JS07.4.A REGIONAL B-CELL MEDIATED IMMUNOSUPPRESSION IDENTIFIED THROUGH SPATIAL AND SINGLE-CELL TRANSCRIPTOMIC ANALYSIS OF CHORDOMA
Authors: Kada Benotmane J , Arrieta V A , Zhao J , Hou D , Katz J , Pandey S , Cholak M , Sonabend A , Horbinski C , Miska J , Stupp R , Lesniak M , Heiland D , Chang C 
Published: September 2023

BACKGROUND

Chordomas, rare indolent neoplasms, mainly occur in the skull base or lower spine. Therapies, including surgery and radiotherapy, often fail to impede local recurrence. Though checkpoint inhibition therapy shows promise, recent immunotherapy trials failed to reach endpoints. Here, we aim to investigate the immunological landscape of chordomas using spatial and single-cell transcriptomics, and TCR/BCR profiling, elucidating cellular interplay and the intricate mechanisms governing the immunosuppressive tumor microenvironment.

MATERIAL AND METHODS

We generated a comprehensive single-cell atlas of the chordoma neoplastic landscape and its associated microenvironment, incorporating paired single-cell transcriptomic samples from blood and tumor cells of six patients, as well as single-cell BCR and TCR sequencing data. Utilizing scGEN, we integrated pre-annotated gene expression datasets and identified both established and novel antigen binding patterns by employing TCR Bidirectional Encoder Representations from Transformers (BERT). Moreover, we conducted GeoMx Digital Spatial Profiler (DSP) analysis by selecting regions of interest (ROIs) that encompass critical immunological and malignant niches. We also curated and quantified cell distributions in immunohistochemical staining for a total of 107 chordomas.

RESULTS

Utilizing pseudo-temporal mapping, we delineated the trajectories of CD8 and CD4 T cells in chordomas, spanning from blood to tumor stroma and encompassing naïve, memory, cytotoxic, and T cell exhaustion profiles. Through an integrated TCR profiling methodology, we observed extratumoral clonal expansion of cytotoxic and memory T cells in the blood, whereas the majority of intratumoral T cells with shared motifs exhibited terminal exhaustion. Leveraging TCR-BERT, we identified binding patterns exclusively enriched in exhausted T cell receptors' binding sites and uncovered shared motifs within the reactive tumor-infiltrating compartment, implying the existence of potential reservoirs for anti-tumor immunity. Investigating the cell-cell interactions driving intratumoral exhaustion, we identified M2 tumor-associated macrophages and a plasma cell phenotype-like subset upregulating TGFB and IL10 expression, referred to as regulatory B cells (Bregs). Spatial profiling substantiated the proximity of regulatory B cells and exhausted T cells within immunosuppressive niches, suggesting an underexplored mechanism contributing to tumor-derived T cell exhaustion.

CONCLUSION

Regulatory B-cells have been identified in the TME of various solid tumors, including colorectal, breast, cervical, and ovarian carcinomas. Our study emphasizes the role of regulatory B cells in the chordoma immune environment, providing crucial insights into novel immunosuppressive mechanisms and pathways leading to T cell exhaustion in chordoma.