Biology subjects

Sen, A.

Publications and source records attributed to Sen, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Interaction between time-of-day and oxytocin efficacy in mice and humans with and without gestational diabetes

Management of labor in women with diabetes is challenging due to the high risk of peri- and postpartum complications. To avoid cesarean section and assist with labor progression, Pitocin, a synthetic oxytocin, is frequently used to induce and augment labor. However, the efficacy of Pitocin is often compromised in diabetic pregnancies, leading to increased cesarian delivery. As diabetes deregulates the bodys circadian timekeeping system and the time-of-day of the first Pitocin administration contributes to labor duration, our objective was to determine how the time of day and the circadian clock gene, Bmal1, gates oxytocin efficacy. Our studies in mice show that, compared to the rest phase of the day (lights on), the uterotonic efficacy of oxytocin is significantly increased during the active phase (lights off). Using in vitro studies, a myometrium-specific Bmal1 conditional knockout mouse model, and a mouse model of food-induced gestational diabetes, we find that Bmal1 is crucial for maintaining oxytocin receptor expression and response in the myometrium in mice. These findings also translate to humans, where oxytocin-induced human myometrial cell contraction is time-of-day dependent, and retrospective clinical data suggest that administration of Pitocin in the morning should be considered for pregnant women with gestational diabetes.

physiology↗

bioRxiv2024

Scrutinized lipid utilization disrupts Amphotericin-B responsiveness in clinical isolates of Leishmania donovani

The management of Leishmania donovani (LD), responsible for fatal visceral leishmaniasis (VL), faces increasing challenges due to rising drug-unresponsiveness, leading to increasing treatment failures. While hypolipidemia characterizes VL, LD, a cholesterol auxotroph, relies on host lipid scavenging for its intracellular survival. The aggressive pathology, in terms of increased organ parasite load, observed in hosts infected with antimony-unresponsive-LD (LD-R) as compared to their sensitive counterparts (LD-S), highlights LD-Rs heightened reliance on host lipids. Here we report that LD-R-infection promotes fluid-phase endocytosis in the host, selectively accumulating neutral lipids while excluding oxidized-LDL. LD-R enhances the fusion of endocytosed LDL-vesicles with its phagolysosomal membrane and inhibits cholesterol mobilization from these vesicles by suppressing NPC-1. This provides LD-R amastigotes with excess lipids, supporting their rapid proliferation and membrane synthesis. This excess LDL-influx leads to an eventual accumulation of neutral lipid droplets around LD-R amastigotes, thereby increasing their unresponsiveness towards Amphotericin-B, a second-line amphiphilic antileishmanial. Notably, VL patients showing relapse with Amphotericin-B treatment exhibited significantly lower serum LDL and cholesterol than cured cases. Treatment with Aspirin, a lipid droplet blocker, reduced lipid droplets around LD-R amastigotes, restoring Amphotericin-B responsiveness.

microbiology↗

bioRxiv2024

Microbiome signatures of virulence in the oral-gut-brain axis influence Parkinson's disease and cognitive decline pathophysiology

The human microbiome is increasingly recognized for its crucial role in the development and progression of neurodegenerative diseases. While the gut-brain axis has been extensively studied, the contribution of the oral microbiome and gut-oral tropism in neurodegeneration has been largely overlooked. Cognitive impairment (CI) is common in neurodegenerative diseases and develops on a spectrum. In Parkinsons Disease (PD) patients, CI is one of the most common non-motor symptoms but its mechanistic development across the spectrum remains unclear, complicating early diagnosis of at-risk individuals. Here, we generated 228 shotgun metagenomics samples of the gut and oral microbiomes across PD patients with either mild cognitive impairment (PD-MCI) or dementia (PDD), and a healthy cohort, to study the role of the gut and oral microbiomes on CI in PD. In addition to revealing compositional and functional signatures, the role of pathobionts, and dysregulated metabolic pathways of the oral and gut microbiome in PD-MCI and PDD, we also revealed the importance of oral-gut translocation in increasing abundance of virulence factors in PD and CI. The oral-gut virulence was further integrated with saliva metaproteomics and demonstrated their potential role in dysfunction of host immunity and brain endothelial cells. Our findings highlight the significance of the oral-gut-brain axis and underscore its potential for discovering novel biomarkers for PD and CI.

microbiology↗

bioRxiv2024

Heterogeneity in chromatin structure drives core regulatory pathways in B-cell Acute Lymphoblastic Leukemia

B-cell acute lymphoblastic leukemia (B-ALL) is the most common pediatric malignancy. Based on gene expression profiling, B-ALL can be classified into distinct transcriptional subtypes with differing disease outcomes. Many of these transcriptional subtypes are defined by mutations in transcription factors and chromatin-modifying enzymes, but how such diverse mutations lead to distinct transcriptional subtypes remains unclear. To illuminate the chromatin regulatory landscape in B-ALL, we analyzed 3D genome organization, open chromatin, and gene expression in 53 primary patient samples. At the level of 3D genome organization, we identified chromatin interactions that vary across transcriptional subtypes. These sites of variable 3D chromatin interactions correlate with local gene expression changes and are enriched for core drivers of B-ALL observed in genome-wide CRISPR knock-out screens. Sites of variable 3D genome interactions are frequently shared across multiple transcriptional subtypes and are enriched for open chromatin sites found in normal B-cell development but repressed in mature B-cells. Within an individual patient sample, the chromatin landscape can resemble progenitor chromatin states at some loci and mature B-cell chromatin at others, suggesting that the chromatin in B-ALL patient tumor cells is in a partially arrested immature state. By analyzing transcriptomic data from large cohorts of B-ALL patients, we identify gene expression programs that are shared across transcriptional subtypes, associated with B-cell developmental stages, and predictive of patient survival. In combination, these results show that the 3D genome organization of B-ALL reflects B-cell developmental stages and helps illustrate how B-cell developmental arrest interacts with transcriptional subtypes to drive B-ALL.

cancer biology↗

bioRxiv2024

Dynamic convergence of autism disorder risk genes across neurodevelopment

Over three hundred and seventy-three risk genes, broadly enriched for roles in neuronal communication and gene expression regulation, underlie risk for autism spectrum disorder (ASD) and developmental delay (DD). Functional genomic studies of subsets of these genes consistently indicate a convergent role in neurogenesis, but how these diverse risk genes converge on a smaller number of biological pathways in mature neurons is unclear. To uncover shared downstream impacts between neurodevelopmental disorder (NDD) risk genes, here we apply a pooled CRISPR approach to contrast the transcriptomic impacts of targeting 29 NDD loss-of-function genes across human induced pluripotent stem cell (hiPSC)-derived neural progenitor cells, glutamatergic neurons, and GABAergic neurons. Points of convergence vary between the cell types of the brain and are greatest in mature glutamatergic neurons, where they broadly target not just synaptic and epigenetic, but unexpectedly, mitochondrial biology. The strongest convergent networks occur between NDD genes with common co-expression patterns in the post-mortem brain, biological annotations, and clinical associations, suggesting that convergence may one-day inform patient stratification and treatment. Towards this, ten out of eleven drugs tested that were predicted to reverse convergent signatures in human cells and/or arousal and sensory processing behaviors in zebrafish ameliorated at least one behavioral phenotype in vivo. Altogether, robust convergence in post-mitotic neurons represents a clinically actionable therapeutic window.

genetics↗

bioRxiv2024

Dynamic stress- and inflammatory-based regulation of psychiatric risk loci in human neurons

The immune environment influences neurodevelopment and subsequent clinical trajectories for psychiatric outcomes in childhood and adolescence. Yet it remains unclear if the impact of maternal and fetal immune activation varies with distinct polygenic risk profiles. Therefore, here we catalogue genotype and environment (GxE) interactions, contrasting allele-specific regulatory activity between inflammatory cues. We report a cue-specific neuronal massively parallel reporter assay (MPRA) of 152 loci from genome-wide association study (GWAS) linked to ten brain traits/disorders, empirically dissecting the impact of interleukin-6 (IL-6) and interferon-alpha (IFN) on transcriptional activity. In human induced pluripotent stem cell (hiPSC)-derived glutamatergic neurons, 1,156 active candidate regulatory risk sequences (MPRA-active CRSs) are resolved, including 267 with variant-specific effects (MPRA-emVars) and 61 with variant-by-cytokine interaction effects (interaction MPRA-emVars). Broadly, neuronal immune-mediated regulatory activity is associated with differences in transcription factor binding and chromatin accessibility, the gene targets of which show pleiotropic enrichments for brain, metabolic, and immune disorders. Dynamic genetic regulation mediates neuroimmune effects, informing our understanding of the genomics of psychiatric and neurological traits, mechanisms governing pleiotropy across disorders, and how immune mechanisms mediate genetic risk.

genetics↗

bioRxiv2024

Comprehensive gene expression analysis of organoid-derived healthy human colonic epithelium and cancer cell line by stimulated with live probiotic bacteria

The large intestine has a dense milieu of indigenous bacteria, generating a complex ecosystem with crosstalk between individual bacteria and host cells. In vitro host cell modeling and bacterial interactions at the anaerobic interphase have elucidated the crosstalk molecular basis. Although classical cell lines derived from patients with colorectal cancer including Caco-2 cells are used, whether they adequately mimic normal colonic epithelial physiology is unclear. To address this, we performed transcriptome profiling of Caco-2 and Monolayer cells derived from healthy Human Colonic Organoid (MHCO) cultured hemi-anaerobically. Coculture with the anaerobic gut bacteria, Bifidobacterium longum subsp. longum differentiated the probiotic effects of test cells from those of physiologically normal intestinal and colorectal cancer cells. We cataloged non- or overlapping gene signatures where gene profiles of Caco-2 cells represented absorptive cells in the small intestinal epithelium, and MHCO cells showed complete colonic epithelium signature, including stem/progenitor, goblet, and enteroendocrine cells colonocytes. Characteristic gene expression changes related to lipid metabolism, inflammation, and cell-cell adhesion were observed in cocultured live Bifidobacterium longum and Caco-2 or MHCO cells. B. longum-stimulated MHCO cells exhibited barrier-enhancing characteristics, as demonstrated in clinical trials. Our data represent a valuable resource for understanding gut microbe and host cell communication.

ecology↗

bioRxiv2024

Differential effects of aging and epilepsy in discriminating and reactivating memories

How are memories stored and subsequently retrieved? Pattern separation and pattern completion are distinct neurocognitive hippocampal processes that are thought to facilitate encoding and retrieval of memories. However, the way in which these operations affect the quality of memory remains unclear and there is currently no single behavioural task in humans to measure both mechanisms simultaneously. Here, we describe a novel paradigm which provides a distinct measure of each process and apply it to people with focal epilepsy, a condition associated with hippocampal dysfunction, comparing them with healthy young and older participants. Pattern separation and pattern completion were observed in healthy younger individuals. A specific deficit in pattern completion was identified in people with focal epilepsy, while the healthy older cohort showed degraded ability to perform pattern separation. To understand the underlying mechanisms, we simulated human performance using an auto-associative neural network. Modelling indicated that disruption in different populations of neurons could explain the observed memory profiles. These findings show that pattern separation and pattern completion are distinct processes that can be measured from a single behavioural task and are differentially affected by focal epilepsy and aging.

neuroscience↗

bioRxiv2023

Cytoskeletal activation of NHE1 regulates cell volume and DNA methylation

Mammalian cells can rapidly respond to osmotic and hydrostatic pressure imbalances during an environmental change, generating large fluxes of water and ions that alter cell volume within minutes. While the role of ion pump and leak in cell volume regulation has been well-established, the potential contribution of the actomyosin cytoskeleton and its interplay with ion transporters is unclear. We discovered a cell volume regulation system that is controlled by cytoskeletal activation of ion transporters. After a hypotonic shock, normal-like cells (NIH-3T3, MCF-10A, and others) display a slow secondary volume increase (SVI) following the immediate regulatory volume decrease. We show that SVI is initiated by hypotonic stress induced Ca2+ influx through stretch activated channel Piezo1, which subsequently triggers actomyosin remodeling. The actomyosin network further activates NHE1 through their synergistic linker ezrin, inducing SVI after the initial volume recovery. We find that SVI is absent in cancer cell lines such as HT1080 and MDA-MB-231, where volume regulation is dominated by intrinsic response of ion transporters. A similar cytoskeletal activation of NHE1 can also be achieved by mechanical stretching. On compliant substrates where cytoskeletal contractility is attenuated, SVI generation is abolished. Moreover, cytoskeletal activation of NHE1 during SVI triggers nuclear deformation, leading to a significant, immediate transcriptomic change in 3T3 cells, a phenomenon that is again absent in HT1080 cells. While hypotonic shock hinders ERK-dependent cell growth, cells deficient in SVI are unresponsive to such inhibitory effects. Overall, our findings reveal the critical role of Ca2+ and actomyosin-mediated mechanosensation in the regulation of ion transport, cell volume, transcriptomics, and cell proliferation.

biophysics↗

bioRxiv2023

Optogenetic determination of dynamic and cell-type-specific chloride equilibrium potentials

Optogenetics has revolutionized neurobiological research by providing tools for modulating neuronal activity. As these tools utilise light-activated ion fluxes, they afford new opportunities to examine the nature of transmembrane ion gradients. Traditional investigation into the equilibrium potential for chloride (ECl) has been limited to studying endogenous chloride-permeable receptors. Here we demonstrate the utility of using a light-activated chloride channel, stGtACR2, to probe somatic ECl in rodent. This agonist-independent optogenetic strategy is validated in vitro and in vivo, captures differences in ECl dynamics following manipulations of endogenous chloride fluxes, and reveals distinct resting ECl across genetically-defined neuronal subpopulations. Using this approach to challenge chloride homeostasis, we uncover cell-specific ECl dynamics that are supported by the differential expression of endogenous handling mechanisms. Our findings establish an optical method for investigating transmembrane chloride gradients and thereby expand the repertoire of optogenetics.

neuroscience↗

bioRxiv2023

A paper based microfluidic platform combining LAMP-CRISPR/Cas12a for fluorometric detection of nucleic acids

Nucleic acid isothermal amplification methods are advantageous for point-of-care (POC) diagnostics because of their precision, sensitivity, and low power requirements. Loop-mediated isothermal amplification (LAMP) is an established method, renowned for its nucleic acid amplification efficiency and robust amplification of semi purified target nucleic acids. However, LAMP may be prone to non-specific amplification causing false positives and therefore fails to replace PCR as the gold standard method in clinical testing. We show that LAMP combined with clustered regularly interspaced short palindromic repeats (CRISPR) technology is an effective alternative for overcoming the limitations of LAMP alone. Nucleic acids are first isothermally pre-amplified to enrich for targets, then specific amplification detection signals are generated by sequences of RNA guided recognition of amplicons. We are the first to demonstrate a paper based microfluidic system for detecting pathogen nucleic acids in samples by combining the power of LAMP and CRISPR technology. We show that although LAMP may produce non-specific amplification, the possibility of detecting a false positive can be eliminated by combining LAMP with CRISPR based detection. We demonstrate that a paper based microfluidic platform has the potential to compete with the conventional Nucleic acid testing (NAT) technologies not only in terms of robustness but also in terms of cost and complexity.

bioengineering↗

bioRxiv2023

Active cortical networks promote shunting fast synaptic inhibition in vivo

Fast synaptic inhibition determines neuronal response properties in the mammalian brain and is mediated by chloride-permeable ionotropic GABA-A receptors (GABAARs). Despite their fundamental role, it is still not known how GABAARs signal in the intact brain. Here we use in vivo gramicidin recordings to investigate synaptic GABAAR signaling in mouse cortical pyramidal neurons under conditions that preserve native transmembrane chloride gradients. In anaesthetized cortex, synaptic GABAARs exert classic hyperpolarizing effects. In contrast, GABAAR-mediated synaptic signaling in awake cortex is found to be predominantly shunting. This is due to more depolarized GABAAR equilibrium potentials (EGABAAR), which are shown to result from the high levels of synaptic activity that characterize awake cortical networks. The EGABAAR observed in awake cortex can facilitate the decoupling of local networks, which improves the ability of the network to discriminate stimuli. Our findings therefore suggest that GABAAR signaling adapts to optimize cortical functions.

neuroscience↗

bioRxiv2022

Yeast and Mammalian Epsins Use Different Determinants for Localization and Function: Role of Clathrin/AP2/Ubiquitin Binding Motifs and Poly-Glutamine Stretches

Epsins are endocytic adaptor proteins involved in the internalization of important membrane proteins such as EGFR and Notch ligands. Therefore, this protein family impacts critical signaling pathways and processes such as cell migration and cytokinesis and is ultimately required for embryo development in mammals and cell viability in yeast. Intriguingly, although Epsins are conserved and display similar binding determinants, the process of endocytosis in yeast and mammals exhibit some dramatic mechanistic differences. Therefore, we wondered if the function of Epsins in these organisms are similar and are similarly regulated or they also differ. Since proper and timely localization is needed for function, we determined what elements target Epsins to endocytic sites in yeast vs mammals. Specifically, using a systematic/combinatorial mutagenesis approach we produced a collection of yeast and human Epsin mutated variants that was tested for localization at endocytic sites and for function. Our results showed that the intrinsically disordered carboxy-terminus holds the major determinants (involved in binding of ubiquitin, AP2, clathrin and EH domain-containing proteins) for proper intracellular localization of different Epsin paralogs and homologs in yeast and mammals, while also having a major impact on function. Importantly, we established hierarchies of carboxy-terminal binding determinants for sustaining Epsin localization which turned to be different for human vs. yeast cells; favoring clathrin and AP2 binding in the former and recognition of cargo and EH domain-containing proteins for the latter. Further, we found evidence in both systems that yeast Epsins also use for localization regions of the protein that were until now of unknown functional relevance, i.e., glutamine-rich sequences. Interestingly, some molecular determinants within the Epsin molecule seem to have functional importance beyond its contribution to localization to endocytic sites. Based on these findings, we propose working models for Epsin function and recruitment to membranes/endocytic sites at different maturation stages.

cell biology↗

bioRxiv2022

Deletion mapping of regulatory elements for GATA3 reveals a distal T helper 2 cell enhancer involved in allergic diseases

The GATA3 gene is essential for T cell differentiation and is surrounded by risk variants for immune traits. Interpretation of these variants is challenging because the regulatory landscape of GATA3 is complex with dozens of potential enhancers spread across a large topological associating domain (TAD) and gene expression quantitative trait locus (eQTL) studies provide limited evidence for variant function. Here, we perform a tiling deletion screen in Jurkat T cells to identify 23 candidate regulatory elements. Using small deletions in primary T helper 2 (Th2) cells, we validate the function of five of these elements, two of which contain risk variants for asthma and allergic diseases. We fine-map genome-wide association study (GWAS) signals in a distal regulatory element, 1 Mb downstream, to identify 14 candidate causal variants. Small deletions spanning candidate rs725861 decrease GATA3 expression in Th2 cells suggesting a causal mechanism for this variant in allergic diseases. Our study demonstrates the power of integrating GWAS signals with deletion mapping and identifies critical regulatory sequences for GATA3.

genomics↗

bioRxiv2022

Quantification of salt stress in wheat leaves by Raman spectroscopy and machine learning

The salinity level of the growing medium has diverse effects on the development of plants, including both physical and biochemical changes. To determine the salt stress level of a plant endures, one can measure these structural and chemical changes. Raman spectroscopy and biochemical analysis are some of the most common techniques in the literature. Here, we present a combination of machine learning and Raman spectroscopy with which we can both find out the biochemical change that occurs while the medium salt concentration changes and predict the level of salt stress a wheat sample experiences accurately using our trained regression models. In addition, by applying different machine learning algorithms, we compare the level of success for different algorithms and determine the best method to use in this application. Production units can take actions based on the quantitative information they get from the trained machine learning models related to salt stress, which can potentially increase efficiency and avoid the loss of crops.

biophysics↗

bioRxiv2021

Vitronectin acts as a key regulator of adhesion and migration in umbilical cord-derived MSCs under different stress conditions

Mesenchymal stem cell (MSC)-based therapy gets compromised as adverse microenvironmental conditions like nutrient deprivation, ischemia, hypoxia at the target site affect migration, engraftment and viability, of MSCs post transplantation. To improve the treatment efficacy, it is critical to identify factors involved in regulating migration and adhesion of MSCs under such microenvironmental stress conditions. In our study, we observed that human Whartons jelly-derived MSCs (WJ-MSCs) exhibited increase in cell spread area and adhesion, with reduction in cellular migration under serum starvation stress. The changes in adhesion and migration characteristics were accompanied by formation of large number of super mature focal adhesions along with extensive stress fibres and altered ECM gene expression with notable induction in vitronectin (VTN) expression. NF-{kappa}{beta} was found to be a positive regulator of VTN expression while ERK pathway regulated it negatively. Molecular and phenotypic comparison studies with inhibition of these signalling pathways or knocking down of VTN under serum starvation established the correlation between increase in VTN expression and increased cellular adhesion with corresponding reduction in cell migration. VTN knockdown also resulted in reduction of super mature focal adhesions and extensive stress fibres, which were formed under serum starvation. Additionally, VTN induction was not detected in hypoxia-treated WJ-MSCs, and the MSCs showed no significant change in the adhesion or migration properties under hypoxia. However, when VTN expression was induced under hypoxia by ERK pathway inhibition, similar increase in cell spread area and adhesion were observed. Our study thus highlights VTN as a key player which is induced under serum starvation stress and possibly regulates the adhesion and migration properties of WJ-MSCs via focal adhesion signalling.

cell biology↗

bioRxiv2021

Enzyme Catalysis Enhances Lateral Lipid Motility and Directional Particle Transport on Membranes

The dynamic interplay between the composition of lipid membranes and the behavior of membrane-bound enzymes is critical to the understanding of cellular function and viability, and the design of membrane-based biosensing platforms. While there is a significant body of knowledge on how lipid composition and dynamics affect membrane-bound enzymes, little is known about how enzyme catalysis influences the motility and lateral transport in lipid membranes. Using enzymes-attached lipids in supported bilayers (SLB), we show catalysis-induced enhanced lateral diffusion of lipids in the bilayer. Enhancing the membrane viscosity by increasing the cholesterol content in the bilayer suppresses the overall diffusion but not the relative diffusion enhancement of the enzyme-attached lipids. We also provide direct evidence of catalysis-induced membrane fluctuations leading to the enhanced diffusion of passive tracers resting on the SLB. Additionally, by using active enzyme patches, we demonstrate the directional transport of tracers on SLBs. These are first steps in understanding diffusion and transport in lipid membranes due to active, out-of-equilibrium processes that are the hallmark of living systems. In general, our study demonstrates how active enzymes can be used to control diffusion and transport in confined 2-D environments.

biophysics↗

bioRxiv2021

Enzyme Aggregation and Fragmentation Induced by Catalysis Relevant Species

It is usually assumed that enzymes retain their native structure during catalysis. However, the aggregation and fragmentation of proteins can be difficult to detect and sometimes conclusions are drawn based on the assumption that the protein is in its native form. We have examined three model enzymes, alkaline phosphatase (AkP), hexokinase (HK) and glucose oxidase (GOx). We find that these enzymes aggregate or fragment after addition of chemical species directly related to their catalysis. We used several independent techniques to study this behavior. Specifically, we found that glucose oxidase and hexokinase fragment in the presence of D-Glucose but not L-glucose, while hexokinase aggregates in the presence of Mg2+ ion and either ATP or ADP at low pH. Alkaline phosphatase aggregates in the presence of Zn2+ ion and inorganic phosphate. The aggregation of hexokinase and alkaline phosphatase does not appear to attenuate their catalytic activity. Our study indicates that specific multimeric structures of native enzymes may not be retained during catalysis and suggests pathways for different enzymes to associate or separate over the course of substrate turnover.

biophysics↗