Long Noncoding RNA and Cancer: A New Paradigm

Construction of a novel prognostic model based on lncRNAs-related to DNA damage repair for predicting the prognosis of clear cell renal cell carcinoma

BACKGROUND

CcRCC has the characteristics of high aggression, high metastasis, high mortality, wide tumour heterogeneity and variable clinical course. The purpose of this study was to explore the potential value of lncRNAs-related to DNA damage repair (DDR) in predicting the prognosis of ccRCC by construction and verification a novel prognostic model.

METHODS

RNA-seq data and clinical data of ccRCC were downloaded from public databases. Subsequently, Pearson correlation analysis and differential expression analysis were performed to identify DElncRNAs-related to DDR. Then, through univariate Cox analysis and LASSO analysis, the DElncRNAs-related to DDR associated with prognosis were screened for the construction of novel risk score prognostic model. In addition, functional annotation, tumour mutation burden, immune correlation and drug sensitivity analyses were performed based on risk score to assess the characteristics of patients in different risk score groups.

RESULTS

Based on univariate Cox analysis and LASSO analysis, four best DElncRNAs-related to DDR were selected. Subsequently, a novel risk score prognostic model based on these four DElncRNAs was constructed through LASSO. Multivariate Cox analysis showed that risk score and age were independent prognostic factors for ccRCC (p < 0.05). Functional enrichment analysis showed that DDR-related biological processes were mainly enriched in the high risk group. The highly mutated genes in the high and low risk groups were the same (VHL, PBRM1 and TTN), but they also had their own unique mutated genes. Pearson correlation analysis showed that the risk score was significantly (p < 0.05) positively correlated with the infiltration degree of CD8 T cells evaluated by six algorithms. In addition, it was found that the high and low risk groups had different sensitivities to the drugs Etoposide, Imatinib, Sorafenib, Bosutinib and Sunitinib.

CONCLUSION

A novel prognostic model was constructed based on four DElncRNAs-related to DDR. The model has satisfactory accuracy in predicting survival of ccRCC patients.

Research progress on the mechanism of tumor cell ferroptosis regulation by epigenetics

Cancer remains a significant barrier to human longevity and a leading cause of mortality worldwide. Despite advancements in cancer therapies, challenges such as cellular toxicity and drug resistance to chemotherapy persist. Regulated cell death (RCD), once regarded as a passive process, is now recognized as a programmed mechanism with distinct biochemical and morphological characteristics, thereby presenting new therapeutic opportunities. Ferroptosis, a novel form of RCD characterized by iron-dependent lipid peroxidation and unique mitochondrial damage, differs from apoptosis, autophagy, and necroptosis. It is driven by reactive oxygen species (ROS)-induced lipid peroxidation and is implicated in tumorigenesis, anti-tumor immunity, and resistance, particularly in tumors undergoing epithelial-mesenchymal transition. Moreover, ferroptosis is associated with ischemic organ damage, degenerative diseases, and aging, regulated by various cellular metabolic processes, including redox balance, iron metabolism, and amino acid, lipid, and glucose metabolism. This review focuses on the role of epigenetic factors in tumor ferroptosis, exploring their mechanisms and potential applications in cancer therapy. It synthesizes current knowledge to provide a comprehensive understanding of epigenetic regulation in tumor cell ferroptosis, offering insights for future research and clinical applications.

Exosome-derived SLC12A2-DT promotes macrophage M2 polarization-mediated hepatocellular carcinoma progression

BACKGROUND

Previous scholarly research highlights the indispensable roles of tumor-associated macrophages (TAMs) and exosomes in the progression of hepatocellular carcinoma (HCC). However, the nuanced molecular mechanisms by which tumor-derived exosomal lncRNAs interact with TAMs to modulate macrophage polarization and HCC proliferation remain largely obscure.

METHOD

Clinical specimens were subjected to sequencing and bioinformatics analysis, revealing the previously unreported SLC12A2-DT. The presence of exosomes was assessed via transmission electron microscopy and differential ultracentrifugation. In vivo and in vitro coculture experiments were employed to elucidate the functions of exosomal SLC12A2-DT. RNA pull-down assays, dual-luciferase reporter assays, and mass spectrometry were utilized to delineate the mechanisms by which exosomal SLC12A2-DT regulates the interaction between HCC cells and M2 macrophages.

RESULTS

Our study revealed the aberrant upregulation of SLC12A2-DT expression in HCC, particularly in advanced stages, and its association with poor prognosis in HCC patients. Notably, SLC12A2-DT-induced M2 macrophage polarization significantly induced lung metastasis in a murine HCC model. We subsequently confirmed that HCC cell-derived exosomal SLC12A2-DT induced M2 macrophage polarization by specifically binding to GSK3β/β-catenin and downregulating the degradation of ubiquitinated β-catenin, leading to Wnt signaling pathway activation. Furthermore, we revealed that KLF4 transcriptionally repressed SLC12A2-DT expression in HCC cells.

CONCLUSION

These findings suggest that tumor-derived exosomal SLC12A2-DT facilitates HCC progression by modulating the interplay between HCC cells and TAMs through the Wnt/GSK3β/β-catenin signaling pathway.

In vitro investigation of epigenetic regulators related to chemo-resistance and stemness of CD133+VE cells sorted from U87MG cell line

Glioblastoma (GBM) is the most common and malignant adult primary brain tumor with frequent relapse and resistance to therapies. Glioma stem cells, a rare population, is thought to be the reason behind the treatment's failure. It is imperative to investigate the disease mechanisms and identify the biomarkers by which glioma stem cells would contribute to treatment relapse and resistance to already available chemotherapeutic agents. The CD133+VE cells were isolated from U87MG cell line and characterized by morphological features, cell viability, self-renewal efficiency, migration potential and karyotyping. Doxorubicin Cisplatin, Irinotecan, Etoposide and Temozolomide were used to determine the anti-proliferative effect on CD133+VE cells. Confocal microcopy was used to localize the chemotherapeutic agents in the CD133+VE cells. In quest of epigenetic biomarkers, RNA sequencing was performed to find the role of lncRNAs in stemness and resistance to therapies. U87cell line and CD133-VE cells were kept as controls for all the experiments. It was found that CD133+VEcells were highly proliferative with increased migration potential, elevated IC50 values against chemotherapeutic agents and showed distinct karyotyping related to pluripotency. Chemotherapeutic agent such as Doxorubicin was localized outside the nucleus revealing the drug resistance as evident by confocal microscopy. RNA sequencing revealed 126 differentially expressed lncRNAs (DELs) in CD133+VEcells among which lncRNA LOXL1-AS1 was highly upregulated and lncRNA PAX8-AS1 was significantly downregulated. These lncRNAs has been reported to be related to drug resistance, migration and epithelial- to- mesenchymal transmission (EMT), self-renewal and stemness properties contributing to poor prognosis and disease relapse.

Association of long non-coding RNA in lipid metabolism: Implications in leukemia

Cancer has high mortality rate and occupies second position among major diseases. Despite extensive research and therapies, in every nook and corner of the world, death rate is increasing exponentially. Hallmarks of cancer are benchmarks of cancer cells describing the fundamental principle and capabilities of the cells transforming from normal to malignant tumour. One of the major ones among them is the deregulation of cellular metabolism or metabolic reprogramming, involving alterations in glucose and lipid metabolism. Progressive research in this area has visualized the vital role of lncRNAs in lipid metabolism with respect to AML. lncRNAs involve in various cellular processes and also contribute for significant functions of the cell like chromatin remodelling, transcriptional activation and repression, gene regulation, immune response, cell differentiation, and cell cycle regulation, in addition to oncogenic processes such as proliferation, angiogenesis, migration, and apoptosis. Structural similarities are observed among mRNAs and lncRNAs in terms of poly A-tail and 5' cap however protein-coding regions are lacking. A large body of evidence has shown that lncRNAs directly or indirectly mediate lipid metabolism by activating downstream genes. Considering their potential involvement in leukemia, these lncRNAs can be explored and considered as biomarkers for therapeutics, prognosis, and diagnosis. The present review is planned to summarize the functional classification of lncRNAs, the role of lipid metabolism in cancer, different lncRNAs involved in leukemia, and different cancer types related to lipid metabolism.

Unveiling EIF5A2: A multifaceted player in cellular regulation, tumorigenesis and drug resistance

The eukaryotic initiation factor 5A2 gene (EIF5A2) is a highly conserved and multifunctional gene that significantly influences various cellular processes, including translation elongation, RNA binding, ribosome binding, protein binding and post-translational modifications. Overexpression of EIF5A2 is frequently observed in multiple cancers, where it functions as an oncoprotein. Additionally, EIF5A2 is implicated in drug resistance through the regulation of various molecular pathways. In the review, we describe the structure and functions of EIF5A2 in normal cells and its role in tumorigenesis. We also elucidate the molecular mechanisms associated with EIF5A2 in the context of tumorigenesis and drug resistance. We propose that the biological roles of EIF5A2 in regulating diverse cellular processes and tumorigenesis are clinically significant and warrant further investigation.

LncRNA ZFAS1 promotes the transformation from prostatitis to prostate cancer via myddosome assembly-mediated activation of NF-κB signaling

BACKGROUND

Prostatitis is a critical factor in promoting carcinogenesis, but the key molecular mechanisms remain unknown. Long noncoding RNA (lncRNA) ZFAS1 was reported to be involved in the development of human cancers including prostate cancer and some inflammatory diseases. This research aims at investigating the function of ZFAS1 in regulating prostatitis to prostate cancer transformation and the underlying mechanism.

METHODS

A prostatitis-cancer transformation cell model RWPE-1/THP-1 was established by co-culturing human prostate epithelial cells RWPE-1 with human acute monocytic leukemia cells THP-1. CCK-8, colony formation, and flow cytometry assays were used to detect the effects of ZFAS1 knockdown or overexpression on the proliferation and apoptosis and malignant transformation ability of the model cells. The influence of ZFAS1 knockdown on the levels of apoptosis-related proteins, MyD88 protein aggregation in cell lysate and pellet fractions, and the phosphorylation of IKKβ, IκBα, and NF-κB p65 in RWPE-1/THP-1 cells. Immunofluorescence staining was used to detect NF-κB p65 nuclear translocation in RWPE-1/THP-1 cells. ST2825 was used to further confirm whether ZFAS1 affects prostatitis to prostate cancer transformation by regulating NF-κB pathway through modulating MYD88 dimerization and the subsequent myddosome assembly.

RESULTS

ZFAS1 expression was markedly increased in RWPE-1/THP-1 cells. ZFAS1 silencing repressed the proliferation and facilitated the apoptosis of RWPE-1/THP-1 cells. P-IKKβ, p-IκBα and p-p65 protein levels and NF-κB p65 nuclear translocation were significantly enhanced in RWPE-1/THP-1 cells, which were reversed by ZFAS1 knockdown. ZFAS1 knockdown exerted the same inhibitory effects as ST2825 treatment on the degree of MyD88 aggregation and NF-κB pathway activation in RWPE-1/THP-1 cells, suggesting that ZFAS1 knockdown inactivated the NF-κB pathway in RWPE-1/THP-1 cells through suppressing MYD88 dimerization and the subsequent myddosome assembly. In addition, ST2825 treatment overturned the influence of ZFAS1 overexpression on the proliferation and apoptosis of RWPE-1/THP-1 cells.

CONCLUSION

ZFAS1 promotes prostatitis to cancer transformation by activating the NF-κB signaling through promoting MYD88 dimerization and the subsequent myddosome assembly.

Application of non‑coding RNAs in tumors (Review)

Tumors are associated with the highest mortality rates worldwide. For more than a decade, research has focused on the genetic involvement of proteins in cancer; however, a complete class of molecular non‑coding (nc)RNAs have been discovered in recent years, and these are considered to be associated with cancer. Notably, ncRNAs are highly conserved and multifunctional. These interact with multiple signaling pathways, influencing cell cycle progression and various physiological processes. Therefore, the present review aimed to investigate ncRNA, microRNA, transfer RNA‑derived small RNA, PIWI‑interacting RNA and long non‑coding RNA to further understand the associated generation processes, functional mechanisms and therapeutic roles in tumors. The present review demonstrated the critical role of ncRNAs in tumors, and may provide a novel theoretical basis for the role of ncRNAs as biomarkers or therapeutic tools in the treatment of cancer.

Unlocking the Mysteries of Breast Cancer: The Role of Epigenetics in Diagnosis, Treatment, and Beyond

OBJECTIVES

Breast cancer is an intricate and varied disease exhibiting a range of molecular subgroups and clinical consequences. Epigenetic alterations have become essential players in the pathophysiology of breast cancer because they control gene expression without changing the DNA sequence. This review provides a comprehensive overview of epigenetics' diagnostic, prognostic, and therapeutic implications in breast cancer. This review aims to present a comprehensive study of the function of epigenetics in breast cancer, emphasizing current developments and potential avenues for future research.

METHODS

A narrative review methodology involved an extensive literature search and selection to gather relevant studies and trial data. PubMed, Embase, and Web of Science databases were searched using relevant keywords such as "epigenetics," "breast cancer," "DNA methylation," "histone modification," "noncoding RNA," and "linical trials." Relevant studies and clinical trial data were selected and synthesized to summarize the topic comprehensively.

RESULTS

The review synthesizes critical findings from current research, underscoring the pivotal role of epigenetic mechanisms in breast cancer initiation, progression, and therapeutic response. It highlights the potential of epigenetic biomarkers for diagnosis and prognosis and the promise of epigenetic-targeted therapies in breast cancer management. Furthermore, the review outlines future directions for research, emphasizing the importance of elucidating the dynamic interplay between epigenetic alterations and tumor microenvironments in shaping breast cancer phenotypes.

CONCLUSIONS

Epigenetic modifications influence breast cancer progression, diagnosis, and therapy. Emerging biomarkers and targeted treatments hold promise, but further research is essential to refine their clinical application and improve personalized cancer management strategies.

Clinical significance of a new early diagnostic model for bladder cancer based on genome-wide microarray profiling of serum exosomal lncRNAs

PURPOSE

The aim of our report was to recognize bladder cancer (BC)-specific serum exosome-derived long non-coding RNAs (lncRNAs) profile for early diagnosis of BC.

METHODS

Potential BC-specific exosomal lncRNA indicators were discerned by genome-wide microarray profiling analysis of serum exosomes from 10 healthy participants and 10 early stage BC patients (Ta and T1), followed by multi-stage validation through quantitative real-time PCR (qRT-PCR) in BC cells, culture solution as well as 200 serum specimens and 50 tissue specimens from non-muscle-invasive bladder cancer (NMIBC) patients. The diagnostic panel was established using logistic regression and evaluated by receiver-operating characteristic (ROC) curve.

RESULTS

In the training stage, a diagnostic panel was constructed based on three up-regulated exosomal lncRNAs (G023016, RP11-553N19.1, and LINC0087) in NMIBC patients compared with healthy controls, yielding an area under ROC curve (AUC) of 0.827. We verified tumor-derived origin of these three lncRNAs which existed steadily in serum because of being enclosed in exosomes. The three-lncRNA panel was demonstrated to perform well in terms of NMIBC diagnosis, revealing AUC values of 0.809 and 0.812, respectively, in the following expanded validation stage and double-blind stage which was demonstrated to be significantly superior to that of urine cytology in double-blind stage (AUC = 0.630) (P < 0.0001). Moreover, serum exosome-derived G023016 significantly associated with tumor grade and TNM stage (P = 0.006 and P < 0.001, respectively), and LINC0087 significantly associated with TNM stage (P = 0.023).

CONCLUSION

The three-exosomal lncRNA signature could function as qualified blood-based non-invasive indicator for early diagnosis of BC.

LINC02154 Promotes Esophageal Squamous Cell Carcinoma Progression via the PI3K-AKT-mTOR Signaling Pathway by Interacting With IGF2BP2

As important types of noncoding RNAs, long noncoding RNAs (lncRNAs) have been found to be involved in the progression of various cancers. Accumulating evidence indicates that LINC02154 plays a critical role in cancer progression, but the underlying mechanisms regulating esophageal squamous cell carcinoma (ESCC) remain unclear. Here, we found that LINC02154 is significantly upregulated in ESCC cell lines and ESCC tissues. LINC02154 knockdown significantly inhibited the proliferation and migration of ESCC cells in vitro and suppressed the progression of ESCC in vivo. Mechanistically, LINC02154 can bind to IGF2BP2 and activate the PI3K-AKT-mTOR signaling pathway. High expression of LINC02154 is positively correlated with poor prognosis in ESCC patients. In conclusion, LINC02154 functions as an oncogenic factor to facilitate ESCC progression through the IG2BP2-PI3K-AKT-mTOR pathway and has the potential to be a promising diagnostic marker and therapeutic target for ESCC patients.

Small protein ERSP encoded by LINC02870 promotes triple negative breast cancer progression via IRE1α/XBP1s activation

Clinical treatment options for triple-negative breast cancer (TNBC) are currently limited to chemotherapy because of a lack of effective therapeutic targets. Recent evidence suggests that long noncoding RNAs (lncRNAs) encode bioactive peptides or proteins, thereby playing noncanonical yet significant roles in regulating cellular processes. However, the potential of lncRNA-translated products in cancer progression remains largely unknown. In this study, we identified a previously undocumented small protein encoded by the lncRNA LINC02870. This protein is localized at the endoplasmic reticulum (ER) and participates in ER stress, thus, we named it the endoplasmic reticulum stress protein (ERSP). ERSP was highly expressed in TNBC tissues, and elevated LINC02870 content was correlated with poor prognosis in TNBC patients. Loss of ERSP inhibited TNBC growth and metastasis both in vitro and in vivo. The pro-oncogenic effects of ERSP could be attributed to its selective activation of the IRE1α/XBP1s branch. ERSP enhances the unfolded protein response (UPR) by interacting with XBP1s, facilitating the nuclear accumulation of XBP1s, thereby promoting the expression of ER stress-related genes. These findings highlight the regulatory role of the lncRNA-encoded protein ERSP in ER stress and suggest that it is a potential therapeutic target for TNBC.

POCALI: Prediction and Insight on CAncer LncRNAs by Integrating Multi-Omics Data with Machine Learning

Long non-coding RNAs (lncRNAs) are receiving increasing attention as biomarkers for cancer diagnosis and therapy. Although there are many computational methods to identify cancer lncRNAs, they do not comprehensively integrate multi-omics features for predictions or systematically evaluate the contribution of each omics to the multifaceted landscape of cancer lncRNAs. In this study, an algorithm, POCALI, is developed to identify cancer lncRNAs by integrating 44 omics features across six categories. The contributions of different omics are explored to identifying cancer lncRNAs and, more specifically, how each feature contributes to a single prediction. The model is evaluated and benchmarked POCALI with existing methods. Finally, the cancer phenotype and genomics characteristics of the predicted novel cancer lncRNAs are validated. POCALI identifies secondary structure and gene expression-related features as strong predictors of cancer lncRNAs, and epigenomic features as moderate predictors. POCALI performed better than other methods, especially in terms of sensitivity, and predicted more candidates. Novel POCALI-predicted cancer lncRNAs have strong relationships with cancer phenotypes, similar to known cancer lncRNAs. Overall, this study facilitates the identification of previously undetected cancer lncRNAs and the comprehensive exploration of the multifaceted feature contributions to cancer lncRNA prediction.

Targeting GPX4 to Induce Ferroptosis Overcomes Chemoresistance Mediated by the PAX8-AS1/GPX4 Axis in Intrahepatic Cholangiocarcinoma

The standard regimen of gemcitabine combined with cisplatin offers limited clinical benefits in the treatment of advanced intrahepatic cholangiocarcinoma (ICC) due to intrinsic or acquired resistance. Currently, effective biomarkers to predict and improve chemotherapy resistance in ICC are lacking. Here, it is reported that a long non-coding RNA (lncRNA), PAX8-AS1, reduces the efficacy of standard chemotherapeutic drugs. Mechanistically, PAX8-AS1 activates NRF2 by binding to p62, thereby promoting GPX4 transcription, and stabilizes GPX4 mRNA through interaction with IGF2BP3. The PAX8-AS1/GPX4 axis inhibits ferroptosis and promotes resistance to gemcitabine and cisplatin. In preclinical models, the combination of the GPX4 inhibitor JKE-1674 with gemcitabine and cisplatin exhibits superior antitumor efficacy. These findings suggest a promising therapeutic strategy to improve chemotherapy efficacy in advanced ICC.

Novel exosome-associated LncRNA model predicts colorectal cancer prognosis and drug response

BACKGROUND

Exosomes are extracellular vesicles that carry various biological substances and have potential as functional mediators in cancers. However, little is known about special molecules in colorectal cancer (CRC) exosomes and their immunological functions.

AIMS

Using genomic data from the TCGA-CRC cohort, we constructed a prognostic model based on exosome-related lncRNA for the first time, and the biological role of MIR4713HG in CRC was deeply analyzed.

METHOD

In this study, we downloaded the gene expression data and clinical data of CRC from the TCGA database. The limma package, SVM-REF and univariate Cox analysis were used to screen out core ERG (CERG) in CRC. LASSO and multivariate Cox regression analyses were used to filter out CERG-related LncRNA and construct a risk score. We explored the distribution and expression levels of ERG in immune cell types by scRNA-seq data. xCell was used to calculate the infiltration levels of stromal cells and immune cells in CRC. KM plotter was used for immunotherapy evaluation of core ERG. Next, we further provide colony formation assay, Transwell assay and xenograft models to understand the carcinogenic effect of MIR4713HG.

RESULT

First, 43 differentially expressed ERG and 7 CERG were obtained. We explored the expression and distribution levels of CERG in 9 types of cells by scRNA-seq data. In addition, two key exosome-associated LncRNA (MIR4713HG and ZEB1-AS1) were obtained, and a risk score (EALncRI) was constructed. EALncRI could accurately predict the prognosis of CRC. Based on the EALncRI, we constructed a nomogram that is easy to use in clinical practice, which can more accurately and stably predict the prognosis of CRC patients. Furthermore, EALncRI was significantly correlated with the expression of 5 HLA molecules and 13 immune checkpoint molecules. MIR4713HG showed a good predictive effect in the overall survival of patients with immunotherapy evaluation. Knocking down the expression of MIR4713HG significantly inhibited proliferation and migration, and also impaired subcutaneous tumor growth in nude mice.

CONCLUSION

In this study, a variety of machine learning algorithms were used to construct the EALncRI based on ERG, which can effectively predict the prognosis and distinguish the immune landscape of CRC. More importantly, we conducted an in-depth study on MIR4713HG, which may become an important therapeutic target in CRC.

Role of exosomes in castration-resistant prostate cancer

Prostate cancer (PCa) is one of the most common urological malignancies in older male patients. Castration-resistant prostate cancer (CRPC) is an aggressive and refractory stage of PCa and is the leading cause of PCa-related deaths. Exosomes are small spherical vesicles with a lipid bilayer membrane structure, secreted by cells, which carry large amounts of nucleic acids, proteins, lipids, and various important reactive small molecules. Numerous studies have demonstrated that exosomes are involved in the development of CRPC by delivering various biomolecules that regulate biological processes in recipient cells. Despite the advancement in treatments, CRPC remains poorly managed, underscoring the urgent need for novel treatment strategies.As research into exosomes continues, they have shown significant potential in the diagnosis and treatment of CRPC.Unlike previous reviews,this review not only provides an overview of exosomes but also comprehensively explores their role in the CRPC tumor microenvironment, angiogenesis, immune escape, metastasis, and drug resistance, with a focus on the potential value of exosomes in the diagnosis and treatment of CRPC.The literature review includes studies published up to June 2024, and the search strategy involved exosomes, CRPC, diagnosis,and treatment using Pubmed.

Construction and validation of a prognostic model for colorectal cancer based on migrasome-related long non-coding RNAs

Background

Colon adenocarcinoma (COAD) is a globally prevalent and deadly malignancy of the digestive system. Recently, migrasomes have gained significant attention as important regulators of tumor cell migration and metastasis. The current research developed a highly accurate prognostic model using migrasome-related long non-coding RNAs (lncRNAs) in COAD, providing new insights for prognostic assessment and immunotherapy of COAD patients.

Methods

RNA sequencing data from COAD patients were acquired from The Cancer Genome Atlas Program (TCGA) database to construct a prognostic lncRNA model based on known migrasome-related genes (MRGs). The model's predictive accuracy was then assessed using concordance index (C-index) analysis, nomograms, principal component analysis, and receiver operating characteristic curves. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to identify significant differences in biological functions and signaling pathways associated with differentially expressed genes in the high-risk subgroup. A comprehensive evaluation of the model incorporated clinical-pathological features, tumor microenvironment, and chemotherapy sensitivity. The expression levels of prognostic genes in COAD patients were validated via quantitative reverse transcription polymerase chain reaction (RT-qPCR). Furthermore, the role of LCMT1-AS1 in colorectal cancer was examined through CCK-8 assays, colony formation assays, and Transwell experiments.

Results

Migrasome-related lncRNAs were identified as robust prognostic predictors for COAD. Multivariate analysis revealed that the risk score derived from these lncRNAs is an independent prognostic factor for COAD. Patients in the low-risk group exhibited significantly longer overall survival (OS) compared to those in the high-risk group. Accordingly, the nomogram prediction model we developed, which integrates clinical features and risk scores, demonstrated excellent prognostic performance. In vitro experiments further showed that LCMT1-AS1 promotes the proliferation and migration of COAD cells.

Evaluation of LncRNAs CBR3-AS1 and PCA3 expression in Gastric cancer and their correlation to clinicopathological variables

BACKGROUND

Gastric cancer (GC) is a multifactorial disease with a high death rate due to the unknown mechanisms involved in the developing, progressing, and late diagnosing GC. Several cancers have been linked to Long non-coding RNAs (lncRNAs), including GC, through differential expression. They play a crucial role in tumorigenesis pathways as modulatory factors, making them intriguing clinical and diagnostic biomarkers for many malignancies. This study's objective is to compare the lncRNAs CBR3-AS1 and PCA3 expression levels in tumoral tissues to marginal tissues and the clinicopathological features of patients.

METHODS AND RESULTS

100 GC patients' tumoral and marginal tissue samples from Tabriz's Valiasr Hospital were gathered for this case-control research. To determine the expression level of PCA3 and CBR3-AS1 lncRNAs in GC, total RNA was extracted, and the qRT-PCR technique was employed. Compared to adjacent marginal tissues, the tumor tissue of patients with GC showed a significant increase in the expression levels of PCA3 and CBR3-AS1 (P < 0.0001). The expression ratio of lncRNA CBR3-AS1 and PCA3 did not significantly correlate with clinicopathological variables. The ROC curve's findings lead to the conclusion that the genes lncRNAs PCA3 and CBR3-AS1, with AUC values of 0.68 and 0.79, respectively, suggest that they could play carcinogenic roles in GC and may act as moderate diagnostic biomarkers for GC.

CONCLUSIONS

In GC, CBR3-AS1 and PCA3 may be utilized as therapeutic targets and prognostic biomarkers, respectively.

Comprehensive analysis of the LINC01122/TPD52 axis as a predictive biomarker in prostate adenocarcinoma

Prostate cancer (PCa) ranks among the most prevalent malignant tumors worldwide. The pivotal role of competitive endogenous RNA (ceRNA) regulatory networks in numerous cancer types has been underscored. However, the specific characteristics of the ceRNA network in PCa remained unknown. This study aims to elucidate the ceRNA regulatory network associated with phosphatase and tensin homolog (PTEN) and to identify potential prognostic markers for PCa. The Cancer Genome Atlas (TCGA) database was employed to extract the expression patterns of long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs). LINC01122-hsa-miR-34c-5p/hsa-miR-449a-TPD52 ceRNA network regarding the prognosis of PCa was explored via bioinformatics analysis. Through correlation analysis, we investigated the LINC01122/TPD52 axis within the ceRNA network, identifying it as a significant clinical prognostic marker for PCa. Subsequent analyses indicated that hypomethylation was responsible for the abnormal upregulation of the LINC01122/TPD52 axis. Furthermore, immune infiltration analysis revealed the impact of the LINC01122/TPD52 axis on the tumor immune microenvironment and the progression of PCa. Finally, a nomogram was constructed to forecast the 1-year, 3-year, and 5-year survival probabilities of PCa patients. In summary, our study demonstrates the significant role of the ceRNA-based LINC01122/TPD52 axis in the progression of PCa and its correlation with prognosis.

Integrative analysis of cuproptosis-related lncRNAs for prognostic risk assessment and tumor immune microenvironment evaluation in laryngeal squamous cell carcinoma

Long non-coding RNAs (lncRNAs) play a pivotal role in tumor prognostic models. This study targets cuproptosis-related lncRNAs in laryngeal squamous cell carcinoma (LSCC) using RNA-seq data from The Cancer Genome Atlas (TCGA)-LSCC. Differentially expressed genes were identified, and Pearson correlation analysis pinpointed cuproptosis-related lncRNAs. Combining clinical data, a prognostic risk model was constructed using LASSO Cox regression and Cox proportional hazards analyses. Nine lncRNAs (LINCO1473, SNHG12, AC007938.3, AC040970.1, AC023669.1, AL158166.2, GIHCG, AC007240.3, and AC011370.1) were identified, with GIHCG showing significant correlation with LSCC prognosis. GIHCG's competing endogenous RNAs (ceRNA) and co-expression networks (CEN) were established, revealing sensitivity to drugs like BMS-509744, YM155, and KU-55933. Silencing of GIHCG inhibited migration, invasion, EMT, and other biological processes in LSCC cells, suggesting GIHCG as a potential therapeutic target. Moreover, METTL16-mediated m6A methylation regulates GIHCG expression. In conclusion, this study successfully established a prognostic model comprising nine cuproptosis-related lncRNAs, accurately predicting LSCC prognosis, and highlighted the crucial role of GIHCG as a novel nucleic acid biomarker in regulating LSCC progression.

Long noncoding RNAs and HPV-related cervical cancer: Uncovering molecular mechanisms and clinical applications

Cervical cancer (CC) is the primary cause of cancer-related mortality among women in developing countries and is the most prevalent disease linked to human papillomavirus (HPV). Over 70 % of CC cases result from persistent infections with high-risk HPV types. The virus typically targets the mucocutaneous epithelium, generating viral particles in mature epithelial cells, which leads to disruptions in normal cell-cycle regulation and promotes uncontrolled cellular proliferation. This unchecked cell division results in the accumulation of genetic damage, contributing to the pathogenesis of CC. While HPV infection is a key etiological factor, the disease's progression also necessitates the involvement of genetic and epigenetic influences. One of the epigenetic regulators, long noncoding RNAs (lncRNAs), are characterized by transcripts exceeding 200 nucleotides. These molecules play crucial roles in various cellular processes, including transcription regulation, RNA metaboli35 per 100,000sm, and apoptosis. Investigating the specific roles of lncRNAs in modulating gene expression related to the oncogenic mechanisms of CC, particularly in the context of high-risk HPV infections, may provide valuable insights for diagnostic and therapeutic advancements. Herein, we first review key molecular mechanisms by which lncRNAs interfere with CC-related HPV development. Then, diagnostic, prognostic, and therapeutic potentials of these lncRNA molecules will be highlighted in depth. The focus of this article is on the role of lncRNAs associated with HPV-related CC, emphasizing the investigation of signaling pathways and their underlying molecular mechanisms. Furthermore, we explore the therapeutic potential and diagnostic relevance of the most significant lncRNAs in the context of CC, thereby highlighting their importance in advancing treatment strategies and improving patient outcomes.

Long noncoding RNA FAM111A-DT promotes aggressiveness of papillary thyroid cancer via activating NF-κB signaling

PURPOSE

Long noncoding RNAs (lncRNAs) play crucial regulatory roles in the tumorigenesis and progression of various cancers. However, the functional roles of lncRNAs in papillary thyroid cancer (PTC) remain unclear. In this study, we investigated the functional role of the lncRNA FAM111A-DT in PTC progression and the underlying mechanisms.

METHODS

Different expression levels of lncRNAs in PTC were compared via analysis of the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Bioinformatics analyses and qRT‒PCR were used to investigate the expression of FAM111A-DT in PTC. Cell proliferation was measured via CCK8, EdU, colony formation, and flow cytometry assays. Cell migration and invasion were examined by wound healing and Transwell assays. Apoptosis was detected via flow cytometry. RNA sequencing, qRT‒PCR, Western blot, immunofluorescence and dual-luciferase reporter assays were performed to assess the underlying mechanisms involved.

RESULTS

FAM111A-DT was highly expressed in PTC and associated with poor prognosis, thyroid dedifferentiation, various clinical features and the BRAFV600E mutation in PTC patients. Overexpression of FAM111A-DT enhanced the proliferation, migration and invasion of PTC cells while reducing their degree of apoptosis. The NF-κB signaling pathway was activated in FAM111A-DT-overexpressing PTC cells. The NF-κB inhibitor PDTC attenuated the promotive effects of FAM111A-DT on aggressive phenotypes and NF-κB pathway activity in PTC cells.

CONCLUSION

FAM111A-DT is upregulated in PTC, and its expression is associated with poor clinical outcomes. FAM111A-DT plays an oncogenic role by, at least partially, activating the NF-κB signaling pathway.

AKT1E17K-Interacting lncRNA SVIL-AS1 Promotes AKT1 Oncogenic Functions by Preferentially Blocking AKT1E17K Dephosphorylation

AKT1E17K is a gain-of-function mutation that constitutively activates the PI3K-AKT pathway. However, how AKT1E17K is regulated in cancer pathogenesis remains elusive. Here, RNA immunoprecipitation sequencing (RIP-seq) is performed to interrogate the AKT1E17K-interacting lncRNAs and identify that SVIL-AS1 preferentially binds to AKT1E17K rather than AKT1WT proteins. It is found that SVIL-AS1 enhances AKT1 phosphorylation and downstream signaling. SVIL-AS1 knockdown dramatically inhibits the growth of AKT1E17K cells in vitro and in vivo. Notably, AKT1 and SVIL-AS1 interaction is AKT1 phosphorylation-dependent. SVIL-AS1 also interacts with PPP2R2A, a subunit of phosphatase PP2A holoenzyme, and blocks the binding of PPP2R2A to AKT1E17K to prevent AKT1 dephosphorylation. Moreover, AKT1E17K cells are not effectively inhibited by the allosteric AKT inhibitor, whereas silencing SVIL-AS1 sensitizes AKT1E17K cells to AKT1 allosteric inhibitor, as well as the PI3Kα inhibitor. In breast cancer tissues, SVIL-AS1 is highly expressed and associated with p-AKT1 level and poor prognosis of patients. Together, the findings discover a novel lncRNA regulator of mutant oncoprotein which preferentially prevents AKT1E17K dephosphorylation. Targeting SVIL-AS1 may help to improve the responses to inhibitors of the PI3K-AKT pathway, especially in AKT1E17K mutant tumors.

Curcumin: Epigenetic Modulation and Tumor Immunity in Antitumor Therapy

Curcumin (turmeric) is the main ingredient of the Chinese herbal turmeric rhizome, used to treat tumors, diabetes, inflammation, neurodegenerative diseases, cardiovascular diseases, metabolic syndrome, and liver diseases. The antitumor effects of curcumin have received even more attention. One of the main mechanisms of the antitumor effects includes inhibition of tumor invasion and migration, induction of tumor cell apoptosis, and inhibition of various cell signaling pathways. It has been found that the antitumor biological activity of curcumin in the body is associated with epigenetic mechanisms. That also implies that curcumin may act as a potential epigenetic modulator to influence the development of tumor diseases. The immune system plays an essential role in the development of tumorigenesis. Tumor immunotherapy is currently one of the most promising research directions in the field of tumor therapy. Curcumin has been found to have significant regulatory effects on tumor immunity and is expected to be a novel adjuvant for tumor immunity. This paper summarizes the antitumor effects of curcumin from four aspects: molecular and epigenetic mechanisms of curcumin against a tumor, mechanisms of curcumin modulation of tumor immunotherapy, reversal of chemotherapy resistance, and a novel drug delivery system of curcumin, which provide new directions for the development of new antitumor drugs.

Epigenetic regulation in oogenesis and fetal development: insights into m6A modifications

The unique physiological structure of women has led to a variety of diseases that have attracted the attention of many people in recent years. Disturbances in the reproductive system microenvironment lead to the progression of various female tumours and pregnancy disorders. Numerous studies have shown that epigenetic modifications crucially influence both oogenesis and foetal development. m6A, a modification at the mRNA level, consists of three parts, namely, writers, erasers, and readers, which are involved in several biological functions, such as the nucleation and stabilisation of mRNAs, thereby regulating the development of reproductive system diseases. In this manuscript, we delineate the constituents of m6A, their biological roles, and advancements in understanding m6A within the maternal-foetal immunological context. In addition, we summarise the mechanism of m6A in gynaecological diseases and provide a new perspective for targeting m6A to delay the progression of reproductive system diseases in clinical practice.

LncRNA FTX promotes colorectal cancer radioresistance through disturbing redox balance and inhibiting ferroptosis via miR-625-5p/SCL7A11 axis

BACKGROUND

Radiotherapy is widely employed in colorectal cancer (CRC) treatment, but the occurrence of radioresistance severely limits the clinical benefit to patients and significantly contributes to treatment failure and recurrent metastasis.

AIM

To explore the role and underlying mechanism of the lncRNA FTX in radiotherapy resistance in CRC.

METHODS

LncRNA FTX expression in colorectal parent cells (HT29 and HCT116) and radioresistant cells (HT29R and HCT116R) was determined by real-time quantitative PCR, and the viability of HT29R-shFTX and HCT116R-shFTX cells under ionizing radiation was evaluated using the cell counting kit-8 assay and colony formation experiment. The levels of glutathione and reactive oxygen species in cells after irradiation were determined, and the association between ferroptosis and lncRNA FTX expression in cancer cells was tested. A dual-luciferase assay was used to validate gene interactions. A xenotransplantation mouse model was established to explore the effects of FTX on the CRC tumor radiosensitivity in vivo.

RESULTS

FTX was upregulated in radioresistant CRC cells, and FTX knockdown inhibited cell survival and increased cell ferroptotic death in response to ionizing radiation. Moreover, lncRNA FTX restricted the SLC7A11 expression by sponging with miR-625-5p, and inhibition of the lncRNA FTX or SLC7A11 significantly increased cellular oxidant levels and DNA damage to ionizing radiation in cancer cells. However, SLC7A11 overexpression reversed the effects of decreased FTX levels on ferroptosis and high oxidation levels in cancer cells exposed to ionizing radiation.

CONCLUSION

Inhibition of the lncRNA FTX/miR-625-5p/SLC7A11 axis can induce ferroptosis and disturb intracellular redox balance, further sensitizing CRC cells to ionizing radiation, suggesting its potential as a therapeutic target for improving CRC response to radiation therapy.

The LncRNA RMST-miR-4295-ITPR1 axis: a key mechanism in regulating autophagy in triple-negative breast cancer cells

BACKGROUND

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with poor prognosis and limited treatment options. Autophagy targeting plays a complex role in tumor resistance. The role of long noncoding RNA (LncRNA) RMST in TNBC progression and its potential involvement in autophagy regulation remain largely unexplored.

METHODS

We performed a bioinformatics analysis using transcriptome sequencing data to identify differentially expressed genes related to autophagy and the LncRNA-miRNA-mRNA axis in TNBC. The effects of the LncRNA RMST-miR-4295-ITPR1 axis on TNBC cell proliferation and migration were investigated using CCK-8, EdU, Transwell, and wound healing assays. Additionally, a series of in vitro experiments, including flow cytometry, transmission electron microscopy, and western blotting, were performed to evaluate the role of the LncRNA RMST-miR-4295-ITPR1 axis in regulating autophagy.

RESULTS

LncRNA RMST competes with ITPR1 mRNA for miR-4295 binding, thereby relieving the miR-4295-mediated suppression of ITPR1 and increasing ITPR1 expression. Overexpression of LncRNA RMST or ITPR1 significantly inhibited TNBC cell proliferation and migration, promoted apoptosis, and enhanced autophagy. Conversely, miR-4295 overexpression reversed these effects, confirming the regulatory role of the LncRNA RMST-miR-4295-ITPR1 axis in autophagy in TNBC.

CONCLUSIONS

Our findings indicate that the LncRNA RMST-miR-4295-ITPR1 axis plays a crucial role in regulating autophagy in TNBC cells. The modulation of this axis may represent a novel therapeutic strategy for inhibiting TNBC progression and overcoming chemoresistance.

LINC00892 as a Prognostic Biomarker in Lung Adenocarcinoma: Role in Immune Infiltration and EMT Suppression

Lung adenocarcinoma (LUAD) is a prevalent and aggressive form of lung cancer with poor prognosis, largely due to late-stage diagnosis and limited therapeutic options. Recent studies suggest that long noncoding RNAs (lncRNAs) play critical roles in cancer progression and immune modulation, emerging as potential therapeutic targets. In this study, we investigated the expression and functional role of LINC00892 in LUAD using RNA sequencing data from The Cancer Genome Atlas (TCGA) and functional assays in vitro and in vivo. We found that LINC00892 is significantly downregulated in LUAD tissues compared to normal tissues, and lower LINC00892 expression correlates with poorer overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI), particularly in younger patients and those with early-stage disease. Bioinformatic analyses revealed that LINC00892 expression is positively correlated with immune cell infiltration, including CD4+ and CD8+ T cells, and negatively correlated with tumor-promoting Th2 cells, suggesting its role in shaping the tumor immune microenvironment. In vitro functional assays showed that LINC00892 overexpression inhibits LUAD cell proliferation, migration, and invasion while promoting apoptosis. Mechanistically, LINC00892 upregulation was found to suppress epithelial-mesenchymal transition (EMT) by increasing E-cadherin expression and decreasing levels of N-cadherin, vimentin, and slug. Additionally, in an in vivo mouse xenograft model, LINC00892 overexpression suppressed tumor growth and metastasis, accompanied by enhanced immune cell infiltration such as CD4+ and CD8+ T cells. Collectively, these findings suggest that LINC00892 acts as a tumor suppressor in LUAD by modulating immune infiltration and EMT, highlighting its potential as a prognostic biomarker and therapeutic target.

The Regulatory Role of NcRNAs in Pyroptosis and Disease Pathogenesis

Non-coding RNAs (ncRNAs), as critical regulators of gene expression, play a pivotal role in the modulation of pyroptosis and exhibit a close association with a wide range of diseases. Pyroptosis is a form of programmed cell death mediated by inflammasomes, characterized by cell membrane perforation, release of inflammatory cytokines, and a robust immune response. Recent studies have revealed that ncRNAs influence the initiation and execution of pyroptosis by regulating the expression of pyroptosis-related genes or modulating associated signaling pathways. This review systematically summarizes the molecular mechanisms and applications of ncRNAs in diseases such as cancer, infectious diseases, neurological disorders, cardiovascular diseases, and metabolic disorders. It further explores the potential of ncRNAs as diagnostic biomarkers and therapeutic targets, elucidates the intricate interactions among ncRNAs, pyroptosis, and diseases, and provides novel strategies and directions for the precision treatment of related diseases.

Predictive model for prognosis, immune microenvironment and drug sensitivity of colon carcinoma based on cuproptosis-related genes

BACKGROUND

Colon cancer is a major cause of morbidity and mortality worldwide. Copper-induced cell death, known as cuproptosis, is a form of apoptosis that has been extensively studied in human diseases and is widely associated with tumor progression, prognosis, and immune response. However, the role of cuproptosis-related genes (CRGs) in the tumor microenvironment (TME) of colon cancer remains unclear.

OBJECTIVE

This study aims to explore the role of cuproptosis-related long non-coding RNAs (lncRNAs) in predicting the prognosis of colon cancer and to establish a risk prediction model based on these lncRNAs to guide clinical decisions and improve patient outcomes.

METHODS

A total of 19 cuproptosis-related genes were collected, and 1330 lncRNAs associated with cuproptosis were identified. Seven cuproptosis-related lncRNAs with prognostic value were selected from The Cancer Genome Atlas (TCGA) database. Using R software (version 4.1.0), the expression levels of the 19 genes were extracted, and the subjects were divided into high- and low-risk subgroups. A risk score model was developed based on cuproptosis-related genes and the seven co-expressed lncRNAs. The dataset was randomly split into a training set and a validation set. Analysis of clinicopathologic features, TME infiltration, and mutations was conducted, and nomogram predictions were validated using calibration plots to assess the predictive accuracy of the model.

RESULTS

The high-risk group had significantly shorter overall survival compared to the low-risk group (P<0.001), and the risk score was an independent prognostic factor (P<0.001). In the training set, the AUC values at 1, 3, and 5 years were 0.666, 0.621, and 0.669, respectively. Furthermore, low-risk patients had a higher survival rate. The genetic markers also correlated with tumor immune cell infiltration, clinical features, and prognosis.

CONCLUSION

This study established a novel method based on cuproptosis-related lncRNAs to predict the prognosis of colon cancer. The model has potential clinical applications in identifying patients sensitive to immunotherapy and antitumor treatments, thereby enhancing precision treatment strategies for colon cancer.

Liver cancer-specific prognostic model developed using endoplasmic reticulum stress-related LncRNAs and LINC01011 as a potential therapeutic target

Liver cancer is a serious malignancy worldwide, and long noncoding RNAs (lncRNAs) have been implicated in its prognosis.It remains unclear how lncRNAs related to endoplasmic reticulum stress (ERS) influence liver cancer prognosis. Here, we analyzed RNA and clinical data from the Cancer Genome Atlas and sourced ERS-related genes from the Molecular Signatures Database. Co-expression analysis identified ERS-related lncRNAs, and Cox regression analysis as well as least absolute shrinkage and selection operator regression highlighted three lncRNAs for a prognostic model. Based on median risk scores, we classified patients into two risk groups. The high-risk group displayed poor prognosis, and this finding was validated in the test set. According to consistency clustering, the patients were assigned to two clusters, and tumor microenvironment scores were computed. Patients with a high mutation burden had worse outcomes. Furthermore, immune infiltration analysis indicated more immune cells and mutations in checkpoint molecules among high-risk individuals. Drug sensitivity varied between the risk groups. LINC01011 was selected for functional assays. Colony formation assay and CCK-8 assay revealed that silencing LINC01011 suppressed liver cancer cell proliferation. Transwell and scratch assays indicated that silencing LINC01011 inhibited liver cancer cell migration. Western blotting assay revealed that inhibiting LINC01011 induced apoptosis and simultaneously inhibited epithelial-mesenchymal transition. These findings confirm the validity of the prognostic model and indicate that LINC01011 could serve as a potential research target.

Frequent dysregulation of multiple circular RNA isoforms with diverse regulatory mechanisms in cancer - Insights from circFNDC3B and beyond: Why unique circular RNA identifiers matter

Circular RNAs (circRNAs) are post-transcriptional regulators generated through backsplicing of pre-mRNAs, primarily comprising exons of host genes. A single host gene may produce multiple circRNA isoforms with distinct structures and sequences. Dysregulated circRNA expression has been implicated in tumorigenesis. This review aims to investigate the selection and regulatory roles of circRNA isoforms in cancer using the extensively studied hsa_circFNDC3B and thirteen other circRNAs as study models. Interrogation of literature and databases, particularly the circBase, confirms that host genes generate a plethora of circRNA isoforms; however, only a small subset of isoforms is validated as dysregulated in tumor tissues. Notably, two or more isoforms of the same circRNA are frequently dysregulated in cancer. Structurally, short isoforms retaining 5'-proximal exons are preferentially selected, but for long host genes, circRNAs may arise from mid- or 3'-regions. We identify dysregulation of seven circFNDC3B isoforms across twelve cancer types and multi-isoforms in nine of the other thirteen circRNAs also in multiple cancers. MicroRNA sponging appears to be the major regulatory mechanism, but possible biased study designs raise concerns. Using circFNDC3B and circZFR as examples, we show inconsistency and inadequacy in circRNA nomenclature in different databases and the literature, underscoring the urgent need for a universally accepted standardized central circRNA database. As an interim measure, we propose guidelines for circRNA nomenclature in journal publications. Our findings caution against indiscriminate clinical use of specific circRNA isoforms as biomarkers or therapeutic targets without further validation.

Development and validation of a novel endoplasmic reticulum stress-related lncRNA signature in laryngeal squamous cell carcinoma

Endoplasmic reticulum stress (ERS) is an intracellular process in which improperly folded proteins lead to a cellular stress response. How endoplasmic reticulum stress contributes to the onset and progression of laryngeal squamous cell carcinoma remains unclear. Our research aimed to find an ERS signature to forecast the prognosis of laryngeal squamous cell carcinoma and to investigate its potential biological functions. LSCC sample data obtained from The Cancer Genome Atlas (TCGA) database were co-expressed with ERS- related genes, and then a prognostic signature on the basis of endoplasmic reticulum stress- related lncRNAs (ERS-related lncRNAs) was constructed by differential analysis and Cox regression analysis. Survival analysis, TMB, consensus cluster analysis, drug sensitivity analysis, immune analysis and clinical drug prediction were carried out on the model. Finally, the function of LHX1-DT was verified by in vitro experiments. From the TCGA-LSCC cohort, 35 significantly different ERS-related lncRNAs were identified. A prognostic signature consisting of three lncRNAs (AC110611.2, LHX1-DT, and AL157373.2) was identified. Kaplan-Meier analysis demonstrated the predictive ability of the model for overall survival. Calibration curves and receiver operating characteristic curves were validated and showed high predictive accuracy. Ultimately, the experimental results verified the expression of LHX1-DT in LSCC.

Novel Biological Strategies for Melanoma Therapy: A Focus on lncRNAs and Their Targeting

Increasing evidence revealed that restoring the correct expression of lncRNAs could have implications in the management of melanoma patients. In this context, here, we aim to dissect the main characteristics of lncRNAs altered in melanoma and their crosstalk with the signaling pathways involved in the progression of this disease. We also highlight the role of nucleic acid-based techniques and natural compounds (i.e., phytochemicals) as a therapeutic tool to increase or silence their expression in cancer cells. Finally, we explore the advances in nanotechnologies as delivery systems to efficiently carry these chemicals into cancer cells, thus limiting their potential off-target effects. The analysis of the literature showed that HOTAIR, MALAT1, and H19 are the oncogenic lncRNAs most studied in melanoma, while MEG3 is an important tumor suppressor decreased in this cancer. The aberrant expression of these lncRNAs affects several hallmarks of cancer, e.g., proliferation, motility, and epithelial to mesenchymal transition, promoting the melanoma plasticity and drug resistance. In this frame, siRNA, antisense oligonucleotide, and CRISPR-Cas9 genome editing appear to be the most effective nucleic acid strategies to restore the physiologic expression of lncRNA, while curcumin, resveratrol, and quercetin are the main phytochemicals able to target and influence the expression of lncRNAs altered in cancer. Overall, this study provides a comprehensive overview regarding the role of lncRNAs in the phenotype plasticity of melanoma cells and their potential targeting using RNA-based therapy and natural products.

Bone metastases of prostate cancer: Molecular mechanisms, targeted diagnosis and targeted therapy (Review)

Prostate cancer (PCa) is second only to lung cancer in terms of death among men worldwide. Advanced PCa frequently results in bone metastases, which occur in ~90% of patients and frequently result in severe skeleton‑related events. Currently, the treatment for this disease is limited to alleviating its clinical symptoms and cannot provide a complete cure. Therefore, the development of novel treatment strategies is particularly important. In recent years, numerous novel strategies for the diagnosis and treatment of PCa have emerged, resulting in good clinical efficacy. For example, strategies targeting prostate specific membrane antigen, poly ADP‑ribose polymerase and programmed cell death protein 1 have been applied to PCa‑induced bone metastasis, and have shown initial efficacy and great potential. Therefore, understanding the molecular mechanisms underlying the formation of bone metastases in patients with PCa is of importance for the effective management of this disease. The purpose of the present review is to comprehensively outline the roles of protein‑coding genes and non‑coding RNAs in the development of bone metastases of PCa to elucidate their significance in the management of PCa. The aim is to offer clinicians and researchers a comprehensive understanding of this topic.

The Long Noncoding RNA Gall Bladder Cancer-Associated Suppressor of Pyruvate Carboxylase Inhibits the Proliferation, Migration, and Invasion of Colorectal Cancer Cells and Induces Their Apoptosis

This study aimed to determine the role of the long noncoding RNA (lncRNA) gall bladder cancer-associated suppressor of pyruvate carboxylase (SOD2-1) in the progression of colorectal cancer (CRC). A total of 23 pairs of specimens, including CRC tissues and adjacent normal tissues, were collected, and the expression of lncRNA SOD2-1 (lnc-SOD2-1) was measured. lnc-SOD2-1 function was examined using HCT15 and HCT116 cells. A lnc-SOD2-1 overexpression vector was designed and transfected into both cell lines. MTS and colony formation assays were used to determine cell viability. Flow cytometry and terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end-labeling assays were performed to measure apoptosis. Cell migration and invasion were evaluated using the Transwell assay. Migration and invasion markers were validated using quantitative reverse transcription-polymerase chain reaction and western blot analysis. The results indicated that the expression of lnc-SOD2-1 was downregulated in CRC tissues. lnc-SOD2-1 overexpression evidently decreased cell viability and led to the formation of fewer cell colonies. lnc-SOD2-1 overexpression induced ~ twofold higher apoptosis than the control group. lnc-SOD2-1 overexpression reduced the proportion of migratory and invasive cells to 50% and 75% of the control group, respectively. lnc-SOD2-1 overexpression significantly decreased the expression of matrix metalloproteinase-2 and -9. In conclusion, lnc-SOD2-1 may act as a tumor suppressor that inhibits the proliferation, migration, and invasion of CRC cells and induces their apoptosis.

Dysregulation of GAS5-miRNA-Mediated Signaling Pathways in Cancer Pathobiology: A Comprehensive Exploration of Pathways Influenced by this Axis

The long non-coding RNA Growth Arrest-Specific 5 (GAS5) is pivotal in modulating key signaling pathways by functioning as a molecular sponge for microRNAs (miRNAs). GAS5 is notably recognized for its antitumor properties, primarily through its ability to sequester oncogenic miRNAs, thereby influencing critical pathways such as p53, Wnt/β-catenin, and PI3K/Akt, all of which are integral to cell proliferation, apoptosis, and metastasis. The disruption of GAS5-miRNA interactions has been implicated in various malignancies, reinforcing its potential as both a biomarker and a therapeutic target. This paper delves into the intricate signaling cascades affected by GAS5-miRNA interactions and thoroughly investigates the diagnosis and treatment prospects associated with GAS5. Moreover, it addresses both the challenges and opportunities for translational applicability of these findings in clinical environments. The study emphasizes GAS5's significance within the cancer molecular landscape and posits that precise modulation of GAS5-miRNA interactions could catalyze transformative developments in cancer diagnostics and therapeutic approaches. This comprehensive review not only highlights the critical role of non-coding RNAs in cancer biology but also aims to lay the groundwork for future investigations aimed at harnessing these insights for therapeutic interventions.

CTCF enhances pancreatic cancer progression via FLG-AS1-dependent epigenetic regulation and macrophage polarization

CCCTC-binding factor (CTCF) regulates chromatin organization and is upregulated in pancreatic ductal adenocarcinoma (PDAC). We found that CTCF interacts with HNRNPU through a FLG-AS1-dependent mechanism, facilitating the recruitment of EP300 and activation of the m6A reader IGF2BP2. This activation promotes histone lactylation at the promoter region of IGF2BP2 stimulating the proliferation of PDAC cells. IGF2BP2 enhanced the mRNA stability of CSF1 and MYC. Moreover, FLG-AS1 directly interacts with HNRNPU to modulate alternative splicing of CSF1, thus promoting the M2 polarization of tumor associated macrophages (TAMs) in PDAC. The results indicated that CTCF-induced oncogenic modification of histone lactylation, m6A and alternative spilcing as multi-regulation modes of TAMs reprogramming in PDAC and identifies CTCF as a potential therapeutic target for PDAC immunotherapy whose inhibition M2 polarization through the IGF2BP2/CSF1/CSF1R axis. Curaxin combined with gemcitabine treatment has shown promising antitumor efficacy against PDAC.

N4-Acetylcytidine-Mediated CD2BP2-DT Drives YBX1 Phase Separation to Stabilize CDK1 and Promote Breast Cancer Progression

Long noncoding RNAs (lncRNAs) play critical roles in the initiation and progression of breast cancer. However, the specific mechanisms and biological functions of lncRNAs in breast cancer remain incompletely understood. Bioinformatics analysis identifies a novel lncRNA, CD2BP2-DT, that is overexpressed in breast cancer and correlates with adverse clinicopathological features and poor overall survival. Both in vivo and in vitro experiments demonstrate that CD2BP2-DT promotes proliferation of breast cancer cells. Mechanistically, NAT10 mediates the N4-acetylcytidine (ac4C) modification of CD2BP2-DT, enhancing its RNA stability and expression. More importantly, CD2BP2-DT enhances the stability of CDK1 mRNA by mediating YBX1 phase separation, thereby promoting the proliferation of breast cancer cells. In conclusion, the lncRNA CD2BP2-DT is identified as a crucial driver of breast cancer cell proliferation through the YBX1/CDK1 axis, highlighting its potential as a promising biomarker and therapeutic target for breast cancer.

Analysis of Long Noncoding RNA in Fatty Acid Metabolism to Identify Prognostic Markers and Predict Immunotherapy Response in Low-Grade Glioma

BACKGROUND

Low-grade gliomas (LGGs) are notorious for their difficult early-stage diagnosis, limited treatment options, and poor prognosis, making them a focal point in cancer research. Long noncoding RNAs (lncRNAs) have been identified as regulators of metabolic reprogramming in tumor cells, offering new directions for LGG treatment.

METHODS

This study employed data from The Cancer Genome Atlas, focusing on key fatty acid metabolism-related lncRNA. A risk scoring model was developed using univariate/multifactorial and least absolute shrinkage and selection operator Cox regression. Additionally, the study evaluated the role of these prognostic lncRNAs in LGG progression by assessing associations between LGG immune markers and tumor drug resistance. Finally, functional enrichment analysis highlighted the molecular roles of these lncRNAs.

RESULTS

In this study, a total of 14 prognostic lncRNAs were obtained. The risk model demonstrated excellent validity and reliability, making it a superior predictor of prognosis among patients with varying LGG risks. Among the identified lncRNAs, GHET-1 was notably associated with LGG sensitivity to current chemotherapy options and might be a crucial lncRNA affecting LGG progression. High-risk patients exhibited T-helper cell-mediated immunosuppression, potentially paving new paths for future LGG immunotherapy.

CONCLUSIONS

Focusing on lncRNA regulation and fatty acid metabolism reprogramming, this study established an innovative prognostic prediction model for LGGs, showing outstanding validity and reliability. The findings offer new molecular and cellular targets for the future development of LGG treatments.

Gene and transcript expression patterns, coupled with isoform switching and long non-coding RNA dynamics in adipose tissue, underlie the longevity of Ames dwarf mice

Our study investigates gene expression in adipose tissue of Ames dwarf (df/df) mice, whose deficiency in growth hormone is linked to health and extended lifespan. Recognizing adipose tissue influence on metabolism, aging, and related diseases, we aim to understand its contribution to the health and longevity of df/df mice. We have identified gene and transcript expression patterns associated with critical biological functions, including metabolism, stress response, and resistance to cancer. Intriguingly, we identified genes that, despite maintaining unchanged expression levels, switch between different isoforms, impacting essential cellular functions such as tumor suppression, oncogenic activity, ATP transport, and lipid biosynthesis and storage. The isoform switching is associated with changes in protein domains, retention of introns, initiation of nonsense-mediated decay, and emergence of intrinsically disordered regions. Moreover, we detected various alternative splicing events that may drive these structural alterations. We also found changes in the expression of long non-coding RNAs (lncRNAs) that may be involved in the aging process and disease resistance by regulating crucial genes in survival and metabolism. Through weighted gene co-expression network analysis, we have linked four lncRNAs with 29 genes, which contribute to protein complexes such as the Mili-Tdrd1-Tdrd12 complex. Beyond safeguarding DNA integrity, this complex also has a wider impact on gene regulation, chromatin structure, and metabolic control. Our detailed investigation provides insight into the molecular foundations of the remarkable health and longevity of df/df mice, emphasizing the significance of adipose tissue in aging and identifying new avenues for health-promoting therapeutic strategies.

Construction of a Prognostic Model for Cervical Cancer Related to lncRNA Based on Differential Co-expression Network and Functional Study of Key Gene EGFR-AS1

Cervical cancer is a common gynecological malignancy, and the average age of onset is decreasing gradually. Therefore, an effective predictive model is urgently needed to improve the personalized treatment of cervical cancer patients. Long non-coding RNAs (lncRNAs) play crucial roles in the occurrence, development, and prognosis of malignant tumors. In this study, we used cervical cancer multi-omics data and single-cell sequencing data for analysis, and established a 33-lncRNA-CESC model by using the random forest algorithm in ensemble learning and mRNA and lncRNA co-expression network technology. The results demonstrated that the model exhibited strong discriminative ability, accuracy, and clinical utility. Furthermore, we investigated the relationship between the model and immune cell infiltration. Enrichment analysis revealed associations between the model and cellular proliferation as well as epidermal growth factor receptor (EGFR) signaling pathways. Subsequently, attention was directed toward the gene EGFR-AS1 in the model, which was identified within the co-expression network and exhibited a significant association with patient prognosis. Additionally, EGFR-AS1 was found to be specifically associated with FAM83B. Analysis of single-cell data confirmed that FAM83B plays a role in the late stage of cervical cancer development mainly through the EGFR signaling pathway. Functional experiments showed that knockdown of either EGFR-AS1 or FAM83B inhibited cervical cancer cell proliferation and migration capabilities, and the phosphorylated ERK and AKT levels. In addition, there was a mutual regulatory effect between EGFR-AS1 and FAM83B expression. In conclusion, this study identifies that EGFR-AS1 served as a key factor in our 33-lncRNA-CESC model and potentially interacted with FAM83B to regulate the EGFR pathway which significantly impacting cervical cancer development.

D-bait: A siDNA for regulation of DNA-protein kinases against DNA damage and its implications in cancer

siDNA fragments, also called Dbait and Pbait, are small DNA oligonucleotides of 30-32 base pairs that cause impairment in DNA repair pathways. Like siRNA and miRNA molecules, which lead to the degradation of mRNA molecules through the Argonaute and Drosha machinery, respectively, Dbait molecules act as false DNA damage signals and trigger and exhaust the DNA repair machinery. In normal cells with no significant DNA damage, the influence of these molecules is negligible. However, in cancer, when there is heavy DNA damage due to replication and anticancer therapies, the cancer cell is heavily dependent on DNA repair proteins to keep the genome intact and limit breaks. This phenomenon primarily occurs during radiation therapy, as significant DNA damage surpasses several DNA repair mechanisms, causing an accumulation of unrepaired lesions and ultimately leading to cell death. This review explores the therapeutic capacity of siDNA molecules in cancer treatment by stimulating the repair mechanisms in cells that depend on DNA repair pathways. For aggressive malignancies such as glioblastoma, prostate cancer, and colorectal cancer, the use of siDNA as a radiosensitizer, especially when combined with other treatments, increases the vulnerability of tumor cells to radiation-induced DNA damage, hence potentially enhancing therapy results.

Comprehensive identification of a migrasomes-associated long non-coding RNA signature to predict the prognosis and treatment options in colon adenocarcinoma

BACKGROUND

Migrasomes, recently discovered cellular substructures, may play a crucial role in cancer progression, treatment response, and prognosis. However, the prognostic value of migrasome-associated long non-coding RNAs (lncRNAs) in colon adenocarcinoma (COAD) remains unexplored.

METHODS

RNA-seq data from 459 COAD patients, including clinical characteristics and outcome information, were obtained from The Cancer Genome Atlas. A risk model was constructed through co-expression analysis of migrasome genes and lncRNAs, followed by Cox regression and least absolute shrinkage and selection operator analysis to identify prognostic lncRNAs. Functional enrichment analyses were performed to elucidate underlying biological mechanisms. Immune landscape characterization utilized ESTIMATE, CIBERSORT, Tumor Immune Estimation Resource (TIME), and single-sample Gene Set Enrichment Analysis (ssGSEA). Drug sensitivity analysis was conducted for select therapeutic agents.

RESULTS

Nine prognostic lncRNAs (AC010463.3, AL590483.4, AP005264.1, ZEB1-AS1, AC104088.1, PRKAR1B-AS2, AC009315.1, SUCLG2-AS1, and AC006111.2) were identified and incorporated into a risk model. Low-risk patients demonstrated significantly improved survival outcomes. The model exhibited independent prognostic capability, with AUCs of 0.783, 0.749, and 0.713 for one-, three-, and five-year survival, respectively, in the training cohort. High-risk patients displayed reduced overall survival and elevated tumor mutation burden. Additionally, these patients showed decreased sensitivity to therapeutic agents, including Oxaliplatin, Irinotecan, and 5-Fluorouracil.

CONCLUSION

Our novel migrasome-associated lncRNA signature demonstrates robust predictive capacity for both prognosis and chemotherapeutic sensitivity in COAD, potentially facilitating personalized treatment strategies and improved patient management.

Identification of mitochondrial permeability transition-related lncRNAs as quantitative biomarkers for the prognosis and therapy of breast cancer

Breast cancer (BC) continues to pose a global health threat and presents challenges for treatment due to its high heterogeneity. Recent advancements in the understanding of mitochondrial permeability transition (MPT) and the regulatory roles of long non-coding RNAs (lncRNAs) offer potential insights for the stratification and personalized treatment of BC. Although the association between MPT and lncRNAs has not been widely studied, a few research studies have indicated a regulatory impact of lncRNAs on MPT, further deepening the understanding of the tumor. To identify reliable biomarkers associated with MPT for managing BC, bulk RNA-seq data of MPT-related lncRNAs acquired from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) project were utilized to assess BC patients. A scoring system, termed the MPT-related score (MPTRscore), was developed using LASSO-Cox regression on data from 1,029 BC patients from TCGA-BRCA. Meanwhile, the superior prognostic accuracy of the MPTRscore was demonstrated by comparing it with biomarkers, including PAM50 subtyping for standardization. Subsequently, a clinical prediction model was created by incorporating the MPTRscore and clinical variables. This analysis revealed two distinct MPTRscore groups characterized by different biomolecular processes, tumor microenvironment (TME) patterns, and clinical outcomes. The MPTRscore was further investigated through unsupervised consensus clustering of TCGA-BRCA based on MPTRscore-related prognostic genes. Additionally, the MPTRscore was identified as an independent prognostic factor for BC and showed guiding utility in immunotherapy and chemotherapy response. Specifically, patients with a low MPTRscore exhibited better prognosis and treatment responses compared to those with a high MPTRscore. Significantly, the relevance of clustering results and MPTRscore was found to be mediated by lncRNA transcript RP11-573D15.8-018. In conclusion, MPTRscore-related clusters were identified in BC, and an integrative score was developed as a biomarker for predicting BC prognosis and therapeutic response. Additionally, molecular interactions underlying the relationship between MPTRscore-related clusters and MPTRscore were uncovered, proving insights for BC stratification. These findings may aid in prognosis determination and therapeutic decision-making for BC patients.

Non-coding RNAs as key regulators of epithelial-mesenchymal transition in breast cancer

This study examines the critical role of non-coding RNAs (ncRNAs) in regulating epithelial-mesenchymal transition (EMT) in breast cancer, a prevalent malignancy with significant metastatic potential. EMT, wherein cancer cells acquire mesenchymal traits, is fundamental to metastasis. ncRNAs-such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs)-modulate EMT by influencing gene expression and signaling pathways, affecting cancer cell migration and invasion. This review consolidates recent findings on ncRNA-mediated EMT regulation and explores their diagnostic and therapeutic potential. Specifically, miRNAs inhibit EMT-related transcription factors, while lncRNAs and circRNAs regulate gene expression through interactions with miRNAs, impacting EMT progression. Given the influence of ncRNAs on metastasis and therapeutic resistance, advancing ncRNA-based biomarkers and treatments holds promise for improving breast cancer outcomes.

A novel prognostic signature based on m5C‑related LncRNAs and its immunological characteristics in colon adenocarcinoma

BACKGROUND

Colon adenocarcinoma (COAD) has high mortality rates due to frequent resistance to treatment. 5-methylcytosine (m5C) is a crucial epigenetic modification of RNA, closely associated with tumorigenesis in various cancers. This study focuses on developing an m5C-related long non-coding RNA (lncRNA) signature to predict prognosis and explore potential therapeutic targets.

METHODS

Using data from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO), we analyzed 18 m5C regulatory genes and their associated lncRNAs in COAD samples. Prognostic lncRNAs were identified through univariate Cox regression, and a risk model was constructed through LASSO regression analyses. Kaplan-Meier survival and receiver operating characteristic analyses were employed to validate the prognostic ability of the signature. Additionally, functional enrichment and immune infiltration analyses were conducted to investigate underlying biological pathways and immune characteristics of the risk groups. Tumor mutation burden and drug sensitivity analyses were also performed. Functional validation of NR2F2-AS1 was conducted through in vitro experiments.

RESULTS

We established a risk score signature comprising six lncRNAs associated with m5C regulators. Patients were classified into high- and low-risk groups based on the median risk score. This prognostic signature demonstrated significant accuracy and was independent of other clinical features. Immune cell infiltration analysis revealed correlations between the risk signature and various immune cell subtypes. Drug sensitivity analysis indicated the potential therapeutic value of our prognostic signature. Functional experiments confirmed that NR2F2-AS1 acts as a risk factor in the proliferation of colon cancer cells.

CONCLUSIONS

The m5C-related lncRNA signature serves as a reliable prognostic indicator for colon adenocarcinoma and provides new insights into the tumor immune microenvironment.

Analysis of expression characteristics of ferroptosis-related lncRNAs in gastrointestinal cancer patients in Asia

BACKGROUND

Asian cancer patients have become the highest morbidity and mortality group, and gastrointestinal tumors account for the majority of them, so it is urgent to find effective targets. Therefore, ferroptosis-related lncRNAs models were established to predict the prognosis and clinical immune characteristics of GI cancer.

METHODS

RNA sequencing and clinical data were collected from the TCGA database (LIHC, STAD, ESCA, PAAD, COAD, CHOL, and READ) of patients with gastrointestinal cancer in Asia. Download ferrodroptosis genes from FerrDb. Through R language, differential genes were identified, prognostic related LncRNAs were screened, and risk scores were obtained by risk formula to build models. Survival analysis, risk heat map, COX regression and ROC were used to evaluate the risk model. Establish Nomogram and clinically relevant heat maps. GSEA software was used to analyze gene enrichment and immune-related characteristics in high and low risk groups. LncRNA expression was validated through paired sample differential analysis and qRT-PCR, and the drug sensitivity of genes was also analyzed.

RESULTS

The transcriptome data of 297 cases and clinical data of 322 cases were downloaded from TCGA, and the intersection of ferroptosis-related genes were obtaine. Cox analysis revealed 48 ferroptosis-related LncRNAs associated with prognosis. Through survival analysis, risk heatmap, COX regression and ROC, it was found that the risk model was highly accurate and efficient in predicting prognosis. KEGG-related GSEA enrichment analysis showed that 12 related pathways were significantly expressed in the low-risk group. Four immune-related functions were significantly higher in the high-risk group than in the low-risk group, and the expression of all immune checkpoints were significantly higher in the high-risk group than in the low-risk group. The three LncRNAs in the model exhibited varying expression levels across different tumors and obtained drug sensitivity data.

CONCLUSIONS

Our results reveal innovative and strong evidence that ferroptosis-related lncRNAs can be used as biomarkers for the treatment and prognosis of Asian GI cancer.

Development of LncRNA Biomarkers in Extracellular Vesicle of Amniotic Fluid Associated with Antenatal Hydronephrosis

Background: Antenatal hydronephrosis (ANH) is the most common congenital renal and urinary tract anomaly, and parenchymal damage and renal fibrosis due to pathological hydronephrosis are the main causes of end-stage renal disease in children and chronic kidney disease in adults. At present, there is no validated biomarker for ANH, and diagnostic criteria other than prenatal ultrasonography (US) assessment are lacking. Therefore, we assessed to determine if biomarkers extracted from amniotic fluid small extracellular vesicles (sEVs) might be used as ANH diagnosis. Methods: With congenital ureteropelvic junction obstruction (UPJO) as the ultimate diagnosis, 10 pregnant women with Grade III-IV ANH and 10 normal pregnant women were recruited. The sEVs were extracted from amniotic fluid supernatant of all samples. Transcriptomic sequencing of sEVs in the discovery cohort identified the differential expression profiles for ANH. The known differentially expressed lncRNAs (DE-lncRNAs) were assessed by qRT-PCR in the validation cohort. Results: We explored the global RNA expression in sEVs from amniotic fluid. The differential expression profiles of both mRNAs and lncRNAs were related to fetal kidney development. Six known DE-lncRNAs were identified for ANH, and three of those with high expression were verified in more ANH samples. In particular, the upregulated LINC02863 and its target genes were associated with renal development and morphogenesis. The four predicted novel lncRNAs in high expression were also related to mesenchymal morphogenesis and the STAT3 signaling pathway and may play roles in ANH. Conclusions: We identified differentially expressed RNAs of all species in the sEVs from amniotic fluid, and the validated known DE-lncRNAs might serve as promising diagnostic biomarkers for ANH.

Prognostic modeling of disulfidptosis gene-associated lncRNAs aids in identifying the tumor microenvironment and guiding the selection of therapy

INTRODUCTION

Gliomas, a type of malignant tumor, are marked by a short survival period and an unfavorable prognosis. Disulfide stress, which arises from an overabundance of intracellular cystine, can initiate disulfidoptosis, an emerging form of cell death. The link between gliomas and disulfidoptosis has not been extensively explored. This study breaks new ground by investigating the correlation between glioma prognosis and lncRNAs associated with disulfidoptosis, with the aim of improving glioma treatment strategies.

METHODS

We analyzed 10 long non-coding RNAs (lncRNAs) co-expressed with disulfidoptosis genes, retrieved clinical information and gene expression profiles from glioma and normal groups in the TCGA database, and developed a prognostic model for lncRNAs based on this data. The receiver operating characteristic curve (ROC) was used to evaluate and validate the model's reliability. Furthermore, the Kaplan-Meier survival curve was employed to assess the disparity in overall survival (OS) among patients with varying risk scores. We also examined the tumor microenvironment (TME), immune cell infiltration, immune-related functions, tumor mutational burden (TMB), and OncoPredict in samples with differing risk scores. To confirm the expression variations of genes associated with prognostic models in cell lines, quantitative polymerase chain reaction (qPCR) was employed.

RESULTS

Eleven long non-coding RNAs (lncRNAs) were identified for constructing prognostic models by analyzing lncRNAs associated with disulfidoptosis genes using Cox regression and LASSO regression analyses. The study's findings indicate that these 11 key lncRNAs serve as independent predictors of overall survival (OS) in glioma patients. Moreover, the frequency with which patients of varying risk scores opt for immune checkpoint blockade (ICB) therapy and chemotherapy not only differs but also their responses to these treatments are significantly distinct, suggesting that the risk score could be a predictive factor for treatment response.

CONCLUSIONS

This research sheds light on the characteristics of disulfidoptosis in glioma, revealing that patterns of disulfidoptosis in patients can be effectively assessed using a risk score. Consequently, the judicious application of this prognostic model can significantly inform clinical treatment strategies and precision medicine for glioma, potentially improving patient outcomes.