Biology subjects

Sahoo, A.

Publications and source records attributed to Sahoo, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Confluent growth state dependent transcriptomic adaptation in A549 lung cancer cells

Cell confluency is a major determinant of cell-cell communication, protein interactions, access to nutrients, and signalling dynamics, thereby significantly impacting biological outcomes. Lung cancer cells like A549 are widely used as screening models for scientific studies wherein their growth in vitro progress from non-confluent to confluent growth. In this study, we investigated the transcriptomic adaptations associated with the transition of A549 cells from baseline non-confluent to confluent growth. Comparative transcriptomic analysis between confluent and cells at baseline identified 815 upregulated and 671 downregulated transcripts. Pathway enrichment analysis of deregulated transcripts in confluent cells revealed enhanced cholesterol and sterol biosynthetic pathways, along with suppression of chromosomal segregation and mitotic pathways. At confluency, an increased expression of glucose transporters (SLC2, SLC60, and SL37 families) and glycolytic pathways, and a decrease in amino acid transporters (SLC1, SLC7, SLC38, and SLC36) and amino acid metabolic pathways is observed. A reduced one-carbon metabolic signature (SHMT2, DHFR, and MTHFD2) and enhanced fatty acid precursor synthesis (HMGCLL1, ALDH6A1, and AASS) were also observed at confluency. 1H NMR profiling of culture media revealed higher glucose and glutamine utilisation with lactate accumulation during culture maturation. Collectively, the data suggest transcriptome-level rewiring in A549 cells with preferential biosynthesis of lipids and sterols at confluency and underscore the importance of considering culture maturity in cancer biology, metabolism, and therapeutic studies.

systems biology↗

bioRxiv2025

Non-human primate LIBRA-Seq accelerates neutralizing antibody discovery in RM vaccinated against HIV-1

Broadly neutralizing antibodies (bNAbs) exhibit protective efficacy against HIV-1 infection making them an ideal archetype for HIV-1 vaccine design. Presently, no vaccine candidate has induced antibody responses capable of meaningful protection against the swathe of circulating, difficult to neutralize tier 2 HIV-1 viruses. However, the development of stabilized, native-like envelope (Env) trimers such as BG505.SOSIP.664.T332N (BG505 SOSIP) has marked a significant advancement in vaccine design, due to their ability to elicit NAbs that neutralize tier 2 viruses in rhesus macaques (RM). NAb development following envelope trimer immunization in RM remains poorly understood, with hypothesized contributions from genetic variation at the IG loci, naive B cell repertoire, and differential gene expression in B cell lineages. To address these knowledge gaps, we have developed a set of BG505 SOSIP probes capable of recovering paired clonotype identity, antigen specificity, and gene expression of B cells in a high throughput fashion. These probes were constructed by conjugating biotinylated BG505 SOSIP to streptavidin covalently linked to both sc-RNA-Seq compatible DNA oligonucleotides and flow cytometry compatible fluorophores. Using these reagents, we isolated and sequenced BG505 SOSIP specific memory B cells from the PBMCs of an RM that developed high titers of neutralizing antibodies. To benchmark the accuracy of our technology, we compared our recovered heavy and light chain sequences to those identified from the same animal using conventional methodology and recovered 100% of previously identified NAbs. We then applied this technology to recover BG505 SOSIP specific memory B cells from five additional vaccinated RMs, cloned 34 antibodies for functional characterization, and identified ten antibodies with autologous neutralizing activity. Author SummaryUnderstanding how effective antibodies arise after HIV vaccination is essential for developing a protective vaccine, yet studying these responses in non-human primates has been limited by low- throughput methods. In this study, we adapted a high-throughput single-cell sequencing approach to identify HIV envelope-specific antibodies from vaccinated rhesus macaques. This method allowed us to recover paired antibody sequences together with their antigen specificity from thousands of individual B cells. We successfully identified known neutralizing antibodies and discovered additional antibodies capable of neutralizing HIV across multiple animals. Our analysis revealed that vaccine-elicited antibody responses were dominated by a small number of expanded lineages, with shared genetic features among animals with stronger neutralization. These findings demonstrate that this approach can efficiently define the antibody repertoires generated by HIV vaccines and provide a powerful tool for evaluating and improving immunogens in preclinical vaccine studies.

immunology↗

bioRxiv2025

Study of Protein-Protein Interactions in Septin Assembly: Multiple amphipathic helix domains cooperate in binding to the lipid membrane

Septins are a conserved family of cytoskeletal proteins known for sensing micron-scale membrane curvature via amphipathic helix (AH) domains. While cooperative interactions in septin assembly have been suggested, the molecular mechanisms governing membrane binding and assembly remain unclear. Building on prior findings, we use all-atom molecular dynamics simulations to examine how single and paired extended AH domains, derived from Cdc12, interact with lipid bilayers. A single membrane-bound AH adopts a curved conformation. In solution, a second AH peptide preferentially interacts with the bound peptide through conserved salt bridges, favoring an antiparallel arrangement. Simulations of covalently linked AH tandems confirm this configuration. Dual membrane-bound peptides induce lipid packing defects, reduce tail order, and exhibit slight membrane displacement, suggesting curved membranes may better accommodate multiple AH domains. Our findings advance the mechanistic understanding of septin-membrane interactions and highlight the role of cooperative AH domain binding in stabilizing higher-order structures.

biophysics↗

bioRxiv2025

Prolonged autophagy induction correlates with host cell protein reduction in CHO cell culture

Autophagy, a cellular recycling process regulated by the CLEAR signaling pathway, plays a pivotal role in maintaining cellular homeostasis. We hypothesize that this process may regulate and reduce HCP levels by targeting intracellular proteins and organelles for degradation. This study investigates the relationship between autophagy induction and the reduction of high-risk host cell proteins (HCPs), including polysorbate-degrading enzymes (PSDEs), to enhance the stability of therapeutic biologics such as monoclonal antibodies (mAbs). Using clonal analysis, we identified upregulation of the CLEAR pathway in one clone, correlating with a significant reduction in lipase activity and PSDE abundance. Furthermore, autophagy modulators, such as 3-methyladenine (3-MA), selectively decreased PSDE levels in both batch and fed-batch cultures. This resulted in 62% reduction in lipase activity that corresponded to a 22% improvement in polysorbate-80 stability. Additionally, 3-MA treatment increased mAb specific productivity and altered glycosylation profiles, increasing afucosylation and galactosylation levels. These findings highlight autophagy induction as a promising strategy to modulate product quality profiles and reduce high-risk HCPs in biologics production.

bioengineering↗

bioRxiv2025

Basic-Leucine-Zipper Transcription Factors Regulate Selective Molecular Phenotypes in Regulatory T Cells During IL-2-Induced Activation

Regulatory T (Treg) cells have long been recognized as modulators of immunological tolerance and homeostasis. Previously, we used scRNA-seq to reveal significant Treg heterogeneity in response to IL-2-induced activation. Herein, we leveraged enrichment analyses, as well as bulk and single-nucleus multi-omics in splenic and lung Tregs, to uncover and confirm the importance of transcription factors (TFs) and chromatin remodeling in Treg activation. Multiple bZIP TF motifs showed increased chromatin accessibility post IL-2 treatment, with correlated transcriptional changes resembling Th1 and Th2 molecular phenotypes, further confirmed by spatial ATAC-seq. By combining gene perturbation and CUT&RUN assays before and after Treg stimulation, we show that bZIP TFs, such as BATF and BACH1, are critical to IL-2-induced Treg activation, coordinating epigenetic and transcriptional changes that selectively drive T-helper phenotypes and metabolic pathways.

genomics↗

bioRxiv2025

Discovery of Chemical Tools for Polysorbate-Degradative Enzyme Control in Biopharmaceutical Upstream Process via Multi-Omic Profiling of Host Cell Clones

Host cell proteins are process-related impurities in biotherapeutics and can potentially pose risks to patient safety and product quality. Specifically, certain host cell-derived enzymes, including lipases, can degrade the formulation excipient polysorbate (PS) in biopharmaceutical formulations, affecting drug product stability in liquid formulations. We leveraged multi-omics approaches, including transcriptomics, proteomics, and activity-based protein profiling (ABPP), to identify mechanisms that regulate PS-degradative enzyme (PSDE) abundance and to develop strategies for their control. Comparative multiomics analysis of two monoclonal antibodies (mAb)-producing host cell clones revealed differential lipase profiles at the mRNA, protein, and enzyme activity levels and associated increased lipase activity with upregulated lipid catabolic pathways such as the fatty acid beta oxidation pathway. Further, for the first time in the literature, we identified peroxisome proliferator-activated receptor {gamma} (PPAR{gamma}) as a key regulator of PSDEs in manufacturing Chinese Hamster Ovary (CHO) cells. Downregulation of the PPAR{gamma} pathway with its antagonists resulted in selective reduction of PSDE levels and improved PS stability without compromising mAb productivity or quality. This study highlights the potential of PPAR{gamma} modulators as chemical tools for PSDE control at the gene regulation level, offering significant implications for biopharmaceutical process development and control.

bioengineering↗

bioRxiv2024

EGDiff: An Experiment-Guided Diffusion model for protein conformational ensemble generation

Understanding protein conformation is key to understanding their function. Importantly, most proteins adopt multiple conformations with non-trivial ensemble distributions that change depending on their environment to perform functions like catalysis, signaling, and transport. Recently, machine learning techniques, especially deep generative models, have been employed to develop protein conformation generators. These models, known as unified protein ensemble samplers, are trained on the PDB dataset and can generate diverse protein conformation ensembles given a protein sequence. However, their reliance solely on structural data from the PDB, which primarily captures folded protein states, restricts the diversity of the generated ensembles and can result in physically unrealistic conformations. In this paper, we overcome these challenges by introducing ExEnDiff, an experiment-guided diffusion model for protein conformation generation. ExEnDiff integrates experimental measurements as a physical prior, enabling the generation of protein conformations with desired properties. Our experiments on a variety of fast-folding and intrinsically disordered proteins demonstrate that ExEnDiff significantly advances the capabilities of current unified protein ensemble samplers. With little computational cost, ExEnDiff can capture important proteins configuration properties and the underlying Boltzmann distribution, paving the way for a next-generation molecular dynamics engine. We further demonstrate the effectiveness of ExEnDiff to capture conformational changes in the presence of mutations and as an efficient tool for determining a reasonable CV space for protein ensembles. With these results, ExEnDiff is well-poised to push the study of protein ensembles into a data-rich regime currently available to few problems in biology.

biophysics↗

bioRxiv2024

Martini without the twist: Unveiling a mechanically correct microtubule through bottom-up coarse-graining in Martini 3

Microtubules are essential cytoskeletal filaments involved in cell motility, division, and intracellular transport. These biomolecular assemblies can exhibit complex structural be-haviors influenced by various biophysical factors. However, simulating microtubule systems at the atomistic scale is challenging due to their large spatial scales. Here, we present an approach utilizing the Martini 3 Coarse-Grained (CG) model coupled with an appropriate elastic network to simulate microtubule-based systems accurately. By iteratively optimiz-ing the elastic network parameters, we matched the structural fluctuations of CG hetero-dimer building blocks to their atomistic counterparts. Our efforts culminated in a [~] 200nm microtubule built with [~] 6 million interaction-centers that could reproduce experimentally observed mechanical properties. Our aim is to employ these CG simulations to investigate specific biophysical phenomena at a microscopic level. These microscopic perspectives can provide valuable insights into the underlying mechanisms and contribute to our knowledge of microtubule-associated processes in cellular biology. With MARTINI 3 CG simulations, we can bridge the gap between computational efficiency and molecular detail, enabling in-vestigations into these biophysical processes over longer spatio-temporal scales with amino acid-level insights.

biophysics↗

bioRxiv2024

diaPASEF Enables High-throughput Proteomic Analysis of Host Cell Proteins for Biopharmaceutical Process Development

Monitoring and quantifying host cell proteins (HCPs) in biotherapeutics production processes is crucial to ensure product quality, stability, and safety. Liquid chromatography-mass spectrometry (LC-MS) analysis has emerged as an important tool for identifying and quantifying individual HCPs. However, LC-MS-based approaches face challenges due to the wide dynamic range between HCPs and the therapeutic protein, as well as laborious sample preparation and long instrument time. To address these limitations, we evaluated the application of parallel accumulation-serial fragmentation combined with data-independent acquisition (diaPASEF), to HCP analysis for biopharmaceutical process development applications. We evaluated different library generation strategies and LC methods, demonstrating the suitability of these workflows for various HCP analysis needs such as in-depth characterization and high-throughput analysis of process intermediates. Remarkably, the diaPASEF approach enabled the quantification of hundreds of HCPs that were undetectable by a standard data-dependent acquisition mode while considerably improving sample requirement, throughput, coverage, quantitative precision, and data completeness.

bioengineering↗

bioRxiv2024

Conformational landscapes of Huntingtin's polyQ domain and variations in its aggregate morphology

Huntingtons disease (HD) is a fatal neurodegenerative disorder resulting from an abnormal expansion of polyglutamine (polyQ) repeats in the N terminus of the Huntingtin protein. When the polyQ tract surpasses 35 repeats, the mutated protein undergoes misfolding, culminating in the formation of intracellular aggregates. Research in mouse models suggests that HD pathogenesis involves the aggregation of N-terminal fragments of the Huntingtin protein (htt). These early oligomeric assemblies of htt, exhibiting diverse characteristics during aggregation, are implicated as potential toxic entities in HD. However, a consensus on their specific structures remains elusive. Understanding the heterogeneous nature of htt oligomers provides crucial insights into disease mechanisms, emphasizing the need to identify various oligomeric conformations as potential therapeutic targets. Employing coarse-grained molecular dynamics, our study aims to elucidate the mechanisms governing the aggregation process and resultant aggregate architectures of htt. The polyQ tract within htt is flanked by two regions: an N-terminal domain (N17) and a short C-terminal proline-rich segment. We conducted self-assembly simulations involving five distinct N17 + polyQ systems with polyQ lengths ranging from 7 to 45, utilizing the ProMPT force field. Prolongation of the polyQ domain correlates with an increase in {beta}-sheet-rich structures. Longer polyQ lengths favor intra-molecular {beta}-sheets over inter-molecular interactions due to the folding of the elongated polyQ domain into hairpin-rich conformations. Importantly, variations in polyQ length significantly influence resulting oligomeric structures. Shorter polyQ domains lead to N17 domain aggregation, forming a hydrophobic core, while longer polyQ lengths introduce a competition between N17 hydrophobic interactions and polyQ polar interactions, resulting in densely packed polyQ cores with outwardly distributed N17 domains. Additionally, at extended polyQ lengths, we observe distinct oligomeric conformations with varying degrees of N17 bundling. These findings can help explain the toxic gain-of function that htt with expanded polyQ acquires. Author summaryOur study delves into Huntingtons disease (HD), a devastating neurodegenerative disorder triggered by abnormal expansions of polyglutamine repeats in the Huntingtin protein. When these repeats exceed a critical threshold, the protein misfolds, leading to the formation of harmful intracellular aggregates. Using computational techniques, we explored the intricate process by which these aggregates form and examined their complex structures. Our findings shed light on the diverse nature of the protein fragments involved in HD pathology, emphasizing the importance of identifying various structural forms as potential targets for therapeutic intervention. We observed that changes in the length of the polyglutamine tract significantly impact the resulting aggregate structures, revealing insights into the disease mechanism. Specifically, we found that an expansion of the polyglutamine domain leads to distinct aggregate morphologies. In addition, the way the first 17 amino acids of these protein fragments pack against each other in the aggregates depends on the length of the polyglutamine repeats. By uncovering these structural intricacies, our study contributes to a deeper understanding of HD and may pave the way for the development of targeted treatments aimed at disrupting or preventing the formation of toxic protein aggregates.

biophysics↗

bioRxiv2023

Analysis of the genome-scale metabolic model of Bacillus subtilis to design novel in-silico strategies for native and recombinant L-asparaginase overproduction

L-asparaginase is an enzyme with widescale use in the food and medicine industry. It is used as a chemotherapeutic drug in the treatment of acute lymphoblastic leukemia. Limitations of side effects associated with commercially available L-asparaginase necessitate the search for alternative sources. Bacillus subtilis is an emerging host for the production of chemicals and therapeutic products. This study deals with L-asparaginase production in Bacillus subtilis using systems metabolic engineering approach. System biology offers a detailed understanding of organism metabolism at the network level unlike the conventional molecular approach of metabolic engineering allowing one to study the effects of metabolite production on growth. Metabolism of Bacillus subtilis is studied using genome-scale metabolic model iYO844 which consists of relationships between the genes and proteins present in Bacillus subtilis. Also, the model contains information about all the metabolic reactions and pathways allowing convenient metabolic engineering methods. Computational methods like flux balance analysis, flux variability analysis, robustness analysis, etc. are carried out to study the metabolic capabilities of Bacillus subtilis. The model predicted a specific growth rate of 0.6242 h-1, which was comparable to the experimental value. Further, the model is used to simulate recombinant L-asparaginase production generating a maximum production rate of 0.4028 mmol gDW-1 h-1. Flux scanning based on enforced objective flux and OptKnock design strategies are used for strain development of Bacillus subtilis for higher production of both native and recombinant L-asparaginase.

systems biology↗

bioRxiv2022

Dynamic Phosphorylation Regulates Eukaryotic Translation Initiation Factor 4A Activity During the Cell Cycle

The eukaryotic translation initiation factor 4A (eIF4A) resolves mRNA structures to support protein synthesis, yet little is known about its regulation. Here we analyzed eIF4A phosphorylation during alternate stages of the cell cycle, and found three residues near the DEAD box motif (T73, T146, and S177) underwent substantial phosphorylation changes. Phosphomimetic mutations T73D and T146D led to G2/M phase arrest, and abolished eIF4A interaction with RNA, suggesting eIF4A activity is needed for completion of cell division. In addition to these repressive events, we found that S177, a site immediately adjacent to the DEAD-box, showed diametrically opposed phosphorylation, with only phosphorylated S177 present during G1/S arrest and dephosphorylated S177 peptides during G2/M arrest. Phosphomimetic S177D eIF4A increased polysome levels and enhanced normally reduced eIF4A-eIF4G-interaction during G2/M, while phosphodeficient S177A decreased polysome levels and reduced growth, suggesting phosphorylation of S177 enhances eIF4A-mediated translation during G1/S. Together these results suggest that dynamic phosphorylation of eIF4A S177 serves to stimulate translation during G1/S, while inhibitory phosphorylation of additional sites holds the potential to rapidly transition eIF4A to an inactive state and turn off translation. These results also suggest an important role for eIF4A in coupling translation to cell cycle stages.

molecular biology↗

bioRxiv2021

Functional network motifs defined through integrationof protein-protein and genetic interactions

Cells are enticingly complex systems. The identification of feedback regulation is critically important for understanding this complexity. Network motifs defined as small graphlets that occur more frequently than expected by chance have revolutionized our understanding of feed-back circuits in cellular networks. However, with their definition solely based on statistical over-representation, network motifs often lack biological context, which limits their usefulness. Here, we define functional network motifs (FNMs) through the systematic integration of genetic interaction data that directly informs on functional relationships between genes and encoded proteins. Occurring two orders of magnitude less frequently than conventional network motifs, we found FNMs significantly enriched in genes known to be functionally related. Moreover, our comprehensive analyses of FNMs in yeast showed that they are powerful at capturing both known and putative novel regulatory interactions, thus suggesting a promising strategy towards the systematic identification of feedback regulation in biological networks. Many FNMs appeared as excellent candidates for the prioritization of follow-up biochemical characterization, which is a recurring bottleneck in the targeting of complex diseases. More generally, our work highlights a fruitful avenue for integrating and harnessing genomic network data.

bioinformatics↗

bioRxiv2021

Reference-free cell-type deconvolution of pixel-resolution spatially resolved transcriptomics data

Recent technological advancements have enabled spatially resolved transcriptomic profiling but at multi-cellular pixel resolution, thereby hindering the identification of cell-type-specific spatial patterns and gene expression variation. To address this challenge, we developed STdeconvolve as a reference-free approach to deconvolve underlying cell-types comprising such multi-cellular pixel resolution spatial transcriptomics (ST) datasets. Using simulated as well as real ST datasets from diverse spatial transcriptomics technologies comprising a variety of spatial resolutions such as Spatial Transcriptomics, 10X Visium, DBiT-seq, and Slide-seq, we show that STdeconvolve can effectively recover cell-type transcriptional profiles and their proportional representation within pixels without reliance on external single-cell transcriptomics references. STdeconvolve provides comparable performance to existing reference-based methods when suitable single-cell references are available, as well as potentially superior performance when suitable single-cell references are not available. STdeconvolve is available as an open-source R software package with the source code available at https://github.com/JEFworks-Lab/STdeconvolve.

bioinformatics↗

bioRxiv2021

Changes at V2 apex of HIV-1 Clade C trimer enhance elicitation of autologous neutralizing and broad V1V2-scaffold antibodies

HIV-1 clade C envelope immunogens that elicit both neutralizing and non-neutralizing V1V2-scaffold specific antibodies (protective correlates from RV144 human trial) are urgently needed due to the prevalence of this clade in the most impacted regions worldwide. To achieve this, we introduced structure-guided changes followed by consensus-C sequence-guided optimizations at the V2-region to generate UFO-v2-RQH173 trimer. This improved the abundance of native-like trimers and carried an intrinsic dynamic V2-loop. Following immunization of rabbits, the wild-type protein failed to elicit any autologous neutralizing antibodies but UFO-v2-RQH173 elicited both autologous neutralizing and broad V1V2-scaffold antibodies. The variant with 173Y modification in V2-region, most prevalent among HIV-1 sequences, showed decreased ability in displaying native-like V1V2 epitope with time in-vitro and elicited antibodies with lower neutralizing and higher V1V2-scaffold activities. Our results identify a clade C C.1086-UFO-v2-RQH173 trimer capable of eliciting improved neutralizing and V1V2-scaffold antibodies, and reveal the importance of V2-region in tuning this.

immunology↗

bioRxiv2021

Conformational clamping by a membrane ligand activates the EphA2 receptor

The EphA2 receptor is a promising drug target for cancer treatment, since EphA2 activation can inhibit metastasis and tumor progression. It has been recently described that the TYPE7 peptide activates EphA2 using a novel mechanism that involves binding to the single transmembrane domain of the receptor. TYPE7 is a conditional transmembrane (TM) ligand, which only inserts into membranes at neutral pH in the presence of the TM region of EphA2. However, how membrane interactions can activate EphA2 is not known. We systematically altered the sequence of TYPE7 to identify the binding motif used to activate EphA2. With the resulting six peptides, we performed biophysical and cell migration assays that identified a new potent peptide variant. We also performed a mutational screen that determined the helical interface that mediates dimerization of the TM domain of EphA2 in cells. These results, together with molecular dynamic simulations, allowed to elucidate the molecular mechanism that TYPE7 uses to activate EphA2, where the membrane peptide acts as a molecular clamp that wraps around the TM dimer of the receptor. We propose that this binding mode stabilizes the active conformation of EphA2. Our data, additionally, provide clues into the properties that TM ligands need to have in order to achieve activation of membrane receptors.

biophysics↗

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

Dendrimer-targeted immunosuppression of microglia reactivity super-accelerates photoreceptor regeneration in the zebrafish retina

Muller glia (MG) function as injury-induced retinal stem cells in zebrafish but not mammals. Insights from zebrafish, however, have been used to stimulate limited regenerative responses from mammalian MG. Microglia/macrophages regulate MG stem cell activity in the chick, zebrafish and mouse. We previously showed that dexamethasone can accelerate retinal regeneration in zebrafish. Similarly, microglia ablation enhances regenerative outcomes in the mouse retina. Targeted immunomodulation may therefore enhance the regenerative potential of human MG. Nanoparticle-based immunomodulation is an emerging field with immense therapeutic potential. Here, we investigated how regeneration-enhancing dexamethasone treatments alter microglia behavior and how dendrimer-based targeting of dexamethasone to reactive microglia impact retinal regeneration kinetics. Intravital time-lapse imaging revealed specific dexamethasone-induced changes in microglia reactivity. Dendrimer-conjugated dexamethasone treatments resulted in: 1) decreased toxicity, 2) selective targeting of reactive microglia and, 3) "super-accelerated" retinal regeneration kinetics. These data support the use of dendrimer-based drug formulations for modulating microglia reactivity in degenerative disease contexts, especially as therapeutic strategies for promoting regenerative responses to neuronal cell loss.

neuroscience↗