IL2RA+VSIG4+ tumor-associated macrophage is a key subpopulation of the immunosuppressive microenvironment in anaplastic thyroid cancer

Extensive infiltration of tumor-associated macrophages was correlated poor prognosis in anaplastic thyroid cancer (ATC). However, the heterogeneity and characteristics of the ATC-associated macrophages (ATAMs) in ATC remain far from clear. We combined single-cell RNA-sequencing analysis and gene expression microarray datasets to assess the molecular signature of ATAMs. Compared with normal thyroid-associated macrophages (NTAMs), 778 differentially expressed genes (DEGs) significantly changed in ATAMs compared with NTAMs. These DEGs were correlated with oxidative phosphorylation (M2 phenotype) and phagocytosis (M1 phenotype). Moreover, ATAMs highly expressed pro-tumor genes associated with angiogenesis, fibrosis, metalloprotease activity, and metastasis. Notably, we identified one ATC-specific subset, IL2RA+ VSIG4+ ATAMs, co-expressed M1 and M2 markers. The infiltration of IL2RA+ VSIG4+ ATAMs showed strong correlation with BRAF and RAS signaling, and its high infiltration was associated with favorable prognosis in thyroid-cancer patients. IL2RA+ VSIG4+ ATAMs were associated with increased tumor-infiltrating lymphocytes (B cells, CD8+ T cells, Tregs). IL2RA+ VSIG4+ ATAMs interacted with CD8+ T cells and Tregs through immune checkpoints (such as LGALS9_HAVCR2), cytokines (such as CXCL10_CXCR3), and receptors (such as CSF1R_CSF1), thereby forming an immunosuppressive microenvironment. Multiplex immunohistochemistry staining and coculture experiment confirmed that ATC cancer cells were able to induce the polarization of IL2RA+ VSIG4+ ATAMs. Besides, we identified several novel ATC-specific immune checkpoint genes including the immunosuppressive molecule VSIG4, LAIR1, and LILRB2. Expression of VSIG4 was also significantly correlated with tumor-infiltrating lymphocytes (B cells, CD8+ T cells, Tregs). In conclusion, our study revealed an ATC-specific ATAM subset with bifunctional phenotype, which provided a comprehensive insight to delineate the molecular characteristics of ATC-associated macrophages. •The characteristics and heterogeneity of TAMs in ATC are comprehensively delineated at single-cell level and validated.•We identify IL2RA+VSIG4+ TAMs as an ATC-specific subset co-exist M1 and M2 signatures, and correlated with better prognosis.•IL2RA+VSIG4+ TAMs correlate with high TILs infiltration, while they present immune checkpoint to inhibit antitumor activity.•The novel ATC-specific immune checkpoints VSIG4, LAIR1, and LILRB2 presented on ATAMs are identified