Biology subjects

Kosik, K. S.

Publications and source records attributed to Kosik, K. S..

At least 19 recordsLinked to original sources

bioRxiv2026

Disrupted Brain Organoid Circuitry, Structural Organization, and Spine Morphology in 7q11.23 Copy Number Variant Syndromes

The 7q11.23 chromosomal region represents a model of gene dosage-dependence, where a hemizygous deletion causes Williams Syndrome (WS) and a duplication leads to 7q11.23 Duplication Syndrome (Dup7). It is not understood how these copy number variations (CNVs) disrupt development and functional cortical circuit assembly. Utilizing iPSC-derived cerebral organoids and longitudinal imaging from post-differentiation day 30 to 150, we characterized the aberrant neural rosette morphogenesis in WS and Dup7 during early stages, establishing an early structural divergence from control lines. We observed accelerated early cortical rosette morphogenesis in WS, characterized by a premature increase in both rosette number and layer thickness compared to controls. In contrast, Dup7 organoids consistently exhibit a significantly lower number and reduced thickness of rosettes from early stages onward. This early structural disruption progressively impacted synaptic-level architecture as the organoids matured. Dendritic spine characterization at later stages revealed Dup7 organoids exhibited a significantly higher dendritic spine density compared to WS. Pharmacological antagonism of CCR5 (C-C chemokine receptor type 5) with Maraviroc significantly enhanced dendritic spine density in control and WS organoids; however, this effect was absent in Dup7. To determine how these structural anomalies translate into circuit-level behavior, we performed longitudinal calcium imaging using GCaMP. Control organoids sustained synchronized activity and high spike correlations at all time points. This synchronization was delayed and highly transient in WS organoids, and completely abolished in Dup7 organoids, which exhibit significantly low spike correlations at all stages. Developmentally, GABA changes from acting as an excitatory signal in the immature brain to an inhibitory signal as the brain matures. As control lines matured gabazine-induced desynchronization progressively diminished, but persisted in WS organoids. Dup7 organoids failed to establish synchronization at any developmental time point, but displayed a negligible increased synchrony following gabazine treatment. These functional aberrations were paralleled by genotype-specific defects in structural organization, specifically in rosette morphogenesis and dendritic spine density. Collectively, our findings demonstrate that 7q11.23 CNVs trigger pathogenic neurodevelopmental defects by derailing the trajectories of structural organization, circuit assembly, and functional synchronization during cortical maturation.

neuroscience↗

bioRxiv2026

Emergent topological structure in spontaneous brain-organoid activity

Neural activity is widely held to organize on low-dimensional structure embedded in a high-dimensional state space. Persistent homology reads such structure directly from the pattern of pairwise correlations, without assuming in advance which variables are relevant. We apply persistent homology to microelectrode-array (MEA) recordings of spontaneous activity from human (Lancaster) and mouse (Pasca) cortical organoids, spanning 26-234 simultaneously sorted units, and ask whether topological data analysis resolves structure at the node counts that neural recordings actually deliver. Building weighted networks in correlation space and characterizing them by Vietoris-Rips filtration, we find that the first homology (H1, loops) rises significantly above a rate- and population-preserving null in 14 of 18 datasets. This loop structure occupies a non-redundant core: it is robust to random removal of units yet disrupted by targeted removal of the units that carry it. Topological richness grows with network size, and second homology (H2) emerges significantly above the null only in the larger networks. These results show that persistent homology resolves structured topology in neural recordings at the scale experiments actually deliver.

neuroscience↗

bioRxiv2026

High-Throughput Screening Identifies Small-Molecule Inhibitors of the Tau-LRP1 Interaction

The cellular uptake and propagation of tau are central features of tauopathies, including Alzheimers disease, and are mediated by the endocytic receptor low-density lipoprotein receptor-related protein 1 (LRP1). While prior studies have implicated LRP1 in tau binding and internalization, the biochemical features of this interaction and its suitability for therapeutic targeting remain incompletely defined. Here, we establish a quantitative and scalable framework to interrogate the tau-LRP1 interaction and identify small-molecule modulators. We engineered and purified the LRP1 ligand-binding domain 4 (BD4), a key region mediating tau interaction, and developed multiple orthogonal assays, including fluorescence polarization, split luciferase complementation, and time-resolved FRET, to measure LRP1-BD4 interactions with tau and a known peptide ligand. Across assay formats, we observe consistent binding affinities in the nanomolar range and demonstrate competitive displacement by tau, receptor-associated protein (RAP), and a peptide ligand, supporting overlapping binding interfaces. Leveraging these platforms, we performed small molecule high-throughput screening and identified a set of candidate inhibitors of the LRP1-BD4-tau interaction. Selected compounds reduced tau uptake in a cellular assay, phenocopying competitive inhibition by tau and a peptide ligand. Together, these studies define the LRP1-BD4-tau interaction as a biochemically tractable and druggable interface and establish an integrated discovery pipeline linking mechanistic characterization to functional cellular outcomes. This work provides a foundation for the development of therapeutic strategies targeting LRP1-mediated tau uptake.

biochemistry↗

bioRxiv2026

BAG2 Condensates Couple Proteostasis to CD8+T Cell Surveillance

Protein aggregation, impaired degradation, and immune activation are central hallmarks of neurodegenerative diseases, yet how these processes are coordinated remains unclear. Here, we identify Immune-Protein Degradation Bodies (I-PDBs), a previously unrecognized class of BAG2-driven, phase-separated organelles that integrate protein quality control with adaptive immunity. IFN{gamma} induce I-PDB formation at the endoplasmic reticulum (ER), where they concentrate immunoproteasome components, MHC-I peptide-loading machinery, and ER-associated chaperones. I-PDBs redirect proteostatic cargo from centrosomal aggregation pathways to spatially restricted degradation sites optimized for antigenic peptide generation, coupling selective substrate clearance to CD8 T cell engagement. Using a cellular model of aggregation-prone tau, we show that I-PDBs capture pathological tau fibrils at ER-microtubule interfaces and process them into potentially antigenic peptides, thus reducing the load of aggregation-prone tau peptides. We term this mechanism the Proteostasis-Associated Immune Relay (PAIR), establishing I-PDBs as critical hubs linking proteostasis to immune surveillance with broad implications for disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/719751v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@16fa503org.highwire.dtl.DTLVardef@ba7607org.highwire.dtl.DTLVardef@19ae5bdorg.highwire.dtl.DTLVardef@60fdf7_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIIFN{gamma} drives BAG2-dependent Immune-Protein Degradation Bodies (I-PDBs) C_LIO_LII-PDBs assemble at the endoplasmic reticulum and are enriched in immunoproteasome and MHC-I machinery C_LIO_LII-PDBs shunt misfolded proteins, including pathological tau, away from aggresomes C_LIO_LII-PDBs couple proteostasis to antigen presentation, enhancing CD8 T cell recognition C_LIO_LIThe Proteostasis-Associated Immune Relay (PAIR) defines a pathway linking proteostasis to adaptive immunity C_LI

cell biology↗

bioRxiv2026

A recurrent neural network model of chronic pain development and recovery

Chronic pain presents a leading challenge in the world today for both clinicians and researchers. Because chronic pain is difficult to explain and treat, it is often managed with opioids despite providing limited relief and contributing to dependence and misuse. Persistent pain can be maintained by altered central nervous system processing even in the absence of distinct tissue damage or disease, which may limit the efficacy of conventional pharmacological therapies that target nociceptive signal transmission rather than maladaptive central nervous system dynamics often present in those with chronic pain. Although neuroimaging studies have identified this shift from nociceptive to emotional circuits during pain chronification, a quantitative framework linking these neural changes to longitudinal pain trajectories or recovery is lacking. We present a parsimonious firing-rate model that can account for the development of and recovery from chronic pain, which is based on the theoretical framework established by Wilson and Cowan. The model provides a quantitative explanation of how sensitization, anxiety, and fear maintain pain even after an injury has healed, and how calming stimulus downregulates these processes to facilitate recovery. A study applying the same principles as the model produced an average pain decrease of 3.5 on the Visual Analog Scale (VAS), with all subjects experiencing a reduction in pain. These results, coupled with our model and findings in prior studies, suggest that increasing calming stimulus can reduce pain without necessitating pharmacological or invasive, resource-intensive interventions.

neuroscience↗

bioRxiv2026

Systematic analysis of RhoGAP expression and function in border cell morphology and migration

Rho family GTPases are central hubs in the signaling and cytoskeletal networks that govern cell morphology and behavior. GTPase-activating proteins (GAPs) inactivate them by accelerating GTP hydrolysis. However, a systematic analysis of GAPs in cell migration is lacking. Here, we report screens for RhoGAP expression and function in migratory Drosophila border cells. Constitutively active Cdc42, Rac, or Rho causes defects, demonstrating that negative regulation is critical. Integrating single-cell RNAseq with published datasets reveals that most of the 22 RhoGAPs are expressed in border cells. RNAi knockdown shows most RhoGAPs are functionally required. We developed automated image analysis tools to sensitively and objectively classify border cell morphologies, defining a normal morphological phase space. RhoGAP perturbations push clusters outside this range. In-depth analysis of RhoGAPp190 reveals that loss-of-function resembles Rho hyperactivation and gain-of-function resembles myosin II inhibition. Thus, complex spatiotemporal sculpting of RhoGTPase activities requires diverse RhoGAPs within a single cell type to control morphology and motility in vivo.

cell biology↗

bioRxiv2026

Neuronal Population Effects of Ketamine on Human Brain Organoids

Ketamines rapid neuropsychiatric actions emerge from interactions that span receptors, cells, and circuits, but their net effects on human neuronal population dynamics remain incompletely defined. Here we combine human dorsal forebrain organoids with high-density microelectrode arrays (MEAs) to quantify ketamines effects from spikes to networks. In 6-month-old organoids, acute ketamine (20{square}g/mL) abolished population bursting while neuronal firing continued mostly unchanged. Spike sorting revealed that mean firing rates declined but not silenced after ketamine Reductions were concentrated within a subset of burst-driver units previously defined as "backbone". Functional connectivity, estimated with the spike time tiling coefficient (STTC), decreased globally after ketamine. Backbone units displayed elevated connectivity at baseline but were functionally disconnected by ketamine. Graph construction from STTC uncovered widespread network reconfiguration, characterized by redistribution of edges from backbone to non-backbone units leading to loss of hubs and less-interconnected communities. Re-exposure after chronic ketamine treatment no longer silenced population bursting, indicating tolerance. Together, these results show that ketamine acutely silences human organoid networks by disconnecting backbone units, while chronic exposure induces tolerance to re-silencing while reducing the number of backbone units and leaving the network less active and less connected. The organoid-MEA platform provides a scalable, human-relevant system for dissecting circuit-level drug effects.

neuroscience↗

bioRxiv2025

Progranulin loss induces mitochondrial dysfunction and ferroptosis in human cerebral organoids

Loss-of-function mutations in the granulin (GRN) gene cause frontotemporal dementia when the mutations are heterozygous and neuronal ceroid lipofuscinosis, a lysosomal storage disease, when homozygous. While it is well established that disease-causing GRN mutations decrease progranulin (PGRN) levels, leading to neurodegeneration, the cellular and molecular mechanisms underlying these conditions remain poorly understood. In this study, we utilized human induced pluripotent stem cell (iPSC) derived forebrain organoids to investigate the impact of PGRN homozygous deficiency on neuronal and glial cell populations. Through single-cell RNA sequencing, we identified robust downregulation of the mitochondrial oxidative phosphorylation pathway in PGRN KO organoids. In line with these results, PGRN KO organoids showed decreased mitochondrial respiration. Furthermore, our study demonstrated that PGRN loss induced increased levels of reactive oxygen species (ROS), lipid peroxidation and iron accumulation. Finally, we observed increased vulnerability to ferroptotic cell death in PGRN KO organoids. Our findings suggest that mitochondrial dysfunction and impaired responses to oxidative stress are early manifestations of PGRN loss, and offer insights into the molecular mechanisms driving neurodegeneration caused by PGRN deficiency. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/691344v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@c477e5org.highwire.dtl.DTLVardef@9b61eforg.highwire.dtl.DTLVardef@13aadeborg.highwire.dtl.DTLVardef@1702929_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO Proposed molecular mechanisms that lead to ferroptosis of PGRN KO cells. Created with BioRender.com. C_FIG

neuroscience↗

bioRxiv2025

Tracking tau and cellular responses in human iPSC-microglia from uptake to seedable secretion in extracellular vesicles

The templated spread of tau aggregates in tauopathies has been attributed to neuron-to- neuron spread, but microglia have also been implicated through mouse studies. Here we examine in detail the uptake, processing, release and seeding of tau using human iPS- derived microglia (iMGL). We show that tau is taken up by iMGL via LRP1 and heparan sulfate proteoglycans, with a role for LRRK2 in LRP1 trafficking, and that phagocytosed fibrils can escape into the cytoplasm. Monomeric tau has minimal effects on iMGL, but recombinant or brain-derived tau fibrils induce a shift towards chemokine and interferon response subtypes, alongside downregulation of homeostatic and MHC genes. Endogenous tau protein is undetectable in iMGL, and monomeric internalised tau is digested to completion, but fibrillar tau is more resistant to degradation and becomes phosphorylated on two specific residues. Finally, fibrillar tau is released by iMGL, visualized within extracellular vesicles by cryo-EM, and can seed tau aggregation in downstream neurons.

cell biology↗

bioRxiv2025

Structure-specific Mini-Prion Model for Alzheimer's Disease Tau Fibrils

A critical discovery of the past decade is that tau protein fibrils adopt disease-specific hallmark structures in each tauopathy. The faithful generation of synthetic fibrils adopting hallmark structures that can serve as targets for developing diagnostic and/or therapeutic strategies remains a grand challenge. We report on a rational design of synthetic fibrils built of a short peptide that adopts a critical structural motif in tauopathy fibrils found in Alzheimers Disease (AD) and Chronic Traumatic Encephalopathy (CTE). They serve as minimal prions with exquisite seeding competency, in vitro and in tau biosensor cells, for recruiting tau constructs ten times larger its size en route to AD or CTE fibril structures. We demonstrate that the generation of AD and CTE-like fibril structures is dramatically catalyzed in the presence of mini-AD prions and further influenced by salt composition in solution. Double Electron-Electron Resonance studies confirmed the preservation of AD-like folds across multi-generational seeding. Fibrils formed with the full AD/CTE-like core show strong seeding competency, with their templating effect dominating over the choice of salt composition that tunes the initial selection of AD- and CTE-like fibril populations. The mini-AD prions serve as a potent catalyst with templating capabilities that offer a novel strategy to design pathological tau fibril models.

biophysics↗

bioRxiv2025

Protein-Like Polymer for Inhibition of Tau Fibril Propagation in Human-Derived Models of Neurodegeneration

The misfolding, aggregation, and spread of tau protein fibrils underlie tauopathies, a diverse class of neurodegenerative diseases for which effective treatments remain elusive. Among these are corticobasal dementia (CBD) and progressive supranuclear palsy (PSP), canonical examples of 4-repeat (4R) tauopathies characterized by tau isoforms exclusively with four microtubule-binding repeat domains. We target this 4R tau isoform-specific mechanism by focusing on misfolded taus distinctive stem-loop-stem structural motif formed by the junction of the 4R-defining alternatively spliced exon and the adjacent constitutive exon. A synthetic peptide based on this stem-loop-stem sequence can induce aggregation and spread in an isoform-specific manner. Here, we develop a protein-like polymer (PLP) in which multiple copies of this synthetic peptide form a brush-like structure capable of preventing tau aggregation by binding and capping fibril ends in vitro, in human brain organoids, and in cellular models with an EC50 of 105 {+/-} 14 nM. PLPs demonstrate robust activity against fibrils derived from CBD and PSP patient brains and a PS19 mouse tauopathy model. Previous tau-targeted treatments have primarily focused on broad tau clearance, aggregation inhibition, or microtubule stabilization, often lacking isoform specificity and precision. In contrast, this approach targets the 4R tau isoforms unique structural motif, offering a tailored therapeutic intervention for diseases like CBD and PSP. Supported by prior studies showing blood-brain barrier penetrance and safety profiles, this tau-binding PLP offers a promising translational path toward clinical applications in tauopathy treatment.

neuroscience↗

bioRxiv2025

Protective mechanisms against Alzheimer's Disease in APOE3-Christchurch homozygous astrocytes

The APOE3-Christchurch (APOE3-Ch) variant has been linked to reduced Alzheimers Disease (AD) risk, but its protective mechanisms remain unclear. This study explores the neuroprotective phenotype of APOE3-Ch astrocytes, focusing on lipid metabolism and tau processing. APOE3-Ch astrocytes demonstrate enhanced tau oligomer uptake via HSPG- and LRP1-mediated pathways, facilitated by elevated HSPG expression, and achieve superior tau degradation through lysosomal pathways and proteasomal pathways, in contrast to wild-type astrocytes, which primarily use proteasomal mechanisms. Transcriptomic analysis reveals upregulation of genes involved in endocytosis and cell projection assembly, explaining enhanced tau uptake and clearance in APOE3-Ch astrocytes. Lipidomic profiling identifies reduced levels of pathological lipids such as ceramides and gamma-linolenic acid (GLA), potentially mitigating neuroinflammation. These findings provide insight into the protective mechanisms of APOE3-Ch astrocytes and underscore their potential as therapeutic targets for tauopathy and neurodegeneration in AD. TeaserAPOE3-Christchurch astrocytes enhance tau clearance and mitigate neurotoxic lipid accumulation, unveiling protective mechanisms against Alzheimers.

neuroscience↗

bioRxiv2023

Protosequences in human cortical organoids model intrinsic states in the developing cortex

Neuronal firing sequences are thought to be the basic building blocks of neural coding and information broadcasting within the brain. However, when sequences emerge during neurodevelopment remains unknown. We demonstrate that structured firing sequences are present in spontaneous activity of human and murine brain organoids and ex vivo neonatal brain slices from the murine somatosensory cortex. We observed a balance between temporally rigid and flexible firing patterns that are emergent phenomena in human and murine brain organoids and early postnatal murine somatosensory cortex, but not in primary dissociated cortical cultures. Our findings suggest that temporal sequences do not arise in an experience-dependent manner, but are rather constrained by an innate preconfigured architecture established during neurogenesis. These findings highlight the potential for brain organoids to further explore how exogenous inputs can be used to refine neuronal circuits and enable new studies into the genetic mechanisms that govern assembly of functional circuitry during early human brain development.

neuroscience↗

bioRxiv2023

Tau P301L mutation promotes core 4R tauopathy fibril fold through near-surface water structuring and conformational rearrangement

Tau forms toxic fibrillar aggregates in a family of neurodegenerative diseases known as tauopathies. The faithful replication of tauopathy-specific fibril structures is a critical gap for developing diagnostic and therapeutic tools. This study debuts a strategy of identifying a critical segment of tau that forms a folding motif that is characteristic of a family of tauopathies and isolating it as a standalone peptide that form seeding-competent fibrils. The 19-residue jR2R3 peptide (295-313) spanning the R2/R3 splice junction of tau, in the presence of P301L, forms seeding-competent amyloid fibrils. This tau fragment contains the hydrophobic VQIVYK hexapeptide that is part of the core of every pathological tau fibril structure solved to-date and an intramolecular counter-strand that stabilizes the strand-loop-strand (SLS) motif observed in 4R tauopathy fibrils. This study shows that P301L exhibits a duality of effects: it lowers the barrier for the peptide to adopt aggregation-prone conformations and enhances the local structuring of water around the mutation site that facilitates site-specific dewetting and in-register stacking of tau to form cross {beta}-sheets. We solve a 3 [A] cryo-EM structure of jR2R3-P301L fibrils with a pseudo 21 screw symmetry in which each half of the fibrils cross-section contains two jR2R3-P301L peptides. One chain adopts a SLS fold found in 4R tauopathies that is stabilized by a second chain wrapping around the SLS fold, reminiscent of the 3-fold and 4-fold structures observed in 4R tauopathies. These jR2R3-P301L fibrils are able to template full length tau in a prion-like fashion. Significance StatementThis study presents a first step towards designing a tauopathy specific aggregation pathway by engineering a minimal tau prion building block, jR2R3, that can template and propagate distinct disease folds. We present the discovery that P301L--among the widest used mutations in cell and animal models of Alzheimers Disease--destabilizes an aggregation-prohibiting internal hairpin and enhances the local surface water structure that serves as an entropic hotspot to exert a hyper-localized effect in jR2R3. Our study suggests that P301L may be a more suitable mutation to include in modeling 4R tauopathies than for modelling Alzheimers Disease, and that mutations are powerful tools for the purpose of designing of tau prion models as therapeutic tools.

biophysics↗

bioRxiv2023

A Small Tau Fragment Specifically Templates Four Repeat Tau Aggregates Through Multiple Generations

Prion-like spread of disease-specific tau conformers is a hallmark of all tauopathies. A 19-residue probe peptide containing a P301L mutation and spanning the R2/R3 splice junction of tau, folds and stacks into seeding-competent fibrils and induces aggregation of 4R, but not 3R tau. These tau peptide fibrils propagate aggregated intracellular tau over multiple generations, have a high {beta}- sheet content, a colocalized lipid signal, and adopt a well-defined U-shaped fold found in 4R tauopathy brain-derived fibrils. Fully atomistic replica exchange molecular dynamics (MD) simulations were used to compute the free energy landscapes of the conformational ensemble of the peptide monomers. These identified an aggregation-prohibiting {beta}-hairpin structure and an aggregation-competent U-fold unique to 4R tauopathy fibrils. Guided by MD simulations, we identified that the N-terminal-flanking residues to PHF6, which slightly vary between 4R and 3R isoforms, modulate seeding. Strikingly, when a single amino acid switch at position 305 replaced the serine of 4R tau with a lysine from the corresponding position in the first repeat of 3R tau, the seeding induced by the 19-residue peptide was markedly reduced. Conversely, a 4R tau mimic with three repeats, prepared by replacing those amino acids in the first repeat with those amino acids uniquely present in the second repeat, recovered aggregation when exposed to the 19- residue peptide. These peptide fibrils function as partial prions to recruit naive 4R tau--ten times the length of the peptide--and serve as a critical template for 4R tauopathy propagation. These results hint at opportunities for tau isoform-specific therapeutic interventions. Significance StatementA structural motif corresponding to a short junction sequence spanning R2 and R3 forms fibrils that adopt a fold characteristic of 4R tauopathy fibrils and induces misfolding of the larger tau protein with loss of microtubule binding and a prion-like specificity for 4R tau. Simulations, validated experimentally, pinpointed the specific amino acids in the peptide that can toggle its properties between aggregation competent and incompetent. The modifications suggest design principles for a therapeutic intervention potentially capable of disaggregating tau or preventing its aggregation in the 4R tauopathies.

molecular biology↗

bioRxiv2022

SUMO2 Protects Against Tau-induced Synaptic and Cognitive Dysfunction

Abnormal intracellular accumulation of Tau aggregates is a hallmark of Alzheimers disease (AD) and other Tauopathies, such as Frontotemporal dementia (FTD), which can be caused by mutations of Tau. Mutated and pathological Tau can undergo a range of post-translational modifications (PTMs) that might trigger or modulate disease pathology. Recent studies indicate that modification of wild type Tau by Small ubiquitin-like modifier SUMO isoform 1 (SUMO1) controls Tau hyperphosphorylation and aggregation, suggesting that SUMOylation acts as a central regulator of Taus biochemical properties. Besides SUMO1, Tau is modified by SUMO2/3, however the consequences of this modification have not been investigated. Here, using viral approaches on primary hippocampal neurons, transgenic mice expressing mutant Tau and SUMO2, and iPSC-derived neurons from FTD patients, we evaluated whether SUMO2/3 conjugation modifies the neurodegenerative disease pathology associated with the aggregation-prone mutant Tau P301L, P301S, and R406W variants. We found that mutant forms of Tau are targets of SUMO2/3, and SUMO2/3 conjugation is neuroprotective. Importantly, expression of mutant Tau is accompanied by a significant reduction of SUMO2/3 conjugation levels, and restoring levels of SUMO2 reduces mutant Tau aggregation and phosphorylation in all model systems Furthermore, overexpression of SUMO2 restores levels of pre- and post-synaptic markers, associated with a complete rescue of the LTP and memory deficits in transgenic mice expressing mutant Tau. These findings bring to light the potential therapeutic implication of manipulating SUMO conjugation to detoxify Tau through PTM-based approaches.

neuroscience↗

bioRxiv2022

Automated detection of extracellular action potentials from single neurons

Multi-electrode arrays (MEAs) non-invasively record extracellular action potentials (eAPs, also known as spikes) from hundreds of neurons simultaneously. However, because extracellular electrodes sample from the local electrical field, each electrode can detect eAPs from multiple nearby neurons. Interpreting spike trains at individual electrodes of high-density arrays requires spike sorting, a computational process which groups eAPs from single units based on assumptions of how spike waveforms correlate with different neuronal sources. Additionally, when experimental conditions result in changes to eAP waveforms, spike sorting routines may have difficulty correlating eAPs from multiple neurons at single electrodes before and after such waveform changes. We present here a novel, empirical method for unambiguously isolating eAPs from individual, uniquely identifiable neurons, based on automated multi- point detection of action potential propagation. This method is insensitive to changes in eAP waveform morphology because it makes no assumptions about the relationship between spike waveform and neuronal source. Our algorithm for automated detection of action potential propagation produces a fingerprint that uniquely identifies those spikes from each neuron. By unambiguously isolating eAPs from multiple neurons in each recording, on a range of platforms and experimental preparations, our method now enables high-content screening with contemporary MEAs. We outline the limitations and strengths of propagation-based isolation of eAPs from single neurons and propose how our automated method complements spike sorting and could be adapted to in vivo use.

neuroscience↗

bioRxiv2021

Self-organized morphogenesis of a human neural tube in vitro by geometric constraints

Understanding how human embryos develop their shape is a fundamental question in physics of life with strong medical implications. However, it is challenging to study the dynamics of organ formation in humans. Animals differ from humans in key aspects, and in particular in the development of the nervous system. Conventional organoids are quantitatively unreproducible and exhibit highly variable morphology. Here we present a morphologically reproducible and scalable approach for studying human organogenesis in a dish, which is compatible with live imaging. We achieve this by precisely controlling cell fate pattern formation in 2D stem cell sheets, while allowing for self-organization of tissue shape in 3D. Upon triggering neural pattern formation, the initially flat stem cell sheet undergoes folding morphogenesis and self-organizes into a millimeter long anatomically accurate model of the neural tube, covered by epidermis. We find that neural and epidermal human tissues are necessary and sufficient for folding morphogenesis in the absence of mesoderm activity. Furthermore, we find that molecular inhibition of tissue contractility leads to defects similar to neural tube closure defects, consistent with in vivo studies. Finally, we discover that neural tube shape, including the number and location of hinge points, depends on neural tissue size. This suggests that neural tube morphology along the anterior posterior axis depends on neural plate geometry in addition to molecular gradients. Our approach provides a new path to study human organ morphogenesis in health and disease.

developmental biology↗