miR-361-5p as a promising qRT-PCR internal control for tumor and normal breast tissues

Autor: Ali Sharifi-Zarchi, Seyed Javad Mowla, Saeid Rahmani, Sogol Ghanbari, Nahid Nafissi, Adel Salimi
Rok vydání: 2021
Předmět:
Oncology
Pathology and Laboratory Medicine
Biochemistry
Correlation
Prostate cancer
Breast Tumors
Gene expression
Medicine and Health Sciences
Breast
Multidisciplinary
Reverse Transcriptase Polymerase Chain Reaction
Prostate Cancer
Prostate Diseases
Middle Aged
Reference Standards
Nucleic acids
Real-time polymerase chain reaction
Medicine
Female
Anatomy
Research Article
medicine.medical_specialty
Clinical Pathology
Science
Urology
Breast Neoplasms
Biology
Malignant Tumors
Breast cancer
Text mining
Internal medicine
Breast Cancer
microRNA
Genetics
medicine
Humans
Non-coding RNA
Differentiated Tumors
Survival analysis
Natural antisense transcripts
Biology and life sciences
business.industry
Reproductive System
Cancers and Neoplasms
medicine.disease
Gene regulation
MicroRNAs
Genitourinary Tract Tumors
RNA
business
Breast Tissue
Zdroj: PLoS ONE
PLoS ONE, Vol 16, Iss 6, p e0253009 (2021)
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0253009
Popis: Background One of the most widely used evaluation methods in miRNA experiments is qRT-PCR. However, selecting suitable internal controls (IC) is crucial for qRT-PCR experiments. Currently, there is no consensus on the ICs for miRNA qRT-PCR experiments in breast cancer. To this end, we tried to identify the most stable (the least expression alteration) and promising miRNAs in normal and tumor breast tissues by employing TCGA miRNA-Seq data and then experimentally validated them on fresh clinical samples. Methods A multi-component scoring system was used which takes into account multiple expression stability criteria as well as correlation with clinical characteristics. Furthermore, we extended the scoring system for more than two biological sub-groups. TCGA BRCA samples were analyzed based on two grouping criteria: Tumor & Normal samples and Tumor subtypes. The top 10 most stable miRNAs were further investigated by differential expression and survival analysis. Then, we examined the expression level of the top scored miRNA (hsa-miR-361-5p) along with two commonly used ICs hsa-miR-16-5p and U48 on 34 pairs of Primary breast tumor and their adjacent normal tissues using qRT-PCR. Results According to our multi-component scoring system, hsa-miR-361-5p had the highest stability score in both grouping criteria and hsa-miR-16-5p showed significantly lower scores. Based on our qRT-PCR assay, while U48 was the most abundant IC, hsa-miR-361-5p had lower standard deviation and also was the only IC capable of detecting a significant up-regulation of hsa-miR-21-5p in breast tumor tissue. Conclusions miRNA-Seq data is a great source to discover stable ICs. Our results demonstrated that hsa-miR-361-5p is a highly stable miRNA in tumor and non-tumor breast tissue and we recommend it as a suitable reference gene for miRNA expression studies in breast cancer. Additionally, although hsa-miR-16-5p is a commonly used IC, it’s not a suitable one for breast cancer studies.
Databáze: OpenAIRE
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