The Role of Non-coding RNAs in Oncology

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.

Exploring the roles and clinical potential of exosome-derived non-coding RNAs in glioma

Non-coding accounts for 98 %-99 % of the human genome and performs many essential regulatory functions in eukaryotes, involved in cancer development and development. Non-coding RNAs are abundantly enriched in exosomes, which play a biological role as vectors. Some biofunctional non-coding RNAs are specifically designed as exosomes for the treatment of cancers such as glioma. Glioma is one of the most common primary tumors within the skull and has varying degrees of malignancy and histologic subtypes of grades I-IV. Gliomas are characterized by high malignancy and an abundant blood supply due to rapid cell proliferation and vascularization, often with a poor prognosis. Exosomal non-coding RNAs can be involved in the tumorigenesis process of glioma from multiple directions, such as angiogenesis, tumor proliferation, metastatic invasion, immune evasion, apoptosis, and autophagy. Therefore, non-coding RNAs in exosomes are suitable as markers or therapeutic targets for early diagnosis of diseases and for predicting the prognosis of a variety of diseases. Regulating exosome production and the level of exosomal non-coding RNA expression may be a new approach to prevent or eliminate glioma. In this review, we review the origin and characteristics of exosomal non-coding RNAs, and introduce the functional studies of exosomal non-coding RNAs in glioma and their potential clinical applications, in order to broaden new ideas for the treatment of glioma.

tRF-23-R9J89O9N9:A novel liquid biopsy marker for diagnosis of hepatocellular carcinoma

BACKGROUND

Non-coding small RNA, specifically tRNA-derived small RNAs (tsRNAs), are readily detectable in cancer patients, exhibit remarkable stability, and are present in high abundance. They play a significant role in tumor development. However, the clinical significance of serum tsRNAs in hepatocellular carcinoma (HCC) remains poorly understood. In this study, we explored the impact of a novel tsRNA, named tRF-23-R9J89O9N9, in the adjuvant diagnosis, disease monitoring, and prognosis assessment of HCC.

METHODS

The tRF-23-R9J89O9N9 was identified as the target molecule through screening the The Cancer Genome Atlas(TCGA) database. Its expression levels were measured using qRT-PCR. Various methods, including agarose gel electrophoresis, Sanger sequencing, gradient dilution experiments, room temperature stability tests, and repeated freeze-thaw assessments, were employed to evaluate the performance of tRF-23-R9J89O9N9. The correlation between tRF-23-R9J89O9N9 levels and clinicopathological parameters was analyzed using the χ2 test. The diagnostic value of tRF-23-R9J89O9N9 in HCC was assessed with ROC curve analysis, while the prognostic value was evaluated using Kaplan-Meier curves.

RESULTS

Serum tRF-23-R9J89O9N9 expression levels were significantly elevated in HCC patients, while levels in postoperative patients were restored to those of healthy subjects. Additionally, the expression of tRF-23-R9J89O9N9 related to TNM stage(P = 0.009), lymph node metastasis(P＜0.0001), and degree of differentiation(P＜0.0001). Furthermore, the combination of AFP, PIVKA-II, and CEA greatly improved the diagnostic value for HCC. Serum tRF-23-R9J89O9N9 was also identified as a potential biomarker for dynamic monitoring and prognosis of HCC.

CONCLUSIONS

tRF-23-R9J89O9N9 may regard as a potential novel biomarker for the adjuvant diagnosis of HCC.

Targeting ncRNAs to overcome metabolic reprogramming‑mediated drug resistance in cancer (Review)

The emergence of resistance to antitumor drugs in cancer cells presents a notable obstacle in cancer therapy. Metabolic reprogramming is characterized by enhanced glycolysis, disrupted lipid metabolism, glutamine dependence and mitochondrial dysfunction. In addition to promoting tumor growth and metastasis, metabolic reprogramming mediates drug resistance through diverse molecular mechanisms, offering novel opportunities for therapeutic intervention. Non‑coding RNAs (ncRNAs), a diverse class of RNA molecules that lack protein‑coding function, represent a notable fraction of the human genome. Due to their distinct expression profiles and multifaceted roles in various cancers, ncRNAs have relevance in cancer pathophysiology. ncRNAs orchestrate metabolic abnormalities associated with drug resistance in cancer cells. The present review provides a comprehensive analysis of the mechanisms by which metabolic reprogramming drives drug resistance, with an emphasis on the regulatory roles of ncRNAs in glycolysis, lipid metabolism, mitochondrial dysfunction and glutamine metabolism. Furthermore, the present review aimed to discuss the potential of ncRNAs as biomarkers for predicting chemotherapy responses, as well as emerging strategies to target ncRNAs that modulate metabolism, particularly in the context of combination therapy with anti‑cancer drugs.

HHLA3 Silencing Suppresses KRAS-Mutant Non-Small-Cell Lung Cancer Cell Progression Through Triggering MYEOV-Mediated Ferroptosis

KRAS mutation is one of the most common mutational events in non-small-cell lung cancer (NSCLC). However, due to the complex signaling pathways and high biological heterogeneity of KRAS-mutant NSCLC, the current clinical treatment for patients with KRAS mutations still faces many difficulties. The oncogenic effector in KRAS-mutant NSCLC was screened using GEO data sets. CCK-8, colony formation, transwell, and flow cytometry were conducted to assess the malignant phenotype of KRAS-mutant NSCLC cells. The indicators intracellular Fe2+, ROS, GSH, and MDA levels were employed to reflect the ferroptosis of cells. The mechanism of myeloma overexpressed (MYEOV) in KRAS-mutant NSCLC was explored from the perspective of noncoding RNA (ncRNA) and validated by rescue experiments. MYEOV presented a high expression trend in KRAS-mutant NSCLC specimens. MYEOV silencing effectively repressed the malignant phenotype and promoted ferroptosis of NSCLC cells carrying KRAS mutations. Based on bioinformation analysis and a series of rescue experiments, we established the HHLA3/miR-139-5p/MYEOV regulatory network in KRAS-mutant NSCLC cells and disclosed that HHLA3 served as a molecular sponge for miR-139-5p to regulate MYEOV expression. The mechanism of MYEOV and its ncRNA network affecting the progression of KRAS-mutant NSCLC revealed in this study intends to provide a theoretical basis for KRAS-mutant NSCLC treatment.

Exosomal circRNAs: key modulators in breast cancer progression

Breast cancer (BC) poses significant challenges globally, necessitating a deeper understanding of its complexities. Exosomes are cell-specific secreted extracellular vesicles of interest, characterized by a lipid bilayer structure. Exosomes can carry a variety of bioactive components, including nucleic acids, lipids, amino acids, and small molecules, to mediate intercellular signaling. CircRNAs are a novel class of single-stranded RNA molecules, characterized by a closed-loop structure. CircRNAs mainly exert ceRNA functions to intricately modulate gene expression and signaling pathways in breast cancer, influencing tumor progression and therapeutic responses. The unique packaging of circRNAs within exosomes serves as novel genetic information transmitters, facilitating communication between BC cells and microenvironmental cells, thereby regulating critical aspects of BC progression, immune evasion, and drug resistance. Besides, exosomal circRNAs possess the capabilities of serving as diagnostic and therapeutic biomarkers of BC, due to their stability, specificity, and regulatory roles in tumorigenesis and metastasis. Therefore, this review aims to elucidate the novel roles and mechanisms of exosomal circRNAs in BC progression, as well as their potential for diagnosis and therapeutics. The ongoing investigations of exosomal circRNAs will potentially revolutionize treatment paradigms and improve patient outcomes of BC.

Plasma-Derived Small Extracellular Vesicles miR- 182 - 5p Is a Potential Biomarker for Diagnosing Major Depressive Disorder

Depression, particularly major depressive disorder (MDD), is a debilitating neuropsychiatric condition characterized by high disability rates, primarily driven by chronic stress and genetic predispositions. Emerging evidence highlights the critical role of microRNAs (miRNAs) in the pathogenesis of depression, with plasma-derived small extracellular vesicles (sEVs) emerging as promising biomarkers. In this study, we collected peripheral blood plasma samples from patients diagnosed with MDD, as assessed by the Hamilton Depression Rating scale, alongside healthy individuals serving as controls. Plasma-derived sEVs were isolated via ultracentrifugation, followed by high-throughput sequencing of miRNAs encapsulated within sEVs, and finally image acquisition and differential expression analysis. Our results revealed a significant elevation of miR-182-5p in plasma-derived sEVs from MDD patients compared to healthy controls, a finding further validated in chronic mild stress (CMS) models. Further analysis suggested that miRNAs encapsulated within sEVs may influence depression onset and progression by modulating hypothalamic-pituitary-adrenal (HPA) axis activity. These findings underscore the potential of miRNAs and their target genes as novel biomarkers, offering improved diagnostic accuracy and therapeutic efficacy for MDD.

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.

An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation

Cancer cells frequently upregulate ribosome production to support tumorigenesis. While small nucleolar RNAs (snoRNAs) are critical for ribosome biogenesis, the roles of other classes of noncoding RNAs in this process remain largely unknown. Here, we performed CRISPR interference (CRISPRi) screens to identify essential long noncoding RNAs (lncRNAs) in renal cell carcinoma (RCC) cells. This revealed that an alternatively spliced isoform of lncRNA colorectal neoplasia differentially expressed (CRNDE) containing an ultraconserved element (UCE), referred to as CRNDEUCE, is required for RCC cell proliferation. CRNDEUCE localizes to the nucleolus and promotes 60S ribosomal subunit biogenesis. The UCE of CRNDE functions as an unprocessed C/D box snoRNA that directly interacts with ribosomal RNA precursors. This facilitates delivery of eukaryotic initiation factor 6 (eIF6), a key 60S biogenesis factor, which binds to CRNDEUCE through a sequence element adjacent to the UCE. These findings highlight the functional versatility of snoRNA sequences and expand the known mechanisms through which noncoding RNAs orchestrate ribosome biogenesis.

PTPRG-AS1 regulates the KITLG/KIT pathway through the ceRNA axis to promote the malignant progression of gastric cancer and the intervention effect of Compound Kushen injection on it

Gastric cancer (GC) is a common malignant tumor with high mortality, recurrence, and metastasis rates. Compound Kushen injection (CKI) combination chemotherapy has been clinically used for the treatment of GC in China for many years, but its underlying mechanisms of action remain unclear. Recent reports have highlighted the important role of the competing endogenous RNA (ceRNA) mechanism of noncoding RNA (ncRNA) and messenger RNA (mRNA) formation in GC and other tumors. This study aimed to investigate the effects of CKI on GC from the ceRNA perspective. We confirmed the inhibitory effect of CKI on GC in mouse models and cell lines. By examining the GC cell lines sensitive to CKI treatment, we developed the CNScore method to analyze the ceRNA network, revealing that the CKI-GC ceRNA network promotes GC proliferation and metastasis through the PTPRG-AS1/hsa-miR-421/KITLG axis. Finally, we constructed GC cell models with PTPRG-AS1 overexpression or knockdown and GC liver metastasis models and found that PTPRG-AS1 can sponge hsa-miR-421, releasing KITLG and promoting GC proliferation and metastasis through the KITLG/KIT pathway. Taken together, CKI can suppress these malignant phenotypes by regulating the PTPRG-AS1/hsa-miR-421/KITLG axis.

Non-coding RNAs in thoracic disease: Barrett's esophagus and esophageal adenocarcinoma

Esophageal adenocarcinoma (EAC) is a highly aggressive malignancy with increasing incidence and poor survival rates, primarily due to late-stage diagnosis. This cancer often develops from Barrett's Esophagus (BE), a precancerous condition linked to chronic gastroesophageal reflux disease (GERD). The transition from BE to EAC is a complex multistep process involving numerous genetic, epigenetic, and molecular changes that lead to the malignant transformation of the esophageal epithelium. Despite advancements in understanding the molecular mechanisms underlying EAC, early detection and effective treatment options remain limited, highlighting an urgent need for innovative diagnostic and therapeutic strategies. Recent research has focused on non-coding RNAs (ncRNAs), which play crucial roles in regulating gene expression and cellular processes relevant to cancer progression. Various types of ncRNAs, including microRNAs, long non-coding RNAs, and circular RNAs, have been implicated in the development of BE and EAC by modulating key signaling pathways such as Wnt/β-catenin and NF-κB. Additionally, ncRNAs are stable in biological fluids, presenting opportunities for their use as non-invasive biomarkers for early detection and monitoring of EAC. This review aims to elucidate the involvement of ncRNAs in the progression from BE to EAC, their potential as therapeutic targets, and their emerging roles in intercellular communication. We will also discuss the challenges in translating ncRNA research into clinical applications, emphasizing their promise in revolutionizing early detection and treatment strategies for EAC.

Exosomes delivering miR-129-5p combined with sorafenib ameliorate hepatocellular carcinoma progression via the KCTD1/HIF-1α/VEGF pathway

BACKGROUND

Potassium channel tetramerization domain-containing 1 (KCTD1) plays a critical role in transcriptional regulation and adipogenesis, but its significance in hepatocellular cancer (HCC) has not been reported.

METHODS

Immunohistochemistry, Western blotting and quantitative real-time PCR analysis were performed to assess the expression of KCTD1 and related genes in HCC cells. MTT assays, colony formation, cell migration, invasion and the in-vivo mouse models were utilized to evaluate the function of KCTD1 in HCC progression. Co-immunoprecipitation, chromatin immunoprecipitation and luciferase reporter assays were conducted to elucidate the molecular mechanisms of KCTD1 in HCC.

RESULTS

KCTD1 expression was increased in human HCC tissues and closely associated with advanced tumor stages. KCTD1 overexpression enhanced growth, migration, and invasion of Huh7 and HepG2 cells both in vitro and in vivo, while KCTD1 knockdown reversed these effects in MHCC97H cells. Mechanistically, KCTD1 interacted with hypoxia-inducible factor 1 alpha (HIF-1α) and enhanced HIF-1α protein stability with the inhibited prolyl-hydroxylases (PHD)/Von Hippel-Lindau (VHL) pathway, consequently activating the Vascular Endothelial Growth Factor (VEGF)/VEGFR2 pathway in HCC cells. Sorafenib and KCTD1 knockdown synergistically inhibited intrahepatic tumor growth following in situ injection of MHCC97H cells. miR-129-5p downregulated KCTD1 by binding to KCTD1 3'UTR. Finally, 45 µg exosomes from miR-129-5p-overexpressing MHCC97H cells combined with 25 mg/kg sorafenib to decrease HCC tumor size.

CONCLUSIONS

These results suggested that KCTD1 protects HIF-1α from degradation and activates the VEGF signaling cascade to enhance HCC progression. Therefore, KCTD1 may serve as a novel target of HCC and pave the way for an efficient combined therapy in advanced HCC.

Role of noncoding RNA and protein interaction in pancreatic cancer

ABSTRACT

Noncoding RNAs (ncRNAs) are a class of RNA molecules with little or no protein-coding potential. Emerging evidence indicates that ncRNAs are frequently dysregulated and play pivotal roles in the pathogenesis of pancreatic cancer. Their aberrant expression can arise from chromosomal abnormalities, dysregulated transcriptional control, and epigenetic modifications. ncRNAs function as protein scaffolds or molecular decoys to modulate interactions between proteins and other biomolecules, thereby regulating gene expression and contributing to pancreatic cancer progression. In this review, we summarize the mechanisms underlying ncRNA dysregulation in pancreatic cancer, emphasize the biological significance of ncRNA-protein interactions, and highlight their clinical relevance. A deeper understanding of ncRNA-protein interactions is essential to elucidate molecular mechanisms and advance translational research in pancreatic cancer.

Current landscape of hypoxia in thyroid cancer pathogenesis and treatment

Thyroid cancer, the most prevalent endocrine malignancy, exhibits diverse clinical behaviors ranging from indolent to highly aggressive forms. A critical factor influencing the progression and treatment resistance of thyroid cancer is hypoxia-a condition characterized by inadequate oxygen supply to the tumor microenvironment. Hypoxia induces the stabilization of hypoxia-inducible factors (HIFs), particularly HIF-1α and HIF-2α, drive various oncogenic processes such as epithelial-mesenchymal transition (EMT), angiogenesis, metabolic reprogramming, and immune evasion. These processes contribute to the aggressive phenotypes observed in poorly differentiated and anaplastic thyroid cancers. This review explores the molecular mechanisms by which hypoxia and HIFs influence thyroid cancer pathogenesis, focusing on key signaling pathways, including NF-κB, Wnt/β-catenin, Hedgehog, and others. Furthermore, we discuss potential therapeutic strategies targeting the hypoxic microenvironment, such as HIF inhibitors and natural compounds, which have shown promise in preclinical studies. Understanding the role of hypoxia in thyroid cancer not only offers insights into the disease's progression but also highlights new avenues for therapeutic intervention aimed at improving patient outcomes.

Engineering Gizmos for Short Cancer Genetic Fragments Discrimination

Currently, mankind is fiercely struggling with cancer. Recently, we have been winning the battle against cancer through precision medicine and accompanying diagnostic methods, and we are raising many hopes with blockbuster drugs. It would be even better if we could read the cancer nucleotide sequence, identify them in advance, and suggest treatments simultaneously. However, this may be an impossible dream because it takes a lot of time and effort to diagnose and ensure all the long gene sequences of cancer at once. Thus, victory will be even closer if a rapid and accurate diagnosis of the cancer-specific gene biomarkers that will soon be imprinted can be made. With the advent of nanotechnology, a new short cancer diagnostic toolkit has been proposed to achieve the goal. This review presents a small diagnostic device that detects certain cancers' genetic fragments (simply 'Gizmo'). The development of numerous diagnostic methods has focused on (1) directly detecting pre-selectively targeted genes using novel diagnostic systems, and (2) indirectly detecting substantial improvements in diagnostic sensitivity only through detection signal amplification without existing gene amplification steps. Our fight against cancer is not a dream, but the result of success, and it is assumed that victory will accelerate as soon as possible.

Therapeutic potential of synthetic microRNA mimics based on the miR-15/107 consensus sequence

MicroRNA expression is frequently suppressed in cancer, and previously we demonstrated coordinate downregulation of multiple related microRNAs of the miR-15/107 group in malignant pleural mesothelioma (PM). From an alignment of the miR-15 family and the related miR-103/107, we derived a consensus sequence and used this to generate synthetic mimics. The synthetic mimics displayed tumour suppressor activity in PM cells in vitro, which was greater than that of a mimic based on the native miR-16 sequence. These mimics were also growth inhibitory in cells from non-small cell lung (NSCLC), prostate, breast and colorectal cancer, and sensitised all cell lines to the chemotherapeutic drug gemcitabine. The increased activity corresponded to enhanced inhibition of the expression of target genes and was associated with an increase in predicted binding to target sites, and proteomic analysis revealed a strong effect on proteins involved in RNA and DNA processes. Applying the novel consensus mimics to xenograft models of PM and NSCLC in vivo using EGFR-targeted nanocells loaded with mimic led to tumour growth inhibition. These results suggest that mimics based on the consensus sequence of the miR-15/107 group have therapeutic potential in a range of cancer types.

Single-molecule resolution of macromolecules with nanopore devices

Nanopore-based electrical detection technology holds single-molecule resolution and combines the advantages of high sensitivity, high throughput, rapid analysis, and label-free detection. It is widely applied in the determination of organic and biological macromolecules, small molecules, and nanomaterials, as well as in nucleic acid and protein sequencing. There are a wide variety of organic polymers and biopolymers, and their chemical structures, and conformation in solution directly affect their ensemble properties. Currently, there is limited approach available for the analysis of single-molecule conformation and self-assembled topologies of polymers, dendrimers and biopolymers. Nanopore single-molecule platform offers unique advantages over other sensing technologies, particularly in molecular size differentiation of macromolecules and complex conformation analysis. In this review, the classification of nanopore devices, including solid-state nanopores (SSNs), biological nanopores, and hybrid nanopores is introduced. The recent developments and applications of nanopore devices are summarized, with a focus on the applications of nanopore platform in the resolution of the structures of synthetic polymer, including dendritic, star-shaped, block copolymers, as well as biopolymers, including polysaccharides, nucleic acids and proteins. The future prospects of nanopore sensing technique are ultimately discussed.

Circulating non-coding RNAs as a tool for liquid biopsy in solid tumors

Solid tumors are significant causes of global mortality and morbidity. Recent research has primarily concentrated on finding pathology-specific molecules that can be acquired non-invasively and that can change as the disease progresses or in response to treatment. The focus of research has moved to RNA molecules that are either freely circulating in body fluids or bundled in microvesicles and exosomes because of their great stability in challenging environments, ease of accessibility, and changes in level in response to therapy. In this context, there are many non-coding RNAs that can be used for this purpose in liquid biopsies. Out of these, microRNAs have been extensively studied. However, there has been an increase of interest in studying long non-coding RNAs, piwi interacting RNAs, circular RNAs, and other small non-coding RNAs. In this article, an overview of the most researched circulating non-coding RNAs in solid tumors will be reviewed, along with a discussion of the significance of these molecules for early diagnosis, prognosis, and therapeutic targets. The publications analyzed were extracted from the PubMed database between 2008 and June 2024.

A seven-LncRNA signature for prognosis prediction of patients with lung squamous cell carcinoma through tumor immune escape

Background

Lung squamous cell carcinoma (LUSC) is a malignant disease associated with poor therapeutic responses and prognosis. Preliminary studies have shown that the dysregulation of long non-coding RNAs (LncRNAs) is linked to cancer development and prognosis. However, research on the role of LncRNAs in LUSC remains limited.

Methods

In this study, we aimed to develop a LncRNA signature for improved prognostic prediction in LUSC and to elucidate the underlying mechanisms. We utilized expression data of LncRNAs and clinical information from 471 LUSC patients in The Cancer Genome Atlas (TCGA), randomly dividing them into a training set (n=236) and a testing set (n=235).

Results

A prognostic signature model comprising seven LncRNAs was constructed using multivariate Cox regression analysis based on the training set. Using a risk score cutoff value of -0.12 (log2-transformed), patients were categorized into high-risk (n=101) and low-risk (n=370) groups. The high-risk group demonstrated significantly worse overall survival (OS) compared to the low-risk group (p<0.0001). The risk score showed strong prognostic predictive ability for LUSC patients, as evidenced by the area under the ROC curve (AUC: 0.66, 0.67, and 0.67) and nomogram analysis (C-index, calibration, and decision curve analysis) for 1-, 3-, and 5-year survival predictions. Independent prognostic factors for LUSC were identified, including risk group (HR=0.3, 95% CI: 0.22-0.4), stage (HR=1.78, 95% CI: 1.28-2.48), and age (HR=1.02, 95% CI: 1.00-1.04). KEGG enrichment analysis revealed that mRNAs influenced by the seven targeted LncRNAs, associated with immune evasion, were primarily linked to pathways such as chemical carcinogenesis, Th17 cell differentiation, NF-κB signaling, and proteoglycans in cancer. Expression levels of 14 target genes related to tumor immune tolerance were significantly suppressed, with eight confirmed via real-time PCR and western blot analysis. Additionally, CIBERSORT analysis of immune cell-related gene expression between normal and LUSC tissues indicated activation of the immune system in LUSC patients.

Conclusion

In conclusion, our findings highlight the clinical significance of the seven LncRNA signature in predicting survival outcomes for LUSC patients.

lncRNA TUG1 and kidney diseases

Long noncoding RNAs (lncRNAs) cover a large class of transcribed RNA molecules that are more than 200 nucleotides in length. An increasing number of studies have shown that lncRNAs control gene expression through different mechanisms and play important roles in a range of biological processes including growth, cell differentiation, proliferation, apoptosis, and invasion. TUG1 was originally discovered in a genomic screen of taurine-treated mouse retinal cells. Previous evidences pointed out that lncRNA TUG1 could inhibit apoptosis and the release of inflammatory factors, improve mitochondrial function, thereby protecting cells from damage, and showing a protective role of TUG1 in diseases. Given that TUG1 has multiple targets and can interfere with multiple steps in the oncogenic process, it has been proposed as a therapeutic target. In this review, we summarize the research progress of lncRNA TUG1 in kidney diseases in the past 8 years, and discuss its related molecular mechanisms.

Expression Levels of Plasma YRNAs in Colorectal Cancer as a Potential Noninvasive Biomarker

PURPOSE

Colorectal cancer (CRC) is identified as the second leading cause of cancer-associated deaths worldwide. Therefore, there is ongoing research to discover new potential biomarkers enabling early and noninvasive diagnosis of the disease. YRNAs, a novel class of non-coding RNAs, have been identified as a new player in carcinogenesis and an independent class of clinical biomarkers in various malignancies. Nevertheless, the role of plasma YRNAs in CRC diagnosis and prognosis remains unknown. Therefore, the current study aimed to investigate the clinical significance of plasma YRNAs as a noninvasive biomarker for CRC.

METHODS

Plasma YRNAs expression was assessed in 50 newly diagnosed CRC patients as well as 50 age- and sex-matched healthy controls using quantitative reverse transcription polymerase chain reaction.

RESULTS

All plasma YRNAs expression levels were significantly higher in CRC patients than in controls. A significant correlation was observed between YRNA1 and YRNA3, and between YRNA1 and YRNA4. However, no significant correlation between YRNA1 and YRNA5 was identified. Plasma YRNA1 expression showed the highest diagnostic performance for the detection of CRC using the receiver operating characteristic curve analysis, with a sensitivity of 92% and a specificity of 90%. Nevertheless, when the four YRNAs were combined in a single ROC analysis, sensitivity decreased to 80%, while the specificity remained virtually unchanged. Moreover, significant association was observed between plasma YRNA1 and YRNA3 and tumor stage, grade, lymph node presence, metastasis, and lymphovascular invasion.

CONCLUSIONS

Plasma YRNA may serve as a potential noninvasive biomarker for the diagnosis and prognosis of CRC with high sensitivity and specificity vs. healthy controls.

The Role of Non-Coding RNAs in MYC-Mediated Metabolic Regulation: Feedback Loops and Interactions

Metabolic reprogramming is a hallmark of cancer, crucial for supporting the rapid energy demands of tumor cells. MYC, often deregulated and overexpressed, is a key driver of this shift, promoting the Warburg effect by enhancing glycolysis. However, there remains a gap in understanding the mechanisms and factors influencing MYC's metabolic roles. Recently, non-coding RNAs (ncRNAs) have emerged as important modulators of MYC functions. This review focuses on ncRNAs that regulate MYC-driven metabolism, particularly the Warburg effect. The review categorizes these ncRNAs into three main groups based on their interaction with MYC and examines the mechanisms behind these interactions. Additionally, we explore how different types of ncRNAs may collaborate or influence each other's roles in MYC regulation and metabolic function, aiming to identify biomarkers and synthetic lethality targets to disrupt MYC-driven metabolic reprogramming in cancer. Finaly, the review highlights the clinical implications of these ncRNAs, providing an up-to-date summary of their potential roles in cancer prognosis and therapy. With the recent advances in MYC-targeted therapy reaching clinical trials, the exciting potential of combining these therapies with ncRNA-based strategies holds great promise for enhancing treatment efficacy.

Exploring the roles of ncRNAs in prostate cancer via the PI3K/AKT/mTOR signaling pathway

Although various treatment options are available for prostate cancer (PCa), including androgen deprivation therapy (ADT) and chemotherapy, these approaches have not achieved the desired results clinically, especially in the treatment of advanced chemotherapy-resistant PCa. The PI3K/AKT/mTOR (PAM) signaling pathway is a classical pathway that is aberrantly activated in cancer cells and promotes the tumorigenesis, metastasis, resistance to castration therapy, chemoresistance, and recurrence of PCa. Noncoding RNAs (ncRNAs) are a class of RNAs that do not encode proteins. However, some ncRNAs have recently been shown to be differentially expressed in tumor tissues compared with noncancerous tissues and play important roles at the transcription and posttranscription levels. Among the types of ncRNAs, long noncoding RNAs (lncRNAs), microRNAs (miRNAs), circular RNAs (circRNAs), and Piwi-interacting RNAs (piRNAs) can participate in the PAM pathway to regulate PCa growth, metastasis, angiogenesis, and tumor stemness. Therefore, ncRNA therapy that targets the PAM signaling pathway is expected to be a novel and effective approach for treating PCa. In this paper, we summarize the types of ncRNAs that are associated with the PAM pathway in PCa cells as well as the functions and clinical roles of these ncRNAs in PCa. We hope to provide novel and effective strategies for the clinical diagnosis and treatment of PCa.

Transcriptome profiling of serum exosomes by RNA-Seq reveals lipid metabolic changes as a potential biomarker for evaluation of roxadustat treatment of chronic kidney diseases

The incidence of chronic kidney disease (CKD) is increasing globally; however, effective preventive and therapeutic strategies are currently limited. Roxadustat is being clinically used to treat renal anemia in CKD patients to reduce anemia-related complications and improve patients' life quality. Exosomes are small vesicles carrying important information that contribute to cell-to-cell communication and are present in various body fluids. However, little is known about the role of serum exosomes and their association with CKD after roxadustat treatment. Next-generation sequencing approaches have revealed that exosomes are enriched in noncoding RNAs and thus exhibit great potential as sensitive nucleic acid biomarkers in various human diseases. In this study, we aimed to identify the changed mRNAs-lncRNAs after roxadustat treatment as novel biomarkers for assessing the efficiency of the treatment. Through our study using RNA-seq data, we identified 957 mRNAs (626 upregulated and 331 downregulated after roxadustat treatment) and 914 lncRNAs (444 upregulated and 470 downregulated) derived from exosomes that were significantly changed, which was highly correlated to lipid metabolism. Our analysis through whole transcriptome profiling of exosome RNAs encompasses an identified differentially expressed mRNA-lncRNA regulatory axis in a larger patient cohort for the validation of suitable biomarkers for assessing CKD after roxadustat treatment.

The NcRNA/Wnt axis in lung cancer: oncogenic mechanisms, remarkable indicators and therapeutic targets

Early diagnosis of lung cancer (LC) is challenging, treatment options are limited, and treatment resistance leads to poor prognosis and management in most patients. The Wnt/β-catenin signaling pathway plays a vital role in the occurrence, progression, and therapeutic response of LC. Recent studies indicate that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) function as epigenetic regulators that can promote or inhibit Wnt/β-catenin signaling by interacting with Wnt proteins, receptors, signaling transducers, and transcriptional effectors, thereby affecting LC cell proliferation, metastasis, invasion, and treatment resistance. Deepening our understanding of the regulatory network between ncRNAs and the Wnt/β-catenin signaling pathway will help overcome the limitations of current LC diagnosis and treatment methods. This article comprehensively reviews the regulatory mechanisms related to the functions of ncRNAs and the Wnt/β-catenin pathway in LC, examining their potential as diagnostic and prognostic biomarkers and therapeutic targets, aiming to offer new promising perspectives for LC diagnosis and treatment.

The functions and modifications of tRNA-derived small RNAs in cancer biology

Recent progress in noncoding RNA research has highlighted transfer RNA-derived small RNAs (tsRNAs) as key regulators of gene expression, linking them to numerous cellular functions. tsRNAs, which are produced by ribonucleases such as angiogenin and Dicer, are classified based on their size and cleavage positions. They play diverse regulatory roles at the transcriptional, post-transcriptional, and translational levels. Furthermore, tRNAs undergo various modifications that influence their biogenesis, stability, functionality, biochemical characteristics, and protein-binding affinity. tsRNAs, with their aberrant expression patterns and modifications, act as both oncogenes and tumor suppressors. This review explores the biogenetic pathways of tsRNAs and their complex roles in gene regulation. We then focus on the importance of RNA modifications in tsRNAs, evaluating their impact on the biogenesis and biological functions on tsRNAs. Furthermore, we summarize recent data indicating that tsRNAs exhibit varied expression profiles across different cancer types, highlighting their potential as innovative biomarkers and therapeutic targets. This discussion integrates both existing and new knowledge about tsRNAs, emphasizing their importance in cancer biology and clinical advancement.

Molecular Interplay Between Non-Coding RNAs and Connexins and Its Possible Role in Cancer

Non-coding RNAs (ncRNAs) are sequences that do not encode for proteins and play key roles in different cellular processes, including cell proliferation and differentiation. On the other hand, connexins (Cxs) are transmembrane proteins that principally allow intercellular communication. In pathological conditions such as cancer, there is a deregulation in the expression and/or function of ncRNAs and Cxs, which in turn leads to an enhancement in the aggressive phenotype, such as a greater proliferative and invasive capacity. This suggests a plausible interplay between ncRNAs and Cxs. Based on that, this review aims to summarize the current knowledge regarding this relationship and to analyze how it may influence the development of aggressive traits in cancer cells and the clinicopathological features of cancer patients. Finally, we discuss the potential of ncRNAs and Cxs as promising clinical biomarkers for cancer diagnosis, prognosis, and therapeutic targeting.

EGFR-induced lncRNA TRIDENT promotes drug resistance in non-small cell lung cancer via phospho-TRIM28-mediated DNA damage repair

Long noncoding RNAs (lncRNAs) play numerous roles in cellular biology and alterations in lncRNA expression profiles have been implicated in a variety of cancers. Here, we identify and characterize a lncRNA, TRIM28 Interacting DNA damage repair Enhancing Noncoding Transcript (TRIDENT), whose expression is induced upon epithelial growth factor receptor (EGFR) activation, and which exerts pro-oncogenic functions in EGFR-driven non-small cell lung cancer. Knocking down TRIDENT leads to decreased tumor-cell proliferation in both in vitro and in vivo model systems and induces sensitization to chemotherapeutic drugs. Using ChIRP-MS analysis we identified TRIM28 as a protein interactor of TRIDENT. TRIDENT promotes phosphorylation of TRIM28 and knocking down TRIDENT leads to accumulation of DNA damage in cancer cells via decreased TRIM28 phosphorylation. Altogether, our results reveal a molecular pathway in which TRIDENT regulates TRIM28 phosphorylation to promote tumor cell growth and drug resistance. Our findings suggest that TRIDENT can be developed as a biomarker or therapeutic target for EGFR mutant non-small cell lung cancer.

Non-coding RNAs: emerging biomarkers and therapeutic targets in cancer and inflammatory diseases

Non-coding RNAs (ncRNAs) have a significant role in gene regulation, especially in cancer and inflammatory diseases. ncRNAs, such as microRNA, long non-coding RNAs, and circular RNAs, alter the transcriptional, post-transcriptional, and epigenetic gene expression levels. These molecules act as biomarkers and possible therapeutic targets because aberrant ncRNA expression has been directly connected to tumor progression, metastasis, and response to therapy in cancer research. ncRNAs' interactions with multiple cellular pathways, including MAPK, Wnt, and PI3K/AKT/mTOR, impact cellular processes like proliferation, apoptosis, and immune responses. The potential of RNA-based therapeutics, such as anti-microRNA and microRNA mimics, to restore normal gene expression is being actively studied. Additionally, the tissue-specific expression patterns of ncRNAs offer unique opportunities for targeted therapy. Specificity, stability, and immune responses are obstacles to the therapeutic use of ncRNAs; however, novel strategies, such as modified oligonucleotides and targeted delivery systems, are being developed. ncRNA profiling may result in more individualized and successful treatments as precision medicine advances, improving patient outcomes and creating early diagnosis and monitoring opportunities. The current review aims to investigate the roles of ncRNAs as potential biomarkers and therapeutic targets in cancer and inflammatory diseases, focusing on their mechanisms in gene regulation and their implications for non-invasive diagnostics and targeted therapies. A comprehensive literature review was conducted using PubMed and Google Scholar, focusing on research published between 2014 and 2025. Studies were selected based on rigorous inclusion criteria, including peer-reviewed status and relevance to ncRNA roles in cancer and inflammatory diseases. Non-English, non-peer-reviewed, and inconclusive studies were excluded. This approach ensures that the findings presented are based on high-quality and relevant sources.

The Common Hallmarks and Interconnected Pathways of Aging, Circadian Rhythms, and Cancer: Implications for Therapeutic Strategies

The intricate relationship between cancer, circadian rhythms, and aging is increasingly recognized as a critical factor in understanding the mechanisms underlying tumorigenesis and cancer progression. Aging is a well-established primary risk factor for cancer, while disruptions in circadian rhythms are intricately associated with the tumorigenesis and progression of various tumors. Moreover, aging itself disrupts circadian rhythms, leading to physiological changes that may accelerate cancer development. Despite these connections, the specific interplay between these processes and their collective impact on cancer remains inadequately explored in the literature. In this review, we systematically explore the physiological mechanisms of circadian rhythms and their influence on cancer development. We discuss how core circadian genes impact tumor risk and prognosis, highlighting the shared hallmarks of cancer and aging such as genomic instability, cellular senescence, and chronic inflammation. Furthermore, we examine the interplay between circadian rhythms and aging, focusing on how this crosstalk contributes to tumorigenesis, tumor proliferation, and apoptosis, as well as the impact on cellular metabolism and genomic stability. By elucidating the common pathways linking aging, circadian rhythms, and cancer, this review provides new insights into the pathophysiology of cancer and identifies potential therapeutic strategies. We propose that targeting the circadian regulation of cancer hallmarks could pave the way for novel treatments, including chronotherapy and antiaging interventions, which may offer important benefits in the clinical management of cancer.

circPRMT10 regulated by QKI hypermethylation attenuates lung tumorigenesis induced by tobacco carcinogen NNK

Chronic exposure to environmental carcinogens is a major cause of tumorigenesis. A potent tobacco-specific nitrosamine carcinogen, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), exhibits high carcinogenicity to induce lung cancer. However, the function and mechanism of circular RNA (circRNA) in chemical carcinogenesis, especially the regulation of circRNA formation upon exposure to environmental chemicals, remain unclear. This study identified that circPRMT10 (hsa_circ_0009048) was downregulated in NNK-exposed human bronchial epithelial cells (16HBE and BEAS-2B). Additionally, the RNA-binding protein Quaking (QKI) was responsible for the biogenesis of circPRMT10 through its binding interaction with the flanking introns of circPRMT10. Moreover, NNK exposure resulted in hypermethylation of the QKI promoter, leading to QKI downregulation, which ultimately affected circPRMT10 formation. Using a cell model of chronic exposure to low-dose NNK, we found that overexpression of circPRMT10 significantly inhibited NNK-induced lung carcinogenesis by suppressing cell proliferation, cell cycle progression, and xenograft tumor growth. Finally, moesin (MSN) was identified as a downstream target of circPRMT10 via RNA pull-down and western blot assays and demonstrated a potential role in the regulation of lung cancer development. In conclusion, our findings reveal the underlying mechanisms of circRNA biogenesis following exposure to chemical carcinogens, providing novel insights into the role of circRNAs in chemical carcinogenesis.

MMnc: multi-modal interpretable representation for non-coding RNA classification and class annotation

MOTIVATION

As the biological roles and disease implications of non-coding RNAs continue to emerge, the need to thoroughly characterize previously unexplored non-coding RNAs becomes increasingly urgent. These molecules hold potential as biomarkers and therapeutic targets. However, the vast and complex nature of non-coding RNAs data presents a challenge. We introduce MMnc, an interpretable deep-learning approach designed to classify non-coding RNAs into functional groups. MMnc leverages multiple data sources-such as the sequence, secondary structure, and expression-using attention-based multi-modal data integration. This ensures the learning of meaningful representations while accounting for missing sources in some samples.

RESULTS

Our findings demonstrate that MMnc achieves high classification accuracy across diverse non-coding RNA classes. The method's modular architecture allows for the consideration of multiple types of modalities, whereas other tools only consider one or two at most. MMnc is resilient to missing data, ensuring that all available information is effectively utilized. Importantly, the generated attention scores offer interpretable insights into the underlying patterns of the different non-coding RNA classes, potentially driving future non-coding RNA research and applications.

AVAILABILITY AND IMPLEMENTATION

Data and source code can be found at EvryRNA.ibisc.univ-evry.fr/EvryRNA/MMnc.

CASCADES, a novel SOX2 super-enhancer-associated long noncoding RNA, regulates cancer stem cell specification and differentiation in glioblastoma

Glioblastoma is the most common primary malignant brain tumor in adults, with a median survival of just over 1 year. The failure of available treatments to achieve remission in patients with glioblastoma (GBM) has been attributed to the presence of cancer stem cells (CSCs), which are thought to play a central role in tumor development and progression and serve as a treatment-resistant cell repository capable of driving tumor recurrence. In fact, the property of "stemness" itself may be responsible for treatment resistance. In this study, we identify a novel long noncoding RNA (lncRNA), cancer stem cell-associated distal enhancer of SOX2 (CASCADES), that functions as an epigenetic regulator in glioma CSCs (GSCs). CASCADES is expressed in isocitrate dehydrogenase (IDH)-wild-type GBM and is significantly enriched in GSCs. Knockdown of CASCADES in GSCs results in differentiation towards a neuronal lineage in a cell- and cancer-specific manner. Bioinformatics analysis reveals that CASCADES functions as a super-enhancer-associated lncRNA epigenetic regulator of SOX2. Our findings identify CASCADES as a critical regulator of stemness in GSCs that represents a novel epigenetic and therapeutic target for disrupting the CSC compartment in glioblastoma.

N6-methyladenosine modification of 3'tRF-AlaAGC impairs PD-1 blockade efficacy by promoting lactic acid accumulation in the tumor microenvironment of gastric carcinoma

The balance between CD8+ T cells and regulatory T (Treg) cells in the tumor microenvironment (TME) plays a crucial role in the immune checkpoint inhibition (ICI) therapy in gastric carcinoma (GC). However, related factors leading to the disturbance of TME and resistance to ICI therapy remain unknown. In this study, we applied N6-methyladenosine (m6A) small RNA Epitranscriptomic Microarray and screened out 3'tRF-AlaAGC based on its highest differential expression level and lowest inter-group variance. N6-methyladenosine modification significantly enhanced the stability of 3'tRF-AlaAGC, which strengthened glycolysis and lactic acid (LA) production in GC cells by binding to PTBP1 (Polypyrimidine Tract Binding Protein 1). In the peritoneal GC implantation model established in huPBMC-NCG mice, 3'tRF-AlaAGC significantly increased the proportion of PD1+ Treg cells. Furthermore, in high-LA environments driven by glucose consumption of GC cells, Treg cells actively uptake LA through MCT1, facilitating NFAT1 translocation into the nucleus and enhancing PD1 expression, whereas PD1 expression by effector T cell is diminished. Meanwhile, T cell suppression assays were performed under low-LA or high-LA conditions, and the proliferation of CD8+ T cells was dampened by adding Sintilimab in a high-LA but not in a low-LA environment, suggesting the preferential activation of PD1+ Treg cell. These findings deciphered the complexities of the immune microenvironment in GC, providing prospects for identifying robust biomarkers that could improve the evaluation of therapeutic effectiveness and prognosis in immune therapy for GC.

CircFak promotes mechanical force-induced osteogenesis via FAK/AKT phosphorylation

OBJECTIVES

Orthodontic treatment is widely applied for addressing orofacial skeletal deformities, with the remodeling of the alveolar bone under mechanical force being the key factor. FAK is essential for cellular response to mechanical force. However, the function of circFak has never been reported. In this study, the microarrays showed that circFak may affect osteogenesis under mechanical force. We aimed to verify the effect of circFak in force-related bone remodeling and investigate the underlying mechanisms.

METHODS

Arraystar microarrays were used to identify differentially expressed circRNAs and microRNAs in response to mechanical stress. The subcellular distribution of circFak was analyzed via RT‒qPCR and FISH. ALP and ARS staining assays were performed to investigate the effects of circFak on osteogenesis. RNA sequencing, bioinformatics analysis, dual-luciferase reporter assays, and RNA immunoprecipitation were accomplished to discover the molecular mechanisms of circFak. AAV-sh-circFak mouse models with tooth movements were established. The role of circFak under mechanical force in vivo was assessed via immunofluorescence and micro-CT analyses.

RESULTS

CircFak expression was significantly upregulated under mechanical force. Osteogenic capacity of osteoblasts was positively correlated with the level of circFak. CircFak promoted mechanical force-induced osteogenesis through miR-425-5p/Ccn3 pathway, and further stimulated the phosphorylation of its parental sourced protein FAK. Our murine models showed that AAV-mediated circFak silencing suppressed osteogenesis.

CONCLUSION

CircFak could obviously promote osteogenesis under mechanical force and may possess ability to become a novel biomarker for prognosis of orthodontic treatments.

Enzyme-Responsive Nanoparachute for Targeted miRNA Delivery: A Protective Strategy Against Acute Liver and Kidney Injury

MicroRNA (miRNA)-based therapy holds significant potential; however, its structural limitations pose a challenge to the full exploitation of its biomedical functionality. Framework nucleic acids are promising owing to their transportability, biocompatibility, and functional editability. MiRNA-125 is embedded into a nucleic acid framework to create an enzyme-responsive nanoparachute (NP), enhancing the miRNA loading capacity while preserving the attributes of small-scale framework nucleic acids and circumventing the uncertainty related to RNA exposure in conventional loading methods. An enzyme-sensitive sequence is designed in NP as a bioswitchable apparatus for cargo miRNAs release. NP is compared with conventional delivery modes and delivery vehicles, confirming its excellent transportability and sustained release properties. Moreover, NP confers good enzyme and serum resistance to the cargo miRNAs. Simultaneously, it can easily deliver miRNA-125 to liver and kidney lesions owing to its passive targeting properties. This allows for Keap1/Nrf2 pathway regulation and p53 protein targeting in the affected tissues. Additionally, NP negatively regulates the expression of Bax and Caspase-3. These combined actions help to inhibit oxidation, prevent cell cycle arrest, and reduce the apoptosis of liver and kidney cells. Consequently, this strategy offers a potential treatment for acute liver and kidney injury.

The epigenetic landscape of brain metastasis

Brain metastasis represents a significant challenge in oncology, driven by complex molecular and epigenetic mechanisms that distinguish it from primary tumors. While recent research has focused on identifying genomic mutation drivers with potential clinical utility, these strategies have not pinpointed specific genetic mutations responsible for site-specific metastasis to the brain. It is now clear that successful brain colonization by metastatic cancer cells requires intricate interactions with the brain tumor ecosystem and the acquisition of specialized molecular traits that facilitate their adaptation to this highly selective environment. This is best exemplified by widespread transcriptional adaptation during brain metastasis, resulting in aberrant gene programs that promote extravasation, seeding, and colonization of the brain. Increasing evidence suggests that epigenetic mechanisms play a significant role in shaping these pro-brain metastasis traits. This review explores dysregulated chromatin patterns driven by chromatin remodeling, histone modifications, DNA/RNA methylation, and other epigenetic regulators that underpin brain metastatic seeding, initiation, and outgrowth. We provide novel insights into how these epigenetic modifications arise within both the brain metastatic tumor and the surrounding brain metastatic tumor ecosystem. Finally, we discuss how the inherent plasticity and reversibility of the epigenomic landscape in brain metastases may offer new therapeutic opportunities.

Unravelling the Regulatory Roles of lncRNAs in Melanoma: From Mechanistic Insights to Target Selection

Melanoma is the deadliest form of skin cancer, and its treatment poses significant challenges due to its aggressive nature and resistance to conventional therapies. Long non-coding RNAs (lncRNAs) represent a new frontier in the search for suitable targets to control melanoma progression and invasiveness. Indeed, lncRNAs exploit a wide range of regulatory functions along chromatin remodeling, gene transcription, post-transcription, transduction, and post-transduction to ultimately tune multiple cellular processes. The understanding of this intricate and flexible regulatory network orchestrated by lncRNAs in pathological conditions can strategically support the rational identification of promising targets, ultimately speeding up the setup of new therapeutics to integrate the currently available approaches. Here, the most recent findings on lncRNAs involved in melanoma will be analyzed. In particular, the functional links between their mechanisms of action and some frequently underestimated features, like their different subcellular localizations, will be highlighted.

Circulating Biomarkers of Thyroid Cancer: An Appraisal

Thyroid cancer is the most prevalent endocrine cancer. The prognosis depends on the type and stage at diagnosis. Thyroid cancer treatments involve surgery, possibly followed by additional therapeutic options such as hormone therapy, radiation therapy, targeted therapy and chemotherapy. Besides the well-known thyroid tumor biomarkers, new circulating biomarkers are now emerging. Advances in genomic, transcriptomic and proteomic technologies have allowed the development of novel tumor biomarkers. This review explores the current literature data to critically analyze the benefits and limitations of routinely measured circulating biomarkers for the diagnosis and monitoring of thyroid cancer. The review also sheds light on new circulating biomarkers, focusing on the challenges of their use in the clinical management of thyroid cancer, underlining the need for the identification of a new generation of circulating biomarkers.

MicroRNAs in the Mitochondria-Telomere Axis: Novel Insights into Cancer Development and Potential Therapeutic Targets

The mitochondria-telomere axis is recognized as an important factor in the processes of metabolism, aging and oncogenesis. MicroRNAs (miRNAs) play an essential function in this complex interaction, having an impact on aspects such as cellular homeostasis, oxidative responses and apoptosis. In recent years, miRNAs have been found to be crucial for telomeric stability, as well as for mitochondrial behavior, factors that influence cell proliferation and viability. Furthermore, mitochondrial miRNAs (mitomiRs) are associated with gene expression and the activity of the cGAS/STING pathway activity, linking mitochondrial DNA recognition to immune system responses. Hence, miRNAs maintain a link to mitochondrial biogenesis, metabolic changes in cancer and cellular organelles. This review focuses on the roles of a variety of miRNAs in cancer progression and their potential application as biomarkers or therapeutic agents.

A Programmable Automatic Cascade Machinery for Single-Molecule Profiling of Multiple Noncoding RNAs in Breast Tissues

Noncoding RNAs (ncRNAs) are identified as critical regulatory molecules in tumorigenesis and progression. Investigating the expression patterns of multiple ncRNAs in living cells and tissues may facilitate the diagnosis of cancers. Herein, we develop a programmable automatic cascade machinery for single-molecule profiling of multiple ncRNAs. This method involves two successive amplification events that can convert extremely low-abundance target ncRNAs into abundant FAM/Cy5 molecules for the generation of amplified fluorescence signals. The subsequent single-molecule detection can identify piR-36026 with the FAM signal and DSCAM-AS1 with the Cy5 signal. Due to the high efficiency of automatic cascade machinery and the high signal-to-noise ratio of single-molecule imaging, this method can achieve sensitive detection of multiple ncRNAs with a detection limit of 44.67 aM for piR-36026 and 45.71 aM for DSCAM-AS1, and it can measure endogenous piR-36026 and DSCAM-AS1 at the single-cell level. Moreover, the profiling of piR-36026 and DSCAM-AS1 in healthy tissues and breast cancer tissues demonstrates the feasibility of the proposed method in cancer diagnostics. By programming the recognition sequences of dumbbell probes, this method can be extended to measure other cancer-related ncRNAs, with great prospects in clinical applications.

The roles and therapeutic potential of exosomal non-coding RNAs in microglia-mediated intercellular communication

Exosomes, which are small extracellular vesicles (sEVs), serve as versatile regulators of intercellular communication in the progression of various diseases, including neurological disorders. Among the diverse array of cargo they carry, non-coding RNAs (ncRNAs) play key regulatory roles in various pathophysiological processes. Exosomal ncRNAs derived from distinct cells modulate their reciprocal crosstalk locally or remotely, thereby mediating neurological diseases. Nevertheless, the emerging role of exosomal ncRNAsin microglia-mediated phenotypes remains largely unexplored. This review aims to summarise the biological functions of exosomal ncRNAs and the molecular mechanisms that underlie their impact on microglia-mediated intercellular communication, modulating neuroinflammation and synaptic functions within the landscape of neurological disorders. Furthermore, this review comprehensively described the potential applications of exosomal ncRNAs as diagnostic and prognostic biomarkers, as well as innovative therapeutic targets for the treatment of neurological diseases.

TFAP2A-regulated CRNDE enhances colon cancer progression and chemoresistance via RIPK3 interaction

Colon cancer (CC) is a common malignancy with rising incidence worldwide. Despite advances in treatment strategies, many patients still face a poor prognosis due to the development of drug resistance. Long non-coding RNAs (lncRNAs) have emerged as important regulators of various biological processes and have been implicated in cancer progression. Among them, colorectal neoplasia differentially expressed (CRNDE) has drawn attention for its potential roles in different cancers. However, its specific functions in CC remain unclear. In this study, we identified CRNDE as highly expressed in CC, contributing to tumor progression and drug resistance. Mechanically, CRNDE is regulated by the transcription factor TFAP2A. Additionally, CRNDE inhibits pyroptosis, a form of programmed cell death, by promoting the ubiquitin-mediated degradation of RIPK3, thereby reducing the sensitivity of CC cells to 5-fluorouracil (5-FU). Our findings suggest that the TFAP2A/CRNDE/RIPK3 axis plays critical roles in colon cancer progression and chemoresistance, highlighting potential therapeutic targets for improving treatment outcomes.

Theoretical perspectives and clinical applications of non-coding RNA in lung cancer metastasis: a systematic review

Lung cancer is one of the deadliest malignancies worldwide, with distant metastasis being a major cause of death. However, the specific mechanisms of lung cancer metastasis remain unclear. NcRNAs, a widely present type of non-coding RNAs in the body, constitute about 98% of the human genome, lacking protein-coding capacity but involved in various cellular processes such as proliferation, apoptosis, invasion, and migration. Studies have shown that ncRNAs play a crucial role in the metastasis of lung cancer, although research in this area is limited. This review summarizes the biological origins and functions of ncRNAs, their specific roles and mechanisms in lung cancer metastasis, and discusses their potential for early screening and therapeutic applications in lung cancer. Furthermore, it outlines the challenges in translating basic advancements of ncRNAs in lung cancer metastasis into clinical practice.

Mechanisms for Orofacial Pain: Roles of Immunomodulation, Metabolic Reprogramming, Oxidative Stress and Epigenetic Regulation

Background and Objectives: Orofacial pain corresponds to pain sensitization originating from the facial and oral regions, often accompanied by diagnostic complexity due to a multitude of contributory factors, leading to significant patient distress and impairment. Here, we have reviewed current mechanistic pathways and biochemical aspects of complex orofacial pain pathology, highlighting recent advancements in understanding its multifactorial regulation and signaling and thus providing a holistic approach to challenging it. Materials and Methods: Studies were identified from an online search of the PubMed database without any search time range. Results: We have discussed neuron-glia interactions and glial cell activation in terms of immunomodulatory effects, metabolism reprogramming effects and epigenetic modulatory effects, in response to orofacial pain sensitization comprising different originating factors. We have highlighted the fundamental role of oxidative stress affecting significant cellular pathways as well as cellular machinery, which renders pain pathology intricate and multidimensional. Emerging research on the epigenetic modulation of pain regulatory genes in response to molecular and cellular environmental factors is also discussed, alongside updates on novel diagnostic and treatment approaches. Conclusions: This review deliberates the integrative perspectives and implications of modulation in the immune system, glucose metabolism, lipid metabolism and redox homeostasis accompanied by mitochondrial dysfunction as well as epigenetic regulation accommodating the effect of dysregulated non-coding RNAs for an interdisciplinary understanding of pain pathology at the molecular level, aiming to improve patient outcomes with precise diagnosis offering improved pain management and treatment.

Non-Coding RNAs in Cancer: Structure, Function, and Clinical Application

We are on the brink of a paradigm shift in both theoretical and clinical oncology. Genomic and transcriptomic profiling, alongside personalized approaches that account for individual patient variability, are increasingly shaping discourse. Discussions on the future of personalized cancer medicine are mainly dominated by the potential of non-coding RNAs (ncRNAs), which play a prominent role in cancer progression and metastasis formation by regulating the expression of oncogenic or tumor suppressor proteins at transcriptional and post-transcriptional levels; furthermore, their cell-free counterparts might be involved in intercellular communication. Non-coding RNAs are considered to be promising biomarker candidates for early diagnosis of cancer as well as potential therapeutic agents. This review aims to provide clarity amidst the vast body of literature by focusing on diverse species of ncRNAs, exploring the structure, origin, function, and potential clinical applications of miRNAs, siRNAs, lncRNAs, circRNAs, snRNAs, snoRNAs, eRNAs, paRNAs, YRNAs, vtRNAs, and piRNAs. We discuss molecular methods used for their detection or functional studies both in vitro and in vivo. We also address the challenges that must be overcome to enter a new era of cancer diagnosis and therapy that will reshape the future of oncology.

NAPTUNE: nucleic acids and protein biomarkers testing via ultra-sensitive nucleases escalation

In an era where swift and precise diagnostic capabilities are paramount, we introduce NAPTUNE (Nucleic acids and Protein Biomarkers Testing via Ultra-sensitive Nucleases Escalation), an innovative platform for the amplification-free detection of nucleic acids and protein biomarkers in less than 45 minutes. Using a tandem cascade of endonucleases, NAPTUNE employs apurinic/apyrimidinic endonuclease 1 (APE1) to generate DNA guides, enabling the detection of target nucleic acids at femtomolar levels. The sensitivity is elevated to attomolar levels through the action of Pyrococcus furiosus Argonaute (PfAgo), which intensifies probe cleavage, thereby boosting both sensitivity and specificity within an innovative in-situ cascade circuit. This technology not only streamlines rapid, onsite diagnostics without pre-amplification but also demonstrates exceptional accuracy in identifying a broad spectrum of nucleic acids and crucial cancer-related protein biomarkers directly from clinical samples. The development of a portable device for point-of-care testing further underscores NAPTUNE's potential to transform diagnostic processes, especially in resource-limited environments, marking a significant diversity forward in medical diagnostics and patient care.

Whole transcriptome and proteome analyses identify ncRNAs and mRNAs to predict competing endogenous RNA networks in hepatitis B virus-induced hepatocellular carcinoma

The presence of the Hepatitis B virus (HBV) is considered as a valuable risk factor of hepatocellular carcinoma (HCC). To more deeply comprehend the molecular mechanism and transcriptome of HBV-induced HCC, we utilized tandem mass tagging (TMT)-based quantitative proteomics analysis and whole-transcriptome sequencing to analyze three sets of matched HepG2 hepatoma cells and HBV-positive HepAD38 cells. The differentially expressed (DE) proteins (1596), mRNAs (5263), miRNAs (581), lncRNAs (2672) and circRNAs (222) were subjected to differential expression and enrichment analyses in order to thoroughly assess the gene-regulatory circuits of HBV-induced HCC. Subsequently, the amounts of 321 DEproteins-DEmRNAs with common alterations were confirmed. According to functional pathway analysis, the DEproteins-DEmRNAs were primarily linked to signaling pathways, amino acid metabolism, and cellular function. Furthermore, the viability and significance of the ceRNA regulatory networks, LOC105377730/miR-4726-5p/FHL2 and hsa_circ_0001098/miR-2110/IGF2BP1, were randomly chosen and confirmed. Our work provides a valuable asset in terms of understanding regulatory activities at the RNA level, and might reveal fresh information about the fundamental mechanism and potential therapeutic targets of HBV-induced HCC.

CircDUSP16 mediates the effect of triple-negative breast cancer in pirarubicin via the miR-1224-3p/TFDP2 axis

Triple-negative breast cancer (TNBC) is an aggressive molecular subtype of breast cancer characterized by a high recurrence rate, poor prognosis, and elevated mortality. Identifying novel molecular targets is crucial for developing more effective therapeutic strategies against TNBC. Recent studies have highlighted the role of circular RNAs (circRNAs) in the progression of TNBC. In this study, we identified and validated that circDUSP16 (hsa_circ_0003855) is significantly upregulated in TNBC cells, tissues, and plasma exosomes. Functional assays in vitro demonstrated that overexpression of circDUSP16 promoted the proliferation, migration and invasion of TNBC cells, weathers circDUSP16 knockdown exerted the opposite effect. In vivo studies confirmed that circDUSP16 knockdown can inhibit tumor growth. Using bioinformatics analysis, circDUSP16/miR-1224-3p/TFDP2 pathway was predicted and cascaded. Mechanistically, circDUSP16 was shown to promote the progression of TNBC via the miR-1224-3p/TFDP2 axis. Additionally, THP, a commonly used anthracycline chemotherapy drug, was found to downregulate circDUSP16, suggesting that its therapeutic effects on TNBC may be mediated through circDUSP16/miR-1224-3p/TFDP2 pathway. Our findings suggest that circDUSP16 is a promising biomarker and potential therapeutic target for TNBC.

A bioswitchable delivery system for microRNA therapeutics based on a tetrahedral DNA nanostructure

As microRNAs (miRNA) regulate almost all physiopathological activities in the human body, miRNA therapeutics that deliver miRNA regulators have attracted considerable attention in the field of nucleic acid drug development. The use of tetrahedral DNA nanostructures to deliver miRNA regulators is promising because of their simple fabrication, enhanced cell entry, effective tissue penetration, biocompatibility and functional editability. This protocol extension builds on our previous protocol for the use of tetrahedral DNA nanostructures and was designed to establish an updated bioswitchable delivery system (BDS) for achieving controlled cargo loading and release. A ribonuclease H-sensitive sequence is designed as a bioswitchable apparatus for the targeted release of the miRNA regulator. The functional sequence of the miRNA regulator and minimal secondary structure formation tendency during annealing are two key points in cargo design. We provide two BDS design strategies; BDS-A comprises an intact DNA tetrahedron with the RNA cargo hanging outside, offering the merits of lower cost, simplicity, and more direct structural design. In the BDS-B design, the RNA regulators are embedded into the DNA tetrahedron, which is beneficial for dermal tissue permeation applications. Following sequence design in Oligo 7 and Tiamat, the BDS assembly is completed and then ribonuclease H achieves controlled release of the miRNA regulator by triggering the bioswitchable apparatus. This is verified via polyacrylamide and agarose gel electrophoresis or fluorophore modifications. Both BDSs show promising cellular membrane permeability, tissue permeability and target inhibition in vitro and in vivo. The assembly and characterization of the BDS can be completed in 4 d, and the validation time for biostability and biological applications will depend on the specific use.