Mesenchymal stromal/stem cell (MSC) therapy demonstrates inconsistent benefit in systemic lupus erythematosus (SLE). This study investigated whether SLE plasma exosomes contribute to this variability by reprogramming MSC phenotype and function, with a focus on CD166+CD106+MSC subset and the underlying molecular mechanisms.

Plasma exosomes isolated from 47 SLE patients and 47 matched healthy controls were characterized and applied to treat MSCs. After being exposed to SLE exosomes, MSC phenotype, proliferation, apoptosis, immunosuppressive capacity, and migration were assessed. CD166+CD106+ and CD166+CD120b+ subsets were FACS-sorted for RNA-sequencing and bioinformatic analysis. Key signaling pathways were validated using lentiviral knockdown of Ras-related protein 1 (Rap1) and Ras-related C3 botulinum toxin substrate 1 (Rac1). Proteomic profiling of SLE exosomes identified differentially expressed proteins, followed by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein–protein interactions (PPI )analyses to map the Rap1/AKT/mTOR network, and their functional role was tested by overexpressing G protein subunit beta 1 (GNB1) in CD166+CD106+MSCs. 

SLE plasma exosomes were efficiently internalized by MSCs, leading to downregulation of surface markers including CD166, CD120b, CD106, CD26 at both mRNA and protein levels and a specific reduction of CD166+CD106+ and CD166+CD120b+ subsets. While immunosuppressive function and migration were largely unaffected, SLE exosomes significantly suppressed CD166+CD106+MSC and CD166+CD120b+MSC proliferation but induced apoptosis. Transcriptomics of CD166+CD106+MSCs identified 82 differentially expressed genes (DEGs) enriched for Rap1 and Rac1 signaling. GO and KEGG analyses indicated that these DEGs were primarily involved in signal transduction and apoptosis. Consistently, SLE exosomes reduced phosphorylation along the RAP1–AKT–mTOR axis, with minimal effects on p38 or JNK1. RAP1 knockdown heightened apoptotic phenotype, which was partially rescued by mTOR activation. Proteomics analyses highlighted RAP1/AKT/mTOR connectivity with upregulated GNB1 as key nodes. GNB1 overexpression in CD166+CD106+MSCs suppressed RAP1/AKT/mTOR signaling and augmented apoptosis, supporting GNB1 as a candidate mediator of SLE exosome–induced MSC heterogeneity.

SLE plasma exosomes, via elevated GNB1, selectively deplete CD166+CD106+MSC subsets through disruption of Rap1/AKT/mTOR pathway, which may contribute to heterogeneous MSC therapy responses in SLE. Our findings revealed the GNB1–Rap1–AKT–mTOR axis as a target for precision MSC optimization.