Laser capture microdissection and miRNA expression profiling of different tissue morphologies in triple-negative breast cancer

Triple negative breast cancers (TNBC) are a morphologically and genetically heterogeneous group of breast cancers with uncertain prediction of biological behavior and response to therapy. The aim of our study was to analyze miRNAs expression within areas of TNBCs with different cellular morphology. We performed laser capture microdissection with PALM MicroBeam system from Zeiss and subsequent expression profiling with Affymetrix GeneChip miRNA 4.0 Arrays to identify distinct classes of miRNAs deregulated in respective tissue morphologies. The study was approved by the Ethics Committee of the University Hospital Olomouc and Medical Faculty of Palacky University in compliance with the Helsinki Declaration (Ref No. 111/15). According to the Czech Law (Act. no. 373/11, and its amendment Act no. 202/17), it is not necessary to obtain informed consent in fully anonymised retrospective studies on formalin-fixed paraffin-embedded tissues. At least one tissue block for each patient was retained in the archive to allow future clinical use such as re-evaluation or further studies. We assembled a set of selected 25 TNBC cases to determine miRNA expression levels in relation to present focal carcinoma in situ (CIS), spindle cell, apocrine, invasive and other tumor morphologies within individual TNBCs. We excluded all tumors which were not complete (core-cut biopsies) and which were treated by previous neoadjuvant chemotherapy. Thus, the cohort of tumors were of limited size, varied from 5 to 20 mm (pathological tumor stage pT1a – pT1c), with an average size of 13.4 mm (median 15 mm). Despite the triple negative phenotype, we also excluded the histological tumor types associated with favourable prognosis (adenoid cystic carcinomas).