Biology subjects

Kaur, K.

Publications and source records attributed to Kaur, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Pyroptotic cell-derived factors promote osteoclast differentiation

The NLRP3 D301N substitution, the murine ortholog of the human D303N variant, causes NLRP3 constitutive activation (NLRP3CA) and inflammasome assembly. Here, we show that priming signals induced by lipopolysaccharide (LPS) are sufficient to trigger GSDMD-dependent pyroptosis in NLRP3CA-expressing bone marrow-derived macrophages (BMDMs), but not in wild-type (NLRP3WT) cells. NLRP3CA mice exhibit elevated IL-1{beta} secretion and LDH release in bone marrow supernatants under both basal and LPS-challenged conditions. Other cytokines (e.g., TNF-) increased comparably between genotypes, indicating that NLRP3CA specifically amplifies inflammasome-dependent responses. Conditioned medium (CM) from LPS-treated NLRP3CA BMDMs significantly enhanced osteoclast (OC) differentiation in vivo and in vitro compared to NLRP3WT CM, as did bone marrow supernatants from NLRP3CA mice. This osteoclastogenic activity was largely independent of IL-1{beta}, as demonstrated by experiments using IL-1{beta}-deficient NLRP3CA BMDMs, IL-1{beta}-neutralizing antibodies, and genetic deletion of the IL-1 receptor. The osteoclastogenic factors were primarily soluble proteins, as heat inactivation and proteinase K digestion markedly reduced OC formation. Extracellular vesicles (EVs) from NLRP3CA CM modestly promoted OC differentiation, but EV-depleted supernatants retained full activity, indicating that the primary mediators are soluble proteins not carried within EVs. Together, these findings establish NLRP3CA as a well-controlled model for studying pyroptosis and demonstrate that pyroptotic cells release soluble proteins that drive osteoclastogenesis independently of IL-1{beta}.

cell biology↗

bioRxiv2026

Systematic CRISPRi perturbation of 1,408 autism risk genes maps multilevel transcriptional convergence in human cortical neurons

Genetic heterogeneity in autism spectrum disorder (ASD) complicates the identification of shared molecular pathways amenable to therapeutic intervention. Here, we perform a CRISPRi Perturb-seq screen targeting 1,408 ASD risk genes in human embryonic stem cell-derived immature cortical neurons and profile the resulting transcriptomic effects by single-cell RNA sequencing. We identify 215 ASD risk genes whose repression induces significant global transcriptomic dysregulation. Leveraging this functional atlas, we characterize candidate genes based on transcriptional similarity to established ASD hub genes. We identify gene programs recurrently dysregulated across perturbations, anchored by processes governing microtubule dynamics, neuron differentiation, cell migration, and transmembrane transport. We further identify CHAMP1 as a previously unrecognized regulator of Wnt signaling and define specific ASD risk genes that modulate the rate of cortical neuron differentiation. Analysis of differentially expressed genes reveals both convergent and perturbation-specific downstream transcriptional responses. Together, these findings provide a multilevel map of transcriptomic convergence in ASD and establish a framework for identifying both pathway-level and genotype-specific therapeutic strategies.

neuroscience↗

bioRxiv2026

Novel human monoclonal antibodies with enhanced sensitivity for lipoarabinomannan antigens present in urines of TB patients

Lipoarabinomannan (LAM) is a useful biomarker for detection of M. tuberculosis infection and disease. Related antigens can be detected in urine samples of TB patients by combinations of monoclonal antibodies (mAbs) directed against specific epitopes expressed in LAM. While sensitive for samples from patients with active TB disease who have HIV-1 co-infections, these assays are less effective for other populations, and there is therefore a need for more sensitive antibodies that can improve the sensitivity of these assays. Here we characterize the antigen and epitope specificities, sequence diversity and isotype dependencies of eight LAM-specific human mAbs that target five distinct arabinose- and mannose-dependent epitopes present in LAM and lipoarabinomannan (LM). Whereas all of the mAbs recognized ManLAM, only a few, including A194-01, consistently detected antigens in TB+ urine samples. Converting A194-01 from the IgG1 to the IgM isotype resulted in broader recognition of poly-Ara glycan epitopes, and increased sensitivity for clinical antigens when combined with several capture reagents, including RU95-C1, a novel antibody targeting the mannan domain of LAM. These results define novel epitopes that are differentially expressed in bacterial and urinary forms of LAM, and identify novel antibody combinations which possess enhanced diagnostic utility for clinical forms of LAM.

immunology↗

bioRxiv2026

Arousal state alters brain network switching and moderates cognitive task performance

Arousal relates to cognitive performance, but the neural underpinnings of this relationship remain unclear. One candidate marker is switching rate, a dynamic measure that has been linked to cognition and has been speculated to be sensitive to arousal. However, whether switching rate is altered across arousal states has not been directly tested. Here, using fMRI together with concurrent eye monitoring and EEG, we examined how the switching rates of the default mode, salience, and central executive networks are altered across arousal states. Default mode and anterior salience networks exhibited significant differences in switching rates across arousal states determined with eye tracking. Notably, thalamic subregions showed arousal-dependent changes in switching rate that were replicated across independent datasets and arousal measures. Additionally, arousal moderated the relationship between average network switching and performance on a relational processing task. Together, these findings suggest that switching rate may index neural underpinnings of arousal-dependent cognition.

neuroscience↗

bioRxiv2025

Entropy of the resting state cortex in epilepsy

BackgroundEpilepsy has long been conceptualised as a disorder in which aberrant brain dynamics extend beyond the epileptogenic zone. Evidence demonstrates that loss of entropy is a generic feature of pathological dynamics in the brain, including the ictal state. However, the impact of recurrent seizures on entropy in the interictal state remains unknown. MethodsResting state magnetoencephalography (MEG) scans and resection masks of 32 individuals with epilepsy who had Engel I outcome post-surgery were retrospectively retrieved. Using co-registered FreeSurfer parcellations, we reconstructed the source localised MEG time series and computed sample entropy for 114 regions of interest. We then tested the association of entropy with the resected volume of the brain, and additional clinical variables including the age of seizure onset, seizure frequency and duration of epilepsy. To further understand the temporal relationship between seizure onset and entropy in the interictal state, we collected and computed sample entropy for week-long EEG traces from leucine-rich glioma inactivated 1 monoclonal antibody (LGI1-mAb) rodent models of autoimmune encephalitis (n=5) and control rats (n=5). ResultsIn individuals with epilepsy, a lower age of seizure onset was associated with lower mean sample entropy of the whole cortex (Spearmans rho =0.60, p<0.001; partial correlation =0.41, p=0.021). Entropy did not differ between the resected and non-resected regions of the brain. Furthermore, LGI1-mAb treated rodents showed a persistent decrease in sample entropy as compared to control rats, after the onset of seizures, and this difference was greatest during periods of highest seizure frequency (p<0.001). ConclusionRecurrent seizures are associated with a persistent decrease in entropy, even in the interictal state, and this decrease was found to be most profound and affecting the whole cortex in patients who had a lower age of seizure onset.

neuroscience↗

bioRxiv2025

Staphylococcus aureus inhibits the NLRP3 inflammasome in macrophages during the early phases of intracellular infection, but not the late phases

Staphylococcus aureus (S. aureus) is a highly virulent pathogen responsible for chronic infections such as osteomyelitis. Although its interaction with the host immune system has been widely studied, the specific role of inflammasomes in regulating the infection within macrophages remains unclear. We investigated this question using bone marrow-derived macrophages infected with S. aureus and observed a significant reduction in intracellular bacterial load beginning at 18 hours post-infection (hpi), which continued through 96 hpi. Notably, robust activation of the NLRP3 inflammasome--including inflammasome assembly, IL-1{beta} and GSDMD maturation, and pyroptosis--occurred only after 18 hpi. This led us to hypothesize that S. aureus suppresses inflammasome activation during early infection. Supporting this, infected BMDMs failed to respond robustly to LPS and nigericin up to 18 hpi, with partial recovery at later timepoints, suggesting that S. aureus initially inhibits NLRP3 signaling to persist within macrophages but is later counteracted by the host response.

immunology↗

bioRxiv2025

A Drosophila Tonic Motor Neuron Reinnervates Ectopic Muscles Fully Deprived of Native Tonic and Phasic Inputs

Motor neurons (MNs) form precise neuromuscular junctions (NMJs) during development, but the extent to which individual MNs can reinnervate fully denervated muscles in vivo remains poorly understood. In the Drosophila larva, each muscle is co- innervated by a tonic and a phasic glutamatergic MN. Here, we show that the tonic MN1 undergoes robust heterosynaptic sprouting and forms ectopic NMJs when neighboring muscles are deprived of both their native tonic and phasic inputs. This structural plasticity is not induced by silencing, but instead requires the physical ablation of adjacent MNs. Live imaging of the same MN1 axons in individual animals reveals that sprouting initiates early and expands progressively across larval stages. In contrast, phasic MNs show minimal remodeling, indicating that tonic MNs possess a greater intrinsic capacity for neuroplasticity. Notably, as MN1 establishes new synapses on targets it does not normally innervate, it redistributes pre-synaptic territory across both native and ectopic muscles. These findings identify a subtype-specific, injury-induced rewiring program in an intact motor circuit.

neuroscience↗

bioRxiv2025

NLRP3 inflammasome is regulated in osteoclasts through a Tmem178-dependent mechanism that restricts calcium influx

Osteoclasts (OCs) differentiate from macrophages in response to RANKL. Here, we investigated the role of the NLRP3 inflammasome in mouse macrophages, with or without exposure to RANKL. Unexpectedly, we found that NLRP3 expression gradually declined during osteoclastogenesis but could be restored with LPS treatment. LPS and nigericin robustly activated this inflammasome in macrophages, as expected, but not in OCs. Mechanistically, we identified Tmem178, a protein that restrains Ca2+ release from the endoplasmic reticulum (ER) and highly expressed in OCs, as an inhibitor of this inflammasome. Notably, NLRP3 inflammasome activation was robust in OCs lacking Tmem178 or wild-type (WT) OCs exposed to high calcium concentrations. In vivo studies demonstrated that under the conditions where OCs efficiently release Ca2+ from bone, inflammasome formation was enhanced. Furthermore, deletion of Nlrp3 rescued osteopenia in Tmem178-/- mice. Thus, we found that Tmem178 uniquely restricts Ca2+ release from ER in OCs, thereby suppressing NLRP3 inflammasome activation. One Sentence SummaryThe NLRP3 inflammasome is silenced in the OC lineage by Tmem178 to prevent pathological bone loss.

immunology↗

bioRxiv2025

Influence of simplifications on FE modelling of mandible and TMJ implants

End-stage temporomandibular joint (TMJ) disorders often necessitate joint replacement to restore bilateral mastication. Patient-specific TMJ implants typically rely on detailed in silico modelling derived from subject-specific computed tomography (CT) scans of the mandible. However, generating highly detailed finite element (FE) models is computationally expensive. Although structural simplifications of the mandible are known to influence mechanical behaviour, their quantitative impact on TMJ implant evaluation has not been systematically investigated. This study examines the influence of three modelling simplifications on stress-strain predictions in intact and implanted mandibles: (i) a detailed segmented mandible with tissue-specific material properties (Model 1), (ii) a simplified mandible comprising cortical bone only (Model 2), and (iii) a further simplified mandible excluding dental crowns (Model 3). Both narrow and standard TMJ implants were analysed under osseointegrated and non-osseointegrated conditions, resulting in fifteen FE models. Physiological clenching activities were simulated. Compared with the detailed model, simplified models showed reductions of up to 50% in maximum principal strain in bone and up to 44% in von Mises stress in TMJ implants, while preserving spatial stress-strain trends. These findings indicate that simplified models may be suitable for preliminary implant design, whereas detailed FE modelling remains essential for final pre-clinical evaluation.

bioengineering↗

bioRxiv2025

Benchmarking and optimizing Perturb-seq in differentiating human pluripotent stem cells

Perturb-seq is a powerful approach to systematically assess how genes and enhancers impact the molecular and cellular pathways of development and disease. However, technical challenges have limited its application in stem cell-based systems. Here, we benchmarked Perturb-seq across multiple CRISPRi modalities, on diverse genomic targets, in multiple human pluripotent stem cells, during directed differentiation to multiple lineages, and across multiple sgRNA delivery systems. To ensure cost-effective production of large-scale Perturb-seq datasets as part of the Impact of Genomic Variants on Function (IGVF) consortium, our optimized protocol dynamically assesses experiment quality across the weeks-long procedure. Our analysis of 1,996,260 sequenced cells across benchmarking datasets reveals shared regulatory networks linking disease-associated enhancers and genes with downstream targets during cardiomyocyte differentiation. This study establishes open tools and resources for interrogating genome function during stem cell differentiation.

genomics↗

bioRxiv2024

High-dimensional mediation analysis to elucidate the role of metabolites in the association between PFAS exposure and reduced SARS-CoV-2 IgG in pregnancy

We previously found that per- and polyfluoroalkyl substances (PFAS) mixture exposure is inversely associated with SARS-CoV-2 IgG (IgG) antibody levels in pregnant individuals. Here, we aim to identify metabolites mediating this relationship to elucidate the underlying biological pathways. This cross-sectional study included 59 pregnant participants from a US-based pregnancy cohort. Untargeted metabolomic profiling was performed using Liquid Chromatography-High Resolution Sass spectrometry (LC-HRMS), and weighted Quantile Sum (WQS) regression was applied to assess the PFAS and metabolites mixture effects on IgG. Metabolite indices positively or negatively associated with IgG levels were constructed separately and their mediation effects were examined independently and jointly. The PFAS- index was negatively associated with IgG levels (beta=-0.315, p<0.001), with PFHpS and PFHxS as major contributors. Two metabolite-indices were constructed, one positively (beta=1.249, p<0.001) and one negatively (beta=-1.200, p<0.001) associated with IgG. Key contributors for these indices included trigonelline, adipate, p-octopamine, and n-acetylproline. Analysis of a single mediator showed that 74.6% (95% CI: 45.9%, 98.0%) and 68.6% (95% CI: 41.8%, 94.1%) of the PFAS index-IgG total effect were mediated by the negative and positive metabolites-indices, respectively. Joint analysis of the metabolite-indices indicated a cumulative mediation effect of 83.8% (95% CI: 58.1%, 98.7%). Enriched pathways associated with these metabolites indices were phenylalanine, tyrosine, and tryptophan biosynthesis and arginine metabolism. We observed significant mediation effects of plasma metabolites on the PFAS-IgG relationship, suggesting that PFAS is associated with alteration in the balance of plasma metabolites that contributes to reduced plasma IgG production.

bioinformatics↗

bioRxiv2024

Biomechanical Evaluation of Temporomandibular Joint Implants Under Complete Mastication Cycle

To ensure the long-term success of temporomandibular joint (TMJ) implants, it is imperative to understand their biomechanical performances. This study aims to compare the biomechanical performance of two stock implants (narrow and standard) under unilateral and bilateral clenching during both osseointegrated and non-osseointegrated conditions. Finite element models of a human mandible were developed from QCT data, with the left TMJ being replaced by the implants. Six clenching tasks were simulated to evaluate stress and strain distributions in the mandible and implants. Ipsilateral clenching produced higher mandibular strains, while contralateral clenching generated larger implant stresses. Furthermore, intercuspal biting was found to have produced the highest strain (1750-1880 {micro}{varepsilon}) and stress ([~]17 MPa) in the mandible. Osseointegration reduced stresses (up to 0.14 MPa) and strains (up to 30 {micro}{varepsilon}) in mandible as well as stresses in mandibular components (up to 48 MPa) and screws (up to 71 MPa). However, during non-osseointegrated conditions, stresses in cortical bone were higher for standard TMJ implant as compared to narrow implant. This suggests possible preference of narrow implant over standard ones.

bioengineering↗

bioRxiv2024

Synovial fluid transcriptome dynamics in osteoarthritis progression: Implications in pathogenesis

BackgroundOsteoarthritis, a degenerative joint disease associated with various pathological manifestations in the joint including cartilage loss, alterations in subchondral bone and synovial inflammation. ObjectiveThis study aimed to elucidate the transcriptional and molecular changes in synovial fluid associated with OA progression, focusing on differential gene expression and pathway enrichment across OA grades. MethodologyPatients with different OA grades were recruited from PGIMER, Chandigarh, following the KL classification. Microarray analysis was conducted to study the transcriptional profiles in different OA grades using a fold-change (FC) cutoff of 2 and a p-value cutoff of 0.05, followed by pathway analysis performed using GSEA and STRING database. Selected genes from microarray and pathway analysis were validated using qRT-PCR. ResultsMicroarray analysis reveals distinct gene expression patterns corresponding to different OA stages (KL grade 2 to KL grade 4). Notably, the upregulation of AMTN and DKK2, alongside the downregulation of MSLN, highlighted their roles in pathological mineralization and disrupted bone remodeling in OA. Pathway enrichment analysis revealed significant changes in immune response, inflammation related pathways and cellular processes such as autophagy and programmed cell death, indicating their involvement in disease progression. Furthermore, mitochondrial dysfunction and impaired autophagy were linked to increased inflammation in advanced OA. ConclusionThese findings suggest that targeting mineralization and inflammatory pathways could offer novel therapeutic avenues for OA management.

pathology↗

bioRxiv2024

Broad-spectrum RNA antiviral inspired by ISG15-/- deficiency

Type I interferons (IFN-I) are cytokines with potent antiviral and inflammatory capacities. IFN-I signaling drives the expression of hundreds of IFN-I stimulated genes (ISGs), whose aggregate function results in the control of viral infection. A few of these ISGs are tasked with negatively regulating the IFN-I response to prevent overt inflammation. ISG15 is a negative regulator whose absence leads to persistent, low-grade elevation of ISG expression and concurrent, self-resolving mild autoinflammation. The limited breadth and low-grade persistence of ISGs expressed in ISG15 deficiency are sufficient to confer broad-spectrum antiviral resistance. Inspired by ISG15 deficiency, we have identified a nominal collection of 10 ISGs that recapitulate the broad antiviral potential of the IFN-I system. The expression of the 10 ISG collection in an IFN-I non-responsive cell line increased cellular resistance to Zika, Vesicular Stomatitis, Influenza A (IAV), and SARS-CoV-2 viruses. A deliverable prophylactic formulation of this syndicate of 10 ISGs significantly inhibited IAV PR8 replication in vivo in mice and protected hamsters against a lethal SARS-CoV-2 challenge, suggesting its potential as a broad-spectrum antiviral against many current and future emerging viral pathogens. One-Sentence SummaryHuman inborn error of immunity-guided discovery and development of a broad-spectrum RNA antiviral therapy

immunology↗

bioRxiv2023

A study of machine learning techniques for Automated Karyotyping System

Genetic abnormalities constitute a considerable share of all the existing societal healthcare issues. There has been a dire need for the automation of chromosomal analysis, hence supporting laboratory workers in effective classification and identifying such abnormalities. Nevertheless, with many modern image processing techniques, like Karyotyping, improved the life expectancy and the quality of life of such cases. The standard image-based analysis procedures include Pre-processing, Segmentation, Feature extraction, and Classification of images. When explicitly considering Karyotyping, the processes of Segmentation and Classification of chromosomes have been the most complex, with much existing literature focusing on the same. Various model-based machine learning models have proven to be highly effective in solving existing issues and building an artificial intelligence-based, autonomous-centric karyotyping system. An autonomous Karyotyping System will connect the pre-processing, Segmentation, and classification of metaphase images. The review focuses on machine learning-based algorithms for efficient classification accuracy. The study has the sole motive of moving towards an effective classification method for karyotype metaphase images, which will eventually predict the fetuss abnormalities more effectively. The studys results shall benefit future researchers working in this area.

bioengineering↗

bioRxiv2023

Chemotherapy activates inflammasomes to cause inflammation-associated bone loss

Chemotherapy is a widely used treatment for a variety of solid and hematological malignancies. Despite its success in improving the survival rate of cancer patients, chemotherapy causes significant toxicity to multiple organs, including the skeleton, but the underlying mechanisms have yet to be elucidated. Using tumor-free mouse models, which are commonly used to assess direct off-target effects of anti-neoplastic therapies, we found that doxorubicin caused massive bone loss in wild-type mice, a phenotype associated with increased number of osteoclasts, leukopenia, elevated serum levels of danger-associated molecular patterns (DAMPs; e.g., cell-free DNA and ATP) and cytokines (e.g., IL-1{beta} and IL-18). Accordingly, doxorubicin activated the absent in melanoma (AIM2) and NLR family pyrin domain containing 3 (NLRP3) inflammasomes in macrophages and neutrophils, causing inflammatory cell death pyroptosis and NETosis, which correlated with its leukopenic effects. Moreover, the effects of this chemotherapeutic agent on cytokine secretion, cell demise, and bone loss were attenuated to various extent in conditions of AIM2 and/or NLRP3 insufficiency. Thus, we found that inflammasomes are key players in bone loss caused by doxorubicin, a finding that may inspire the development of a tailored adjuvant therapy that preserves the quality of this tissue in patients treated with this class of drugs.

cell biology↗

bioRxiv2023

Effects of aluminum-salt, CpG and emulsion adjuvants on the stability and immunogenicity of a virus-like particle displaying the SARS-CoV-2 receptor binding domain (RBD)

Second-generation COVID-19 vaccines with improved immunogenicity (e.g., breadth, duration) and availability (e.g., lower costs, refrigerator stable) are needed to enhance global coverage. In this work, we formulated a clinical-stage SARS-CoV-2 receptor binding domain (RBD) virus-like particle (VLP) vaccine candidate (IVX-411) with widely available adjuvants. Specifically, we assessed the in vitro storage stability and in vivo mouse immunogenicity of IVX-411 formulated with aluminum-salt adjuvants (Alhydrogel, AH and Adjuphos, AP), without or with the TLR-9 agonist CpG-1018 (CpG), and compared these profiles to IVX-411 adjuvanted with an oil-in-water nano-emulsion (AddaVax, AV). Although IVX-411 bound both AH and AP, lower binding strength of antigen to AP was observed by Langmuir binding isotherms. Interestingly, AH- and AP-adsorbed IVX-411 had similar storage stability profiles as measured by antigen binding assays (competitive ELISAs), but the latter displayed higher pseudovirus neutralizing titers (pNT) in mice, at levels comparable to titers elicited by AV-adjuvanted IVX-411. CpG addition to alum (AP or AH) resulted in a marginal trend of improved pNTs in stressed samples only, yet did not impact the storage stability profiles of IVX-411. In contrast, previous work with AH-formulations of a monomeric RBD antigen showed greatly improved immunogenicity and decreased stability upon CpG addition to alum. At elevated temperatures (25, 37{degrees}C), IVX-411 formulated with AH or AP displayed decreased in vitro stability compared to AV-formulated IVX-411and this rank-ordering correlated with in vivo performance (mouse pNT values). This case study highlights the importance of optimizing antigen-adjuvant interactions to develop low cost, aluminum-salt adjuvanted recombinant subunit vaccine candidates.

immunology↗

bioRxiv2022

Molecular engineering of a cryptic epitope in Spike RBD improves manufacturability and neutralizing breadth against SARS-CoV-2 variants

There is a continued need for sarbecovirus vaccines that can be manufactured and distributed in low- and middle-income countries (LMICs). Subunit protein vaccines are manufactured at large scales at low costs, have less stringent temperature requirements for distribution in LMICs, and several candidates have shown protection against SARS-CoV-2. We previously reported an engineered variant of the SARS-CoV-2 Spike protein receptor binding domain antigen (RBD-L452K-F490W; RBD-J) with enhanced manufacturability and immunogenicity compared to the ancestral RBD. Here, we report a second-generation engineered RBD antigen (RBD-J6) with two additional mutations to a hydrophobic cryptic epitope in the RBD core, S383D and L518D, that further improved expression titers and biophysical stability. RBD-J6 retained binding affinity to human convalescent sera and to all tested neutralizing antibodies except antibodies that target the class IV epitope on the RBD core. K18-hACE2 transgenic mice immunized with three doses of a Beta variant of RBD-J6 displayed on a virus-like particle (VLP) generated neutralizing antibodies (nAb) to nine SARS-CoV-2 variants of concern at similar levels as two doses of Comirnaty. The vaccinated mice were also protected from challenge with Alpha or Beta SARS-CoV-2. This engineered antigen could be useful for modular RBD-based subunit vaccines to enhance manufacturability and global access, or for further development of variant-specific or broadly acting booster vaccines.

bioengineering↗