Cell surface proteins

• Diseases are caused by aberrant cell function. These functions are executed by proteins interacting with other proteins and clustering.

• This dynamic interactome represents a vast and unstudied dimension in translational research with massive potential as novel types of biomarkers, drug targets, and discoveries of new therapeutic avenues.

• Protein interactomics by Proximity Networks delivers this new exciting omics dimension.

Herein we present the Proximity Network Assay, where 150 target proteins are positioned in a DNA-based spatial network of >40,000 nodes from single cells without optics. Barcoded antibodies bound to target proteins are subjected to in situ rolling circle amplification, generating multiple barcode copies subsequently serving as spatial network nodes to several other proximal neighbors via hybridization of a linker-oligonucleotide. Pairs of proximal barcodes are inserted into the two ends of the linker by gap-fill ligation, readable by DNA sequencing. At nanoscale resolution in 3D, Proximity Networks will be applicable to high throughput protein interactomics studies in immuno oncology-, hematology-, and cell therapy research.