Biology subjects

Jainarayanan, A. K.

Publications and source records attributed to Jainarayanan, A. K..

14 recordsLinked to original sources

bioRxiv2025

Isolation of functional supramolecular attack particles (SMAPs)

High density cultures of the GMP compatible NK-92 natural killer cell line release heterogeneous extracellular particles (EP), notably extracellular vesicles (EV) and non-vesicular extracellular particles (NVEP). The NVEP include a small proportion of supramolecular attack particles (SMAPs), the direct cytotoxic potential of which suggests therapeutic promise, yet scalable enrichment and functional evaluation alongside other extracellular particles (EPs) have been lacking. Here, we develop a high-resolution serial size-exclusion liquid chromatography (SELC) workflow that resolves EPs into 4 fractions F1-F4, in which EV are enriched in F2 and SMAPs are enriched in F3. Multi-modal characterization using Nanoparticle Tracking Analysis (NTA), Nano Flow Cytometry (Nano FCM), Transmission Electron Microscopy (TEM), Total Internal Reflection Microscopy (TIRFM) and Proteomics) demonstrated that F2 NK-92 EVs are [~]130-150 nm particles enriched for complement proteins, whereas SMAPs (F3) are 100-110 nm particles enriched for cytotoxic proteins (PRF1, GZMB) and SMAP shell components (e.g., THBS1, THBS4). Functionally, Ca2+-stabilized SMAPs (F3) trigger caspase-3-dependent apoptosis in tumor cell lines with robust dose responses, while F2 lacks direct cytotoxicity in vitro. Ex vivo, F3 SMAPs kill patient-derived breast cancer and chronic lymphocytic leukaemia cells (CLL) in a concentration-dependent manner. In NSG mice, intra-tumoral treatment with SMAPs (F3) restrains the growth of aggressive B16F10 melanoma and PANC-1 pancreatic cancer, confirming in vivo functionality. These results establish a scalable method to isolate and compare NK-derived particle classes and provide a foundation for targeted SMAP engineering as a promising approach for treatment of solid tumours. Significance StatementCell therapies face barriers in solid tumours, including lack of entry and suppression. NK cells release extracellular particles (EPs), including supramolecular attack particles (SMAPs), that can traffic into tumour tissue. We define a practical, scalable chromatography process that resolves NK-derived SMAPs from other EPs and demonstrate that SMAPs induce caspase mediated apoptosis in vitro and engage in cytotoxic lymphocyte independent anti-tumour activity in vivo. These insights open a route to engineering and testing SMAP-based therapeutics to overcome limitations of whole-cell approaches in solid cancers.

immunology↗

bioRxiv2025

STAT3 phosphorylation in the rheumatoid arthritis immunological synapse

Targeting the JAK/STAT pathway has emerged as a key therapeutic strategy for managing Rheumatoid Arthritis (RA). JAK inhibitors suppress cytokine-mediated signaling, including the critical IL-6/STAT3 axis, thereby effectively targeting different aspects of the pathological process. However, despite their clinical efficacy, a subset of RA patients remains refractory to JAK inhibition, underscoring the need for alternative approaches. Here, we identify a novel JAK-independent mechanism of STAT3 activation, which is triggered by the formation of the immunological synapse (IS) in naive CD4+ T cells. Our data demonstrates that Lck mediates the TCR-dependent phosphorylation of STAT3 at the IS, highlighting this pathway as a previously unrecognized hallmark of early T cell activation. Furthermore, we show that the synaptic Lck/TCR-STAT3 pathway is compromised in RA. This discovery highlights a new therapeutic target for RA beyond JAK inhibitors, offering potential avenues for treating patients resistant to current therapies.

immunology↗

bioRxiv2024

A resource for extracellular vesicles from activated CD4 T cells that relay pro-inflammatory signals

CD4 T helper cells (TH cells) play a vital role in coordinating and amplifying the immune response to specific pathogens. They constitutively produce different kinds of extracellular vesicles (EVs), which mediate cell-to cell communication and play diverse roles in immune regulation and inflammatory processes. Here we provide a resource documenting the composition of activated TH cell EVs and demonstrating their ability to instigate pro-inflammatory response in antigen-presenting cells (APCs). EVs were characterized by lipidomics, proteomics, and NanoFCM. The activated TH cells derived EVs (act-EVs) were found to be enriched in TH cell-specific proteins, transmembrane and cytosolic EV marker proteins, and HLA proteins relative to resting CD4 T cells EVs (rest-EVs). The pro-inflammatory effect of act-EVs vs rest-EVs on donor matched APCs were characterized by chemokine and cytokine profiling and flow cytometry analysis. There was no discernible contrast in endotoxin levels between act-EVs and rest-EVs. Functional distinctions were seen to arise from variations in the content and composition of these EVs. Moreover, we validated our findings with an in-vivo investigation in mice, demonstrating the recruitment of monocytes, dendritic cells (DCs), neutrophils, and NK cells in the spleen, accompanied by the release of pro-inflammatory cytokines in the serum after administering act-EVs. In summary, this study sheds light on the role of TH cell released EVs in modulating the immune response during pro-inflammatory responses and this resource provides a foundation for development of novel therapeutics on EV based scaffolds.

immunology↗

bioRxiv2024

Synaptic synergy of T cell receptor and interleukin 2 receptor in CD8+ T cells

Interleukin 2 (IL2) promotes T cell proliferation and differentiation, making it a central target in immunotherapies. T cells fine-tune their sensitivity to and consumption of IL2 by regulating surface expression and composition of the IL2 receptor. Following antigen recognition, IL2 receptor signaling is shared through polarized interactions in T cell aggregates. However, how IL2 function is integrated during earlier antigen-dependent T cell synapses is unknown. Here, we demonstrate a synergistic effect between the T cell receptor (TCR) and IL2 receptor signaling at the immunological synapse of CD8+ T cells with supported lipid bilayers. TCR and IL2 signaling overlapped in space and time, potentiating each other when simultaneously triggered. Immuno-STATs, a safe and effective new class of immunotherapeutics, which fuse IL2 and peptide-major histocompatibility complex (pMHC) in a single molecule to expand antigen-specific CD8+ T cells, enhanced both TCR and IL2 signaling and promoted antigen specific T-T immunological synapses.

immunology↗

bioRxiv2021

Synthetic Antigen Presenting cells reveal the diversity and functional specialization of extracellular vesicles composing the fourth signal of T cell immunological synapses.

The T cell Immunological Synapse (IS) is a pivotal hub for the regulation of adaptive immunity by endowing the exchange of information between cells engaged in physical contacts. Beyond the integration of antigen (signal one), co-stimulation (signal two), and cytokines (signal three), the IS facilitates the delivery of T-cell effector assemblies including supramolecular attack particles (SMAPs) and extracellular vesicles (EVs). How these particulate outputs differ among T -cell subsets and how subcellular compartments and signals exchanged at the synapse contribute to their composition is not fully understood. Here we harnessed bead-supported lipid bilayers (BSLBs) as a tailorable and versatile technology for the study of synaptic particle biogenesis and composition in different T-cell subsets, including CART. These synthetic antigen-presenting cells (APCs) facilitated the characterisation of trans-synaptic vesicles (tSV) as a heterogeneous population of EVs comprising among others PM-derived synaptic ectosomes and CD63+ exosomes. We harnessed BSLB to unveil the factors influencing the vesicular release of CD40L, as a model effector, identifying CD40 trans presentation, T-cell activation, ESCRT upregulation/recruitment, antigen density/potency, co-repression by PD-1 ligands, and its processing by ADAM10 as major determinants. Further, BSLB made possible the comparison of microRNA (miR) species associated with tSV and steadily released EVs. Altogether, our data provide evidence for a higher specialisation of tSV which are enriched not only in effector immune receptors but also in miR and RNA-binding proteins. Considering the molecular uniqueness and functional complexity of the tSV output, which is also accompanied by SMAPs, we propose their classification as signal four. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/445691v3_ufig1.gif" ALT="Figure 1"> View larger version (67K): org.highwire.dtl.DTLVardef@100f3aorg.highwire.dtl.DTLVardef@57adfforg.highwire.dtl.DTLVardef@6052fcorg.highwire.dtl.DTLVardef@1e85c21_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIBead Supported Lipid Bilayers (BSLB) reconstituting antigen-presenting cells support synapse assembly by T cells and the release of effector particles. C_LIO_LIBSLB facilitate the dissection of the cellular machineries and synapse composition shaping the released tSV. C_LIO_LItSV and their steadily released counterparts have a different composition. TSV show a higher enrichment of effectors including immune receptors, miR, RNA- and other nucleic acid-binding proteins, than EVs. C_LI

immunology↗

bioRxiv2021

QPromoters: Sequence based prediction of promoter strength in Saccharomyces cerevisiae

Promoters play a key role in influencing transcriptional regulation for fine-tuning expression of genes. Heterologous promoter engineering has been a widely used concept to control the level of transcription in all model organisms. The strength of a promoter is mainly determined by its nucleotide composition. Many promoter libraries have been curated but few have attempted to develop theoretical methods to predict the strength of promoters from its nucleotide sequence. Such theoretical methods are not only valuable in the design of promoters with specified strength, but are also meaningful to understand the mechanism of promoters in gene transcription. In this study, we present a theoretical model to describe the relationship between promoter strength and nucleotide sequence in Saccharomyces cerevisiae. We infer from our analysis that the -49 to 10 sequence with respect to the Transcription Start Site represents the minimal region that can be used to predict the promoter strength. We present an online tool https://qpromoters.com/ that takes advantage of this fact to quickly quantify the strength of the promoters.

synthetic biology↗

bioRxiv2021

iGEM comes of age: trends in its research output.

The international Genetically Engineered Machine (iGEM) is an educational benchmark in synthetic biology. Eighteen years after its inception, it has also catalysed the infusion of synthetic biology with interdisciplinary fundamental and translational research as well as with inspired young scientists. Here, we communicate a quantitative analysis of compiled published work associated to iGEM projects, highlighting trends in their dissemination and versatility. As iGEM comes of age, we anticipate it will continue to revolutionise, alongside SynBio, several disciplines of science and industries through the development of synthetic biological systems towards a sustainable future.

scientific communication and education↗

bioRxiv2019

Insilico analysis of structural and functional impact of SNPs in Pleckstrin

Pleckstrin (PLEK) gene has been associated with a variety of disorders including autoimmune, inflammatory diseases and cancer. Mutation in this gene has been reported to be associated with autoimmune celiac disease (CD), increased atrophy in multiple sclerosis (MS), obstructive sleep apnea (OSA), abdominal aortic aneurysms, over expression in inflammatory disorders including periodontis, risk for ependymoma relapse, bladder cancer, melanoma, lung, and colorectal cancer revealing the importance of study of the PLEK. PLEK gene has been reported from other animals and therefore we have studied the molecular evolution of the PLEK gene by insilico approaches. Single nucleotide polymorphisms (SNPs), in humans have been reported to cause potential structure-function alteration in proteins. In this study we have tried to understand by insilico approaches the (i) molecular evolution of PLEK and (ii) the impact of potentially deleterious single non-synonymous SNPs (nsSNPs) on the structure and function of Pleckstrin protein. We report for the first time using molecular dynamic simulation (MDS), the impact of SNPrs17035364 and rs3816281 on the structural alterations of Pleckstrin with implications in altering its biological function which may find importance as diagnostic markers.

bioinformatics↗

bioRxiv2019

Invariant Genes in Human Genomes

With large-scale human genome and exome sequencing, a lot of focus has gone in studying variations present in genomes and their associations to various diseases. Since major emphasis has been put on their variations, less focus has been given to invariant genes in the population. Here we present 60,706 genomes from the ExAC database to identify population specific invariant genes. Out of 1,336 total genes drawn from various population specific invariant genes, 423 were identified to be mostly (allele frequency less than 0.001) invariant across different populations. 46 of these invariant genes showed absolute invariance in all populations. Most of these common invariant genes have homologs in primates, rodents and placental mammals while 8 of them were unique to human genome and 3 genes still had unknown functions. Surprisingly, a majority were found to be X-linked and around 50% of these genes were not expressed in any tissues. The functional analysis showed that the invariant genes are not only involved in fundamental functions like transcription and translation but also in various developmental processes. The variations in many of these invariant genes were found to be associated with cancer, developmental diseases and dominant genetic disorders.

genomics↗

bioRxiv2018

Pharmacophore-driven Identification of N-Methyl-D-Receptor Antagonists as Potent Neuroprotective Agents Validated Using In-Vivo Studies

Alzheimers disease (AD), the most widespread cause of dementia is delineated by progressive cognitive impairment in the elderly people. During its progression, N-Methyl-D-Aspartate receptor antagonists are known to play a key role in the mechanisms of learning and memory. Extensive side effects alongside other effects on learning and memory have limited the therapeutic significance of various blockers and antagonists of the NMDA receptor. In this study, we identify potential compounds targeted against NMDA. In order to reveal the essential structural features for NMDA receptor, three-dimensional pharmacophore models are constructed based on a set of known NMDA inhibitors. This is followed by virtual screening which results in novel chemical compounds having the potential to inhibit NMDA. The lead compounds are then subjected to molecular docking and assessed by a scoring function, which results in two compounds with high Libdock scores. These compounds also show interactions with important residues at the active site. The compounds are shortlisted on the basis of high estimated activity, fit values, LibDock score, no violation to Lipinskis and availability for procuring.\n\nOf the shortlisted compounds, one compound satisfying the entire aforementioned criterion is further tested using in-vivo studies on mice with the help of an eight-arm radial maze. The pharmacophore-based virtual screening protocol presented in this study pave the way forward to address the unmet medical need of Alzheimer disease.

bioinformatics↗

bioRxiv2018

Spatio-Temporal Network Dynamics of Genes Underlying Schizophrenia

Schizophrenia (SZ) is a debilitating mental illness with multigenic etiology and high heritability. Despite extensive genetic studies the molecular etiology stays enigmatic. A systems biology study had suggested a protein-protein interaction (PPI) network for SZ with 504 novel PPIs amongst which several genes happen to be drug targets of existing FDA approved drugs. Although the PPI network presented all possible pairs of interactions (known and novel), it lacks a spatio-temporal information. The onset of psychiatric disorders is predominantly in adolescent and young adult stages, often accompanied by subtle structural abnormalities in multiple regions of the brain. Hence, there is a need to redefine the generic PPI network as a function of time (developmental stages) and space (brain regions). The availability of BrainSpan atlas data allowed us to redefine the SZ interactome as a function of space and time. The absence of non-synonymous variants in centenarians and non-psychiatric ExAC database allowed us to identify the variants of criticality. The expression of candidate genes in different brain regions and during developmental stages, responsible for cognitive processes as well as the onset of disease were studied. A subset of novel interactors detected in the network was further validated using gene-expression data of psychiatric postmortem brains. From the long list of drug targets proposed from the interactome study and based on the microarray gene-expression results, we have shortlisted a probable subset of 10 drug targets (targeted by 34 FDA approved drugs) coalescing into 81 biological pathways, that could be potentially repurposed for neuropsychiatric disorders.

bioinformatics↗

bioRxiv2018

Identification of novel and structurally diverse N-Methyl-D-Aspartate Receptor Antagonists: Successful Application of Pharmacophore Modeling, Virtual Screening and Molecular Docking

In view of \"excitotoxic\" effects of glutamate, wherein excessive excitatory input causes increase in intracellular Ca2+ and ultimately cell death, NMDA receptor has emerged as an important target for treatment and prevention of several neurological disorders, like Alzheimer disease. Prompted by the successful application of in-silico pharmacophore-based virtual screening in lead identification, we have made an effort to implement in-silico protocols to identify novel NMDA receptor antagonist. A series of novel benzo[b]quinolizinium cations as NMDA receptor antagonists have been used as a starting point to develop prognostic pharmacophore models. The most predictive pharmacophore model (hypothesis 1), consisting of four features, namely, one hydrogen bond acceptor, one hydrophobic and two ring aromatic, showed a correlation (r) of 0.89, root mean square of 0.259, and the cost difference of 43.01 bits between null and fixed cost. The model was thoroughly validated and subjected to a chemical database search, which lead to the identification of 400 hits from NCI and Maybridge databases which were checked for Lipinskis violation and predictive potency.\n\nThis reduced the list to 10 compounds, out of which, two most potent compounds were subjected to molecular docking using Libdock software and interestingly, all the docked conformations showed hydrogen bond interactions with important amino acids Tyr214, His88, Thr174, Val169 and Arg121. In summary, through our validated pharmacophore-based virtual screening protocol, we have identified two potent, structurally diverse, druggable and novel NMDA receptor antagonist which might be of great help to address the unmet medical need of Alzheimer disease.

bioinformatics↗

bioRxiv2018

AchE-OGT dual inhibitors: Potential Partners in Handling Alzheimer’s Disease

The emerging role of O-GlcNAc Transferase (OGT) and tau protein in Alzheimers disease (AD) holds promises for the treatment of this life-threatening neurodegenerative disorder. In view of the availability of 3D structure of OGT, we attempted to develop structure-based pharmacophore model to elucidate specific structural requirements for binding of inhibitors to the active site of OGT. During the course of study we discovered that donepezil, an old and trusted Acetylcholinesterase (AchE) inhibitor also possess the pharmacophoric sites important for interaction with OGT active site. To further explore the specific interactions of donepezil with OGT, we performed molecular docking studies using CDocker. The results of molecular docking and structure-based pharmacophore mapping revealed that donepezil has the required structural features to interact with various OGT active site amino acids like Lys842, His920, Leu653, Gly654, Asn838, and Thr921 in addition to its AchE interaction abilities. Our findings could be an important breakthrough in the design of OGT specific and/or AchE OGT dual inhibitors.

bioinformatics↗

bioRxiv2018

Intronic miRNA Mediated Gene Expression Regulation Controls Protein Crowding Inside the Cell

SUMMARYGene regulatory effects of microRNAs at a posttranscriptional level has been established over the last decade. In this study, we analyze the interaction networks of mRNA translation regulation through intronic miRNA, under various tissue-specific cellular contexts, taking into account the thermodynamic affinity, kinetics, and the presence of competitive interactors. This database, and analysis has been made available through an open-access web-server, miRiam, to promote further exploration.\n\nHere we report that expression of genes involved in Apoptosis Processes, Immune System Processes, Translation Regulator Activities, and Molecular Transport Activities within the cell are predominately regulated by miRNA mediation. Our findings further indicate that this regulatory effect has a profound effect in controlling protein crowding inside the cell. A miRNA mediated gene expression regulation serves as a temporal regulator, allowing the cellular machinery to temporarily pause the translation of mRNA, indicating that the miRNA-mRNA interactions may be important for governing the optimal usage of cell volume.

bioinformatics↗