Biology subjects

Verma, S.

Publications and source records attributed to Verma, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Autoimmune CD4+T cells Cause Meibomian Gland Dysfunction

Sjogren disease (SjD) is an autoimmune disease driven by autoreactive CD4+T cells that leads to an immune-mediated loss of lacrimal glands. Meibomian glands are lipid-producing glands in the eyelids that help prevent tear evaporation. While the role of T cells in lacrimal gland-mediated destruction is well established, it is unknown whether pathogenic T cells can cause MG dysfunction (MGD). Herein, we investigated whether autoreactive CD4+T cells induce MGD and characterized the pathophysiologic mechanisms using an adoptive transfer model. T cells were isolated from CD25KO (CD4KO) or wild-type (CD4WT) mice, transferred into Rag1KO mice. Further, CD4KO cells were co-adoptively transferred with WT regulatory T cells (CD4KO+TregsWT). Our results demonstrate that CD4KO recipients had MG dropout, CD4+IFN-{gamma}+ infiltration, increased MHC II presentation within the periglandular area, MG fibrosis, and decreased lipid production and upregulation of pathways related to inflammation, including Type II interferon signaling. Rag1KO, CD4WT, and CD4KO+TregsWT recipients exhibited minimal inflammation in the periglandular MG area. These results indicate that autoimmune CD4+T cells are sufficient to cause MGD, and healthy young regulatory T cells can prevent T-cell-mediated damage. Taken together, our findings provide mechanistic insights into the pathogenesis autoimmune SjD, and could impact how patients are managed in the clinic.

pathology↗

bioRxiv2025

Spatial Regulation of Lysosomal Vesicle Acidification Along the Axon via mRAVE-Dependent v-ATPase Assembly

Lysosomal acidification is essential for neuronal homeostasis, supporting degradative clearance and metabolic signaling in all neuronal domains. Yet, how lysosomal acidification is spatially regulated within neurons remains unclear. Here, we show that assembly of the membrane-embedded V0 and cytosolic V1 domains of the vacuolar H-ATPase (v-ATPase) -- the proton pump that drives lysosomal acidification -- governs spatial and functional lysosome diversity. In non-neuronal cells, V1-V0 association is higher in perinuclear lysosomes, correlating with increased acidity of this population. In neurons, axonal V0-positive vesicles move bidirectionally, whereas V1-V0 -positive vesicles move almost exclusively in the retrograde direction, consistent with the higher acidity of retrograde lysosomal vesicles. Depletion of DMXL2, a subunit of the mRAVE complex that promotes V1-V0 assembly, reduces V1 association, acidification, transport, and proteolytic activity of retrograde lysosomal vesicles in the axon. Together, these findings reveal a spatially regulated mechanism for the acidification of axonal lysosomal vesicles and identify mRAVE-dependent v-ATPase assembly as a key determinant of this process. Subjects: Organelles, Trafficking, Disease

cell biology↗

bioRxiv2025

AnnotateAnyCell: Open-Source AI Framework for Efficient Annotation in Digital Pathology

AO_SCPLOWBSTRACTC_SCPLOWManual annotation of histopathological whole slide images remains a critical bottleneck for computational pathology and clinical AI deployment, requiring prohibitive expert time at scale. Here we present an open-source semi-supervised framework combining active contrastive learning with iterative human-in-the-loop feedback for efficient cellular annotation and classification. The pipeline integrates Cellpose segmentation, UMAP-based latent space visualization, and contrastive learning with pseudolabel propagation, evaluated on five whole slide images of canine invasive urothelial carcinoma across low, intermediate, and high histological grades at 40x magnification. Latent space clustering-guided annotation required 47 minutes compared to 63 minutes for sequential annotation, a 25% reduction (95% CI 18-32%). Classification accuracy reached 96.3% {+/-} 1.2% for mitotic figures and 98.3% {+/-} 1.4% for nucleoli using 1,075 labeled samples, with nucleoli classification achieving 95.5% {+/-} 1.5% accuracy from only 215 samples. Inter-annotator agreement was high for chromatin ({kappa} = 1.00) and nucleoli ({kappa} = 0.95) but moderate for mitotic figures ({kappa} = 0.58) and nuclear shape ({kappa} = 0.36), reflecting intrinsic morphological ambiguity in these categories. This framework substantially reduces annotation burden while achieving expert-level accuracy for well-defined morphological features, providing a scalable path toward AI-assisted diagnostics in resource-constrained pathology settings.

pathology↗

bioRxiv2025

GRAYU: Graph-based Database integrating Ayurvedic formulations, medicinal plants, phytochemicals and diseases

The translation of Indias extensive traditional knowledge on indigenous medicinal plants into modern therapeutic solutions is contingent upon a systematic framework. While traditional Indian medicine offers a rich source of therapeutic leads, this knowledge is often not structured for modern computational analysis, creating a barrier to systematic drug discovery. To this end, we present GRAYU, a curated and comprehensive online database that integrates data across multiple categories, connecting 1039 traditional formulations to 12,949 indigenous plants, 129,542 phytochemicals, and 13,480 indicated diseases. It also provides insights into 1,382,362 plant-phytochemical, 116,824 plant-disease, 2,405 plant-formulation, and 4,087 formulation-disease associations. Case studies on phytochemical analogs, sustainable plant substitution, and disease-network pharmacology showcased the potential of integrative graphs to decode shared molecular signatures and therapeutic networks across traditional Ayurvedic formulations. GRAYU represents a user-friendly resource for researchers to investigate complex bio-associations and formulate novel therapeutic hypotheses, with insights from traditional Indian medicine. GRAYU is available at https://caps.ncbs.res.in/GRAYU/.

bioinformatics↗

bioRxiv2025

Molecular Configuration, Regulation and Function of Heterochannel Electrical Synapses

Neuron-specific expression of particular gap junction channel components defines the configuration and functional properties of electrical synapses. However, how a neuron utilises multiple, simultaneously expressed channel proteins - connexins or innexins -to make meaningful connections with distinct synaptic partners remains largely unknown. Using the posterior mechanosensory circuit in C. elegans, we discovered that individual electrical synapses can be formed by clustering together molecularly distinct gap junction channel-types made of three different innexin proteins, INX-1, UNC-7, and UNC-9. In this previously unknown configuration, which we term as heterochannel synapses, molecularly distinct gap junction channel types functionally collaborate to regulate posterior touch sensory behaviour, enhancing functional robustness. We show that the synaptic trafficking of the molecularly different channel types within a heterochannel synapse is independently regulated by discrete and conserved kinesin motor proteins, while distinct molecular pathways involving channel-specific retrograde kinesins regulate their turnover. These independent, channel-specific regulations also make individual synapse-level alterations in the composition of heterochannel synapses possible under altered environmental conditions, providing a novel mechanism for electrical synapse plasticity. Finally, we present evidence of heterochannel electrical synapses in C. elegans locomotory circuits and in the cerebellar Purkinje neurons of zebrafish larvae. Altogether, we demonstrate a novel heterochannel organization of electrical synapses, their regulation, and functional importance, which may be a conserved feature of metazoan nervous system.

neuroscience↗

bioRxiv2025

Coronavirus protein interaction mapping in bat and human cells identifies molecular and genetic switches for immune evasion and replication

Coronaviruses, including SARS-CoV-2, can cause severe disease in humans, whereas reservoir hosts like Rhinolophus bats remain asymptomatic. To investigate how host-specific protein-protein interactions (PPIs) influence infection, we generated comparative PPI maps for SARS-CoV-2 and its bat-origin relative RaTG13 using affinity purification-mass spectrometry (AP-MS) in human and Rhinolophus ferrumequinum (RFe) bat cells. This approach identified both conserved and virus- and host-specific interactions that regulate infection dynamics. Notably, SARS-CoV-2 required a non-synonymous mutation in nucleocapsid to replicate in bat cells expressing human ACE2 and TMPRSS2. Analysis of the viral protein Orf9b revealed differential interactions with mitochondrial proteins Tom70 and MTARC2. A single residue difference in Orf9b between SARS-CoV-2 and RaTG13 functions as a molecular switch, weakening Tom70 binding and immune evasion in human cells while enhancing interaction with the bat-specific restriction factor MTARC2. These findings demonstrate how a single-residue substitution can reshape virus-host interactions and contribute to immune evasion and host adaptation.

systems biology↗

bioRxiv2025

Immunologic insights into the critical epitopes of HIV-1 and structure-based characterization of cross-reactive antibodies

HIV-1 escape from neutralizing antibodies even in the presence of strong host immunity is associated with variations in envelope proteins that drive antigenic diversification. The virus exploits the error-prone nature of reverse transcriptase and the high mutation rate as key survival strategies. However, the rate of production of new variations occurs at relatively slow pace. Interestingly, the immune system often produces cross-reactive antibodies, with anticipated role in neutralizing point mutations in HIV surface proteins by cross-reacting with mutants and tolerating them. In light of this paradox, we explored the mystery of immune evasion and antibody promiscuity by screening single chain variable fragment (scFvs) antibodies against several crucial HIV-1 gp41 epitopes using a phage display library. These findings underscore the broader significance of cross-reactive antibodies. Here, high-affinity cross-reactive scFvs showed physiologically relevant affinities with peptide epitopes, their analogs, and the native HIV-1 gp41 protein. We determined the crystal structure of a high-affinity cross-reactive scFv, DE94, and obtained insights into the molecular interactions of scFv antibodies with peptide epitopes and its natural mutants using molecular docking studies. This analysis of cross-reactive antibodies could contribute to the therapeutic development against immune-evading pathogens and paves the way for innovative strategies for combating viral infections, including emerging global threats.

biophysics↗

bioRxiv2025

Functional rescue of a fatal ERAD mutation via alternative splicing

Endoplasmic reticulum (ER)-associated degradation (ERAD) is essential for cellular proteostasis, with the SEL1L-HRD1 protein complex targeting misfolded proteins in the ER for proteasomal degradation. Disruption of this pathway underlies a recently identified infant-onset neurodevelopmental disorder (ENDI syndrome), characterized by profound developmental delay, microcephaly, and immune deficiency. Its most severe form, ENDI with agammaglobulinemia (ENDI-A), is driven by a bi-allelic SEL1L Cys141Tyr (C141Y) mutation within the fibronectin II (FNII) domain, for which no treatment currently exists. Here, we serendipitously uncover a striking mechanism of intrinsic rescue in knock-in mouse models of the C141Y mutation: enhanced usage of an alternative splice donor site within exon 4 bypasses the mutant FNII-encoding region, restoring ERAD activity and rescuing key disease phenotypes including perinatal lethality, growth retardation, B cell deficiency, and neurodevelopmental defects. Building on this discovery, we demonstrate that antisense oligonucleotide (ASO)-mediated exon skipping in patient-derived fibroblasts generates a truncated yet functional SEL1L protein, fully rescuing ERAD function and ER proteostasis. These results establish RNA splicing modulation as a viable therapeutic strategy for ERAD deficiency and extend the clinical potential of exon-skipping therapy to diseases of protein misfolding. ONE-SENTENCE SUMMARYThis study reports the discovery of using antisense oligonucleotides (ASOs) to rescue the biallelic SEL1L C141Y variant, offering a potential therapeutic strategy.

cell biology↗

bioRxiv2025

Structural and Evolutionary Analysis of Human Growth Hormone Variants

Human growth hormone (GH) exerts its pleiotropic effects by binding to its receptor (GHR), leading to receptor dimerization and activation. We combined structural, evolutionary, and genetic analyses to elucidate the critical determinants of GH-GHR interaction and the impact of disease-causing mutations. Protein contact analysis revealed the specific amino acid residues involved in two distinct binding interfaces between GH and two chains of GHR. ConSurf analysis demonstrated significant sequence conservation in the receptor-binding regions of GH across species, highlighting their functional importance. A comprehensive list of known disease-causing mutations in GH was compiled and mapped to these binding interfaces and conserved regions. Computational site-directed mutagenesis (SDM) analysis predicted the impact of several mutations on protein stability, revealing both stabilizing and destabilizing effects. Sequence comparisons with orthologs from various species further supported the evolutionary conservation of key functional residues. Integrated analysis of contact residues between GH and GHR showed a strong correlation between receptor-binding residues, evolutionary conservation, and the occurrence of disease-associated mutations. These findings underscore the critical role of specific GH residues in mediating high-affinity interaction with its receptor, and how mutations in these conserved contact points can disrupt binding affinity and/or protein stability, ultimately leading to growth disorders. This multi-faceted approach provides valuable insights into the molecular mechanisms underlying growth hormone deficiency and related syndromes.

pharmacology and toxicology↗

bioRxiv2025

Lack of motor defects and ALS-like neuropathology in heterozygous Sptlc1 Exon 2 deletion mice

Mutations in the human SPTLC1 gene have recently been linked to early onset amyotrophic lateral sclerosis (ALS), characterized by global atrophy, motor impairments, and symptoms such as tongue fasciculations. All known ALS-linked SPTLC1 mutations cluster within exon 2 and a specific variant, c.58G>T, results in exon 2 skipping. However, it is unclear how the exon 2 deletion affects SPTLC1 function in vivo and contributes to ALS pathogenesis. Leveraging the high genomic sequence similarity between mouse and human SPTLC1, we created a novel mouse model with a CRISPR/Cas9-mediated deletion of exon 2 in the endogenous murine Sptlc1 locus. While heterozygous mice did not develop motor defects or ALS-like neuropathology, homozygous mutants died prematurely. These findings indicate that Sptlc1 {Delta}Exon2 heterozygous mice do not replicate the disease phenotype but provide valuable insights into SPTLC1 biology and serve as a useful resource for future mechanistic studies.

neuroscience↗

bioRxiv2025

A single mutation in the DSL motif of the acyl carrier protein can prevent its in vivo modification by E. coli Holo-acyl carrier protein synthase (AcpS)

E. coli expression system is the method of choice to obtain high yields of a pure protein. However, there is always a chance that an overexpressed protein shares structural or sequence homology with the substrate of an E. coli enzyme. In such cases, the expressed protein may be partially or fully converted into the product. A notable example is the expression of acyl carrier proteins (ACP) in E. coli. Since most type II ACPs of the fatty acid synthesis pathway (FAS) have a conserved helix II, the carrier proteins are recognized as a substrate by Holo-acyl carrier protein synthase (AcpS). Thus, most ACPs express as partially or fully loaded proteins in E. coli. This undesirable modification is a concern when the objective is to obtain milligram amounts of apo-ACP. Here, using an approach combining mutagenesis, enzyme activity, and NMR, we probed for residues in ACP that can prevent this in vivo modification, without affecting Sfp (Surfactin synthetase activating enzyme) function. Taking cues from the E. coli ACP-AcpS structure (PDB 5VCB), charge neutralization mutations were designed at five different positions in EcACP that participate in ion-pair interaction with AcpS. Three of the mutants expressed solely as apo-ACP in E. coli viz. D35N, E41A and E47A/E48A. However, only the D35N mutant could be converted into holo-/acyl-ACP using Sfp in vitro, establishing mutagenesis as a viable strategy to prevent undesired modifications in vivo. As proof of principle, the mutation was applied to two unrelated ACPs that express primarily as modified proteins in E. coli -Mus musculus mitochondrial FAS ACP (MmACP) and Salmonella Typhimurium invasion acyl carrier protein (IacP). Single D35N mutation of the ACPs prevented their in vivo modification by AcpS, and the mutants were efficiently converted into holo-ACP by Sfp in vitro. These results demonstrate that D35N mutagenesis is a useful strategy to express apo-ACP in E. coli and is applicable across all type II ACPs. Furthermore, we show that holo-IacP and holo-MmACP are not recognized as substrates by AcpH (E. coli Acyl carrier protein hydrolase), and therefore they express predominantly as modified proteins in E. coli.

biochemistry↗

bioRxiv2025

Hypoxia-inducible factor 2α promotes protective Th2 cell responses during intestinal helminth infection

Th2 cells must sense and adapt to the tissue milieu in order to provide protective host immunity and tissue repair. Here, we examined the mechanisms promoting Th2 cell differentiation and function within the small intestinal lamina propria. Single cell RNA-seq analyses of CD4+ T cells from the small intestinal lamina propria of helminth infected mice revealed high expression of the gene Epas1, encoding the transcription factor hypoxia-inducible factor 2a (HIF2). In vitro, exposure to hypoxia or genetic HIF2 activation promoted Th2 cell differentiation, even under non-polarizing conditions. In mice, HIF2 activation in CD4+ T cells promoted intestinal Th2 cell accumulation in the absence of infection, and HIF2-deficiency impaired CD4+ T cell-mediated host immunity to intestinal helminth infection. Our findings identified hypoxia, and the oxygen-regulated transcription factor Hypoxia-Inducible Factor 2 (HIF2), as key regulators of Th2 cell differentiation and function within the small intestine.

immunology↗

bioRxiv2025

Thermodynamic uncertainty relation constraints information transmission through cell signaling systems

Cell signaling systems are involved in sensing changes in the environment by activating a set of transcription factors (TF) that typically diffuse within the nucleus to trigger transcription of the required genes. The TFs can diffuse randomly in and out of the nucleus leading to fluctuations in different components which severely limits the accuracy of estimating environmental input. The diffusion usually happens through the nuclear pore complexes which enables the tf protein to enter the nucleus either passively or actively depending on its size. In this study, we explored the role of diffusion on the information transmission capacity of a set of tfs using a coupled mathematical and machine learning approaches to experimental data in yeast under several stress conditions. We found that the the activation followed by biased diffusion of transcription factors (TF) towards the nucleus triggers amplifying magnitude of the overall TF currents towards the nucleus as well as reduces the fluctuations. In fact, to our surprise the diffusion rate estimated from the data is found to be positively correlated with the protein mass, indicating the possibility of active diffusion since a negative correlation is expected in case of passive diffusion. The active diffusion in fact facilitates faster entry to the nucleus enabling faster information transmission with nuclear protein concentration as output. Additionally, higher copy number of the TF also improves information transmission by reducing overall noise in the output. However, improved information owing to faster active diffusion and higher copy number comes at an extra cost of increased entropy production due to the inherent thermodynamic uncertainty relation (TUR)for non-equilibrium systems. A linear optimization analysis demonstrates a corelation between the protein size and the optimized protein number which corroborates the actual observation. Thus, experimental measurements coupled with diffusion based theoretical models demonstrate the role of diffusion on optimizing cellular information processing.

systems biology↗

bioRxiv2025

Developmental synaptic pruning in the olivo-cerebellar circuit sculpts predictive processing

Developmental synaptic pruning is thought to refine neural circuits by eliminating excess connectivity, but whether this process changes the computations performed by developing circuits remains poorly understood. Here, we show that synaptic pruning sharpens neural representations in the developing zebrafish cerebellum. Climbing fiber (CF) inputs to Purkinje neurons (PNs) progressively transition from poly- to predominantly mono-innervation during the first two weeks of life. In vivo whole-cell recordings reveal that individual CFs convey distinct sensorimotor information, and that convergence of differently tuned CFs degrades the precision of PN representations. As this convergence is reduced during development, PN responses become more selective and temporally precise. Later-stage PNs also exhibit stronger predictive responses to expected sensory events and enhanced responses to violations of those expectations, accompanied by improved behavioral adaptation. These findings suggest that developmental synaptic pruning is not simply a process of reducing excess connectivity, but can contribute to the functional specialization of neural circuits by sharpening neuronal representations and enabling increasingly precise predictive sensorimotor computations.

neuroscience↗

bioRxiv2024

Genomic Architecture of the Resistance to Phytophthora Cactorum 2 (RPc2) Locus in Strawberry (Fragaria x ananassa)

Phytophthora crown rot (PhCR), caused by Phytophthora cactorum, is a soilborne disease with broad impacts to cultivated strawberries in the United States and worldwide. While a resistance locus, RPc2, has been identified in octoploid strawberries, the underlying genomic architecture and mechanism remain unclear. Here, we fine-mapped the RPc2 region to 546 kb, containing 92 genes, and constructed a chromosome-scale haplotype-phased genome of resistant breeding selection FL 16.33-8. Comparative genome analyses with high-quality octoploid reference genomes, Florida Brilliance (FaFB1) and Royal Royce (FaRR1), identified two candidate genes, Wall Associated Kinase 1 (WAK1) and Cyclic Nucleotide Gated Channel 1 (CNGC1). Gene functions were validated using an Agrobacterium-mediated transient expression assay. Furthermore, by leveraging the population structure of the RPc2 locus among genetically diverse breeding populations, we unveiled the complexity of genetic architecture and recent selective sweeps associated with RPc2. Notably, the predominant resistant haplotype (RPc2-H3) is prevalent in most commercial strawberry varieties in the US. The findings from this study are facilitating the advancement of genome-assisted breeding strategies for resistance to PhCR in strawberries. SummaryO_LIPhytophthora crown rot (PhCR), caused by the soilborne pathogen Phytophthora cactorum, is a disease with broad impacts to cultivated strawberries worldwide. The Resistance to Phytophthora Cactorum 2 (RPc2) locus is widespread in important cultivars and is a target of selection in breeding programs. Despite its importance, the genomic architecture and mechanisms of RPc2 remain poorly characterized. C_LIO_LIWe performed fine-mapping and delimited the genomic region to a 546 kb segment containing 92 genes. We developed a chromosome-scale haplotype-phased genome from an elite resistant line, FL16.33-8, and made comparisons to reference genomes of Florida Brilliance (FaFB1) and Royal Royce (FaRR1) to uncover gene sequence and structural variants in resistant accessions. C_LIO_LIThrough comparative genomics and transcriptome profiling, we identified three candidate genes, Wall Associated Kinase 1 (WAK1) and Cyclic Nucleotide Gated Channel 1 (CNGC1) and CNGC2. The functions of these genes were validated using a simplified Agrobacterium-mediated transformation method for transient gene expression in strawberry crowns and roots. C_LIO_LIAn examination of the population structure of the RPc2 locus among genetically diverse accessions (N=1029) revealed that the predominant H3 resistant haplotype is widespread in breeding accessions in the US, supporting the findings of a previous study on recent selective sweeps associated with RPc2. Results from this study are advancing genome-assisted breeding strategies for enhancing resistance to PhCR in strawberry. C_LI

plant biology↗

bioRxiv2024

Mechanistic insights into the inhibition of dengue virus NS5 methyltransferase by herbacetin

Herbacetin (HC) is a naturally occurring flavonoid compound with a dual antiviral mechanism. It inhibits the polyamine biosynthetic pathway and targets the methyltransferase (MTase) enzyme of the dengue and chikungunya virus. However, understanding the detailed inhibition mechanism of DENV MTase by HC remains unclear. The crystal structure of DENV3 nonstructural protein 5 (NS5) MTase in complex with HC and S-adenosyl-L-homocysteine presented in this study gives structural insights into the inhibition mechanism. Structural analysis revealed that HC binds to the cap 0 RNA site near the GTP binding site in the DENV3 NS5 MTase, and fluorescence polarization assay demonstrated HC inhibits GTP binding with an inhibition constant Ki value of [~] 0.43 {micro}M. This is the first study that identified an inhibitor that targets the conserved RNA-binding region of NS5 MTase, suggesting its potential as a highly effective scaffold for broad-spectrum antiviral agents against orthoflaviviruses. ImportanceDengue virus (DENV) is a vector-borne disease affecting global health, and no antiviral treatment is available for Dengue fever. DENV NS5 methyltransferase (DENV NS5 MTase) is a viral RNA capping enzyme essential for the virus replication. This study demonstrated that herbacetin (HC), a natural flavonoid, blocked the binding of GTP to NS5 MTase and inhibited the enzyme. In addition to DENV3, HC effectively inhibited the replication of DENV1,2, and 4 serotypes. The crystal structure of the DENV3 NS5 MTase in complex with HC revealed that HC binds at the cap 0 RNA binding site, which is close to the GTP binding site and thereby perturbs the spatial arrangement of GTP binding site residues. HC, as the first identified inhibitor that targets the conserved RNA-binding site of DENV3 NS5 MTase, presents a potential scaffold for the development of new antiviral drugs.

microbiology↗

bioRxiv2024

Limited O-specific polysaccharide (OSP)-specific functional antibody responses in young children with Shigella infection in Bangladesh

Shigellosis is the second leading cause of diarrheal death in children younger than five years of age globally. At present, there is no broadly licensed vaccine against shigella infection. Previous vaccine candidates have failed at providing protection for young children in endemic settings. Improved understanding of correlates of protection against Shigella infection and severe shigellosis in young children living in endemic settings is needed. Here, we applied a functional antibody profiling approach to define Shigella-specific antibody responses in young children versus older individuals with culture-confirmed shigellosis in Bangladesh, a Shigella endemic area. We analyzed Shigella-specific antibody isotypes, FcR binding and antibody-mediated innate immune cell activation in longitudinal serum samples collected at clinical presentation and up to 1 year later. We found that higher initial Shigella O-specific polysaccharide (OSP)-specific and protein-specific IgG and Fc{gamma}R binding levels correlated with less severe disease regardless of patient age, but that individuals under 5 years of age developed a less prominent class switched, FcR-binding, functional and durable antibody response against both OSP and protein Shigella antigens than older individuals. Focusing on the largest cohort, we found that functional S. flexneri 2a OSP-specific responses were significantly induced only in individuals over age 5 years, and that these responses promoted monocyte phagocytosis and activation. Our findings suggest that in a Shigella endemic region, young children with shigellosis harbor a functional antibody response that fails to maximally activate monocytes; such a response may be important in facilitating subsequent innate cell clearance of Shigella, especially via recruitment and activation of polymorphonuclear cells capable of directly killing Shigella.

immunology↗

bioRxiv2024

Sequence and structural analysis of adaptors of Toll-like receptor 4 sheds light on the evolutionary trajectory and functional emergence

1.Type 4 Toll-like receptors 4 (TLR4) recognise lipopolysaccharides (LPS) from bacteria as their conventional ligands and undergo downstream signalling to produce cytokines. They mediate the signalling either by the TIRAP-MyD88 complex or by the TRAM-TRIF complex. The MyD88 pathway is common to all other TLRs, whereas the TRAM-TRIF complex is largely exclusive to TLR4. We studied the TIR domain of TRAM and TRIF homologue proteins, that are crucial for downstream signalling. From our previous work on pan-genome-wide survey, we find Callorhincus milli to be the ancestral organism with both TRAM and TRIF proteins. To gain a deeper insight about the functioning of these proteins and comparison with the adaptor proteins in Homo sapiens, we performed TRAM and TRIF dimer docking to model the TRAM-TRIF complex of representative organisms across various taxa. These provide us insights to ascertain a possible interaction surface, calculate the energetics, electrostatic potential, and then employ Normal Mode Analysis (NMA) to examine fluctuating, interacting and specific residue clusters which can be important for the protein functioning in both organisms. We also performed molecular dynamics simulations of these complexes and cross validated the functionally important residues using network parameters. While the critical residues of TIRAP, TRIF, and MyD88 were preserved, we found that the important residues of TRAM signalling were not conserved in Callorhincus milli. This suggests the presence of functional TIRAP-MyD88 mediated TLR4 signalling and TRIF mediated TLR3 signalling in the ancestral species. The overall biological function of this signalling domain appears to be gradually acquired through the orchestration of several motifs through evolutionary scale.

bioinformatics↗