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bioRxiv · 10.1101/2021.05.26.445719

In vivo selection of nanobodies to target the tumor immune microenvironment for immunotherapy development

Sekar, T. V.·Elghonaimy, E.·Swancutt, K. L.·Whitney, M.·Aguilera, T. A.
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Abstract

In the rapidly advancing field of synthetic biology, there is a critical need for technology to discover targeting moieties for therapeutic biologics. We developed INSPIRE-seq, an approach that utilizes a nanobody library and next-generation sequencing to identify nanobodies selected for complex environments. INSPIRE-seq enables the parallel enrichment of immune cell-binding nanobodies that penetrate the tumor microenvironment. Clone enrichment and specificity varies across immune cell subtypes in the tumor, lymph node, and spleen. INSPIRE-seq identified a dendritic cell binding clone that binds PHB2. Single-cell RNA sequencing revealed a connection with cDC1s, and immunofluorescence confirmed nanobody-PHB2 colocalization along cell membranes. Structural modeling and docking studies assisted binding predictions and will guide nanobody selection. In this work, we demonstrate that INSPIRE-seq offers an unbiased approach to examine complex microenvironments and assist in the development of nanobodies, which could serve as active drugs, modified to become drugs, or used as targeting moieties.

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Sekar, T. V., Elghonaimy, E., Swancutt, K. L., Whitney, M., Aguilera, T. A.. 2021-05-29. In vivo selection of nanobodies to target the tumor immune microenvironment for immunotherapy development. https://doi.org/10.1101/2021.05.26.445719

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