Non-coding RNA in cancer

Targeted delivery systems of siRNA based on ionizable lipid nanoparticles and cationic polymer vectors

As an emerging therapeutic tool, small interfering RNA (siRNA) had the capability to down-regulate nearly all human mRNAs via sequence-specific gene silencing. Numerous studies have demonstrated the substantial potential of siRNA in the treatment of broad classes of diseases. With the discovery and development of various delivery systems and chemical modifications, six siRNA-based drugs have been approved by 2024. The utilization of siRNA-based therapeutics has significantly propelled efforts to combat a wide array of previously incurable diseases and advanced at a rapid pace, particularly with the help of potent targeted delivery systems. Despite encountering several extracellular and intracellular challenges, the efficiency of siRNA delivery has been gradually enhanced. Currently, targeted strategies aimed at improving potency and reducing toxicity played a crucial role in the druggability of siRNA. This review focused on recent advancements on ionizable lipid nanoparticles (LNPs) and cationic polymer (CP) vectors applied for targeted siRNA delivery. Based on various types of targeted modifications, we primarily described delivery systems modified with receptor ligands, peptides, antibodies, aptamers and amino acids. Finally, we discussed the challenges and opportunities associated with siRNA delivery systems based on ionizable LNPs and CPs vectors.

Decoding intricate interactions between m6A modification with mRNAs and non-coding RNAs in cervical cancer: Molecular mechanisms and clinical implications

N6-methyladenosine (m6A) methylation is the most prevalent RNA modification that is regulated by three regulatory factors: "writers", "erasers" and "readers". m6A modification regulates RNA stability and other mechanisms, including translation, cleavage, and degradation. Current research has demonstrated that m6A methylation is involved in the regulation of occurrence and development of cancers by controlling the expression of cancer-related genes. This review summarizes the role of m6A modification on messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs) in cervical cancer (CC). We highlight the dual role of m6A regulatory factors, which act as oncogenes or tumor suppressors depending on the cellular context and downstream targets. Additionally, we examine how ncRNAs reciprocally regulate m6A modification in two ways: by guiding the deposition or removal of m6A modifications on RNA targets, and by modulating the expression of m6A regulatory factors. These interactions further contribute to tumor progression. Furthermore, the therapeutic potential of targeting m6A modification has been emphasized in CC. Moreover, recent advances in small-molecule inhibitors targeting m6A regulators and RNA-based therapies which may offer new treatment strategies have been summarized. Finally, we discuss the current challenges in m6A modification research and provide suggestions for future research directions. This review aims to deepen the understanding of m6A modification in CC and contribute to the development of targeted and personalized treatment strategies.

Tumor heterogeneity and resistance in glioblastoma: the role of stem cells

Glioblastoma multiforme (GBM) is one of the most aggressive and treatment-resistant brain tumor, characterized by its heterogeneity and the presence of glioblastoma stem cells (GSCs). GSCs are a subpopulation of cells within the tumor that possess self-renewal and differentiation capabilities, contributing to tumor initiation, progression, and recurrence. This review explores the unique biological properties of GSCs, including their molecular markers, signalling pathways, and interactions with the tumor microenvironment. We discuss the mechanisms by which GSCs evade conventional therapies, such as enhanced DNA repair and metabolic plasticity, which complicate treatment outcomes. Furthermore, we highlight recent advancements in identifying novel biomarkers and therapeutic targets that may improve the efficacy of treatments aimed at GSCs. The potential of targeted therapies, including immunotherapy and combination strategies, is also examined to overcome the challenges posed by GSCs. Ultimately, a deeper understanding of GSC biology is essential for developing personalized treatment approaches that can enhance patient outcomes in glioblastoma.

ncRNAs as Key Regulators in Gastric Cancer: From Molecular Subtyping to Therapeutic Targets

Gastric cancer (GC) poses a major global health challenge, underscoring the need for advanced diagnostic and therapeutic approaches. Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), have emerged as pivotal regulators in GC, with their dysregulated expression driving key processes such as tumorigenesis, metastasis, immune evasion, and chemoresistance. The functional diversity of ncRNAs across different GC molecular subtypes highlights their potential as biomarkers for improved subtype classification and patient stratification. Beyond their diagnostic value, ncRNAs demonstrate critical regulatory functions in tumor biology, establishing these RNA molecules as promising targets for therapeutic development. Strategies based on RNA hold considerable promise for addressing critical challenges such as immune escape and drug resistance by modulating key signaling pathways. These approaches can enhance immune responses, reprogram the tumor microenvironment, and reverse resistance mechanisms that compromise treatment efficacy, thereby improving clinical outcomes. Although ncRNAs represent a promising frontier in GC precision medicine, further research is required to fully harness their clinical potential.

LncRNA PVT1 promotes proliferation and migration in gallbladder adenocarcinoma by modulating miR-2355-5p/AGO1 axis

To investigate how lncRNA plasmacytoma variant translocation 1 (PVT1) contributed to the pathogenesis of gallbladder adenocarcinoma (GBA). Bioinformatics techniques were used to analyze differentially expressed lncRNA, and downstream miRNA and mRNA were identified using databases. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) and western blotting were utilized to analyze the RNA and protein expressions in different cells. The binding relationships between different genes were confirmed utilizing luciferase assay and RNA Immunoprecipitation (RIP) assay. Cell growth and migration were examined through CCK-8, colony formation, and Transwell assays. Several in vivo experiments were utilized to determine how the PVT1/miR-2355-5p/AGO1 pathway on tumor growth. Elevated PVT1 was observed in GBA cells, which may further aggravate cell malignant properties. Based on bioinformatics analysis, an interaction between miR-2355-5p and either PVT1 or AGO1 was identified, which was confirmed utilizing dual luciferase reporter assays and RIP assays. Silencing PVT1 (si-PVT1) led to a reduction in AGO1 expression, while depletion of miR-2355-5p reversed this effect. In vivo, PVT1 knockdown significantly inhibited tumor growth, an effect that was reversed by miR-2355-5p downregulation. This study showed that PVT1 facilitated GBA progression via the modulation of the miR-2355-5p/AGO1 axis. These findings underscored the potential therapeutic significance of targeting the lncRNA PVT1 in the treatment of GBA.

Noncoding RNAs and their influence on maternal mental health: insights into perinatal depression: a review

Perinatal depression profoundly influences the psychological and physiological well-being of women both during and after pregnancy. This condition encompasses depressive symptoms that manifest as antenatal as well as postnatal depression. Noncoding RNAs (ncRNAs), including microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), are integral to various cellular processes and have been implicated in the pathophysiology of perinatal depression. These ncRNAs are involved in the regulation of gene expression, maintenance of neuronal function, and modulation of stress responses. Dysregulation of ncRNAs, particularly lncRNAs and miRNAs, has been associated with psychiatric disorders, including perinatal depression. This review explores the classification and functions of ncRNAs, their biological roles, and the evidence linking them to perinatal depression. The investigation of ncRNAs in the context of perinatal depression holds promise for the development of novel therapeutic strategies and the enhancement of health outcomes for both mothers and their children. Future research should prioritize the standardization of methodologies and approaches in this field.

Long noncoding RNA LINC01811 sponges miR-214-3p and upregulates YAP1 thereby promoting the migration and invasion of colorectal cancer

Long non-coding RNAs (lncRNAs) exert significant influence on the development of cancer. However, their role in colorectal cancer (CRC) is not fully clarified. The expression levels of LINC01811 in CRC samples were determined using differential expression analysis and validated by RT-qPCR assays. Transwell assays were conducted to investigate the biological function of LINC01811 in CRC. To elucidate the mechanism by which LINC01811 acts as a molecular sponge for miR-214-3p and regulates YAP1 expression, binding site analysis, Luciferase reporter assay, RT-qPCR, and Western blotting were employed. We identified a novel oncogenic lncRNA LINC01811 in CRC tissues and cell lines. Our results showed that the suppression of LINC01811 significantly reduced CRC cell invasion and migration by regulating epithelial-mesenchymal transition-related markers, including MMP2, MMP9, vimentin, and E-cadherin in vitro. Furthermore, LINCO1811 modulated YAP1 expression by sequestering miR-214-3p, thereby promoting CRC progression by suppressing its activity. In summary, this study identified a novel lncRNA LINC01811 involved in CRC progression through the miR-214-3p/YAP1 axis.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-025-04292-8.

Organoid modeling identifies USP3-AS1 as a novel promoter in colorectal cancer liver metastasis through increasing glucose-driven histone lactylation

Dysregulation of long non-coding RNAs (lncRNAs) is common in colorectal cancer liver metastasis (CRLM). Emerging evidence links lncRNAs to multiple stages of metastasis from initial migration to colonization of distant organs. In this study we investigated the role of lncRNAs in metabolic reprogramming during CRLM using patient-derived organoid (PDO) models. We established five pairs of PDOs from primary tumors and matched liver metastatic lesions, followed by microarray analysis. We found that USP3-AS1 was significantly upregulated in CRLM-derived PDOs compared to primary tumors. High level of USP3-AS1 was positively associated with postoperative liver metastasis and negatively correlated with the prognosis of colorectal cancer (CRC) patients. Overexpression of USP3-AS1 significantly enhanced both sphere formation efficiency and liver metastasis in PDOs. Gene set enrichment analysis revealed that USP3-AS1 upregulation significantly enriched glycolysis and MYC signaling pathways. Metabolomics analysis confirmed that USP3-AS1 promoted glycolysis in PDOs, whereas glycolysis inhibition partially attenuated the effects of USP3-AS1 overexpression on PDO growth and liver metastasis. We revealed that USP3-AS1 stabilized MYC via post-translational deubiquitination, thereby promoting glycolysis. We demonstrated that USP3-AS1 increased the stability of USP3 mRNA, resulting in higher USP3 protein expression. The elevated USP3 protein then interacted with MYC and promoted its stability by deubiquitination. The USP3-AS1-MYC-glycolysis regulatory axis modulated liver metastasis by promoting H3K18 lactylation and CDC27 expression in CRC. In conclusion, USP3-AS1 is a novel promoter of CRLM by inducing histone lactylation.

EIF4A3-Induced hsa_circ_0118578 Expression Enhances the Tumorigenesis of Papillary Thyroid Cancer

Background: Circular RNA (circRNA) plays a regulatory role in the malignancy of papillary thyroid cancer (PTC). However, the role of a novel circRNA, hsa_circ_0118578, in PTC is not yet fully understood. This report focuses on unveiling hsa_circ_0118578's effect on PTC cell malignancy and reveals its mechanism in PTC progression. Methods: Levels of hsa_circ_0118578 in PTC were assessed by quantitative real-time polymerase chain reaction (qRT-PCR). The functional roles of hsa_circ_0118578 in PTC cell malignancy were evaluated through Transwell, 5-ethynyl-2'-deoxyuridine (EdU), and wound healing assays. A xenograft model in nude mice was used to examine the effects of hsa_circ_0118578's in vivo. The interaction between eukaryotic translation initiation factor 4A3 (EIF4A3) and hsa_circ_0118578 was confirmed using RNA-binding protein immunoprecipitation, qRT-PCR, and Western blotting. Results: Hsa_circ_0118578 with high expression in PTC tissues was associated with higher tumor node metastasis stage, lymph node metastasis, as well as poor differentiation. Cell functional assays demonstrated that silencing hsa_circ_0118578 inhibited PTC cell proliferation, invasion, and migration. In the xenograft assay, tumorigenicity of PTC cells in vivo was reduced following hsa_circ_0118578 suppression. Additionally, EIF4A3, as an RNA-binding protein, was shown to interact with hsa_circ_0118578 to stabilize its expression in PTC cells. Conclusions: Upregulated hsa_circ_0118578 in PTC interacts with EIF4A3 to exert oncogenic effects by enhancing hsa_circ_0118578 stability, contributing to PTC development. These findings shed light on the oncogenic role of hsa_circ_0118578 in PTC and suggest it as a potential therapeutic target.

TPX2 promotes papillary renal cell carcinoma progression by forming a ceRNA with LINC00894

PURPOSE

Papillary renal cell carcinoma (pRCC), particularly type 2, is associated with a poor prognosis. This study aimed to identify molecular mechanisms underlying pRCC progression and explore potential therapeutic targets to improve patient outcomes.

METHODS

TPX2 expression was analyzed in tumor samples from patients with type 2 pRCC. In vitro experiments were conducted to assess the effects of TPX2 and LINC00894 knockdown and overexpression on the proliferation and migration of Caki-2 and ACHN cells. Immunohistochemical analysis of tissue microarrays was performed to evaluate the associations between TPX2 expression and clinicopathological characteristics in type 2 pRCC patients.

RESULTS

Elevated TPX2 expression was significantly associated with a worse prognosis in type 2 pRCC patients and served as an independent risk factor for overall survival. Knockdown of TPX2 in Caki-2 and ACHN cells significantly reduced cell proliferation and migration. Additionally, LINC00894 was highly expressed in type 2 pRCC and correlated with poor prognosis. Mechanistically, miR-660-5p targeted the TPX2 3' UTR, promoting TPX2 degradation, while LINC00894 competitively bound to miR-660-5p, protecting TPX2 from miRNA-mediated degradation and exerting a pro-oncogenic effect. Immunohistochemical analysis revealed significant correlations between TPX2 expression and clinicopathological features, including tumor thrombus volume, tumor diameter, pathological TNM stage, and Fuhrman grade.

CONCLUSION

This study underscores the critical role of TPX2 in type 2 pRCC progression and highlights its potential as a prognostic biomarker and therapeutic target. The TPX2/LINC00894/miR-660-5p regulatory axis provides novel insights into the molecular mechanisms driving pRCC and offers a promising avenue for improving patient prognosis.

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.

Present progress in biomarker discovery of endometrial cancer by multi-omics approaches

Endometrial cancer (EC), a prevalent and intricate disease, is associated with a poor prognosis among gynecological malignancies. Its incidence rising globally underscores the urgent need for biomarkers detection in both research and clinical settings. Over the past decade, we've witnessed rapid advancements in biological methodologies and techniques. A multitude of omics technologies, encompassing genomic/transcriptomic sequencing and proteomic/metabolomic mass spectrometry, have been extensively employed to analyze both tissue and liquid samples derived from EC patients. The integration of multi-omics data has not only broadened our understanding of the disease but also unearthed valuable biomarkers specific to EC. This review encapsulates the recent progress and future prospects in the application of multi-omics technologies in EC research, emphasizing the potential of multi-omics in uncovering novel biomarkers and enhancing clinical assessments.

Advances in CRISPR/Cas13a-based biosensors for non-coding RNA detection

Non-coding RNAs play crucial roles in disease initiation and progression, making them promising biomarkers for early diagnosis and treatment monitoring. Conventional nucleic acid diagnostic methods, including polymerase chain reaction (PCR), next-generation sequencing (NGS), and enzyme-linked immunosorbent assay (ELISA), alongside emerging techniques such as single-molecule fluorescence in situ hybridization (smFISH), nanopore sequencing, and single-cell RNA sequencing (scRNA-seq), face inherent limitations in detecting regulatory non-coding RNAs. These challenges include laborious workflows, prolonged processing times, and technical complexities, hindering their broad applicability in rapid and high-throughput RNA analysis. CRISPR/Cas13a-based biosensors, integrated with various signal transduction systems-such as fluorescence, electrochemistry, colorimetry, surface-enhanced Raman spectroscopy (SERS)-show great promise for real-world diagnostic applications. This review provides a comprehensive overview of the CRISPR/Cas13a-mediated RNA detection mechanism, the development of CRISPR/Cas13a-based biosensors, and their integration with innovative signal detection methods. Additionally, we highlight the progress in portable detection devices, including lateral flow assay strips and smartphone-based platforms. Finally, the review discusses the current challenges and future prospects of CRISPR/Cas13a-based biosensors, particularly in the context of clinical diagnostics and personalized medicine.

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.

Interactions between long non-coding RNAs and m6 A modification in cancer

Long non-coding RNAs (lncRNAs) are a class of transcripts exceeding 200 nucleotides (nt) in length, which are broadly implicated in a broad spectrum of physiological and pathological processes, including allelic imprinting, genome packaging, chromatin remodeling, transcriptional activation and disruption, as well as the occurrence and progression of oncogenesis. N6-methyladenosine (m6 A) methylation stands as the most prevalent RNA modification, affecting multiple facets of RNA biology such as stability, splicing, transport, translation, degradation, and tertiary structure. Aberrant m6 A modifications are intimately implicated in cancer progression. In recent years, there has been a growing number of studies illuminating the dynamic interplay between lncRNAs and m6 A modifications, revealing that lncRNAs can modulate the activity of m6 A regulators, while m6 A not only affects the structural integrity but also the translational efficiency and stability of lncRNAs. Together, the interactions between lncRNAs and m6 A modifications significantly impact downstream oncogenes, cancer suppressor genes, cellular metabolism, epithelial-mesenchymal transition, angiogenesis, drug transport, DNA homology repair, and epigenetics, subsequently influencing tumorigenesis, metastasis, and drug resistance. This article endeavors to clarify the functions and mechanisms of lncRNAs and m6 A modifications interaction in cancer to provide promising insights for cancer diagnosis and therapeutic strategies.

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.

Classical biomarkers and non-coding RNAs associated with diagnosis and treatment in gastric cancer

One of the most prevalent malignant tumors worldwide, stomach cancer still has a high incidence and fatality rate in China, and the number of young people developing early-onset gastric cancer is steadily increasing. The 5-year survival rate of stomach cancer is typically 30%-35%, the prognosis is bad, the patients' quality of life is low, and the progression of advanced gastric cancer cannot be effectively managed despite the use of surgical surgery, chemotherapy, and other medicines. We urgently need molecular biomarkers with high specificity and sensitivity to increase the early gastric cancer detection rate, extend patient survival, and improve patient quality of life. The initial diagnosis of gastric cancer primarily depends on gastroscopy and biopsy, and invasive procedures cause significant discomfort to patients. Similar to this, treating advanced and metastatic stomach cancer is a pressing issue that requires attention. More and more immune checkpoint molecules have been discovered, and corresponding inhibitors are gradually being applied to clinical diagnosis and treatment. Recently, some non-coding RNAs have begun to be used as new targets for the treatment of gastric cancer. Some non-coding RNAs are highly present in the serum or urine of gastric cancer patients and can be used as diagnostic markers or prognostic indicators. Many clinical trials targeting non-coding RNAs have also shown good therapeutic effects. In general, targeting non-coding RNAs has shown good therapeutic effects. The biomarkers for gastric cancer detection and treatment are reviewed in this article, focusing on the new non-coding RNAs used in diagnosis, prognosis, and treatment. Patients with stomach cancer should have access to more precise and efficient diagnosis and treatment choices as a result of ongoing technological advancements and thorough research.

Long noncoding RNA VPS9D1-AS1 promotes angiogenesis in colorectal cancer by regulating the VEGFA signalling pathway

To clarify the mechanism of long non-coding RNA VPS9D1-AS1 affecting angiogenesis in colorectal cancer (CRC). Western blot and qRT-PCR assays were performed to detect the expression of VPS9D1-AS1 in colorectal cancer. The effects of VPS9D1-AS1 regulating VEGFA and affecting the proliferation, migration and invasion of human umbilical vein endothelial cells (HUVECs) were examined using cell biology, in vitro tubeformation and Chorioallantoic membrane vascular assay. Chromatin Immunoprecipitation (ChIP) and dual luciferase assays were performed to verify the specific sites of transcription factor binding to the promoter region of VPS9D1-AS1. VPS9D1-AS1 is highly expressed in colorectal cancer. Interfering with VPS9D1-AS1 inhibited the proliferation, invasion and migration of HUVECs. Mechanistically, VPS9D1-AS1 can promote angiogenesis by upregulating VEGFA expression and activating the downstream PI3K/AKT pathway. In addition, CEBPB is a transcription factor of VPS9D1-AS1 predicted by database, and the results of ChIP experiments showed that CEBPB could directly bind to the VPS9D1-AS1 promoter region at the -698 bp to -794 bp site. The results of dual luciferase assay showed that CEBPB could enhance VPS9D1-AS1 promoter activity and promote its transcription. VPS9D1-AS1 can be activated by CEBPB transcription factor and target VEGFA to activate its downstream pathway to promote colorectal cancer angiogenesis, which may suggest that VPS9D1-AS1 is critical for regulating colorectal cancer angiogenesis.

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.

METTL16-dependent miR-146b-5p m6A modification remodeling sensitize NSCLC to osimertinib via activating PI3K/AKT signaling

BACKGROUND

Non-small-cell lung cancer (NSCLC) is one of the most common malignant tumors, with poor prognosis and increasing osimertinib therapy resistance. Revealing mechanisms of NSCLC progression and therapy resistance remains critical. The aim of this study was to elucidate the molecular mechanism of miR-146b-5b-5p m6A modification and underlying function in regulating the proliferation and osimertinib resistance of NSCLC.

METHODS

TCGA, GEO datasets were used to analyze the differential expression of miR-146b-5p in NSCLC and adjacent tissues, and its impact on prognosis. Then the effects of miR-146b-5p on the proliferation and osimertinib of A549 and HCC827 cells were investigated through proliferation experiments, colony formation assay and IC50 assay. The regulatory mechanism of miR-146b-5p on the PI3K/AKT signaling pathway and its interaction in cancer progression were investigated through Western blots, dual-luciferase reporter assay, and rescue experiments.

RESULTS

miR-146b-5p was significantly upregulated in NSCLC tissue and represented worse prognosis. miR-146b-5p mimic significantly enhanced proliferation and osimertinib resistance, while miR-146b-5p inhibitor inhibited above phenotype. Through bioinformatic analysis and experimental results, miR-146b-5p interacted directly with PTEN mRNA and activated subsequent signaling pathway activation. PI3K/AKT inhibitor could eliminate the tumorigenic effects of miR-146b-5p mimic on the progression of NSCLC, while PI3K/AKT agonist could rescue the inhibition effect of miR-146b-5p inhibitor group cells. Further, methyltransferase METTL16 is responsible for miR-146b m6A modification. Modified miR-146b-5p promotes osimertinib resistance through downstream PI3K/AKT activation.

CONCLUSIONS

In summary, we found that METTL16 mediated miR-146b-5p m6A modification promoted the proliferation and osimertinib resistance of NSLCL by activating PI3K/AKT signaling pathway. Our study is expected to provide a novel insight and potential therapeutic target for NSCLC osimertinib resistance.

Targeting the epigenetic regulation of ferroptosis: a potential therapeutic approach for sepsis-associated acute kidney injury

Sepsis is a syndrome of organ dysfunction caused by the invasion of pathogenic microorganisms. In clinical practice, patients with sepsis are prone to concurrent acute kidney injury, which has high morbidity and mortality rates. Thus, understanding the pathogenesis of sepsis-associated acute kidney injury is of significant clinical importance. Ferroptosis is an iron-dependent programmed cell death pathway, which is proved to play a critical role in the process of sepsis-associated acute kidney injury through various mechanisms. Epigenetic regulation modulates the content and function of nucleic acids and proteins within cells through various modifications. Its impact on ferroptosis has garnered increasing attention; however, the role of epigenetic regulation targeting ferroptosis in sepsis-associated acute kidney injury has not been fully elucidated. Growing evidence suggests that epigenetic regulation can modulate ferroptosis through complex pathway networks, thereby affecting the development and prognosis of sepsis-associated acute kidney injury. This paper summarizes the impact of ferroptosis on sepsis-associated acute kidney injury and the regulatory mechanisms of epigenetic regulation on ferroptosis, providing new insights for the targeted therapy of sepsis-associated acute kidney injury.

CircRNA (circ)_0007823 Contributes to Triple-Negative Breast Cancer Progression and Cisplatin Resistance via the miR-182-5p/FOXO1 Pathway

Cisplatin (DDP) is used for the clinical management of triple-negative breast cancer (TNBC). However, the development of drug resistance limits its therapeutic efficacy. Circular RNAs (circRNAs) are known to be involved in tumor DDP resistance. In our previous study, we reported that circ_0007823 expression is downregulated and correlated with adverse prognosis in TNBC. However, its association with DDP resistance remains unclear. This study aimed to determine the role of circ_0007823 and miR-182-5p in DDP-resistant TNBC and explore the underlying mechanisms. First, expression profiles circ_0007823, microRNA (miR)-182-5p, and forkhead box O1 (FOXO1) in TNBC cells were determined. Additionally, biological characteristics of cells, including apoptosis, cell cycle, proliferation, and migration, were analyzed using various assays. Luciferase reporter and rescue assays were used to determine the correlations among circ_0007823, miR-182-5p, and FOXO1 expression. MiR-182-5p was overexpressed in DDP-resistant TNBC cells. MiR-182-5p knockdown suppressed the invasiveness and increased the apoptosis of drug-resistant cells, contributing to G1 arrest and S phase reduction. Mechanistically, circ_0007823 targeted miR-182-5p, and its overexpression drastically reduced the promotional effects of the miR-182-5p mimic on the aggression and transfer ability of drug-resistant cells. Furthermore, FOXO1 overexpression increased the sensitivity of cells to DDP and reduced their malignant progression. Therefore, FOXO1 was established as the downstream target of miR-182-5p that may be used to treat DDP-resistant TNBC. In summary, circ_0007823 overexpression attenuated DDP resistance in TNBC via the miR-182-5p-FOXO1 axis, indicating the therapeutic potential of circ_0007823 DDP-resistant TNBC treatment.

The Role of Non-coding RNAs in Diabetic Retinopathy: Mechanistic Insights and Therapeutic Potential

Diabetic retinopathy (DR) is the most common ocular complication in diabetic patients, accounting for a significant proportion of diabetes-related eye diseases. Approximately one-third of diabetic patients worldwide are affected by DR. Microvascular diseases, which can lead to severe visual impairment or even blindness, pose a significant threat to the quality of life and visual function of patients. However, the underlying cellular mechanisms of DR remain unclear. Recent studies have discovered that, apart from traditional pathological mechanisms, epigenetic mechanisms may alter key biological processes through gene expression dysregulation, thereby promoting the onset and progression of DR. Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), play crucial roles in gene regulation and disease pathways. Taking this into account, exploring innovative therapies and developing effective management strategies is crucial. This review focuses on the latest research on ncRNAs in DR, emphasizing their regulatory functions in cell proliferation, apoptosis, and inflammatory responses, and discusses the potential mechanisms by which ncRNAs accelerate disease progression. Additionally, the article highlights the potential role of exosome-associated ncRNAs in DR, proposing their use as early diagnostic markers and targeted therapeutic tools. By integrating current research, this review aims to provide guidance for future studies and promote the advancement of precision diagnostics and therapeutic efficacy in DR.

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.

Noncoding RNA (ncRNA)-mediated regulation of TLRs: critical regulator of inflammation in tumor microenvironment

Toll-like receptors (TLRs) are central components of the innate immune system as they recognize molecular patterns associated with pathogens and cellular damage and initiate immune responses using MyD88- and TRIF-dependent pathways. In contrast to being very useful for immune defense, dysregulated TLR signaling may be involved in diseases, such as cancer and autoimmune conditions. In cancer, TLRs create an environment that supports tumorigenesis and growth. In addition to this, a class of multifunctional noncoding RNAs (ncRNAs), including miRNAs, lncRNAs, and circRNAs, regulate gene expression without encoding proteins. MiRNAs regulate gene expression in a fine-tuned manner, while lncRNAs and circRNAs do so via diverse mechanisms. Notably, these ncRNAs interact, where lncRNAs and circRNAs function as competing endogenous RNAs and ceRNA, affecting miRNA activity. This interaction has a vital role in cancer pathology, in influencing that of various oncogenes and tumor suppressors in the tumor microenvironment; hence, modulation of ncRNAs could also be a great promising therapeutic approach. In this context, interplay between TLRs and ncRNAs is of paramount importance as they influence various parameters of the tumor microenvironment. TLR signaling works upon the expression of ncRNAs, while ncRNAs work back to regulate TLR signaling in return. An example of this includes miRNA targeting of components of the TLR; lncRNAs induced by TLR signaling possibly would favor tumor progression. Pharmacological interventions directed toward inhibiting these TLR pathways could be the model to halt malignancy by hampering pro-tumor inflammation and boosting immune responses against neoplasms. Hence, the review will highlight the complicated contrast of ncRNAs and TLRs within human cancer. By connecting the mechanisms, the researchers may study more about tumorigenesis and gather up new, innovative notions regarding therapeutic targeting.

The Application of Non-Coding RNAs as Biomarkers, Therapies, and Novel Vaccines in Diseases

Non-coding RNAs (ncRNAs) are a class of RNAs that largely lack the capacity to encode proteins. They have garnered significant attention due to their central regulatory functions across numerous cellular and physiological processes at transcriptional, post-transcriptional, and translational levels. Over the past decade, ncRNA-based therapies have gained considerable attention in the diagnosis, treatment, and prevention of diseases, and many studies have revealed a significant relationship between ncRNAs and diseases. At the same time, due to their tissue specificity, an increasing number of projects have focused on the application of ncRNAs as biomarkers in diseases, as well as the design and development of novel ncRNA-based vaccines and therapies for clinical use. These ncRNAs may also drive research into the potential molecular mechanisms and complex pathogenesis of related diseases. However, new biomarkers need to be validated for their clinical effectiveness. Additionally, to produce safe and stable RNA products, factors such as purity, precise dosage, and effective delivery methods must be ensured to achieve optimal bioactivity. These challenges remain key issues in the clinical application of ncRNAs. This review summarizes the prospects of ncRNAs as potential biomarkers, as well as the current research status and clinical applications of ncRNAs in therapies and vaccines, and discusses the challenges and expectations of ncRNAs in disease diagnosis and drug therapy.

Apelin/APJ: Another Player in the Cancer Biology Network

The apelinergic system exerts multiple biological activities in human pathologies, including cancer. Overactivation of apelin/APJ, which has been detected in many malignant tumors, and the strong correlation with progression-free and overall survival, suggested the role of an oncogene for the apelin gene. Emerging evidence sheds new light on the effects of apelin on cellular functions and homeostasis in cancer cells and supports a direct role for this pathway on different hallmarks of cancer: "sustaining proliferative signaling", "resisting cell death", "activating invasion and metastasis", "inducing/accessing vasculature", "reprogramming cellular metabolism", "avoiding immune destruction" and "tumor-promoting inflammation", and "enabling replicative immortality". This article reviews the currently available literature on the intracellular processes regulated by apelin/APJ, focusing on those pathways correlated with tumor development and progression. Furthermore, the association between the activity of the apelinergic axis and the resistance of cancer cells to oncologic treatments (chemotherapy, immunotherapy, radiation) suggests apelin/APJ as a possible target to potentiate traditional therapies, as well as to develop diagnostic and prognostic applications. This issue will be also covered in the review.

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 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.

The Role of M6A LncRNA Modification in Papillary Thyroid Cancer

Thyroid Cancer (TC) is the most common endocrine cancer, of which papillary thyroid cancer (PTC), a well-differentiated type of TC, accounts for 80-90%. Long non-coding RNAs (lncRNAs), which comprise non-protein-coding segments of the genome, have been found to play a crucial role in various biological processes, including cancer development. The activity of lncRNAs is modified through epigenetic modifications, with N6-Methyladenosine (m6A) modifications implicated in the progression of several malignancies. The activity of m6A is further regulated by modifying enzymes classified as "readers", writers", and "erasers", of which specific enzymes have been found to play a role in various aspects of PTC. Recent research has highlighted the significance of m6A modification in regulating the expression and function of lncRNAs associated with PTC pathogenesis. Dysregulation of this process implicates tumor proliferation, invasion, and metastasis, with subsequent impact on prognosis. Therefore, understanding the interplay between m6A modification and lncRNAs provides valuable insights into the molecular mechanisms underlying PTC progression. This narrative review aims to explore the established role of several prominent m6A modifying enzymes and lncRNAs on cancer pathogenesis and seeks to clarify the function of these enzymes in PTC pathogenesis.

Roles of autophagy and long non-coding RNAs in gastric cancer

Gastric cancer (GC) is one of the most aggressive malignancies worldwide and is characterized by its poor prognosis and resistance to conventional therapies. Autophagy and long non-coding RNAs (lncRNAs) play critical yet complex roles in GC, functioning as both tumor suppressors and promoters depending on the disease stage and context. Autophagy influences cellular homeostasis and metabolism, whereas lncRNAs regulate gene expression through epigenetic modifications, RNA sponging, and protein interactions. Notably, the interplay between lncRNAs and autophagy modulates tumor progression, metastasis, chemoresistance, and the tumor microenvironment. This study explored the intricate relationship between lncRNAs and autophagy in GC, highlighting their roles in pathogenesis and treatment resistance. By addressing current knowledge gaps and proposing innovative therapeutic strategies, we have emphasized the potential of targeting this dynamic interplay for improved diagnostic and therapeutic outcomes.

Influence of Magnesium Ions and Crowding Agents on Structure and Stability of RNA Aptamers

Aptamers bind to their targets with exceptional affinity and specificity. However, their intracellular application is hampered by the lack of knowledge about the effect of the cellular milieu on the RNA structure/stability. In this study, cellular crowding was mimicked using polyethylene glycol (PEG), and the crucial role of Mg2+ ions in stabilizing the structure of an RNA aptamer was investigated. Increasing the concentration of Mg2+ or PEG increased the thermal stability of the aptamer. The crowding effect lowered the requirement of the Mg2+ ion to form the binding-competent conformer of the aptamer. This suggests that crowding and other factors may compensate for a lower concentration of Mg2+ for proper folding of aptamers inside cells. Selective 2'-hydroxyl acylation and primer extension (SHAPE) probing permitted residue-level analysis of the aptamer. Mg2+ and/or PEG were shown to be involved in increasing the rigidity or flexibility of different regions of the aptamer. Fluorescence correlation spectroscopy showed a significantly low hydrodynamic radius (RH) in the presence of molecular crowders and Mg2+ ions. We believe that the decreased water activity due to crowding may be responsible for reduced RH. Our results show that in a crowded environment, the RNA aptamer was exposed to conformers that were not available to it in simple buffer solutions or solely in the presence of lower concentrations of Mg2+.

From diagnosis to therapy: The role of LncRNA GAS5 in combatting some cancers affecting women

Long non-coding RNAs (lncRNAs) are a collection of non-coding RNA molecules that consist of more than 200 nucleotides. In human malignancies, these lncRNAs exhibit abnormal expression patterns and play a significant role in either suppressing or promoting tumor growth. They achieve this by modulating various functions and mechanisms within cancer cells, including proliferation, invasion, metastasis, apoptosis, and resistance to different therapeutic approaches. The downregulation of long non-coding RNA growth arrest‑specific transcript 5 (GAS5) has been observed in multiple tumor types, indicating its role as a tumor suppressor in cancer. GAS5 exhibits interactions with various proteins, DNA, and microRNAs (miRNAs), leading to the upregulation of several mRNAs encoding suppressor proteins like PTEN. Consequently, this upregulation inhibits tumor growth. In this review, we have examined the existing literature concerning the expression of GAS5 and its diagnostic significance in female tissue-specific cancers, including breast, cervical, ovarian, and endometrial cancers. Additionally, we have explored its interactions with different miRNAs and its impact on cancer progression and resistance to therapy in these malignancies.

Perspectives of exosomal ncRNAs in the treatment of bone metabolic diseases: Focusing on osteoporosis, osteoarthritis, and rheumatoid arthritis

Bone metabolic disorders, constituting a group of prevalent and grave conditions, currently have a scarcity of therapeutic alternatives. Over the recent past, exosomes have been at the forefront of research interest, owing to their nanoparticulate nature and potential for therapeutic intervention. ncRNAs are a class of heterogeneous transcripts that they lack protein-encoding capacity, yet they can modulate the expression of other genes through multiple mechanisms. Mounting evidence underscores the intricate role of exosomes as ncRNAs couriers implicated in the pathogenesis of bone metabolic disorders. In this review, we endeavor to elucidate recent insights into the roles of three ncRNAs - miRNAs, lncRNAs, and circRNAs - in bone metabolic ailments such as osteoporosis, osteoarthritis, and rheumatoid arthritis. Additionally, we examine the viability of exosomal ncRNAs as innovative, cell-free modalities in the diagnosis and therapeutic management of bone metabolic disorders. We aim to uncover the critical function of exosomal ncRNAs within the context of bone metabolic diseases.

Hepatitis B Virus X Protein promotes VWF-mediated HCC progression through ST8SIA6-AS1/miR-3150b-3p/ASCL1 axis

Hepatocellular carcinoma (HCC) is one of the most prevalent malignant tumors, often with a poor prognosis. The HBx protein, encoded by the hepatitis B virus (HBv), is significantly associated with the pathogenesis of HCC. Although studies suggested that the von Willebrand factor (vWF) is key to the progression of HCC associated with HBv, the underlying mechanisms are largely obscure. Here we report that high vWF expression predicts poor prognosis in HCC patients infected with HBv. In vitro studies have shown that vWF enhances the migration, invasion, proliferation, and epithelial-mesenchymal transition (EMT) of HCC associated with HBv, and also inhibits apoptosis. We demonstrated that HBv-encoded oncogene X protein (HBx), a core protein of HBv expression can facilitate the transcription of vWF through the upregulation of ASCL1. Furthermore, miR-3150b-3p, which is negatively regulated by HBx, was screened to bind to the 3'UTR of ASCL1 and mediate ASCL1 silencing. Finally, we found that ST8SIA6-AS1 is positively regulated by HBx, which could sponge miR-3150b-3p, consequently impacting the expression of ASCL1 and ultimately alters the protein levels of vWF. In conclusion, our study identified that Hepatitis B Virus X Protein affected vWF level in HBv-related HCC through ST8SIA6-AS1/miR-3150b-3p/ASCL1 axis, which in turn promoted tumor malignant progression.

AC074117.1/miR-193a-3p axis regulates the malignant progression of uterine corpus endometrial carcinoma via the m6A-related gene ALKBH5

Uterine corpus endometrial carcinoma (UCEC) is one of the most common gynecological malignancies, with an annually increasing incidence and a poor prognosis. lncRNAs and microRNAs regulate the progression of UCEC through ceRNA networks. Additionally, m6A modification plays various roles in UCEC, and abnormal regulation of it can directly affect tumor progression. However, the role of m6A-associated ceRNA networks in UCEC remains unclear. This study showed that the AC074117.1/miR-193a-3p axis promoted the malignant progression of UCEC through ALKBH5, an m6A demethylase. MeRIP assay indicated that ALKBH5 regulated m6A modification in UCEC. Gene set enrichment analysis and cell proliferation and migration assays showed that the AC074117.1/miR-193a-3p/ALKBH5 axis regulated the proliferation and migration of UCEC cells. With regard to mechanistic analysis, dual-luciferase reporter assay demonstrated that AC074117.1 acted as a ceRNA for miR-193a-3p, influencing the expression of ALKBH5. Furthermore, rescue experiments validated that the regulatory effects of miR-193a-3p on the malignant progression of UCEC relied on ALKBH5 to some extent. Altogether, this study revealed an m6A-related ceRNA network in UCEC, which may serve as a target for early diagnosis and treatment.

HAS-CIRCpedia-5280 sponges miR-4712-5p inhibited colon cancer autophagyinduced by human beta-defensin-1

BACKGROUND

Among all malignancies, colorectal cancer ranks third in incidence rate and second in mortality rate. Human beta-defensin-1 (hBD-1) has broad-spectrum antimicrobial properties, and it plays an important role in the tumor microenvironment. Circular ribonucleic acids (circRNAs) regulate the proliferation and progression of colorectal cancer cells via cancer-related signaling pathways.

METHODS

Cell proliferation was assessed using the Cell Counting Kit-8 assay to determine the optimal hBD-1 concentration. Intracellular autophagic vesicles were visualized via monodansylcadaverine staining. In addition, the levels of AKT and mammalian target of rapamycin (mTOR)-associated signaling proteins were analyzed via Western blot analysis. CircRNA microarrays and quantitative real-time polymerase chain reaction were used to identify differentially expressed circRNAs in colon cancer cell lines. The functional role of HAS-CIRCpedia-5280 in vitro was demonstrated by overexpressing HAS-CIRCpedia-5280 and inhibiting miR-4712-5p. HAS-CIRCpedia-5280 could be a sponge of miR-4712-5p, mimicking the effect induced by HAS-CIRCpedia-5280 overexpression in colon cancer cells.

RESULTS

hBD-1 inhibited the proliferation of colon cancer cells and increased the number of intracellular autophagic vesicles. In addition, hBD-1 inhibited the AKT/mTOR signaling pathway, thereby enhancing cellular autophagy. Further, the interaction of HAS-CIRCpedia-5280 and miR-4712-5p was investigated. hBD-1 upregulated the expression level of HAS-CIRCpedia-5280 and downregulated the expression level of miR-4712-5p in colon cancer cells. Subsequently, the overexpression of HAS-CIRCpedia-5280 or the inhibition of miR-4712-5p activated the AKT/mTOR signaling pathway, leading to cellular autophagy inhibition. Conversely, the mimicry of miR-4712-p counteracted the effect of HAS-CIRCpedia 5280 overexpression in colon cancer cells by inhibiting the activation of the AKT/mTOR signaling pathway and, thereby, enhancing cellular autophagy.

CONCLUSION

hBD-1 can have an inhibitory effect against cell proliferation in colon cancer SW-620/HCT-116 cells via the HAS-CIRCpedia-5280/miR-4712-5p-mediated activation of autophagy.

Unraveling the mechanisms of glioblastoma's resistance: investigating the influence of tumor suppressor p53 and non-coding RNAs

Glioblastoma (GB) is one of the most fatal CNS malignancies, and its high resistance to therapy and poor outcomes have made it one of the primary challenges in oncology. Resistance to standard therapy, i.e., radio-chemotherapy with temozolomide, is one of the principal causes of the poor prognostic outcomes of GB. Finding the molecular basis of GB resistance to therapy is key to creating effective solution approaches. The general problem of GB resistance is supervised by cancer suppressive protein, p53, and has become a very special interest in molecular research in recent decades. The principal aim of this manuscript is to perform a comprehensive survey on the complex network of interactions developed by p53 with non-coding RNAs (ncRNA) in the context of GB resistance. The present article details the functional aspects of p53 as a cellular stress response protein, including its roles in apoptosis, cell cycle regulation, and DNA repair in glioblastoma (GB), along with the disruption of p53 and its involvement in chemoresistance (CR). It also highlights several classes of ncRNAs, namely microRNAs, long ncRNAs, and circular RNAs, that manipulate p53 signaling in GB-CR. The article likewise explains how disruption in the expression of these ncRNAs can promote GB-CR and how it interacts with essential cellular functions, such as proliferation, apoptosis, and DNA repair. The manuscript also describes the potential of targeting p53 and ncRNAs with their diagnostic and prognostic potential as novel promising therapeutics for GB. Nevertheless, ncRNA-based biomarkers still present challenges for their suitability in GB resistance. However, modern research continues to discover novel prediction targets, potentially enhancing patient outcomes and therapeutic options. Therefore, the neutralization of this intricate regulatory network of GB resistance might have a primary clinical effect in fighting GB resistance therapy and thus might lead to a substantial increase in patient survival and quality of life.

LINC01088 prevents ferroptosis in glioblastoma by enhancing SLC7A11 via HLTF/USP7 axis

BACKGROUND

Glioblastoma multiforme (GBM)is a highly aggressive malignancy of the central nervous system characterized by poor survival rates. Ferroptosis, an iron-dependent cell death pathway, is a promising therapeutic target for GBM. However, current treatments targeting cell death pathways have not yielded expected results. Long noncoding RNAs (lncRNAs) have been implicated in tumour proliferation, however, their role in ferroptosis in GBM remains underexplored. This study investigated the interplay between the lncRNA LINC01088 and ferroptosis in GBM to identify novel therapeutic strategies.

METHODS

We conducted gain- and loss-of-function studies to assess the impact of LINC01088 on GBM tumourigenesis and ferroptosis both in vitro and in vivo. Bioinformatics, dual-luciferase reporter assays, chromatin immunoprecipitation, RNA pulldown, mass spectrometry, RNA immunoprecipitation (RIP), and transcriptome sequencing were utilized to elucidate the mechanisms underlying LINC01088 expression and its downstream effects on ferroptosis.

RESULTS

The transcription factor specificity protein 1 (SP1) was identified as the promoter of LINC01088 transcription, which facilitated GBM progression. LINC01088 was found to inhibit ferroptosis and promote malignancy. Mechanistically, LINC01088 stabilized HLTF by enhancing its interaction with USP7 and preventing ubiquitin-mediated degradation. The stabilization of HLTF led to the upregulation of SLC7A11, which inhibits ferroptosis in GBM. Rescue experiments confirmed that altering HLTF levels reversed the ferroptotic phenotypes associated with LINC01088 modulation.

CONCLUSION

This study revealed a novel SP1/LINC01088/HLTF/USP7/SLC7A11 axis that regulates ferroptosis in GBM, highlighting LINC01088 as a potential therapeutic target for ferroptosis-dependent GBM treatment.

KEY POINTS

LINC01088 is transcriptionally upregulated by SP1. LINC01088 acts as a scaffold platform to bind USP7 and HLTF. USP7, as a deubiquitinating enzyme of HLTF, participates in inhibiting the ubiquitin-proteasome degradation of HLTF. HLTF transcriptionally upregates the expression of downstream SLC7A11, and ferroptosis of GBM cells was inhibited.

LINC00942 Accelerates Esophageal Cancer Progression by Raising PRKDC Through Interaction With PTBP1

Aberrantly expressed LINC00942 is participated in the progression of several cancers. However, the function of LINC00942 in esophageal cancer (ESCA) is unclear. The objective of this study was to explore the effect of LINC00942 on ESCA and its possible molecular mechanisms. First, differentially expressed lncRNAs in ESCA were analyzed using GSE192662 microarray. catRAPID omics v2.1 was applied to predict the proteins that might interact with LINC00942. SDS-PAGE silver staining assay, RNA pull down, and RIP assay were utilized to validate proteins interacting with LINC00942. Then, RNA seq was applied to detect the downstream targets of PTBP1, and KEGG enrichment analysis was used to analyze the genes involved in proliferation and migration-related signaling pathways. In addition, CCK-8, EdU and transwell were used to detect the impact of LINC00942 on ESCA cell function. Bioinformatics revealed that LINC00942 was significantly overexpressed in ESCA. Patients in low-expression of LINC00942 had an obviously better prognosis. After LINC00942 knockdown, the proliferation and migration of TE-1 and OE19 were dramatically reduced. Subsequently, PTBP1 was found to interact with LINC00942, and PRKDC was a downstream target of PTBP1. Functional analysis showed that TE-1 and OE19 cell proliferation and migration were markedly elevated after LINC00942 overexpression, and knockdown of PRKDC significantly reversed this effect. Mechanistically, LINC00942 promoted PRKDC expression by interacting with PTBP1. In summary, LINC00942 facilitated the proliferation and migration of ESCA cells via binding to PTBP1 to promote PRKDC expression.

Exosomal CircMFN2 Enhances the Progression of Pituitary Adenoma via the MiR-146a-3p/TRAF6/NF-κB Pathway

BACKGROUND

 Pituitary adenoma (PA) is a common intracranial endocrine tumor, but no precise target has been found for effective prediction and treatment of PA.

METHODS

 Quantitative reverse transcription polymerase chain reaction (qRT‒PCR) analysis showed that circMFN2 could affect the expression of miR-146a-3p in PA samples. Moreover, we used Western blotting to evaluate the expression levels of TRAF6 and NF-κB markers. The EdU assay, scratch wound healing assay, and Matrigel invasion assay were performed to assess the potential function of this pathway in PA cells. Based on the bioinformatic analysis including KEGG, gene ontology (GO) analysis, and microarray analysis, we evaluated the efficacy of circMFN2 as a potential biomarker for diagnosing PA, and we aimed to determine the mechanism of action in PA cells.

RESULTS

 Our findings indicate that there is a significant increase in the expression of circMFN2 in tissues, serum, and exosomes in the invasive group compared with the noninvasive and normal groups. Furthermore, this difference was statistically significant both preoperatively and postoperatively. To clarify its function, we downregulated this gene, and the experimental results suggested that the motility and proliferative capacity were reduced in vitro. In addition, rescue assays showed that miR-146a-3p could successfully reverse the inhibitory effect of circMFN2 knockdown on motility and proliferation in PA cells. Moreover, downregulation of circMFN2 and miR-146a-3p significantly changed the expression of TRAF6 and NF-κB.

CONCLUSION

 This study identified that circMFN2 regulates miR-146a-3p to promote adenoma development partially via the TRAF6/NF-κB pathway and may be a potential therapeutic target for PA.

The regulatory role of ZFAS1/miRNAs/mRNAs axis in cancer: a systematic review

Objectives

Recently, we and others have demonstrated the involvement of Zinc Finger Antisense 1 (ZFAS1) in cancer development. However, the intricate interplay of ZFAS1 with miRNAs and mRNAs remains to be fully understood.

Materials and methods

We followed PRISMA guidelines to retrieve and assess the available literature on the topic "ZFAS1/miRNA/mRNA axis" and "Cancer" from databases such as PubMed, Google Scholar, and ScienceDirect. We also used bioinformatic webtools for analyzing the potential miRNA targets of ZFAS1 and its role in survival of cancer patients along with their role in various biological functions and pathways.

Results

Our literature search and bioinformatic analysis reveals that ZFAS1 serves as a sponge for numerous miRNAs. Among the various targeted miRNAs, miR-150-5p stands out as significantly correlated with ZFAS1 across multiple databases (p-value = 3.27e-16, R-value = -0.346). Additionally, our Kaplan-Meier survival analysis indicates a noteworthy association between ZFAS1 expression levels and overall poor prognosis and survival rates in ovarian, sarcoma, and pancreatic cancers. We also underscore the involvement of various signaling pathways, including Signal Transducer and Activator of Transcription 3 (STAT3), Spindle and Kinetochore-associated Protein 1 (SKA1), Lysophosphatidic acid receptor 1 (LPAR1), and Wnt β-catenin, in cancer development through the ZFAS1/miRNAs/mRNAs axis. Furthermore, we identify ZFAS1's pivotal roles in diverse molecular processes, such as RNA binding and ribonucleoprotein formation.

Conclusion

In conclusion, this review comprehensively summarizes the latest advancements in understanding the regulatory relationships among ZFAS1, miRNAs, and mRNAs, emphasizing their collective role in cancer development to propose innovative avenues for cancer treatment. We believe that the intricate relationship among the ZFAS1-miRNA-mRNA axis may yield potential therapeutic targets for effective cancer management.

Comprehensive Analysis Identifies Hsa_circ_0058191 as a Potential Drug Resistance Target in Multiple Myeloma

Background

Multiple Myeloma (MM) is the second most common hematologic malignancy, which exhibits strong resistance to bortezomib, the first-line treatment. Circular RNAs (circRNAs) are increasingly considered as important drivers of drug resistance across various cancers, but their roles in multiple myeloma are not well understood.

Aim

To investigate and identify potential circRNA targets and their roles in the mechanisms of bortezomib resistance.

Methods

Bortezomib-resistant MM patient-specific circRNAs were screened using Arraystar circRNA microarrays. The MM circRNA dataset from the GEO database was analyzed with GEO2R to identify candidate circRNAs associated with MM progression and drug resistance. CircRNA-forming and loop-forming sites, along with their structures, were identified via Sanger sequencing. The identified circRNA was validated by qRT-PCR in MM patients with and without bortezomib resistance. Bioinformatic analysis through CircInteractome was conducted to predict potential miRNA and RBP binding for the core circRNAs. Metascape was employed to perform RBP pathway analysis to identify specific biological processes in circRNAs.

Results

The hsa_circ_0058191 was found to be overexpressed in bortezomib-resistant MM patient samples, suggesting its pivotal role in drug resistance mechanisms. The interaction of hsa_circ_0058191 with miR-660 and AGO2 as determined through bioinformatic predictions, indicated that it regulates RNA modification and mRNA regulation pathways. These molecular interactions expand our understanding of the mechanisms of drug resistance in multiple myeloma.

Conclusion

This study identified the role of hsa_circ_0058191 in the development of drug resistance in MM, which provides a theoretical foundation for designing potential therapeutic strategies to prevent drug resistance.

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.

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.

Aberrant SNHG expression predicts poor prognosis in esophageal cancer using meta-analysis and bioinformatics analysis

BACKGROUND

Small nucleolar RNA host gene (SNHG) family were reported involved in various biological processes and may be used as a promising prognostic marker in esophageal cancer (EC). A meta-analysis was performed to investigate the relationship between SNHG expression and prognosis of EC in this study.

METHODS

Relevant databases were browsed to obtain suitable publications. Hazard ratio (HR) with 95% confidence interval (CI) were extracted to explore the association between SNHG expression and EC prognosis. Odds ratio (OR) with 95%CI were extracted to assess the association between SNHG expression and other clinicopathological parameters. Sensitivity analysis and publication bias were performed to explore the reliability and robustness of the results. Bio-informatics has been explored in order to confirm our conclusions more comprehensively.

RESULTS

16 studies comprising 1229 patients were enrolled. The results showed that increasing SNHG expression indicated worse overall survival (HR: 1.392, 95%CI = 0.876-1.908). SNHG2, SNHG5, and SNHG12 were down-regulated, while other SNHGs were up-regulated in EC. In populations with low expression of SNHG2, SNHG5, and SNHG12, increasing SNHG expression predicted a favorable cancer prognosis (HR: 0.511, 95%CI = 0.322-0.700). Conversely, in populations with high expression of other SNHGs, SNHG expression indicated poor prognosis (OR: 2.340, 95%CI = 1.744-2.936). Elevated SNHG expression also implied advanced TNM stage (OR 1.578, 95%CI = 1.273-1.956) and lymph node metastasis (OR: 1.533, 95%CI = 1.205-1.950).

CONCLUSION

Increased expression of SNHG2, SNHG5, and SNHG12, and decreased expression of other SNHGs tended to have a favorable prognosis in patients with EC. These findings suggest that SNHG may serve as a prognostic marker and therapeutic target for EC.

Noncoding RNA profiling in omentum adipose tissue from obese patients and the identification of novel metabolic biomarkers

Background

Obesity, a prevalent metabolic disorder, is linked to perturbations in the balance of gene expression regulation. Noncoding RNAs (ncRNAs), including long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs), play pivotal roles in regulating gene expression. The aim of this study was to identify additional ncRNA candidates that are implicated in obesity, elucidating their potential as key regulators of the pathogenesis of obesity.

Methods

We identified distinct ncRNA expression profiles in omental adipose tissue in obese and healthy subjects through comprehensive whole-transcriptome sequencing. Subsequent analyses included functional annotation with GO and KEGG pathway mapping, validation via real-time quantitative polymerase chain reaction (qRT‒PCR), the exploration of protein‒protein interactions (PPIs), and the identification of key regulatory genes through network analysis.

Results

The results indicated that, compared with those in healthy individuals, various lncRNAs, circRNAs, and miRNAs were significantly differentially expressed in obese subjects. Further verifications of top changed gene expressions proved the most genes' consistence with RNA-sequencing including 11 lncRNAs and 4 circRNAs. Gene network analysis highlighted the most significant features associated with metabolic pathways, specifically ENST00000605862, ENST00000558885, and ENST00000686149. Collectively, our findings suggest potential ncRNA therapeutic targets for obesity, including ENST00000605862, ENST00000558885, and ENST00000686149.

Silencing of LINC01278 promotes sensitivity of non-small cell lung cancer cells to osimertinib by targeting miR-324-3p/ZFX axis

Osimertinib has been demonstrated to be effective for improving the prognosis of patients with epidermal growth factor receptor mutation-positive lung cancer. However, osimertinib resistance inevitably emerges throughout the treatment course. This study explored the function and mechanism of long noncoding RNA LINC01278 in osimertinib-resistant NSCLC cells. Osimertinib-resistant non-small cell lung cancer (NSCLC) cells were established by treating PC9 and HCC827 cells with increasing doses of osimertinib for over 6 months. LINC01278 expression in parental and drug-resistant cells (PC9-OR and HCC827-OR) was measured by polymerase chain reaction. Cell counting kit 8 assays were used to examine cell viability and half-maximal inhibitory concentration values. The effects of LINC01278 knockdown on cell proliferation and apoptosis were measured by colony formation assays and flow cytometry. A luciferase reporter assay was performed to verify the interaction between LINC01278 and miR-324-3p or the binding ability between miR-324-3p and ZFX. Protein levels of ZFX and apoptotic markers in NSCLC cells were measured by western blotting. As shown by experimental results, LINC01278 was highly expressed in osimertinib-resistant NSCLC cells compared to its expression in parental cells. The silencing of LINC01278 improved the sensitivity of drug-resistant cells towards osimertinib. LINC1278 depletion inhibited osimertinib-resistant cell proliferation while promoting cell apoptosis. LINC01278 interacted with miR-324-3p to regulate ZFX expression. ZFX could be targeted by miR-324-3p in PC9-OR and HCC827-OR cells. ZFX overexpression counteracted the suppressive impact of LINC01278 silencing on the malignant behavior of PC9-OR and HCC827-OR cells. In conclusion, LINC01278 knockdown alleviates osimertinib resistance of NSCLC cells by regulating downstream miR-324-3p and ZFX.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10616-024-00673-8.

The role and mechanism of epigenetics in anticancer drug-induced cardiotoxicity

Cardiovascular disease is the main factor contributing to the global burden of diseases, and the cardiotoxicity caused by anticancer drugs is an essential component that cannot be ignored. With the development of anticancer drugs, the survival period of cancer patients is prolonged; however, the cardiotoxicity caused by anticancer drugs is becoming increasingly prominent. Currently, cardiovascular disease has emerged as the second leading cause of mortality among long-term cancer survivors. Anticancer drug-induced cardiotoxicity has become a frontier and hot topic. The discovery of epigenetics has given the possibility of environmental changes in gene expression, protein synthesis, and traits. It has been found that epigenetics plays a pivotal role in promoting cardiovascular diseases, such as heart failure, coronary heart disease, and hypertension. In recent years, increasing studies have underscored the crucial roles played by epigenetics in anticancer drug-induced cardiotoxicity. Here, we provide a comprehensive overview of the role and mechanisms of epigenetics in anticancer drug-induced cardiotoxicity.

LncRNA MIR600HG inhibits laryngeal cancer development by mediating the miR-424-5p/BTG2 axis

Laryngeal carcinoma is the predominant kind of tumor seen under the category of head and neck malignancies. LncRNA MIR600HG affects tumor morphology in numerous cancer types. However, the function of MIR600HG in laryngeal cancer remains unclear. Protein and gene expressions were analyzed by using western blot and quantitative real time polymerase chain reaction. Cells proliferation and migration were evaluated by EdU and transwell assays. Flow cytometry was performed to detect cells apoptosis. The interaction between MIR600HG or B-cell translocation gene 2 (BTG2) and miR-424-5p was analyzed by dual luciferase reporter assay and RNA immunoprecipitation. The expression of MIR600HG in laryngeal cancer tissues was lower than that in normal tissues, and low expression of MIR600HG was associated with poor prognosis in laryngeal cancer. Furthermore, overexpression of MIR600HG resulted in a reduction in cellular proliferation and the promotion of apoptosis in both HEp-2 and Tu-212. Mechanically, miR-424-5p was a direct target of MIR600HG, and overexpression of MIR600HG reduced miR-424-5p expression. Furthermore, BTG2 was a target gene of miR-424-5p and miR-424-5p upregulation suppressed the expression of BTG2. In addition, overexpression of BTG2 inhibited laryngeal cancer progression, whereas MIR600HG knockdown or miR-424-5p overexpression reversed the role of BTG2. This work suggested that MIR600HG represses laryngeal tumor development by regulating the miR-424-5p/BTG2 axis, which provides new molecules for early diagnosis of laryngeal cancer in the future.