Analysis of Hyperexpanded T Cell Clones in SARS-CoV-2 Vaccine-Associated Liver Injury by Spatial Proteomics and Transcriptomics

Background and aims: SARS-CoV-2 vaccine-associated liver injury (SVALI) is a rare event and its pathophysiology remains unclear. Previous studies have found an oligoclonal CD8+ T cell infiltrate and SARS-CoV-2 spike antigen-specific T cells in the liver of patients with SVALI. Therefore, we aimed to characterise the immune infiltrate in a liver explant from a patient with severe SVALI. Methods: T cell receptor sequencing, a novel combined multiplex immunofluorescence (mIF)-RNA in situ hybridisation (RISH) approach, and single cell spatial transcriptomics with the Xenium in situ platform were used to identify, track and characterise specific T cell clones in this liver sample. Results: T cell repertoire analysis revealed hyperexpanded clones with CDR3 sequences similar to previously identified SARS-CoV-2 spike antigen-specific T cells. The hyperexpanded clones were localised throughout the whole liver, but the concentration was higher at the portal interface. Many hyperexpanded T cells expressed cytotoxic granzymes A, B and K, but also tissue-resident markers such as CXCR6, CD69 and KLRB1. Conclusions: Spatial proteomics and spatial transcriptomics techniques allowed the localisation and characterisation of hyperexpanded CD8+ T cell clones at single cell level. They exhibited cytotoxic and tissue-resident memory properties, suggesting their involvement in the pathogenesis of SVALI.