Accelerating target deconvolution for therapeutic antibody candidates using highly parallelized genome editing

Abstract

Therapeutic antibodies are transforming the treatment of cancer and autoimmune diseases. Today, a key challenge is finding antibodies against new targets. Phenotypic discovery promises to achieve this by enabling discovery of antibodies with therapeutic potential without specifying the molecular target a priori. Yet, deconvoluting the targets of phenotypically discovered antibodies remains a bottleneck; efficient deconvolution methods are needed for phenotypic discovery to reach its full potential. Here, we report a comprehensive investigation of a target deconvolution approach based on pooled CRISPR/Cas9. Applying this approach within three real-world phenotypic discovery programs, we rapidly deconvolute the targets of 38 of 39 test antibodies (97%), a success rate far higher than with existing approaches. Moreover, the approach scales well, requires much less work, and robustly identifies antibodies against the major histocompatibility complex. Our data establish CRISPR/Cas9 as a highly efficient target deconvolution approach, with immediate implications for the development of antibody-based drugs.

Sequence enrichment profiles enable target-agnostic antibody generation for a broad range of antigens

“…PDD is a well-validated strategy for first-in-class small-molecule drug discovery, 6 , 34 , 35 and we and others have used PDD to identify first-in-class antibodies to, e.g., CD52, 8 ICAM-1, 9 CD32b, 10 , 11 and TNFR2, 12 several of which are currently in clinical development. 36 , 37 , 38 , 39 , 40 By combining prediction-based antibody discovery with appropriate functional screening 11 , 41 and our recently described high-throughput CRISPR-based method for target deconvolution, 42 biologic PDD can be taken to the next level, directly on par with small-molecule PDD.…”

Identification of lamprey variable lymphocyte receptors that target the brain vasculature

“…Commonly used pull down methods to identify receptor-ligand interactions are notoriously complicated for membrane tethered proteins 67 , 68 . However, expression cloning methods 25 and rapidly advancing gene editing approaches could be deployed to determine the specific targets recognized by the VLR-Fcs 69 .…”

CRISPR in cancer biology and therapy

“…or biologic therapies 229,230 . For example, Sheltzer and colleagues 231 used a CRISPR KO approach to show that in some cases, drugs entering clinical trials that are presumed to inhibit a single protein can engage more than one target, and this offtarget activity is important for drug response.…”

“…For example, Sheltzer and colleagues 231 used a CRISPR KO approach to show that in some cases, drugs entering clinical trials that are presumed to inhibit a single protein can engage more than one target, and this offtarget activity is important for drug response. Mattsson et al 230 used an elegant screenbased strategy to define the cellsurface targets of dozens of antibodies. Such approaches streamline the validation of novel antibodybased therapeutics.…”