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

Abstract

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.