Cell-level integration of gene expression and B cell receptor data captures complementary B cell information

Authors

Aron, E., Gabernet, G., Sabuwala, B., Yaari, G., Kleinstein, S.

Abstract

Single-cell B cell analyses commonly define relationships among cells using gene expression (GEX), although paired B cell receptor (BCR) sequences provide complementary information about receptor features, differentiation, and clonal relationships. We evaluated multiple approaches for integrating paired GEX and BCR data into cell-level representations and compared their ability to capture complementary aspects of B cell biology. We compared BCR representations based on language-model embeddings and engineered sequence features across multiple integration strategies. Spaces dominated by BCR language-model embeddings captured broad sequence and clonal information but could distort cell type relationships, as assessed using independent cell surface protein measurements. In contrast, concatenating GEX with selected BCR features (isotype, somatic hypermutation frequency, and CDRH3 length) incorporated receptor information while retaining transcriptional and surface-protein-associated structure. The resulting space reduced discordance between GEX-based cell type annotations and BCR characteristics and revealed B-cell substructure supported by both transcriptional and receptor-derived features. Thus, integrating GEX and BCR data captures complementary biological information and provides a richer foundation for single-cell B cell analysis.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 23 Oct 2026.

Stats

1-terrible, 9-excellent. How would you rate this preprint? Sign in in to submit your rating.

Post a comment

You need to be signed in to post comments. You can sign in here.

Comments

There are no comments yet.