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| Item Type: | Preprint |
|---|---|
| Title: | circVDJ-seq for T cell clonotype detection in single-cell and spatial multi-omics |
| Creators Name: | Plumbom, Izabela, Obermayer, Benedikt, Raspe, Raphael, Pascual-Reguant, Anna, Theurillat, Ilan, Pentimalli, Tancredi M., Hsieh, Yu-Hsin, Gil, Marine, Dietrich, Carola, Seeger-Zografakis, Michaela, Quedenau, Claudia, Wilde, Jeannine, Braeuning, Caroline, Fischer, Cornelius, Schuelke, Markus, Ludwig, Leif S., Eggert, Angelika, Rajewsky, Nikolaus, Borodina, Tatiana, Beule, Dieter, Altmueller, Janine, Radbruch, Helena, Hauser, Anja and Conrad, Thomas |
| Abstract: | Monitoring T cell clonality in human tissues provides important insights into adaptive immune response mechanisms in cancer, infectious diseases, and autoimmunity. However, retrieving VDJ sequence 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 TCR profiling from 3’-directed workflows such as single-nucleus RNA sequencing, RNA+ATAC multi-omics, and spatial transcriptomics. Application of circVDJ-seq to freshly resected neuroblastomas, and post-mortem 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: | bioRxiv |
| Publisher: | Cold Spring Harbor Laboratory Press |
| Article Number: | 2025.09.16.675546 |
| Date: | 18 September 2025 |
| Official Publication: | https://doi.org/10.1101/2025.09.16.675546 |
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