SPaCeD: Spatial Point Process Distances for Pairing the Heavy and Light Chains of B Cell Receptors from Spatial BCR-seq

Abstract

B cells mediate anti-tumor immunity through B cell receptors (BCRs) composed of paired heavy and light chains. Leveraging spatial transcriptomics, we introduce SPaCeD, a framework that infers heavy-light chain pairs by integrating expression matrices with spatial distances between point patterns derived via optimal transport. Applied to ovarian and breast cancer datasets and simulation scenarios, SPaCeD improves pairing accuracy and stability compared with existing methodology (Repair), particularly for pairs with lower spatial expression.