Biology subjects

Kumari, M.

Publications and source records attributed to Kumari, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Avian Diversity and Community Structure in Magadh University Campus Landscape, Bodh Gaya

University campuses function as important refugia for biodiversity within an increasingly urbanizing landscape. Magadh University (MU) is among the oldest universities of Bihar, India, located in Bodh Gaya, a place of spiritual tourism, near a UNESCO heritage site. The campus hosts a mosaic of heterogeneous habitats, rich vegetation and dense canopy cover along with varied range of anthropogenic interferences. This study mainly focusses on measuring the alpha diversity of avifaunal species and persistence across four seasons from July 2025 to June 2026 at MU. A total of 78 bird species belonging to 41 families and 16 orders were recorded using a combination of point count, line transect and acoustic monitoring. The study revealed that the order Passeriformes was the most species-rich (47.44%). Muscicapidae was the most species-rich family (6 species). Relatively high Shannon diversity (H') = 3.278, low Simpson's dominance (D = 0.062) and a high Pielou's evenness (J) = 0.751 indicated the avian community was distributed across diverse assemblage. Species richness estimates from Chao1 (78.5), iChao1 (79.02) and ACE (79.53) were comparable to recorded 78 species, indicating sampling completeness. Observed species were further classified into five major feeding guilds, majority of which were insectivorous species. 77 of the observed species were classified as Least Concern while Coracias benghalensis was categorized as Near Threatened. These findings demonstrate that the MU campus supports significant taxonomic, functional and temporal avian assemblage, highlighting the conservation values of the campus landscapes within rapidly urbanizing regions.

zoology↗

bioRxiv2026

Hepatic Differentiation of Human Pluripotent Stem Cells into Functional In Vitro Models Recapitulating Native Liver Complexity for MASLD Modelling

Human in vitro hepatic models that accurately recapitulate liver function are essential for fundamental and translational research; however, currently utilised models for disease modelling and drug discovery lack physiological fidelity and require prolonged culture time. Here, we present a streamlined 10-day protocol for efficient and reproducible differentiation of human pluripotent stem cells into hepatocyte like cells (HLCs) and hepatic liver organoids (HLOs). Both models exhibited mature hepatocyte differentiation, as evidenced by albumin secretion and CYP3A4 metabolic activity. Interestingly, HLOs display enhanced multicellular complexity incorporating endothelial, stellate, and macrophage populations along with hepatocytes, thereby more closely recapitulating the native liver microenvironment than HLCs. Here, steatosis was induced in both platforms, which resulted in triglyceride accumulation and upregulated lipogenic markers (DGAT1, DGAT2). However, only HLOs recapitulated advanced disease characteristics, including inflammatory (IL-10) and fibrotic (alpha SMA, COL1A1) responses. Resmetirom, a thyroid hormone receptor-{beta} agonist, significantly reduced steatosis and restored molecular signatures in both models. Additionally, transplanted HLOs demonstrated prolonged survival and displayed host-derived vascularization, thereby validating in vivo maturation. Collectively, HLCs provides a rapid and physiologically relevant liver model, with HLOs offering superior utility for disease modelling, therapeutic evaluation, and regenerative applications due to their enhanced functional and physiological relevance.

cell biology↗

bioRxiv2026

Solvent ordering in a fully packaged RNA bacteriophage and the mechanics of genome delivery

Self-assembly of an RNA virus requires a thermodynamic state stable enough to confine the highly charged genome yet primed for genome delivery. By simulating the behavior of every atom in a packaged bacteriophage, we determined the physical factors enabling such a state to emerge. We show that the electrical charge of the RNA genome is neutralized by both a cloud of mobile counterions and polarized water that exhibits a long-range order despite stochastic motion of the unstructured parts of the genome. Acting as an intermolecular glue, the solvent equipoises self-repulsion of the RNA genome with attraction of RNA to specific sites at the capsid, accommodating the mechanical stress produced by the capsids fluctuations. Simulations of genome extraction show that specific RNA-protein contacts can withstand extreme forces, supporting mechanical extraction as a mechanism of genome delivery. Together, our findings detail how self-assembled viruses balance the conflicting biophysical demands of confinement and infection.

biophysics↗

bioRxiv2026

Cardiomyocytes execute pro- and anti-inflammatory signaling of IFNγ-induced GBP5 by differential regulation of the inflammasome

Infiltration of conventional immune cells has been ascribed as the fundamental drivers of innate immune signaling in the damaged myocardium. However, the emerging intrinsic immunoregulatory potential of cardiomyocytes still remains poorly understood. Interferon gamma (IFN{gamma}) is a pleiotropic cytokine with context-dependent detrimental as well protective role in regulating cardiac inflammatory circuits. The prevailing view of IFN{gamma} as a prime pro-inflammatory cytokine has been challenged due to its paradoxical actions both as an inducer as well as negative regulator of inflammation, but the players involved in these converse processes remains enigmatic. Here we show that cardiomyocytes exhibit a cell-autonomous immunocompetent response upregulating innate inflammatory signaling upon type I and type II IFN stimulus. Notably, hiPSC-derived cardiomyocytes display a robust increase in guanylate binding protein 5 (GBP5), one of the major IFN{gamma}-induced GTPase involved in inflammasome signaling, followed by upregulation of AIM2/CASP1 pathway whereas NLRP3 levels remain unaltered by IFN{gamma} stimulation. GBP5 knockdown and overexpression studies in hiPSC-derived cardiomyocytes identify GBP5/TGF{beta} axis as a non-canonical anti-inflammatory feedback regulation on the IFN{gamma}-induced inflammatory cascade.

cell biology↗

bioRxiv2026

OmniDetect: a plant-produced universal IgG binder replacing secondary antibodies in immunoassays

High sensitivity in immunodetection technologies has long been a priority for both diagnostic kit development and routine laboratory research. We developed a recombinant fusion protein, OmniDetect-G3, as an alternative to conventional HRP-conjugated secondary antibodies, and successfully produced it in plants. OmniDetect-G3 binds to primary IgG antibodies regardless of host species, and also recognizes chicken IgY. In comparative analyses, OmniDetect-G3 exhibits 165-381% higher sensitivity than commercial secondary antibodies in western blot analysis and 30%-1145% higher sensitivity in ELISA, depending on commercial products tested. Moreover, OmniDetect-G3 showed robust performance when used with sera from vaccinated animals (porcine and bovine). The chemiluminescence signal generated by OmniDetect-G3 remained stable up to 30 minutes after reaction initiation. These findings indicate that plant-produced OmniDetect-G3 has strong potential as a universal mimetic to animal-derived HRP-conjugated secondary antibodies, offering simplified immunoassay workflows and improved detection efficiency.

immunology↗

bioRxiv2026

Multicellular signaling and partial recovery define reverse cardiac remodeling

Heart failure results from maladaptive multicellular remodeling triggered by sustained biomechanical stress. Although mechanical unloading can promote reverse remodeling, recovery is frequently incomplete and its mechanistic basis remains unclear. Using a reversible murine pressure-overload model combined with bulk and single-nucleus transcriptomics, we demonstrate that reverse remodeling represents an actively maintained yet constrained multicellular state. Unloading improved cardiac function and partially restored extracellular matrix and metabolic programs, whereas inflammatory and mitochondrial dysfunction signatures persisted. Cardiomyocytes and endothelial cells largely re-established homeostatic transcriptional states, while fibroblasts retained activated programs that dominated residual pathology. Multicellular factor analysis delineated a reversible metabolic stress program and a persistent inflammatory-mitochondrial program coordinated across cardiac cell types. Cell-cell communication analysis identified lymphatic endothelial cells as key instructive regulators of recovery. Notably, lymphatic-derived Reelin directly suppressed pathological fetal gene activation in murine and human cardiomyocytes, uncovering a previously unrecognized lymphoangiocrine mechanism that constrains myocardial recovery in chronic heart failure.

molecular biology↗

bioRxiv2025

TRIM24 preserves cardiomyocyte immune quiescence by repressing interferon/STAT signaling

Innate immune activation in cardiomyocytes is a key driver of inflammatory heart disease and heart failure progression, yet the mechanisms by which cardiomyocytes maintain transcriptional immune quiescence remain poorly understood. TRIM24, a multidomain chromatin reader implicated in cancer and inflammation, has not been previously studied in the heart. Here, we investigated whether TRIM24 regulates interferon/STAT-driven inflammatory programs and paracrine signaling in cardiomyocytes. Single-nucleus RNA sequencing revealed a pronounced downregulation of TRIM24 specifically in cardiomyocytes from human ischemic cardiomyopathy, a change not detected by bulk RNA-sequencing in either human or mouse myocardial infarction samples, likely due to masking by non-cardiomyocyte cell populations. Fractionated protein analysis further demonstrated that TRIM24 is enriched in cardiomyocyte nuclei. Functional studies in neonatal rat ventricular cardiomyocytes showed that TRIM24 represses interferon-stimulated and STAT-dependent genes, including Mx1, Irf7, and Ifit3. ChIP-Seq revealed TRIM24 occupancy at STAT-bound regulatory regions, suggesting cooperative suppression of inflammatory gene networks. Mechanistically, TRIM24 decreased Stat1a/b and Stat3 transcription, reduced protein abundance, and inhibited phosphorylation independently of proteasomal degradation; these effects were partially reversible by bromodomain inhibition. Functionally, TRIM24 overexpression dampened paracrine macrophage recruitment, whereas TRIM24 depletion amplified it. Collectively, these findings identify TRIM24 as a cardiomyocyte-enriched chromatin regulator that restrains STAT1/3 signaling and suppresses paracrine inflammatory activation. TRIM24 acts as a transcriptional safeguard of immune quiescence in the heart and represents a potential therapeutic target for limiting cardiac inflammation.

molecular biology↗

bioRxiv2025

Poly(ADP-ribose) Polymerase 1 Deficiency Attenuates Amyloid Pathology, Neurodegeneration, and Cognitive Decline in a Familial Alzheimer Disease Model

Poly(ADP-ribose) (PAR) polymerase-1 (PARP1) has been implicated in DNA damage responses and neuroinflammation in Alzheimers disease (AD), yet its role in amyloid-{beta} (A{beta}) pathology remains unclear. Here, we show that PARP1 activation drives A{beta} pathology and neurodegeneration. Using a sensitive ELISA, we observed significantly elevated PAR levels in the cerebrospinal fluid (CSF) of patients with mild cognitive impairment (MCI) and AD compared to controls. In vitro, oligomeric A{beta}1-42 activated PARP1 and induced DNA damage, while genetic or pharmacological inhibition of PARP1 conferred neuroprotection. In vivo, PARP1 knockout in the 5XFAD mouse model of amyloidosis led to reduced amyloid plaque burden, preserved synaptic and neuronal integrity, attenuated glial activation and neuroinflammation, and rescued cognitive deficits. Mechanistically, PARP1 deficiency decreased amyloid precursor protein (APP) and BACE1 levels, altered {gamma}-secretase complex composition, and enhanced A{beta} degradation via neprilysin. These findings position PARP1 as a critical mediator of A{beta} toxicity and neurodegeneration, suggesting its inhibition as a promising therapeutic strategy for AD. Significance StatementOur study identifies poly(ADP-ribose) (PAR) as an elevated biomarker in the cerebrospinal fluid of patients with mild cognitive impairment and Alzheimers disease, correlating with established markers of amyloid pathology. We demonstrate that PARP1, the enzyme responsible for PAR synthesis, is activated by neurotoxic A{beta}1-42 and mediates neuronal death, amyloid plaque formation, neuroinflammation, and cognitive deficits in a mouse model of AD. Importantly, genetic ablation of PARP1 not only protects neurons from A{beta} toxicity but also reduces amyloid burden by suppressing A{beta} production and enhancing its degradation. These findings highlight PARP1 as a critical regulator of amyloid pathology and neurodegeneration, and suggest that PARP1 inhibition may offer a promising therapeutic avenue for Alzheimers disease by simultaneously targeting multiple pathogenic mechanisms.

neuroscience↗

bioRxiv2025

The Ca2+ Channel CYCLIC NUCLEOTIDE GATED CHANNEL13 (CNGC13) regulates systemic wound signalling and immunity against Spodoptera herbivory

Insect herbivory elicits rapid and complex signalling responses in plants, including membrane depolarization, cytosolic Ca2+ elevation and activation of jasmonate-mediated defense pathways in local and systemic leaves. These early events are orchestrated by calcium-permeable channels and regulatory components that generate stimulus-specific cytosolic Ca2+ signatures. However, the molecular mechanisms that generate long-distance Ca2+ propagation and systemic immune activation on herbivory remain poorly defined. Here, we identify CYCLIC NUCLEOTIDE GATED CHANNEL13 (CNGC13) as a novel plasma membrane-localized, phloem-expressed Ca2+ channel that is essential for systemic wound signalling and defense against lepidopteran pest, Spodoptera litura in Arabidopsis thaliana. CNGC13 is rapidly induced by wounding and herbivory, mediates cytosolic Ca2+ influx, and is required for efficient propagation of Ca2+ signals from wounded to distal leaves. Loss of CNGC13 compromises the thioglucosidase-dependent breakdown of aliphatic glucosinolates into aglucones/isothiocyanates within the vascular tissue, which are essential for wounding-induced systemic Ca2+ wave propagation. Consequently, cngc13 mutants display impaired systemic jasmonate accumulation in distal leaves, reduced glucosinolate levels and enhanced herbivore susceptibility. CNGC13 is also required for AtPep-induced Ca2+ elevation and Reactive Oxygen Species (ROS) signalling and interacts with the receptor kinase, PEPR2, implicating it in DAMP-mediated immune responses. Although CNGC13 and CNGC19 function cooperatively in herbivore defense, they do not physically interact, suggesting independent but converging roles. Our study identifies CNGC13 as a vasculature-localized Ca2+-permeable channel that functions downstream of PEPR2 receptor, to sustain systemic signalling, operating in a distinct yet converging pathway alongside known glutamate receptor-like channels during long-distance wound responses. SignificancePlants must detect and respond to insect herbivory rapidly by activating systemic immunity to trigger defense responses. Calcium (Ca2+) signalling plays a central role in this defense network, yet the identities and specific functions of Ca2+ channels involved in long-distance herbivory signalling remain poorly understood. Here, we identify the plasma membrane-localized channel CYCLIC NUCLEOTIDE GATED CHANNEL13 (CNGC13) as a key integrator of mechanical damage perception, ricca factor-mediated systemic signalling, and jasmonate-dependent defense against Spodoptera herbivory in Arabidopsis. CNGC13 facilitates systemic Ca2+ wave propagation, activates jasmonate and glucosinolate biosynthesis, and promotes the perception of damage-associated molecular pattern (DAMP) molecules to confer herbivore resistance. This work uncovers a previously uncharacterized calcium channel that plays a crucial dual role in systemic wound signalling.

plant biology↗

bioRxiv2024

Mitophagy Facilitates Cytosolic Proteostasis to Preserve Cardiac Function

BackgroundProtein quality control (PQC) is critical for maintaining sarcomere structure and function in cardiac myocytes, and mutations in PQC pathway proteins, such as CRYAB (arginine to glycine at position 120, R120G) and BAG3 (proline to lysine at position 209, P209L) induce protein aggregate pathology with cardiomyopathy in humans. Novel observations in yeast and mammalian cells demonstrate mitochondrial uptake of cytosolic protein aggregates. We hypothesized that mitochondrial uptake of cytosolic protein aggregates and their removal by mitophagy, a lysosomal degradative pathway essential for myocardial homeostasis, facilitates cytosolic protein quality control in cardiac myocytes. MethodsMice with inducible cardiac myocyte specific ablation of TRAF2 (TRAF2icKO), which impairs mitophagy, were assessed for protein aggregates with biochemical fractionation and super-resolution imaging in comparison to floxed controls. Induced pluripotent stem cell (iPSC)-derived cardiac myocytes with R120G knock-in to the CRYAB locus were assessed for localization of the CRYAB protein. Transgenic mice expressing R120G CRYAB protein (R120G-TG) were subjected to both TRAF2 gain-of-function (with AAV9-cardiac Troponin T promoter-driven TRAF2 transduction) and TRAF2 loss-of-function (with tamoxifen-inducible ablation of one Traf2 allele) in cardiac myocytes to determine the effect of mitophagy modulation on cardiac structure, function, and protein aggregate pathology. ResultsCardiomyocyte-specific ablation of TRAF2 results accumulation of mitochondrial and cytosolic protein aggregates and DESMIN mis-localization to protein aggregates. Isolated mitochondria take up cardiomyopathy-associated aggregate-prone cytosolic chaperone proteins, namely arginine to glycine (R120G) CRYAB mutant and proline to lysine (P209L) BAG3 mutant. R120G-CRYAB mutant protein increasingly localizes to mitochondria in human and mouse cardiomyocytes. R120G-TG mice demonstrate upregulation of TRAF2 in the mitochondrial fraction with increased mitophagy as compared with wild type. Adult-onset inducible haplo-insufficiency of TRAF2 resulted in accelerated mortality, impaired left ventricular systolic function and increased protein aggregates in R120G-TG mice as compared with controls. Conversely, AAV9-mediated TRAF2 transduction in R120G-TG mice reduced mortality and attenuated left ventricular systolic dysfunction, with reduced protein aggregates and restoration of normal localization of DESMIN, a cytosolic scaffolding protein chaperoned by CRYAB, as compared with control AAV9-GFP group. ConclusionsTRAF2-mediated mitophagy in cardiac myocytes facilitates removal of cytosolic protein aggregates and can be stimulated to ameliorate proteotoxic cardiomyopathy.

cell biology↗

bioRxiv2024

Phosphorylation of CRYAB Induces a Condensatopathy to Worsen Post-Myocardial Infarction Left Ventricular Remodeling.

Protein aggregates are emerging therapeutic targets in rare monogenic causes of cardiomyopathy and amyloid heart disease, but their role in more prevalent heart failure syndromes remains mechanistically unexamined. We observed mis-localization of desmin and sarcomeric proteins to aggregates in human myocardium with ischemic cardiomyopathy and in mouse hearts with post-myocardial infarction ventricular remodeling, mimicking findings of autosomal-dominant cardiomyopathy induced by R120G mutation in the cognate chaperone protein, CRYAB. In both syndromes, we demonstrate increased partitioning of CRYAB phosphorylated on serine-59 to NP40-insoluble aggregate-rich biochemical fraction. While CRYAB undergoes phase separation to form condensates, the phospho-mimetic mutation of serine-59 to aspartate (S59D) in CRYAB mimics R120G-CRYAB mutants with reduced condensate fluidity, formation of protein aggregates and increased cell death. Conversely, changing serine to alanine (phosphorylation-deficient mutation) at position 59 (S59A) restored condensate fluidity, and reduced both R120G-CRYAB aggregates and cell death. In mice, S59D CRYAB knock-in was sufficient to induce desmin mis-localization and myocardial protein aggregates, while S59A CRYAB knock-in rescued left ventricular systolic dysfunction post-myocardial infarction and preserved desmin localization with reduced myocardial protein aggregates. 25-Hydroxycholesterol attenuated CRYAB serine-59 phosphorylation and rescued post-myocardial infarction adverse remodeling. Thus, targeting CRYAB phosphorylation-induced condensatopathy is an attractive strategy to counter ischemic cardiomyopathy.

cell biology↗

bioRxiv2024

Systematic investigation of interindividual variation of DNA methylation in human whole blood

Interindividual genetic variability is well characterised, but we still lack a complete catalogue of loci displaying variable and stable epigenetic patterns. Here, we report a catalogue of stable and variable interindividual DNA methylation in human whole blood by analysing the DNA methylation patterns in 3642 individuals using the IlluminaEPIC array. Our results showed that 41,216 CpGs display stable methylation (SMPs) and 34,972 CpGs display variable methylation levels (VMPs). This catalogue will be a useful resource for interpretation of results when associating epigenetic signals to phenotypes. We observed that SMPs are highly enriched in CpG islands, depleted at CpG shelves and open sea regions of the genome. In addition, we found that the VMPs were under higher genetic control than the SMPs and that trans mQTL pairs are often located in the same TAD or connected by chromatin loops. A subset of these VMPs (784) were classified as putative epialleles and our results demonstrate that these loci located in regulatory regions exhibit a link with gene expression.

genomics↗

bioRxiv2022

Epigenetic markers of adverse lifestyle identified among night shift workers

BackgroundEpigenetic changes in the form of DNA methylation (DNAm) may act as biological markers of risk factors or adverse health states. We investigated associations between night shift work and established DNAm predictors of lifestyle, and compared them with those observed between night shift work and self-reported or conventionally-measured phenotypes. MethodsIn two cohort studies, Generation Scotland (GS) (n=7,028) and Understanding Society (UKHLS) (n=1,175), we evaluated associations between night shift work and four lifestyle factors (body mass index, smoking, alcohol, education) using both conventionally-measured phenotypes and DNA methylation-based scores proxying the phenotypes. DNA methylation-based measures of biological ageing were also generated using six established "epigenetic clocks". Meta-analysis of GS and UKHLS results was conducted using inverse-variance weighted fixed effects. ResultsNight shift work was associated with higher BMI (0.79; 95%CI 0.02, 1.56; p=0.04) and lower education (-0.18; -0.30, -0.07; p=0.002). There was weak evidence of association between night shift work and DNAm scores for smoking (0.06, -0.03, 0.15; p=0.18) and education (-0.24; -0.49, 0.01; p=0.06) in fully adjusted models. Two of the epigenetic age measures demonstrated higher age acceleration among night shift workers (0.80; 0.42, 1.18; p<0.001 for GrimAge and 0.46; 0.00, 0.92; p=0.05 for PhenoAge). ConclusionsNight shift work is associated with phenotypic and DNAm-based measures of lower education. Night shift work was also related to DNAm predictors of smoking and ageing.

genetics↗

bioRxiv2022

An Efficient Approach for SARS-CoV-2 Monoclonal Antibody Production via Modified mRNA-LNP Immunization

Throughout the COVID-19 pandemic, many prophylactic and therapeutic drugs have been evaluated and introduced. Among these treatments, monoclonal antibodies (mAbs) that bind to and neutralize SARS-CoV-2 virus have been applied as complementary and alternative treatments to vaccines. Although different methodologies have been utilized to produce mAbs, traditional hybridoma fusion technology is still commonly used for this purpose due to its unmatched performance record. In this study, we coupled the hybridoma fusion strategy with mRNA-lipid nanoparticle (LNP) immunization. This time-saving approach can circumvent biological and technical hurdles, such as difficult to express membrane proteins, antigen instability, and the lack of posttranslational modifications on recombinant antigens. We used mRNA-LNP immunization and hybridoma fusion technology to generate mAbs against the receptor binding domain (RBD) of SARS-CoV-2 spike (S) protein. Compared with traditional protein-based immunization approaches, inoculation of mice with RBD mRNA-LNP induced higher titers of serum antibodies. In addition, the mAbs we obtained can bind to SARS-CoV-2 RBDs from several variants. Notably, RBD-mAb-3 displayed particularly high binding affinities and neutralizing potencies against both Alpha and Delta variants. In addition to introducing specific mAbs against SARS-CoV-2, our data generally demonstrate that mRNA-LNP immunization may be useful to quickly generate highly functional mAbs against emerging infectious diseases.

immunology↗

bioRxiv2022

Broadly neutralizing antibodies against Omicron variants of SARS-CoV-2 derived from mRNA-lipid nanoparticle-immunized mice

The COVID-19 pandemic continues to threaten human health worldwide, as new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged. Currently, the predominant circulating strains around the world are Omicron variants, which can evade many therapeutic antibodies. Thus, the development of new broadly neutralizing antibodies remains an urgent need. In this work, we address this need by using the mRNA-lipid nanoparticle immunization method to generate a set of Omicron-targeting monoclonal antibodies. Five of our novel K-RBD-mAbs show strong binding and neutralizing activities toward all SARS-CoV-2 variants of concern (Alpha, Beta, Gamma, Delta and Omicron). Notably, the epitopes of these five K-RBD-mAbs are overlapping and localized around K417 and F486 of the spike protein receptor binding domain (RBD). Chimeric derivatives of the five antibodies (K-RBD-chAbs) neutralize Omicron sublineages BA.1 and BA.2 with low IC50 values that range from 5.7 to 12.9 ng/mL. Additionally, we performed antibody humanization on a broadly neutralizing chimeric antibody to create K-RBD-hAb-62, which still retains excellent neutralizing activity against Omicron. Our results collectively suggest that these five therapeutic antibodies may effectively combat current and emerging SARS-CoV-2 variants, including Omicron BA.1 and BA.2. Therefore, the antibodies can potentially be used as universal neutralizing antibodies against SARS-CoV-2.

immunology↗

bioRxiv2022

Evaluation of nanopore sequencing for epigenetic epidemiology: a comparison with DNA methylation microarrays

Most epigenetic epidemiology to date has utilized microarrays to identify positions in the genome where variation in DNA methylation is associated with environmental exposures or disease. However, these profile less than 3% of DNA methylation sites in the human genome, potentially missing affected loci and preventing the discovery of disrupted biological pathways. Third generation sequencing technologies, including Nanopore sequencing, have the potential to revolutionise the generation of epigenetic data, not only by providing genuine genome-wide coverage but profiling epigenetic modifications direct from native DNA. Here we assess the viability of using Nanopore sequencing for epidemiology by performing a comparison with DNA methylation quantified using the most comprehensive microarray available, the Illumina EPIC array. We implemented a CRISPR-Cas9 targeted sequencing approach in concert with Nanopore sequencing to profile DNA methylation in three genomic regions to attempt to rediscover genomic positions that existing technologies have shown are differentially methylated in tobacco smokers. Using Nanopore sequencing reads, DNA methylation was quantified at 1,779 CpGs across three regions, providing a finer resolution of DNA methylation patterns compared to the EPIC array. The correlation of estimated levels of DNA methylation between platforms was high. Furthermore, we identified 12 CpGs where hypomethylation was significantly associated with smoking status, including 10 within the AHRR gene. In summary, Nanopore sequencing is a valid option for identifying genomic loci where large differences in DNAm are associated with a phenotype and has the potential to advance our understanding of the role differential methylation plays in the aetiology of complex disease.

neuroscience↗

bioRxiv2022

Omicron-specific mRNA vaccine induced potent neutralizing antibody against Omicron but not other SARS-CoV-2 variants

The emerging SARS-CoV-2 variants of concern (VOC) harbor mutations associated with increasing transmission and immune escape, hence undermine the effectiveness of current COVID-19 vaccines. In late November of 2021, the Omicron (B.1.1.529) variant was identified in South Africa and rapidly spread across the globe. It was shown to exhibit significant resistance to neutralization by serum not only from convalescent patients, but also from individuals receiving currently used COVID-19 vaccines with multiple booster shots. Therefore, there is an urgent need to develop next generation vaccines against VOCs like Omicron. In this study, we develop a panel of mRNA-LNP-based vaccines using the receptor binding domain (RBD) of Omicron and Delta variants, which are dominant in the current wave of COVID-19. In addition to the Omicron- and Delta-specific vaccines, the panel also includes a "Hybrid" vaccine that uses the RBD containing all 16 point-mutations shown in Omicron and Delta RBD, as well as a bivalent vaccine composed of both Omicron and Delta RBD-LNP in half dose. Interestingly, both Omicron-specific and Hybrid RBD-LNP elicited extremely high titer of neutralizing antibody against Omicron itself, but few to none neutralizing antibody against other SARS-CoV-2 variants. The bivalent RBD-LNP, on the other hand, generated antibody with broadly neutralizing activity against the wild-type virus and all variants. Surprisingly, similar cross-protection was also shown by the Delta-specific RBD-LNP. Taken together, our data demonstrated that Omicron-specific mRNA vaccine can induce potent neutralizing antibody response against Omicron, but the inclusion of epitopes from other variants may be required for eliciting cross-protection. This study would lay a foundation for rational development of the next generation vaccines against SARS-CoV-2 VOCs.

microbiology↗

bioRxiv2022

Glycation renders alpha-synuclein oligomeric strain and modulates microglia activation

-Synuclein is known to involve in the pathogenesis of Parkinsons diseases (PD) and related disorders. However, it is unclear how its aggregation causes neuronal degeneration and neuroinflammation. Due to intrinsic disorder nature, -synuclein produces a large number of structural ensembles and diverse aggregation intermediates. The post-translational modifications add a new layer of complexity to the aggregation mechanism. Recently, it has been demonstrated that glycation of -synuclein restricts into oligomeric intermediates and causes neuronal toxicity. However, the understanding of aggregation mechanism, dopaminergic neuronal death, and neuroinflammation by the glycated -synuclein is yet to be elucidated. The present study aims to address how glycated synuclein differs in oligomerization and neuroinflammation. The glycation of -synuclein perturbs the aggregation kinetics and prevents the fibrilization through the alteration of surface charges of N-terminal domain residues which prevents membrane binding and seed amplification mechanism. Mass spectrometry-based proteomics analysis of BV2 cells treated with glycated oligomers provides evidence of alteration of endocytic mechanism, mitochondrial dysfunction, and inflammatory cascade. Here, we show that -synuclein oligomers strongly bind to TLR2 and activate the TLR2 mediated signaling. However, glycated -synuclein oligomers impair the TLR2 binding and compromise TLR2 signaling. Interestingly, we also find that the glycated -synuclein oligomers favor NLRP3 inflammasome mediated neuroinflammation compared to non- glycated -synuclein oligomers. In conclusion, our findings suggest that microglia response towards -synuclein is conformation-specific and glycated oligomers can contribute to neurodegeneration differently.

neuroscience↗