Abstract B057: Decoding tumor microenvironment and resistance following immune checkpoint inhibition therapy in anaplastic thyroid carcinoma

Abstract Purpose: The vast majority of patients with anaplastic thyroid carcinoma (ATC) without BRAF V600E mutations have limited therapeutic options. We sought to investigate why only a third of ATC patients have tumor responses to immune checkpoint inhibition (ICI) with dual anti-programmed death-1 (PD-1) and anti cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) blockade (PMID: 39446365) in hopes of identifying novel therapeutic targets in this population. Methods: To dissect the tumor immune-microenvironment and understand mechanisms of response & resistance to ICI, we performed GEMX-FLEX single-nucleus RNA sequencing (snRNA-seq) on archival pre-ICI (baseline) and post-ICI (surgical) primary tumor samples obtained from a real-world cohort of six patients with ATC who received nivolumab (anti-PD-1) and ipilimumab (anti-CTLA-4) in neoadjuvant/ palliative setting. Results: 5/6 (83.3%) patients had BRAF wild type disease. 2 pre-ICI, 1 oligo-progressive on ICI (lymph node) and 4 post-ICI treatment (Rx) surgical samples underwent snRNA-seq, of which 2 sets were paired. Out of 4 post-Rx thyroid samples, 2 (50%) had residual ATC component, while 2 (50%) did not, i.e. with pathologic complete response of ATC component. snRNA-seq resulted in diverse cell type capture (epithelial, fibroblast, perivascular, macrophages, T cells etc.) and strong recovery of canonical cell type markers (EPCAM, COL1A1, PDGFRB, CD8A, CD4, CD163 etc.) in ATC samples. In the post-Rx samples with no residual ATC, there was evidence of emergent memory T cell phenotypes. Memory CD8 and CD4 T cells strongly expressing CXCR4 were retained at the tumor scar in these samples, potentially related to strong CXCL12 expression by fibroblasts, which may drive durable anti-tumor immunity. The other two post-Rx specimens with residual ATC showed divergent ICI-resistant microenvironments: one immune-excluded and other highly inflamed. snRNA-seq in the paired pre- and post-Rx sample with residual ATC (immune-excluded) suggested that TGF beta signaling in fibroblasts may drive CD8 exclusion and suppressive M1-like to M2-like tumor-associated macrophage polarization. The majority of the remaining T cells were naïve non-tumor-reactive bystanders in this post-ICI sample. In the other post-ICI sample with a residual ATC component and highly inflamed microenvironment, chronic inflammation by type I and II interferon (IFN) signaling appeared to be driving negative feedback mechanisms, evidenced by upregulation of known immune suppressive factors like IDO1 and RIPK1. Conclusions: This is the first characterization of the effects of ICI on the tumor microenvironment in human ATC samples, revealing putative mechanisms of response and resistance. Induction of memory CXCR4+ T cells may drive response, while divergent ICI resistance mechanisms exist, including immune exclusion and chronic inflammation. These results reflect scenarios where clinical responses to ICI allowed surgical resection of primary tumors; future experiments will analyze samples with and without clinical response to ICI therapy. Citation Format: Kartik Sehgal, Kevin Bi, Theodora Pappa, Justine A. Barletta, Laura A. Goguen, Rosh K. Sethi, Eleni M. Rettig, Glenn J. Hanna, Erik K. Alexander, Gerard M. Doherty, Yashika Rustagi, Anwesha Nag, Aaron R. Thorner, Michael J. Dennis, Jonathan D. Schoenfeld, Ravindra Uppaluri, David A. Barbie, Kathleen B. Yates, Robert T. Manguso, Robert I. Haddad. Decoding tumor microenvironment and resistance following immune checkpoint inhibition therapy in anaplastic thyroid carcinoma [abstract]. In: Proceedings of the AACR Immuno-Oncology Conference (AACR IO): Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2026 Feb 18-21; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2026;14(2 Suppl):Abstract nr B057.