Spatial transcriptomics reveals distinct phenotype of proliferating and interferon-activated T lymphocytes in macrophage activation syndrome driven liver inflammation in systemic juvenile idiopathic arthritis

Identify pathways and candidate biomarkers that distinguish various liver pathologies in systemic juvenile idiopathic arthritis (SJIA) with the focus on liver-predominant macrophage activation syndrome (SJIA-MAS). Formalin-fixed, paraffin-embedded liver tissues from SJIA-MAS ( n = 6), SJIA without MAS ( n = 1), autoimmune hepatitis (AIH, n = 7), familial HLH (FHLH, n = 6), steatohepatitis (SH, n = 3), and controls (Ctrl, n = 3) were analyzed by histology and using the NanoString GeoMx Digital Spatial Profiler (DSP). CD3E, CD68 and cytokeratin 8/18 antibodies were used to select regions enriched for T lymphocytes, macrophages, or hepatocytes, respectively. Spatially resolved gene expression data was Q3-normalized and subjected to principal component and clustering analysis. Differentially expressed genes were identified using Mann-Whitney U-test. Histologically, SJIA-MAS liver biopsies were distinguished by extensive portal and intra-sinusoidal expansion of activated CD163 + histiocytes and T lymphocytes (predominantly CD8+). Spatial transcriptomics revealed a markedly distinct phenotype in T lymphocyte enriched regions in SJIA-MAS liver tissue. In addition to pathways driving activation and survival, T lymphocyte regions in SJIA-MAS were distinguished by activation of IFNƔ-induced signaling including CXCL9 overexpression. Strong IFN-induced signatures were also observed in hepatocyte-enriched areas in SJIA-MAS and FHLH. T cell regions in SJIA-MAS could be distinguished by upregulated IFN-induced signaling. Considering that T cells have emerged as the main source of IFN-Ɣ in MAS, this may reflect an amplification loop contributing to uncontrolled activation and expansion of these cells. Our data also suggest that in SJIA-MAS, IFN-Ɣ may be a direct driver of liver injury and, therefore, serve as a therapeutic target.