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Updated: Jun 16, 2026
Clinicopathological Analysis of miRNA Expression in Breast Cancer Tissues by Using miRNA In Situ Hybridization
Published on: June 7, 2016
Differential expression of NEAT1 and miR-506-3p in triple-negative breast cancer: potential tissue-based diagnostic
Mohammad Samani1, Ali Samareh2, Aliasghar Tirgar3
1Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran.
Objectives:
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer (BC) characterized by the absence of estrogen receptor (ER), progesterone receptor (PR), and HER2 expression, and is one of the most challenging cancers to treat. Non-coding RNAs have been identified as potential biomarkers for various diseases, including cancer. Identifying these biomarkers may facilitate early diagnosis and improve treatment strategies. Therefore, this study aimed to evaluate the non-coding RNAs NEAT1 and miR-506-3p expression levels in TNBC patients.
Methods:
Formalin-fixed, paraffin-embedded (FFPE) tumor tissues and paired adjacent non-tumor tissues were obtained from 35 TNBC patients. Total RNA was extracted, and the expression levels of NEAT1 and miR-506-3p were quantified by qPCR using GAPDH and U6 as internal controls, respectively. Relative expression was analyzed by the 2-ΔΔCt method. Statistical analyses included comparison of gene expression fold changes, assessment of associations with clinicopathological features, Spearman correlation analysis, and receiver-operating characteristic (ROC) curve analysis.
Results:
NEAT1 was significantly upregulated (≈eightfold, P < 0.0001) and miR-506-3p was markedly downregulated (≈fivefold, P < 0.0001) in tumor tissues compared to adjacent non-tumor samples. Elevated NEAT1 expression was significantly associated with the younger age group, necrosis, calcification status, larger tumor size, and vascular invasion, whereas no significant associations were observed with BMI, tumor grade, or lymph-node involvement (P > 0.05). MiR-506-3p expression showed no significant clinicopathological differences in subgroup analysis. A significant inverse correlation was observed between NEAT1 and miR-506-3p levels (rs = -0.33, P < 0.05). ROC curve analysis showed promising discriminatory performance for NEAT1 in the present cohort (AUC = 0.9563, 95% CI 0.9165-0.9961; estimated sensitivity = 1.00, specificity = 0.77) and moderate discriminatory performance for miR-506-3p (AUC = 0.7971, 95% CI 0.6946-0.8997). A logistic regression model combining both markers showed improved discrimination in this dataset (AUC = 0.9739).
Conclusion:
Our findings suggest that NEAT1 and miR-506-3p exhibit opposite expression patterns in TNBC tissues and may serve as complementary tissue-based candidate diagnostic biomarkers. Their combined use showed improved discriminatory performance in this cohort; however, larger independent validation studies are required before a clinical diagnostic application can be proposed.
Insights
Triple-negative breast cancer (TNBC) shows altered expression of NEAT1 and miR-506-3p. These non-coding RNAs may serve as complementary biomarkers for TNBC diagnosis, with combined use improving accuracy.
Area of Science:
- Oncology
- Molecular Biology
- Biomarker Discovery
Background:
- Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype lacking ER, PR, and HER2 expression, posing treatment challenges.
- Non-coding RNAs are emerging as critical regulators in cancer and potential diagnostic biomarkers.
- Identifying novel biomarkers is crucial for early TNBC diagnosis and improved therapeutic strategies.
Purpose of the Study:
- To evaluate the expression levels of NEAT1 and miR-506-3p in TNBC patients.
- To assess the potential of NEAT1 and miR-506-3p as diagnostic biomarkers for TNBC.
Main Methods:
- Quantitative PCR (qPCR) was used to measure NEAT1 and miR-506-3p expression in 35 TNBC tumor tissues and adjacent non-tumor tissues.
- Statistical analyses included fold change analysis, correlation studies, and receiver-operating characteristic (ROC) curve analysis.
- Clinicopathological associations and combined diagnostic performance were evaluated.
Main Results:
- NEAT1 was significantly upregulated (eightfold) and miR-506-3p was markedly downregulated (fivefold) in TNBC tissues compared to non-tumor samples (P < 0.0001).
- Elevated NEAT1 expression correlated with younger age, necrosis, calcification, larger tumor size, and vascular invasion.
- ROC analysis indicated promising discriminatory performance for NEAT1 (AUC=0.9563) and moderate performance for miR-506-3p (AUC=0.7971); combined use improved discrimination (AUC=0.9739).
Conclusions:
- NEAT1 and miR-506-3p exhibit opposing expression patterns in TNBC, suggesting their potential as complementary tissue-based diagnostic biomarkers.
- The combination of NEAT1 and miR-506-3p demonstrated enhanced diagnostic performance in the studied cohort.
- Further validation in larger independent cohorts is necessary prior to clinical application.
