Biology subjects

Kulkarni, A.

Publications and source records attributed to Kulkarni, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Caveolin-1 dependent regulation of cell-matrix interphase in 3D collagen gels.

Cell and extracellular matrix (ECM) interactions are essential for maintaining tissue function and homeostasis. Changes in the biochemical or mechanical properties of the ECM can lead to diseases such as fibrosis or cancer. In a 3D microenvironment, cell-matrix interaction is vital to how cells sense and respond to biochemical and biophysical cues. This study examines the reciprocal interactions between fibroblasts and collagen in 3D hydrogels. We quantitatively measured changes in collagen branch number and junctions in 3D hydrogels using confocal reflectance microscopy and existing analysis protocols. This reveals the impact small changes in collagen concertation (1.0 vs 1.5 mg/ml) over time (15 minutes to 4 hours) have on 3D gels. Embedded in 3D hydrogels, wild-type mouse fibroblasts differentially affect collagen organisation in their immediate proximity with changing concentration and time. This regulation is interestingly lost in Caveolin-1 null fibroblasts with altered stiffness, mechanosensing and cytoskeletal regulation. Inhibition of the Rho-ROCK pathway (known to be changed in Caveolin-1 null fibroblasts) drives cellular protrusions and concentration-dependent 3D collagen organisation in wildtype fibroblasts, but surprisingly not in Caveolin-1 null fibroblasts. This depends on dynamin-dependent endocytosis, which, when inhibited, disrupts ROCK-dependent protrusions and alters collagen organisation in 3D collagen. Together, these observations quantitatively demonstrate how cells respond at the cell-matrix interphase to subtle changes in collagen concentration and organisation in 3D hydrogels, regulated by the presence of Caveolin-1. Statement of SignificanceThis study highlights the critical role of Caveolin-1 in cell-mediated regulation of the extracellular matrix (ECM) in a 3D microenvironment. Using confocal reflectance microscopy, we demonstrate that subtle changes in collagen concentration significantly influence collagen organisation over time. While wild-type fibroblasts exhibit dynamic, concentration-dependent regulation of the cell-matrix interphase, Caveolin-1 null fibroblasts lose this regulation. Furthermore, Rho-ROCK pathway inhibition promotes protrusions and collagen reorganisation in wild-type cells but not Caveolin-1 null fibroblasts. Dynamin-dependent endocytosis also emerges as a key modulator of this process. These findings provide quantitative insights into how mechanosensing and cytoskeletal regulation, dependent on endocytosis can control the cell-matrix interphase, with possible implications for understanding disease-associated matrix changes.

cell biology↗

bioRxiv2025

Semi-automatic Geometrical Reconstruction and Analysis of Filopodia Dynamics in 4D Two-Photon Microscopy Images

BackgroundFilopodia are thin and dynamic membrane protrusions that play a crucial role in cell migration, axon guidance, and other processes where cells explore and interact with their surroundings. Historically, filopodial dynamics have been studied in great detail in 2D in cultured cells, and more recently in 3D culture as well as living brains. However, there is a lack of efficient tools to trace and track filopodia in 4D images of complex brain cells. ResultsTo address this issue, we have developed a semi-automatic workflow for tracing filopodia in 3D images and tracking the traced filopodia over time. The workflow was developed based on high-resolution data of photoreceptor axon terminals in the in vivo context of normal Drosophila brain development, but devised to be applicable to filopodia in any system, including at different temporal and spatial scales. In contrast to the pre-existing methods, our workflow relies solely on the original intensity images without the requirement for segmentation or complex preprocessing. The workflow was realized in C++ within the Amira software system and consists of two main parts, dataset pre-processing, and geometrical filopodia reconstruction, where each of the two parts comprises multiple steps. In this paper, we provide an extensive workflow description and demonstrate its versatility for two different axo-dendritic morphologies, R7 and Dm8 cells. Finally, we provide an analysis of the time requirements for user input and data processing. ConclusionTo facilitate simple application within Amira or other frameworks, we share the source code, which is available at https://github.com/zibamira/filopodia-tool.

neuroscience↗

bioRxiv2025

Functional alignment of protein language models via reinforcement learning

Protein language models (pLMs) enable generative design of novel protein sequences but remain fundamentally misaligned with protein engineering goals, as they lack explicit understanding of function and often fail to improve properties beyond those found in nature. We introduce Reinforcement Learning from eXperimental Feedback (RLXF), a general framework that aligns protein language models with experimentally measured functional objectives, drawing inspiration from the methods used to align large language models like ChatGPT. Applied across five diverse protein families, RLXF improves generation of high-functioning variants beyond pre-trained baselines. We demonstrate this with CreiLOV, an oxygen-independent fluorescent protein, where RLXF-aligned models generate sequences with significantly enhanced fluorescence, including the most fluorescent CreiLOV variants reported to date. Our results indicate that RLXF-aligned models effectively integrate the evolutionary knowledge encoded in pre-trained pLMs with experimental observations, improving the success rate of generated sequences and enabling the discovery of synergistic mutation combinations that are difficult to identify through zero-shot or evolutionary approaches. RLXF provides a scalable and accessible approach to steer generative models toward desired biochemical properties, enabling function-driven protein design beyond the limits of natural evolution.

bioengineering↗

bioRxiv2025

Multi-step genomics on single cells and live cultures in sub-nanoliter capsules

Single-cell sequencing methods uncover natural and induced variation between cells. Many functional genomic methods, however, require multiple steps that cannot yet be scaled to high throughput, including assays on living cells. Here we develop capsules with amphiphilic gel envelopes (CAGEs), which selectively retain cells and large analytes while being freely accessible to media, enzymes and reagents. Capsules enable high-throughput multi-step assays combining live-cell culture with genome-wide readouts. We establish methods for barcoding CAGE DNA libraries, and apply them to measure persistence of gene expression programs in cells by capturing the transcriptomes of tens of thousands of expanding clones in CAGEs. The compatibility of CAGEs with diverse enzymatic reactions will facilitate the expansion of the current repertoire of single-cell, high-throughput measurements and extension to live-cell assays.

genomics↗

bioRxiv2025

Resilience to Endoplasmic Reticulum Stress Mitigates Calcium-Dependent Membrane Hyperexcitability Underlying Late Disease Onset in SCA6

An enduring puzzle in many inherited neurological disorders is the late onset of symptoms despite expression of function-impairing mutant protein early in life. We examined the basis for onset of impairment in Spinocerebellar ataxia type 6 (SCA6), a canonical late-onset neurodegenerative ataxia which results from a polyglutamine expansion in the voltage gated calcium channel, Cav2.1. Cerebellar Purkinje cell spiking abnormalities are seen concurrent with motor impairment in SCA6 mice but the basis for these changes in spiking is unknown. We identify endoplasmic reticulum (ER) calcium depletion as the cause for Purkinje cell spiking abnormalities and that the impairments in Purkinje cell spiking are unrelated to Cav2.1 ion-flux function. Further, intact inhibitory neurotransmission in the cerebellar cortex is necessary for Purkinje neurons to exhibit spiking abnormalities in SCA6 mice. Based on serial cerebellar transcriptome analysis, we define a mechanism of disease that is related to ER stress. Further, our studies support a model whereby proteotoxicity from misfolded mutant Cav2.1 is mitigated by a HSP90-dependent unfolded protein response (UPR) and that age-related breakdown of this response causes motor dysfunction and aberrant Purkinje cell spiking. Redundant pathways of the UPR mediate this resilience to ER stress. These studies elucidate a mechanism of resilience connecting aberrant proteostasis and calcium-dependent intrinsic membrane hyperexcitability to explain delayed disease onset more widely in age-dependent neurodegenerative disease. Significance StatementAdvancing age is the single most important risk factor for neurodegenerative disease. Understanding how age intersects with genetic risk is therefore a critical challenge for neurodegenerative disease research. SCA6, a canonical late-onset degenerative cerebellar ataxia, results from a polyQ expansion in the voltage gated calcium channel, Cav2.1, encoded by CACNA1A. We define a mechanism of disease in SCA6 that is related to ER stress and unrelated to impaired calcium flux function of Cav2.1. Age-related decompensation of a HSP90-dependent unfolded protein response leads to disease onset. Mutant Cav2.1 misfolding as the basis for disease in SCA6 provides insight into a novel role for channelopathies to behave as proteinopathies and helps understand resilience to proteotoxicity more widely in adult-onset neurodegenerative disease.

neuroscience↗

bioRxiv2025

All-Optical Strategies to Minimize Photo-Bleaching in Reversibly Switchable Fluorescent Proteins

Photo-bleaching is a general hurdle of fluorescence-based techniques that becomes even more severe in high- resolution microscopy that relies on prolonged, focused and complex illumination sequences. Strategies to reduce photo-bleaching require chemical modifications of the cell media, which often stave off physiological cellular conditions. Here, we outline an all-optical strategy to minimize photo-bleaching in reversibly switching fluorescent proteins (RSFPs), a class of probes used in several super-resolution and protein-multiplexing imaging techniques. By identifying the photobleaching pathways, we developed novel imaging schemes to increase the number of ON- OFF photo-switching cycles based on a designed modulation of the on-switching light or a co-irradiation with red- shifted light. By rationalizing the photo-cycle, we expand multiplexing strategies with RSFPs to high- spatiotemporal resolutions while maintaining the accuracy and recording longer time-lapse imaging of sub-cellular structures with both confocal microscopy and parallelized RESOLFT nanoscopy.

biophysics↗

bioRxiv2025

Invasive lobular carcinoma integrated multi-omics analysis reveals silencing of Arginosuccinate synthase and upregulation of nucleotide biosynthesis in tamoxifen resistance

Invasive Lobular Carcinoma (ILC), a distinct subtype of breast cancer is hallmarked by E-Cadherin loss, slow proliferation, and strong hormone receptor positivity. ILC faces significant challenges in clinical management due to advanced stage at diagnosis, late recurrence, and development of resistance to endocrine therapy - a cornerstone of ILC treatment. To elucidate the mechanisms underlying endocrine resistance in ILC, ILC cell lines (MDA-MB-134-VI, SUM44PE) were generated to be resistant to tamoxifen, a selective estrogen receptor modulator. The tamoxifen-resistant (TAMR) cells exhibit a 2-fold increase tamoxifen IC50 relative to parental cells. Metabolomics and RNA-sequencing revealed deregulation of alanine, aspartate, and glutamate metabolism, purine metabolism, and arginine and proline metabolism in TAMR cells. Among the fifteen commonly dysregulated genes in these pathways, low ASS1 expression was identified in the TAMR cells and was significantly correlated with poor outcome in ILC patients, specifically in the context of endocrine therapy. Our study reveals methylation mediated silencing of ASS1 in TAMR cells as a likely mechanism of downregulation. Demethylation restored ASS1 expression and correspondingly reduced tamoxifen IC50 toward parental levels. Nucleic acid biosynthesis is augmented in TAMR cells, evidenced by increase in nucleotide intermediates. Both TAMR cell lines demonstrated increased expression of several nucleic acid biosynthesis enzymes, including PAICS, PRPS1, ADSS2, CAD, and DHODH. Furthermore, CAD, the key multifunctional protein of de novo pyrimidine biosynthesis pathway is differentially activated in TAMR cells. Treating TAMR cell with Decitabine, a demethylating agent, or Farudodstat, a pyrimidine biosynthesis inhibitor, markedly augmented efficacy of tamoxifen. Collectively, our study unveils ASS1 downregulation as a novel mechanism underlying acquired tamoxifen resistance in ILC and establishes a metabolic link between ASS1 and nucleic acid biosynthesis. Restoring ASS1 expression or inhibiting pyrimidine biosynthesis restored tamoxifen sensitivity. ASS1 could be a potential biomarker and therapeutic target in tamoxifen resistant ILC patients, warranting further investigation.

cancer biology↗

bioRxiv2025

MiRNA-501-3p and MiRNA-502-3p: A Promising Biomarker Panel for Alzheimer's Disease

INTRODUCTIONAlzheimers disease (AD) lacks a less invasive and early detectable biomarker. Here, we investigated the biomarker potential of miR-501-3p and miR-502-3p using different AD sources. METHODSMiR-501-3p and miR-502-3p expressions were evaluated in AD CSF exosomes, serum exosomes, familial and sporadic AD fibroblasts and B-lymphocytes by qRT-PCR analysis. Further, miR-501-3p and miR-502-3p expressions were analyzed in APP, Tau cells and media exosomes. RESULTSMiR-501-3p and miR-502-3p expressions were significantly upregulated in AD CSF exosomes relative to controls. MiRNA levels were high in accordance with amyloid plaque and NFT density in multiple brain regions. Similarly, both miRNAs were elevated in AD and MCI serum exosomes compared to controls. MiR-502-3p expression was high in fAD and sAD B-lymphocytes. Finally, miR-501-3p and miR-502-3p expression were elevated intracellularly and secreted extracellularly in response to APP and Tau pathology. DISCUSSIONThese results suggest that miR-501-3p and miR-502-3p could be promising biomarkers for AD.

neuroscience↗

bioRxiv2024

Diploid origins, adaptation to polyploidy, and the beginning of rediploidization in allotetraploid Arabidopsis suecica

Polyploidization, followed by genome downsizing, is a recurrent evolutionary cycle that dramatically reshapes genome structure. Newly formed polyploids must quickly adjust their cell division machinery to maintain stable chromosome inheritance, while long-term stabilization involves rediploidization, returning the genome to a diploid-like state. Here, we investigate the origin and early genome evolution of Arabidopsis suecica, a hybrid polyploid derived from A. thaliana and A. arenosa Leveraging a recent genome assembly for A. suecica along with population level whole-genome resequencing of all three species, we identify the closest progenitors to A. suecica and use this knowledge to examine genes under positive selection and to assess compensatory dynamics between homeologs carrying loss-of-function mutations. Our findings show that both parental species were diploid, including the paternal A. arenosa progenitor. We identify evidence for de novo adaptation to allopolyploidy within the A. arenosa sub-genome of A. suecica, including genes involved in homolog pairing and recombination. Although relaxed purifying selection is evident, likely due to the genome-wide redundancy, we observe functional compensation between homeologous gene pairs in A. suecica: when one copy loses function, the other maintains it Together, these findings revise the origin of A. suecica and identify early genome stabilization mechanisms, including evidence for meiotic adaptation and mutational buffering through homeologous gene compensation.

genomics↗

bioRxiv2024

Hypusinated and unhypusinated isoforms of eIF5A exert distinct effects in models of pancreas development and function

Hypusination of eukaryotic translation initiation factor 5A (eIF5A) is essential for its role in translation elongation and termination. Although the function of hypusinated eIF5A (eIF5AHyp) in cellular proliferation is well-characterized, the role of its unhypusinated form (eIF5ALys) remains unclear. We hypothesized that eIF5ALys exerts independent effects on cellular replication and metabolism distinct from the loss of eIF5AHyp. To test this hypothesis, we utilized zebrafish and mouse models with inducible knockdowns of deoxyhypusine synthase (DHPS) and eIF5A to investigate their roles in cellular growth. Gene expression analysis via RNA sequencing and morphometric measurements of pancreas and {beta}-cell mass were performed to assess phenotypic changes and identify affected biological pathways. Loss of DHPS in zebrafish resulted in significant defects in pancreatic growth, accompanied by the dysregulation of mRNA translation, neurogenesis, and stress pathways. By contrast, knockdown of eIF5A had minimal impact on pancreas development, suggesting that the effects of DHPS loss are not solely due to the lack of eIF5AHyp. In mice, {beta} cell-specific deletion of DHPS impaired {beta} cell mass expansion and glucose tolerance, while eIF5A deletion had no statistically significant effects. These findings reveal an independent role for eIF5ALys in regulating developmental and functional responses and that a balance in levels of the hypusinated and unhypusinated isoforms of eIF5A may be pivotal in cellular phenotypes in health and disease.

cell biology↗

bioRxiv2024

Organ-specific electrophile responsivity mappingin live C. elegans

Proximity labeling technologies are limited to indexing localized protein residents. Such data-- although valuable--cannot inform on small-molecule responsivity of local residents. We here bridge this gap by demonstrating in live C. elegans how electrophile-sensing propensity in specific organs can be quantitatively mapped and ranked. Using this method, >70% of tissue-specific responders exhibit novel responsivity, independent of tissue-specific abundance. One responder, cyp-33e1--for which both human and worm orthologs are electrophile responsive--marshals stress-dependent gut functions, despite manifesting uniform abundance across all tissues studied. Cyp-33e1s localized electrophile responsivity operates site-specifically, triggering multifaceted responses: electrophile sensing through the catalytic-site cysteine results in partitioning between enzyme inhibition and localized production of a critical metabolite that governs global lipid availability, whereas a rapid dual-cysteine site-specific sensing modulates gut homeostasis. Beyond pinpointing chemical actionability within local proteomes, tissue-specific electrophile responsivity mapping illuminates otherwise intractable locale-specific metabolite signaling and stress response programs influencing organ-specific decision-making. IN BRIEFContext-specific protein reactivity is a cornerstone of biological stress responsivity, and thus has important ramifications for drug discovery; no current method can inform on these parameters. Here we debut a method that cartographs locale-specific actionability to reactive metabolites; Cyp-33e1, a gut-specific responder, emerged to partition between electrophile-driven localized enzymatic turnover that triggers gut-specific metabolite production shaping global lipid storage, and localized electrophile sensing that marshals global stress response. HIGHLIGHTSO_LILocalis-REX maps organ-specific electrophile-responsive proteins in worms C_LIO_LIHits are neither identified by organ-specific Ultra-ID nor biased by localized expression C_LIO_LIHits are enriched in proteins functionally relevant to stress-related phenotypes C_LIO_LILocalized responsivity of gut-specific hit, cyp-33e1, shapes global lipid availability C_LI

molecular biology↗

bioRxiv2024

Effect of differential protection regimes on the diversity and composition of woody plants in the Western Ghats

Human interference in forests is inevitable, and despite significant conservation efforts, many forest areas continue to suffer from anthropogenic pressures. The forests of the Northern Western Ghats (NWG) exhibit varying degrees of protection, including private, community, and legal frameworks. However, the tree diversity within these protection regimes remains underexplored. This study aims to assess tree diversity, composition, and structure across four protection regimes using a transect-cum-quadrat method, with four quadrats (20x20 m) along a single transect line. Data collected included species richness, individual counts, girth at breast height (GBH), basal area, and a combined disturbance index (CDI). Approximately 50% commonality was observed among sites across the four protection regimes. Protected Areas (PA) and Reserved Forests (RF) exhibited higher tree densities compared to Sacred Groves (SG) and Private Forests (PV). Notably, Sacred Groves, despite experiencing high disturbance levels, displayed a similar tree variety to PAs and RFs. While species composition across the four regimes was comparable, structural elements such as tree density and basal area varied significantly. Sacred Groves were predominantly characterized by older trees, whereas RFs and PAs were primarily populated by younger trees. These findings underscore the critical need for targeted conservation strategies that address the unique challenges faced by each protection regime. Enhanced conservation planning is essential to mitigate the impacts of disturbances, such as climate change and land use changes, which threaten the biodiversity of these forests. The study highlights the importance of preserving Sacred Groves and emphasizes the role of community involvement in conservation efforts to safeguard endemic species and maintain ecological balance in the NWG.

ecology↗

bioRxiv2024

L-Phenylalanine is a metabolic checkpoint of human Th2 cells

After the primary response, circulating memory CD4+T effector and T regulatory cells (Treg) regulate recall responses, which are impaired in allergy. Using mass spectrometry, we discovered distinct metabolomes of these cells in humans and their unique enrichment in amino acids. By assessing energy metabolism in in vitro and ex vivo single-cell analyses, we determined that increased intracellular L-phenylalanine boosts glycolysis while limiting OXPHOS in CD4+T, memory CD4+T and Th2, but not in Treg cells. L-phenylalanine also restrains memory CD4+T proliferation in an IL4I1-dependent manner and inhibits Th2 cell proliferation and differentiation. RNA-sequencing, metabolomics, flow cytometry and proteomics, validated in vitro and across patients cohorts, revealed an impairment in LAT1-dependent transport of L-phenylalanine into Th2 cells in allergy with an increase in its intracellular processing, accompanied by an expansion of pathogenic Th2 cells. Thus, our study identifies L-phenylalanine as a checkpoint in the development, energy metabolism and function of Th2 cells.

immunology↗

bioRxiv2024

First Detection of Recombinant Enterovirus G Carrying a Torovirus Papain-like cysteine protease Gene from India

Enterovirus G (EV-G) comprising 20 genotypes (G1-G20) are associated with in a various disease conditions in pig populations. The recombination between homologous EV-G is a driving force behind evolution but the recombination with virus from heterologous family is rare event. Presently, two types of recombinant EV-G strains containing torovirus papain like cysteine protease (PLCP) at 2C-3A junction (Type I) and in place of structural proteins (Type II) are reported. The present study conducted to reveal RNA virome in diarrheic piglets faeces retrieved genome coding for complete polyprotein of EV-G1. The detected EV-G1 strain represents first type I recombinant from India. The polyprotein of strain exhibiting 97% amino acid identity was closely related with Chinese strain. Furthermore, the EV-G1-PLCP strain was found to be originated from South Korean, Chinese, and Japanese strains with breakpoints at nucleotide (nt) position 1323 and 4725. Genetic and phylogenetic analysis of VP1 and PLCP of study strain demonstrated its closeness to EV-G1-PLCP strains from South Korea KOR/KNU-1811/2018/G1-PLCP. The present study advances the knowledge about genetic evolution of EV-G from gaining virulence gene from different virus family.

microbiology↗

bioRxiv2024

A Curated Cell Life Imaging Dataset of Immune-enriched Pancreatic Cancer Organoids with Pre-trained AI Models

Tumor organoids are three-dimensional in vitro models which can recapitulate the complex mutational landscape and tissue architecture observed in cancer patients, providing a realistic tumor microenvironment for testing novel therapies, including immunotherapies. A significant challenge in organoid research in oncology lies in developing efficient and reliable methods for segmenting organoid images, quantifying organoid growth, regression and response to treatments, as well as predicting the behavior of organoid systems. Up to now, a curated dataset of organoids co-cultured with immune cells is not available. To address this gap, we present a new public dataset, comprising both phase-contrast images of murine and patient-derived tumor organoids of one of the deadliest cancer types, the Pancreatic Ductal Adenocarcinoma, co-cultured with immune cells, and state-of-the-art algorithms for object detection and segmentation. Our dataset, OrganoIDNetData, encompassing 190 images with 33906 organoids, can be a potential common benchmark for different organoids segmentation protocols, moving beyond the current practice of training and testing these algorithms on isolated datasets.

cancer biology↗

bioRxiv2024

Broad de-regulated U2AF1 splicing is prognostic and augments leukemic transformation via protein arginine methyltransferase activation

The role of splicing dysregulation in cancer is underscored by splicing factor mutations; however, its impact in the absence of such rare mutations is poorly understood. To reveal complex patient subtypes and putative regulators of pathogenic splicing in Acute Myeloid Leukemia (AML), we developed a new approach called OncoSplice. Among diverse new subtypes, OncoSplice identified a biphasic poor prognosis signature that partially phenocopies U2AF1-mutant splicing, impacting thousands of genes in over 40% of adult and pediatric AML cases. U2AF1-like splicing co-opted a healthy circadian splicing program, was stable over time and induced a leukemia stem cell (LSC) program. Pharmacological inhibition of the implicated U2AF1-like splicing regulator, PRMT5, rescued leukemia mis-splicing and inhibited leukemic cell growth. Genetic deletion of IRAK4, a common target of U2AF1-like and PRMT5 treated cells, blocked leukemia development in xenograft models and induced differentiation. These analyses reveal a new prognostic alternative-splicing mechanism in malignancy, independent of splicing-factor mutations. Statement of significanceUsing a new in silico strategy we reveal counteracting determinants of patient survival in Acute Myeloid Leukemia that co-opt well-defined mutation-dependent splicing programs. Broad poor-prognosis splicing and leukemia stem cell survival could be rescued through pharmacological inhibition (PRMT5) or target deletion (IRAK4), opening the door for new precision therapies. Competing InterestsConflict-of-interest disclosure: DTS. serves on the scientific advisory board at Kurome Therapeutics; is a consultant for and/or received funding from Kurome Therapeutics, Captor Therapeutics, Treeline Biosciences, and Tolero Therapeutics; and has equity in Kurome Therapeutics. AV has received research funding from GlaxoSmithKline, BMS, Jannsen, Incyte, MedPacto, Celgene, Novartis, Curis, Prelude and Eli Lilly and Company, has received compensation as a scientific advisor to Novartis, Stelexis Therapeutics, Acceleron Pharma, and Celgene, and has equity ownership in Throws Exception and Stelexis Therapeutics.

cancer biology↗

bioRxiv2024

Sleep need driven oscillation of glutamatergic synaptic phenotype

Sleep loss increases AMPA-synaptic strength and number in the neocortex. However, this is only part of the synaptic sleep loss response. We report increased AMPA/NMDA EPSC ratio in frontal-cortical pyramidal neurons of layers 2-3. Silent synapses are absent, decreasing the plastic potential to convert silent NMDA to active AMPA synapses. These sleep loss changes are recovered by sleep. Sleep genes are enriched for synaptic shaping cellular components controlling glutamate synapse phenotype, overlap with autism risk genes and are primarily observed in excitatory pyramidal neurons projecting intra-telencephalically. These genes are enriched with genes controlled by the transcription factor, MEF2c and its repressor, HDAC4. Sleep genes can thus provide a framework within which motor learning and training occurs mediated by sleep-dependent oscillation of glutamate-synaptic phenotypes.

neuroscience↗

bioRxiv2024

Negative allosteric modulation of cannabinoid CB1 receptor signaling suppresses opioid-mediated tolerance and withdrawal without blocking opioid antinociception

The direct blockade of CB1 cannabinoid receptors produces therapeutic effects as well as adverse side-effects that limit their clinical potential. CB1 negative allosteric modulators (NAMs) represent an indirect approach to decrease the affinity and/or efficacy of orthosteric cannabinoid ligands or endocannabinoids at CB1. We recently reported that GAT358, a CB1-NAM, blocked opioid-induced mesocorticolimbic dopamine release and reward via a CB1-allosteric mechanism of action. Whether a CB1-NAM dampens opioid-mediated therapeutic effects such as analgesia or alters other unwanted side-effects of opioids remain unknown. Here, we characterized the effects of GAT358 on nociceptive behaviors in the presence and absence of morphine. We examined the impact of GAT358 on formalin-evoked pain behavior and Fos protein expression, a marker of neuronal activation, in the lumbar dorsal horn. We also assessed the impact of GAT358 on morphine-induced slowing of colonic transit, tolerance, and withdrawal behaviors. GAT358 attenuated morphine antinociceptive tolerance without blocking acute antinociception. GAT358 also reduced morphine-induced slowing of colonic motility without impacting fecal boli production. GAT358 produced antinociception in the presence and absence of morphine in the formalin model of inflammatory nociception and reduced the number of formalin-evoked Fos protein-like immunoreactive cells in the lumbar spinal dorsal horn. Finally, GAT358 mitigated the somatic signs of naloxone-precipitated, but not spontaneous, opioid withdrawal following chronic morphine dosing in mice. Our results support the therapeutic potential of CB1-NAMs as novel drug candidates aimed at preserving opioid-mediated analgesia while preventing their unwanted side-effects. Our studies also uncover previously unrecognized antinociceptive properties associated with an arrestin-biased CB1-NAMs. HighlightsO_LICB1 negative allosteric modulator (NAM) GAT358 attenuated morphine tolerance C_LIO_LIGAT358 reduced morphine-induced slowing of colonic motility but not fecal production C_LIO_LIGAT358 was antinociceptive for formalin pain alone and when combined with morphine C_LIO_LIGAT358 reduced formalin-evoked Fos protein expression in the lumbar spinal cord C_LIO_LIGAT358 mitigated naloxone precipitated withdrawal after chronic morphine dosing C_LI

neuroscience↗