Biology subjects

Kim, P. S.

Publications and source records attributed to Kim, P. S..

At least 19 recordsLinked to original sources

bioRxiv2025

Modelling Immune Dynamics in Locally Advanced MSI-H/dMMR Colorectal Cancer with Neoadjuvant Pembrolizumab Treatment: From Differential Equations to an Agent-Based Framework

Colorectal cancer (CRC) is the third most common malignancy worldwide, and accounts for approximately 10% of all cancers and an estimated 850,000 deaths annually. Within CRC, MSI-H/dMMR tumours are highly immunogenic due to their high mutational burden and neoantigen load, yet can evade immunosurveillance via PD-1/PD-L1-mediated signalling. Pembrolizumab, an anti-PD-1 antibody approved for unresectable or metastatic MSI-H/dMMR CRC, is emerging as a promising neoadjuvant option in the locally advanced setting, inducing rapid, deep and durable immune responses. In this work, we construct a minimal model of neoadjuvant pembrolizumab therapy in locally advanced MSI-H/dMMR CRC (laMCRC) using ordinary differential equations (ODEs), providing a highly extensible model that captures the main immune dynamics involved. On the other hand, agent-based models (ABMs) naturally capture stochasticity, interactions at an individual level, and discrete events that lie beyond the scope of differential-equation formulations. As such, we also convert our ODE model, with parameters calibrated to experimental data, to an ABM, preserving its dynamics while providing a flexible platform for future mechanistic investigation and modelling.

cancer biology↗

bioRxiv2025

Intercellular forces driving stratification in a two-layer corneal epithelium: Insight from a Voronoi cell-based simulation model

The cornea is a self-renewing, multilayered tissue maintained with remarkable precision. Its outermost layer, the corneal epithelium, consists of five to seven stratified cell layers, sustained by two coordinated processes: the centripetal migration of transit amplifying cells (TACs) from peripheral limbal epithelial stem cells (LESCs), and delamination (vertical movement) of cells between layers. Despite this well-organized renewal, the mechanisms governing epithelial stratification remain largely unknown. In this study, we present a two-dimensional Voronoi cell-based model that captures the dynamics of epithelial stratification. Our model incorporates two distinct epithelial layers--the basal and the suprabasal layers--and accounts for key cellular processes. These processes are mediated by mechanical interactions such as cell-substrate adhesion, as well as horizontal and vertical intercellular forces. Our simulations show that cell delamination, which drives stratification, is strongly linked to TAC proliferation. In contrast, LESC division remains largely unchanged, suggesting that TACs buffer LESC activity, consistent with the slow-cycling nature of stem cells. This reveals that processes weakening the cell-to-substrate interaction will enhance the turnover of epithelial cells without the need for external growth factor induction, which is a notable finding. Interestingly, although increased shedding promotes division and delamination, excessive shedding leads to mechanical compensation via cell stretching in the upper layers. This mechanical response explains the presence of enlarged cells in the superficial layers of the corneal epithelium. Our model reveals a direct link between the shedding rate and the centripetal velocity of clonal growth, predicting that increased surface cell loss accelerates cell movement-a response similar to wound healing, where cells rapidly migrate to restore the damaged area. These results highlight how cell size, migration, and turnover are tightly coupled, and offer deeper insights into how physical forces work together to maintain and rapidly restore epithelial integrity. Author summaryThe cornea is the eyes clear outer layer, helping to protect the eye and focus light for sharp vision. Its outermost surface is made up of several layers of cells that are constantly renewed to keep the tissue healthy. This renewal happens through two main processes: new cells are produced by stem cells on the edge of the cornea and move inward, while older cells gradually move upward through the layers and eventually shed from the surface. However, the exact way these movements and layers are controlled is still not fully understood. In this study, we developed a computer model to explore how these cells grow, move, and replace one another over time. The model includes the physical forces, such as how strongly cells stick to each other and to the surface beneath them. Our results show that the upward movement of cells plays an important role in how often cells divide. We also found that when surface cells are lost more quickly such as in injury the cells below respond by dividing and moving faster to repair the surface. This helps us better understand how the cornea repairs itself and maintains its protective surface.

cell biology↗

bioRxiv2025

Optimising Chemotherapy for Locally Advanced High-Grade Serous Ovarian Cancer via Delay-Differential Equations

Ovarian cancer is the deadliest gynaecological cancer and the fourth leading cause of cancer deaths in women. High-grade serous ovarian cancer (HGSOC) accounts for 75% of cases, and chemotherapy resistance and relapse occur in 85% of patients, leading to a 5-year survival of 45%. Currently, the literature lacks comprehensive immunobiological models of HGSOC, and developing such models could provide critical insights into the diseases underlying mechanisms and interactions within the tumour microenvironment. We address this by constructing an immunobiological model using delay differential equations and then optimise chemotherapy regimens to maximise efficacy, minimise toxicity, and improve treatment efficiency for first-line treatment. The model consists of two compartments, the tumour site and tumour-draining lymph node, with immune processes such as DC maturation, T cell priming and proliferation, and cytokine interactions modelled. Parameter values are estimated using experimental data from ovarian cancer tissue samples as well as the TCGA OV database. The results indicate that low-dose dose more frequent chemotherapy provides comparable results to the standard regimen with a lower toxicity, and alternative dosing strategies with rest weeks can allow patients to recover from the toxic side effects of chemotherapy.

cancer biology↗

bioRxiv2025

Optimisation of pembrolizumab therapy for de novo metastatic MSI-H/dMMR colorectal cancer using data-driven delay integro-differential equations

Colorectal cancer (CRC), the third most commonly diagnosed cancer worldwide, presents a growing public health concern, with 20% of new diagnoses involving de novo metastatic disease and up to 80% of these patients presenting with unresectable metastatic lesions. Microsatel-lite instability-high (MSI-H) CRC and deficient mismatch repair (dMMR) CRC constitute 15% of all CRC, and 4% of metastatic CRC, and, while less responsive to conventional chemotherapy, exhibit notable sensitivity to immunotherapy, especially programmed cell death protein 1 (PD-1) checkpoint inhibitors such as pembrolizumab. Despite this, there is a significant need to optimise immunotherapeutic regimens to maximise clinical efficacy and patient quality of life whilst minimising financial burden. In this work, we adapt our mechanistic model for locally advanced MSI-H/dMMR CRC to de novo metastatic MSI-H/dMMR CRC (dnmMCRC), deriving model parameters from pharmacokinetic, bioanalytical, and radiographic studies, as well as bulk RNA-sequencing data deconvolution from the TCGA COADREAD and GSE26571 datasets. We finally optimised treatment with pembrolizumab to balance efficacy, efficiency, and toxicity in dnmMCRC, comparing against currently FDA-approved regimens, analysing factors influencing treatment success and comparing immune dynamics to those in locally advanced disease.

cancer biology↗

bioRxiv2024

Large-scale Signal Propagation Modes in the Human Brain

The brains large-scale temporal dynamics play a crucial role in understanding its operations, but developing a cohesive framework to integrate the potentially extensive array of spatiotemporal patterns remains elusive. Our work addresses this gap by identifying multiple large-scale signal propagation modes in resting-state fMRI time series under a unified methodological framework. We found five distinct modes that effectively predict future blood-oxygen-level-dependent (BOLD) signal dynamics, each reconciling transitions between well-known large-scale brain networks into coherent spatiotemporal units. By utilizing these coherent units, our approach circumvents the need to explore combinatorial explosion of transitions between potential states, enabling parsimonious modeling and effective prediction of whole-brain temporal evolution. Each mode captures specific operational dimensions of neural resource allocation, ensuring their interpretability. Importantly, we showed that complex spatiotemporal features emerge from the superposition of these few propagation modes, unifying a broad spectrum of well-known brain dynamics phenomena. Our results lay the groundwork for a unified framework to understand large-scale spatiotemporal brain organization. Moreover, individual differences in mode expression profiles correlate with general cognitive abilities, exhibit heritability, and demonstrate cross-task stability, underscoring their functional significance. This could lead to efficient methods for characterizing functional fingerprints and advancing diagnostic approaches for neurological disorders.

neuroscience↗

bioRxiv2024

Bilateral Symmetry and Asymmetry in the C. elegans Connectome: A Graph-Theoretic Analysis based on Redundancy Measures

Understanding the balance between symmetry and asymmetry in animal nervous systems is crucial for unraveling the complexities of neural architectures and their functions. Previous studies have primarily focused on morphological symmetry, such as neuron placement, leaving the symmetry in the functional architecture largely unexplored. The current study investigates this aspect within the Caenorhabditis elegans connectomes by introducing a graph-theoretic approach. By defining a mirror-symmetry index, we quantitatively assess the symmetry in these connectomes, revealing a significant level of bilateral symmetry alongside notable asymmetry. Our approach also incorporates measures including connectivity similarity, motif-fingerprint differences, and path-compensation index to evaluate the networks functional redundancy and its capacity to compensate for unilateral disturbances. Here we show the C. elegans connectomes robust bilateral symmetry, which not only facilitates similar functions across neuron pairs but also ensures resilience against disruptions. This redundancy is not confined to symmetrical connections; it also includes asymmetric ones, adding to the neural networks complexity. An in-depth analysis into different neuron types shows varied redundancy levels: high in interneurons, moderate in motor neurons, and low in sensory neurons. This pattern suggests a strategic neural design where diverse inputs from sensory neurons, coupled with the stable integration by interneurons, lead to coordinated actions through motor neurons. This study advances our understanding of neural connectomes, offering insights into the intricate balance of symmetry and asymmetry in neural systems and their implications for complex, adaptive behaviors.

neuroscience↗

bioRxiv2024

Single-Sequence, Structure Free Allosteric Residue Prediction with Protein Language Models

Large language models trained on protein amino acid sequences have shown the ability to learn general coevolutionary relationships at scale, which in turn contain useful structural and functional information. Here we show that attention maps, matrices of learned pairwise relationships between residues, also include information about allostery. This enables prediction of allosteric relationships with no task-specific training, requiring only a single input sequence and no structural information. Attention maps outperform state-of-the-art structure-based and sequence coevolution-based allosteric residue prediction models on a well-curated benchmark set of 24 allosteric proteins. For K-Ras, an allosterically regulated GTPase, attention maps correlate best with allosteric residues influencing binding identified in deep mutational scanning data. For the beta-2 adrenergic receptor, an allosterically regulated GPCR, attention maps correlate best when compared to experimental alanine-scanning mutational data identifying allosteric relationships influencing signaling. These results enable allosteric relationship prediction in a single-sequence, structure-free manner.

biochemistry↗

bioRxiv2024

Engineering a SARS-CoV-2 vaccine targeting the RBD cryptic-face via immunofocusing

The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is the main target of neutralizing antibodies. Although they are infrequently elicited during infection or vaccination, antibodies that bind to the conformation-specific cryptic face of the RBD display remarkable breadth of binding and neutralization across Sarbecoviruses. Here, we employed the immunofocusing technique PMD (protect, modify, deprotect) to create RBD immunogens (PMD-RBD) specifically designed to focus the antibody response towards the cryptic-face epitope recognized by the broadly neutralizing antibody S2X259. Immunization with PMD-RBD antigens induced robust binding titers and broad neutralizing activity against homologous and heterologous Sarbecovirus strains. A serum-depletion assay provided direct evidence that PMD successfully skewed the polyclonal antibody response towards the cryptic face of the RBD. Our work demonstrates the ability of PMD to overcome immunodominance and refocus humoral immunity, with implications for the development of broader and more resilient vaccines against current and emerging viruses with pandemic potential. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/597541v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@12f1b1eorg.highwire.dtl.DTLVardef@19d6adforg.highwire.dtl.DTLVardef@1d392ccorg.highwire.dtl.DTLVardef@14aa8a2_HPS_FORMAT_FIGEXP M_FIG C_FIG SYNOPSISUsing the immunofocusing technique protect, modify, deprotect (PMD) we engineer SARS-CoV-2 receptor-binding domain (RBD) immunogens that generate broadly neutralizing antibodies against the conserved cryptic face. The ability to refocus humoral immunity to broadly conserved epitopes has important implications for the design of universal vaccines.

immunology↗

bioRxiv2024

Evolution of human pair bonds as a consequence of male-biased mating sex ratios?

Compared to our closest primate relatives, human life history involves greater longevity, which includes a distinctive postmenopausal life stage. The extension of the human lifes-pan (and continued fertility in old males) without lengthening female fertility directly changes the ratio of fertile males to fertile females, called the adult sex ratio (ASR). Additionally, this affects a more fine-grained ratio, the operational sex ratio (OSR), defined as the ratio of males to females currently able to conceive. Here, we construct an ODE model with minimal age structure, in which males compete for paternities using either a multiple-mating or mate-guarding strategy. Our focus is on investigating the differences of strategy choice between populations with chimpanzee-like and human-like life histories. By simulating the system, we determine the dominant strategy and its dependence on various parameter combinations. We introduce a new measure we call the lifetime paternity opportunities (LPO) of a given male strategy. The LPO directly calculates the payoffs of different male strategies and hence enables us to predict when strategies may shift. Our results show that an increase in OSR and ASR correlates well with a change in the dominant strategy from multiple mating to guarding.

evolutionary biology↗

bioRxiv2023

Inverse folding of protein complexes with a structure-informed language model enables unsupervised antibody evolution

Large language models trained on sequence information alone are capable of learning high level principles of protein design. However, beyond sequence, the three-dimensional structures of proteins determine their specific function, activity, and evolvability. Here we show that a general protein language model augmented with protein structure backbone coordinates and trained on the inverse folding problem can guide evolution for diverse proteins without needing to explicitly model individual functional tasks. We demonstrate inverse folding to be an effective unsupervised, structure-based sequence optimization strategy that also generalizes to multimeric complexes by implicitly learning features of binding and amino acid epistasis. Using this approach, we screened [~]30 variants of two therapeutic clinical antibodies used to treat SARS-CoV-2 infection and achieved up to 26-fold improvement in neutralization and 37-fold improvement in affinity against antibody-escaped viral variants-of-concern BQ.1.1 and XBB.1.5, respectively. In addition to substantial overall improvements in protein function, we find inverse folding performs with leading experimental success rates among other reported machine learning-guided directed evolution methods, without requiring any task-specific training data.

synthetic biology↗

bioRxiv2023

Design of universal Ebola virus vaccine candidates via immunofocusing

Ebola virus causes hemorrhagic fever in humans and poses a significant threat to global public health. Although two viral vector vaccines have been approved to prevent Ebola virus disease, they are distributed in the limited ring vaccination setting and only indicated for prevention of infection from orthoebolavirus zairense (EBOV) - one of three orthoebolavirus species that have caused previous outbreaks. Ebola virus glycoprotein GP mediates viral infection and serves as the primary target of neutralizing antibodies. Here we describe a universal Ebola virus vaccine approach using structure-guided design of candidates with hyperglycosylation that aims to direct antibody responses away from variable regions and toward conserved epitopes of GP. We first determined the hyperglycosylation landscape on Ebola virus GP and used that to generate hyperglycosylated GP variants with two to four additional glycosylation sites to mask the highly variable glycan cap region. We then created vaccine candidates by displaying wild-type or hyperglycosylated GP variants on ferritin nanoparticles (Fer). Immunization with these antigens elicited potent neutralizing antisera against EBOV in mice. Importantly, we observed consistent cross-neutralizing activity against Bundibugyo virus and Sudan virus from hyperglycosylated GP-Fer with two or three additional glycans. In comparison, elicitation of cross-neutralizing antisera was rare in mice immunized with wild-type GP-Fer. These results demonstrate a potential strategy to develop universal Ebola virus vaccines that confer cross-protective immunity against existing and emerging filovirus species. SIGNIFICANCE STATEMENTEbola virus outbreaks cause hemorrhagic fever with high mortality rates. Current viral vaccines require cold-chain storage and are distributed in limited ring vaccination settings. They are only indicated for protection against orthoebolavirus zairense (EBOV), one of three human-pathogenic Ebola virus species. Here we harness hyperglycosylation as an immunofocusing approach to design universal Ebola virus vaccine candidates based on Ebola virus glycoprotein (GP) displayed on ferritin nanoparticles (Fer). Compared with wild-type GP-Fer, immunization with hyperglycosylated GP-Fer elicited potently neutralizing antisera against EBOV, and more importantly, consistent cross-neutralizing activity against the other two orthoebolavirus species. Our work shows that immunofocusing antibody responses toward conserved and neutralizing epitopes of GP represents a promising strategy for vaccine design against antigenically diverse Ebola virus species.

immunology↗

bioRxiv2023

Decreased efficacy of a COVID-19 vaccine due to mutations present in early SARS-CoV-2 variants of concern

With the SARS-CoV-2 virus still circulating and evolving, there remains an outstanding question if variant-specific vaccines represent the optimal path forward, or if other strategies might be more efficacious towards providing broad protection against emerging variants. Here, we examine the efficacy of strain-specific variants of our previously reported, pan-sarbecovirus vaccine candidate, DCFHP-alum, a ferritin nanoparticle functionalized with an engineered form of the SARS-CoV-2 spike protein. In non-human primates, DCFHP-alum elicits neutralizing antibodies against all known VOCs that have emerged to date and SARS-CoV-1. During development of the DCFHP antigen, we investigated the incorporation of strain-specific mutations from the major VOCs that had emerged to date: D614G, Epsilon, Alpha, Beta, and Gamma. Here, we report the biochemical and immunological characterizations that led us to choose the ancestral Wuhan-1 sequence as the basis for the final DCFHP antigen design. Specifically, we show by size exclusion chromatography and differential scanning fluorimetry that mutations in the VOCs adversely alter the antigens structure and stability. More importantly, we determined that DCFHP without strain-specific mutations elicits the most robust, cross-reactive response in both pseudovirus and live virus neutralization assays. Our data suggest potential limitations to the variant-chasing approach in the development of protein nanoparticle vaccines, but also have implications for other approaches including mRNA-based vaccines.

biochemistry↗

bioRxiv2023

Formulation development and comparability studies with an aluminum-salt adjuvanted SARS-CoV-2 Spike ferritin nanoparticle vaccine antigen produced from two different cell lines

The development of safe and effective second-generation COVID-19 vaccines to improve affordability and storage stability requirements remains a high priority to expand global coverage. In this report, we describe formulation development and comparability studies with a self-assembled SARS-CoV-2 spike ferritin nanoparticle vaccine antigen (called DCFHP), when produced in two different cell lines and formulated with an aluminum-salt adjuvant (Alhydrogel, AH). Varying levels of phosphate buffer altered the extent and strength of antigen-adjuvant interactions, and these formulations were evaluated for their (1) in vivo performance in mice and (2) in vitro stability profiles. Unadjuvanted DCFHP produced minimal immune responses while AH-adjuvanted formulations elicited greatly enhanced pseudovirus neutralization titers independent of [~]100%, [~]40% or [~]10% of the DCFHP antigen adsorbed to AH. These formulations differed, however, in their in vitro stability properties as determined by biophysical studies and a competitive ELISA for measuring ACE2 receptor binding of AH-bound antigen. Interestingly, after one month of 4{degrees}C storage, small increases in antigenicity with concomitant decreases in the ability to desorb the antigen from the AH were observed. Finally, we performed a comparability assessment of DCFHP antigen produced in Expi293 and CHO cells, which displayed expected differences in their N-linked oligosaccharide profiles. Despite consisting of different DCFHP glycoforms, these two preparations were highly similar in their key quality attributes including molecular size, structural integrity, conformational stability, binding to ACE2 receptor and mouse immunogenicity profiles. Taken together, these studies support future preclinical and clinical development of an AH-adjuvanted DCFHP vaccine candidate produced in CHO cells.

immunology↗

bioRxiv2022

A ferritin-based COVID-19 nanoparticle vaccine that elicits robust, durable, broad-spectrum neutralizing antisera in non-human primates

While the rapid development of COVID-19 vaccines has been a scientific triumph, the need remains for a globally available vaccine that provides longer-lasting immunity against present and future SARS-CoV-2 variants of concern (VOCs). Here, we describe DCFHP, a ferritin-based, protein-nanoparticle vaccine candidate that, when formulated with aluminum hydroxide as the sole adjuvant (DCFHP-alum), elicits potent and durable neutralizing antisera in non-human primates against known VOCs, including Omicron BQ.1, as well as against SARS-CoV-1. Following a booster [~]one year after the initial immunization, DCFHP-alum elicits a robust anamnestic response. To enable global accessibility, we generated a cell line that can enable production of thousands of vaccine doses per liter of cell culture and show that DCFHP-alum maintains potency for at least 14 days at temperatures exceeding standard room temperature. DCFHP-alum has potential as a once-yearly booster vaccine, and as a primary vaccine for pediatric use including in infants.

immunology↗

bioRxiv2022

Structure-guided stabilization improves the ability of the HIV-1 gp41 hydrophobic pocket to elicit neutralizing antibodies

The hydrophobic pocket found in the N-heptad repeat (NHR) region of HIV-1 gp41 is a highly conserved epitope that is the target of various HIV-1 neutralizing monoclonal antibodies. Although the high conservation of the pocket makes it an attractive vaccine candidate, it has been challenging to elicit potent anti-NHR antibodies via immunization. Here, we solved a high-resolution structure of the NHR mimetic IQN17, and, consistent with previous ligand-bound gp41 pocket structures, we observed remarkable conformational plasticity of the pocket. The high malleability of this pocket led us to test whether we could improve the immunogenicity of the gp41 pocket by stabilizing its conformation. We show that the addition of five amino acids at the C-terminus of IQN17, to generate IQN22, introduces a stabilizing salt bridge at the base of the peptide that rigidifies the pocket. Mice immunized with IQN22 elicited higher avidity antibodies against the gp41 pocket and a more potent, albeit still weak, neutralizing response against HIV-1 compared to IQN17. Stabilized epitope-focused immunogens could serve as the basis for future HIV-1 fusion-inhibiting vaccines.

biochemistry↗

bioRxiv2022

Designing epitope-focused vaccines via antigen reorientation

A major challenge in vaccine development, especially against rapidly evolving viruses, is the ability to focus the immune response toward evolutionarily conserved antigenic regions to confer broad protection. For example, while many broadly neutralizing antibodies against influenza have been found to target the highly conserved stem region of hemagglutinin (HA-stem), the immune response to seasonal influenza vaccines is predominantly directed to the immunodominant but variable head region (HA-head), leading to narrow-spectrum efficacy. Here, we first introduce an approach to controlling antigen orientation based on the site-specific insertion of short stretches of aspartate residues (oligoD) that facilitates antigen-binding to alum adjuvants. We demonstrate the generalizability of this approach to antigens from the Ebola virus, SARS-CoV-2, and influenza and observe enhanced antibody responses following immunization in all cases. Next, we use this approach to reorient HA in an "upside down" configuration, which we envision increases HA-stem exposure, therefore also improving its immunogenicity compared to HA-head. When applied to HA of H2N2 A/Japan/305/1957, the reoriented H2 HA (reoH2HA) on alum induced a stem-directed antibody response that cross-reacted with both group 1 and 2 influenza A HAs. Our results demonstrate the possibility and benefits of antigen reorientation via oligoD insertion, which represents a generalizable immunofocusing approach readily applicable for designing epitope-focused vaccine candidates. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/521291v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@185f949org.highwire.dtl.DTLVardef@b132a9org.highwire.dtl.DTLVardef@174fcc8org.highwire.dtl.DTLVardef@17fb872_HPS_FORMAT_FIGEXP M_FIG C_FIG Seasonal influenza vaccines induce a biased antibody response against the variable head of hemagglutinin, whereas conserved epitopes on the stem are a target for universal vaccines. Here we show that reorienting HA in an "upside-down" configuration sterically occludes the head and redirects the antibody response to the more exposed stem, thereby inducing broad cross-reactivity against hemagglutinins from diverse influenza strains.

immunology↗

bioRxiv2022

Enhancing HIV-1 neutralization by increasing the local concentration of MPER directed bnAbs

Broadly neutralizing antibodies (bnAbs) against the membrane-proximal external region (MPER) of the gp41 component of the HIV-1 envelope (Env) are characterized by long hydrophobic heavy-chain complementarity-determining regions (HCDR3s) that interact with MPER and some viral membrane lipids, to achieve increased local concentrations. Here, we show that increasing the local concentration of MPER-directed bnAbs at the cell surface via binding to the high affinity Fc receptor (Fc{gamma}RI) potentiates their ability to prevent viral entry in a manner analogous to the previously reported observation whereby the lipid binding activity of MPER bnAbs increases their concentration at the viral surface membrane. However, binding of MPER-directed bnAb 10E8 to Fc{gamma}RI abolishes the neutralization synergy that is seen with the N-heptad repeat (NHR)-targeting antibody D5_AR and NHR-targeting small molecule enfuvirtide (T20), possibly due to decreased accessibility of the NHR in the Fc{gamma}RI-10E8-MPER complex. Taken together, our results suggest that lipid-binding activity and Fc{gamma}RI-mediated potentiation function in concert to improve the potency of MPER-directed bnAbs by increasing their local concentration near the site of viral fusion. Therefore, lipid-binding may not be a strict requirement for potent neutralization by MPER-targeting bnAbs, as alternative methods can achieve similar increase in local concentration while avoiding potential liabilities associated with immunologic host tolerance. Author summaryThe trimeric glycoprotein Env is the only viral protein expressed on the surface of HIV-1, is the target of broadly neutralizing antibodies, and is the focus of most vaccine development efforts. Broadly neutralizing antibodies targeting the membrane proximal external region (MPER) of Env show lipid-binding characteristics and modulating this interaction affects neutralization. In this study, we tested the neutralization potencies of variants of the MPER-targeting antibody 10E8 with different viral membrane-binding and host Fc{gamma}RI-binding capabilities. Our results suggest that binding to both lipid and Fc{gamma}RI improves the neutralization potency of MPER-directed antibodies by concentrating the antibody at sites of viral fusion. As such, lipid-binding may not be uniquely required for MPER-targeting broadly neutralizing antibodies, as alternative methods to increase local concentration can achieve similar improvements in potency.

microbiology↗

bioRxiv2022

HIV-1 neutralization tiers are not relevant for inhibitors targeting the pre-hairpin intermediate

HIV-1 strains are categorized into one of three neutralization tiers based on the relative ease by which they are neutralized by plasma from HIV-1 infected donors not on antiretroviral therapy; tier-1 strains are particularly sensitive to neutralization while tier-2 and tier-3 strains are increasingly difficult to neutralize. Most broadly neutralizing antibodies (bnAbs) previously described target the native prefusion conformation of HIV-1 Envelope (Env), but the relevance of the tiered categories for inhibitors targeting another Env conformation, the pre-hairpin intermediate, is not well understood. Here we show that two inhibitors targeting distinct highly-conserved regions of the pre-hairpin intermediate have strikingly consistent neutralization potencies (within [~]100-fold for a given inhibitor) against strains in all three neutralization tiers of HIV-1; in contrast, best-in-class bnAbs targeting diverse Env epitopes vary by more than 10,000-fold in potency against these strains. Our results indicate that antisera-based HIV-1 neutralization tiers are not relevant for inhibitors targeting the pre-hairpin intermediate and highlight the potential for therapies and vaccine efforts targeting this conformation.

immunology↗