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Series GSE162670 Query DataSets for GSE162670
Status Public on Mar 04, 2021
Title Laser capture microdissection and miRNA expression profiling of different tissue morphologies in triple-negative breast cancer
Platform organism synthetic construct
Sample organism Homo sapiens
Experiment type Non-coding RNA profiling by array
Summary 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.
Overall design 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).
Web link
Contributor(s) Bouchal J, Koleckova M, Kolar Z
Citation(s) 33664322
Submission date Dec 04, 2020
Last update date Mar 06, 2021
Contact name Jan Bouchal
Phone +420585639570
Organization name Palacky University
Department Department of Clinical and Molecular Pathology
Lab Laboratory of Molecular Pathology
Street address Hnevotinska 3
City Olomouc
ZIP/Postal code CZ-77900
Country Czech Republic
Platforms (1)
GPL19117 [miRNA-4] Affymetrix Multispecies miRNA-4 Array
Samples (74)
GSM4956542 normal, biological rep 1
GSM4956543 normal, biological rep 2
GSM4956544 normal, biological rep 3
BioProject PRJNA682594

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE162670_ESet.RData.gz 14.7 Mb (ftp)(http) RDATA
GSE162670_RAW.tar 51.7 Mb (http)(custom) TAR (of CEL)
GSE162670_RMA_normalized_matrix.txt.gz 1.4 Mb (ftp)(http) TXT
Processed data are available on Series record

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