Spatially resolved single-cell transcriptome analysis of mycosis fungoides reveals distinct biomarkers GNLY and FYB1 compared to psoriasis and chronic spongiotic dermatitis

Early mycosis fungoides (MF) and inflammatory dermatoses including psoriasis and chronic spongiotic dermatitis are often difficult to differentiate. We explored diagnostic markers differentiating MF from psoriasis and chronic spongiotic dermatitis via spatially resolved single-cell transcriptome analysis. Single-cell transcriptomics of intraepidermal T cells of MF patches, psoriasis and chronic spongiotic dermatitis were analyzed using CosMx^TM spatial molecular imager utilizing surface markers, including CD3 and CD4. An immunohistochemical study with potential markers was performed to verify clinical utility. Compared to psoriasis and chronic spongiotic dermatitis, 41 upregulated differentially expressed genes (DEGs) in MF were associated with T-cell receptor (TCR) signaling pathway and apoptosis regulation. Protein-protein interaction network analysis of these DEGs revealed a main cluster associated with TCR signaling. Pathway enrichment analysis showed that apoptosis, Th17 cell differentiation, and TCR signaling pathways were enriched in MF. GNLY and FYB1, DEGs with the highest fold change values, were selected as potential diagnostic biomarkers for MF. For immunohistochemistry, biopsy specimens from 150 patients diagnosed with patch MF with CD4⁺ immunophenotype (n = 56), psoriasis (n = 48), and chronic eczema (n = 46) were included. The sensitivity and specificity of GNLY for distinguishing MF and psoriasis/chronic spongiotic dermatitis were 67.9% and 93.6%, respectively. For FYB1, those values were 73.2% and 69.2%, respectively. The AUC values of GNLY and FYB1 were 0.86 and 0.79, respectively. In conclusion, GNLY and FYB1 can be promising diagnostic biomarkers for differentiating early-stage MF from psoriasis and chronic spongiotic dermatitis.