Low dose IFNγ remodels enhancer landscape to potentiate mesenchymal stromal cell activation

Interferon gamma (IFNγ) priming is a prominent approach to enhance the immune-regulatory capacity of mesenchymal stromal cells (MSCs). Despite its potential, the concentration of IFNγ vary between studies, and how MSCs response to different concentrations of IFNγ is unclear.

MSCs were treated with various concentrations of IFNγ (0, 1, 5, 10, 50, and 100 ng/mL) for 48 h. Followed by RNA sequencing (RNA-seq) and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to profile gene expression and chromatin accessibility, respectively. Integrative analysis was conducted to elucidate the epigenetic regulation of MSCs response to different doses of IFNγ.

We found that low dose IFNγ (1 ng/mL) treatment was sufficient to induced significant changes in gene expression and chromatin accessibility. RNA-seq revealed that IFNγ activated genes involved in immune response and inactivated genes related to cell-cycle regulation. ATAC-seq showed that IFNγ reduced global enhancer accessibility of MSCs, possibly by downregulation of the SWI/SNF complex. Moreover, IFNγ selectively opened enhancer regions associated with immune response genes while closing regions linked to proliferation-related genes. Motif enrichment analysis identified binding sites for transcription factors such as IRF and AP-1 family members in open and closed regions, respectively, highlighting selective regulatory mechanisms.

This study demonstrates that low dose IFNγ is sufficient to modulate the transcriptional and epigenetic landscape of MSCs by selectively altering enhancer landscape. Our results provide insights into the regulatory mechanisms underlying IFNγ priming and offer a resource for the rational design of strategies to optimize MSC licensing for therapeutic applications.