JAK-centric explainable few-shot gene-expression diagnosis framework for alopecia via MultiPLIER priors and relation-style set-to-set comparison

Alopecia areata (AA) and androgenetic alopecia (AGA) both present with hair loss but require different therapies, and reliable biomarkers to guide treatment remain lacking. We integrated bulk and single-cell RNA-seq to compare JAK–STAT signaling in AA versus AGA. In AA, 257 immune-enriched differentially expressed genes (DEGs) were identified; WGCNA and consensus machine learning (LASSO, SVM-RFE, random forest) yielded six candidate hub genes, and external validation narrowed these to four key genes–granzyme A (GZMA), interleukin-2 receptor β (IL2RB) and γ (IL2RG) chains, and eomesodermin (EOMES). Building on these biology-anchored features, we introduced an interpretable few-shot deep learning classifier as an explainable AI alternative to a nomogram: bulk expression profiles are projected onto pathway/cell-type–aligned MultiPLIER latent variables (a frozen prior), the latent channels are re-weighted via element-wise multiplication with the expression levels of the key hub genes, and a Relation-style set-to-set comparator then aggregates support–query similarities (Hadamard mapping + permutation-invariant aggregation) before a shallow head predicts AA versus control. This prior-informed approach enables robust discrimination under limited sample conditions while retaining mechanistic interpretability, thereby exemplifying a next-generation XAI solution for small-cohort genomic diagnosis. Cross-database functional annotation and wet-lab validation (RT-qPCR and Western blot) in independent AA/AGA/healthy scalp samples confirmed that the IL2RB/IL2RG–EOMES–GZMA axis is selectively activated at both mRNA and protein levels in AA. Single-cell analysis localized GZMA to cytotoxic T cells and IL2RG to proliferating lymphocytes, outlining an EOMES + CD 8 + T-cell GZMA–IL2RB/IL2RG cytotoxic loop driving JAK–STAT hyperactivation in AA. Drug–gene network analysis linked these targets to JAK inhibitors and cyclosporine. AGA showed no comparable JAK–STAT perturbation, consistent with its androgen-centric biology. In summary, this four-gene loop provides a non-invasive AA biomarker and a tractable target for precision JAK blockade, while the proposed few-shot framework offers a general, prior-driven alternative to nomograms for transcriptomic diagnosis in small cohorts, illustrating an XAI-driven diagnostic approach for precision medicine.