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| Item Type: | Article |
|---|---|
| Title: | circVDJ-seq for T cell clonotype detection in single-cell and spatial multi-omics |
| Creators: |
Plumbom, Izabela  ORCID: https://orcid.org/0009-0006-3720-3700, Obermayer, Benedikt ORCID: https://orcid.org/0000-0002-9116-630X, Raspe, Raphael, Pascual-Reguant, Anna, Theurillat, Ilan ORCID: https://orcid.org/0000-0002-1125-1951, Pentimalli, Tancredi Massimo ORCID: https://orcid.org/0000-0002-8461-7918, Hsieh, Yu-Hsin ORCID: https://orcid.org/0000-0003-3037-8728, Gil, Marine ORCID: https://orcid.org/0000-0002-3885-7806, Dietrich, Carola, Seeger-Zografakis, Michaela, Quedenau, Claudia ORCID: https://orcid.org/0000-0002-6846-4915, Wilde, Jeannine, Braeuning, Caroline ORCID: https://orcid.org/0009-0007-1439-9920, Fischer, Cornelius ORCID: https://orcid.org/0000-0003-0329-2435, Schuelke, Markus ORCID: https://orcid.org/0000-0003-2824-3891, Seitz, Volkhard, Ludwig, Leif S. ORCID: https://orcid.org/0000-0002-2916-2164, Eggert, Angelika, Rajewsky, Nikolaus ORCID: https://orcid.org/0000-0002-4785-4332, Borodina, Tatiana ORCID: https://orcid.org/0000-0002-6978-016X, Beule, Dieter ORCID: https://orcid.org/0000-0002-3284-0632, Altmueller, Janine ORCID: https://orcid.org/0000-0003-4372-1521, Radbruch, Helena ORCID: https://orcid.org/0000-0001-6941-3397, Hauser, Anja Erika and Conrad, Thomas ORCID: https://orcid.org/0000-0001-5618-6295
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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. |
| Keywords: | TCR Sequencing, Single-Cell Immune Profiling, Adaptive Immunity, Spatial Transcriptomics, Tumor Microenvironment |
| Source: | Genome Medicine |
| ISSN: | 1756-994X |
| Publisher: | BioMed Central |
| Volume: | 18 |
| Number: | 1 |
| Page Range: | 84 |
| Date: | 11 June 2026 |
| Official Publication: | https://doi.org/10.1186/s13073-026-01691-1 |
| PubMed: | View item in PubMed |
| Related to: |
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