Biology subjects

Sheff, J.

Publications and source records attributed to Sheff, J..

3 recordsLinked to original sources

bioRxiv2026

Interconnecting ADC Structure with Tumor Cell Biology with Multimodal Learning

Antibody-drug conjugates (ADCs) represent a significant advancement in cancer therapy, yet their development remains constrained by high attrition rates driven by an incomplete understanding of how ADC chemical design interconnects with tumor biology. Compounding this challenge, the field has converged on a narrow set of redundant structural components, and current linker-payload systems that do not share a single mechanism of action. Existing drug response prediction frameworks cannot resolve this multidimensional complexity, relying predominantly on genomic inputs while protein-level biology is challenging to integrate. To address this, we developed a multimodal machine learning platform interconnecting ADC structural parameters with tumor cell biology across thousands of curated structure-activity datapoints, including multi-omics profiles from 1,479 human tumor cell lines and protein-level inputs from a unique model (GENCEP) that derives complete proteomic signatures. The model was validated through blinded retrospective evaluation and, critically, large coverage prospective prediction of cytotoxicity across 159 ADC-cell line combinations spanning five antigens, four mechanistically distinct linker-payload systems, and eight tumor types, most with no prior published associated ADC data. Performance surpassed industry benchmarks established for small molecule therapeutic modalities, demonstrating that protein-informed multimodal integrated framework is effective at capturing cytotoxic determinants at scale.

pharmacology and toxicology↗

bioRxiv2024

Broadly Reactive Anti-VHH Antibodies for Characterizing, Blocking, or Activating Nanobody-Based CAR-T Cells

Production of chimeric antigen receptor T cell (CAR-T) therapies is dependent on the use of antibody reagents to label, isolate, and/or expand T cell products. We sought to create antibody-based tools that directly target the variable domain of heavy-chain only antibodies (VHH or nanobody) used in some CAR molecules. Two murine antibodies were identified which bind to distinct epitopes in the conserved framework regions of llama-derived VHHs, and not to human VH domains. We produced a high-quality dual-clonal anti-VHH antibody product which reacts with over 98% of VHH proteins, regardless of their antigenic specificity. Anti-VHH binding did not disrupt VHH/antigen interaction, and thus could be used for secondary labeling to assess cellular or tissue reactivity of VHH molecules. Despite not interfering with antigen binding, anti-VHH antibodies potently inhibited VHH-CAR function, blocking CAR-T activation and cytolytic killing of target cells. When immobilized, anti-VHH antibodies could also be applied for activation and expansion of VHH CAR-T cells, inducing 730-fold mean expansion, >94% CAR purity, with retained CD8/CD4 heterogeneity. Functionally, anti-VHH antibody-expanded CAR-T cells maintained strong antigen specific activity without functional exhaustion. Overall, these data identify a useful new tool for understanding and manipulating VHH-based CAR-T cells. Funding SourceThis work was funded by the National Research Council Canada Disruptive Technology Solutions Cell and Gene Therapy challenge program, and BioCanRx Declaration of interestsThe anti-VHH antibodies reported here are the subject of a provisional patent application by the National Research Council of Canada

immunology↗

bioRxiv2021

Arsenal of Nanobodies for Broad-Spectrum Countermeasures against Current and Future SARS-CoV-2 Variants of Concerns

Nanobodies offer several potential advantages over mAbs for the control of SARS-CoV-2. Their ability to access cryptic epitopes conserved across SARS-CoV-2 variants of concern (VoCs) and feasibility to engineer modular, multimeric designs, make these antibody fragments ideal candidates for developing broad-spectrum therapeutics against current and continually emerging SARS-CoV-2 VoCs. Here we describe a diverse collection of 37 anti-SARS-CoV-2 spike glycoprotein nanobodies extensively characterized as both monovalent and IgG Fc-fused bivalent modalities. The panel of nanobodies were shown to have high intrinsic affinity; high thermal, thermodynamic and aerosolization stability; broad subunit/domain specificity and cross-reactivity across many VoCs; wide-ranging epitopic and mechanistic diversity; high and broad in vitro neutralization potencies; and high neutralization efficacies in hamster models of SARS-CoV-2 infection, reducing viral burden by up to six orders of magnitude to below detectable levels. In vivo protection was demonstrated with anti-RBD and previously unreported anti-NTD and anti-S2 nanobodies. This collection of nanobodies provides a therapeutic toolbox from which various cocktails or multi-paratopic formats could be built to tackle current and future SARS-CoV-2 variants and SARS-related viruses. Furthermore, the high aerosol-ability of nanobodies provides the option for effective needle-free delivery through inhalation.

bioengineering↗