SpaceBar enables clone tracing in spatial transcriptomic data

Kinsler, G.; Fagan, C.; Li, H.; Kaster, J.; Dunne, M.; Vander Velde, R. J.; Boe, R. H.; Shaffer, S.; Herlyn, M.; Raj, A.; Heyman, Y.

doi:10.1101/2025.02.10.637514

bioRxiv · 10.1101/2025.02.10.637514

SpaceBar enables clone tracing in spatial transcriptomic data

Kinsler, G.·Fagan, C.·Li, H.·Kaster, J.·Dunne, M.·Vander Velde, R. J.·Boe, R. H.·Shaffer, S.·Herlyn, M.·Raj, A.·Heyman, Y.

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Abstract

We report a cellular barcoding strategy, SpaceBar, that enables simultaneous clone tracing and spatial transcriptomics profiling. Our approach uses a library of 96 synthetic barcode sequences that can be robustly detected by imaging based spatial transcriptomics (seqFISH), delivered such that each cell is labeled with a combination of barcodes. We used these barcodes to label melanoma cells in a tumor xenograft model and profiled both clone identity and spatial gene expression in situ. We developed a gene scoring metric that quantifies how strongly gene expression is driven by intrinsic cellular cues or extrinsic environmental signals. Our framework distinguishes between clonal dynamics and environmentally-driven transcriptional regulation in complex tissue contexts.

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Kinsler, G., Fagan, C., Li, H., Kaster, J., Dunne, M., Vander Velde, R. J., Boe, R. H., Shaffer, S., Herlyn, M., Raj, A., Heyman, Y.. 2025-02-14. SpaceBar enables clone tracing in spatial transcriptomic data. https://doi.org/10.1101/2025.02.10.637514

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