Biology subjects

Jaiswal, D.

Publications and source records attributed to Jaiswal, D..

5 recordsLinked to original sources

bioRxiv2026

Defining the Antigenic Topology and Prospective Binding Breadth of Vaccination-induced SARS-CoV-2 Neutralizing Antibodies

Antibodies that neutralize SARS-CoV-2 primarily target the viral spike glycoprotein, yet the breadth of these responses is continually challenged by viral evolution. While extensive structural studies have defined epitopes across the spike protein, how antibodies elicited by the initial mRNA vaccination campaigns perform against subsequently emerging variants remains an important question. Here, we structurally and functionally characterize a panel of early plasmablast-derived human monoclonal antibodies isolated following primary mRNA vaccination, targeting both the receptor-binding domain (RBD) and the N-terminal domain (NTD) of spike. Using cryo-electron microscopy, variant-binding analyses, and viral-fusion inhibition assays, we observe that antibodies directed against immunodominant regions of the RBD and NTD are highly potent but more frequently impacted by variant-associated mutations. In contrast, antibodies engaging a conserved hydrophobic pocket within the NTD exhibit broader reactivity and neutralize through distinct molecular mechanisms. Together, these findings extend prior structural studies of spike-directed antibodies by prospectively assessing the breadth of vaccine-elicited antibodies against later variants and identifying structural features associated with differential escape sensitivity. These results contribute to a growing understanding of how early vaccine-induced antibody repertoires relate to subsequent viral evolution. One sentence summaryAntibody epitopes on SARS-CoV-2 spike determine prospective breadth and vulnerability to viral evolution.

immunology↗

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↗

bioRxiv2024

Defining a highly conserved B cell epitope in the receptor binding motif of SARS-CoV-2 spike glycoprotein

SARS-CoV-2 mRNA vaccines induce robust and persistent germinal centre (GC) B cell responses in humans. It remains unclear how the continuous evolution of the virus impacts the breadth of the induced GC B cell response. Using ultrasound-guided fine needle aspiration, we examined draining lymph nodes of nine healthy adults following bivalent booster immunization. We show that 77.8% of the B cell clones in the GC expressed as representative monoclonal antibodies recognized the spike protein, with a third (37.8%) of these targeting the receptor binding domain (RBD). Strikingly, only one RBD-targeting mAb, mAb-52, neutralized all tested SARS- CoV-2 strains, including the recent KP.2 variant. mAb-52 utilizes the IGHV3-66 public clonotype, protects hamsters challenged against the EG.5.1 variant and targets the class I/II RBD epitope, closely mimicking the binding footprint of ACE2. Finally, we show that the remarkable breadth of mAb-52 is due to the somatic hypermutations accumulated within vaccine-induced GC reaction. One Sentence SummaryBooster SARS-CoV-2 mRNA vaccine recruits and broadens GC B cell responses targeting a highly conserved site on receptor binding domain of spike glycoprotein.

immunology↗

bioRxiv2024

Dissecting human monoclonal antibody responses from mRNA- and protein-based XBB.1.5 COVID-19 monovalent vaccines

The emergence of highly contagious and immune-evasive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has required reformulation of coronavirus disease 2019 (COVID-19) vaccines to target those new variants specifically. While previous infections and booster vaccinations can enhance variant neutralization, it is unclear whether the monovalent version, administered using either mRNA or protein-based vaccine platforms, can elicit de novo B-cell responses specific for Omicron XBB.1.5 variants. Here, we dissected the genetic antibody repertoire of 603 individual plasmablasts derived from five individuals who received a monovalent XBB.1.5 vaccination either with mRNA (Moderna or Pfizer/BioNtech) or adjuvanted protein (Novavax). From these sequences, we expressed 100 human monoclonal antibodies and determined binding, affinity and protective potential against several SARS-CoV-2 variants, including JN.1. We then select two vaccine-induced XBB.1.5 mAbs, M2 and M39. M2 mAb was a de novo, antibody, i.e., specific for XBB.1.5 but not ancestral SARS-CoV-2. M39 bound and neutralized both XBB.1.5 and JN.1 strains. Our high-resolution cryo-electron microscopy (EM) structures of M2 and M39 in complex with the XBB.1.5 spike glycoprotein defined the epitopes engaged and revealed the molecular determinants for the mAbs specificity. These data show, at the molecular level, that monovalent, variant-specific vaccines can elicit functional antibodies, and shed light on potential functional and genetic differences of mAbs induced by vaccinations with different vaccine platforms. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=43 SRC="FIGDIR/small/602781v1_ufig1.gif" ALT="Figure 1000"> View larger version (16K): org.highwire.dtl.DTLVardef@7c4708org.highwire.dtl.DTLVardef@11b66acorg.highwire.dtl.DTLVardef@1f1cec7org.highwire.dtl.DTLVardef@3e72fe_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2021

Set4 coordinates the activity of histone deacetylases and regulates stress-responsive gene expression within subtelomeric regions in yeast

The yeast chromatin protein Set4 is a member of the Set3-subfamily of SET domain proteins which play critical roles in the regulation of gene expression in diverse developmental and environmental contexts, although they appear to lack methyltransferase activity. The molecular functions of Set4 are relatively unexplored, likely due to its low abundance in standard growth conditions. We previously reported that Set4 promotes survival during oxidative stress and regulates expression of stress response genes via stress-dependent chromatin localization. In this study, global gene expression analysis and investigation of histone modification status has revealed a role for Set4 in maintaining gene repressive mechanisms within yeast subtelomeres under both normal and stress conditions. We show that Set4 works in a partially overlapping pathway to the SIR complex and the histone deacetylase Rpd3 to maintain proper levels of histone acetylation and expression of stress response genes encoded in subtelomeres. This role for Set4 is particularly critical for cells under hypoxic conditions, and the loss of Set4 decreases cell fitness and cell wall integrity in hypoxia. These findings uncover a new regulator of subtelomeric chromatin that is key to stress defense pathways and demonstrate a function for yeast Set4 in regulating repressive, heterochromatin-like environments.

genetics↗