Biology subjects

Kumar, K.

Publications and source records attributed to Kumar, K..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Cytokine Dynamics and Oxidative Stress in Host Cells Stimulated with Drug-Resistant and Sensitive Mycobacterium tuberculosis Isolates

BackgroundThe immune response to Mycobacterium tuberculosis (M. tuberculosis) is central to the pathogenesis of tuberculosis (TB), yet the immune dynamics induced by drug-resistant strains remain underexplored. Understanding the hosts immune response to both drug-sensitive and drug-resistant M. tuberculosis isolates is crucial for elucidating the mechanisms of pathogenesis and resistance. This study aims to assess the cellular immune responses, including PBMC proliferation, cytokine secretion (IL-4 and IL-17a), and reactive oxygen species (ROS) production in response to live drug-sensitive and drug-resistant M. tuberculosis clinical isolates. MethodsPeripheral blood mononuclear cells (PBMCs) from PPD-negative and PPD-positive healthy volunteers were stimulated with live M. tuberculosis isolates, including MDR, SI-resistant, and sensitive strains. The immune responses were assessed by evaluating cell proliferation, secretion of IL-4 and IL-17a cytokines, and ROS production over a 9-day period. ResultsPBMCs from PPD-positive individuals exhibited a higher proliferative response compared to PPD-negative individuals, indicating more robust immune memory. IL-4 secretion was low but varied among samples, with higher levels observed in response to MDR isolates, suggesting a potential role in immunopathology. IL-17a levels increased over time, particularly in PPD-positive individuals, and MDR strains elicited a stronger response than sensitive isolates. ROS production was significantly elevated in response to resistant strains, reflecting the hosts oxidative defense mechanisms. ConclusionThis study demonstrates distinct immune responses to drug-resistant M. tuberculosis isolates, with variations in cell proliferation, cytokine secretion, and ROS production. These findings provide insights into the immune dynamics during infection with resistant strains and underscore the importance of genotype-environment interactions in TB pathogenesis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/626310v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1bb9ad6org.highwire.dtl.DTLVardef@1b268e7org.highwire.dtl.DTLVardef@52800org.highwire.dtl.DTLVardef@85234b_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

Monovalent Pseudo-Natural Product Degraders Supercharge the Native Degradation of IDO1 by KLHDC3

Targeted protein degradation (TPD) modulates protein function beyond inhibition of enzyme activity or protein-protein interactions. Most degrader drugs function by directly mediating proximity between a neosubstrate and hijacked E3 ligase. Here, we identified pseudo-natural products derived from (-)-myrtanol, termed iDegs that inhibit and induce degradation of the immunomodulatory enzyme indoleamine-2,3-dioxygenase 1 (IDO1) by a distinct mechanism. iDegs boost IDO1 ubiquitination and degradation by the cullin-RING E3 ligase CRL2KLHDC3, which we identified to natively mediate ubiquitin-mediated degradation of IDO1. Therefore, iDegs increase IDO1 turnover using the native proteolytic pathway. In contrast to clinically explored IDO1 inhibitors, iDegs reduce formation of kynurenine by both inhibition and induced degradation of the enzyme and, thus, would also modulate non-enzymatic functions of IDO1. This unique mechanism of action may open up new therapeutic opportunities for the treatment of cancer beyond classical inhibition of IDO1.

cell biology↗

bioRxiv2024

White adipose tissue remodeling in Little Brown Myotis (Myotis lucifugus) with white-nose syndrome

White-nose syndrome (WNS) is a fungal wildlife disease of bats that has caused precipitous declines in certain Nearctic bat species. A key driver of mortality is premature exhaustion of fat reserves, primarily white adipose tissue (WAT), that bats rely on to meet their metabolic needs during winter. However, the pathophysiological and metabolic effects of WNS have remained ill-defined. To elucidate metabolic mechanisms associated with WNS mortality, we infected a WNS susceptible species, the Little Brown Myotis (Myotis lucifugus), with Pseudogymnoascus destructans (Pd) and collected WAT biopsies for histology and targeted lipidomics. These results were compared to the WNS-resistant Big Brown Bat (Eptesicus fuscus). A similar distribution in broad lipid class was observed in both species, with [~]60% of total WAT consisting of triacylglycerides (TAGs). We found several baseline differences in WAT chemical composition between species. M. lucifugus WAT had significantly higher levels of measured TAGs ([~]30%). Higher lipid levels in E. fuscus WAT were primarily sphingomyelins and glycerophosphoethanolamines (PEs), along with glycerophospholipids (GPs) dominated by unsaturated or monounsaturated moieties and n-6 (18:2, 20:2, 20:3, 20:4) fatty acids. These differences between M. lucifugus and E. fuscus may indicate dietary differences that lead to differential "fuel" reserves that are available during torpor. Following Pd-infection, we found that perturbation to WAT reserves occurs in M. lucifugus, but not in the resistant E. fuscus. A total of 36 GPs (primarily PEs) were higher in Pd-infected M. lucifugus, indicating perturbation to the WAT structural component. In addition to changes in lipid chemistry, smaller adipocyte sizes and increased extracellular matrix deposition was observed in Pd-infected M. lucifugus. This is the first study to describe WAT lipidomic composition of bats with different susceptibilities to WNS and highlights that recovery from WNS may require repair from adipose remodeling in addition to replenishing depot fat during spring emergence.

biochemistry↗

bioRxiv2024

Select DYRK1A Inhibitors Enhance Both Proliferation and Differentiation in Human Pancreatic Beta Cells

The small molecule DYRK1A inhibitor, harmine, induces human beta cell proliferation, expands beta cell mass, enhances expression of beta cell phenotypic genes, and improves human beta cell function in vitro and in vivo. It is unknown whether the "pro-differentiation effect" is a DYRK1A inhibitor class-wide effect. Here we compare multiple commonly studied DYRK1A inhibitors. Harmine, 2-2c and 5-IT increase expression of PDX1, MAFA, NKX6.1, SLC2A2, PCSK1, MAFB, SIX2, SLC2A2, SLC30A8, ENTPD3 in normal and T2D human islets. Unexpectedly, GNF4877, CC-401, INDY, CC-401 and Leucettine fail to induce expression of these essential beta cell molecules. Remarkably, the pro-differentiation effect is independent of DYRK1A inhibition: although silencing DYRK1A induces human beta cell proliferation, it has no effect on differentiation; conversely, harmine treatment enhances beta cell differentiation in DYRK1A-silenced islets. A careful screen of multiple DYRK1A inhibitor kinase candidate targets was unable to identify pro-differentiation pathways. Overall, harmine, 2-2c and 5-IT are unique among DYRK1A inhibitors in their ability to enhance both beta cell proliferation and differentiation. While beta cell proliferation is mediated by DYRK1A inhibition, the pro-differentiation effects of harmine, 2-2c and 5-IT are distinct, and unexplained in mechanistic terms. These considerations have important implications for DYRK1A inhibitor pharmaceutical development.

molecular biology↗

bioRxiv2024

Effects of gene dosage on cognitive ability: A function-based association study across brain and non-brain processes

Genomic Copy Number Variants (CNVs) that increase risk for neurodevelopmental disorders are also associated with lower cognitive ability in general population cohorts. Studies have focussed on a small set of recurrent CNVs, but burden analyses suggested that the vast majority of CNVs affecting cognitive ability are too rare to reach variant-level association. As a result, the full range of gene-dosage-sensitive biological processes linked to cognitive ability remains unknown. To investigate this issue, we identified all CNVs >50 kilobases in 258k individuals from 6 general population cohorts with assessments of general cognitive abilities. We performed a CNV-GWAS and functional burden analyses, which tested 6502 gene-sets defined by tissue and cell-type transcriptomics as well as gene ontology disrupted by all rare coding CNVs. CNV-GWAS identified a novel duplication at 2q12.3 associated with higher performance in cognitive ability. Among the 864 gene-sets associated with cognitive ability, only 11% showed significant effects for both deletions and duplication. Accordingly, we systematically observed negative correlations between deletion and duplication effect sizes across all levels of biological observations. We quantified the preferential effects of deletions versus duplication using tagDS, a new normalized metric. Cognitive ability was preferentially affected by cortical, presynaptic, and negative-regulation gene-sets when duplicated. In contrast, preferential effects of deletions were observed for subcortical, post-synaptic, and positive-regulation gene-sets. A large proportion of gene-sets assigned to non-brain organs were associated with cognitive ability due to low tissue specificity genes, which were associated with higher sensitive to haploinsufficiency. Overall, most biological functions associated with cognitive ability are divided into those sensitive to either deletion or duplications.

genetics↗

bioRxiv2024

Apoptotic proteins in Leishmania donovani: In silico screening, modelling, and validation by knock-out and gene expression analysis

Visceral leishmaniasis (VL), a life-threatening vector-borne illness that disproportionately affects children and elderly immunocompromised people, is a primary tropical neglected disease. No apoptotic partner proteins in L. donovani have been reported yet, which might contribute to the knowledge of parasite cell death and the establishment of alternative therapeutics. We used the Orthologues algorithm to search for the mammalian Bcl-2 family proteins orthologs, one anti-apoptotic and two pro-apoptotic, in L. donovani. We also included a pro-death aquaporin (AQP) protein due to its characteristic BH3 domain, which is known to interact with pro-apoptotic proteins in mammals. Molecular docking and molecular dynamics simulation studies were conducted to assess the protein-protein interaction between the identified apoptotic proteins and mimic mammalian intrinsic apoptotic pathways. The results showed that the pro-apoptotic protein interacted with the hydrophobic pocket of the anti-apoptotic ortholog, forming a stable complex, which may represent a critical event in the apoptotic pathways of leishmaniasis. To further establish an apoptotic pathway in L. donovani, we used several CRISPR-Cas9 approaches to target the identified proteins. The pure knocked population mutants, and episomal over-expressing mutant cells were exposed to apoptotic stimuli. TUNEL assay and quantitative expression profiling suggested that these proteins are needed during the parasites apoptosis and could play a role in the parasites survival. Author SummaryVisceral leishmaniasis, a fatal systemic infection affecting internal organs, is one of three types of leishmaniasis in mammals alongside cutaneous and mucocutaneous leishmaniasis. It predominantly occurs in tropical and subtropical climatic zones, Leishmania donovani predominant in the Indian subcontinent and Leishmania infantum in the Mediterranean basin, the Middle East, Central Asia, South America, and Central America. This disease primarily affects children, immunocompromised adults, and the elderly. L donovani, transmitted by the infected sandflies complete its life cycle in humans, serving as reservoir. During its life cycle, at a particular stage, the parasite undergoes apoptotic-like events, yet underlying proteins or key factors remain unidentified. Using computational methods, we screened the L. donovani genome for potential candidate genes of the Bcl-2 family apoptotic proteins. We biologically/experimentally validated our in-silico findings using molecular editing tools like CRISPR-Cas9, advancing our understanding of the parasites apoptotic pathway. Targeting this pathway could lead to more effective therapeutics against visceral leishmaniasis.

microbiology↗

bioRxiv2024

Unique functional neuroimaging signatures of genetic versus clinical high risk for psychosis

Background22q11.2 Deletion Syndrome (22qDel) is a copy number variant (CNV) associated with psychosis and other neurodevelopmental disorders. Adolescents at clinical high risk for psychosis (CHR) have subthreshold psychosis symptoms without known genetic risk factors. Whether common neural substrates underlie these distinct high-risk populations is unknown. We compared functional brain measures in 22qDel and CHR cohorts and mapped results to biological pathways. MethodsWe analyzed two large multi-site cohorts with resting-state functional MRI (rs-fMRI): 1) 22qDel (n=164, 47% female) and typically developing (TD) controls (n=134, 56% female); 2) CHR individuals (n=244, 41% female) and TD controls (n=151, 46% female) from the North American Prodrome Longitudinal Study-2. We computed global brain connectivity (GBC), local connectivity (LC), and brain signal variability (BSV) across cortical regions, testing case-control differences for 22qDel and CHR separately. Group difference maps were related to published brain maps using autocorrelation-preserving permutation. ResultsBSV, LC, and GBC are significantly disrupted in 22qDel compared with TD controls (False Discovery Rate q<0.05). Spatial maps of BSV and LC differences are highly correlated with each other, unlike GBC. In CHR, only LC is significantly altered versus controls, with a different spatial pattern compared to 22qDel. Group differences map onto biological gradients, with 22qDel effects strongest in regions with high predicted blood flow and metabolism. Conclusion22qDel and CHR exhibit divergent effects on fMRI temporal variability and multi-scale functional connectivity. In 22qDel, strong and convergent disruptions in BSV and LC not seen in CHR individuals suggest distinct functional brain alterations.

neuroscience↗

bioRxiv2024

Exploring variations in lipids among drug-resistant and sensitive Mycobacterium tuberculosis by Thin layer chromatography and mass spectrometry

Mycobacterium tuberculosis (M.tb) lipids are important in the host-pathogen interplay, variation in the lipids organization of cell wall can act as an adaptive response. Specific cell wall structures can possibly result in suboptimal intracellular concentrations of anti-TB drugs, which favors the acquisition of drug resistance. Therefore, lipids from M.tb (drug resistant and sensitive) were analyzed by 2D-thin layer chromatography and mass spectrometry. GraphPad Prism was used to perform Mann Whitney-U test to determine the statistical significance. Difference observed for total lipid content among different resistant isolates was insignificant. However, increase in phospholipids was identified in multi-drug resistant (MDR) isolate compared to sensitive isolate. Isoniazid, streptomycin-isoniazid, and isoniazid-ethambutol resistant isolates showed increased alpha-mycolic acids. MDR isolate showed a marginal decrease in alpha- and keto-form. Mycolipenic acid was seen only in sensitive isolate, and mycosanoic acids were observed in all the resistant isolates. Among the resistant isolates, there was an insignificant increase in the total phthiocerol dimycocerosates and sulfolipids. Drug resistance was associated with compositional imbalance of lipids. However, investigations to determine whether the changes notices are induced by the drugs is to be explored, which could give an insight into the drug resistant organisms pathogenesis.

microbiology↗

bioRxiv2024

Characterization, structure and inhibition of the human succinyl-CoA:glutarate-CoA transferase, a genetic modifier of glutaric aciduria type 1

Glutaric Aciduria Type 1 (GA1) is a serious inborn error of metabolism with no pharmacological treatments. A novel strategy to treat this disease is to divert the toxic biochemical intermediates to less toxic or non-toxic metabolites. Here, we report a novel target, SUGCT, which we hypothesize suppresses the GA1 metabolic phenotype through decreasing glutaryl-CoA. We report the structure of SUGCT, the first eukaryotic structure of a type III CoA transferase, develop a high-throughput enzyme assay and a cell-based assay, and identify valsartan and losartan carboxylic acid as inhibitors of the enzyme validating the screening approach. These results may form the basis for future development of new pharmacological intervention to treat GA1.

biochemistry↗

bioRxiv2023

Ultrasound-Assisted Hydrolysis of Food Waste using Glucoamylase: Statistical Optimization and Mechanistic Analysis with Molecular Simulations

Food waste represents a promising and cost-effective resource for synthesizing value-added products through a fermentative pathway. Preceding fermentation, the hydrolysis of food waste into monomeric sugars is a crucial step. This study presents a comprehensive investigation of food waste hydrolysis, encompassing experimental and computational approaches, using glucoamylase (GLCM) enzyme. Initial optimization of hydrolysis parameters was conducted through the Box-Behnken design of experiments, resulting in a total reducing sugar yield (TRS) of 263.4 mg/g biomass under optimized conditions within 42 hours. Sonication of hydrolysis mixture at 35 kHz at 20% duty cycle, yielded a 4x reduction in hydrolysis time with 22% enhancement in TRS yield (320 mg/g biomass). Analysis of GLCMs secondary structure revealed sonication-induced changes through FTIR spectra deconvolution in both control and test experiments. Sonication led to a reduction in -helix content and an increase in random coil content. Molecular dynamics simulations, including molecular docking, unveiled the majority of amino acid residues associated with the GLCM binding pocket in the -helix and random coil regions. Consequently, sonication widened the binding pockets, facilitating easier transport of substrate and product. This effect translated into improved reaction kinetics in food waste hydrolysis. Research HighlightsO_LIStatistical optimization of food waste hydrolysis: TRS yield = 263.4 mg/g in 42 h C_LIO_LI4x reduction of hydrolysis time, 22% rise in TRS yield with 35 kHz sonication C_LIO_LISonication reduced -helix content & increased random coil content of glucoamylase C_LIO_LIMolecular docking simulation to deduce mechanism of ultrasound-assisted hydrolysis C_LIO_LIMD simulations reveal widening of binding pockets and enhancing catalytic efficiency C_LI

biochemistry↗

bioRxiv2023

Acetone-Butanol-Ethanol (ABE) fermentation with Clostridial Co-cultures for Enhanced Biobutanol Production

This study investigates acetone-butanol-ethanol (ABE) fermentation, a process using solventogenic Clostridium species to produce acetone, butanol, and ethanol. Recent biotechnological advancements, such as omics, systems biology, and metabolic engineering, have reignited interest in butanol production, responding to the increasing gasoline costs and the demand for sustainable energy systems. This study unravels the distinct physiological attributes of C. acetobutylicum (Cac) and C. pasteurianum (Cpa), significantly impacting sustainable bioenergy technologies. Employing response surface methodology (RSM), we embarked on a comprehensive statistical optimization journey in the co-culture system, Cac MTCC 11274 and Cpa MTCC 116, enhancing biobutanol production from mixed substrates. A spectrum of process parameters was scrutinized, encompassing the ratio of Cac and Cpa inoculum, sodium concentration, and the ratio of xylose to glucose. Statistical analysis revealed salt concentrations profound influence on biomass, total alcohol, and butanol production. The culmination of these endeavors yielded highly promising outcomes: a butanol concentration of 12.1 {+/-} 0.45 g L-1 (model prediction: 11.87 g L-1), biomass of 4.15 {+/-} 0.03 (model prediction: 4.06 OD600), and ABE concentration of 23.1 {+/-} 0.55 g L-1 (model prediction: 22.45 g L-1). These results represent a significant leap forward in bioenergy technologies, offering both practical insights and sustainable solutions for enhanced biofuel production.

microbiology↗

bioRxiv2023

Increased susceptibility for pathogenesis of post-traumatic epilepsy in offspring exposed to deltamethrin during gestation and ameliorative effects of dietary curcumin

Deltamethrin (DLT) is a most potent and widely used pesticide that does not cross Blood Brain Barrier (BBB) in adults. While it considered as safe, its lipophilic properties makes it a neurotoxic substance specially in early stages of brain development. It has shown neurotoxic effects on the brain by hyper-excitation of neurons. Epilepsy is a neurological disorder with recurring seizures where epileptogenesis occurs due to hyperexcitation of neurons. In various kinds of epilepsy, post-traumatic epilepsy (PTE) is a common epilepsy in children due to traumatic brain injury (TBI). PTE, however reportedly alleviated by curcumin in rats. Therefore, in the current study, we assessed the effect of gestational DLT exposure on the severity of PTE. The pregnant rats were injected with 0.75mg/kg-b/w of DLT dissolved in 1% DMSO each day of gestation between days 7-15. Epilepsy was induced four months postnatally, and curcumin was orally administered by oral gavage. ECoG, behavioral tests, Golgi Staining, immunofluorescence, and immunohistochemistry was performed to assess the pathogenesis, severity of epilepsy, and mitigating effects of curcumin. The results indicated the neurotoxic effects of DLT by raising the severity of seizures in an electrophysiological and behavioral manner. PTE decreased the dendritic branching and arborization. Sodium channel overexpression is an important reason for the hyperexcitation of neurons during the pathogenesis of epilepsy. DLT enhanced the increase in expression of both sodium channel subunits NaV1.1 and NaV1.6 during epileptogenesis. Similarly, synaptic markers PSD95 and SYP decreased. Astrocytic and microglial activation increased during pathogenesis of PTE. The antiepileptic effects of curcumin alleviated the effects on electrobehavioral response, neuronal arborization, and levels of NaVs, PSD95, SYP, GFAP and Iba1 in epilepsy. However, DLT raised the severity and susceptibility of epilepsy and decreased the antiepileptic effects on gestationally DLT-exposed epileptic animals. Our result demonstrates the gestational neurotoxic exposure of DLT increased the severity and susceptibility for PTE while decreasing the antiepileptic effects of curcumin.

neuroscience↗

bioRxiv2023

Influence of amino acid substitutions in capsid proteins of coxsackievirus B5 on free chlorine and thermal inactivation

The sensitivity of enteroviruses to disinfectants varies among genetically similar variants and coincides with amino acid changes in capsid proteins, though the effect of individual substitutions remains unknown. Here, we employed reverse genetics to investigate how amino acid substitutions in coxsackievirus B5 (CVB5) capsid proteins affect its sensitivity to free chlorine and heat treatment. Of ten amino acid changes hypothesized to coincide with free chlorine resistance, none significantly reduced the chlorine-sensitivity, indicating a minor role of the capsid composition in chlorine sensitivity of CVB5. Conversely, we observed reduced heat sensitivity in mutants with substitutions at the C-terminal region of the viral protein 1. Cryo-electron microscopy revealed that these changes affect the assembly of intermediate viral states (particle A and E), suggesting that the mechanism for reduced heat sensitivity could be related to improved molecular packing of CVB5, resulting in greater stability and/or altered dynamics of virus uncoating during infection.

microbiology↗

bioRxiv2023

Cheminformatics analysis of multi-target structure-activity landscape of environmental chemicals binding to human endocrine receptors

In human exposome, environmental chemicals can target, and disrupt different endocrine axes, ultimately leading to several endocrine disorders. Such chemicals, termed endocrine disrupting chemicals (EDCs), can promiscuously bind to different endocrine receptors and lead to varying biological endpoints. Thus, understanding the complexity in molecule-receptor binding of environmental chemicals can aid in the development of robust toxicity predictors. Towards this, the ToxCast project has generated the largest resource on the chemical-receptor activity data for environmental chemicals that were screened across various endocrine receptors. However, the heterogeneity in the multi-target structure-activity landscape of such chemicals is not yet explored. In this study, we systematically curated the chemicals targeting 8 human endocrine receptors, their activity values and biological endpoints from the ToxCast chemical library. We employed dual-activity difference and triple-activity difference maps to identify single-, dual-, and triple-target cliffs across different target combinations. We annotated the identified activity cliffs through matched molecular pair (MMP) based approach, and observed that a small fraction of activity cliffs form MMPs. Further, we structurally classified the activity cliffs and observed that R-group cliffs form the highest fraction among the cliffs identified in various target combinations. Finally, we leveraged the mechanism of action (MOA) annotations to analyze structure-mechanism relationships, identified strong MOA-cliffs and weak MOA-cliffs, for each of the 8 endocrine receptors. Overall, insights from this first study analyzing the structure-activity landscape of environmental chemicals targeting multiple human endocrine receptors, will likely contribute towards the development of better toxicity prediction models for characterizing the human chemical exposome.

pharmacology and toxicology↗

bioRxiv2023

Polyimide-Based Flexible Multi-Electrode Arrays: Synthesis, Microfabrication, and in-vivo Validation

Neurological disorders such as epilepsy, Parkinsons disease, are rising globally, with conditions like drug-resistant epilepsy affecting millions of patients for whom traditional pharmacological treatments are ineffective. Implantable neural devices have shown great promise in managing these conditions, but their accessibility is limited due to high costs and the availability of suitable biocompatible materials.Thin film implantable neural interfaces hold immense promise over conventional clinical electrodes, offering higher resolution, flexibility, and improved integration with neural tissue. However, their widespread use, especially for flexible interfaces, is limited by the lack of customizable and medical grade materials. We report a novel synthesis method for ISO 10993-11 compliant polyamic acid that enables the fabrication of biocompatible polyimide films tailored for neural implants. Using this material, we developed 4 and 32 channel depth and surface electrodes, including custom whole brain ECoG arrays. These were implanted in the laforin knockout mice, a validated model of drug-resistant epilepsy, to monitor spontaneous seizures. Both acute and 12 day recordings demonstrated mechanical flexibility, long term stability, and excellent biocompatibility. This study presents a clinically safe material platform and a complete fabrication pathway for building thin film neural interfaces, paving the way for broader clinical use in applications such as epilepsy monitoring and stereo EEG.

bioengineering↗

bioRxiv2023

Analysis of structure-activity and structure-mechanism relationships among thyroid stimulating hormone receptor binding chemicals by leveraging ToxCast library

Thyroid stimulating hormone receptor (TSHR) is an integral part of the hypothalamic-pituitary-thyroid axis. Notably, dysregulation in TSHR activation in humans can lead to adverse effects such as Graves disease, hypothyroidism and Hashimotos disease. Moreover, animal studies have shown that binding of endocrine disrupting chemicals (EDCs) with TSHR can lead to developmental toxicity. Several such chemicals have also been screened for their adverse physiological effects in human cell lines through various high-throughput assays under the ToxCast project. The vast resource of data generated through ToxCast has enabled the development of different toxicity predictors, but they can be limited in their predictive ability due to the heterogeneity in structure-activity relationships among chemicals. In an attempt to explore this heterogeneity, we systematically investigated structure-activity and structure-mechanism relationships among the TSHR binding chemicals from ToxCast. By employing structure-activity similarity (SAS) map, we identified 79 activity cliffs among 509 chemicals in the TSHR agonist dataset and 69 activity cliffs among 650 chemicals in the TSHR antagonist dataset. Further, by using the matched molecular pair (MMP) approach, we find that the resultant activity cliffs (MMP-cliffs) are a subset of activity cliffs identified via the SAS map approach. Moreover, by leveraging ToxCast mechanism of action (MOA) annotations for chemicals common to both TSHR agonist and antagonist datasets, we identified 3 chemical pairs as Strong MOA-cliffs and 19 chemical pairs as Weak MOA-cliffs. In conclusion, the insights from this systematic analysis of the structure-activity as well as the structure-mechanism relationships of TSHR binding chemicals are likely to inform ongoing efforts towards development of better predictive toxicity models for characterizing the chemical exposome.

pharmacology and toxicology↗

bioRxiv2023

Using rare genetic mutations to revisit structural brain asymmetry

Asymmetry between the left and right brain is a key feature of brain organization. Hemispheric functional specialization underlies some of the most advanced human-defining cognitive operations, such as articulated language, perspective taking, or rapid detection of facial cues. Yet, genetic investigations into brain asymmetry have mostly relied on common variant studies, which typically exert small effects on brain phenotypes. Here, we leverage rare genomic deletions and duplications to study how genetic alterations reverberate in human brain and behavior. We quantitatively dissected the impact of eight high-effect-size copy number variations (CNVs) on brain asymmetry in a multi-site cohort of 552 CNV carriers and 290 non-carriers. Isolated multivariate brain asymmetry patterns spotlighted regions typically thought to subserve lateralized functions, including language, hearing, as well as visual, face and word recognition. Planum temporale asymmetry emerged as especially susceptible to deletions and duplications of specific gene sets. Targeted analysis of common variants through genome-wide association study (GWAS) consolidated partly diverging genetic influences on the right versus left planum temporale structure. In conclusion, our gene-brain-behavior mapping highlights the consequences of genetically controlled brain lateralization on human-defining cognitive traits.

neuroscience↗

bioRxiv2023

SWI/SNF complex-mediated chromatin remodelling is vital for cell surface adhesin repression and immune evasion

Immune evasion is critical for fungal virulence. However, how the human opportunistic pathogen Candida glabrata (Cg) accomplishes this is unknown. Here, using micrococcal nuclease-sequencing, RNA-sequencing, macrophage-signalling and genetic analyses, we demonstrate that chromatin reorganization in macrophage-internalized Cg, via CgSnf2 (ATPase subunit of the SWI/SNF chromatin remodelling complex), leads to upregulation and downregulation of immunosuppressive seven mannosyltransferase-cluster (CgMT-C) and immunostimulatory cell surface adhesin EPA1 genes, respectively. Consistently, EPA1 overexpression and CgMT-C deletion led to increased IL-1{beta} (pro-inflammatory cytokine) production and reduced Cg proliferation in macrophages. Further, CgSNF2 deletion evoked increased IL-1{beta} secretion, and the consequent killing of macrophage-internalized Cg, with elevated IL-1{beta} levels being partially reversed in Akt-, p38-, NF-{kappa}B- or NLRP3 inflammasome-inhibited macrophages. Importantly, macrophages respond to multiple Candida pathogens via NF-{kappa}B-dependent IL-1{beta} production, underscoring NF-{kappa}B signallings role in fungal diseases. Finally, we present the first genome-wide nucleosome map of macrophage-internalized Cg consisting of [~]12,000 dynamic and 70,000 total nucleosomes. Altogether, our findings directly link the nucleosome positioning-based chromatin remodelling to fungal immunomodulatory molecule expression, which dictates Cg fate in host immune cells.

microbiology↗