S6K1 amplification confers innate resistance to CDK4/6 inhibitors through activating c-Myc pathway in patients with estrogen receptor-positive breast cancer

Abstract

Background CDK4/6 inhibitors combined with endocrine therapy has become the preferred treatment approach for patients with estrogen receptor-positive metastatic breast cancer. However, the predictive biomarkers and mechanisms of innate resistance to CDK4/6 inhibitors remain largely unknown. We sought to elucidate the molecular hallmarks and therapeutically actionable features of patients with resistance to CDK4/6 inhibitors. Methods A total of 36 patients received palbociclib and endocrine therapy were included in this study as the discovery cohort. Next-generation sequencing of circulating tumour DNA in these patients was performed to evaluate somatic alterations associated with innate resistance to palbociclib. Then the candidate biomarker was validated in another independent cohort of 104 patients and publicly available datasets. The resistance was verified in parental MCF-7 and T47D cells, as well as their derivatives with small interfering RNA transfection and lentivirus infection. The relevant mechanism was examined by RNA sequencing, chromatin immunoprecipitation and luciferase assay. Patient-derived organoid and patient-derived xenografts studies were utilized to evaluated the antitumor activity of rational combinations. Results In the discovery cohort, S6K1 amplification (3/35, 9%) was identified as an important reason for innate resistance to CDK4/6 inhibitors. In the independent cohort, S6K1 was overexpressed in 15/104 (14%) patients. In those who had received palbociclib treatment, patients with high-expressed S6K1 had significantly worse progression free survival than those with low S6K1 expression (hazard ratio = 3.0, P = 0.0072). Meta-analysis of public data revealed that patients with S6K1 amplification accounted for 12% of breast cancers. Breast cancer patients with high S6K1 expression had significantly worse relapse-free survival (hazard ratio = 1.31, P < 0.0001). In breast cancer cells, S6K1 overexpression, caused by gene amplification, was sufficient to promote resistance to palbociclib. Mechanistically, S6K1 overexpression increased the expression levels of G1/S transition-related proteins and the phosphorylation of Rb, mainly through the activation of c-Myc pathway. Notably, this resistance could be abrogated by the addition of mTOR inhibitor, which blocked the upstream of S6K1, in vitro and in vivo. Conclusions S6K1 amplification is an important mechanism of innate resistance to palbociclib in breast cancers. Breast cancers with S6K1 amplification could be considered for combinations of CDK4/6 and S6K1 antagonists.

P2RX7 promotes osteosarcoma progression and glucose metabolism by enhancing c-Myc stabilization

“…With the use of CDK4/6 inhibitors in preclinical and clinical settings, the relationship between c-Myc and CDK4/6 has been better elucidated. Importantly, c-Myc activation is responsible for both innate [ 66 ] and induced resistance [ 67 , 68 ] to CDK4/6 inhibition therapy. Moreover, the combination of CDK4/6 inhibitors with CDK2 [ 69 , 70 ] or ERK [ 71 ] inhibition can overcome c-Myc-dependent resistance.…”

CDK4/6 inhibitor resistance in estrogen receptor positive breast cancer, a 2023 perspective

“…c-Myc is also activated downstream of kinases such as S6K1. Elevated S6K1 have been reported in 9%–14% of breast cancer patients and studies have demonstrated that elevated S6K1 drives palbociclib resistance via activation of c-Myc signaling pathways in preclinical models and clinical breast cancer samples ( Mo et al, 2022 ).…”

Systematic Analysis of Network-driven Adaptive Resistance to CDK4/6 and Estrogen Receptor Inhibition using Meta-Dynamic Network Modelling

“…Moreover, our analysis also makes predictions about additional protein nodes/interactions that have not yet been identified by the literature. Known mechanisms of resistance to CDK4/6 inhibitors include: Rb loss/mutations [56,57], CDK4/6 overexpression [58][59][60], loss of ER expression [58,61,62], loss of PTEN [63], reduced expression/activity of p21 and p27 [64][65][66], activation of mTOR complexes [67,68], activation of PI3K and PI3K signalling pathways [61,69], activation of PDK1 [70], upregulation of FGFR [71,72], AKT amplification and/or over-activation [73], E2F amplification and/or over-activation [74], MAPK pathway activation [75][76][77], c-Myc activity [78,79], cyclin E overexpression and increased CDK2-cyclin E complex formation [43,44,80,81]. Known mechanisms of resistance to ER inhibitors include mutations that induce the constitutive activation of ER [82,83], loss of ER activity [84,85], activation of PI3K and MAPK signalling [86,87], overexpression of c-Myc [88,89] and loss of p21 and p27 [90,91].…”