Biology subjects

Phelps, N.

Publications and source records attributed to Phelps, N..

10 recordsLinked to original sources

bioRxiv2026

Germinal centers can persist for up to one year with declining somatic hypermutation and ongoing plasma cell output

The total duration of primary germinal center (GC) responses, and how B cell evolution changes as these responses mature, remain poorly defined. Here, longitudinal sampling of rhesus macaques immunized with HIV Envelope protein revealed that a single slow-delivery prime sustained ongoing GCs for nearly a year without additional antigen. Somatic hypermutation (SHM) accumulated throughout these prolonged responses, but its rate declined substantially over time, independent of both priming strategy and boosting. Over the same period, subdominant non-base Env specificities became increasingly represented within the GC response. Delaying boosting until after primary GC contraction increased recruitment of recalled memory B cells into the GC response. Bone marrow plasma cells were generated throughout prolonged GC maturation, with the timing of their generation modulated by booster timing. Together, these findings reveal how GCs evolve across nearly a year and how this prolonged maturation shapes the memory and plasma cell compartments that underpin long-term humoral immunity.

immunology↗

bioRxiv2026

Neural mechanisms underlying leg muscle responses during cervical transcutaneous spinal cord stimulation

Transcutaneous spinal cord stimulation (tSCS) of the cervical spinal cord has been thought to modulate lumbar networks, leading to the hypothesis that leg muscle recruitment may occur via recruitment of long-range spinal connections between cervical and lumbar circuits. To directly test this hypothesis, we compared arm and leg muscle responses elicited in unimpaired participants (N = 12) by cervical tSCS with the anodes placed over the iliac crests, with the anodes placed over the clavicles, and with lumbar tSCS as a control for leg muscle recruitment via the posterior root-muscle reflex. The idea of tSCS targeting cervico-lumbar connectivity would suggest that cervical stimulation could evoke responses in leg muscles. However, in our experiments, leg responses via cervical tSCS were only observed when the anodes were placed over the iliac crests, but not over the clavicles. These leg muscle responses had shorter latencies than those with lumbar tSCS and showed minimal post-activation depression, indicating efferent rather than afferent recruitment. Therefore, changes in leg muscle excitability by cervical-iliac tSCS previously attributed to descending cervical circuits could instead be explained by direct recruitment of efferent fibers near the iliac anodes. These findings suggest that cervical tSCS alone does not engage leg muscle motoneurons via long-range spinal or bidirectional pathways. Therefore, our study highlights the need to carefully consider electrode configuration when interpreting cervical tSCS mechanisms and additional or unexpected rehabilitative effects that extend caudally from the cervical spinal cord.

neuroscience↗

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

CryoEM Structures of Antibodies Elicited by Germline-Targeting HIV MPER Epitope-Scaffolds

Applying cryoEM to small protein complexes is usually challenging due to their lack of features for particle alignment. Here, we characterized antibody responses to 21 kDa HIV membrane-proximal external region germline-targeting (MPER-GT) immunogens through cryoEM by complexing them with 10E8 or Fabs derived from MPER-GT immunized animals. Distinct antibody-antigen interactions were analyzed using atomic models generated from cryoEM maps. Mutagenesis screening revealed off-target mAbs that do not compete with 10E8 bind non-MPER epitopes, and the two most dominant epitopes were verified by cryoEM. The structures of 10E8-class on-target Fabs showed binding patterns that resemble the YxFW motif in the 10E8 HCDR3 loop. Additionally, we demonstrate that high-resolution maps can be generated from heterogeneous samples with pooled competing Fabs. Overall, our findings will facilitate the optimization of MPER GT-antigens and push the size limit for cryoEM-based epitope mapping with smaller antigens and heterogeneous antibody mixes. HighlightsO_LIElucidate the structural basis of increased 10E8 affinity to GT12 over GT10.2 C_LIO_LICryoEM epitope mapping reveals three main binding sites on MPER-GT immunogens C_LIO_LIProof of concept for application of CryoEM epitope mapping to small immunogens C_LIO_LIStructural characterization and MD analysis confirms 10E8-like interactions of the MPER-specific Fabs C_LI

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

Transient effects in corticospinal and reticulospinal tract excitability induced by motor skill and isometric resistance training

Motor skill and resistance training are commonly used in rehabilitation to enhance neural plasticity. Nonetheless, how each modality impacts the excitability of corticospinal and reticulospinal pathways controlling the lower limb remains poorly understood. Here, we tested how single 30-minute sessions of cue-paced motor skill and isometric resistance training modulate corticospinal, reticulospinal, and spinal excitability in unimpaired adults (N = 23). Using motor-evoked potentials via transcranial magnetic stimulation, we found that both training types increased corticospinal excitability, with more substantial effects following motor skill training. In contrast, reticulospinal tract excitability--assessed by StartReact responses--and spinal excitability--assessed by H/M ratios, F-wave response amplitude, and persistence--remained largely unchanged. These results suggest that short-term training selectively enhances corticospinal tract excitability without a measurable impact on spinal or reticulospinal circuits. This pathway-specific response may inform strategies for targeting neural plasticity in rehabilitation.

neuroscience↗

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↗

bioRxiv2020

B cells expressing authentic naive human VRC01-class BCRs can be primed and recruited to germinal centers in multiple independent mouse models

Animal models of human antigen-specific B cell receptors (BCR) generally depend on "inferred germline" sequences, and thus their relationship to authentic naive human B cell BCR sequences and affinities is unclear. Here, BCR sequences from authentic naive human VRC01-class B cells from healthy human donors were selected for the generation of three new BCR knock-in mice. The BCRs span the physiological range of affinities found in humans, and use three different light chains (VK3-20, VK1-5, and VK1-33) found among subclasses of naive human VRC01-class B cells and HIV broadly neutralizing antibodies (bnAbs). The germline-targeting HIV immunogen eOD-GT8 60mer is currently in clinical trial as a candidate bnAb vaccine priming immunogen. To attempt to model human immune responses to the eOD-GT8 60mer, we tested each authentic naive human VRC01-class BCR mouse model under rare human physiological B cell precursor frequency conditions. B cells with high (HuGL18HL) or medium (HuGL17HL) affinity BCRs were primed, recruited to germinal centers, accrued substantial somatic hypermutation, and formed memory B cells. Precursor frequency and affinity interdependently influenced responses. Taken together, these experiments utilizing authentic naive human VRC01-class BCRs validate a central tenet of germline-targeting vaccine design and extend the overall concept of the reverse vaccinology approach to vaccine development.

immunology↗