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Mishra, B.

Publications and source records attributed to Mishra, B..

At least 37 records · Page 2Linked to original sources
bioRxiv2023

Integrative systems biology framework discovers common gene regulatory signatures in multiple mechanistically distinct inflammatory skin diseases

AimMore than 20% of the population across the world is affected by non-communicable inflammatory skin diseases including psoriasis, atopic dermatitis, hidradenitis suppurativa, rosacea, etc. Many of these chronic diseases are painful and debilitating with limited effective therapeutic interventions. However, recent advances in psoriasis treatment have improved the effectiveness and provide better management of the disease. Similar effective treatments are also needed for other chronic skin disorders regulated molecular pathogenesis. This study aims to identify common regulatory pathways and master regulators that regulate molecular pathogenesis. MethodsWe designed an integrative systems biology framework to identify the significant regulators across several inflammatory skin diseases. We exploited the gene co-expression-, and protein-protein interaction-based networks to identify shared genes and pro components in different diseases with relevant functional implications. Further, we utilized network analytics to unravel the high-priority proteins, that play a crucial role in disease pathogenesis. ResultsWith conventional transcriptome analysis we identified 55 shared genes, which are enriched in several immune-associated pathways in eight inflammatory skin diseases. Our correlation-based co-expression networks identified the core co-expression networks and the integrative multi-omics interactomes providing core interactions across four of the eight diseases. Next, by implementing network analytics, we unraveled 55 high-value proteins as significant regulators in molecular pathogenesis. We believe that these significant regulators should be explored with critical experimental approaches to identify the putative drug targets for more effective treatments. As an example, we identified IKZF1 as a shared significant master regulator in three inflammatory skin diseases, which can serve as a putative drug target with known disease-derived molecules for developing efficacious combinatorial treatments for hidradenitis suppurativa, atopic dermatitis, and rosacea. ConclusionThe conventional transcriptome results identify huge complexity among inflammatory skin diseases, which demands a systems biology perspective for comprehensive understanding. The proposed framework is very modular, which can indicate a significant path of molecular mechanism-based drug development from complex transcriptomics data and other multi-omics data.

systems biology↗
bioRxiv2023

Staphyloccocus aureus biofilm, in the absence of planktonic bacteria, produces factors that activate counterbalancing inflammatory and immune-suppressive genes in human monocytes

Staphyloccocus aureus (S. aureus) is a major bacterial pathogen in orthopedic periprosthetic joint infection (PJI). S. aureus forms biofilms that promote persistent infection by shielding bacteria from immune cells and inducing an antibiotic-resistant metabolic state. We developed an in vitro system to study S. aureus biofilm interactions with primary human monocytes in the absence of planktonic bacteria. In line with previous in vivo data, S. aureus biofilm induced expression of inflammatory genes such as TNF and IL1B, and their anti-inflammatory counter-regulator IL-10. S. aureus biofilm also activated expression of PD-1 ligands that suppress T cell function, and of IL-1RA that suppresses differentiation of protective Th17 cells. Gene induction did not require monocyte:biofilm contact and was mediated by a soluble factor(s) produced by biofilm-encased bacteria that was heat resistant and > 3 kD in size. Activation of suppressive genes by biofilm was sensitive to suppression by Jak inhibition. These results support an evolving paradigm that biofilm plays an active role in modulating immune responses, and suggest this occurs via production of a soluble vita-PAMP. Induction of T cell suppressive genes by S. aureus biofilm provides insights into mechanisms that suppress T cell immunity in PJI, and suggest that anti-PD-1 therapy that is modeled on immune checkpoint blockade for tumors may be beneficial in PJI.

immunology↗
bioRxiv2023

The uniqueness of the Brazilian Yellow Fever Virus. Are the vaccines less effective against it?

The years 2016-2019 witnessed the expansion of Yellow Fever Virus (YFV) circulation area in Brazil. Deforestation and mutations in the nsp genes were presumed responsible for the reemergence of YFV in brazil. However, our data analysis involving 200 clinical isolates worldwide including vaccine strains showed two amino acids substitutions exclusively in the Brazilian strains at critical positions (V318A and I335M) in the ED III domain of E protein. Our molecular dynamics analysis involving reference and mutant structures suggests that the mutations significantly changed the conformational rearrangement and folding of the YFV-EDIII domain as revealed by RMSF, PCA, Porcupine plots and secondary structure analysis. Briefly, the regions 324-330, 339-346 and 347-359 had a higher fluctuation than the wild, while regions 313-318 and 379-384 had a lower fluctuation. As reported earlier that the residues E325 and E380 are part of vaccine epitopes and any mutations in these residues reduced the binding of vaccine generated mabs to the epitopes. Hence, it may be speculated from our porcupine plot data analysis that that the commercial YFV vaccines may not be fully effective against the Brazilian strains in particular owing to the fluctuations of these residues. However, future investigation is required to validate the observations.

microbiology↗
bioRxiv2023

Bcl-xL is translocated to the nucleus via CtBP2 to epigenetically promote metastasis

Besides its mitochondria-based anti-apoptotic role, Bcl-xL also travels to the nucleus to promote cancer metastasis by upregulating global histone H3 trimethyl Lys4 (H3K4me3) and TGF{beta} transcription. How Bcl-xL is translocated into the nucleus and how nuclear Bcl-xL regulates H3K4me3 modification are not understood. Here, we report that C-terminal Binding Protein 2 (CtBP2) binds Bcl-xL via its N-terminus and translocates Bcl-xL into the nucleus. Knockdown of CtBP2 by shRNA decreases the nuclear portion of Bcl-xL and reverses Bcl-xL-induced cell migration and metastasis in mouse models. Furthermore, knockout of CtBP2 suppresses Bcl-xL transcription. The binding between Bcl-xL and CtBP2 is required for their interaction with MLL1, a histone H3K4 methyltransferase. Pharmacologic inhibition of MLL1 enzymatic activity reverses Bcl-xL-induced H3K4me3 and TGF{beta} mRNA upregulation as well as cell invasion. Moreover, cleavage under targets and release using nuclease (CUT&RUN) coupled with next generation sequencing reveals that H3K4me3 modifications are particularly enriched in the promotor region of genes encoding TGF{beta} and its signaling pathway in the cancer cells overexpressing Bcl-xL. Altogether, the metastatic function of Bcl-xL is mediated by its interaction with CtBP2 and MLL1.

cancer biology↗
bioRxiv2023

Temporal control by co-factors prevents kinetic trapping in retroviral Gag lattice assembly

For retroviruses like HIV to proliferate, they must form virions shaped by the self-assembly of Gag polyproteins into a rigid lattice. This immature Gag lattice has been structurally characterized and reconstituted in vitro, revealing the sensitivity of lattice assembly to multiple co-factors. Due to this sensitivity, the energetic criterion for forming stable lattices is unknown, as are their corresponding rates. Here, we use a reaction-diffusion model designed from the cryo-ET structure of the immature Gag lattice to map a phase diagram of assembly outcomes controlled by experimentally constrained rates and free energies, over experimentally relevant timescales. We find that productive assembly of complete lattices in bulk solution is extraordinarily difficult due to the large size of this [~]3700 monomer complex. Multiple Gag lattices nucleate before growth can complete, resulting in loss of free monomers and frequent kinetic trapping. We therefore derive a time-dependent protocol to titrate or activate the Gag monomers slowly within the solution volume, mimicking the biological roles of co-factors. This general strategy works remarkably well, yielding productive growth of self-assembled lattices for multiple interaction strengths and binding rates. By comparing to the in vitro assembly kinetics, we can estimate bounds on rates of Gag binding to Gag and the cellular co-factor IP6. Our results show that Gag binding to IP6 can provide the additional time-delay necessary to support smooth growth of the immature lattice with relatively fast assembly kinetics, mostly avoiding kinetic traps. Our work provides a foundation for predicting and disrupting formation of the immature Gag lattice via targeting specific protein- protein binding interactions.

biophysics↗
bioRxiv2022

CXCL4 signaling and gene induction in human monocytes involve a TLR4 response divergent from LPS

The chemokine CXCL4 activates myeloid cells and contributes to the pathogenesis of inflammatory and fibrotic diseases. One mechanism of CXCL4 action is binding of nucleic acids to promote their internalization and activation of endosomal TLRs. However, the signaling pathways and receptors that mediate myeloid cell responses to CXCL4 alone are not well characterized. Here, we report that in primary human monocytes, CXCL4 activated NF-{kappa}B and a TBK1-JNK signaling axis that drive the expression of inflammatory, fibrotic and neutrophil chemokine genes, and also RIPK3-dependent necroptosis. Surprisingly, six distinct lines of evidence targeting TLR4 expression and function suggested a role for TLR4 in CXCL4 responses. However, we were not able to completely dissect the contributions of CXCL4 alone to the observed results versus a contribution from endotoxin contamination. Our findings suggest that the interactions between CXCL4 and TLR4 merit further study.

immunology↗
bioRxiv2022

Changes in m6A RNA methylation of goat lung following PPRV infection

Peste des petits ruminants (PPR) is an acute, highly contagious viral disease of goats and sheep, caused by the Peste des petits ruminants virus (PPRV). Earlier studies suggest the involvement of diverse regulatory mechanisms in PPRV infection. Methylation at N6 of Adenosine called m6A is one such RNA modification that influences various physiological and pathological phenomena. As the lung tissue represents the primary target organ of PPRV, the present study explored the m6A changes and their functional significance in PPRV disease pathogenesis. m6A-seq analysis revealed 1289 m6A peaks to be significantly altered in PPRV infected lung in comparison to normal lung, out of which 975 m6A peaks were hypomethylated and 314 peaks were hypermethylated. Importantly, hypomethylated genes were enriched in Interleukin-4 and Interleukin-13 signaling and various processes associated with extracellular matrix organization. Further, of the 843 differentially m6A containing cellular transcripts, 282 transcripts were also found to be differentially expressed. Functional analysis revealed that these 282 transcripts are significantly enriched in signaling by Interleukins, extracellular matrix organization, cytokine signaling in the immune system, signaling by receptor tyrosine kinases, and Toll-like Receptor Cascades. We also found m6A reader HNRNPC and the core component of methyltransferase complex METTL14 to be highly upregulated than the m6A readers - HNRNPA2B1 and YTHDF1 at the transcriptome level. These findings suggest that alteration in m6A landscape following PPRV is implicated in diverse processes including the Interleukin signaling.

microbiology↗
bioRxiv2022

Do place cells dream of deceptive moves in a signaling game?

We consider the possibility of applying game theory to analysis and modeling of neurobiological systems. Specifically, the basic properties and features of information asymmetric signaling games are considered and discussed as having potential to explain diverse neurobiological phenomena at levels of biological function that include gene regulation, molecular and biochemical signaling, cellular and metabolic function, as well as the neuronal action potential discharge that can represent cognitive variables such as memory and purposeful behavior. We begin by arguing that there is a pressing need for conceptual frameworks that can permit analysis and integration of information and explanations across the many scales of diverse levels of biological function. Developing such integrative frameworks is crucial if we are to understand cognitive functions like learning, memory, and perception. The present work focuses on systems level neuroscience organized around the connected brain regions of the entorhinal cortex and hippocampus. These areas are intensely studied in rodent subjects as model neuronal systems that undergo activity-dependent synaptic plasticity to form and represent memories and spatial knowledge used for purposeful navigation. Examples of cognition-related spatial information in the observed neuronal discharge of hippocampal place cell populations and medial entorhinal head-direction cell populations are used to illustrate possible challenges to information maximization concepts. It may be natural to explain these observations using the ideas and features of information asymmetric signaling games.

neuroscience↗
bioRxiv2021

Phosphorylation dynamics in a flg22 induced, heterotrimeric G protein dependent signaling network in Arabidopsis thaliana reveals a candidate PP2A phosphatase involved in AtRGS1 trafficking

flg22 is a 22-amino peptide released from bacterial flagellin, a Microbe-Associated Molecular Pattern (MAMP) that is recognized by the plant cell as a signal indicating that bacteria are present. On its own, flg22 initiates a rapid increase in cytoplasmic calcium, extracellular reactive oxygen species, and activation of a Mitogen Activated Protein Kinase (MAPK) cascade, all of which are activated within 15 minutes after the cell perceives flg22. Here we show a massive change in protein abundance and phosphorylation state of the Arabidopsis root cell proteome within this 15-minute duration in wildtype and a mutant deficient in G-protein coupled signaling. Integration of phosphoproteome with protein-protein interactome data followed by network topology analyses discovered that many of the flg22-induced phosphoproteome changes fall on proteins that comprise the G protein interactome and on the most highly populated hubs of the immunity network. Approximately 95% of the phosphorylation changes in the G-protein interactome depend on a functional heterotrimeric G protein complex, some occur on proteins that interact directly with components of G-coupled signal transduction. One of these is ATB, a substrate-recognition sub-unit of the PP2A Ser/Thr phosphatase and an interactor to Arabidopsis thaliana REGULATOR OF G SIGNALING 1 protein (AtRGS1), a 7-transmembrane spanning modulator of the nucleotide-binding state of the core G protein complex. AtRGS1 is phosphorylated by BAK1, a component of the flg22 receptor, to initiate AtRGS1 endocytosis. A null mutation of ATB confers high basal endocytosis of AtRGS1, suggesting sustained phosphorylated status. Loss of ATB confers traits associated with loss of AtRGS1. Because the basal level of AtRGS1 is lower in the atb null mutant in a proteasome-dependent manner, we propose that phosphorylation-dependent endocytosis of AtRGS1 is part of a mechanism to degrade AtRGS1 which then sustains activation of the G protein complex. Thus, the role of ATB is now established as a central component of phosphorylation-dependent regulation of system dynamics in innate immunity.

systems biology↗
bioRxiv2021

Lotka-Volterra equations in the presence of Mimicry

This paper studies a novel framework for understanding toxicity and nutritional value of a prey to a predator with utility. Furthermore, it introduces a novel notion of prey mimicry in a multi predator - multi prey system. In addition, the paper also analyzes the dynamics and the stability of equilibrium that arise as a result of the one or more predators inability to distinguish between certain prey. The paper is motivated by the mimicry in the context of adversarial chase involved in the evolution of multiple viral variants in the presence of multiple vaccines - possibly, in a population stratified by a diverse HLA background.

evolutionary biology↗
bioRxiv2021

A chromosome-level genome assembly of the European Beech (Fagus sylvativa) reveals anomalies for organelle DNA integration, repeat content and distribution of SNPs

The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 Mb and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb of the genome in which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome- wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.

genomics↗
bioRxiv2021

Efficient Agony Based Transfer Learning Algorithms for Survival Forecasting

Progression modeling is a mature subfield of cancer bioinformatics, but it has yet to make a proportional clinical impact. The majority of the research in this area has focused on the development of efficient algorithms for accurately reconstructing sequences of (epi)genomic events from noisy data. We see this as the first step in a broad pipeline that will translate progression modeling to clinical utility, with the subsequent steps involving inferring prognoses and optimal therapy programs for different cancers and using similarity in progression to enhance decision making. In this paper we take some initial steps in completing this pipeline. As a theoretical contribution, we introduce a polytime-computable pairwise distance between progression models based on the graph-theoretic notion of "agony". Focusing on a particular progression model we can then use this agony distance to cluster (dis)similarities via multi-dimensional scaling. We recover known biological similarities and dissimilarities. Finally, we use the agony distance to automate transfer learning experiments and show a large improvement in the ability to forecast time to death.

cancer biology↗
bioRxiv2021

Speed limits of protein assembly with reversible membrane localization

Self-assembly is often studied in a three-dimensional (3D) solution, but a significant fraction of binding events involve proteins that can reversibly bind and diffuse along a two-dimensional (2D) surface. In a recent study, we quantified how proteins can exploit the reduced dimension of the membrane to trigger complex formation. Here, we derive a single expression for the characteristic timescale of this multi-step assembly process, where the change in dimensionality renders rates and concentrations effectively time-dependent. We find that proteins can accelerate complex formation due to an increase in relative concentration, driving more frequent collisions which often wins out over slow-downs due to diffusion. Our model contains two protein populations that associate with one another and use a distinct site to bind membrane lipids, creating a complex reaction network. However, by identifying two major rate-limiting pathways to reach an equilibrium steady-state, we derive an accurate approximation for the mean first passage time when lipids are in abundant supply. Our theory highlights how the sticking rate, or effective adsorption coefficient of the membrane is central in controlling timescales. We also derive a corrected localization rate to quantify how the geometry of the system and diffusion can reduce rates of localization. We validate and test our results using kinetic and reaction-diffusion simulations. Our results establish how the speed of key assembly steps can shift by orders-of-magnitude when membrane localization is possible, which is critical to understanding mechanisms used in cells.

biophysics↗
bioRxiv2020

Genomic basis of drought resistance in Fagus sylvatica

In the course of global climate change, central Europe is experiencing more frequent and prolonged periods of drought. The drought years 2018 and 2019 affected European beeches (Fagus sylvatica L.) differently: even in the same stand, drought damaged trees neighboured healthy trees, suggesting that the genotype rather than the environment was responsible for this conspicuous pattern. We used this natural experiment to study the genomic basis of drought resistance with Pool-GWAS. Contrasting the extreme phenotypes identified 106 significantly associated SNPs throughout the genome. Most annotated genes with associated SNPs (>70%) were previously implicated in the drought reaction of plants. Non-synonymous substitutions led either to a functional amino acid exchange or premature termination. A SNP-assay with 70 loci allowed predicting drought phenotype in 98.6% of a validation sample of 92 trees. Drought resistance in European beech is a moderately polygenic trait that should respond well to natural selection, selective management, and breeding. Impact StatementEuropean beech harbours substantial genetic variation at genomic loci associated with drought resistance and the loci identified in this study can help to accelerate and monitor adaptation to climate change.

plant biology↗
bioRxiv2020

Systems Biology behind immunoprotection of both Sheep and Goats after Sungri/96 PPRV vaccination

Immune response is a highly coordinated cascade involving all the subsets of PBMCs. In this study, RNA-Seq analysis of PBMC subsets - CD4+, CD8+, CD14+, CD21+ and CD335+ cells from day 0 and day 5 of Sungri/96 Peste des Petits Ruminants vaccinated sheep and goats was done to delineate the systems biology behind immune - protection of the vaccine in sheep and goats. Assessment of the immune response processes enriched by the differentially expressed genes in all the subsets suggested a strong dysregulation towards development of early inflammatory microenvironment, which is very much required for differentiation of monocytes to macrophages, and for activation and migration of dendritic cells into the draining lymph nodes. The protein - protein interaction networks among the antiviral molecules (IFIT3, ISG15, MX1, MX2, RSAD2, ISG20, IFIT5 and IFIT1) and common DEGs across PBMCs subsets in both the species identified ISG15 to be an ubiquitous hub, that helps in orchestrating antiviral host response against PPRV. IRF7 was found to be the key master regulator activated in most of the subsets in sheep and goats. Most of the pathways were found to be inactivated in B - lymphocytes of both the species indicating that 5 dpv is too early a time point for the B - lymphocytes to react. The cell mediated immune response and humoral immune response pathways were found more enriched in goats than in sheep. Though, animals from both the species survived the challenge, a contrast in pathway activation was observed in CD335+ cells. ImportancePeste des petits ruminants (PPR) by PPRV is an OIE listed acute, contagious transboundary viral disease of small ruminants. Attenuated Sungri/96 PPRV vaccine used all over India against this PPR, provides long-lasting robust innate and adaptive immune response. The early antiviral response was found mediated through type I interferon independent ISGs expression. However, systems biology behind this immune response is unknown. In this study, in vivo transcriptome profiling of PBMC subsets (CD4+, CD8+, CD14+, CD21+ and CD335+) in vaccinated goats and sheep (at 5 days of post vaccination) was done to understand this systems biology. Though there are a few differences in the systems biology across cells (specially the NK cells) between sheep and goats, the co-ordinated response that is inclusive of all the cell subsets was found to be towards induction of strong innate immune response, which is needed for an appropriate adaptive immune response.

systems biology↗
bioRxiv2020

Prediction analysis of SARS-COV-2 entry in Livestock and Wild animals

BackgroundSARS-CoV-2 is a viral pathogen causing life-threatening disease in human. Interaction between spike protein of SARS-CoV-2 and ACE2 receptor on the cells is a potential factor in the infectivity of a host. The interaction of SARS-CoV-2 spike receptor-binding domain with its receptor - ACE2, in different hosts was evaluated to understand and predict viral entry. The protein and nucleotide sequences of ACE2 were initially compared across different species to identify key differences among them. The ACE2 receptor of various species was homology modeled (6LZG, 6M0J, and 6VW1 as a reference), and its binding ability to the spike ACE2 binding domain of SARS-CoV-2 was assessed. Initially, the spike binding parameters of ACE2 of known infected and uninfected species were compared with each Order (of animals) as a group. Finally, a logistic regression model vis-a-vis the spike binding parameters of ACE2 (considering data against 6LZG and 6M0J) was constructed to predict the probability of viral entry in different hosts. ResultsPhylogeny and alignment comparison did not lead to any meaningful conclusion on viral entry in different hosts. Out of several spike binding parameters of ACE2, a significant difference between the known infected and uninfected species was observed for six parameters. However, these parameters did not specifically categorize the Orders (of animals) into infected or uninfected. The logistic regression model constructed revealed that in the mammalian class, most of the species of Carnivores, Artiodactyls, Perissodactyls, Pholidota, and Primates had high probability of viral entry. However, among the primates, African Elephant had low probability of viral entry. Among rodents, hamsters were highly probable for viral entry with rats and mice having a medium to low probability. Rabbits have a high probability of viral entry. In Birds, ducks have a very low probability, while chickens seemed to have medium probability and turkey showed the highest probability of viral entry. ConclusionsMost of the species considered in this study showed high probability of viral entry. This study would prompt us to closely follow certain species of animals for determining pathogenic insult by SARS-CoV-2 and for determining their ability to act as a carrier and/or disseminator.

microbiology↗
bioRxiv2020

Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis

COVID-19 (Coronavirus disease 2019) is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). While the pathophysiology of this deadly virus is complex and largely unknown, we employ a network biology-fueled approach and integrated multiomics data pertaining to lung epithelial cells-specific coexpression network and human interactome to generate Calu-3-specific human-SARS-CoV-2 Interactome (CSI). Topological clustering and pathway enrichment analysis show that SARS-CoV-2 target central nodes of host-viral network that participate in core functional pathways. Network centrality analyses discover 28 high-value SARS-CoV-2 targets, which are possibly involved in viral entry, proliferation and survival to establish infection and facilitate disease progression. Our probabilistic modeling framework elucidates critical regulatory circuitry and molecular events pertinent to COVID-19, particularly the host modifying responses and cytokine storm. Overall, our network centric analyses reveal novel molecular components, uncover structural and functional modules, and provide molecular insights into SARS-CoV-2 pathogenicity.

systems biology↗