title: A gene expression signature of retinoblastoma loss-of-function is a predictive biomarker of resistance to palbociclib in breast cancer cell lines and is prognostic in patients with ER positive early breast cancer.
abstract: Palbociclib is a CDK4/6 inhibitor that received FDA approval for treatment of hormone receptor positive (HR+) HER2 negative (HER2neg) advanced breast cancer. To better personalize patients treatment it is critical to identify subgroups that would mostly benefit from it. We hypothesize that complex alterations of the Retinoblastoma (Rb) pathway might be implicated in resistance to CDK4/6 inhibitors and aim to investigate whether signatures of Rb loss-of-function would identify breast cancer cell lines resistant to palbociclib. We established a gene expression signature of Rb loss-of-function (RBsig) by identifying genes correlated with E2F1 and E2F2 expression in breast cancers within The Cancer Genome Atlas. We assessed the RBsig prognostic role in the METABRIC and in a comprehensive breast cancer meta-dataset. Finally, we analyzed whether RBsig would discriminate palbociclib-sensitive and -resistant breast cancer cells in a large RNA sequencing-based dataset. The RBsig was associated with RB1 genetic status in all tumors (p <7e-32) and in luminal or basal subtypes (p < 7e-11 and p < 0.002, respectively). The RBsig was prognostic in the METABRIC dataset (discovery: HR = 1.93 [1.5-2.4] p = 1.4e-08; validation: HR = 2.01 [1.6-2.5] p = 1.3e-09). Untreated and endocrine treated patients with estrogen receptor positive breast cancer expressing high RBsig had significantly worse recurrence free survival compared to those with low RBsig (HR = 2.37 [1.8 - 3.2] p = 1.87e-08 and HR = 2.62 [1.9- 3.5] p = 8.6e-11, respectively). The RBsig was able to identify palbociclib resistant and sensitive breast cancer cells (ROC AUC = 0,7778). Signatures of RB loss might be helpful in personalizing treatment of patients with HR+/HER2neg breast cancer. Further validation in patients receiving palbociclib is warranted.
authors.affiliation: "Sandro Pitigliani" Translational Research Unit, Hospital of Prato-AUSL Toscana Centro, Istituto Toscano Tumori, Prato, Italy.|"Sandro Pitigliani" Medical Oncology Department, Hospital of Prato-AUSL Toscana Centro, Istituto Toscano Tumori, Prato, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Malorni
authors.affiliation: Laboratorio Nazionale CIB (LNCIB), Area Science Park, and Functional Genomics & Bioinformatics Units, Trieste, Italy.|Bioinformatics Core Facility, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy.
authors.forename: Silvano
authors.initials: S
authors.lastname: Piazza
authors.affiliation: Laboratorio Nazionale CIB (LNCIB), Area Science Park, and Functional Genomics & Bioinformatics Units, Trieste, Italy.
authors.forename: Yari
authors.initials: Y
authors.lastname: Ciani
authors.affiliation: "Sandro Pitigliani" Translational Research Unit, Hospital of Prato-AUSL Toscana Centro, Istituto Toscano Tumori, Prato, Italy.
authors.forename: Cristina
authors.initials: C
authors.lastname: Guarducci
authors.affiliation: "Sandro Pitigliani" Translational Research Unit, Hospital of Prato-AUSL Toscana Centro, Istituto Toscano Tumori, Prato, Italy.
authors.forename: Martina
authors.initials: M
authors.lastname: Bonechi
authors.affiliation: "Sandro Pitigliani" Translational Research Unit, Hospital of Prato-AUSL Toscana Centro, Istituto Toscano Tumori, Prato, Italy.|"Sandro Pitigliani" Medical Oncology Department, Hospital of Prato-AUSL Toscana Centro, Istituto Toscano Tumori, Prato, Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Biagioni
authors.affiliation: "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato-AUSL Toscana Centro, Istituto Toscano Tumori, Prato, Italy.
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Hart
authors.affiliation: Laboratorio Nazionale CIB (LNCIB), Area Science Park, and Functional Genomics & Bioinformatics Units, Trieste, Italy.
authors.forename: Roberto
authors.initials: R
authors.lastname: Verardo
authors.affiliation: "Sandro Pitigliani" Translational Research Unit, Hospital of Prato-AUSL Toscana Centro, Istituto Toscano Tumori, Prato, Italy.|"Sandro Pitigliani" Medical Oncology Department, Hospital of Prato-AUSL Toscana Centro, Istituto Toscano Tumori, Prato, Italy.
authors.forename: Angelo
authors.initials: A
authors.lastname: Di Leo
authors.affiliation: "Sandro Pitigliani" Translational Research Unit, Hospital of Prato-AUSL Toscana Centro, Istituto Toscano Tumori, Prato, Italy.
authors.forename: Ilenia
authors.initials: I
authors.lastname: Migliaccio
mesh_terms: D000970:Antineoplastic Agents / Q000627:therapeutic use*; D015415:Biomarkers / Q000378:metabolism*; D054316:Biomarkers, Pharmacological / Q000378:metabolism; D001943:Breast Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000401:mortality; D045744:Cell Line, Tumor; D051358:Cyclin-Dependent Kinase 4 / Q000037:antagonists & inhibitors; D051361:Cyclin-Dependent Kinase 6 / Q000037:antagonists & inhibitors; D066264:Datasets as Topic; D019008:Drug Resistance, Neoplasm; D050687:E2F1 Transcription Factor / Q000235:genetics / Q000378:metabolism; D050703:E2F2 Transcription Factor / Q000235:genetics / Q000378:metabolism; D005260:Female; D006801:Humans; D009154:Mutation / Q000235:genetics; D010879:Piperazines / Q000627:therapeutic use*; D011379:Prognosis; D011725:Pyridines / Q000627:therapeutic use*; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000378:metabolism; D011960:Receptors, Estrogen / Q000378:metabolism; D016160:Retinoblastoma Protein / Q000235:genetics / Q000378:metabolism*; D016019:Survival Analysis; D059467:Transcriptome
chemical_list: D000970:Antineoplastic Agents; D015415:Biomarkers; D054316:Biomarkers, Pharmacological; D051358:Cyclin-Dependent Kinase 4; D051361:Cyclin-Dependent Kinase 6; D050687:E2F1 Transcription Factor; D050703:E2F2 Transcription Factor; D010879:Piperazines; D011725:Pyridines; D018719:Erb-b2 Receptor Tyrosine Kinases; D011960:Receptors, Estrogen; D016160:Retinoblastoma Protein; C493753:E2F1 protein, human; C493761:E2F2 protein, human; C508053:ERBB2 protein, human; C500026:palbociclib
keywords: CDK4/6 inhibitors; breast cancer; retinoblastoma loss of functions