MON-380 Development of a Prognostic Cell Cycle Progression Score in Preoperative Thyroid Tumor Samples to Predict Prognosis

Abstract Disclosure: A. Bikas: None. E. Su: None. H. Patankar: None. M. Alshalalfa: Veracyte, Inc. Y. Hao: Veracyte, Inc. J.P. Klopper: Veracyte, Inc.. T. Pappa: None. Introduction: Alterations in cell cycle regulatory genes may lead to abnormal cellular proliferation, tumor development, and malignancy. The aim of this study was to characterize the expression of cell cycle proliferation genes in thyroid nodules/cancer and assess the molecular and clinical associations of their expression. Methods: A set of 47 genes implicated in cell cycle progression (CCP) genes (i.e. TOP2A, MKI67) were identified from The Cancer Genome Atlas (TCGA) Thyroid. A CCP activity z-score was derived from the expression of the 47 genes and subsequently associated with genomic alterations and outcomes data in TCGA. In addition, 2,205 fine needle aspiration (FNA) samples with (B)ethesda V/VI cytology sent for Afirma testing were extracted from the Afirma thyroid nodule database. The CCP score was analyzed in reference to TERT promoter mutation status and common oncogenic alterations reported by the Afirma Xpression Atlas (XA - the variant and fusion panel), as well as other molecular markers of tumor aggressiveness. Fisher’s exact test was used to assess statistical differences. Results: TCGA samples were stratified based on the CCP score and then grouped into 4 quartiles (Q4: top 25%, Q3:50-75%, Q2:25-50%, Q1: low 25%). Comparing Q4 to Q1, Q4 was enriched with TERT promoter mutations (14.4% vs 2.4%, p<0.001), disease progression (20% vs 8%, p=0.001), MACIS>8 (9.6% vs 3.2%, p=0.06), and stage IV disease (13.6% vs5.6%, p=0.05). The Q4 group is associated with a shorter time to disease progression (HR:2.56, 95%CI [1.23-5.3], p=0.01) relative to the Q1 group. In Afirma B V/VI samples, Q4 CCP score was more enriched with TERT promoter mutations (11.2% vs 4.9%, p p<0.001) compared to Q1, but less enriched with BRAFV600E (40% vs 69%, p<0.001), and RAS family variants (1.8% vs 6.4%, p<0.001). Within this subset, CCP was negatively correlated with TDS (r= -0.48, p<0.001) but not correlated with ERK activity or BRAF-RAS score. Mutations in genes of the PI3K/AKT/mTOR pathway were present, though in small numbers, in Q3 and Q4 groups, but not in Q1-Q2 groups. The CCP score was not correlated with sex or age. Conclusion: The CCP score may be a useful tool in pre-operative thyroid tumor samples to predict tumor aggressiveness, especially in the absence of known molecular alterations or in intermediate risk mutations (such as BRAFV600E) that present with a heterogeneous histologic phenotype. Interestingly, the highest CCP quartile, associated with worse progression free survival in the TCGA cohort, was less enriched with BRAFV600E compared to the lowest CCP quartile. Future analysis incorporating pathology and recurrence outcomes will be necessary to assess the validity and clinical utility of the preoperative CCP score. Presentation: Monday, July 14, 2025