Biology subjects

Cohen, S. R.

Publications and source records attributed to Cohen, S. R..

10 recordsLinked to original sources

bioRxiv2026

Restoration of Rapid-Eye Movement Sleep During Cocaine Abstinence Reduces Incubation of Cocaine Seeking and Normalizes Dopamine Transporter Function

Progressive increases in cocaine craving or seeking during abstinence from cocaine are thought to contribute to relapse. Recent observations suggest that sleep disruptions during abstinence from cocaine may have a significant influence on cocaine seeking. While the neural mechanisms underlying the association between sleep disruptions and increases in cocaine seeking during abstinence continue to be investigated, alterations in mesolimbic dopamine transmission may be a common factor. In these studies, we assessed whether sleep disruptions during abstinence are associated with incubation of cocaine seeking and dopamine terminal adaptations in the nucleus accumbens core of female and male rats. We observed that intermittent access to cocaine followed by abstinence reduced rapid-eye movement sleep, intensified cue-induced cocaine seeking, and enhanced dopamine uptake and dopamine transporter sensitivity to cocaine. Notably, a sleep restoration procedure that restricted sleep to the light phase (active period) restored rapid-eye movement sleep, prevented incubation of cocaine seeking, and normalized baseline dopamine uptake and dopamine transporter sensitivity to cocaine. These findings indicate that rapid-eye movement sleep disruptions during abstinence contribute to exaggerated cocaine seeking and that dopamine transporter adaptations are a potential molecular substrate through which these changes occur. Thus, interventions that restore sleep during cocaine abstinence may serve as effective behavioral therapies for reducing cocaine craving and preventing subsequent relapse.

neuroscience↗

bioRxiv2025

Non-Invasive Mechanical-Functional Analysis of Individual Liver Mitochondria by Atomic Force Microscopy

Mitochondria play a pivotal role in energy production, signaling, and apoptosis. Yet, probing their functional state at the single-organelle level without invasive labels remains a major challenge. Here, we introduce a novel, label-free approach that leverages Atomic Force Microscopy (AFM) beyond its traditional imaging role, transforming it into a powerful tool for functional analysis of individual, isolated mitochondria. By immobilizing mouse liver mitochondria on polylysine-coated mica, we achieved nanoscale resolution of mitochondrial mechanical properties including height, height fluctuation power spectra, and Youngs modulus, under different respiratory states. Strikingly, fluctuations in mitochondrial height fluctuations below 20 Hz showed robust correlation with the mitochondria membrane potential ({Delta}{Psi}m), a cornerstone of mitochondrial function. This relationship allows AFM to sensitively detect changes in the mitochondria bioenergetic status. Applying this method to mitochondria from liver-specific MTCH2 liver-conditional knockout mice, a model of mitochondrial malfunction, we confirmed AFMs diagnostic potential. The technique reliably distinguished malfunctional mitochondria, mirroring and adding new insights beyond conventional fluorescence assays. By bridging nanomechanics and mitochondrial bioenergetics, this approach paves the way for non-invasive, high-resolution diagnostics at the single-organelle level, holding promise to monitor the actual functional state of mitochondria in clinical settings.

biophysics↗

bioRxiv2025

Phenotypic analysis of 11,125 trio exomes in neurodevelopmental disorders

Genomic sequencing is widely used to identify causative genetic changes in neurodevelopmental disorders, such as autism, intellectual disability, and epilepsy. Most neurodevelopmental disorders also present with diverse clinical features, and delineating the interaction between causative genetic changes and phenotypic features is a key prerequisite for developing personalized therapies. However, assessing clinical features at a scale that parallels genomic sequencing remains challenging. Here, we standardize phenotypic information across 11,125 patient-parent trios with exome sequencing data using biomedical ontologies, analyzing 674,767 phenotypic terms. We find that individuals with de novo variants in 69 out of 261 neurodevelopmental genes exhibit statistically significant clinical similarities with distinct phenotypic fingerprints. We also observe that phenotypic relatedness follows a gradient, spanning from highly similar to dissimilar phenotypes, with intra-gene similarities suggesting clinically distinct subgroups for seven neurodevelopmental genes. For most genetic etiologies, only a small subset of highly phenotypically similar individuals carried de novo variants in the same gene, highlighting the heterogeneous and complex clinical landscape of neurodevelopmental disorders. Our study provides a large-scale overview of the dynamic relationship between genotypes and phenotypes in neurodevelopmental disorders, underscoring how the inherent complexity of these conditions can be deciphered through approaches that integrate genomic and phenotypic data.

genetics↗

bioRxiv2024

Direct computations of viscoelastic moduli of biomolecular condensates

In vitro facsimiles of biomolecular condensates are formed by different types of intrinsically disordered proteins including prion-like low complexity domains (PLCDs). PLCD condensates are viscoelastic materials defined by time-dependent, sequence-specific complex shear moduli. Here, we show that viscoelastic moduli can be computed directly using a generalization of the Rouse model and information regarding intra- and inter-chain contacts that is extracted from equilibrium configurations of lattice-based Metropolis Monte Carlo (MMC) simulations. The key ingredient of the generalized Rouse model is the Zimm matrix that we compute from equilibrium MMC simulations. We compute two flavors of Zimm matrices, one referred to as the single-chain model that accounts only for intra-chain contacts, and the other referred to as a collective model, that accounts for inter-chain interactions. The single-chain model systematically overestimates the storage and loss moduli, whereas the collective model reproduces the measured moduli with greater fidelity. However, in the long time, low-frequency domain, a mixture of the two models proves to be most accurate. In line with the theory of Rouse, we find that a continuous distribution of relaxation times exists in condensates. The single crossover frequency between dominantly elastic versus dominantly viscous behaviors is influenced by the totality of the relaxation modes. Hence, our analysis suggests that viscoelastic fluid-like condensates are best described as generalized Maxwell fluids. Finally, we show that the complex shear moduli can be used to solve an inverse problem to obtain distributions of relaxation times that underlie the dynamics within condensates.

biophysics↗

bioRxiv2024

Optimizing clinical interpretability of functional evidence in epilepsy-related ion channel variants

Variants in genes encoding the voltage-gated ion channels are among the most common monogenic causes of epilepsy and neurodevelopmental disorders. Functional effects of a variant are increasingly important for diagnosis and therapeutic decisions. To incorporate knowledge regarding functional consequences in formal clinical variant interpretation, we developed an approach for evaluating multiple functional measurements within the Bayesian framework of the modified ACMG/AMP guidelines. We analyzed 216 functional assessments of 191 variants in SCN1A (n=74), SCN2A (n=66), SCN3A (n=18), and SCN8A (n=33). Of 20 commonly measured biophysical parameters, the most frequent drivers of overall functional consequence were persistent current (f=0.54), voltage dependence of activation (f=0.51), and voltage dependence of fast inactivation (f=0.40) for gain-of-function and peak current (f=0.87) for loss-of-function. By comparing measurements of 23 benign variants, we determined thresholds by which published data on these four parameters confer Strong evidence of variant pathogenicity (likelihood ratio > 18.7) under the ACMG/AMP rubric. Similarly, we delineated evidence weights for the most common epilepsy-related potassium channel gene, KCNQ2, through reports of 80 pathogenic and 24 benign variants, accounting for heterozygous and homozygous experimental conditions. We collected the resulting categorization of functional data into FENICS, a biomedical ontology of 152 standardized terms for coherent annotation of electrophysiological results. Across 271 variants in SCN1A/2A/3A/8A and KCNQ2, 1,731 annotations are available in ClinVar, facilitating use of this evidence in variant classification. In summary, we introduce and apply an ACMG/AMP-calibrated framework for electrophysiological studies in epilepsy-related channelopathies to delineate the impact of functional evidence on clinical variant interpretation.

genetics↗

bioRxiv2023

Biomolecular condensates form spatially inhomogeneous network fluids

The functions of biomolecular condensates are thought to be influenced by their material properties, and these will be determined by the internal organization of molecules within condensates. However, structural characterizations of condensates are challenging, and rarely reported. Here, we deploy a combination of small angle neutron scattering, fluorescence recovery after photobleaching, and coarse-grained molecular dynamics simulations to provide structural descriptions of model condensates that are formed by macromolecules from nucleolar granular components (GCs). We show that these minimal facsimiles of GCs form condensates that are network fluids featuring spatial inhomogeneities across different length scales that reflect the contributions of distinct protein and peptide domains. The network-like inhomogeneous organization is characterized by a coexistence of liquid- and gas-like macromolecular densities that engenders bimodality of internal molecular dynamics. These insights suggest that condensates formed by multivalent proteins share features with network fluids formed by systems such as patchy or hairy colloids.

biophysics↗

bioRxiv2023

Sequence-encoded grammars determine material properties and physical aging of protein condensates

Biomolecular condensates are viscoelastic materials. Here, we report results from investigations into molecular-scale determinants of sequence-encoded and age-dependent viscoelasticity of condensates formed by prion-like low-complexity domains (PLCDs). The terminally viscous forms of PLCD condensates are Maxwell fluids. Measured viscoelastic moduli of these condensates are reproducible using a Rouse-Zimm model that accounts for the network-like organization engendered by reversible physical crosslinks among PLCDs in the dense phase. Measurements and computations show that the strengths of aromatic inter-sticker interactions determine the sequence-specific amplitudes of elastic and viscous moduli as well as the timescales over which elastic properties dominate. PLCD condensates also undergo physical aging on sequence-specific timescales. This is driven by mutations to spacer residues that weaken the metastability of terminally viscous phases. The aging of PLCD condensates is accompanied by disorder-to-order transitions, leading to the formation of non-fibrillar, beta-sheet-containing, semi-crystalline, terminally elastic, Kelvin-Voigt solids. Our results suggest that sequence grammars, which refer to the identities of stickers versus spacers in PLCDs, have evolved to afford control over the metastabilities of terminally viscous fluid phases of condensates. This selection can, in some cases, render barriers for conversion from metastable fluids to globally stable solids to be insurmountable on functionally relevant timescales.

biophysics↗

bioRxiv2022

The SCN1A Philadelphia variant - a gain-of-function mutation causing an early-onset epileptic encephalopathy

ObjectiveLoss-of-function variants in SCN1A cause Dravet Syndrome, the most common genetic developmental and epileptic encephalopathy (DEE). However, emerging evidence suggests separate entities of SCN1A-related disorders due to gain-of-function variants. Here, we aim to refine the clinical, genetic, and functional electrophysiological features of a recurrent p.R1636Q gain-of-function variant, identified in four individuals at a single center. MethodsIndividuals carrying the recurrent SCN1A p.R1636Q variant were identified through diagnostic testing. Whole-cell voltage-clamp electrophysiological recording in HEK-293T cells was performed to compare the properties of sodium channels containing wild-type Nav1.1 or Nav1.1-R1636Q along with both Nav{beta}1 and Nav{beta}2 subunits, including response to oxcarbazepine. To delineate differences to other SCN1A-related epilepsies, we analyzed electronic medical records. ResultsAll four individuals had an early-onset DEE characterized by focal tonic seizures and additional seizure types starting in the first few weeks of life. Electrophysiological analysis showed a mixed gain-of-function effect with normal current density, a leftward (hyperpolarized) shift of steady-state inactivation, and slower inactivation kinetics leading to a prominent late sodium current (INa). The observed functional changes closely paralleled effects of pathogenic variants in SCN3A and SCN8A at corresponding positions. Both wildtype and variant exhibited sensitivity to block by oxcarbazepine, partially correcting electrophysiological abnormalities of the SCN1A p.R1636Q variant. Clinically, a single individual responded to treatment with oxcarbazepine. Across 51 individuals with SCN1A-related epilepsies, those with the recurrent p.R1636Q variants had the earliest ages of onset. InterpretationThe recurrent SCN1A p.R1636Q variant causes a clinical entity with a wider clinical spectrum than previously reported, characterized by ultra early-onset epilepsy and absence of prominent movement disorder. Functional consequences of this variant lead to mixed loss- and gain-of-function that is partially corrected by oxcarbazepine. The recurrent p.R1636Q variant represents one of the most common causes of early-onset SCN1A-related epilepsies with separate treatment and prognosis implications. Key PointsO_LILoss-of-function variants in SCN1A cause Dravet syndrome, but gain-of-function variants have an emerging clinical spectrum. C_LIO_LIThe SCN1A p.R1636Q variant shows similar overall gain-of-function effects to identical missense variants in other voltage-gated sodium channels. C_LIO_LIFeatures of four unreported individuals with SCN1A p.R1636Q from a single center expand the SCN1A gain-of-function phenotype. C_LIO_LIIndividuals with this variant are recognizable by their ultra early-onset seizures in contrast to Dravet syndrome. C_LI

genetics↗

bioRxiv2022

Condensates of disordered proteins have small-world network structures and interfaces defined by expanded conformations

The formation of membraneless biomolecular condensates is driven by macromolecules with sticker-and-spacer architectures that undergo phase separation coupled to percolation (PSCP). Driving forces for PSCP are governed by the interplay between reversible inter-sticker crosslinks and solvation preferences of spacers. Here, we introduce molecular and mesoscale descriptions of structures within, outside, and at the interfaces of condensates that are formed by prion-like low complexity domains (PLCDs), which are exemplars of intrinsically disordered, linear multivalent proteins. Our studies are based on simulations that accurately describe sequence-specific phase behaviors of PLCDs. We find that networks of reversible, intermolecular, inter-sticker crosslinks organize PLCDs into small-world topologies within condensates. These topologies result from distinct conformational preferences within dense, dilute, and interfacial regions. Specifically, the degree of conformational expansion varies non-monotonically, being most expanded at the interface and most compact in the dilute phase with molecules preferring to be oriented perpendicular to condensate interfaces. This contrasts with dense and dilute phases where molecules are randomly oriented relative to one another. Our results demonstrate that even simple condensates, with only one type of macromolecule, feature inhomogeneous spatial organizations of molecules and interfacial features that likely prime them for being locations of biochemical activity.

biophysics↗

bioRxiv2022

LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways

Lissencephaly-1 (LIS1) is associated with neurodevelopmental diseases and is known to regulate the activity of the molecular motor cytoplasmic dynein. Here we show that LIS1 is essential for the viability of mouse embryonic stem cells (mESCs), and it regulates the physical properties of these cells. LIS1 dosage substantially affects gene expression, and we uncovered an unexpected interaction of LIS1 with RNA and RNA-binding proteins, most prominently the Argonaute complex. We demonstrate that LIS1 overexpression partially rescued the expression of extracellular matrix (ECM) and mechanosensitive genes conferring stiffness to Argonaute null mESCs. Collectively, our data transforms the current perspective on the roles of LIS1 in post- transcriptional regulation underlying development and mechanosensitive processes.

cell biology↗