Abstract
Background: Killer Immunoglobulin-like Receptors (KIRs) are variably expressed on natural killer (NK) and T cells and may regulate immune responses in multiple sclerosis (MS). However, standard reference transcriptomes used in RNA-sequencing fail to capture the full gene and allelic diversity of the KIR locus, limiting the interpretation of KIR+ cell function.
Objective: To characterise KIR+ NK and T cells in MS using multi-omic profiling, integrating high-resolution KIR genotyping, flow cytometry, and transcriptomics, and to investigate the role of KIR+ CD8+ T cells as potential modulators of immune function or therapeutic biomarkers.
Methods: Peripheral blood mononuclear cells from healthy controls and people with MS treated with Tysabri or Ocrevus were profiled using multiparameter flow cytometry. Sorted KIR+ NK cells and matched KIR+ and KIR- CD8+ T cells were analysed by bulk RNA- and TCR-sequencing. High-resolution KIR genotyping was performed to interpret transcriptomic data in the context of gene content, addressing the frequent misalignment between detected KIR transcripts and genotype.
Results: KIR expression on CD8+ T cells was significantly higher in Ocrevus-treated MS compared to Tysabri-treated or healthy controls. In controls, KIR+ CD8+ T cells exhibited a transcriptional profile distinct from KIR- cells, including upregulation of immune modulatory genes and downregulation of T cell signalling and regulation genes. These differences were not observed in MS. In MS, KIR+ CD8+ T cells showed significantly reduced TCR diversity compared to KIR- counterparts.
Conclusion: KIR+ CD8+ T cells in MS show evidence of clonal expansion and altered transcriptional states. However, mismatches between KIR gene content and transcript detection complicate interpretation, highlighting the need for genotyping informed analyses to accurately assess KIR+ T cell and their contribution to immune-mediated diseases.