Abstract PS12-03: p53 loss enables HR+ breast cancer escape from CDK4/6 inhibitor-induced quiescence via CDK2
Authors: Kudo Rei , Safonov Anton , da Silva Edaise M. , Li Qing , Shao Hong , Will Marie , Nakshatri Harikrishna , Reis-Filho Jorge , Goel Shom , Koff Andrew , Weigelt Britta , Khan Qamar , Razavi Pedram , Chandarlapaty Sarat 
Published: May 2024

Background:

Inhibition of CDK4/6 kinases has led to improved clinical outcomes in hormone receptor positive (HR+) breast cancer. While these are highly effective therapies, only a minority of patients experience long-term disease control. We sought to determine the genomic configurations and underlying mechanisms associated with long-term response.

Methods:

To identify genomic patterns associated with clinical outcomes, we analyzed a cohort of 447 patients with metastatic HR+ breast cancer treated at MSK with first-line CDK4/6 inhibitors (CDK4/6i) for which tumor-normal sequencing and long-term clinical follow up were available. To identify the pattern of genomic features associated with longer, intermediate, and short response, we implemented an elastic net Cox regression on binary pathogenic variant status of each gene as well as select clinical features (prior endocrine therapy, endocrine therapy partner, de novo metastatic status). Our principal aim was variable interpretability over pure predictive accuracy. Human HR+ breast cancer models including human breast cancer organoids and cell lines were utilized for mechanistic studies. For validation in a clinical setting, we analyzed the association between Ki67 score after neoadjuvant ribociclib plus endocrine therapy and pre-treatment gene mutation from the FELINE trial [NCT02712723] using a Fisher exact test.

Results:

Our model identified a “longer response” group (n = 124, 27.7%) from patients with a median progression free survival (PFS) of 32.5 months, compared with an “intermediate” (n = 224, 50.1%, median PFS = 13.7 months) and “short response” group (n = 99, 22.1%, median PFS = 5.84 months). TP53 and MDM2 pathogenic variant status were the most important variables to stratify between these groups, obtaining variable selection frequencies of 1.0 and 0.93 and mean hazard ratios of 2.02 and 1.38, respectively. To elucidate the mechanisms whereby the p53 pathway supports long term response, we generated isogenic and patient derived models of TP53 loss or MDM2 overexpression. Using immunoblotting and cell cycle assays, we found that drug-treated p53 KO cells and MDM2 overexpressing cells effectively suppressed RB1 phosphorylation and blocked in G1 after 24-48 hours. However, upon drug withdrawal, these cells could reenter the cell cycle and promote long-term tumor outgrowth. These effects we observed both in vitro and in vivo. Measures of long-term CDK4/6i response such as expression of senescence associated secretory phenotype genes was abrogated by TP53 loss. Mechanistically, we found persistent phosphorylation of the p130 RB1-like protein in the p53 KO cells. Phosphorylation of p130 impaired its interaction with E2F4, thereby blocking DREAM complex assembly and promoting cell cycle reentry. Inhibition of phosphorylation of p130 via p21 overexpression or by selective CDK2 inhibitors could restore irreversible cell cycle arrest in p53 KO cells. The combination of CDK2 and CDK4/6 inhibition led to long-term tumor growth suppression in models with mutant TP53. To validate the human relevance of TP53 mediating CDK4/6i response, we analyzed longitudinal samples from the FELINE trial that evaluated efficacy and feasibility of neoadjuvant ribociclib plus endocrine therapy. Of 45 evaluable patients, 13 (28.9%) harbored a pre-treatment TP53 loss of function variant. Of these 13 cases, 7 (53.8%) did not achieve a low ( &lt; 10%) Ki-67 upon surgical resection as compared to TP53 wildtype tumors (n=32), only one (3.2%) of which did not achieve a low Ki-67 [OR 32.1, 95% CI 3.28 – 1660.3, p = 0.00026].

Conclusion:

Loss of p53 was strongly associated with lack of long-term response to CDK4/6i in patients. Complete inhibition of both CDK4/6 and CDK2 appears to be necessary in order to convert quiescent HR+ tumors cells into durably inhibited and effectively dormant cancers.

Citation Format: Rei Kudo, Anton Safonov, Edaise M. da Silva, Qing Li, Hong Shao, Marie Will, Harikrishna Nakshatri, Jorge Reis-Filho, Shom Goel, Andrew Koff, Britta Weigelt, Qamar Khan, Pedram Razavi, Sarat Chandarlapaty. p53 loss enables HR+ breast cancer escape from CDK4/6 inhibitor-induced quiescence via CDK2 [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PS12-03.