Biology subjects

Roy Chowdhury, R.

Publications and source records attributed to Roy Chowdhury, R..

7 recordsLinked to original sources

bioRxiv2026

Protective pan-betacoronavirus neutralizing antibodies by vaccination

The continued emergence of betacoronaviruses underscores the urgent need for vaccines that provide broadly protective immunity. Here, we present an epitope-focused vaccine strategy targeting the conserved S2 stem-helix region of the spike fusion machinery, a broadly neutralizing antibody-(bnAb) epitope shared across betacoronaviruses yet partially occluded on the native spike. Immunization of non-human primates with engineered S2 stem-helix nanoparticle immunogens, alone or followed by a SARS-CoV-2 BA.1 spike mRNA boost, elicited broadly cross-reactive antibody responses against sarbecoviruses, merbecoviruses, and embecoviruses and neutralized SARS-CoV-2, multiple variants, other sarbecoviruses, and MERS-CoV. Vaccine-elicited monoclonal antibodies displayed broad in-vitro neutralizing activity and protected against both SARS-CoV-2 and MERS-CoV in-vivo. Structural analyses revealed conserved features between rhesus and human stem-helix bnAbs, supporting the translational potential. Overall, our findings provide proof-of-concept that epitope-focused nanoparticle immunogens can target partially occluded, immunoquiescent bnAb epitopes, laying the groundwork for pan-betacoronavirus vaccines that provide broad protection and strengthen pandemic preparedness. ONE SENTENCE SUMMARYEpitope-focused S2 stem-helix nanoparticle immunogens elicit protective broadly neutralizing antibodies (bnAbs) against diverse betacoronaviruses in non-human primates, establishing a framework for development of pan-betacoronavirus vaccines.

immunology↗

bioRxiv2025

Structure-guided design of native-like HIV Env Single Chain Trimers for enhanced stability, immunogenicity, and versatile vaccine delivery

Stabilizing the HIV envelope (Env) trimer in its native prefusion conformation is key to eliciting broadly neutralizing antibodies (bnAbs). We present a generalizable single-chain trimer-(SCT) design platform that enables the production of stable, native-like Env trimers across diverse HIV strains. Using a structure-guided approach, we developed CAP256.SU-SCT9, based on a CAP256.SU Env shown to induce V2-apex bnAbs in humans and rhesus macaques. CAP256.SU-SCT9 trimer exhibited native-like structure, bnAb-specific antigenicity, authentic glycosylation, and compatibility with nucleic acid and nanoparticle delivery. We extended this design strategy to a panel of HIV Envs representing global diversity, and immunogens known to initiate bnAb responses in humans. Structural analyses confirmed that SCTs consistently maintained prefusion-closed conformations, favorable glycan profiles, strong binding to trimer-specific bnAbs, and low reactivity with non-neutralizing antibodies. These findings establish SCT as a versatile platform for HIV trimer immunogen design, with potential to support next-generation vaccines aimed at eliciting protective bnAb responses.

immunology↗

bioRxiv2024

Germinal center BCR maturation in appendicitis reveals a role for antigen-specific adaptive immune responses during disease

Appendicitis is one of the most common abdominal emergencies globally, yet little is understood about the inflammatory mechanisms or potential drivers of disease. Neutrophil inflammation and increased cytokine expression such as IL-6 and IL-8 are hallmarks of appendicitis inflammation. However, early histological studies identified increased T and B cell infiltration during appendicitis, providing support for adaptive immune activation as well, although this has never been investigated in depth. We hypothesized that antigen-dependent activation of the adaptive immune response contributes to appendicitis pathology, in addition to the known innate-mediated processes. Via a series of transcriptomic approaches and lymphocyte repertoire analysis in human appendiceal tissue, we identified evidence of antigen-dependent B cell activation. Increased somatic hypermutation in the germinal center and plasma cell compartment was comprised of presumed high-affinity IgG and IgA B cells. We propose that the appendiceal microbiome acts as a source of antigen, as significant microbial dysbiosis was observed during appendicitis. This dysbiosis was characterized by outgrowth of pathobionts such as Parvimonas and oral biofilm-formers such as Fretibacterium and Fusobacterium, in line with previous reports. We also identified potential loss of epithelial barrier integrity via spatial transcriptomic analysis of the appendiceal epithelium, supporting the possibility of microbial invasion into the tissue during appendicitis. This study provides insight into the inflammatory mechanisms of a common disease and helps to define the immune and microbial compartment of an often-ignored organ, the appendix.

immunology↗

bioRxiv2023

Discerning state estimation and sensory gating, two presumptive predictive signals in mouse barrel cortex

The brain is assumed to contain distinctive predictive systems ranging from sensorimotor to cognitive functions. Here we report the successful functional delineation of two different presumptive predictive systems on the neuronal level, state estimation (SE) and sensory gating (SG), which both attenuate sensory flow during movement. Studying neuronal sensorimotor responses throughout the depth of primary somatosensory cortex in mice trained on a whisker reach task, SE appeared as a learned attenuation of tactile signal flow, due to a suppressive predictive signal, precisely at the time of an experimental sensory consequence. In contrast, SG was observable during a much longer interval after onset of the motor command. Both phenomena are internal, presumptively predictive signals, as blockade of the reafference did not affect them. We speculate that SG may be related to cognitive signals monitoring goals of movements, while SE likely is the expression of the classical notion of the reafference principle.

neuroscience↗

bioRxiv2023

MACI: A machine learning-based approach to identify drug classes of antibiotic resistance genes from metagenomic data

Novel methodologies are now essential for identification of antibiotic resistant pathogens in order to resist them. Here, we are presenting a model, MACI (Machine learning-based Antibiotic resistance gene-specific drug Class Identification) that can take metagenomic fragments as input and predict the drug class of antibiotic resistant genes. We trained the model to learn underlying patterns of genes using the Comprehensive Antibiotic Resistance Database. It comprises of 116 drug classes with a total of 2960 representative sequences. Among these 116 drug classes, we found 22 categories (contributing approximately 85% of the overall sequence-data) surpassed other 94 drug classes based on the number of fragments. The model showed an average precision of 0.83 and a recall of 0.81 for these 22 drug classes. Moreover, the model predicted multidrug resistant classes with higher performance score (precision and recall: 0.9 and 0.88 respectively) compared to single drug resistant categories (0.77 and 0.75). Post to this, we analysed these 22 drug classes to find out class-specific overlapping patterns of nucleotides that led to accurate classification. This way, we found five drug classes viz. "carbapenem;cephalosporin;penam", "cephalosporin", "cephamycin", "cephalosporin;monobactam;penam;penem", and "fluoroquinolone". Additionally, the positions of these significant patterns corroborated with the functional domains of majority of antibiotic resistance genes in that drug class, indicating their biological importance. These class-specific patterns play a pivotal role in rapid identification of some drug classes comprising antibiotic resistance genes. Further analysis showed that bacterial species, containing these five-drug classes, were found to have well-known multidrug resistance property.

bioinformatics↗

bioRxiv2021

The role of antigen recognition in the γδ T cell response at the controlled stage of M. tuberculosis infection.

{gamma}{delta} T cells contribute to host immune defense uniquely; but how they function in different stages (e.g., acute versus chronic) of a specific infection remains unclear. As the role of{gamma}{delta} T cells in early, active Mycobacterium tuberculosis (Mtb) infection is well documented, we focused on elucidating the{gamma}{delta} T cell response in persistent or controlled Mtb infection. Systems analysis of circulating{gamma}{delta} T cells from a South African adolescent cohort identified a distinct population of CD8+{gamma}{delta} T cells that expanded in this state. These cells had features indicative of persistent antigenic exposure but were robust cytolytic effectors and cytokine/chemokine producers. While these{gamma}{delta} T cells displayed an attenuated response to TCR-mediated stimulation, they expressed Natural Killer (NK) cell receptors and had robust CD16 (Fc{gamma}RIIIA)-mediated cytotoxic response, suggesting alternative ways for{gamma}{delta} T cells to control this stage of the infection. Despite this NK- like functionality, the CD8+{gamma}{delta} T cells consisted of highly expanded clones, which utilized TCRs with different V{gamma}/{delta} pairs. Theses TCRs could respond to an Mtb-lysate, but not to phosphoantigens, which are components of Mtb-lysate that activate{gamma}{delta} T cells in acute Mtb infection, indicating that the CD8+{gamma}{delta} T cells were induced in a stage-specific, antigen-driven manner. Indeed, trajectory analysis showed that these{gamma}{delta} T cells arose from naive cells that had traversed distinct differentiation paths in this infection stage. Importantly, increased levels of CD8+{gamma}{delta} T cells were also found in other chronic inflammatory conditions, including cardiovascular disease and cancer, suggesting that persistent antigenic exposure may lead to similar{gamma}{delta} T cell responses.

immunology↗

bioRxiv2020

A facile method of mapping neutralizing HIV-1 epitopes

Identification of specific epitopes targeted by neutralizing antibodies is essential to advance epitope-based vaccine design strategies. We report a facile methodology for rapid epitope mapping of neutralizing antibodies (NAbs) against HIV-1 Envelope (Env) at single residue resolution, using Cys labeling, viral neutralization assays and deep sequencing. This was achieved by the generation of a library of Cys mutations in Env glycoprotein on the viral surface, covalent labeling of the Cys residues using a Cys reactive label that masks epitope residues, followed by infection of the labeled mutant virions in mammalian cells in the presence of NAbs. Env gene sequencing from NAb-resistant viruses was used to accurately delineate epitopes for the NAbs VRC01, PGT128 and PGT151. These agreed well with corresponding experimentally determined structural epitopes previously inferred from NAb:Env structures. HIV-1 infection is associated with complex and polyclonal antibody responses, typically composed of multiple antibody specificities. Deconvoluting the epitope specificities in a polyclonal response is a challenging task. We therefore extended our methodology to map multiple specificities of epitopes targeted in polyclonal sera, elicited in immunized animals as well as in an HIV-1 infected elite neutralizer capable of neutralizing Tier-3 pseudoviruses with high titers. The method can be readily extended to other viruses for which convenient reverse genetics or lentiviral surface display systems are available.

molecular biology↗