PME Immuno Special Seminar - Dr. Evgeni Fiskin

Harnessing Engineered Nanobodies for Target Discovery and Therapeutic Innovation Targeting diseased cells with biologics or cell therapies requires identifying cell surface epitopes that distinguish pathological from healthy states. However, many antigens explored in cancer therapy lack disease exclusivity, leading to on-target, off-tumor toxicities due to unintended targeting of normal cells. Traditional target discovery approaches, such as differential RNA sequencing or proteomics, provide only indirect evidence of targetable epitopes. Meanwhile, direct epitope profiling via oligonucleotide-barcoded antibody panels remains limited by the number of epitopes that can be assayed in parallel, restricting the comprehensive characterization of the cell surface landscape. To overcome these limitations, we developed PHAGE-ATAC, a scalable platform that leverages a high-complexity phage display library of engineered genetically barcoded Nanobodies to systematically map the cellular epitope landscape. PHAGE-ATAC enables single-cell resolution measurements of Nanobody binding profiles, chromatin accessibility, and mitochondrial DNA-based clonal tracing in parallel. We apply this technology to multimodal analysis of primary human cells, sample multiplexing, intracellular protein profiling, and detection of SARS-CoV-2 spike protein in human cell populations. By dramatically expanding the scope of epitope profiling, this platform facilitates the discovery of novel therapeutic targets and advances the development of precision biologics for targeted therapy.