Droplet-based single-cell pairing for high-throughput interaction mapping of antigen-receptor combinations.

Summary

SPLIS deterministically pairs a single antigen-presenting cell with a single receptor-expressing cell in droplets to quantify syncytium formation across spike–ACE2 variant pairs. It reveals both fusion-enhancing and -inhibiting combinations and shows how ACE2 SNPs modulate susceptibility to emerging SARS-CoV-2 spike mutations.

Key Findings

• Developed SPLIS to deterministically co-encapsulate one sender and one receiver cell in droplets and read out fusion by sequencing fused DNA barcodes.
• High-throughput profiling identified spike–ACE2 variant pairs that enhance or inhibit syncytium formation.
• ACE2 single-nucleotide polymorphisms modulate susceptibility to emerging SARS-CoV-2 spike mutations.

Clinical Implications

While preclinical, the approach can prioritize concerning spike mutations and host ACE2 variants for surveillance, guide variant risk assessment, and support precision public health strategies for respiratory virus threats.

Limitations

• Cell–cell fusion is a proxy for entry and may not fully capture multistep viral infection in vivo.
• Generalization to other receptor–ligand systems requires additional validation and engineering.

Future Directions

Extend SPLIS to other respiratory viruses and host receptors, integrate with CRISPR perturbations for causal mapping, and validate key variant pairs in physiologic airway models.