Biology subjects

Agrawal, A.

Publications and source records attributed to Agrawal, A..

At least 109 records · Page 6Linked to original sources

bioRxiv2020

Complimentary action of structured and unstructured domains of epsin supports clathrin-mediated endocytosis at high tension

Membrane tension plays an inhibitory role in clathrin-mediated endocytosis (CME) by impeding the transition of flat plasma membrane to hemispherical clathrin-coated structures (CCSs). Membrane tension also impedes the transition of hemispherical domes to omegashaped CCSs, a necessary step before their internalization via dynamin-mediated membrane scission. However, CME is not completely halted in cells under high tension conditions. Here we find that epsin, a membrane bending protein which inserts its N-terminus H0 helix into lipid bilayer, supports flat-to-dome transition and increases the stability of CCSs at high tension. This discovery is supported by molecular dynamic simulation of the epsin N-terminal homology (ENTH) domain that becomes more structured when embedded in a lipid bilayer. In addition, epsin has an intrinsically disordered protein (IDP) C-terminus domain which induces membrane curvature via steric repulsion. Insertion of H0 helix into lipid bilayer is not sufficient for stable epsin recruitment as deleting the IDP domain in epsin renders it cytosolic. Epsins binding to adaptor protein 2 and clathrin is critical for epsins association with CCSs under high tension conditions, supporting the importance of multivalent interactions in CCSs. Together, our results support a model where the ENTH and IDP domains of epsin have complementary roles to ensure CME initiation and CCS maturation are unimpeded under high tension environments.

cell biology↗

bioRxiv2020

Click-chemistry enabled directed evolution of glycosynthases for bespoke glycans synthesis

Engineering of carbohydrate-active enzymes like glycosynthases for chemoenzymatic synthesis of bespoke oligosaccharides has been limited by the lack of suitable directed evolution based protein engineering methods. Currently there are no ultrahigh-throughput screening methods available for rapid and highly sensitive single cell-based screening of evolved glycosynthase enzymes employing azido sugars as substrates. Here, we report a fluorescence-based approach employing click-chemistry for the selective detection of glycosyl azides (versus free inorganic azides) that facilitated ultrahigh-throughput in-vivo single cell-based assay of glycosynthase activity. This discovery has led to the development of a directed evolution methodology for screening and sorting glycosynthase mutants for synthesis of desired fucosylated oligosaccharides. Our screening technique facilitated rapid fluorescence activated cell sorting of a large library of glycosynthase variants (>106 mutants) expressed in E. coli to identify several novel mutants with increased activity for {beta}-fucosyl-azide activated donor sugars towards desired acceptor sugars, demonstrating the broader applicability of this methodology.

biochemistry↗

bioRxiv2019

Functional characterization and lineage analysis of broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics

Eliciting broadly neutralizing antibodies (bNAbs) against the four dengue virus serotypes (DENV1-4) that are spreading into new territories is an important goal of vaccine design. To delineate bNAb targets, we characterized 28 monoclonal antibodies belonging to expanded and hypermutated clonal families identified by transcriptomic analysis of single plasmablasts from DENV-infected individuals. Among these, we identified two somatically related bNAbs that potently neutralized DENV1-4. Mutagenesis studies revealed that the major recognition determinants of these bNAbs are in E protein domain I, distinct from the only known class of human bNAbs against flaviviruses with a well-defined epitope. B cell repertoire analysis from acute-phase peripheral blood suggested a memory origin and divergent somatic hypermutation pathways for these bNAbs, and a limited number of mutations was sufficient for neutralizing activity. Our study suggests multiple B cell evolutionary pathways leading to DENV bNAbs targeting a novel epitope that can be exploited for vaccine design.

microbiology↗

bioRxiv2019

Leveraging genome-wide data to investigate differences between opioid use vs. opioid dependence in 41,176 individuals from the Psychiatric Genomics Consortium

To provide novel insights into the biology of opioid dependence (OD) and opioid use (i.e., exposure, OE), we completed a genome-wide analysis comparing up to 4,503 OD cases, 4,173 opioid-exposed controls, and 32,500 opioid-unexposed controls. Among the variants identified, rs9291211 was associated with OE (a comparison of exposed vs. unexposed controls; z=-5.39, p=7.2x10-8). This variant regulates the transcriptomic profiles of SLC30A9 and BEND4 in multiple brain tissues and was previously associated with depression, alcohol consumption, and neuroticism. A phenome-wide scan of rs9291211 in the UK Biobank (N>360,000) found association of this variant with propensity to use dietary supplements (p=1.68x10-8). With respect to the same OE phenotype in the gene-based analysis, we identified SDCCAG8 (z=4.69, p=10-6), which was previously associated with educational attainment, risk-taking behaviors, and schizophrenia. In addition, rs201123820 showed a genome-wide significant difference between OD cases and unexposed controls (z=5.55, p=2.9x10-8) and a significant association with musculoskeletal disorders in the UK Biobank (p=4.88x10-7). A polygenic risk score (PRS) based on a GWAS of risk-tolerance (N=466,571) was positively associated with OD (OD cases vs. unexposed controls, p=8.1x10-5; OD cases vs. exposed controls, p=0.054) and OE (exposed controls vs. unexposed controls, p=3.6x10-5). A PRS based on a GWAS of neuroticism (N=390,278) was positively associated with OD (OD cases vs. unexposed controls, p=3.2x10-5; OD cases vs. exposed controls, p=0.002) but not with OE (p=0.671). Our analyses highlight the difference between dependence and exposure and the importance of considering the definition of controls (exposed vs. unexposed) in studies of addiction.

genetics↗

bioRxiv2019

Polygenic Prediction of Substance Use Disorders in Clinical and Population Samples

Genome-wide, polygenic risk scores (PRS) have emerged as a useful way to characterize genetic liability using genotypic data. There is growing evidence that PRS may prove useful to identify those at increased risk for developing certain diseases. The current utility of PRS in relation to alcohol use disorders (AUD) remains an open question. Using data from both a population-based sample [the FinnTwin12 (FT12) study] and a high risk sample [the Collaborative Study on the Genetics of Alcoholism (COGA)], we examined the association between PRSs derived from genome-wide association studies (GWASs) of 1) alcohol dependence/alcohol problems, 2) alcohol consumption, and 3) risky behaviors with AUD and other substance use disorder (SUD) symptoms. Individuals in the top 20%, 10%, and 5% of PRSs had increasingly greater odds of having an AUD compared to the lower end of the continuum in both COGA (80th % OR = 1.95; 90th % OR = 2.03; 95th % OR = 2.13) and FT12 (80th % OR = 1.77; 90th % OR = 2.27; 95th % OR = 2.39). Those in the top 5% reported greater levels of licit (alcohol and nicotine) and illicit (cannabis) SUD symptoms. PRSs can predict elevated risk for SUD in independent samples. However, clinical utility of these scores in their current form is modest. As these scores become more predictive of SUD, they may become useful to practitioners. Improvement in predictive ability will likely be dependent on increasing the size of well-phenotyped discovery samples.

genetics↗

bioRxiv2019

Meta-analysis of problematic alcohol use in 435,563 individuals identifies 29 risk variants and yields insights into biology, pleiotropy and causality

Problematic alcohol use (PAU) is a leading cause of death and disability worldwide. Although genome-wide association studies (GWASs) have identified PAU risk genes, the genetic architecture of this trait is not fully understood. We conducted a proxy-phenotype meta-analysis of PAU combining alcohol use disorder and problematic drinking in 435,563 European-ancestry individuals. We identified 29 independent risk variants, 19 of them novel. PAU was genetically correlated with 138 phenotypes, including substance use and psychiatric traits. Phenome-wide polygenic risk score analysis in an independent biobank sample (BioVU, n=67,589) confirmed the genetic correlations between PAU and substance use and psychiatric disorders. Genetic heritability of PAU was enriched in brain and in genomic conserved and regulatory regions. Mendelian randomization suggested causal effects on liability to PAU of substance use, psychiatric status, risk-taking behavior, and cognitive performance. In summary, this large PAU meta-analysis identified novel risk loci and revealed genetic relationships with numerous other outcomes.

genetics↗

bioRxiv2019

Scalable probabilistic PCA for large-scale genetic variation data

Principal component analysis (PCA) is a key tool for understanding population structure and controlling for population stratification in genome-wide association studies (GWAS). With the advent of large-scale datasets of genetic variation, there is a need for methods that can compute principal components (PCs) with scalable computational and memory requirements. We present ProPCA, a highly scalable method based on a probabilistic generative model, which computes the top PCs on genetic variation data efficiently. We applied ProPCA to compute the top five PCs on genotype data from the UK Biobank, consisting of 488,363 individuals and 146,671 SNPs, in less than thirty minutes. Leveraging the population structure inferred by ProPCA within the White British individuals in the UK Biobank, we scanned for SNPs that are not well-explained by the PCs to identify several novel genome-wide signals of recent putative selection including missense mutations in RPGRIP1L and TLR4.\n\nAuthor SummaryPrincipal component analysis is a commonly used technique for understanding population structure and genetic variation. With the advent of large-scale datasets that contain the genetic information of hundreds of thousands of individuals, there is a need for methods that can compute principal components (PCs) with scalable computational and memory requirements. In this study, we present ProPCA, a highly scalable statistical method to compute genetic PCs efficiently. We systematically evaluate the accuracy and robustness of our method on large-scale simulated data and apply it to the UK Biobank. Leveraging the population structure inferred by ProPCA within the White British individuals in the UK Biobank, we identify several novel signals of putative recent selection.

bioinformatics↗

bioRxiv2019

Anti-inflammatory Role of Curcumin in LPS Treated A549 cells at Global Proteome level and on Mycobacterial infection.

A diet derived agent Curcumin (Diferuloylmethane), demonstrated its clinical application in inflammation, infection and cancer conditions. Nevertheless, its impact on the proteome of epithelial cells of non-small cell lung carcinoma (NSCLC) is yet to be explored. We employed a stable isotope labeling method for cell culture (SILAC) based relative quantitative proteomics and informatics analysis to comprehend global proteome change in A549 cells treated with curcumin and/or Lipopolysaccharide (LPS). Pretreated A549 cells were infected with Mycobacterium tuberculosis H37Rv strain to monitor bacterial load. With exposure to curcumin and LPS, out of the 1492 identified proteins, 305 and 346 proteins showed deregulation respectively. The expression of BID and AIFM1 mitochondrial proteins which play critical role in apoptotic pathway were deregulated in curcumin treated cells. Higher mitochondria intensity was observed in curcumin treated A549 cells than LPS treatment. Simultaneous treatment of curcumin and LPS neutralized the effect of LPS. Curcumin and/or LPS pretreated A549 cells infected with H37Rv, showed successful bacterial internalization. LPS treated A549 cells after infection showed increased bacterial load than curcumin compared to non-treated infected cells. However, simultaneous treatment of curcumin and LPS neutralized the effect of LPS. This study generated molecular evidence to deepen our understanding of the anti-inflammatory role of curcumin and may be useful to identify molecular targets for drug discovery.

biochemistry↗

bioRxiv2019

HER2 Cancer Protrusion Growth Signaling Regulated by Unhindered, Localized Filopodial Dynamics

Protrusions are plasma membrane extensions that are found in almost every cell in the human body. Cancer cell filopodial and lamellipodial protrusions play key roles in the integral processes of cell motility and signaling underlying tumor invasion and metastasis. HER2 (ErbB-2) is overexpressed in diverse types of tumors and regulates PI3K-pathway-mediated protrusion growth. It is known that HER2 resides at breast cancer cell protrusions, but how protrusion-based HER2 spatiotemporal dynamics shape cancer signaling is unclear. Here, we study how HER2 location and motion regulate protrusion signaling and growth using quantitative spatio-temporal molecular imaging approaches. Our data highlight morphologically-segregated features of filopodial and lamellipodial protrusions, in in vitro 2D breast cancer cells and in vivo intact breast tumor. Functional-segregation parallels morphological-segregation, as HER2 and its activated downstream pAKT-PI3K signaling remain spatially-localized at protrusions, provoking new protrusion growth proximal to sites of HER2 activation. HER2 in SKBR3 breast cancer cell filopodia exhibits fast, linearly-directed motion that is distinct from lamellipodia and non-protrusion subcellular regions ([~]3-4 times greater diffusion constant, rapid speeds of 2-3 um2/s). Surprisingly, filopodial HER2 motion is passive, requiring no active energy sources. Moreover, while HER2 motion in lamellipodia and non-protrusion regions show hindered diffusion typical of membrane proteins, HER2 diffuses freely within filopodia. We conclude that HER2 activation, propagation, and functional protrusion growth is a local process in which filopodia have evolved to exploit Brownian thermal fluctuations within a barrier-free nanostructure to transduce rapid signaling. These results support the importance of developing filopodia and other protrusion-targeted strategies for cancer.

cancer biology↗

bioRxiv2019

Reading Increases the Compositionality of Visual Word Representations

Reading causes widespread changes in the brain but its effect on visual word representations is unknown. Reading may facilitate visual processing by forming specialized detectors for longer strings, or by making word responses more predictable from single letters, that is by increasing compositionality. We provide evidence for the latter hypothesis by comparing readers and nonreaders of two Indian languages, Telugu and Malayalam. Readers showed decreased interactions between letters during visual search, which predicted their overall reading fluency. Brain imaging revealed increased compositionality in readers, whereby responses to bigrams were more predictable from single letters. This effect was specific to the lateral occipital region, where activations best matched behavior. Thus, reading facilitates visual processing by increasing the compositionality of visual word representations.

neuroscience↗

bioRxiv2019

A compositional shape code explains how we read jumbled words

We read words and even jubmled wrods effortlessly, but the neural representations underlying this remarkable ability remain unknown. We hypothesized that word processing is driven by a visual representation that is compositional i.e. with string responses systematically related to letters. To test this hypothesis, we devised a model in which neurons tuned to letter shape respond to longer strings by linearly summing letter responses. This letter model explained human performance in both visual search as well as word reading tasks. Brain imaging revealed that viewing a string activates this compositional letter code in the lateral occipital (LO) region, and that subsequent comparisons to known words are computed by the visual word form area (VWFA). Thus, seeing a word activates a compositional letter code that enables efficient reading.

neuroscience↗

bioRxiv2019

Pattern similarity analyses of frontoparietal task coding: Individual variation and genetic influences

Pattern similarity analyses are increasingly used to characterize coding properties of brain regions, but relatively few have focused on cognitive control processes in FrontoParietal regions. Here, we use the Human Connectome Project (HCP) N-back task fMRI dataset to examine individual differences and genetic influences on the coding of working memory load (0-back, 2-back) and perceptual category (Face, Place). Participants were grouped into 105 MZ (monozygotic) twin, 78 DZ (dizygotic) twin, 99 non-twin sibling, and 100 unrelated pairs. Activation pattern similarity was used to test the hypothesis that FrontoParietal regions would have higher similarity for same load conditions, while Visual regions would have higher similarity in same perceptual category conditions. Results confirmed this highly robust regional double dissociation in neural coding, which also predicted individual differences in behavioral performance. In pair-based analyses, anatomically-selective genetic relatedness effects were observed: relatedness predicted greater activation pattern similarity in FrontoParietal only for load coding, and in Visual only for perceptual coding. Further, in related pairs, the similarity of load coding in FrontoParietal regions was uniquely associated with behavioral performance. Together, these results highlight the power of task fMRI pattern similarity analyses for detecting key coding and heritability features of brain regions.

neuroscience↗

bioRxiv2019

Population genomics of the facultatively asexual duckweed Spirodela polyrhiza

O_LIClonal propagation allows some plant species to achieve massive population sizes quickly but also reduces the evolutionary independence of different sites in the genome.\nC_LIO_LIWe examine genome-wide genetic diversity in Spirodela polyrhiza, a duckweed that reproduces primarily asexually.\nC_LIO_LIWe find that this geographically widespread and numerically abundant species has very low levels of genetic diversity. Diversity at nonsynonymous sites relative to synonymous sites is high, suggesting that purifying selection is weak. A potential explanation for this observation is that a very low frequency of sex renders selection in effective. However, there is a pronounced decay in linkage disequilibrium over 40 kb, suggesting that though sex may be rare at the individual level it is not too infrequent at the population level. In addition, neutral diversity is affected by the physical proximity of selected sites, which would be unexpected if sex was exceedingly rare at the population level.\nC_LIO_LIThe amount of genetic mixing as assessed by the decay in linkage disequilibrium is not dissimilar from selfing species such as Arabidopsis thaliana, yet selection appears to be much less effective in duckweed. We discuss alternative explanations for the signature of weak purifying selection.\nC_LI

evolutionary biology↗

bioRxiv2018

Analysis of whole genome-transcriptomic organization in brain to identify genes associated with alcoholism

Alcohol exposure triggers changes in gene expression and biological pathways in human brain. We explored alterations in gene expression in the Pre-Frontal Cortex (PFC) of 65 alcoholics and 73 controls of European descent, and identified 129 genes that showed altered expression (FDR < 0.05) in subjects with alcohol dependence. Differentially expressed genes were enriched for pathways related to interferon signaling and Growth Arrest and DNA Damage-inducible 45 (GADD45) signaling. A coexpression module (thistle2) identified by weighted gene co-expression network analysis (WGCNA) was significantly correlated with alcohol dependence, alcohol consumption, and AUDIT scores. Genes in the thistle2 module were enriched with genes related to calcium signaling pathways and showed significant downregulation of these pathways, as well as enrichment for biological processes related to nicotine response and opioid signaling. A second module (brown4) showed significant upregulation of pathways related to immune signaling. Expression quantitative trait loci (eQTLs) for genes in the brown4 module were also enriched for genetic associations with alcohol dependence and alcohol consumption in large genome-wide studies included in the Psychiatric Genetic Consortium and the UK Biobanks alcohol consumption dataset. By leveraging multi-omics data, this transcriptome analysis has identified genes and biological pathways that could provide insight for identifying therapeutic targets for alcohol dependence.

neuroscience↗

bioRxiv2018

Senescent cells and the dynamics of aging

Genetically-identical organisms age at different rates, but the reason for this is unclear. The rate of aging is due to the accumulation of damage, such as senescent cells (SnC) which are a major driver of aging in mammals, but the accumulation dynamics of SnC are unknown. Here, we combine theory and experiments in mice and find that SnC are rapidly produced and removed with a half-life of days in young mice. In old mice SnC half-life grows to weeks, because SnC saturate their own removal process. This saturation leads to persistent fluctuations known as critical-slowing-down: fluctuations are amplified to long-lasting differences in SnC between individuals at old ages. Rapid turnover with saturating removal is a general framework that may apply to any aging-related form of damage, and can quantitatively explain the demographic laws of mortality in worms, flies, mice and humans.

systems biology↗

bioRxiv2018

Evidence of causal effect of major depression on alcohol dependence: Findings from the Psychiatric Genomics Consortium

BackgroundDespite established clinical associations among major depression (MD), alcohol dependence (AD), and alcohol consumption (AC), the nature of the causal relationship between them is not completely understood.\n\nMethodsThis study was conducted using genome-wide data from the Psychiatric Genomics Consortium (MD: 135,458 cases and 344,901 controls; AD: 10,206 cases and 28,480 controls) and UK Biobank (AC-Frequency: from \"daily or almost daily\" to \"never\", 438,308 individuals; AC-Quantity: total units of alcohol per week, 307,098 individuals). Linkage disequilibrium score regression and Mendelian Randomization (MR) analyses were applied to investigate shared genetic mechanisms (horizontal pleiotropy) and causal relationships (mediated pleiotropy) among these traits.\n\nOutcomesPositive genetic correlation was observed between MD and AD (rgMD-AD=+0.47, P=6.6x10-10). AC-Quantity showed positive genetic correlation with both AD (rgAD-AC-Quantity=+0.75, P=1.8x10-14) and MD (rgMD-AC-Quantity=+0.14, P=2.9x10-7), while there was negative correlation of AC-Frequency with MD (rgMD-AC-Frequency=-0.17, P=1.5x10-10) and a non-significant result with AD. MR analyses confirmed the presence of pleiotropy among these traits. However, the MD-AD results reflect a mediated-pleiotropy mechanism (i.e., causal relationship) with a causal role of MD on AD (beta=0.28, P=1.29x10-6) that does not appear to be biased by confounding such as horizontal pleiotropy. No evidence of reverse causation was observed as the AD genetic instrument did not show a causal effect on MD.\n\nInterpretationResults support a causal role for MD on AD based on genetic datasets including thousands of individuals. Understanding mechanisms underlying MD-AD comorbidity not only addresses important public health concerns but also has the potential to facilitate prevention and intervention efforts.\n\nFundingNational Institute of Mental Health and National Institute on Drug Abuse.\n\nPutting data into contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed up to August 24, 2018, for research studies that investigated causality among alcohol-and depression related phenotypes using Mendelian randomization approaches. We used the search terms \"alcohol\" AND \"depression\" AND \"Mendelian Randomization\". No restrictions were applied to language, date, or article type. Ten articles were retrieved, but only two were focused on alcohol consumption and depression-related traits. The studies were based on genetic variants in alcohol dehydrogenase (ADH) genes only, did not find evidence for a causal effect of alcohol consumption on depression phenotypes, with one study finding a causal effect of alcohol consumption on alcoholism. Both studies noted that future studies are needed with increased sample sizes and clinically derived phenotypes. To our knowledge, no previous study has applied two-sample Mendelian randomization to investigate causal relationships between alcohol dependence and major depression.\n\nTwin studies show genetic factors influence susceptibility to MD, AD, and alcohol consumption. Differently from observational approaches where several studies have investigated the relationship between alcohol-and depression-related phenotypes, very limited use of molecular genetic data has been applied to investigate this issue. Additionally, the use of genetic information has been shown to be less biased by confounders and reverse causation than observation data. However, genetic approaches, like Mendelian randomization, require large sample sizes to be informative.\n\nAdded value of this studyIn this study, we used genome-wide data from the Psychiatric Genomic Consortium and UK Biobank, which include information regarding hundred thousands of individuals, to test the presence of shared genetic mechanisms and causal relationships among major depression, alcohol dependence, and alcohol consumption. The results support a causal influence of MD on AD, while alcohol consumption showed shared genetic mechanisms with respect to both major depression and alcohol dependence.\n\nImplications of all the available evidenceGiven the significant morbidity and mortality associated with MD, AD, and the comorbid condition, understanding mechanisms underlying these associations not only address important public health concerns but also has the potential to facilitate prevention and intervention efforts.

genetics↗

bioRxiv2018

Spatial Control of Neuronal Metabolism Through Glucose-Mediated Mitochondrial Transport Regulation

Eukaryotic cells modulate their metabolism by organizing metabolic components in response to varying nutrient availability and energy demands. In the axons of mammalian neurons, mitochondria have been shown to respond to glucose levels by halting active transport preferentially in high glucose regions. Here, we employ quantitative modeling to explore the physical limits on spatial organization of organelles through such regulated stopping of processive motion, as well as the consequences to cellular metabolism. We delineate the role of key parameters, including cellular glucose uptake and consumption rates, that are expected to modulate mitochondrial distribution and metabolic response in spatially varying glucose conditions. Our quantitative estimates indicate that physiological brain glucose levels fall within the limited range necessary for metabolic enhancement, making this a plausible regulatory mechanism for neuronal metabolic flexibility in the presence of spatially heterogeneous glucose. These findings highlight the role of spatial organization in the regulation of neuronal metabolism, while providing a quantitative framework for the establishment of such organization by control of organelle trafficking.

biophysics↗

bioRxiv2018

Simvastatin mediates inhibition of exosome synthesis, localization, and secretion via multicomponent interventions.

Discovery of exosomes as modulator of cellular communication has added a new dimension to our understanding of biological processes. Exosomes influence the biological systems by mediating trans-communication across tissues and cells, which has important implication for health and disease. Identification of strategies for exosome modulation may pave the way towards better understanding of exosome biology and development of novel therapeutics. In absence of well-characterized modulators of exosome biogenesis, an alternative option is to target pathways generating important exosomal components. Cholesterol represents one such essential component required for exosomal biogenesis. We initiated this study to test the hypothesis that owing to its cholesterol lowering effect, simvastatin, a HMG CoA inhibitor, might be able to alter exosome formation and secretion. Using previously established protocols for detecting secreted exosomes in biological fluids, simvastatin was tested for its effect on exosome secretion under various in-vitro and in-vivo settings. Murine model of AAI was used for further validation of our findings. Utilizing aforementioned systems, we demonstrate exosome-lowering potential of simvastatin in various in-vivo and in-vitro models, of AAI and atherosclerosis. We believe that the knowledge acquired in this study holds potential for extension to other exosome dominated pathologies and model systems.

cell biology↗