Abstract PS2-09-19: Tonsl, an immortalizing oncogene on chr.8q24.3 amplicon, confers intrinsic resistance to cdk4/6 inhibitors in breast cancer

Background: Advanced Estrogen receptor-positive (ER+) breast cancers benefit from the inhibitors of cell-cycle kinases CDK4 and CDK6. However, 20% of breast cancers show intrinsic resistance to these inhibitors. Although the mechanisms of acquired resistance to CDK4/6 inhibitors have been studied extensively, little is known about mechanisms of intrinsic resistance. We had recently reported a gene called TONSL, a DNA repair and chromatin organization-associated gene located on chromosome 8q24.3 amplicon, as an immortalizing oncogene and its overexpression in ER+ breast cancer is associated with poor outcome. In preclinical models, TONSL-immortalized breast epithelial cell lines generated ER+ adenocarcinomas upon transformation. Here we investigated whether TONSL amplification confers intrinsic resistance to CDK4/6 inhibitors. Here we compare the survival of TONSL amplified vs not amplified ER+ breast cancer patients treated with CDK4/6 inhibitors. Methods: 10,980 ER+ breast cancer samples (TONSL amplified, n=313; Not amplified, n=10,667) were analyzed by next-generation sequencing (WES, NovaSeq) and Whole Transcriptome Sequencing (WTS; NovaSeq) (Caris Life Sciences, Phoenix, AZ). Copy number variations were determined using CNVKit. A tissue microarray comprising ∼200 ER+ breast cancers was examined for TONSL and phospho-RB expression levels by immunohistochemistry. The role of TONSL in sensitivity to abemaciclib was examined in vitro in a TONSL amplified ER+ breast cancer cell line (generated from MCF-7 derived tumor in nude mice) with and without shRNA-mediated TONSL knockdown using bromodeoxyuridine (BrdU) incorporation ELISA. Real-world median overall survival (mOS) was derived from insurance claims and calculated from the biopsy to last contact or start of CDK4/6 inhibitor (abemiciclib/palbociclib/ribociclib) to last contact or first to last dose of CDK4/6 inhibitor treatment (time on treatment) using Kaplan-Meier. Statistical significance was assessed using chi-square and Mann-Whitney U and p<0.05 was considered significant. Results: MCF-7 derivative, which is intrinsically resistant to CDK4/6 inhibitor abemaciclib, regained drug sensitivity as assessed using cell proliferation assay upon TONSL knockdown (p<0.05). TONSL amplification/overexpression correlated with elevated RB-loss and P53-loss gene signatures, but not RB phosphorylation. In real-word database, moderate correlations were observed between TONSL copy number and RNA expression (r=0.48, p<0.05). Median age of breast cancer patients with TONSL amplification was lower (62 vs 64, p<0.05) compared to TONSL not amplified. TONSL amplification was more common in Black or African American patients (20% vs 14%, p<0.05), but less common in White patients (68.6% vs 77.7%, p<0.05). TONSL amplified breast cancer patients had worse mOS (28.4 months (m) vs 41.9, HR 1.4, 95% CI 1.2-1.6, p<0.0001) compared to TONSL not amplified. Importantly, TONSL amplified breast cancer patients treated with CDK4/6 inhibitors had worse mOS (41.6 m vs 56.3, HR 1.43, 95% CI 1.1-1.8, p=0.002). Moreover, TONSL amplified breast cancer patients had shorter mOS with palbociclib time on treatment (8.9 m vs 11 m, HR 1.31, 95% CI 1-1.6, p=0.01) compared to TONSL not amplified. Conclusions: TONSL amplification in ER+ breast cancer is associated with poor outcome and is potentially a biomarker of intrinsic resistance to CDK4/6 inhibitors. Since activity of TONSL is governed by multiple protein complexes, disruptors of TONSL-protein complexes could potentially be developed as sensitizers to CDK4/6 inhibitors. Citation Format: H. Nakshatri, A. S. Khatpe, U. R. Kamdar, G. Sandusky, S. K. Althouse, S. K. Deshmukh, S. Wu, N. Kulkarni, L. A. Poole, P. Coelho, M. B. Lustberg, G. W. Sledge, K. D. Miller, P. Bhat-Nakshatri. Tonsl, an immortalizing oncogene on chr.8q24.3 amplicon, confers intrinsic resistance to cdk4/6 inhibitors in breast cancer [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS2-09-19.