Biology subjects

Tripathi, U.

Publications and source records attributed to Tripathi, U..

12 recordsLinked to original sources

bioRxiv2026

iPSC-derived extracellular vesicles rescue deficits in human and mouse models of Parkinsons disease

Parkinsons disease (PD) pathogenesis often involves progressive -synuclein (-Syn)-mediated neuronal dysfunction, yet the earliest cellular events that link -Syn pathology to circuit failure remain poorly defined. Here, we used human induced pluripotent stem cell (iPSC)-derived dopaminergic (DA) neurons from patients carrying the familial A53T SNCA mutation to reconstruct a temporal course of dysfunction in vitro. We identified a biphasic trajectory with an early phase of hyperexcitability, characterized by elevated spontaneous firing, followed by a progressive transition into hypoexcitability as the neurons mature, accompanied by reduced network activity, synaptic dysfunction, and -Syn accumulation. Transcriptomic profiling at the critical transition point revealed a dual transcriptional signature, with upregulation of stress-inflammatory pathways (p53, JAK-STAT, apoptosis) coupled with systematic downregulation of metabolic and synaptic maintenance genes. This molecular profile preceded functional collapse, linking early hyperactivity-driven metabolic stress to subsequent neuronal exhaustion. To counteract this pathology, we used extracellular vesicles (EVs), small membrane-bound particles carrying intercellular signals, as a cell-free treatment approach. Strikingly, treatment with EVs derived from healthy iPSCs completely rescued both electrophysiological deficits and pathological -Syn accumulation, restoring normal firing patterns, synaptic function, and network activity. Consistent with these observations, EV treatment reduced -Syn aggregation and improved motor responses in -Syn fibril-injected mice, which are characterized by pathological -Syn accumulation and motor deficits. Overall, these findings demonstrate that EVs derived from healthy iPSCs can reverse PD-related phenotypes in human and mouse models.

neuroscience↗

bioRxiv2025

Senolytic-Resistant Senescent Cells Have a Distinct SASP Profile and Functional Impact: The Path to Developing Senosensitizers

The senescent cell (SC) fate is linked to aging, multiple disorders and diseases, and physical dysfunction. Senolytics, agents that selectively eliminate 30-70% of SCs, act by transiently disabling the senescent cell anti-apoptotic pathways (SCAPs), which defend those SCs that are pro-apoptotic and pro-inflammatory from their own senescence-associated secretory phenotype (SASP). Consistent with this, a JAK/STAT inhibitor, Ruxolitinib, which attenuates the pro-inflammatory SASP of senescent human preadipocytes, caused them to become "senolytic-resistant". Administering senolytics to obese mice selectively decreased abundance of the subset of SCs that is pro-inflammatory. In cell cultures, the 30-70% of human senescent preadipocytes or human umbilical vein endothelial cells (HUVECs) that are senolytic-resistant (to Dasatinib or Quercetin, respectively) had increased p16INK4a, p21CIP1, senescence-associated {beta}-galactosidase (SA{beta}gal), {gamma}H2AX, and proliferative arrest similarly to the total SC population (comprising senolytic-sensitive plus -resistant SCs). However, the SASP of senolytic-resistant SCs entailed less pro-inflammatory/ apoptotic factor production, induced less inflammation in non-senescent cells, and was equivalent or richer in growth/ fibrotic factors. Senolytic-resistant SCs released less mitochondrial DNA (mtDNA) and more highly expressed the anti-inflammatory immune evasion signal, glycoprotein non-melanoma-B (GPNMB). Transplanting senolytic-resistant SCs intraperitoneally into younger mice caused less physical dysfunction than transplanting the total SC population. Because Ruxolitinib attenuates SC release of pro-apoptotic SASP factors, while pathogen-associated molecular pattern factors (PAMPs) can amplify the release of these factors rapidly (acting as "senosensitizers"), senolytic-resistant and senolytic-sensitive SCs appear to be interconvertible.

cell biology↗

bioRxiv2025

Divergent Excitability of GABAergic Neurons Derived from Bipolar Disorder Patients Shapes Energy Shifts of Network Dynamics, possibly mimicking mania and depression

Bipolar disorder (BD) is characterized by fluctuating mood states, yet the cellular and circuit-level mechanisms distinguishing lithium-responsive (LR) from non-responsive (NR) patients remain elusive. We derived dentate gyrus granule neurons and GABAergic interneurons from induced pluripotent stem cells (iPSCs) of BD patients stratified by lithium response, and from healthy controls. Using patch-clamp electrophysiology, we assessed intrinsic excitability. We further developed a computational model simulating large-scale neuronal networks based on patient-derived electrophysiological properties and ion channel conductance distributions. Granule neurons from both LR and NR patients exhibited hyperexcitability compared to controls. However, GABAergic neurons showed a striking divergence: LR neurons were hyperexcitable, while NR neurons were hypoexcitable. Transcriptomic profiling revealed distinct molecular signatures between NR and LR neurons, including dysregulation of GABA receptor genes (GABRR1). Computational simulations over 10,000 iterations, mimicking long-term network activity, revealed that dentate granule neuron changes alone failed to recapitulate netwrok shifts between global hyperexcitability and global hypoexcitability. Networks incorporating only granule neuron phenotypes entered persistent hyper- or hypoactive states, depending on lithium response. Remarkably, when GABAergic neuron phenotypes were added to the model, both LR and NR networks exhibited spontaneous transitions between high and low activity states, that may be associated with the mood episodes that the patients exhibit. Control networks did not show such bistability. We, therefore, conclude that GABAergic neuronal excitability is a key determinant of lithium responsiveness in BD and critically shapes the emergence of state-shift dynamics in neural networks. These findings suggest that restoring excitatory/inhibitory (E/I) balance via targeted modulation of interneuron function may offer novel therapeutic avenues for BD.

neuroscience↗

bioRxiv2025

Digestive Dimensions of Autism: A Multiscale Exploration of Gut-Brain Interactions

Social communication difficulties characterize autism spectrum disorders (ASD). Gastrointestinal (GI) symptoms are more common in ASD than in the general population. The identification of GI problems in individuals with ASD is challenging due to their altered pain perception and irregular behaviors. Importantly, GI symptoms and ASD can potentially aggravate each other. However, it is unclear if GI problems cause ASD symptoms or vice versa. A crosstalk between the digestive system, gut microbiota, and the central and enteric nervous systems has been repeatedly reported. The enteric nervous system (ENS) regulates the GI tract with the central nervous system (CNS) and the autonomic nervous system (ANS), as well as independently through specific neural circuits. Several mechanisms contribute to GI problems in ASD, including genetic mutations that affect the enteric nervous system (ENS), dysregulation of the ANS, alterations in gut microbiota, unhealthy dietary preferences, and changes in metabolomic profiles. Furthermore, studies have shown molecular and cellular differences in the GI biopsy of children with and without ASD. These findings highlight the unique nature of GI issues in ASD, underscoring the importance of further investigating the changes that occur in the digestive system and enteric nervous system (ENS) in ASD models.

neuroscience↗

bioRxiv2025

Dysregulation of Multiple Solute Carrier genes and Metabolic Deficits in SLC1A4-Mutant Human iPSC-Derived Hippocampal Neurons

Mutations in SLC1A4, which encodes the neuronal amino acid transporter ASCT1, disrupt metabolic and synaptic homeostasis, contributing to neurodevelopmental deficits commonly observed in autism spectrum disorder (ASD). To investigate the underlying molecular mechanisms of SLC1A4-related disorders, we utilized human iPSC-derived hippocampal neurons and applied an integrated multi-omics approach, combining electrophysiology, calcium imaging, metabolomics, proteomics, and transcriptomics. Our findings reveal an initial phase of early neuronal hyperexcitability, driven by increased sodium and potassium currents, followed by a progressive decline in synaptic activity at later stages. Metabolomic analysis identified elevated glycine, serine, and glutamate levels during early differentiation, contributing to excitotoxicity, whereas later glutamate depletion and extracellular matrix (ECM) disruption were associated with synaptic dysfunction. Proteomics data further showed dysregulation in metabolic pathways, amino acid biosynthesis, and fatty acid metabolism pathways during early time points, and in later stage dysregulation in metabolic and ECM-receptor interactions. Additionally, transcriptomic analysis revealed dysregulation in calcium signaling, amino acid metabolism pathways such as valine, leucine and isoleucine degradation, tryptophan metabolism, and glycine, serine, and threonine metabolism. Further investigation of SLC-family transporter genes uncovered disruptions in glutamate and glycine transport, establishing a direct link between amino acid transport dysfunction and neuronal deficits. Collectively, our study demonstrates that SLC1A4 mutations lead to dysregulation of multiple solute carrier protein genes causing metabolic stress, excitability defects, and synaptic abnormalities, providing a molecular framework for understanding SLC1A4-related neurodevelopmental disorders and identifying potential therapeutic targets.

neuroscience↗

bioRxiv2024

Predicting Suicide Risk in Bipolar Disorder patients from Lymphoblastoid Cell Lines genetic signatures

This research investigates the genetic signatures associated with a high risk of suicide in Bipolar disorder (BD) patients through RNA sequencing analysis of lymphoblastoid cell lines (LCLs). By identifying differentially expressed genes (DEGs) and their enrichment in pathways and disease associations, we uncover insights into the molecular mechanisms underlying suicidal behavior. LCL gene expression analysis reveals significant enrichment in pathways related to primary immunodeficiency, ion channel, and cardiovascular defects. Notably, genes such as LCK, KCNN2, and GRIA1 emerged as pivotal in these pathways, suggesting their potential roles as biomarkers. Machine learning models trained on a subset of the patients and then tested on other patients demonstrate high accuracy in distinguishing low and high-risk of suicide in BD patients. Moreover, the study explores the genetic overlap between suicide-related genes and several psychiatric disorders. This comprehensive approach enhances our understanding of the complex interplay between genetics and suicidal behavior, laying the groundwork for future prevention strategies.

neuroscience↗

bioRxiv2023

Synaptic dysfunction and dysregulation of extracellular matrix-related genes in dopaminergic neurons derived from Parkinson's disease sporadic patients and with GBA1 mutations

Parkinsons disease (PD) is a neurodegenerative disease with both genetic and sporadic origins. In this study, we investigated the electrophysiological properties, synaptic activity, and gene expression differences in dopaminergic (DA) neurons derived from induced pluripotent stem cells (iPSCs) of healthy controls, sporadic PD (sPD) patients, and PD patients with GBA1 mutations. Our results demonstrate reduced sodium currents and synaptic activity in DA neurons derived from PD patients with GBA1 mutations, suggesting a potential contribution to PD pathophysiology. We also observed distinct electrophysiological alterations in sPD DA neurons that were dependent on the age of disease onset. RNA sequencing analysis revealed unique dysregulated pathways in early and late-onset sPD neurons, further supporting the notion that molecular mechanisms driving PD may be different between PD patients. In agreement with our previous reports, ECM and focal adhesion genes were the top dysregulated pathways in DA neurons from sPD patients and from patients with GBA1 mutations. Overall, this study gives further confirmation that the convergent functional phenotypes of DA neurons derived from PD patients are synaptic abnormalities and at the transcriptome level, ECM and focal adhesion pathways are highly involved in PD pathology across multiple PD-associated mutations as well as sPD.

neuroscience↗

bioRxiv2022

Upregulated extracellular matrix-related genes and impaired synaptic activity in dopaminergic and hippocampal neurons derived from Parkinson's disease patients with PINK1 and PARK2 mutations

Parkinsons disease (PD) is the second most prevalent neurodegenerative disease. Primary symptoms of PD arise with the loss of dopaminergic (DA) neurons in the Substantia Nigra Pars Compacta, but it affects the hippocampus and cortex also, usually in its later stage. Approximately 15% of PD cases familial with a genetic mutation. Two of the most associated genes with autosomal recessive (AR) early-onset familial PD are PINK1 and PARK2. There is a need for in-vitro studies of these genetic mutations in order to understand the neurophysiological changes in patients neurons that may contribute to neurodegeneration. In this work, we generated and differentiated DA and hippocampal neurons from iPSCs derived from two patients with a double mutation in their PINK1 and PARK2 (one homozygous and one heterozygous) genes and assessed their neurophysiology compared to two healthy controls. We showed that the synaptic activity of PD neurons generated from patients with the PINK1 and PARK2 mutations is impaired in the hippocampus and dopaminergic neurons. Mutant dopaminergic neurons had enhanced excitatory post-synaptic activity. In addition, DA neurons with the homozygous mutation of PINK1 exhibited more pronounced electrophysiological differences compared to the control neurons. Signaling network analysis of RNA sequencing results revealed that Focal adhesion and ECM receptor pathway were the top 2 upregulated pathways in the mutant PD neurons. These phenotypes are reversed to PD phenotypes of other mutations, suggesting that the interaction of the two mutations may yield different mechanisms of PD.

neuroscience↗

bioRxiv2022

Early maturation and hyperexcitability is a shared phenotype of cortical neurons derived from different ASD-causing mutations

Autism Spectrum Disorder (ASD) is characterized mainly by social and sensory-motor abnormal and repetitive behavior patterns. Over hundreds of genes and thousands of genetic variants were reported to be highly penetrant and causative of ASD. Many of these mutations cause comorbidities such as epilepsy and intellectual disabilities (ID). In this study, we measured cortical neurons derived from induced pluripotent stem cells (iPSCs) of patients with four mutations in the genes GRIN2B, SHANK3, UBTF, as well as chromosomal duplication in the 7q11.23 region and compared them to neurons derived from a first-degree relative without the mutation. Using a whole-cell patch-clamp, we observed that the mutant cortical neurons demonstrated hyperexcitability and early maturation compared to control lines. These changes were characterized by increased sodium currents, increased amplitude and rate of excitatory postsynaptic currents (EPSCs), and more evoked action potentials in response to current stimulation in early-stage cell development (3-5 weeks post differentiation). These changes that appeared in all the different mutant lines, together with previously reported data, indicate that an early maturation and hyperexcitability may be a convergent phenotype of ASD cortical neurons.

neuroscience↗

bioRxiv2022

Information theory characteristics improve the prediction of lithium response in bipolar disorder patients using an SVM classifier

Bipolar disorder (BD) is a mood disorder with a high morbidity and death rate. Lithium (Li), a prominent mood stabilizer, is fully effective in roughly 30% of BD patients. The remaining patients respond partially or do not respond at all. Another drug used to treat BD patients is valproate (VPA). Plenty of efforts has been made to understand how these drugs affect the patients neurons. We have performed electrophysiological recordings in patient-derived dentate gyrus (DG) granule neurons for three groups: control individuals, BD patients who respond to Li treatment (LR), and BD patients who do not respond to Li treatment (NR). The recordings were analyzed by the statistical tools of modern information theory, which enabled us to recognize new relationships between the electrophysiological features. These added features included the entropy of several electrophysiological measurements and the mutual information between different types of electrophysiological measurements. Information theory features provided further knowledge about the distribution of the electrophysiological entities, which improved basic classification schemes. These newly added features enabled a significant improvement in our ability to distinguish the BD patients from the control individuals (an improvement from 60% accuracy to 74% accuracy) and the Li responders from the non-responders in the BD population using Support Vector Machine (SVM) classification algorithms (an improvement from 81% accuracy to 99% accuracy). These new tools showed that LR neurons are less distinguishable from control neurons after Li treatment but not after VPA treatment, whereas NR neurons become more distinguishable from control neurons after Li treatment.

neuroscience↗

bioRxiv2020

Partial inhibition of mitochondrial complex I attenuates neurodegeneration and restores energy homeostasis and synaptic function in a symptomatic Alzheimers mouse model

We demonstrate that mitochondrial respiratory chain complex I is an important small molecule druggable target in Alzheimers Disease (AD). Partial inhibition of complex I triggers the AMP-activated protein kinase-dependent signaling network leading to neuroprotection in symptomatic APP/PS1 mice, a translational model of AD. Treatment of APP/PS1 mice with complex I inhibitor after the onset of AD-like neuropathology improved energy homeostasis, synaptic activity, long-term potentiation, dendritic spine maturation, cognitive function and proteostasis, and reduced oxidative stress and inflammation in brain and periphery, ultimately blocking the ongoing neurodegeneration. Therapeutic efficacy in vivo was monitored using translational biomarkers FDG-PET, 31P NMR, and metabolomics. Cross-validation of the mouse and the human AMP-AD transcriptomic data demonstrated that pathways improved by the treatment in APP/PS1 mice, including the immune system response and neurotransmission, represent mechanisms essential for therapeutic efficacy in AD patients.

neuroscience↗

bioRxiv2018

MICU1 modulates MCU ion selectivity and tolerance to manganese stress

The mitochondrial calcium uniporter is a highly selective ion channel composed of species-and tissue-specific structural and regulatory subunits. However, the contribution of each component to uniporter-mediated activity still remains unclear. Here, we employ an evolutionary and synthetic biology approach to investigate the functional inter-dependence between the pore-forming subunit MCU and the EF-hand protein MICU1. Using phylogenetic profiling and genetic complementation analyses, we show that MCU and MICU1 constitute the minimal eukaryotic unit of the uniporter, pointing towards a strong selective pressure behind their co-occurrence. Heterologous reconstitution of MCU-mediated and MICU1-gated mitochondrial calcium entry in vivo in yeast cells demonstrates that MICU1 per se is essential to protect yeast from MCU-dependent manganese cytotoxicity. Accordingly, MICU1 deletion significantly sensitizes human HEK-293 cells to manganese-induced stress. Our study identifies a critical role of MICU1 in the regulation of MCU ion selectivity, with potential implications for patients with MICU1 deficiency.

cell biology↗