Biology subjects

Alavi, N.

Publications and source records attributed to Alavi, N..

9 recordsLinked to original sources

bioRxiv2025

Antibody feedback establishes an affinity brake in the germinal center

Recent advances in mRNA vaccine technology have opened the door to novel types of antigen display, but little is yet known as to how B cells recognize and respond to these formats. By delivering an mRNA-LNP encoded membrane-bound immunogen displaying three conserved HIV-1 Envelope (Env) epitopes to knock-in mouse models with B cell receptors (BCRs) of defined affinities, we investigated how epitope-specific competition shapes germinal center (GC) responses. Co-activation of B cells targeting different epitopes did not alter GC kinetics observed in individual activations, but a striking inverse correlation was observed between BCR affinity and GC residence time in either scenario: high-affinity B cells exhibited shorter persistence in GCs, while those with lower affinity to the antigen were maintained. Furthermore, B cells were able to engage in GC reactions at equivalent rates in the presence or absence of clonal lineages binding the same epitope with similar affinities, while higher-affinity clones suppressed lower-affinity counterparts targeting the same epitope. Spatial transcriptomics revealed plasma-like cells within and adjacent to the GC which, together with the detection of early IgG in draining lymph nodes, suggests that local antibody production from these cells may contribute to feedback-driven kinetics. These findings indicate that a self-modulated local antibody feedback loop may act as a "brake" on epitope-specific recognition--dampening further affinity enhancement for high-affinity B cells and facilitating epitope spreading by redirecting the response toward alternative epitopes.

immunology↗

bioRxiv2025

Deep learning-enabled scaffolding of spatial arrays of PfCSP epitopes

Malaria is a leading cause of disease in developing countries. The licensed malaria vaccine RTS,S/AS01 confers partial protection in part due to the elicitation of circumsporozoite protein (CSP) antibodies, of which those to the CSP repeat and junctional regions offer the most potent protection. Anti-repeat region antibodies, including the protective antibody L9, frequently develop mutations that promote inter-Fab contacts when bound to CSP in "spiral" quaternary structures. As a first step toward the design of immunogens that elicit L9-like antibodies, we utilized generative deep learning models to design epitope-scaffolds that incorporated up to three junctional repeat epitopes with structural conformations and relative spatial orientations matching those of the multivalent complex of CSP bound to three copies of L9. Affinity and structural studies demonstrated accurate scaffolding of two epitopes with the intended relative orientation, and less accurate positioning of the third epitope. This study demonstrates proof of principle for design of multi-epitope scaffolds with pre-determined relative epitope spatial positioning. The study also represents an initial step toward development of multi-epitope immunogens to elicit antibodies that utilize homotypic interactions to bind pathogen in multivalent clusters.

immunology↗

bioRxiv2025

Accurate detection of pathogenic structural variants guided by multi-platform comparison

Structural variants (SVs) are a common cause of human diseases and greatly contribute to inter-individual variability. Their detection represents a significant challenge due to their diversity, size, and enrichment in repetitive regions. With the use of high quality long-read technologies, the majority of these challenges can now be mitigated. However, many downstream applications ranging from clinical diagnostics and genome-wide association studies to large-scale aggregation of population variants continue to rely on short-read-sequencing data due to its high through-put and cost-effectiveness. Thus, the challenges of short-read sequencing SV detection remain a constant and relevant obstacle. We created dicast, a machine-learning method to improve the identification of true-positive SVs from short-read sequencing using genomic context and alignment features. Dicast is driven by a novel and comprehensive benchmark call-set created through the combination of several sequencing technologies and rigorous manual curation. This benchmark set served as the basis for a systematic evaluation of five sequencing platforms and fifteen SV detection methods across different SV classes, sizes, and genomic contexts, enabling us to quantify the strengths and weaknesses of each and inform the training of our model. Leveraging these insights, dicast outperforms state-of-the-art short-read-based callers and consensus approaches, identifying considerably more true-positive variants while maintaining a high precision. We also demonstrate the methods applicability in diagnostic scenarios using putative pathogenic candidates in a limb malformation cohort, as well as known pathogenic variants in atrial fibrillation and neuromuscular disease cohorts. Dicast identifies all known pathogenic variants and 20% more manually confirmed candidate deletions than a consensus approach, and therefore can be used to reliably reduce time-consuming manual inspection in diagnostics. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=153 SRC="FIGDIR/small/655285v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@1c1702aorg.highwire.dtl.DTLVardef@aaecddorg.highwire.dtl.DTLVardef@1a4de08org.highwire.dtl.DTLVardef@ed0811_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Virus glycoprotein nanodisc platform for vaccine design

Transmembrane glycoproteins of enveloped viruses are the targets of neutralizing antibodies and essential vaccine antigens. mRNA-LNP technology allows in situ production of transmembrane glycoproteins upon immunization, but biophysical characterization of transmembrane antigens and in vitro analysis of post-immunization antibody responses typically rely on soluble proteins. Here, we present a methodological platform for assembling transmembrane glycoprotein vaccine candidates into lipid nanodiscs. We demonstrate the utility of the nanodiscs in HIV membrane proximal external region (MPER)-targeting vaccine development by binding assays using surface plasmon resonance (SPR), ex vivo B cell sorting with fluorescence-activated cell sorting (FACS), and by determining the structure of a prototypical HIV MPER-targeting immunogen nanodisc in complex with three broadly neutralizing antibodies (bnAbs), including the MPER bnAb 10E8, to 3.5 [A] by cryogenic electron microscopy (cryo-EM), providing a template for structure-based immunogen design for MPER. Overall, the platform offers a tool for accelerating the development of next-generation viral vaccines.

immunology↗

bioRxiv2025

Antigen avidity drives the durability of the vaccine immune response.

One challenge in vaccine development is designing immunogens that elicit durable immunity. We hypothesized that antigen avidity regulates the magnitude, diversity, and durability of the vaccine immune response. We tested this in multiple preclinical HIV vaccine models using a neoteric mosaic nanoparticle platform. This allowed us to precisely modulate antigen avidity by varying multivalency and affinity independently, whilst keeping other variables constant. Antigen avidity drove seeding, interclonal competition, and immunodominance within germinal centers. High-valency immunogens promoted durable germinal center, memory B cell, serum antibody, and long-lived plasma cell responses. Restricting interclonal competition rescued B cell responses to low-valency immunogens. B cell receptor sequencing revealed that antigen valency had minimal impact on individual somatic hypermutations but promoted clonal diversity. Affinity worked in concert with valency in driving productive B cell responses, with multivalency having dominant influences. The results underscore the importance of antigen avidity in driving durable and diverse vaccine responses.

immunology↗

bioRxiv2025

Vaccination with mRNA-encoded membrane-bound HIV Envelope trimer induces neutralizing antibodies in animal models

A protective vaccine against HIV will likely need to induce broadly neutralizing antibodies (bnAbs) that engage relatively conserved epitopes on the HIV envelope glycoprotein (Env) trimer. Nearly all vaccine strategies to induce bnAbs require the use of relatively complex immunization regimens involving a series of different immunogens, most of which are Env trimers. Producing protein-based clinical material to evaluate such relatively complex regimens in humans presents major challenges in cost and time. Furthermore, immunization with HIV trimers as soluble proteins induces strong non-neutralizing responses to the trimer base, which is normally occluded on the virion. These base responses could potentially detract from the induction of nAbs and the eventual induction of bnAbs. mRNA vaccine platforms offer potential advantages over protein delivery for HIV vaccine development, including increased production speed, reduced cost, and the ability to deliver membrane-bound trimers that might facilitate improved immuno-focusing to non-base epitopes. We report the design of mRNA-delivered soluble and membrane-bound forms of a stabilized native-like Env trimer (BG505 MD39.3), initial immunogenicity evaluation in rabbits that triggered clinical evaluation, and more comprehensive evaluation of B cell, T cell, and antibody responses in non-human primates. mRNA-encoded membrane-bound Env immunization elicited reduced off-target base-directed Env responses and stronger neutralizing antibody responses, compared with mRNA-encoded soluble Env. Overall, mRNA delivery of membrane-bound Env appears promising for enhancing B cell responses to subdominant epitopes and facilitating rapid translation to clinical testing, which should assist HIV vaccine development. One Sentence SummaryHIV envelope trimer mRNA enables membrane-bound expression and represents a functional immunogen in pre-clinical mammalian models.

immunology↗

bioRxiv2024

Diverse priming outcomes under conditions of very rare precursor B cells

Rare B cells can have special pathogen-recognition features giving them the potential to make outsized contributions to protective immunity. However, rare naive B cells infrequently participate in immune responses. We investigated how germline-targeting vaccine antigen delivery and adjuvant selection affect priming of exceptionally rare BG18-like HIV broadly neutralizing antibody-precursor B cells (~1 in 50 million) in non-human primates. Only escalating dose (ED) priming immunization using the saponin adjuvant SMNP elicited detectable BG18-like cells in germinal centers (GCs). All groups had strong GC responses, but only ED+SMNP and bolus+SMNP induced BG18-like memory B cells in >50% of animals. One group had vaccine-specific GC responses equivalent to ED+SMNP, but BG18-like memory B cells were rarely detected. Following homologous boosting, BG18-like memory B cells were more frequent in a bolus priming group, but had lower somatic hypermutation and affinities. This outcome was inversely associated with post-prime antibody titers, suggesting antibody feedback can significantly influence rare precursor B cell responses.

immunology↗

bioRxiv2023

Phase-locking of hippocampal CA3 neurons to distal CA1 theta oscillations selectively predicts memory performance

How the coordination of neuronal spiking activity and brain rhythms between hippocampal subregions supports memory function remains elusive. We studied interregional coordination of CA3 neuronal spiking activity with CA1 theta oscillations by recording electrophysiological signals along the proximodistal axis of the hippocampus in rats performing a high memory demand recognition memory task adapted from humans. We found that CA3 population spiking activity occurs preferentially at the peak of distal CA1 theta oscillations only when animals recalled previously encountered stimuli. In addition, decoding analyses revealed that only population cell firing of proximal CA3 together with that of distal CA1 can predict memory performance in the present non-spatial task. Overall, our work demonstrates an important role of the synchronization of CA3 neuronal activity with CA1 theta oscillations for successful recognition memory.

neuroscience↗

bioRxiv2021

Balancing conservation priorities for grassland and forest specialist bird communities in agriculturally dominated landscapes

Effective conservation planning often requires difficult decisions when at-risk species inhabit economically valuable landscapes or if the needs of multiple threatened species do not align. In the agriculture-dominated landscape of eastern Ontario and southwestern Quebec, Canada, conflicting habitat requirements exist between threatened grassland birds benefiting from certain agriculture practices and those of a diverse woodland bird community dependent on forest recovery. Using multi-scale species distribution models with Breeding Bird Survey (BBS) data, we assessed habitat suitability for 8 threatened grassland and forest specialists within this region. We also identified landscapes that jointly maximize occurrence of the 8 focal species and diversity of the overall grassland and forest communities. Influential habitat associations differed among species at the territory (200m radius) and landscape level (1km), highlighting the importance of considering multiple spatial scales. Species diversity was maximized when forest or grassland/pasture cover approached 40-50%, indicating a positive response to land cover heterogeneity. We identified species diversity hotspots near Lake Huron, as well as along the shore and southeast of the St. Lawrence River. These areas represent mosaic landscapes, balancing forest patches, wetland, grassland/pasture, and row crops such as corn, soybean, and cereals. Despite drastic landscape changes associated with agroecosystems, we demonstrate that targeted habitat protection and enhancement that prioritizes land cover diversity can maximize protection of bird communities with directly contrasting needs. We highlight multiple pathways to achieve this balance, including forest retention or separating row crops with hedgerows and wooded fence-lines, improving flexibility in conservation approaches.

ecology↗