The Interplay between Long Noncoding RNAs and Proteins of the Epigenetic Machinery in Ovarian Cancer

Upregulation of long non-coding RNA ENSG00000267838 is related to the high risk of progression and non-response to chemoradiotherapy treatment for cervical cancer

Cervical cancer (CC) is a global public health concern, primarily caused by persistent infection with oncogenic types of human papillomavirus (HPV). The World Health Organization (WHO) has established a plan to eliminate CC as a public health issue by the year 2100. However, the implementation of the HPV vaccine is impeded by vaccine restrictions and misinformation despite its demonstrated effectiveness. The CC treatment is influenced by the disease stage, with an unfavorable prognosis for those in advanced stages. This study aimed to investigate the potential of long non-coding RNAs (lncRNAs) in CC by identifying and characterizing related lncRNAs, elucidating their regulatory mechanisms and molecular interactions, and analyzing their expression patterns in patients with diverse responses to chemoradiotherapy. Non-stem cells from CC were isolated using flow cytometry sorting and used for total RNA extraction. The RNA was used to build libraries that were subsequently sequenced using the Illumina Nextseq 550.417 lncRNAs that showed differentially expressed between CC patients who responded or not to treatment. Further analysis demonstrated that these lncRNAs significantly interact with several molecules, which play crucial roles in CC progression and therapeutic resistance. Statistical analysis correlated the expression profile of these lncRNAs with treatment efficacy. Three lncRNAs, ENSG00000267838, ENSG00000266340, and FRMD6-AS1, were identified with positive expression related to non-response to chemoradiotherapy and worse progression-free survival in CC patients. Specifically, lncRNA ENSG00000267838 has its up-regulation related to non-response and down-regulation to response to chemoradiotherapy treatment.

Long Non-Coding RNAs in Ovarian Cancer: Mechanistic Insights and Clinical Applications

Background/Objectives: Ovarian cancer is a leading cause of gynecological cancer mortality worldwide, often diagnosed at advanced stages due to vague symptoms and the lack of effective early detection methods. Long non-coding RNAs (lncRNAs) have emerged as key regulators in cancer biology, influencing cellular processes such as proliferation, apoptosis, and chemoresistance. This review explores the multifaceted roles of lncRNAs in ovarian cancer pathogenesis and their potential as biomarkers and therapeutic targets. Methods: A comprehensive literature review was conducted to analyze the structural and functional characteristics of lncRNAs and their contributions to ovarian cancer biology. This includes their regulatory mechanisms, interactions with signaling pathways, and implications for therapeutic resistance. Advanced bioinformatics and omics approaches were also evaluated for their potential in lncRNA research. Results: The review highlights the dual role of lncRNAs as oncogenes and tumor suppressors, modulating processes such as cell proliferation, invasion, and angiogenesis. Specific lncRNAs, such as HOTAIR and GAS5, demonstrate significant potential as diagnostic biomarkers and therapeutic targets. Emerging technologies, such as single-cell sequencing, provide valuable insights into the tumor microenvironment and the heterogeneity of lncRNA expression. Conclusions: LncRNAs hold transformative potential in advancing ovarian cancer diagnosis, prognosis, and treatment. Targeting lncRNAs or their associated pathways offers promising strategies to overcome therapy resistance and enhance personalized medicine. Continued research integrating omics and bioinformatics will be essential to unlock the full clinical potential of lncRNAs in ovarian cancer management.

Developing four cuproptosis-related lncRNAs signature to predict prognosis and immune activity in ovarian cancer

BACKGROUND

There has been a recent discovery of a new type of cell death produced by copper-iron ions, called Cuproptosis (copper death). The purpose of this study was to identify LncRNA signatures associated with Cuproptosis in ovarian cancer that could be used as prognostic indicators.

METHODS

RNA sequencing (RNA-seq) profiles with clinicopathological data from TCGA database were used to select prognostic CRLs and then constructed prognostic risk model using multivariate regression analysis and LASSO algorithms. An independent dataset from GEO database was used to validate the prognostic performance. Combined with clinical factors, we further constructed a prognostic nomogram. In addition, tumor immune microenvironment, somatic mutation and drug sensitivity were analyzed using ssGSEA, GSVA, ESTIMATE and CIBERSORT algorithms.

RESULT

A total of 129 CRLs were selected whose expression levels were significantly related to expression levels of 10 cuproptosis-related genes. The univariate Cox regression analysis showed that 12 CRLs were associated with overall survival (OS). Using LASSO algorithms and multivariate regression analysis, we constructed a four-CRLs prognostic signature in the training dataset. Patients in the training dataset could be classified into high- or low-risk subgroups with significantly different OS (log-rank p < 0.001). The prognostic performance was confirmed in TCGA-OC cohort (log-rank p < 0.001) and an independent GEO cohort (log-rank p = 0.023). Multivariate cox regression analysis proved the four-CRLs signature was an independent prognostic factor for OC. Additionally, different risk subtypes showed significantly different levels of immune cells, signal pathways, and drug response.

CONCLUSION

We established a prognostic signature based on cuproptosis-related lncRNAs for OC patients, which will be of great value in predicting the prognosis patients and may provide a new perspective for research and individualized treatment.

The Long Non-Coding RNA SNHG12 as a Mediator of Carboplatin Resistance in Ovarian Cancer via Epigenetic Mechanisms

Simple Summary

Epithelial ovarian cancer is a lethal malignancy in which recurrence and therapy resistance are the major causes of death. We investigated the transcriptome and DNA methylation profile of ovarian cancer cell lines sensitive and resistant to carboplatin, aiming to identify genes associated with therapy resistance. We focused on long non-coding RNAs (lncRNAs), known as epigenetic regulators of several cellular and biological processes. We found 11 lncRNAs associated with carboplatin resistance, including SNHG12 (small nucleolar RNA host gene 12), also confirmed in an external dataset (The Cancer Genome Atlas). SNHG12 gene silencing increased the sensitivity to carboplatin, giving evidence that this lncRNA contributes to resistance to carboplatin in ovarian cancer cell lines. We also demonstrated that SNHG12 could control the expression of nearby genes probably by altering epigenetic markers and modifying the transcript levels.

Abstract

Genetic and epigenetic changes contribute to intratumor heterogeneity and chemotherapy resistance in several tumor types. LncRNAs have been implicated, directly or indirectly, in the epigenetic regulation of gene expression. We investigated lncRNAs that potentially mediate carboplatin-resistance of cell subpopulations, influencing the progression of ovarian cancer (OC). Four carboplatin-sensitive OC cell lines (IGROV1, OVCAR3, OVCAR4, and OVCAR5), their derivative resistant cells, and two inherently carboplatin-resistant cell lines (OVCAR8 and Ovc316) were subjected to RNA sequencing and global DNA methylation analysis. Integrative and cross-validation analyses were performed using external (The Cancer Genome Atlas, TCGA dataset, n = 111 OC samples) and internal datasets (n = 39 OC samples) to identify lncRNA candidates. A total of 4255 differentially expressed genes (DEGs) and 14529 differentially methylated CpG positions (DMPs) were identified comparing sensitive and resistant OC cell lines. The comparison of DEGs between OC cell lines and TCGA-OC dataset revealed 570 genes, including 50 lncRNAs, associated with carboplatin resistance. Eleven lncRNAs showed DMPs, including the SNHG12. Knockdown of SNHG12 in Ovc316 and OVCAR8 cells increased their sensitivity to carboplatin. The results suggest that the lncRNA SNHG12 contributes to carboplatin resistance in OC and is a potential therapeutic target. We demonstrated that SNHG12 is functionally related to epigenetic mechanisms.

Role of a Pyroptosis-Related lncRNA Signature in Risk Stratification and Immunotherapy of Ovarian Cancer

Background: Pyroptosis is a newly recognized form of cell death. Emerging evidence has suggested the crucial role of long non-coding RNAs (lncRNAs) in the tumorigenesis and progression of ovarian cancer (OC). However, there is still poor understanding of pyroptosis-related lncRNAs in OC. Methods: The TCGA database was accessed for gene expression and clinical data of 377 patients with OC. Two cohorts for training and validation were established by random allocation. Correlation analysis and Cox regression analysis were performed to identify pyroptosis-related lncRNAs and construct a risk model. Results: Six pyroptosis-related lncRNAs were included in the final signature with unfavorable survival data. Subsequent ROC curves showed promising predictive value of patient prognosis. Further multivariate regression analyses confirmed the signature as an independent risk factor in the training (HR: 2.242, 95% CI: 1.598-3.145) and validation (HR: 1.884, 95% CI: 1.204-2.95) cohorts. A signature-based nomogram was also established with a C-index of.684 (95% CI: 0.662-0.705). Involvement of the identified signature in multiple immune-related pathways was revealed by functional analysis. Moreover, the signature was also associated with higher expression of three immune checkpoints (PD-1, B7-H3, and VSIR), suggesting the potential of the signature as an indicator for OC immunotherapies. Conclusion: This study suggests that the identified pyroptosis-related lncRNA signature and signature-based nomogram may serve as methods for risk stratification of OC. The signature is also associated with the tumor immune microenvironment, potentially providing an indicator for patient selection of immunotherapy in OC.

The functions and potential roles of extracellular vesicle noncoding RNAs in gynecological malignancies

Extracellular vesicles (EVs) are small membranous vesicles secreted by multiple kinds of cells and are widely present in human body fluids. EVs containing various constituents can transfer functional molecules from donor cells to recipient cells, thereby mediating intercellular communication. Noncoding RNAs (ncRNAs) are a type of RNA transcript with limited protein-coding capacity, that have been confirmed to be enriched in EVs in recent years. EV ncRNAs have become a hot topic because of their crucial regulating effect in disease progression, especially in cancer development. In this review, we summarized the biological functions of EV ncRNAs in the occurrence and progression of gynecological malignancies. In addition, we reviewed their potential applications in the diagnosis and treatment of gynecological malignancies.

Elevated LINC00909 Promotes Tumor Progression of Ovarian Cancer via Regulating the miR-23b-3p/MRC2 Axis

Ovarian cancer (OC), the third common gynecologic malignancy, contributes to the most cancer-caused mortality in women. However, 70% of patients with OC are diagnosed at an advanced stage, of which the 5-year survival is less than 30%. Long noncoding RNAs (long ncRNAs or lncRNA), a type of RNA with exceeding 200 nucleotides in length but no protein-coding capability, have been demonstrated to involve the pathogenesis of various cancers and show considerable potential in the diagnosis of OC. In this study, we found that the LINC00909 expression in tumor and serum specimens of OC patients was elevated, determined by real-time quantitative, and droplet digital PCR. In receiver operating characteristic (ROC) analysis, our results revealed that serum LINC00909 distinguished cancers from normal ovarian tissue with 87.8% of sensitivity and 69.6% of specificity (AUC, 81.2%) and distinguished serous ovarian cancer from normal ovarian tissue with 90.0% of sensitivity and 75.9% of specificity (AUC, 84.5%). Furthermore, we observed that the tumor and serum LINC00909 level was positively associated with the International Federation of Gynecology and Obstetrics (FIGO) stage and the Eastern Cooperative Oncology Group (ECOG) score (reflecting patients' performance status). Also, patients with low serum LINC00909 level showed a longer overall (hazard ratio, HR = 1.874, p = 0.0004) and progression-free (HR = 1.656, p = 0.0017) survival. Functional assays indicated that the elevation of LINC00909 expression contributes to cell proliferation, migration, and invasion capability of ovarian cancer cells. Besides, we demonstrated that LINC00909 functions as a competing endogenous RNA (ceRNA) of MRC2 mRNA by sponging miR-23-3p, and thereby promotes epithelial-to-mesenchymal transition (EMT) of ovarian cancer cells. Therefore, we highlight that the LINC00909/miR-23b-3p/MRC2 axis is implicated in the pathogenesis of ovarian cancer, and serum LINC00909 may be a promising biomarker for the diagnosis of OC.