Single-Cell Transcriptome of Anaplastic Thyroid Cancer Reveals Immunosuppressive Tumor Microenvironment Remodeling

Anaplastic thyroid cancer (ATC) is a rare but extremely aggressive malignancy responsible for most thyroid cancer-related deaths. To elucidate molecular and immunological characteristics distinguishing ATC from aggressive papillary thyroid cancer (PTC), we performed single-cell RNA sequencing on three ATC and three lethal PTC samples. ATC tumor cells exhibited enhanced inflammatory and immune-related gene expression, and co-activation of MAPK and PI3K pathways. Notably, p53 pathway activity was suppressed in ATC, alongside activation of angiogenic and immune-evasion programs, indicating a shift from proliferation-driven to immune-evasion-oriented signaling. Transcriptional network analysis revealed E2F family activation, including E2F1, E2F7, and E2F8, suggesting CDK-RB-E2F axis dysregulation drives tumor dedifferentiation and proliferation, whereby p53 suppression unleashes E2F-dependent transcriptional reprogramming. Immunoprofiling revealed CD8⁺ T cells in ATC showed elevated exhaustion signatures and high expression of inhibitory immune checkpoint molecules, accompanied by enhanced Treg-CD8⁺ T cell interactions, indicating a dual-layered immunosuppressive mechanism involving both T-cell exhaustion and enhanced Treg-mediated suppression. In addition, we identified antigen-presenting CAFs with altered CD4⁺ T-cell interactions. These findings delineate a comprehensive single-cell landscape of ATC and demonstrate coordinated alterations in tumor-intrinsic signaling and the tumor microenvironment during dedifferentiation, provide a foundation for developing rational combination immunotherapies tailored to the molecular and immunological landscape of thyroid cancer.