MMP9 as a shared immune-related gene in Alzheimer’s and Huntington’s diseases: a cross-tissue transcriptomic analysis

Alzheimer's disease (AD) and Huntington's disease (HD) share neuroinflammatory mechanisms, yet their specific immune microenvironments remain poorly understood. Integrating transcriptomic profiles of peripheral blood and frontal cortex tissues with 2,160 immune-related genes, we analysed their shared immunopathology. Differential analysis identified 64 peripheral and 159 central consistently dysregulated immune genes, intersecting to isolate 10 co-expressed all-immune genes. Functional enrichment highlighted neutrophil and monocyte activation, alongside IL-17 and T-cell receptor signalling pathways. Machine learning (LASSO and Boruta) robustly pinpointed MMP9 as the core shared immune hub gene. External validation revealed MMP9 exhibited modest diagnostic performance in peripheral blood (AD AUC = 0.616; HD AUC = 0.619) but stronger predictive accuracy in brain tissues (AD AUC = 0.825; HD AUC = 0.876). Furthermore, MMP9 expression positively correlated with neutrophil and M0 macrophage infiltration. While modest peripheral accuracy limits its standalone diagnostic utility, this cross-tissue analysis establishes MMP9 as a consistently upregulated candidate molecular indicator of shared neuroinflammation, offering a valuable target for future mechanistic research.