Migliaccio Ilenia, Bonechi Martina, Romagnoli Dario, Boccalini Giulia, Galardi Francesca, Guarducci Cristina, Nardone Agostina, Schiff Rachel, Biganzoli Laura, Malorni Luca, Benelli Matteo
Translational Research Unit, Department of Oncology, Hospital of Prato, Azienda USL Toscana Centro, Prato, Italy.
Department of Oncology, Hospital of Prato, Azienda USL Toscana Centro, Prato, Italy.
NPJ Breast Cancer. 2025 Jul 31;11(1):82. doi: 10.1038/s41523-025-00803-1.
Cyclin dependent kinases 4 and 6 inhibitors have brought great improvements in the treatment of luminal breast cancer, but resistance is a major clinical hurdle. Multiple biomarkers of resistance have been proposed, but none is currently utilized in clinical practice. By performing single-cell RNA sequencing of seven palbociclib-naïve luminal breast cancer cell lines and palbociclib-resistant derivatives, we show that established biomarkers and pathways related to CDK4/6i resistance present marked intra- and inter- cell-line heterogeneity. Transcriptional features of resistance could be already observed in naïve cells correlating with levels of sensitivity (IC50) to palbociclib. Resistant derivatives showed transcriptional clusters that significantly varied for proliferative, estrogen response signatures or MYC targets. This marked heterogeneity was validated in the FELINE trial where, compared to the sensitive ones, ribociclib-resistant tumors developed higher clonal diversity at genetic level and showed greater trascriptional variability for genes associated with resistance. A potential signature of resistance inferred from the cell-line models, positively enriched for MYC targets and negatively enriched for estrogen response markers, was probed on the FELINE trial, separating sensitive from resistant tumors and revealing higher heterogeneity in resistant versus sensitive cells. These data suggest that heterogeneity for CDK4/6 inhibitors resistant markers might facilitate the development of resistance and challenge the validation of clinical biomarkers.
细胞周期蛋白依赖性激酶4和6抑制剂在管腔型乳腺癌的治疗中带来了巨大改善，但耐药性是一个主要的临床障碍。已经提出了多种耐药生物标志物，但目前在临床实践中均未得到应用。通过对七个未使用过哌柏西利的管腔型乳腺癌细胞系及其哌柏西利耐药衍生物进行单细胞RNA测序，我们发现与CDK4/6抑制剂耐药相关的既定生物标志物和信号通路存在显著的细胞内和细胞间异质性。在未使用过药物的细胞中就已经可以观察到与对哌柏西利的敏感性水平（IC50）相关的耐药转录特征。耐药衍生物显示出在增殖、雌激素反应特征或MYC靶点方面有显著差异的转录簇。这种显著的异质性在FELINE试验中得到了验证，在该试验中，与敏感肿瘤相比，瑞博西尼耐药肿瘤在基因水平上产生了更高的克隆多样性，并且在与耐药相关的基因上表现出更大的转录变异性。从细胞系模型推断出的一种潜在耐药特征，在FELINE试验中进行了验证，该特征对MYC靶点呈阳性富集，对雌激素反应标志物呈阴性富集，能够区分敏感肿瘤和耐药肿瘤，并揭示出耐药细胞与敏感细胞相比具有更高的异质性。这些数据表明，CDK4/6抑制剂耐药标志物的异质性可能会促进耐药性的发展，并对临床生物标志物的验证提出挑战。
