High-sensitive spatially resolved T cell receptor sequencing with SPTCR-seq.

Jasim Kada Benotmane, Jan Kueckelhaus, Paulina Will, Junyi Zhang, Vidhya M Ravi, Kevin Joseph, Roman Sankowski, Jürgen Beck, Catalina Lee-Chang, Oliver Schnell, Dieter Henrik Heiland

Nature communications 2023 Nov 16

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Spatial resolution of the T cell repertoire is essential for deciphering cancer-associated immune dysfunction. Current spatially resolved transcriptomic technologies are unable to directly annotate T cell receptors (TCR). We present spatially resolved T cell receptor sequencing (SPTCR-seq), which integrates optimized target enrichment and long-read sequencing for highly sensitive TCR sequencing. The SPTCR computational pipeline achieves yield and coverage per TCR comparable to alternative single-cell TCR technologies. Our comparison of PCR-based and SPTCR-seq methods underscores SPTCR-seq's superior ability to reconstruct the entire TCR architecture, including V, D, J regions and the complementarity-determining region 3 (CDR3). Employing SPTCR-seq, we assess local T cell diversity and clonal expansion across spatially discrete niches. Exploration of the reciprocal interaction of the tumor microenvironmental and T cells discloses the critical involvement of NK and B cells in T cell exhaustion. Integrating spatially resolved omics and TCR sequencing provides as a robust tool for exploring T cell dysfunction in cancers and beyond. © 2023. The Author(s).

Citation

Jasim Kada Benotmane, Jan Kueckelhaus, Paulina Will, Junyi Zhang, Vidhya M Ravi, Kevin Joseph, Roman Sankowski, Jürgen Beck, Catalina Lee-Chang, Oliver Schnell, Dieter Henrik Heiland. High-sensitive spatially resolved T cell receptor sequencing with SPTCR-seq. Nature communications. 2023 Nov 16;14(1):7432