circVDJ-seq for T cell clonotype detection in single-cell and spatial multi-omics

Plumbom, I.; Obermayer, B.; Raspe, R.; Pascual-Reguant, A.; Theurillat, I.; Pentimalli, T. M.; Hsieh, Y.-H.; Gil, M.; Dietrich, C.; Seeger-Zografakis, M.; Quedenau, C.; Wilde, J.; Braeuning, C.; Fischer, C.; Schuelke, M.; Ludwig, L. S.; Eggert, A.; Rajewsky, N.; Borodina, T.; Beule, D.; Altmueller, J.; Radbruch, H.; Hauser, A.; Conrad, T.

doi:10.1101/2025.09.16.675546

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bioRxiv · 10.1101/2025.09.16.675546

circVDJ-seq for T cell clonotype detection in single-cell and spatial multi-omics

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Abstract

Monitoring T cell repertoires in human tissues provides important insights into immune response mechanisms in cancer, infectious diseases, and autoimmunity. However, retrieving VDJ information from single-cell and spatial transcriptomics workflows with 3-barcoding of cDNA remains resource-intensive or requires specialized sequencing equipment. Here, we introduce circVDJ-seq for simplified and cost-efficient T cell receptor (TCR) profiling from 3-directed workflows like single-cell or single-nucleus RNA sequencing, ATAC+RNA multi-omics, and spatial transcriptomics. Application of circVDJ-seq to freshly resected neuroblastomas and postmortem lymph nodes affected by pneumonia or COVID-19 reveals distinct immune microenvironments and T cell clonality patterns, highlighting broad utility across diverse clinical contexts.

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Plumbom, I., Obermayer, B., Raspe, R., Pascual-Reguant, A., Theurillat, I., Pentimalli, T. M., Hsieh, Y.-H., Gil, M., Dietrich, C., Seeger-Zografakis, M., Quedenau, C., Wilde, J., Braeuning, C., Fischer, C., Schuelke, M., Ludwig, L. S., Eggert, A., Rajewsky, N., Borodina, T., Beule, D., Altmueller, J., Radbruch, H., Hauser, A., Conrad, T.. 2025-09-18. circVDJ-seq for T cell clonotype detection in single-cell and spatial multi-omics. https://doi.org/10.1101/2025.09.16.675546

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