Subtype-specific lncRNA signatures: MALAT1 and XIST in breast cancer

Pelin Soytürk; Miray Acer

doi:10.5606/fng.btd.2025.206

Pelin Soytürk, Miray Acer

Department of Molecular Biology and Genetics, Demiroğlu Science University, Faculty of Arts & Science, İstanbul, Türkiye

Keywords: Breast cancer, HER2-positive, long non-coding RNA, luminal A, MALAT1, molecular subtypes, triple-negative breast cancer, XIST.

Abstract

Objectives: The objective of this study was to assess and compare metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), and X-inactive specific transcript (XIST) expression among breast cancer molecular subtypes in vitro, and to evaluate their potential association with subtype-specific biological characteristics.

Materials and methods: The expression levels of MALAT1 and XIST were analyzed in breast cancer cell lines representing three molecular subtypesluminal A (MCF-7), HER2-positive (MDA-MB-453), and triple-negative (MDA-MB-231)-as well as in non-tumorigenic MCF-10A cells, using quantitative real-time PCR. All experiments were performed in triplicate, and statistical analysis was conducted using one-way ANOVA followed by Dunnett tests.

Results: Both MALAT1 and XIST were significantly upregulated in all breast cancer cell lines compared with MCF-10A control (p<0.001). MALAT1 expression was highest in triple-negative MDA-MB-231 cells (6.23-fold), followed by luminal A MCF-7 (3.40-fold) and HER2-positive MDA-MB-453 (3.29-fold). Conversely, XIST showed the highest expression in luminal A MCF-7 cells (6.76-fold), with lower levels in HER2-positive (4.37-fold) and triple-negative breast cancer (TNBC) cells (4.06-fold). Notably, MALAT1 expression was significantly higher in TNBC than in other subtypes (p<0.001), whereas XIST expression in luminal A cells was significantly higher than in HER2+ and TNBC subtypes (p<0.001).

Conclusion: The findings demonstrate clear subtype-specific expression patterns of MALAT1 and XIST in breast cancer. Markedly elevated MALAT1 in TNBC corresponds to its aggressive phenotype and metastatic potential, while predominant XIST expression in luminal A cells may reflect estrogen receptor-related regulatory mechanisms. These differential expression profiles suggest potential roles for these long non-coding ribonucleic acids as subtype-specific biomarkers and therapeutic targets.

Cite this article as: Soytürk P, Acer M. Subtype-specific lncRNA signatures: MALAT1 and XIST in breast cancer. D J Med Sci 2025;11(3):115-121. doi: 10.5606/fng. btd.2025.206.