Immune remodeling after thymectomy in patients with anti-AChR antibodies

Thymectomy is an established treatment for thymoma-associated myasthenia gravis (MG). However, a subset of patients develop new-onset MG after surgery. Although thymectomy affects immune homeostasis, its comprehensive impact on the peripheral immune system remains unclear, particularly at the single-cell transcriptomic level. Therefore, we aimed to characterize immune remodeling following thymectomy in anti-acetylcholine receptor (AChR) antibody-positive patients without overt MG.

Peripheral blood mononuclear cells were collected from three anti-AChR antibody-positive patients before and 7-22 months after thymectomy. Single-cell RNA and T cell receptor (TCR) sequencing were subsequently performed. Cell populations were annotated using SingleR and Azimuth. Differential gene expression was analyzed, followed by gene set enrichment analysis. TCR repertoire diversity was assessed using scRepertoire. Additionally, cell-cell communication was inferred using CellChat.

Thymectomy induced broad immune remodeling characterized by a relative reduction in naïve CD4⁺ and CD8⁺ T cells and a concomitant relative increase in natural killer (NK) cells, particularly the CD56^dim subset. Despite the relative decline in naïve T cells, activation-associated genes were upregulated and inflammatory pathways were enriched in the remaining cells, indicating an activation-associated transcriptional state. Monocyte subsets showed marked transcriptional changes, including upregulation of the expression of immediate early genes and downregulation of that of antigen presentation-related and inflammatory genes, consistent with substantial transcriptional remodeling. Furthermore, cell-cell communication analysis revealed a qualitative shift in the dominant signaling axis after thymectomy. Pre-thymectomy networks were characterized by TNF- and resistin-mediated signaling, whereas post-thymectomy networks were dominated by IFNγ signaling, primarily originating from CD56^dim NK cells and targeting monocyte subsets.

Thymectomy induces coordinated remodeling of the peripheral immune system, which involves reduced thymic output, activation-associated transcriptional changes in T cells, relative increase in the proportion of NK cells, and transcriptional remodeling of monocytes. The dominant inflammatory signaling axis shifts from TNF/resistin-centered to IFNγ-centered communication after thymectomy. This bidirectional immune modulation may underlie both therapeutic effects and susceptibility to post-thymectomy MG, highlighting the importance of intercellular signaling dynamics in maintaining immune homeostasis.