibly sonoporated cells, the entire microtubule network collapsed within 4.0 {+/-} 2.4 min (mean {+/-} s.d.). Whilst in reversibly sonoporated cells, the uptake of the model drug propidium iodide was mild-to-moderate, without drastic cell size changes up to about 1 h post-sonication, irreversibly sonoporated cells presented with substantially higher propidium iodide uptake and shrunk completely within 43.2 {+/-} 10.5 min (mean {+/-} s.d.). Together, our study identified distinct spatiotemporal sequences of interconnected biological responses underlying different fates of sonoporated cells, providing a framework for identifying processes that could be manipulated for safe and effective sonoporation-based drug delivery.

pharmacology and toxicology↗

bioRxiv2025

Astrocyte and neurogenic mechanisms of protective gene therapy prevent brain disease and death due to non-ketotic hyperglycinemia

Genetic defects in glycine decarboxylase (GLDC) cause non-ketotic hyperglycinemia (NKH), a rare and frequently fatal neurometabolic disease, which lacks FDA-approved therapies. We characterized CRISPR Cas9-edited humanized mice expressing a prevalent clinical mutation after administration with a single intraperitoneal dose of a novel recombinant of adeno-associated viral vector 9 expressing GLDC (rAAV9-GLDC). Long term biological activity of rAAV9-GLDC was first validated by assessment of its systemic efficacy over five and ten months in mice. Access of rAAV9 to the brain was confirmed by tracking green fluorescent protein (GFP) after a single intraperitoneal dose of rAAV9-GFP. Over five months, control mock treated GFP-mice showed reduction in astrocytes but not microglia, oligodendrocytes or neurons in the brain. 37% of these animals suffered long term neurological disease and/or death. rAAV9-GLDC boosts astrogenesis without triggering an inflammatory response and confers 100% protection against disease progression and fatality due to NKH.

neuroscience↗

bioRxiv2024

Proteostasis as a fundamental principle of Tau immunotherapy

The microtubule-associated protein Tau is a driver of neuronal dysfunction in Alzheimers disease and numerous other tauopathies. In this process, Tau initially undergoes subtle changes to its abundance, subcellular localisation and a vast array of post-translational modifications including phosphorylation, that progressively result in the proteins aggregation and dysregulation of multiple Tau-dependent cellular processes. Given the various loss- and gain-of-functions of Tau in disease and the brain-wide changes in the proteome that characterise tauopathies, we asked whether targeting Tau would restore the alterations in proteostasis observed in disease. To this end, we generated a novel pan-Tau antibody, RNJ1, that preferentially binds human Tau and neutralises proteopathic seeding activity in multiple cell lines and benchmarked it against a clinically tested pan-Tau antibody, HJ8.5 (murine version of tilavonemab). We next evaluated both antibodies, alone and in combination, in the K3 mouse model of tauopathy, showing reduced Tau pathology and improvements in neuronal function following 14 weekly treatments, without obtaining synergistic effects for the combination treatment. To gain insight into molecular mechanisms contributing to improvements in neuronal function, we employed quantitative proteomics and phosphoproteomics to first establish alterations in K3 mice relative to WT controls at the proteome level. This revealed 342 proteins with differential abundance in K3 mice, which are predominantly involved in metabolic and microtubule-associated processes, strengthening previously reported findings of defects in several functional domains in multiple tauopathy models. We next asked whether antibody-mediated Tau target engagement indirectly affects levels of deregulated proteins in the K3 model. Importantly, both immunotherapies, in particular RNJ1, induced abundance shifts in this protein subset towards a restoration to wild-type levels (proteostasis). A total of 257 of 342 ([~]75.1%) proteins altered in K3 were closer in abundance to WT levels after RNJ1 treatment. The same analysis indicated a similar response in K3 mice treated with HJ8.5, with approximately 72.5% of these altered proteins also showing changes in the same direction as wild-type. Furthermore, analysis of the phosphoproteome showed an even stronger restoration effect with RNJ1, with [~]82.1% of altered phosphopeptides in K3 showing a shift to WT levels, and 75.4% with HJ8.5. Gene set over-representation analysis (ORA) further confirmed that proteins undergoing restoration are involved in biological pathways affected in K3 mice. Together, our study suggests that a Tau immunotherapy-induced restoration of proteostasis links target engagement and treatment efficacy.

neuroscience↗

bioRxiv2023

VAMP2/Munc18-1 domain 3a interaction controls the nanoscale reorganization underpinning vesicular priming

SNARE-mediated secretory vesicle (SV) exocytosis underpins neuronal communication. Munc18-1 orchestrates SNARE complex formation by controlling the opening of syntaxin-1A. How the SV-plasma membrane interface becomes fusion-competent at the nanoscale level is poorly understood. Here, we propose that the interaction of Munc18-1 with VAMP2 during vesicular docking triggers nanoscale re-organization which renders the SV-plasma membrane interface fusion-competent. We identified and mutated key residues in Munc18-1 domain 3a (A297 and T304) hypothesised to impair its interaction with VAMP2. Munc18-1A297H, and to a lesser extent Munc18-1T304H, constrained SVs on the plasma membrane and reduced stimulated secretion, under re-expression conditions in Munc18-1/2 double knockout neurosecretory cells. Moreover, the de-clustering of Munc18-1 in response to activity was lost for both mutants. The interaction of VAMP2 with the Munc18-1 domain 3a therefore controls the re-organization of the nanoscale environment of the docked SV-plasma membrane interface, fostering syntaxin-1A opening and Munc18-1 release to ensure that SNARE assembly only occurs within the confinement of docked vesicles.

neuroscience↗

bioRxiv2023

Senolytic therapy alleviates physiological human brain aging and COVID-19 neuropathology.

Aging is the primary risk factor for most neurodegenerative diseases, and recently coronavirus disease 2019 (COVID-19) has been associated with severe neurological manifestations that can eventually impact neurodegenerative conditions in the long-term. The progressive accumulation of senescent cells in vivo strongly contributes to brain aging and neurodegenerative co-morbidities but the impact of virus-induced senescence in the aetiology of neuropathologies is unknown. Here, we show that senescent cells accumulate in physiologically aged brain organoids of human origin and that senolytic treatment reduces inflammation and cellular senescence; for which we found that combined treatment with the senolytic drugs dasatinib and quercetin rejuvenates transcriptomic human brain aging clocks. We further interrogated brain frontal cortex regions in postmortem patients who succumbed to severe COVID-19 and observed increased accumulation of senescent cells as compared to age-matched control brains from non-COVID-affected individuals. Moreover, we show that exposure of human brain organoids to SARS-CoV-2 evoked cellular senescence, and that spatial transcriptomic sequencing of virus-induced senescent cells identified a unique SARS-CoV-2 variant-specific inflammatory signature that is different from endogenous naturally-emerging senescent cells. Importantly, following SARS-CoV-2 infection of human brain organoids, treatment with senolytics blocked viral retention and prevented the emergence of senescent corticothalamic and GABAergic neurons. Furthermore, we demonstrate in human ACE2 overexpressing mice that senolytic treatment ameliorates COVID-19 brain pathology following infection with SARS-CoV-2. In vivo treatment with senolytics improved SARS-CoV-2 clinical phenotype and survival, alleviated brain senescence and reactive astrogliosis, promoted survival of dopaminergic neurons, and reduced viral and senescence-associated secretory phenotype gene expression in the brain. Collectively, our findings demonstrate SARS-CoV-2 can trigger cellular senescence in the brain, and that senolytic therapy mitigates senescence-driven brain aging and multiple neuropathological sequelae caused by neurotropic viruses, including SARS-CoV-2.

neuroscience↗

bioRxiv2022

Simple within-stride changes in treadmill speed can drive selective changes in human gait symmetry

BackgroundMillions of people worldwide are affected by clinical conditions that result in gait asymmetry (e.g., stroke, cerebral palsy, lower limb amputation). There is a need for customizable rehabilitation approaches that can flexibly target different aspects of gait asymmetry with minimal need for specialized equipment. Here, we studied how simple within-stride changes in treadmill speed could drive selective, predictable changes in human gait symmetry. MethodsIn Experiment 1, ten healthy young adults walked on an instrumented treadmill with and without a closed-loop controller engaged. The controller changed the treadmill speed to 1.50 m/s or 0.75 m/s depending on whether the right or left leg generated propulsive (i.e., forward-directed) ground reaction forces, respectively. In Experiment 2, a separate group of ten healthy young adults walked on the treadmill with and without an open-loop controller engaged. This controller changed the treadmill speed to 1.50 m/s or 0.75 at a prescribed time interval. We used a metronome to guide the participants to step at a series of different time points relative to the controller-driven speed change. We collected kinematic and kinetic data in Experiments 1 and 2. ResultsIn Experiment 1, participants walked with asymmetric kinematics and ground reaction forces when the closed-loop controller was engaged. The leg that accelerated during propulsion (right leg) showed a smaller leading limb angle and a larger trailing limb angle than the leg that decelerated during propulsion (left leg). The right leg also generated smaller propulsive forces than the left leg. In Experiment 2, the patterns of asymmetry in spatiotemporal gait parameters, kinematics, and ground reaction forces depended on the timing of the speed change within the gait cycle. Step times, leading limb angles, and peak propulsion became asymmetric when the treadmill speed changed early in stance. When the treadmill speed changed later in stance, step lengths, step times, and propulsion impulses became asymmetric. ConclusionsSimple manipulations of treadmill speed can drive predictable, selective changes in human gait symmetry. Future work will explore this customizable technique as a potential approach for restoring gait symmetry in clinical populations.

bioengineering↗

bioRxiv2022

Single-molecule imaging reveals Tau trapping at nanometer-sized dynamic hot spots near the plasma membrane

Accumulation of Tau aggregates is a pathological hallmark of Alzheimers disease, but little is known about where these aggregates assemble and how stable these assemblies are. Using quantitative, single-molecule imaging, we show that Tau exhibits spatial and kinetic heterogeneity near the plasma membrane, resulting in the formation of nanometer-sized hot spots smaller than the diffraction limit. The hot spots lasted tens of seconds, much longer than the short dwell time (~40 ms) of Tau on microtubules. Pharmacological and biochemical disruption of Tau/microtubule interactions did not affect hot spot formation, suggesting that these are different from the reported Tau condensation on microtubules. Although cholesterol removal has been shown to reduce Tau pathology, its depletion did not affect Tau hot spot dynamics. Our study identifies an intrinsic dynamic property of Tau near the plasma membrane that may facilitate the formation of assembly sites for Tau to assume its physiological and pathological functions.

neuroscience↗

bioRxiv2022

Evidence of increased Cathepsin B/L and decreased TMPRSS2 usage for cell entry by the SARS-CoV-2 Omicron variant

The SARS-CoV-2 Omicron variant harbours mutations in its spike protein, which may affect its cell entry, tropism, and response to interventions. To elucidate these effects, we developed a mathematical model of SARS-CoV-2 entry into cells and applied it to analyse recent in vitro data. SARS-CoV-2 enters cells using host proteases, either Cathepsin B/L or TMPRSS2. We estimated >4-fold increase and >3-fold decrease in entry efficiency using Cathepsin B/L and TMPRSS2, respectively, of the Omicron variant relative to the original or other strains in a cell type-dependent manner. Our model predicted that Cathepsin B/L inhibitors would be more and TMPRSS2 inhibitors less efficacious against the Omicron than the original strain. Furthermore, the two inhibitor classes would exhibit synergy, although the drug concentrations maximizing synergy would have to be tailored to the Omicron variant. These findings provide insights into the cell entry mechanisms of the Omicron variant and have implications for interventions.

microbiology↗

bioRxiv2021

Immunoinformatic Approach for the identification of T Cell and B Cell Epitopes in the Surface Glycoprotein and Designing a Potent Multiepitope Vaccine Construct Against SARS-CoV-2 including the new UK variant

The emergence of a novel coronavirus in China in late 2019 has turned into a SARS-CoV-2 pandemic affecting several millions of people worldwide in a short span of time with high fatality. The crisis is further aggravated by the emergence and evolution of new variant SARS-CoV-2 strains in UK during December, 2020 followed by their transmission to other countries. A major concern is that prophylaxis and therapeutics are not available yet to control and prevent the virus which is spreading at an alarming rate, though several vaccine trials are in the final stage. As vaccines are developed through various strategies, their immunogenic potential may drastically vary and thus pose several challenges in offering both arms of immunity such as humoral and cell-mediated immune responses against the virus. In this study, we adopted an immunoinformatics-aided identification of B cell and T cell epitopes in the Spike protein, which is a surface glycoprotein of SARS-CoV-2, for developing a new Multiepitope vaccine construct (MEVC). MEVC has 575 amino acids and comprises adjuvants and various cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and B-cell epitopes that possess the highest affinity for the respective HLA alleles, assembled and joined by linkers. The computational data suggest that the MEVC is non-toxic, non-allergenic and thermostable with the capability to elicit both humoral and cell-mediated immune responses. The population coverage of various countries affected by COVID-19 with respect to the selected B and T cell epitopes in MEVC was also investigated. Subsequently, the biological activity of MEVC was assessed by bioinformatic tools using the interaction between the vaccine candidate and the innate immune system receptors TLR3 and TLR4. The epitopes of the construct were analyzed with that of the strains belonging to various clades including the new variant UK strain having multiple unique mutations in S protein. Due to the advantageous features, the MEVC can be tested in vitro for more practical validation and the study offers immense scope for developing a potential vaccine candidate against SARS-CoV-2 in view of the public health emergency associated with COVID-19 disease caused by SARS-CoV-2.

bioinformatics↗

bioRxiv2019

Persons post-stroke restore step length symmetry by walking asymmetrically

BackgroundRestoration of step length symmetry is a common rehabilitation goal after stroke. Persons post-stroke often retain the capacity to walk with symmetric step lengths (\"symmetric steps\"); however, the resulting walking pattern remains effortful. Two key questions with direct implications for rehabilitation have emerged: 1) how do persons post-stroke generate symmetric steps, and 2) why do symmetric steps remain so effortful?\n\nObjectiveTo understand how persons post-stroke generate symmetric steps and how the resulting gait pattern relates to the metabolic cost of transport.\n\nMethodsTen persons post-stroke walked on an instrumented treadmill under two conditions: preferred walking and symmetric stepping (using visual feedback). We recorded kinematic, kinetic, and metabolic data during both conditions.\n\nResultsPersons post-stroke restored step length symmetry using energetically expensive, asymmetric patterns. Impaired paretic propulsion and abnormal vertical movement of the center of mass were evident during both preferred walking and symmetric stepping. These deficits contributed to diminished positive work performed by the paretic limb on the center of mass in both conditions. Decreased positive paretic work correlated with increased metabolic cost of transport, decreased self-selected walking speed, and increased asymmetry in limb kinematics.\n\nConclusionsIt is important to consider the mechanics used to restore symmetric steps when designing interventions to improve walking after stroke. Facilitating symmetric steps via increased paretic propulsion or enabling paretic limb advancement without excessive vertical movement may enable persons post-stroke to walk with a less effortful, more symmetric gait pattern.

neuroscience↗

bioRxiv2019

Deciphering the mechanoresponsive role of β-catenin in Keratoconus epithelium

Keratoconus (KC) a disease with established biomechanical instability of the corneal stroma, is an ideal platform to identify key proteins involved in mechanosensing. This study aims to investigate the possible role of {beta}-catenin as mechanotransducer in KC epithelium. KC patients were graded as mild, moderate or severe using Amsler Krumeich classification. Immunoblotting and tissue immunofluorescence studies were performed on KC epithelium to analyze the expression and localization of {beta}-catenin, E-cadherin, ZO1, -catenin, Cyclin D1, -actinin, RhoA, Rac123. Co-immunoprecipitation (Co-IP) of {beta}-catenin followed by mass spectrometry of mild KC epithelium was performed to identify its interacting partners. This was further validated by using epithelial tissues grown on scaffolds of different stiffness. We observed down regulation of E-cadherin, -catenin, ZO1 and upregulation of Cyclin D1, -actinin and RhoA in KC corneal epithelium. {beta}-catenin Co-IP from mild KC epithelium identified new interacting partners such as StAR-related lipid transfer protein3, Dynamin-1-like protein, Cardiotrophin-1,Musculin, Basal cell adhesion molecule and Protocadherin Fat 1.{beta}-catenin localization was altered in KC which was validated in vitro, using control corneal epithelium grown on different substrate stiffness. {beta}-catenin localization is dependent upon the elastic modulus of the substrate and acts as mechanotransducer by altering its interaction and regulating the barrier function in corneal epithelium.

cell biology↗

bioRxiv2018

Actomyosin-II facilitates long-range retrograde transport of large cargoes by controlling axonal radial contractility

Most mammalian neurons have a narrow axon, which constrains the passage of large cargoes such as autophagosomes that can be larger than the axon diameter. Radial axonal expansion must therefore occur to ensure efficient axonal trafficking. In this study we consistently find that the trafficking speed of various large axonal cargoes is significantly slower than that of small ones, and reveal that the transit of diverse-sized cargoes causes an acute, albeit transient axonal radial expansion, which is immediately restored by constitutive contractility. Using live super-resolution microscopy, we demonstrate that actomyosin-II controls axonal radial contractility and local expansion, and that NM-II filaments associate with periodic F-actin rings via their head domains. Pharmacological inhibition of NM-II activity, significantly increases axon diameter by detaching the NM-II from F-actin, and impacts the trafficking speed, directionality, and overall efficiency of long-range retrograde trafficking. Consequently, prolonged disruption of NM-II activity leads to disruption of periodic actin rings and formation of focal axonal swellings, a hallmark of axonal degeneration.\n\nSummaryAxonal radial contractility and local expansion control the retrograde trafficking of large cargoes. The periodic actomyosin-II network comprises of NM-II filaments and F-actin rings. Loss of actomyosin-II-mediated radial contractility causes defects in axonal trafficking and stability, leading to degeneration.

neuroscience↗