Abstract 6216: Single Cell DNA Sequencing of BRAF Treatment Resistant Anaplastic Thyroid Cancer

Abstract Anaplastic thyroid cancer (ATC) is one of the most lethal cancers. Although dramatic responses to BRAFV600E-mutated ATC are seen with BRAF/MEK inhibition, treatment resistance inevitably develops, limiting survival. In this study we sequentially profiled BRAFV600E-mutated ATC at diagnosis, after BRAF/MEK targeted therapy and at the time of disease recurrence using both bulk and single-cell DNA/RNA sequencing. We profiled (~400-800 single cells) for each patient - Patient 1 (n = 704 cells); Patient 2 (n = 817 cells) and Patient 3 (n = 407 cells). At diagnosis, we show that tumor cell populations were characterized by a predominance of arm-level aneuploidies. Across all patients, there is a sharp decline in tumor cells post BRAF-targeted treatment. Interestingly, we observe at least 2 distinct tumor subclones present in the pre-treatment tumor and subsequently there was an expansion event that occurred in each patient after BRAF treatment. This was associated with acquiring unique copy number aberrations (CNA)events and the dominance of these subclones in the recurrent disease. For Patient 2, we also performed single-cell RNA sequencing and show that the recurrent tumor cells have high proliferation and stem-cell like cell states even though they had higher differentiation scores. Importantly, correlating the scDNAseq identified CNA with the inferred CNA from scRNAseq, we show proof of concept that copy number aberrations can be directly correlated with gene expression changes and gene dosage effects. Collectively our data reveal an early polyclonal dissemination model of clones in BRAF-mutated ATCs and suggests that treatment resistance to BRAF inhibition develops as a results of incomplete elimination of viable tumor cell reservoirs in ATC. Citation Format: Aatish Thennavan, Maxime Tarabichi, Per Wu, Meghan Martin, Ramona Dadu, Maria Cabanillas, Nafia Busaidy, Ying C. Henderson, Mark Zafereo, Michelle D. Williams, Stephen Lai, Nicholas Navin, Jennifer R. Wang. Single cell DNA sequencing of BRAF treatment resistant anaplastic thyroid cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6216.