Long noncoding RNAs (lncRNAs) have been identified as contributors to the development and progression of cancer through various functions and mechanisms. LncRNA GAS5 is downregulated in multiple cancers and acts as a tumor suppressor in breast cancer. GAS5 interacts with various proteins (e.g., E2F1, EZH2, and YAP), DNA (e.g., the insulin receptor promoter), and various microRNAs (miRNAs). In breast cancer, GAS5 binds with miR-21, miR-222, miR-221-3p, miR-196a-5p, and miR-378a-5p that indicates the presence of several elements for miRNA binding (MREs) in GAS5. Mediated by the listed miRNAs, GAS5 is involved in the upregulation of a number of mRNAs of suppressor proteins such as PTEN, PDCD4, DKK2, FOXO1, and SUFU. Furthermore, the aberrant promoter methylation is involved in the regulation of GAS5 gene expression in triple-negative breast cancer and some other carcinomas. GAS5 can stimulate apoptosis in breast cancer via diverse pathways, including cell death receptors and mitochondrial signaling pathways. GAS5 is also a key player in the regulation of some crucial signal pathways in breast cancer, such as PI3K/AKT/mTOR, Wnt/β-catenin, and NF-κB signaling. Through epigenetic and other mechanisms, GAS5 can increase sensitivity to multiple drugs and improve prognosis. GAS5 is thus a promising target in the treatment of breast cancer patients.

Our work aimed to differentiate 20 aberrantly methylated miRNA genes that participate at different stages of development and metastasis of ovarian carcinoma (OvCa) using methylation-specific qPCR in a representative set of clinical samples: 102 primary tumors without and with metastases (to lymph nodes, peritoneum, or distant organs) and 30 peritoneal macroscopic metastases (PMM). Thirteen miRNA genes (MIR107, MIR124-2, MIR124-3, MIR125B-1, MIR127, MIR129-2, MIR130B, MIR132, MIR193A, MIR339, MIR34B/C, MIR9-1, and MIR9-3) were hypermethylated already at the early stages of OvCa, while hypermethylation of MIR1258, MIR137, MIR203A, and MIR375 was pronounced in metastatic tumors, and MIR148A showed high methylation levels specifically in PMM. We confirmed the significant relationship between methylation and expression levels for 11 out of 12 miRNAs analyzed by qRT-PCR. Moreover, expression levels of six miRNAs were significantly decreased in metastatic tumors in comparison with nonmetastatic ones, and downregulation of miR-203a-3p was the most significant. We revealed an inverse relationship between expression levels of miR-203a-3p and those of ZEB1 and ZEB2 genes, which are EMT drivers. We also identified three miRNA genes (MIR148A, MIR9-1, and MIR193A) that likely regulate EMT–MET reversion in the colonization of PMM. According to the Kaplan–Meier analysis, hypermethylation of several examined miRNA genes was associated with poorer overall survival of OvCa patients, and high methylation levels of MIR130B and MIR9-1 were related to the greatest relative risk of death.

Our work aimed to evaluate and differentiate the role of ten lncRNA genes (GAS5, HAND2-AS1, KCNK15-AS1, MAGI2-AS3, MEG3, SEMA3B-AS1, SNHG6, SSTR5-AS1, ZEB1-AS1, and ZNF667-AS1) in the development and progression of epithelial ovarian cancer (EOC). A representative set of clinical samples was used: 140 primary tumors from patients without and with metastases and 59 peritoneal metastases. Using MS-qPCR, we demonstrated an increase in methylation levels of all ten lncRNA genes in tumors compared to normal tissues (p < 0.001). Using RT-qPCR, we showed downregulation and an inverse relationship between methylation and expression levels for ten lncRNAs (r_s < −0.5). We further identified lncRNA genes that were specifically hypermethylated in tumors from patients with metastases to lymph nodes (HAND2-AS1), peritoneum (KCNK15-AS1, MEG3, and SEMA3B-AS1), and greater omentum (MEG3, SEMA3B-AS1, and ZNF667-AS1). The same four lncRNA genes involved in peritoneal spread were associated with clinical stage and tumor extent (p < 0.001). Interestingly, we found a reversion from increase to decrease in the hypermethylation level of five metastasis-related lncRNA genes (MEG3, SEMA3B-AS1, SSTR5-AS1, ZEB1-AS1, and ZNF667-AS1) in 59 peritoneal metastases. This reversion may be associated with partial epithelial–mesenchymal transition (EMT) in metastatic cells, as indicated by a decrease in the level of the EMT marker, CDH1 mRNA (p < 0.01). Furthermore, novel mRNA targets and regulated miRNAs were predicted for a number of the studied lncRNAs using the NCBI GEO datasets and analyzed by RT-qPCR and transfection of SKOV3 and OVCAR3 cells. In addition, hypermethylation of SEMA3B-AS1, SSTR5-AS1, and ZNF667-AS1 genes was proposed as a marker for overall survival in patients with EOC.

Breast cancer (BC) remains one of the leading causes of cancer deaths among women worldwide. Recently, studies of long non-coding RNAs (lncRNAs) involved in the regulation of various signaling pathways in cells have become increasingly important, since they demonstrate great prognostic potential in cancer. The aim of our work was to identify new aberrantly expressed lncRNAs in BC. We identified 30 aberrantly expressed lncRNAs in BC. For most lncRNAs, a decrease in the expression level by 2.34–13.2 times (p < 0.05) was noted, and only for lncRNA TERC, an increase in the expression level by 2.24 times (p = 0.034) was noted. Of greatest interest are the data obtained for the lncRNAs ADAMTS9-AS2, EMX2OS, HOTAIRM1 and MEG3, as they are consistent with the data of the bioinformatic analysis.

Рак яичников относится к наиболее агрессивным и неблагоприятным формам рака у женщин с быстрым прогрессированием и высоким метастатическим потенциалом. Ключевую роль в развитии этого заболевания может играть нарушение эпигенетической регуляции экспрессии длинных некодирующих РНК (днРНК) вследствие аберрантного метилирования их генов. Цель: изучить характер метилирования и экспрессии генов днРНК GAS5, HOTAIR и SNHG6 в опухолях больных раком яичников и оценить связь этих эпигенетических нарушений с прогрессией и метастазированием заболевания. Методы: Анализ уровней метилирования и экспрессии днРНК проводили методом ПЦР в реальном времени на выборке парных (опухоль/норма) образцов, полученных от пациенток с раком яичников. Статистический и корреляционный анализ выполняли в программной среде R. Результаты: Выявлено значимое повышение уровня метилирования генов GAS5, HOTAIR и SNHG6 в опухолевой ткани по сравнению с нормой. Тот же результат показан для генов GAS5 и SNHG6 при прогрессии опухоли, включая метастазирование. Уровень экспрессии при этом для HOTAIR и SNHG6 значимо снижался в опухоли. Выявлена отрицательная корреляция между уровнем метилированием гена SNHG6 и уровнем его экспрессии. Заключение: Полученные данные указывают на важную роль эпигенетической дерегуляции днРНК в патогенезе рака яичников и могут найти применение в прогнозировании и разработке персонализированных подходов к терапии. Ovarian cancer is one of the most aggressive and unfavorable forms of cancer in women with rapid progression and high metastatic potential. A key role in the development of this disease may be played by a disruption in the epigenetic regulation of the expression of long non-coding RNAs (lncRNAs) due to aberrant methylation of their genes. Objective: To study the methylation and expression patterns of the lncRNA genes GAS5, HOTAIR, and SNHG6 in ovarian cancer tumors and evaluate the association of these epigenetic abnormalities with disease progression and metastasis. Methods: Analysis of lncRNA methylation and expression levels was performed by RT-PCR on paired (tumor/normal) samples obtained from ovarian cancer patients. Statistical and correlation analysis was performed in the R software environment. Results: A significant increase in the methylation level of the GAS5, HOTAIR, and SNHG6 genes was observed in tumor tissue compared to normal tissue. The same result was shown for the GAS5 and SNHG6 genes during tumor progression, including metastasis. The expression level for HOTAIR and SNHG6 was significantly decreased in the tumor. A negative correlation was found between the methylation level of the SNHG6 gene and its expression level. Conclusion: The obtained data indicate an important role of epigenetic deregulation of lncRNAs in the pathogenesis of ovarian cancer and may find application in predicting and developing personalized approaches to therapy.