Naaz, S. | bioRxiv Science

bioRxiv2025

Programing Immunogenicity of Dengue EDIII Vaccine Antigens Using Engineered Outer Membrane Vesicles (OMVs)

Dengue is a mosquito-borne viral infection and is more prevalent in the world with no therapeutics and suboptimal vaccine performance against all four serotypes of the dengue virus. Hence, there is an urgent requirement for a non-infectious and non-replicative vaccine candidate that can elicit a balanced and serotype-specific immune response. In this study, we have engineered bacterial outer membrane vesicles (rOMVs) that display EDIII antigens (EDIII rOMVs). The current formulation modulates the expression of costimulatory molecules on antigen-presenting cells (APCs) as well as enhances the uptake and presentation. Subsequently, the EDIII rOMVs elicited a strong antigen-specific polyfunctional response from CD4+ and CD8+ T cells. The robust antibody response was facilitated by a germinal center reaction characterized by high T follicular helper (Tfh) and B cell response levels in the mice that received EDIII rOMVs. Notably, the produced antibodies demonstrated the ability to neutralize all four dengue virus serotypes in an in vitro infection model, indicating its potential role in protective immunity. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/640071v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@689d81org.highwire.dtl.DTLVardef@3c878aorg.highwire.dtl.DTLVardef@1e6b1aaorg.highwire.dtl.DTLVardef@9a5180_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

Deciphering the role of the nanoscale clustering of activating and costimulatory antibodies on T cell activation

In a joint experimental and a modeling effort, we explored the regulation of T cell activation and cytotoxicity by the nanoscale clustering and surface density of activating and costimulatory antibodies. Specifically, we simulated T cells on nanolithographically patterned arrays of clusters of these antibodies, systematically varying the cluster size from intermediate to large and overall antibody density. We found that T-cell activation correlated more with global antibody density than with cluster size, such that at low density arrays were inefficient in activation, while high density arrays saturated the signal. However, when T-cells were exposed to patterns of low global densities but small, very dense clusters, full activation of T cells was achieved. These results could be rationalized using the membrane-fluctuation-model that integrates the cooperative effects between bonds with mechanical feedback from the cell activation. This insight into the spatial organization of activating ligands provides an important understanding of the mechanism of T cell activation and allows for the design of more effective T cell activation platforms for immunotherapy.

immunology↗

bioRxiv2024

Long G4-rich enhancer physically interacts with EXOC3 promoter via a G4:G4 DNA-based mechanism

Enhancers are genomic sequences that function as regulatory elements capable of increasing the transcription of a given gene often located at a considerable distance. The broadly accepted model of enhancer activation involves bringing an enhancer-bound activator protein complex into close spatial proximity to its target promoter through chromatin looping. Equally relevant to the work described herein, roles for guanine (G) rich sequences in transcriptional regulation are now widely accepted. Non-coding G-rich sequences are commonly found in gene promoters and enhancers, and various studies have described specific instances where G-rich sequences regulate gene expression via their capacity to form G-quadruplex (G4) structures under physiological conditions. In light of this, our group previously performed a search for long human genomic stretches significantly enriched for minimal G4 motifs (referred to as LG4s herein) leading to the identification of 301 LG4 loci with a density of at least 80 GGG repeats / 1,000 basepairs (bp) and averaging 1,843 bp in length. Further, in agreement with previous reports indicating that minimal G4s are highly enriched in promoters and enhancers, we found 217/301 LG4 sequences overlap a GeneHancer annotated enhancer, and the gene promoters regulated by these LG4 enhancers were found to be similarly, markedly enriched with G4-capable sequences. Importantly, while the generally accepted model for enhancer:promoter specificity maintains that interactions are dictated by enhancer- and promoter-bound transcriptional activator proteins, the current study was designed to test an alternative hypothesis: that LG4 enhancers physically interact with their cognate promoters via a direct G4:G4 DNA-based mechanism. As such, this work employs a combination of informatic mining and locus-specific immunoprecipitation strategies to establish the spatial proximity of enhancer:promoter pairs within the nucleus then biochemically confirms the ability of individual LG4 ssDNAs to directly and specifically interact with DNA sequences found in their target promoters. In addition, we also identify four single nucleotide polymorphisms (SNPs), occurring within a LG4 enhancer on human chromosome 5, significantly associated with Cystic Fibrosis (CF) lung disease severity (avg. p value = 2.83E-9), presumably due to their effects on the expressions of CF-relevant genes directly regulated by this LG4 enhancer (e.g., EXOC3 and CEP72). Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/577212v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1fee785org.highwire.dtl.DTLVardef@11f0a9org.highwire.dtl.DTLVardef@1cf198corg.highwire.dtl.DTLVardef@1963a55_HPS_FORMAT_FIGEXP M_FIG C_FIG In brief: LG4 enhancers physically interact with gene promoters by forming composite G4 structures where both the LG4 and cognate promoter contribute half of the necessary sequence for G4 formation.

genetics↗