Biology subjects

Gaur, A.

Publications and source records attributed to Gaur, A..

13 recordsLinked to original sources

bioRxiv2026

The IKC-leptin axis functions as a molecular bridge between neurodevelopment and endocrine signaling

Kcnb1, a voltage-gated K channel widely expressed in brain, assembles with integrins to form integrin-K channel complexes (IKCs) in cortex and hypothalamus. Pathogenic KCNB1 variants cause Developmental and Epileptic Encephalopathy (DEE), and Kcnb1-null (Null) mice reproduce core neurodevelopmental defects alongside chronic hypoleptinemia, suggesting a leptin-IKC signaling axis. We find that Kcnb1, integrins, and the leptin receptor (LepR) co-immunoprecipitate and co-localize in cortical neurons. Perinatal leptin supplementation in Null mice improves cognition, corrects cortical anatomy, and restores neuronal migration, dendritic arborization, and synaptic functionality. In primary Null cortical neurons, leptin normalizes dendritic growth and actin remodeling via integrin-dependent mechanisms. By contrast, leptin has modest effects in WT animals and neurons; sensitivity is unmasked by pharmacological manipulation of integrins, and, strikingly, LepR blockade in the absence of exogenous leptin is sufficient to induce Null-like defects in WT neurons. These findings argue that hypoleptinemia alone does not drive the Null phenotype. Instead, they reveal a previously unrecognized, dual-mode model in which LepR signaling is regulated by both its ligand and IKCs. This conceptual advance links IKC-LepR coupling to neurodevelopment and DEE and pinpoints their interface as a tractable therapeutic target.

neuroscience↗

bioRxiv2025

Dynamic flexibility of the gut microbiota to morphine disturbance enables escape from the stable dysbiosis associated with addiction-like behavior

Although opioids are effective analgesics, they can lead to problematic drug use behaviors that underlie opioid use disorder (OUD). Opioids also drive gut microbiota dysbiosis which is linked to altered opioid responses tied to OUD. To interrogate the role of the gut microbiota in a mouse model of OUD, we used a longitudinal paradigm of voluntary oral morphine self-administration to capture multiple facets of drug seeking and preserve both individual behavioral response and gut microbiota variation to examine associations between these two variables. After prolonged morphine consumption, only a subset of mice transitioned to a state we define statistically as compulsive. In compulsive mice, morphine fragmented the microbiota networks which subsequently reorganized to form robust novel connections. In contrast, the communities of non-compulsive mice also changed but were highly interconnected during morphine disturbance and maintained more continuity post morphine suggesting dynamic flexibility. Compulsive mice displayed a greater loss of functional diversity and a shift towards a new stable state dominated by potential pathobionts, whereas non-compulsive mice better preserved genera associated with gut health and broader functional diversity. These findings highlight how persistent and stable gut microbiota dysbiosis aligns with long-term behavioral changes underlying OUD, potentially contributing to relapse.

microbiology↗

bioRxiv2025

Immunogenicity and Structural Features of a Stabilized Clade-C HIV-1 Env Derived from a Pediatric Elite-neutralizer

The envelope (Env) glycoprotein derived from circulating viruses in elite-neutralizers (who naturally develop broadly neutralizing antibodies (bNAbs)), serves as potential template for HIV-1 vaccine design. Herein, we report the structure and immunogenicity of soluble clade-C HIV-1 Env trimer (330) derived from a pediatric elite-neutralizer (AIIMS_330). Using SOSIP, NFL and ferritin-nanoparticle (NP) platforms, we engineered immunogens that preserved native-like Env conformation, exhibited high thermostability and nanomolar affinity for diverse bNAbs, with minimal reactivity to non-neutralizing antibodies. Cryo-EM structure solved at 5 [A] resolution of 330-SOSIP trimer-autologous bNAb 44m complex revealed interactions at GDIR motif, N332 supersite along with additional contacts at E293, K337, K446 and glycans N326, N442, N448, as compared to our previously reported BG505-44m structure. Rabbit immunizations with soluble and NP-displayed formats elicited autologous, and heterologous neutralization of tier-1 clade-C viruses. Herein we define a structurally resolved HIV-1 clade C Env that supports multivalent vaccine strategies and provides mechanistic insights toward rational HIV-1 immunogen design.

immunology↗

bioRxiv2025

M6A reader protein YTHDF3 regulates cardiomyocyte death and atrophy by modulating the alternative splicing program

BackgroundThe functional impact of m6A modifications on RNA is governed by reader proteins that read the m6A marks and process the RNA accordingly. Recent studies have highlighted the importance of m6A reader proteins in the heart. However, the function of a reader protein Ythdf3 in the heart remains completely unknown. ObjectiveWe aim to uncover the function of Ythdf3 in the hearts. Methods& ResultsHere, we show that Ythdf3 is indispensable for the heart, and its knockdown leads to cardiac cachexia evident by cardiomyocyte atrophy, death, and less dense myofibrils visualized by electron microscopy. We also found downregulation of Ythdf3 in response to doxorubicin, and its overexpression rescues doxorubicin-induced cardiomyocyte atrophy and death. Contrary to primarily cytoplasmic localization, we found that Ythdf3 localizes in the cardiomyocyte nucleus. Furthermore, using co-immunoprecipitation coupled with LC-MS/MS, we show that Ythdf3 interacts with splicing proteins like DDX5 and HNRNPU and regulates alternative splicing in the heart. Mechanistically, we found that Ythdf3 regulates the splicing of CaMKII{delta}, and its knockdown leads to an increase in CaMKII{delta}A and CaMKII{delta}C isoforms while a decrease in CaMKII{delta}9 isoform. ConclusionCollectively, Ythdf3 knockdown in the adult heart leads to cardiac cachexia due to the alteration of the splicing program.

cell biology↗

bioRxiv2024

G protein-Coupled Receptor Associated Sorting ProteinGASP1 mediated trafficking of the Glucagon Like Peptide-1Receptor contributes to the development of tolerance toincretin drugs

Incretin mimetic drugs are in widespread use for the treatment of type 2 diabetes and obesity and more recently have been prescribed for weight loss in otherwise healthy individuals. These drugs are all agonists of the glucagon-like peptide 1 receptor (GLP-1R) and function by supplementing effects produced by the endogenous hormone agonist glucagon-like peptide 1 (GLP-1). The therapeutic benefits of these medications, including improved glucose control and weight loss, require continued usage and wane with time. The molecular mechanisms underlying this loss of effect to incretin drugs remain unknown. Following activation by agonist and signaling to G protein, the GLP-1R engages arrestins and is endocytosed. Here we investigated the role of G protein-coupled receptor associated sorting protein 1 (GASP1), a critical regulator of the post-endocytic trafficking of GLP-1R, on tolerance to GLP-1R agonist drug. We found that tolerance to incretin drug was prevented at the cellular, tissue and whole animal level in mice with a selective disruption of the GASP1 protein in beta cells of the pancreatic islet. These studies implicate post-endocytic sorting of the GLP-1R in the loss of effectiveness of incretin therapeutics with prolonged use. These findings also suggest a novel strategy to prevent tolerance by biasing incretin drugs for G protein and away from arrestin engagement.

cell biology↗

bioRxiv2024

Sequence-specific targeting of intrinsically disordered protein regions

Intrinsically disordered proteins and peptides play key roles in biology, but the lack of defined structures and the high variability in sequence and conformational preferences has made targeting such systems challenging. We describe a general approach for designing proteins that bind intrinsically disordered protein regions in diverse extended conformations with side chains fitting into complementary binding pockets. We used the approach to design binders for 39 highly diverse unstructured targets and obtain designs with pM to 100 nM affinities in 34 cases, testing [~]22 designs per target (including polar targets). The designs function in cells and as detection reagents, and are specific for their intended targets in all-by-all binding experiments. Our approach is a major step towards a general solution to the intrinsically disordered protein and peptide recognition problem.

biochemistry↗

bioRxiv2024

Gut dysbiosis was inevitable, but tolerance was not: temporal responses of the murine microbiota that maintain its capacity for butyrate production correlate with sustained antinociception to chronic voluntary morphine

The therapeutic benefits of opioids are compromised by the development of analgesic tolerance, which necessitates higher dosing for pain management thereby increasing the liability for drug dependence and addiction. Rodent models indicate opposing roles of the gut microbiota in tolerance: morphine-induced gut dysbiosis exacerbates tolerance, whereas probiotics ameliorate tolerance. Not all individuals develop tolerance which could be influenced by differences in microbiota, and yet no study design has capitalized upon this natural variation. We leveraged natural behavioral variation in a murine model of voluntary oral morphine self-administration to elucidate the mechanisms by which microbiota influences tolerance. Although all mice shared similar morphine-driven microbiota changes that largely masked informative associations with variability in tolerance, our high-resolution temporal analyses revealed a divergence in the progression of dysbiosis that best explained sustained antinociception. Mice that did not develop tolerance maintained a higher capacity for production of the short-chain fatty acid (SCFA) butyrate known to bolster intestinal barriers and promote neuronal homeostasis. Both fecal microbial transplantation (FMT) from donor mice that did not develop tolerance and dietary butyrate supplementation significantly reduced the development of tolerance independently of suppression of systemic inflammation. These findings could inform immediate therapies to extend the analgesic efficacy of opioids.

systems biology↗

bioRxiv2023

Deletion of arrestin-3 does not alter compulsive morphine-seeking behavior in an oral operant self-administration paradigm

Opioid drugs are potent analgesics that mimic the endogenous opioid peptides, endorphins and enkephalins, by activating the {micro}-opioid receptor. Opioid use is limited by side effects, including significant risk of opioid use disorder. Improvement of the effect/side effect profile of opioid medications is a key pursuit of opioid research, yet there is no consensus on how to achieve this goal. One hypothesis is that the degree of arrestin-3 recruitment to the {micro}-opioid receptor impacts therapeutic utility. However, it is not clear whether increased or decreased interaction of the {micro}-opioid receptor with arrestin-3 would reduce compulsive drug-seeking. To examine this question, we utilized three genotypes of mice with varying abilities to recruit arrestin-3 to the {micro}-opioid receptor in response to morphine in a novel longitudinal operant self-administration model. We demonstrate that arrestin-3 knockout and wild type mice have highly variable drug-seeking behavior with few genotype differences. In contrast, in mice where the {micro}-opioid receptor strongly recruits arrestin-3, drug-seeking behavior is much less varied. We created a quantitative method to define compulsivity in drug-seeking and found that mice lacking arrestin-3 were more likely to meet the criteria for compulsivity whereas mice with enhanced arrestin-3 recruitment did not develop a compulsive phenotype. Our data suggest that opioids that engage both G protein and arrestin-3, recapitulating the endogenous signaling pattern, will reduce abuse liability.

animal behavior and cognition↗

bioRxiv2023

Musashi-2 causes cardiac hypertrophy and heart failure by inducing mitochondrial dysfunction through destabilizing Cluh and Smyd1 mRNA

Regulation of RNA stability and translation by RNA-binding proteins (RBPs) is a crucial process altering gene expression. Musashi family of RBPs comprising Msi1 and Msi2 are known to control RNA stability and translation. However, despite the presence of MSI2 in the heart, its function remains entirely unknown. Here, we aim to explore the cardiac functions of MSI2. We confirmed the presence of MSI2 in the adult mouse, rat heart, and neonatal rat cardiomyocytes. Furthermore, Msi2 was significantly enriched in the hearts cardiomyocyte fraction. Next, using RNA-seq data and isoform-specific PCR primers, we identified, Msi2 isoforms 1, 4, and 5 and two novel putative isoforms labeled as Msi2 isoforms 6 and 7 to be expressed in the heart. Overexpression of Msi2 isoforms led to cardiac hypertrophy in cultured cardiomyocytes. Additionally, Msi2 was also found to be significantly increased in a pressure-overload model of cardiac hypertrophy. To validate the hypertrophic effects, we selected isoforms 4 and 7 due to their unique alternative splicing patterns. AAV9-mediated overexpression of Msi2 isoforms 4 and 7 in murine hearts led to cardiac hypertrophy, dilation, heart failure, and eventually early death, confirming a pathological function for Msi2. Using global proteomics, gene ontology, transmission electron microscopy, and transmembrane potential measurement assays increased MSI2 was found to cause mitochondrial dysfunction in the heart. Mechanistically, we identified Cluh and Smyd1 as direct downstream targets of Msi2. Overexpression of Cluh or Smyd1 inhibited Msi2-induced hypertrophy and mitochondrial dysfunction in cardiomyocytes. Collectively, we show that Msi2 induces hypertrophy, mitochondrial dysfunction, and heart failure.

cell biology↗

bioRxiv2023

Artificial Intelligence uncovers Evolutionarily Conserved Intracellular Allosteric Modulators of GPCR-Gα interface.

Endogenous intracellular allosteric modulators of GPCRs remain largely unexplored, with limited binding and phenotype data available. This gap arises from the lack of robust computational methods for unbiased cavity identification, cavity-specific ligand design, synthesis, and validation across GPCR topology. Here, we developed Gcoupler, an AI-driven generalized computational toolkit that leverages an integrative approach combining de novo ligand design, statistical methods, Graph Neural Networks, and Bioactivity-based ligand prioritization for rationally predicting high-affinity ligands. Using Gcoupler, we interrogated intracellular metabolites that target and regulate the GPCR-G interface (Ste2p-Gpa1p), affecting pheromone-induced programmed cell death in yeast. Our computational analysis, complemented by experimental validations, including genetic screening, multi-omics, site-directed mutagenesis, biochemical assays, and physiological readouts, identified endogenous hydrophobic metabolites, notably sterols, as direct intracellular allosteric modulators of Ste2p. Molecular simulations coupled with biochemical signaling assessment in site-directed Ste2p mutants further confirmed that metabolites binding to GPCR-G obstruct downstream signaling, possibly via a cohesive effect. Finally, by utilizing isoproterenol-induced, GPCR-mediated human and neonatal rat cardiac hypertrophy models, we observed that elevated metabolite levels attenuate hypertrophic response, reinforcing the evolutionary relevance of this mechanism.

bioinformatics↗

bioRxiv2021

hNOP2/NSUN1 Regulates Ribosome Biogenesis through Stabilization of snoRNP Complexes and Cytosine-5 Methylation of 28S rRNA.

5-Methylcytosine (m5C) is a base modification broadly found on various RNAs in the human transcriptome. In eukaryotes, m5C is catalyzed by enzymes of the NSUN family composed of seven human members (NSUN1-7). NOP2/NSUN1 has been primarily characterized in budding yeast as an essential ribosome biogenesis factor required for the deposition of m5C on the 25S ribosomal RNA (rRNA). Although human NOP2/NSUN1 has been known to be an oncogene overexpressed in several types of cancer, its functions and substrates remain poorly characterized. Here we used a miCLIP-seq approach to identify human NOP2/NSUN1 RNA substrates. Our analysis revealed that NOP2/NSUN1 catalyzes the deposition of m5C at position 4447 on the 28S rRNA. We also find that NOP2/NSUN1 binds to the 5ETS region of the pre-rRNA transcript and regulates pre-rRNA processing through non-catalytic complex formation with box C/D snoRNAs. We provide evidence that NOP2/NSUN1 facilitates the recruitment of U3 and U8 snoRNAs to pre-90S ribosomal particles and their stable assembly into snoRNP complexes. Remarkably, expression of both WT and catalytically inactive NOP2/NSUN1 in knockdown background rescues the rRNA processing defects and the stable assembly of box C/D snoRNP complexes, suggesting that NOP2/NSUN1-mediated deposition of m5C on rRNA is not required for ribosome synthesis.

molecular biology↗

bioRxiv2021

Notch-Jagged signaling complex defined by an interaction mosaic

The Notch signaling system links cellular fate to that of its neighbors, driving proliferation, apoptosis, and cell differentiation in metazoans, whereas dysfunction leads to debilitating developmental disorders and cancers. Other than a five-by-five domain complex, it is unclear how the 40 extracellular domains of the Notch1 receptor collectively engage the 19 domains of its canonical ligand Jagged1 to activate Notch1 signaling. Here, using cross-linking mass spectrometry (XL-MS), biophysical and structural techniques on the full extracellular complex and targeted sites,we identify five distinct regions, two on Notch1 and three on Jagged1, that form an interaction network.The Notch1 membrane-proximal regulatory region individually binds to the established Notch1 epidermal growth factor (EGF) 8-13 and Jagged1 C2-EGF3 activation sites, as well as to two additional Jagged1 regions, EGF 8-11 and cysteine-rich domain (CRD). XL-MS and quantitative interaction experiments show that the three Notch1 binding sites on Jagged1 also engage intramolecularly.These interactions, together with Notch1 and Jagged1 ectodomain dimensions and flexibility determined by small-angle X-ray scattering (SAXS), support the formation of backfolded architectures. Combined, the data suggest that critical Notch1 and Jagged1 regions are not distal, but engage directly to control Notch1 signaling, thereby redefining the Notch1-Jagged1 activation mechanism and indicating new routes for therapeutic applications.

molecular biology↗

bioRxiv2019

De novo assembly and annotation of Asiatic lion (Panthera leo persica) genome

We report the first draft of the whole genome assembly of a male Asiatic lion, Atul and whole transcriptomes of five Asiatic lion individuals. Evaluation of genetic diversity placed the Asiatic lion in the lowest bracket of genomic diversity index highlighting the gravity of its conservation status. Comparative analysis with other felids and mammalian genomes unraveled the evolutionary history of Asiatic lion and its position among other felids. The genome is estimated to be 2.3 Gb (Gigabase) long with 62X sequence coverage and is found to have 20,543 protein-coding genes. About 2.66% of the genome is covered by simple sequence repeats (SSRs) and 0.4% is estimated to have segmental duplications. Comparison with seven well annotated genomes indicates the presence of 6,295 single copy orthologs, 4 co-orthologs, 21 paralogs uniquely present in Asiatic lion and 8,024 other orthologs. Assessment of male and female transcriptomes gave a list of genes specifically expressed in the male. Our genomic analyses provide candidates for phenotypes characteristic to felids and lion, inviting further confirmation of their contribution through population genetic studies. An Asiatic lion-specific expansion is detected in the Cysteine Dioxygenase-I (CDO-I) family that is responsible for taurine biosynthesis in cats. Wilms tumor-associated protein (WT1) family, a non-Y chromosome genetic factor underlying male-sex determination and differentiation is found to have undergone expansion, interestingly like that of the human genome. Another protein family, translation machinery-associated protein 7 (TMA7) that has undergone expansion in humans, also expanded in Asiatic lion and can be further investigated as a candidate responsible for mane in lions because of its role in hair follicle morphogenesis.

genomics↗