miRNA signatures of prognostic significance in single hormone receptor-positive breast cancer.
Authors: Senkus-Konefka Elzbieta , Popęda Marta , Kunc Michał , Bieńkowski Michał , Braun Marcin , Lacko Aleksandra , Radecka Barbara , Pikiel Joanna , Litwiniuk Maria , Pogoda Katarzyna , Iżycka-Świeszewska Ewa , Zaczek Anna Joanna , Biernat Wojciech 
Published: June 2022

e12544

Background: Single hormone receptor-positive breast cancer – ER+/PgR– and ER–/PR+, is a distinct entity with vastly undiscovered biology. This study aimed at exploring miRNA profiles of primary tumors of single hormone receptor-positive phenotype and their association with overall survival (OS). Methods: The study group comprised 32 breast cancer patients, collected at 3 Polish centers, with single hormone receptor-positive phenotype, including 14 ER+/PgR– and 18 ER–/PR+ cases, thoroughly characterized for ER (clones: 1D5, EP1 and SP1) and PgR (clone: 636) expression. Expression of 798 miRNAs was profiled using nCounter Human v3 miRNA Expression Assay (NanoString) in each primary tumor sample (FFPE), data available at NCBI GEO (GSE155362). Normalized miRNAs counts were analyzed for the association with OS. Gene targets of miRNAs showing prognostic significance were identified using miRNET 2.0, while their annotation with Gene Ontology Biological Processes was determined with DAVID Bioinformatics Resources 6.8 tool. The results were validated using MINDACT trial dataset [Cardoso et al. 2016]: single hormone receptor-positive (central assessment) cases of ductal histology (including 392 ER+/PgR– and 15 ER–/PR+ cases) where analysed for the prognostic value of gene expression of the identified miRNAs targets. Results: In our cohort, 7 miRNAs showed an association with OS (log-rank test): positive for four: hsa-miR-25-3p (p=0.013), hsa-miR-150-5p (p=0.015), hsa-miR-148a-3p (p=0.038) and hsa-miR-497-5p (p=0.044); and negative for three: hsa-miR-517c-3p (p=0.017), hsa-miR-4284 (p=0.018) and hsa-miR-301a-5p (p=0.029). According to miRNET 2.0, the 4 and 3 prognostic miRNAs have 3801 and 544 gene targets, respectively. The genes targeted by positively associated miRNAs were involved in transcription regulation, vesicle-mediated transport and protein stabilization, while the targets of negatively associated miRNAs were related with mRNA polyadenylation, DNA replication and regulation of DNA-templated transcription. Next, genes targeted by most of miRNAs from either group were identified: 11 targets of positive miRNAs (CANX, CBX5, HIPK1, PDE4DIP, PPM1A, REL, SETD5, SP1, XYLT2, ZMAT3, ZNF460) and 6 targets of negative miRNAs (ARL10, DNAJC28, MTHFD1L, PRPF6, RHOF, TSPAN6). The genes were tested for the association with OS in single hormone receptor-positive subgroup of the MINDACT cohort, with the following significant findings in multivariate analysis including N stage and Ki67 status: PDE4DIP (HR=2.84, p=0.011), CBX5 (HR=2.08, p=0.026) and PRPF6 (HR=0.44, p=0.045). Conclusions: This study identifies 7 miRNAs and their gene targets with a potential prognostic significance in single hormone receptor-positive breast cancer. Thus, several miRNA-mRNA axes merit further investigation both at molecular level and in a separate patient cohort to validate their clinical utility.