Biology subjects

Lin, Z. J.

Publications and source records attributed to Lin, Z. J..

4 recordsLinked to original sources

bioRxiv2025

Rapid elicitation of a new class of neutralizing N332-glycan independent V3-glycan antibodies against HIV-1 in nonhuman primates.

Sequential immunization is a promising approach to elicit broadly neutralizing antibodies (bNAbs) against the HIV-1 Envelope (Env). However, available protocols are inefficient and involve multiple immunizations over long periods of time. Here, we present WIN332, a new engineered Env-immunogen that induces a new class of neutralizing N332-glycan-independent antibodies to the conserved V3-glycan epitope of Env after a single bolus immunization in nonhuman primates. WIN332 binds to precursors of canonical human N332-glycan-dependent (Type-I) V3-glycan bNAbs but also of a first-of-its-class N332-glycan-independent (Type-II) V3-glycan bNAb. A single immunization elicits neutralizing serum and monoclonal antibodies that are boosted and affinity matured with a heterologous immunogen. EMPEM analysis of serum antibodies, antibody cloning and cryo-EM analysis reveal that WIN332 elicits N332-glycan-independent antibodies with remarkable sequence and binding similarities with the most potent human type-I and type-II V3-glycan bNAbs. Thus, WIN332 is a promising vaccine candidate to streamline V3-glycan bNAb elicitation.

immunology↗

bioRxiv2025

Machine learning enables de novo multi-epitope design of plasmodium falciparum circumsporozoite protein to target trimeric L9 antibody

AbstractCurrently approved vaccines for the prevention of malaria provide only partial protection against disease, due to high variability in the quality of induced antibodies. These vaccines present the unstructured central repeat region, as well as the C-terminal domain, of the circumsporozoite protein (PfCSP) of the malaria parasite, Plasmodium falciparum (1). A recently discovered protective monoclonal antibody, L9, recognizes three structured copies of the PfCSP minor repeat. Similarly to other highly potent anti-malarial antibodies, L9 relies on critical homotypic interactions between antibodies for its high protective efficacy (2, 3). Here, we report the design of immunogens scaffolding one copy of PfCSPs minor repeat capable of binding L9. To design immunogens capable of presenting multiple, structure-based epitopes in one scaffold, we developed a machine-learning-driven structural immunogen design pipeline, MESODID, tailored to focus on multi-epitope vaccine targets. We use this pipeline to design multiple scaffolds that present three copies of the PfCSP minor repeat. A 3.6 [A] cryo-EM structure of our top design, minor repeat targeting immunogen (M-TIM), demonstrates that M-TIM successfully orients three copies of L9, effectively recapitulating its critical homotypic interactions. The wide prevalence of repeated epitopes in key vaccine targets, such as HIV-1 Envelope, SARS-CoV-2 spike, and Influenza Hemagglutinin, suggests that MESODID will have broad utility in creating immunogens that incorporate such epitopes, offering a new powerful approach to developing vaccines against a range of challenging infections, including malaria. Significance StatementIn this study, we present a machine learning driven, structure-guided protein design pipeline built specifically for the design of multi-epitope vaccine immunogens. We employ the pipeline here to design and solve the cryo-EM structure of a de novo immunogen that binds and properly orients three copies of the anti-malarial monoclonal antibody L9, producing a promising next-generation malaria vaccine immunogen. This design pipeline could be employed to design any number of structurally constrained multi-epitope immunogens, as well as other proteins designed to bind multiple targets.

biophysics↗

bioRxiv2024

Deep Mining of the Human Antibody Repertoire Identifies Frequent and Immunogenetically Diverse CDRH3 Topologies Targetable by Vaccination

Germline targeting vaccination strategies against highly variable pathogens such as HIV aim to elicit broadly neutralizing antibodies (bnAbs) with particular immunogenetic or structural features. The V2 apex of the HIV Env protein is a promising target for a class of bnAbs that contain conserved structural motifs in the heavy chain complementarity determining region 3 (CDRH3). Here, we show that these structural motifs are targetable by vaccination by characterizing V2 apex axe-like CDRH3s in the human repertoire and developing new immunogens capable of engaging them. We determined the frequency and diversity of axe-like CDHR3s in healthy human donors using a series of structural informatics approaches, finding these precursors in nearly 90% of donors. Axe-targeting immunogens based on the HIV Env Q23.17 bound axe-like precursors in cryo-EM structures, induced V2 apex-specific antibody responses in humanized mice, and induced axe-like heterologous neutralizing antibodies in rhesus macaques infected with a germline-targeted simian-human immunodeficiency virus. These results illustrate a new structure-guided immunoinformatic vaccine design paradigm that can be employed to elicit immunogenetically diverse yet structurally conserved classes of antibodies. Significance StatementMany broadly neutralizing antibodies (bnAbs) utilize modes of epitope recognition dominated by the antibody complementarity determining region 3 (CDRH3). The CDRH3 is the most diverse part of the antibody, posing a challenge for germline targeting vaccine designs that aim to elicit antibodies with particular immunogenetic features. Vaccine design strategies that accommodate CDRH3 variability are therefore needed. Many HIV Env V2 apex bnAbs share "axe-like" CDRH3 microfolds that arise from diverse immunogenetic origins. Here we determined the frequency in humans of B cells with such CDRH3 topologies and designed immunogens to engage their precursors. This work opens a path toward vaccines that engage specific structural classes of B cells, thereby advancing the rational design of immunogens for HIV and other pathogens.

immunology↗

bioRxiv2024

Harnessing molecular mechanism for precision medicine in dilated cardiomyopathy caused by a mutation in troponin T

Familial dilated cardiomyopathy (DCM) is frequently caused by autosomal dominant point mutations in genes involved in diverse cellular processes, including sarcomeric contraction. While patient studies have defined the genetic landscape of DCM, genetics are not currently used in patient care, and patients receive similar treatments regardless of the underlying mutation. It has been suggested that a precision medicine approach based on the molecular mechanism of the underlying mutation could improve outcomes; however, realizing this approach has been challenging due to difficulties linking genotype and phenotype and then leveraging this information to identify therapeutic approaches. Here, we used multiscale experimental and computational approaches to test whether knowledge of molecular mechanism could be harnessed to connect genotype, phenotype, and drug response for a DCM mutation in troponin T, deletion of K210. Previously, we showed that at the molecular scale, the mutation reduces thin filament activation. Here, we used computational modeling of this molecular defect to predict that the mutant will reduce cellular and tissue contractility, and we validated this prediction in human cardiomyocytes and engineered heart tissues. We then used our knowledge of molecular mechanism to computationally model the effects of a small molecule that can activate the thin filament. We demonstrate experimentally that the modeling correctly predicts that the small molecule can partially rescue systolic dysfunction at the expense of diastolic function. Taken together, our results demonstrate how molecular mechanism can be harnessed to connect genotype and phenotype and inspire strategies to optimize mechanism-based therapeutics for DCM. Significance statementDilated cardiomyopathy (DCM), a leading cause of heart failure, is characterized by the inability of the heart to perfuse the body at normal filling pressures. There are multiple causes of DCM, including point mutations in sarcomeric proteins, but most patients receive similar courses of treatment, regardless of the underlying cause of the DCM. Many patients remain unserved by current therapies, and there is a need for new approaches. Here, we use multiscale experimental and computational approaches to demonstrate how knowledge of molecular mechanism can be harnessed to accurately predict the effects of a patient-specific mutation and responses to presumptive therapeutics. Our approach lays the foundation for a precision medicine approach to DCM.

biophysics↗