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73. Jahrestagung der Deutschen Gesellschaft für Neurochirurgie (DGNC)
Joint Meeting mit der Griechischen Gesellschaft für Neurochirurgie

Deutsche Gesellschaft für Neurochirurgie (DGNC) e. V.

29.05. - 01.06.2022, Köln

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Spatial T-cell receptor sequencing (SPTCR-seq) uncovers regional anti-tumour immunity in glioblastoma

Erforschung der regionalen anti-tumor Immunität im Glioblastom mit räumlich aufgelöster T-Zellrezeptor Sequenzierung

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  • presenting/speaker Jasim Kada Benotmane - Universitätsklinikum Freiburg, Klinik für Neurochirurgie, AG Tumormetabolismus MILO Lab, Freiburg i. Br., Deutschland
  • Jan Kückelhaus - Universitätsklinikum Freiburg, Klinik für Neurochirurgie, AG Tumormetabolismus MILO Lab, Freiburg i. Br., Deutschland
  • Paulina Will - Universitätsklinikum Freiburg, Klinik für Neurochirurgie, AG Tumormetabolismus MILO Lab, Freiburg i. Br., Deutschland
  • Oliver Schnell - Universitätsklinikum Freiburg, Klinik für Neurochirurgie, Freiburg i. Br., Deutschland
  • Jürgen Beck - Universitätsklinikum Freiburg, Klinik für Neurochirurgie, Freiburg i. Br., Deutschland
  • Vidhya Madapusi Ravi - Universitätsklinikum Freiburg, Klinik für Neurochirurgie, AG Tumormetabolismus MILO Lab, Freiburg i. Br., Deutschland
  • Kevin Joseph - Universitätsklinikum Freiburg, Klinik für Neurochirurgie, AG Tumormetabolismus MILO Lab, Freiburg i. Br., Deutschland
  • Dieter Henrik Heiland - Universitätsklinikum Freiburg, Klinik für Neurochirurgie, AG Tumormetabolismus MILO Lab, Freiburg i. Br., Deutschland

Deutsche Gesellschaft für Neurochirurgie. 73. Jahrestagung der Deutschen Gesellschaft für Neurochirurgie (DGNC), Joint Meeting mit der Griechischen Gesellschaft für Neurochirurgie. Köln, 29.05.-01.06.2022. Düsseldorf: German Medical Science GMS Publishing House; 2022. DocV284

doi: 10.3205/22dgnc275, urn:nbn:de:0183-22dgnc2750

Published: May 25, 2022

© 2022 Kada Benotmane et al.
This is an Open Access article distributed under the terms of the Creative Commons Attribution 4.0 License. See license information at http://creativecommons.org/licenses/by/4.0/.

Outline

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Objective: An understanding of the diversity of T cell response and clonality in the inherently heterogeneous glioblastoma (GBM) is of paramount importance to explore underlying mechanisms of anti-tumor immunity. Here, we present SPatial T-Cell Receptor sequencing (SPTCR-seq), a novel method to integrate spatially resolved T cell receptor sequencing and RNA-sequencing.

Methods: We performed spatially resolved RNA sequencing using the 10X-Visium technology on 9 primary and recurrent GBMs. After reverse transcriptase of the tissue sections, the harvested cDNA library containing both transcripts and spatial position barcodes is split into the transcriptome and SPTCR-seq workflow. SPTCR-seq is a targeted enrichment of T-cell receptor (TCR) sequences with hybridization-probes followed by Oxford nanopore (ONT) long-read sequencing. To overcome the currently high per-base Error Rate of ONT-sequencing, a neural network (Long-Short-Term Memory Autoencoder) was used to find enriched T cell receptor (CDR3) motifs in the annotated VDJ-rearrangements.

Results: Our data show that clonal evolution of T cells is restricted to regional areas, supported by a significant spatial autocorrelation coefficient (0.6-0.95, padj<0.001). We found increased diversity of T-cell receptor VDJ rearrangements in glioblastoma significantly enriched in areas of myeloid cell infiltration (padj=2.1e10-4). Furthermore, spatial integration of single-cell transcriptomics of T cells revealed a spatial correlation between exhausted T cells (Morans's I 0.76, p=5.26e10-16) and high VDJ diversity. In areas of enriched hypoxic gene expression, we found significantly increased T cell clonality (p=1.01e10-5) with low VDJ diversity (p=1.65e10-6). Inferred copy number changes and small nucleotide variance in these regions showed increased mutational burden. In addition, these areas had lower myeloid infiltration, suggesting that high mutational load and absence of myeloid cells support anti-tumor immunity in segregated areas.

Conclusion: Spatial profiling of TCR sequences through SPTCR-seq is a powerful tool to investigate anti-tumor immunity in GBM and to discover general and personalized targets for immunotherapy.

Figure 1 [Fig. 1]