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Varghese, J. M.

Publications and source records attributed to Varghese, J. M..

4 recordsLinked to original sources

The Anti-inflammatory Drug Leflunomide Inhibits NS2B3 Cluster Formation During Dengue Viral Infection as Revealed by Single Molecule Imaging

A prerequisite for Dengue viral infection is the clustering of NS2B3 viral protein in the infected cell. This calls for drugs capable of reversing the biological processes leading to the declustering of NS2B3 viral complex. In this work, we report a new drug (leflunomide) that shows reversal of NS2B3 clustering, post 24 hours of cell transfection with a recombinant probe (Dendra2-NS2B3) containing the viral complex of interest (NS2B3). To study, we constructed a photoactivable recombinant plasmid for visualizing the activity of the target protein-of-interest (Dendra2-NS2B3). This enabled a better understanding of the underlying biological processes involved in Dengue and the role of NS2B3. The study was performed in a cellular system by transfecting the cell (NIH3T3 -mouse fibroblast cell line), followed by drug treatment studies. A range of physiologically relevant concentrations (250 nM - 10 M) of the FDA-approved drug (leflunomide) was used. The single molecule super-resolution microscopy (scanSM LM) study showed declustering of NS2B3 clusters for concentrations > 250 nM and near complete disappearance of clusters at concentrations > 5 M . Moreover, the associated critical biophysical parameters suggest a substantial decrease in clustered molecules (from 53.2 {+/-} 1.77% for control to 14.89 {+/-} 4.80% at 250 nM, and further reduction to 10.55 {+/-} 2.91% at 500 nM). Moreover, the number of clusters reduced from 46 {+/-} 15 to 13 {+/-} 4, and the number of molecules per cluster decreased from 133 {+/-} 29 to 62 {+/-} 3, with a depletion in large clusters (from 24 to 12). The parameters collectively indicate the clustering nature of NS2B3 viral protein during the infection process at a cellular level and the effect of leflunomide in declustering. The results supported by statistical analysis suggest strong declustering promoted by leflunomide, which holds the promise to contain/treat dengue viral infection. Statement of SignificanceThe fact that there is no approved antiviral approach for Dengue makes it life-threatening and calls for ways to tackle viral infection. Hence, understanding Dengue biology at a single molecule level plays a vital role. In the present super-resolution study, we noted the formation of key viral protein (NS2B3) clusters post 24 hours of transfection in a cellular system. We identified a repurposed FDA-approved drug (Leflunomide) that inhibits the clustering process and promotes declustering at higher drug concentrations. This may become the basis of future studies, which may have therapeutic potential against Dengue.

biophysics↗

Complete genomic assembly of Mauritian cynomolgus macaque killer immunoglobulin-like receptor and natural killer group 2 haplotypes

Mauritian-origin cynomolgus macaques (MCM) serve as a powerful nonhuman primate model in biomedical research due to their unique genetic homogeneity, which simplifies experimental designs. Despite their extensive use, a comprehensive understanding of crucial immune-regulating gene families, particularly killer immunoglobulin-like receptors (KIR) and natural killer group 2 (NKG2), has been hindered by the lack of detailed genomic reference assemblies. In this study, we employ advanced long-read sequencing techniques to completely assemble eight KIR and seven NKG2 genomic haplotypes, providing an extensive insight into the structural and allelic diversity of these immunoregulatory gene clusters. Leveraging these genomic resources, we prototype a strategy for genotyping KIR and NKG2 using short-read, whole exome capture data, illustrating the potential for cost-effective multi-locus genotyping at colony scale. These results mark a significant enhancement for biomedical research in MCMs and underscores the feasibility of broad-scale genetic investigations.

genomics↗

Single-Molecule Super-Resolution Microscopy Reveals Formation of NS2B3 Protein Clusters on Mitochondrial Network Leading to its Fragmentation during the Onset of Dengue (Denv-2) Viral Infection

Understanding viral proteins at single-molecule level and visualizing their dynamics in a cellular environment is challenging. This calls for sophisticated microscopy techniques (such as SMLM) and image-based study that can reveal details with the precision of a single-molecule. Specifically, NS2B3 is recognized as a critical protein complex responsible for proteolytic activity and processing of viral polyprotein during dengue type 2 (Denv - 2) infection. Using single-molecule-based super-resolution imaging, we study the dynamics of NS2B3 protein, its kinetics and its interaction with cell organelles. Two distinct photoactivable recombinant plasmids (mEos-NS2B3 and PAGFP - NS2B3) and a fluorescent recombinant plasmid (eGFP-NS2B3) were constructed to exemplify the role of NS2B3 protein complex. The study was conducted on NIH3T3 cells and optimized transfection protocol was developed. Studies confirmed the formation of NS2B3 clusters on the mitochondrial network. Statistical analysis of super-resolution data (images) helped determine cluster dynamics and facilitated the estimation of critical biophysical parameters (such as, cluster density, number of molecules / cluster and its spread). Results indicate an average NS2B3 cluster area / spread of [~] 0.050 {micro}m2 with a density of 3500mol./ {micro}m2, and an average of [~] 120 NS2B3 molecules per cluster. In addition, regional analysis suggests a direct positive correlation between NS2B3 cluster formation (single-molecule localization microscopy study) and fragmentation of mitochondrial network (confocal microscopy study). To further exemplify, we have carried out time-lapse imaging to visualize formation of NS2B3 clusters and its dynamics. The corresponding cluster parameters (#clusters, #mol/cluster and cluster area) suggests an increase in average #mol/cluster and cluster area. For the first time, single-molecule-based super-resolution imaging study helped reveal the dynamics of NS2B3 clusters in a cellular system. Understanding the underlying dynamics of NS2B3 clustering at the single-molecule level may help to decipher potential drug targets and the ways to disrupt the NS2B3 clusters. The image-based study has immediate implications in the broad field of single molecule imaging, fluorescence microscopy and disease biology. Statement of SignificanceThe arrival of single-molecule super-resolution imaging techniques and image-based study have advanced the field of cell biology, and our understanding of sub-cellular processes with single-molecule precision. Here, we report the first ever application of super-resolution imaging to visualize NS2B3 clusters in a cellular system that directly links to the fragmentation of mitochondrial network. To facilitate the study, two new photoactivable probes (mEos - NS2B3 and P AGF P- NS2B3) with key protein complex, NS2B3 of dengue virus were developed. The study involves cell transfection studies followed by confocal and single-molecule imaging. The correlative biophysical study (comprising of confocal and single-molecule imaging) and estimated cluster parameters corroborates our findings.

pathology↗

Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype

Macaques provide the most widely used nonhuman primate models for studying immunology and pathogenesis of human diseases. While the macaque major histocompatibility complex (MHC) region shares most features with the human leukocyte antigen (HLA) region, macaques have an expanded repertoire of MHC class I genes. Although a chimera of two rhesus macaque MHC haplotypes was first published in 2004, the structural diversity of MHC genomic organization in macaques remains poorly understood due to a lack of adequate genomic reference sequences. We used ultra-long Oxford Nanopore and high-accuracy PacBio HiFi sequences to fully assemble the [~]5.2 Mb M3 haplotype of an MHC-homozygous, Mauritian-origin cynomolgus macaque (Macaca fascicularis). The MHC homozygosity allowed us to assemble a single MHC haplotype unambiguously and avoid chimeric assemblies that hampered previous efforts to characterize this exceptionally complex genomic region in macaques. The high quality of this new assembly is exemplified by the identification of an extended cluster of six Mafa-AG genes that contains a recent duplication with a remarkably similar [~]48.5 kb block of sequence. The MHC class II region of this M3 haplotype is similar to the previously sequenced rhesus macaque haplotype and HLA class II haplotypes. The MHC class I region, in contrast, contains 13 MHC-B genes, four MHC-A genes, and three MHC-E genes (versus 19 MHC-B, two MHC-A, and one MHC-E in the previously sequenced haplotype). These results provide an unambiguously assembled single contiguous cynomolgus macaque MHC haplotype with fully curated gene annotations that will inform infectious disease and transplantation research.

genomics↗