Noncoding RNA therapeutics - challenges and potential solutions

Novel insights into non-coding RNAs and their role in hydrocephalus

A large body of evidence has highlighted the role of non-coding RNAs in neurodevelopment and neuroinflammation. This evidence has led to increasing speculation that non-coding RNAs may be involved in the pathophysiological mechanisms underlying hydrocephalus, one of the most common neurological conditions worldwide. In this review, we first outline the basic concepts and incidence of hydrocephalus along with the limitations of existing treatments for this condition. Then, we outline the definition, classification, and biological role of non-coding RNAs. Subsequently, we analyze the roles of non-coding RNAs in the formation of hydrocephalus in detail. Specifically, we have focused on the potential significance of non-coding RNAs in the pathophysiology of hydrocephalus, including glymphatic pathways, neuroinflammatory processes, and neurological dysplasia, on the basis of the existing evidence. Lastly, we review the potential of non-coding RNAs as biomarkers of hydrocephalus and for the creation of innovative treatments.

Potential mechanisms of non-coding RNA regulation in Alzheimer's disease

Alzheimer's disease, a progressively degenerative neurological disorder, is the most common cause of dementia in the elderly. While its precise etiology remains unclear, researchers have identified diverse pathological characteristics and molecular pathways associated with its progression. Advances in scientific research have increasingly highlighted the crucial role of non-coding RNAs in the progression of Alzheimer's disease. These non-coding RNAs regulate several biological processes critical to the advancement of the disease, offering promising potential as therapeutic targets and diagnostic biomarkers. Therefore, this review aims to investigate the underlying mechanisms of Alzheimer's disease onset, with a particular focus on microRNAs, long non-coding RNAs, and circular RNAs associated with the disease. The review elucidates the potential pathogenic processes of Alzheimer's disease and provides a detailed description of the synthesis mechanisms of the three aforementioned non-coding RNAs. It comprehensively summarizes the various non-coding RNAs that have been identified to play key regulatory roles in Alzheimer's disease, as well as how these non-coding RNAs influence the disease's progression by regulating gene expression and protein functions. For example, miR-9 targets the UBE4B gene, promoting autophagy-mediated degradation of Tau protein, thereby reducing Tau accumulation and delaying Alzheimer's disease progression. Conversely, the long non-coding RNA BACE1-AS stabilizes BACE1 mRNA, promoting the generation of amyloid-β and accelerating Alzheimer's disease development. Additionally, circular RNAs play significant roles in regulating neuroinflammatory responses. By integrating insights from these regulatory mechanisms, there is potential to discover new therapeutic targets and potential biomarkers for early detection and management of Alzheimer's disease. This review aims to enhance the understanding of the relationship between Alzheimer's disease and non-coding RNAs, potentially paving the way for early detection and novel treatment strategies.

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.

Expanded insights into the mechanisms of RNA-binding protein regulation of circRNA generation and function in cancer biology and therapy

RNA-binding proteins (RBPs) regulate the generation of circular RNAs (circRNAs) by participating in the reverse splicing of circRNA and thereby influencing circRNA function in cells and diseases, including cancer. Increasing evidence has demonstrated that the circRNA-RBP network plays a complex and multifaceted role in tumor progression. Thus, a better understanding of this network may provide new insights for the discovery of cancer drugs. In this review, we discuss the characteristics of RBPs and circRNAs and how the circRNA-RBP network regulates tumor cell phenotypes such as proliferation, metastasis, apoptosis, metabolism, immunity, drug resistance, and the tumor environment. Moreover, we investigate the factors that influence circRNA-RBP interactions and the regulation of downstream pathways related to tumor development, such as the tumor microenvironment and N6-methyladenosine modification. Furthermore, we discuss new ideas for targeting circRNA-RBP interactions using various RNA technologies.

β-elemene: A promising natural compound in lung cancer therapy

Lung cancer, a leading cause of cancer-related mortality globally, presents complex challenges in treatment and disease management. This review explores β-elemene, a sesquiterpene from Curcuma wenyujin, emphasising its pharmacological effects and therapeutic mechanisms in lung cancer. Focusing on its roles in modulating cellular pathways, this study details β-elemene's influence on apoptosis, autophagy, ferroptosis, hypoxic responses, metabolic shifts, and cell cycle arrest, as well as its impact on the tumour microenvironment and regulatory pathways (including PI3K/AKT, STAT3, AMPK/MAPK) and non-coding RNAs. The potential of β-elemene as a complementary agent in chemotherapy, radiotherapy, and hyperthermia therapy is examined, underscoring its capability to bolster treatment efficacy and counter drug resistance. The review also addresses current obstacles in clinical use, notably bioavailability issues, and explores innovative delivery systems like liposomes and microemulsions designed to enhance therapeutic delivery. Although preclinical studies indicate significant anti-tumor effects, further research is needed to address clinical translation challenges. Collectively, this review highlights β-elemene's multi-targeted therapeutic potential in lung cancer, advocating for ongoing research to refine its clinical use and optimize patient outcomes.

Ferroptosis-related LncRNAs in diseases

Ferroptosis is a form of regulated cell death (RCD) caused by the accumulation of intracellular iron and lipids and is involved in many pathological processes, including neurodegenerative and cardiovascular diseases, and cancer. Long non-coding RNAs (lncRNAs), RNA molecules exceeding 200 nt in length that do not possess protein coding function can interfere with ferroptosis by binding ferroptosis-related miRNAs or proteins. Recently, ferroptosis-related lncRNAs (FRlncRNAs) have been identified in cancer and non-malignant disease models, including inprediction of drug resistance, intra-tumoral immune infiltration, metabolic reprogramming and mutation landscape. Here, we review FRlncRNAs in cancer and non-malignant diseases, from prognosis to treatment.

The role of curcumin in modulating circular RNAs and long non-coding RNAs in cancer

Cancer is one of the primary causes of human disease and death, with high morbidity and mortality rates. Chemotherapy, one of the most common therapeutic techniques, functions through a variety of mechanisms, including the production of apoptosis and the prevention of tumor development. Herbal medicine has been the subject of numerous investigations due to its potential as a valuable source of innovative anti-cancer products that target multiple protein targets and cancer cell genomes. Curcumin, a polyphenol that is the major bioactive ingredient of turmeric, exhibits pharmacological and biological efficacy with antioxidant, anti-inflammatory, anticancer, cardioprotective, neuroprotective, and hypoglycemic activity in humans and animals. Recent research suggests that curcumin changes noncoding RNA (ncRNA), such as long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs), in various types of cancers. Both circRNAs and lncRNAs are ncRNAs that can epigenetically modulate the expression of multiple genes via post-transcriptional regulation. In this study, we outline curcumin's activities in modulating signaling pathways and ncRNAs in various malignancies. We also described curcumin's regulatory function, which involves blocking carcinogenic lncRNAs and circRNAs while increasing tumor-suppressive ones. Furthermore, we intend to demonstrate how ncRNAs and signaling pathways interact with each other across regulatory boundaries to gain a better understanding of how curcumin fights cancer and create a framework for its potential future therapeutic uses.

LncRNA MKLN1-AS promotes glioma tumorigenesis and growth via activating the Hippo pathway through miR-126-5p/TEAD1 axis

The involvement of long non-coding RNAs (lncRNAs) in glioma carcinogenesis has gradually been identified. Herein, we aimed to explore the function and mechanism of lncRNA muskelin 1 antisense RNA (MKLN1-AS) in glioma cell oncogenic properties. Quantitative real-time polymerase chain reaction was utilized to test the expression of MKLN1-AS, miR-126-5p, and TEAD1 (TEA Domain Transcription Factor 1) mRNA expression. Oncogenic properties of glioma cells were characterized using 5-ethynyl-2'-deoxyuridine, flow cytometry, wound healing, transwell, and tube formation assays, respectively. Levels of TEAD1 protein, mobility-related proteins, and Hippo pathway-related proteins were examined by Western blotting. The binding between miR-126-5p and MKLN1-AS or TEAD1 was confirmed by using dual-luciferase reporter and pull-down assays. The murine xenograft model was established for in vivo analysis. Levels of MKLN1-AS in glioma tissues and cell lines were higher, functionally, MKLN1-AS deficiency could suppress glioma cell proliferation, migration, invasion, and angiogenesis, and induce apoptosis in vitro, as well as impede tumor growth in vivo. Mechanistically, miR-126-5p was targeted by MKLN1-AS, miR-126-5p directly targeted TEAD1. The suppressing effects of MKLN1-AS deficiency on glioma cell oncogenic properties were abolished by TEAD1 overexpression or miR-126-5p inhibition. Besides, MKLN1-AS/miR-126-5p mediates the activation of Hippo pathway by TEAD1. MKLN1-AS knockdown weakened glioma cell oncogenic phenotypes and growth via TEAD1-Hippo pathway through miR-126-5p, indicating a new therapeutic target for glioma molecular therapy.

The role of micro-ribonucleic acid and small interfering-ribonucleic acid in precision nutrition for obesity management

BACKGROUND & AIMS

Precision nutrition aims to tailor dietary interventions based on genetic and molecular profiles. MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are emerging as critical tools in precision obesity management. miRNAs serve as biomarkers for predicting dietary response and obesity risk, while siRNAs provide a targeted approach to silencing obesity-related genes. This review explores the mechanisms, applications, and potential of integrating miRNA and siRNA in personalized dietary strategies to combat obesity.

METHODS

A comprehensive literature review was conducted using Boolean operations to identify studies on miRNAs, siRNAs, and their roles in precision nutrition. The review focused on molecular mechanisms, clinical applications, challenges, and future directions in integrating miRNA detection and siRNA therapy for obesity management.

RESULTS

miRNAs regulate gene expression related to lipid metabolism, adipogenesis, and insulin sensitivity, with miRNA-33 and miRNA-103/107 being notable examples. siRNAs offer precise gene silencing for targets like SREBP-1c and PPARγ, addressing metabolic pathways resistant to dietary interventions. The synergistic integration of miRNAs as biomarkers and siRNAs as therapeutic tools enhances the personalization and efficacy of obesity management.

CONCLUSIONS

The dual application of miRNAs and siRNAs in precision nutrition represents a transformative approach to obesity management. While challenges such as molecular stability and delivery systems persist, advancements in RNA technology and clinical research promise to revolutionize personalized dietary strategies. Future research should focus on large-scale trials and ethical considerations to ensure equitable and effective implementation.

Targeting and engineering biomarkers for prostate cancer therapy

Prostate cancer (PCa) is the second most commonly occurring cancer among men worldwide. Although the clinical management of PCa has significantly improved, a number of limitations have been identified in both early diagnosis and therapeutic treatment. Because multiple studies show that prostate-specific antigen (PSA) screening frequently results in overdiagnosis and overtreatment, the use of PSA alone as a diagnostic marker for PCa screening has been controversial. For individuals with locally advanced or metastatic PCa, androgen deprivation therapy (ADT) is the standard initially successful treatment; nonetheless, the majority of patients will eventually develop lethal metastatic castration-resistant prostate cancer (CRPC). Alternative treatment options, including chemo-, immuno-,or radio-therapy, can only prolong the survival of CRPC patients for several months with the most developing resistance. Considering this background, there is an urgent need to discuss about selective prostate-specific biomarkers that can predict clinically relevant PCa diagnosis and to develop biomarker-driven treatments to counteract CRPC. This review addresses several PCa-specific biomarkers that will assist physicians in determining which patients are at risk of having high-grade PCa, focusing on the clinical relevance of these biomarker-based tests among PCa patients. Secondly, this review highlights the effective use of these markers as drug targets to develop precision medicine or targeted therapies to counteract CRPC. Altogether, translating this biomarker-based research into the clinic will pave the way for the effective execution of personalized therapies for the benefit of healthcare providers, the biopharmaceutical industry, and patients.

LURAP1L-AS1 long noncoding RNA promotes breast cancer progression and associates with poor prognosis

Long noncoding RNAs (lncRNAs) are emerging as critical regulators of cancer biology, yet their roles in breast cancer, particularly in triple-negative breast cancer (TNBC), remain incompletely understood. Through a custom siRNA library screen targeting TNBC-associated lncRNAs in MDA-MB-231 and BT-549 TNBC cell models, we identified LURAP1L-AS1 as a key modulator of TNBC progression. Survival analysis of TNBC patients demonstrated a significant association between elevated LURAP1L-AS1 expression and poor clinical outcomes. LURAP1L-AS1 knockdown significantly impaired colony formation and organoid growth of TNBC models, associated with increased apoptosis thus highlighting its role in promoting tumorigenicity. RNA sequencing of LURAP1L-AS1-depleted cells revealed dysregulation of pathways related to cell proliferation, apoptosis, migration, and RNA processing. Bioinformatics analysis predicted LURAP1L-AS1 to function as a competitive endogenous RNA (ceRNA), sponging key microRNAs, such as miR-7a-5p, miR-101-3p, miR-181a-5p, and miR-27a-3p, thereby modulating oncogenes including EZH2, MCL1, and KRAS, which are linked to increased cancer cell survival, proliferation, and metastasis. In addition to its role in TNBC, correlation analysis using breast cancer patient datasets revealed a significant association between LURAP1L-AS1 and ESR1 expression, suggesting its broader impact across breast cancer subtypes. Concordantly, LURAP1L-AS1 depletion inhibited estrogen receptor-positive (ER+) MCF7 breast cancer cells colony formation and organotypic growth. Our findings establish LURAP1L-AS1 as a functional lncRNA that promotes breast cancer progression, highlighting its potential for use in RNA-based therapies for breast cancer.

Artificial intelligence-driven microRNA signature for early detection of gastric cancer: discovery and clinical functional exploration

BACKGROUND

Gastric cancer (GC) is a leading cause of cancer-related deaths worldwide, with late-stage diagnoses frequently leading to poor outcomes. This underscores the need for effective early-stage gastric cancer (ESGC) diagnostics.

METHODS

We introduce ESGCmiRD, an innovative artificial intelligence-driven strategy that identifies a miRNA signature for ESGC detection by integrating robust expression patterns, ESGC relevance, and regulatory capabilities of microRNA (miRNA) based on multiple networks. Expression and biological roles of miRNAs in GC were validated and explored via bioinformatics analysis and in vitro studies. miRNA-target interaction was confirmed by dual-luciferase reporter assay. Molecular docking predicted miRNA-drug binding affinities, assessing the miRNA signature's therapeutic potential.

RESULTS

ESGCmiRD identified a blood miRNA signature (miR-320b, miR-222-3p, miR-181a-5p, miR-103a-3p, miR-107) for ESGC detection, demonstrated high diagnostic accuracy with AUC values of 0.986, 0.977, 0.815, and 0.811 in the test and three validation sets (GSE211692, TCGA-STAD, and our cohort), respectively. The five miRNAs were overexpressed in ESGC plasma and directly target PTEN, promoting GC cell proliferation, migration, and invasion. Molecular docking suggested Paclitaxel had the strongest potential interaction with these miRNAs.

CONCLUSION

This method identifies a robust miRNA signature for ESGC detection and sheds light on gastric carcinogenesis mechanisms, opening doors for potential therapeutic strategies.

The lncRNA ST18-AS1 suppresses pancreatic cancer progression by enhancing ST18 mRNA stability through anchoring FUS in the cytoplasm

Pancreatic ductal adenocarcinoma (PDAC) is associated with a high mortality rate and short survival time. Long noncoding RNAs (lncRNAs) play a significant role in the progression of PDAC. However, prognostic lncRNAs associated with overall survival (OS) in patients with PDAC remain elusive. RNA sequencing was used to identify differential lncRNA expression between short-term and long-term PDAC patients. We identified a novel lncRNA (ENSG00000253924), termed ST18-AS1 (ST18-associated lncRNA), that is highly expressed in the tissues of long-term PDAC patients. High ST18-AS1 expression was correlated with favorable clinical outcomes, and the upregulation of ST18-AS1 expression in PDAC cell lines suppressed cell proliferation and promoted apoptosis both in vivo and in vitro. The key downstream target regulated by ST18-AS1 was Suppression of tumorigenicity 18 (ST18). We also found that ST18 expression was lower in PDAC tissues compared to non-tumorous adjacent tissues (NATs) and that higher ST18 expression was correlated with better clinical outcomes. Accordingly, the forced expression of ST18 inhibited proliferation and promoted apoptosis in tumor cells. Mechanistic studies showed that ST18-AS1 maintained the stability of ST18 mRNA by binding to Fused in sarcoma (FUS) and anchoring FUS in the cytoplasm. Overall, we identified ST18-AS1 as a novel biomarker that inhibits PDAC cell proliferation and promotes PDAC cell apoptosis through ST18. Targeting ST18-AS1/ST18 may be a potential therapeutic strategy for treating PDAC.

Hybridization chain reaction-based DNA nanoframeworks for biosensing and therapeutic applications

Artificial DNA nanostructures, with their sequence programmability, precise molecular recognition and tunable stimuli responsiveness, bridge material chemistry and biomedicine. Here we detail the design and construction of hybridization chain reaction (HCR)-based DNA nanoframeworks, a class of DNA nanostructures with programmable sequences and customizable functions. HCR is an efficient, enzyme-free amplification strategy that isothermally produces nicked double-stranded DNA with periodically repeated modules via the assembly of two DNA hairpins, triggered by a DNA initiator. In contrast to other available assembly methods for the synthesis of DNA nanostructures, such as tile-mediated assembly, DNA origami and rolling circle amplification, the HCR method offers improved stability and efficiency under mild conditions, without reliance on enzymatic activity. The procedure uses radical polymerization to integrate DNA initiator into nanoframeworks, with overhangs complementary to functional sequences - termed linkers -which are amplified and incorporated through HCR. The linkers enable the incorporation of functional nucleic acid sequences. The HCR-based DNA nanoframeworks facilitate the loading capability of the delivered molecules, showing notable therapeutic efficacy and biosensing sensitivity. Preparation time for HCR-based DNA nanoframeworks ranges from 30 h to 45 h, depending on the payload.

YAP1 promoter-associated noncoding RNA affects Ewing sarcoma cell tumorigenicity by regulating YAP1 expression

BACKGROUND

Ewing sarcomas (ESs) are aggressive paediatric tumours of bone and soft tissues afflicting children and adolescents. Despite current therapies having improved the 5-year survival rate to 70% in patients with localized disease, 25% of patients relapse and most have metastasis at diagnosis. Resistance to chemotherapy, together with the high propensity to metastasize, remain the main causes of treatment failure. Thus, identifying novel targets for alternative therapeutic approaches is urgently needed.

METHODS

Biochemical and functional analyses were carried out to elucidate the mechanism of regulation of YAP1 expression by pncRNA_YAP1-1 in ES cells.

RESULTS

Here, we identified a novel promoter-associated noncoding RNA, pncRNA_YAP1-1, transcribed from the YAP1 promoter in ES cells. We found that pncRNA_YAP1-1 level exerts antitumour effects on ES by destabilizing YAP1 protein. The molecular mechanism relies on the interaction of pncRNA_YAP1-1 with the RNA binding protein FUS, which stabilizes the transcript. Furthermore, pncRNA_YAP1-1 binding to TEAD impairs its interaction with YAP1, thus determining YAP1 translocation into the cytoplasm, its phosphorylation and degradation.

CONCLUSIONS

Overall, our findings reveal a novel layer of regulation of YAP1 protein expression by pncRNA_YAP1-1 in Ewing sarcoma. Considering the role of YAP1 in therapy response and cell propensity to metastasize, our results indicate pncRNA_YAP1-1 as an actionable target that could be exploited to enhance chemotherapy efficacy in Ewing sarcoma.

SIGNIFICANCE

PncRNA_YAP1-1 counteracts the YAP1 oncogenic transcriptional program in Ewing sarcoma cells by interfering with YAP1-TEAD interaction and impairing YAP1 protein stability. These findings uncover a novel treatment option for Ewing sarcoma.

Machine learning approaches for predicting the small molecule-miRNA associations: a comprehensive review

MicroRNAs (miRNAs) are evolutionarily conserved small regulatory elements that are ubiquitous in cells and are found to be abnormally expressed during the onset and progression of several human diseases. miRNAs are increasingly recognized as potential diagnostic and therapeutic targets that could be inhibited by small molecules (SMs). The knowledge of SM-miRNA associations (SMAs) is sparse, mainly because of the dynamic and less predictable 3D structures of miRNAs that restrict the high-throughput screening of SMs. Toward augmenting the costly and laborious experiments determining the SM-miRNA interactions, machine learning (ML) has emerged as a cost-effective and efficient platform. In this article, various aspects associated with the ML-guided predictions of SMAs are thoroughly reviewed. Firstly, a detailed account of the SMA data resources useful for algorithms training is provided, followed by an elaboration of various feature extraction methods and similarity measures utilized on SMs and miRNAs. Subsequent to a summary of the ML algorithms basics and a brief description of the performance measures, an exhaustive census of all the 32 ML-based SMA prediction methods developed so far is outlined. Distinctive features of these methods have been described by classifying them into six broad categories, namely, classical ML, deep learning, matrix factorization, network propagation, graph learning, and ensemble learning methods. Trend analyses are performed to investigate the patterns in ML algorithms usage and performance achievement in SMA prediction. Outlining key principles behind the up-to-date methodologies and comparing their accomplishments, this review offers valuable insights into critical areas for future research in ML-based SMA prediction.

The crosstalk between glutathione metabolism and non-coding RNAs in cancer progression and treatment resistance

Excessive reactive oxygen species (ROS) are closely associated with the initiation and progression of cancers. As the most abundant intracellular antioxidant, glutathione (GSH) plays a critical role in regulating cellular ROS levels, modulating physiological processes, and is intricately linked to tumor progression and drug resistance. However, the underlying mechanisms remain not fully elucidated. Non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), are key regulators of GSH levels. Different ncRNAs modulate various pathways involved in GSH metabolism, and these regulatory targets have the potential to serve as therapeutic targets for enhancing cancer treatment. In this review, we summarize the functions of GSH metabolism and highlight the significance of ncRNA-mediated regulation of GSH in cancer progression, drug resistance, and clinical applications.

Identification of progression related LncRNAs in colorectal cancer aggressiveness

Colorectal cancer (CRC) progression involves complex molecular alterations, including the dysregulation of long non-coding RNAs (lncRNAs). In this study, we identified key progression-related lncRNAs in CRC by integrating transcriptomic data from TCGA and single-cell RNA sequencing (scRNA-seq). Differential expression analysis revealed numerous lncRNAs associated with CRC progression. To systematically prioritize these lncRNAs, we developed a scoring system incorporating multiple progression-related signatures, differential expression, and survival analysis. This approach identified 198 key lncRNAs, including both known (e.g., LINC01615) and novel candidates (e.g., AC007998.3). Experimental validation confirmed that LINC01615 was significantly upregulated in CRC tissues, whereas AC007998.3 was downregulated. Further analyses indicated that these lncRNAs influence CRC progression through cis-, trans-, and post-transcriptional regulation. Patients were classified into distinct molecular subgroups based on lncRNA expression, exhibiting significant differences in prognosis and immune microenvironment composition. The enrichment of progression-related lncRNAs among differentially expressed lncRNAs was statistically significant, reinforcing their functional relevance. Validation across independent datasets demonstrated the robustness of our findings. Our research provides novel insights into the molecular mechanisms underlying CRC progression and highlights the potential of progression-related lncRNAs as prognostic biomarkers and therapeutic targets.

Nebulized inhalation of extracellular vesicles containing SPOCK2 suppresses lung adenocarcinoma progression via MAPK inhibition

Aberrant expression of SPARC/osteonectin, cwcv and kazal-like domains proteoglycan 2 (SPOCK2) plays a role in the development and progression of several human cancers. However, the importance of its expression and function in lung adenocarcinoma (LUAD) remains unclear. The present study aimed to elucidate the role of SPOCK2 in the growth of LUAD and propose a novel therapeutic insight for LUAD through SPOCK2. SPOCK2 protein expression was significantly reduced in LUAD tissues and cells by Immunohistochemical assay and Western blot. CCK-8, colony formation, and Transwell assays were used to demonstrate that SPOCK2 overexpression inhibited both proliferation and migration of LUAD cells in vitro. This inhibition of tumor growth was further confirmed by a LUAD xenograft mouse model in vivo. To explore downstream target signal of SPOCK2 in LUAD, RNA transcriptome sequencing was performed and enrichment analysis showed an association between SPOCK2 expression and the MAPK pathway. Furthermore, HEK293T cells were modified with SPOCK2, and extracellular vesicles (EVs) containing SPOCK2 (SPOCK2-EVs) were collected through ultra-high-speed centrifugation. Interestingly, co-culture with SPOCK2-EVs significantly increased SPOCK2 levels within LUAD cells. Furthermore, SPOCK2-EVs effectively inhibited LUAD growth in vitro and in vivo studies. Because directly injecting SPOCK2-EVs into tumors presents challenges for internal organs, we investigated the efficacy of nebulized SPOCK2-EVs for LUAD treatment. Consistent with our findings from intratumoral injection, nebulized inhalation of SPOCK2-EVs resulted in significant inhibition of LUAD growth. These results strongly suggest that SPOCK2 released by HEK293T-EVs can effectively inhibit LUAD tumor growth and hold promise for future clinical translation in cancer therapy.

RNA therapeutics-An evaluation of potential occupational health hazards and a strategy to establish occupational exposure limits (OELs)

RNA therapeutics represent a rapidly expanding and innovative group of pharmaceuticals. These new modalities necessitate the establishment of Occupational Exposure Limits (OELs) to ensure safe occupational handling. While there is an established methodology for setting OELs for small molecule therapeutics, this methodology is not readily applicable to large molecule RNA therapeutics that deserve additional considerations in their safety assessment, particularly for aspects related to their unique modes of action. This research, which involves an extensive review of the data available for RNA therapeutics to derive substance-specific OELs and to propose a strategy for low-characterized RNA therapeutics, fills this crucial gap. It is recommended to apply an activity correction factor (ACF) in the OEL formula for large molecules, as representative of the "α" in the OEL formula for small molecules, considering differences in route of administration, critical effects, mechanism of action, and the RNA delivery platform. Additionally, it is proposed to consider lower OEL values for mRNA vaccines as compared to other RNA therapeutics. Finally, it is suggested that the exposure assessment experience that has already been acquired when handling therapeutic proteins can also be used to define containment strategies for RNA therapeutics.

MicroRNA-induced reprogramming of tumor-associated macrophages for modulation of tumor immune microenvironment

Tumor-associated macrophages (TAMs) are abundant in the tumor microenvironment and typically exhibit pro-tumoral phenotypes. TAMs overexpress the signal regulatory protein alpha (SIRPα) receptor on their surface, which interacts with CD47 on tumor cells to inhibit their phagocytic activity. In this study, we developed lipid nanoparticles modified with an anti-SIRPα antibody (aSIRPα) for the targeted delivery of microRNA-155 (miR155@aSIRPα-LNP) to TAMs, aiming to enhance their anti-tumoral phenotypes within the tumor microenvironment. The aSIRPα modification not only facilitated nanoparticle uptake by TAMs rather than B16F10 cells, but also blocked the anti-phagocytosis signal by disrupting the interaction between SIRPα and CD47 on cancer cells. This dual functionality enhanced the expression of anti-tumoral phenotype markers in TAMs and activated macrophage-mediated phagocytosis of tumor cells. In a melanoma model, intratumoral administration of miR155@aSIRPα-LNP to B16F10 tumor-bearing mice reprogrammed TAMs toward anti-tumoral phenotypes. The anti-tumoral cytokines released by these TAMs remodeled the immunosuppressive tumor microenvironment, increasing cytotoxic T cell infiltration and reducing the regulatory T cell population, inhibiting tumor progression. This approach indicates the potential of miRNA-based therapies to overcome the limitations of current immunotherapies in treating cold solid tumors. Overall, the results suggest that delivering miR155 to TAMs by targeting SIRPα is a promising strategy for modulating the immunosuppressive tumor microenvironment in cancer immunotherapy.

RNA research for drug discovery: Recent advances and critical insight

The field of RNA research has experienced significant changes and is now at the forefront of contemporary drug development. This narrative overview explores the scientific developments and historical turning points in RNA research, emphasising the field's critical significance in the development of novel therapeutics. Important discoveries like antisense oligonucleotides (ASOs), mRNA therapies, and RNA interference (RNAi) have created novel treatment options that can be targeted, such as the ground-breaking mRNA vaccinations against COVID-19. Advances in high-throughput sequencing, single-cell RNA sequencing, and epitranscriptomics have further unravelled the complexity of RNA biology, shedding light on the intricacies of gene regulation and cellular diversity. The integration of computational tools and bioinformatics has propelled the identification of RNA-based biomarkers and the development of RNA therapeutics. Despite significant progress, challenges such as RNA stability, delivery, and off-target effects persist, necessitating continuous innovation and ethical considerations. This review provides a critical insight into the current state and prospects of RNA research, emphasising its transformative potential in drug discovery. By examining the interplay between technological advancements and therapeutic applications, we underscore the promising horizon for RNA-based interventions in treating a myriad of diseases, marking a new era in precision medicine.

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.

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

PURPOSE

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

METHODS

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

RESULTS

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

CONCLUSION

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

LncRNA-GPHN Regulates Epilepsy by Inhibiting Apoptosis via the miR-320/YWHAH Axis in an Immature Rat Model of Status Epilepticus

Long non-coding RNAs (lncRNAs) play significant roles in neurological diseases, including epilepsy. Our previous study identified lncRNA-GPHN as specifically downregulated in a rat model of status epilepticus (SE). Investigate the role and regulatory mechanism of lncRNA-GPHN in the pathogenesis of epilepsy. SE rat and in vitro cell models were used to analyse expression dynamics, cellular localisation, and effects of lncRNA-GPHN on epileptic seizures, followed by HE staining, Nissl staining, and TUNEL staining. Luciferase Reporter assay, ChIRP assay, real-time quantitative PCR, and Western blotting accompanied with TUNEL assay and whole-cell patch-clamp techniques were employed to determine the molecular mechanism in lncRNA-GPHN regulating epilepsy in neurons. Post-seizure, lncRNA-GPHN in SE rats' hippocampus was markedly downregulated, hitting a nadir at 24 h. FISH and qPCR confirmed its cytoplasmic localization in neurons. EEG showed that lncRNA-GPHN overexpression significantly curtailed seizure frequency and intensity, elevating the threshold, while MWM results pointed to enhanced cognition in SE rats. Histological staining revealed less neuronal damage and better cellular integrity in overexpressing rats, accompanied with a reduction in neuronal apoptosis. In vitro, lncRNA-GPHN reduced neuronal excitability and epileptic potentials dose-dependently. q-PCR and ChIRP showed lncRNA-GPHN upregulates YWHAH by sequestering miR-320. Dual-luciferase and Western blot validated miR-320's direct suppression of YWHAH and lncRNA-GPHN's counteracting effect. TUNEL staining confirmed that miR-320 overexpression increased apoptosis, mitigated by lncRNA-GPHN overexpression and further reduced with combined overexpression. lncRNA-GPHN ameliorates epilepsy by inhibiting apoptosis via the miR-320/YWHAH axis, providing insights into epilepsy pathogenesis and potential targeted therapeutic strategies.

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

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

miR-574-3p and miR-125a-5p in Adipose-Derived Mesenchymal Stem Cell Exosomes Synergistically Target TGF-β1/SMAD2 Signaling Pathway for the Treatment of Androgenic Alopecia

Androgenetic alopecia is the most common hair loss disorder, influenced by distinct genetic factors and intricate environmental factors. The exosomes (Exos) from adipose-derived mesenchymal stem cells (ADMSCs) have diverse effects, including the promotion of cell proliferation, inhibition of apoptosis, analgesia, and enhancement of wound healing. MicroRNAs are essential components of the paracrine secretion of ADMSC-derived Exos. This study revealed that ADMSC-derived Exos could counteract the impairment of dermal papilla cells induced by dihydrotestosterone by inhibiting the TGF-β1 signaling pathway`s activation. Two miRNAs-miR-574-3p and miR-125a-5p-were identified as being predominantly expressed and specifically targeting TGF-β1 and SMAD2, respectively. Notably, individually knocking down miR-574-3p or miR-125a-5p did not affect the therapeutic efficacy of ADMSC-derived Exos. Yet, when both miR-574-3p and miR-125a-5p were concurrently knocked down, the efficacy of ADMSC-derived Exos was markedly reduced. Ultimately, our findings indicate that ADMSC-derived Exos target the TGF-β1/SMAD2 signaling pathway through miR-574-3p and miR-125a-5p, which are integral to the therapeutic action of ADMSC-derived Exos on dihydrotestosterone-induced dermal papilla cells and androgenetic alopecia murine models. This discovery offers significant insights into the pathogenesis of androgenetic alopecia and suggests potential therapeutic approaches. Further investigation into the role and interaction of these miRNAs in ADMSC-derived Exos may lead to the development of more precise and efficacious treatments for androgenetic alopecia.

Neurodegenerative disease-associated microRNAs acting as signaling molecules modulate CNS neuron structure and viability

BACKGROUND

Dysregulation of microRNA (miRNA) expression in the brain is a common feature of neurodegenerative diseases. Beyond their conventional role in regulating gene expression at the post-transcriptional level, certain miRNAs can act extracellularly as signaling molecules. Our study elucidates the identity of such miRNA species serving as ligands for membrane receptors expressed in central nervous system (CNS) neurons and the impact of such miRNAs on neurons in the context of neurodegenerative disease.

METHODS

We combined a machine learning approach with the analysis of disease-associated miRNA databases to predict Alzheimer's disease (AD)-associated miRNAs as potential signaling molecules for single-stranded RNA-sensing Toll-like receptors (TLRs) 7 and 8. TLR-expressing HEK-Blue reporter cells, primary murine microglia, and human THP-1 macrophages were used to validate the AD miRNAs as ligands for human and mouse TLR7 and/or TLR8. Interaction between mouse cortical neurons and extracellularly applied AD miRNAs was analyzed by live cell imaging and confocal microscopy. Transcriptome changes in cortical neurons exposed to AD miRNAs were assessed by RNAseq and RT-qPCR. The extracellular AD miRNAs' effects on CNS neuron structure were investigated in cell cultures of murine primary cortical neurons and iPSC-derived human cortical neurons by immunocytochemistry. We employed a mouse model of intrathecal injection to assess effects of AD miRNAs acting as signaling molecules on neurons in vivo.

RESULTS

We identified the AD-associated miRNAs miR-124-5p, miR-92a-1-5p, miR-9-5p, and miR-501-3p as novel endogenous ligands for TLR7 and/or TLR8. These miRNAs being extracellularly stable and active were taken up by murine cortical neurons via endocytosis and induced changes in neuronal inflammation-, proliferation-, and apoptosis-related gene expression. Exposure of both murine and human cortical neurons to the AD-associated miRNAs led to alterations of dendrite and axon structure, synapse protein expression, and cell viability in a sequence-dependent fashion. Extracellular introduction of the AD miRNAs into the cerebrospinal fluid of mice resulted in both changes in neuronal structure and synapses, and neuronal loss in the cerebral cortex. Most of the observed extracellular miRNA-induced effects on cortical neurons involved TLR7/8 signaling.

CONCLUSION

Neurodegenerative disease-associated miRNAs in extracellular form act as signaling molecules for CNS neurons including human cortical neurons, thereby modulating their structure and viability.

Long non-coding RNA LRTOR drives osimertinib resistance in non-small cell lung cancer by boosting YAP positive feedback loop

The therapeutic efficacy of osimertinib (OSI) in EGFR-mutant lung cancer is ultimately limited by the onset of acquired resistance, of which the mechanisms remain poorly understood. Here, we identify a novel long non-coding RNA, LRTOR, as a key driver of OSI resistance in non-small cell lung cancer (NSCLC). Clinical data indicate that elevated LRTOR expression correlates with poor prognosis in OSI-resistant patients. Functionally, LRTOR promotes tumor growth and confers OSI resistance both in vitro and in vivo. Mechanistically, LRTOR shields YAP from LATS-mediated phosphorylation at Ser127 and Ser381, preventing its proteasomal degradation. Furthermore, LRTOR facilitates the interaction between YAP and KCMF1, promoting K63-linked ubiquitination, nuclear translocation of YAP, and formation of the YAP/TEAD1 transcriptional complex, which in turn triggers the transcription of LRTOR, establishing a positive feedback loop that amplifies oncogenic signaling of YAP and consequently induces OSI resistance. LRTOR depletion by siRNA restores OSI sensitivity in resistant tumors, as demonstrated in patient-derived organoid xenograft models. Our findings unveil LRTOR as a central regulator of OSI resistance in NSCLC and propose it as a promising therapeutic and prognostic target for overcoming acquired OSI resistance in EGFR-mutant lung cancer.

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.

LncRNA PVT1 Promotes the Progress of Hypertrophic Scar via Regulating the Proliferation and Migration of Myofibroblasts Through Targeting miR-29a-3p/STAT3

Purpose

Hypertrophic scar (HS) is a common clinical disease during skin injury recovery. Although medicines have been listed for treatment, none are universally effective, and the details of the underlying molecular regulation are yet to be revealed. This research was aimed at exploring the clinical value of lncRNA PVT1 in HS formation and its potential mechanisms in human hyperplastic scar myofibroblasts (HSFs).

Patients and Methods

Fifty-seven HS patients were enrolled. RT-qPCR was conducted to examine the RNA levels of lncRNA PVT1, miR-29a-3p and STAT3. CCK-8, Transwell, and flow cytometry were used to analyze cell proliferation, migration, and apoptosis. The targeting relationship of PVT1/miR-29a-3p and miR-29a-3p/STAT3 was proved by the dual luciferase reporter.

Results

Relative expression of lncRNA PVT1 in human HS tissues was higher compared with normal tissues. LncRNA PVT1 silencing slowed proliferation and migration and accelerated apoptosis in human HSFs. miR-29a-3p was downregulated in human HS tissues, which was negatively correlated with PVT1 levels. LncRNA PVT1 was covalently bound to miR-29a-3p. miR-29a-3p played an important role in the proliferation, migration, and apoptosis of human HSFs. miR-29a-3p inhibitor rescued the negative influence of lncRNA PVT1 silencing on cells. STAT3 was covalently linked to miR-29a-3p.

Conclusion

LncRNA PVT1 was a potential biomarker for HS and regulated the biological behavior of human HSFs via miR-29a-3p/STAT3.

Long non-coding RNAs as therapeutic targets in head and neck squamous cell carcinoma and clinical application

Head and neck squamous cell carcinoma (HNSCC) is a major global health burden, often associated with poor prognosis and limited therapeutic options. Long non-coding RNAs (lncRNAs), a diverse group of non-coding RNA molecules > 200 nucleotides in length, have emerged as critical regulators in the pathogenesis of HNSCC. This review summarizes the mechanisms through which certain lncRNAs regulate chromatin modification, mRNA splicing, and interactions with RNA-binding proteins and contribute to the development and progression of HNSCC. Interaction of lncRNAs with key oncogenic pathways, such as PI3K/AKT and Wnt/β-catenin, highlights their importance in tumor progression. The role of lncRNAs, such as ELDR, MALAT1, NEAT1, HOTAIR, and UCA1, which promote cell proliferation, metastasis, immune evasion, and therapy resistance is discussed. Moreover, several lncRNAs are being evaluated in clinical trials for their potential as biomarkers, reflecting their clinical significance. We further address the challenges and opportunities for targeting lncRNA therapeutically, highlighting the promise of lncRNA-based interventions for personalized cancer treatment. Gaining insight into the function of lncRNAs in HNSCC could pave the way for novel therapeutic strategies to potentially improve patient outcomes.

Long noncoding RNA semaphorin 6A-antisense RNA 1 reduces hepatocellular carcinoma by promoting semaphorin 6A mRNA degradation

BACKGROUND

Hepatocellular carcinoma (HCC) is a prevalent malignant tumor with a poor prognosis, which is often associated with chronic hepatitis B virus infection in China. Our previous study has shown that long non-coding RNA semaphorin 6A-antisense RNA 1 (SEMA6A-AS1) was significantly downregulated in hepatitis B virus-related HCC and associated with poor prognosis.

AIM

To explore the underlying mechanism of SEMA6A-AS1 in HCC progression.

METHODS

The expression levels of SEMA6A-AS1 and SEMA6A were detected using quantitative polymerase chain reaction, immunohistochemistry and Western blot. A growth curve, colony formation, wound-healing and transwell (with or without Matrigel) assays were respectively performed to assess the proliferation, migration and invasion abilities of HCC cells. Cell cycle and apoptosis assays were performed by flow cytometry. To investigate the potential mechanism underpinning SEMA6A-AS1, we utilized tagged RNA affinity purification, dual luciferase reporter assay and immunofluorescence.

RESULTS

Downregulation of SEMA6A-AS1 in HCC was negatively correlated with SEMA6A protein expression. SEMA6A was upregulated in HCC and correlated with high alpha-fetoprotein level, high Edmondson-Steiner grade and poor prognosis. SEMA6A-AS1 significantly inhibited the proliferation, migration and invasion of HCC cells by combining with SEMA6A mRNA and promoting its degradation. SEMA6A protein promoted the proliferation, migration and invasion of HCC cells by regulating the actin cytoskeleton.

CONCLUSION

Our findings suggest that SEMA6A-AS1 can inhibit HCC progression through decreasing SEMA6A expression by promoting its mRNA degradation. SEMA6A-AS1 may be a prognostic biomarker and therapeutic target for HCC.

Long noncoding RNAs in acute myeloid leukemia: biomarkers, prognostic indicators, and treatment potential

Long noncoding RNAs (lncRNAs) have been recognized as significant modulators of gene expression and are essential for various biological functions, even though they don't appear to have the ability to encode proteins. Originally considered dark matter, lncRNAs have been recognized as being dysregulated and contributing to the onset, progression, and resistance to treatment of acute myeloid leukemia (AML). AML is a prevalent type of leukemia characterized by the disruption of myeloid cell differentiation, leading to an increased number of immature myeloid progenitor cells. Currently, the need for novel biomarkers and treatment targets to enhance therapeutic alternatives has led to a focus on lncRNAs as possible indicators for prognostic, therapeutic, and diagnostic systems in various human cancers, including AML. Recent research has recognized a limited set of lncRNAs as possible prognostic biomarkers or diagnoses in AML. This review evaluates the key research that highlights the significance of lncRNAs in AML and discusses their roles and impacts on the disease. Furthermore, we intend to underscore the importance of lncRNAs as new and trustworthy markers for the diagnosis, prediction, drug resistance, and targets for treatment in AML.

CircTADA2A stabilizes p53 via interacting with TRIM28 and suppresses the maintenance of FLT3-ITD acute myeloid leukemia

Internal tandem duplication mutations in the FMS-like tyrosine kinase 3 (FLT3-ITDs) occur in 25%-30% of acute myeloid leukemia (AML) cases and are associated with adverse prognosis. RNA-based therapeutics exhibit significant potential for treating diseases, prompting us to develop a novel circular RNA (circRNA)-based therapeutic strategy for FLT3-ITD AML. Here, we find circTADA2A is downregulated in FLT3-ITD AML patients. We further demonstrate that the downregulation of circTADA2A is critical for the proliferation of human FLT3-ITD AML cells, the sustenance of AML, and the self-renewal of leukemia stem/initiating cells (LSCs/LICs). Mechanistically, circTADA2A inhibits the TRIM28/MDM2 complexes formation by competitively binding to TRIM28, resulting in decreased levels of p53 ubiquitination and activating the p53 pathway. Importantly, in vitro transcription of circTADA2A and in vivo delivery via lipid nanoparticles (LNPs) significantly enhance the elimination of FLT3-ITD leukemia cells in combination with quizartinib treatment. In conclusion, our work uncovers the crucial functions of circTADA2A in the maintenance of FLT3-ITD AML and highlights a translationally important circTADA2A-based therapeutic approach for FLT3-ITD AML treatment.

circDHX33 suppresses glycolysis, malignant proliferation, and metastasis in prostate cancer by interacting with RNA-binding protein IGF2BP2 to destabilize its protein

Prostate cancer (PCa) is a malignant tumor characterized by dependence on androgens and enhanced glycolytic processes in response to the energy demands of rapid proliferation. This study delved into the role of circDHX33 interacting with IGF2BP2 in regulating the malignant behavior of PCa. circRNA expression data from PCa tissues and normal tissues were selected from the GEO database, and differentially expressed circRNAs were screened out. circDHX33 expression in clinical PCa samples was verified by RT-qPCR. Cellular experiments included cell culture, RNA interference and overexpression assays, as well as the use of Transwell migration invasion assay and EdU cell proliferation assay to assess the effect of circDHX33 on the proliferation and migration of PC-3 cells. In addition, its regulatory effect on energy metabolism in tumor cells was assessed by glycolysis assay. FISH assay, RNA pull-down, silver staining assay, and RIP were used to evaluate the interaction between circDHX33 and IGF2BP2. circDHX33 expression was significantly reduced in PCa tissues relative to normal tissues. Overexpression of circDHX33 significantly inhibited the glycolytic activity, proliferative capacity, and migratory and invasive abilities of PC-3 cells, and this effect was closely related to its reduction of IGF2BP2 protein stability. Knockdown of IGF2BP2 could reverse the malignant behavior of cells enhanced by circDHX33 knockdown. In addition, the direct intracellular interaction between circDHX33 and IGF2BP2 was verified. circDHX33 inhibits glycolysis and malignant proliferation in PCa through interaction with IGF2BP2, suggesting its potential as a potential therapeutic target.

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

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

Cellular and Molecular Mechanisms of Innate Memory Responses

There has been an increasing effort to understand the memory responses of a complex interplay among innate, adaptive, and structural cells in peripheral organs and bone marrow. Trained immunity is coined as the de facto memory of innate immune cells and their progenitors. These cells acquire epigenetic modifications and shift their metabolism to equip an imprinted signature to a persistent fast-responsive functional state. Recent studies highlight the contribution of noncoding RNAs and modulation of chromatin structures in establishing this epigenetic readiness for potential immune perturbations. In this review, we discuss recent studies that highlight trained immunity-mediated memory responses emerging intrinsically in innate immune cells and as a complex interplay with other cells at the organ level. Lastly, we survey epigenetic contributors to trained immunity phenotypes-specifically, a recently discovered regulatory circuit coordinating the regulation of a key driver of trained immunity.

Noncoding RNA as potential therapeutics to rescue mitochondrial dysfunction in cardiovascular diseases

Noncoding RNAs (ncRNAs) are critical regulators of mitochondrial function in cardiovascular diseases. Several studies have explored the manipulation of ncRNAs in mitochondrial dysfunction in different cardiovascular disease contexts, however, there is a dearth of information on the exploration of these noncoding RNAs as actual therapeutics to ameliorate cardiovascular diseases. This systematic review examines the roles of various ncRNAs in modulating mitochondrial dysfunction across major cardiovascular diseases and how they can be targeted to the mitochondria. A comprehensive literature search was conducted using Web of Science and Scopus databases, following the PRISMA guidelines. Original research articles in the English language, focusing on ncRNAs and mitochondrial dysfunction in specific cardiovascular diseases, were eligible for inclusion. A total of 76 studies were included in the systematic review with up to 100 ncRNAs identified as therapeutic biomarkers. The identified ncRNAs participate in regulating mitochondrial processes including oxidative phosphorylation (OXPHOS), fission/fusion dynamics, apoptosis, and calcium handling in cardiovascular diseases. Mitochondrial targeting moieties including mitochondrial targeting cell-penetrating peptides, mitochondrial targeting liposomes, and aptamers can be conjugated to ncRNAs and delivered to the heart via various injection routes including the pericardium or the myocardium. However, significant challenges remain in developing effective delivery methods to modulate these ncRNAs in vivo.

Intravenous and oral administration of the synthetic RNA drug, TY1, reverses heart failure with preserved ejection fraction in mice

TY1, a synthetic non-coding RNA (ncRNA) bioinspired by small Y RNAs abundant in extracellular vesicles (EVs), decreases cGAS/STING activation in myocardial infarction and thereby attenuates inflammation. Motivated by the concept that heart failure with preserved ejection fraction (HFpEF) is a systemic inflammatory disease, we tested TY1 in a murine model of HFpEF. Intravenous TY1, packaged in a transfection reagent, reversed the cardiac and systemic manifestations of HFpEF in two-hit obese-hypertensive mice, without inducing weight loss. The effects of TY1 were specific, insofar as they were not reproduced by a control RNA of the same nucleotide content but in scrambled order. TY1 consistently suppressed myocardial stress-induced MAP kinase signaling, as well as downstream inflammatory, fibrotic, and hypertrophic gene pathways in heart tissue. TY1 not only prevented but actually reversed key pathological processes underlying HFpEF, with no evidence of toxicity. Most noteworthy from a practical perspective, the effects of intravenous TY1 were reproduced by feeding HFpEF mice an oral micellar formulation of TY1. As the prototype for a novel class of ncRNA drugs which target cell stress, TY1 exhibits exceptional disease-modifying bioactivity in HFpEF.

Cleavage of Structured RNAs Is Accelerated by High Affinity DNAzyme Agents

DNAzymes (Dz) have been suggested as sequence-specific agents for cleaving RNA for therapeutic purposes. This concept paper discusses the challenges of Dz 10-23 design to effciently cleave folded RNA substrates. Dz with traditionally designed RNA binding arms (Tm~37 °C) have low affinity to the folded RNA substrates, which limits the overall cleavage rate. The RNA cleavage can be facilitated using Dz with high-affinity arms. However, this strategy is efficient only for cleaving RNA into folded RNA products. The unfolded products inhibit multiple substrate turnover. In a more general approach, Dz should be equipped with additional RNA binding arms to achieve tight RNA binding. This can be accomplished by bivalent and multivalent Dz constructs that have multiple catalytic cores. In all cases, high selectivity toward single nucleotide variations can be achieved in addition to multiple turnovers. The presence of RNase H, which plays a role in the antisense effect of oligonucleotide gene therapy agents, stabilizes the Dz:RNA complex and reduces its selectivity but significantly increases RNA cleavage efficiency. This work proposes changes in the algorithms of Dz design, which can help in constructing potent Dz agents for RNA inhibition both in cell cultures and in vivo. The concept article is supplemented with a quiz, which tests knowledge of the main concepts discussed in this work.

LINC01235 Promotes Clonal Evolution through DNA Replication Licensing-Induced Chromosomal Instability in Breast Cancer

Despite the development of HER2-targeting drugs such as trastuzumab and T-DXd, treatment resistance is a substantial challenge, often leading to relapse and distant metastasis. Tumor heterogeneity in HER2-positive breast cancer drives the evolution of resistant clones following therapeutic stress. However, the targetable drivers of anti-HER2 treatment resistance are not thoroughly identified. This study aims to use neoadjuvant-targeted therapy cohorts and a patient-derived organoid in vitro treatment model to uncover the potential targetable drivers of anti-HER2 treatment resistance. it is found that LINC01235 significantly enhances DNA replication licensing and chromosomal instability, fostering clonal expansion and evolution, and ultimately increasing resistance to therapeutic interventions. LINC01235 regulates global H3K27ac, H3K9ac, and H3K36me3 modifications, promotes H2A.Z expression in regulatory regions, and increases the accessibility of DNA licensing factors to their promoter regions. XRCC5 is identified as a key component for maintaining genomic stability, crucial for LINC01235's role in replication licensing. Furthermore, therapeutic strategies targeting LINC01235, including the use of antisense oligonucleotides or ATR inhibitors, which showed promise in overcoming treatment resistance are explored. These findings underscore the pivotal role of LINC01235 in driving resistance mechanisms and highlight novel avenues for targeted therapies to improve the outcomes of patients with HER2-positive breast cancer.

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.

Toehold-Based CRISPR-dCas9 Transcriptional Activation Platform for Spatiotemporally Controllable Gene Therapy in Tumor and Diabetic Mouse Models

The CRISPR-Cas system has been extensively employed as a genome editing tool with the dCas9-based transcriptional activation system emerging as a particularly promising approach for gene editing in the treatment of diseases at the gene level. Nevertheless, the challenge of achieving effective spatiotemporal control of the transcriptional activation system of dCas9 has thus far restricted its broader application. In this study, we present an miRNA-responsive CRISPR-dCas9 transcriptional activation (mCTA) system. This system is capable of responding specifically to exogenous and endogenous miRNAs in mammalian cells and enables the specific imaging of miRNAs during neural development or in the deep tissues of mice. Furthermore, the replacement of downstream functional genes with DTA has been demonstrated to result in the effective apoptosis of tumor cells and inhibition of xenografted tumor growth in mice. Finally, in a diabetic mouse model, the m122CTA system was shown to reduce the blood glucose in diabetic mice via the activation of PDX-1 gene. Our work provides an effective platform for miRNA imaging and gene therapy via spatiotemporal control of gene regulation.

A narrative review of papillary thyroid carcinoma-related long non-coding RNAs and their relevance to malignant tumors

Background and Objective

In recent years, research on the relationship between papillary thyroid carcinoma (PTC) and long non-coding RNAs (lncRNAs) has been burgeoning. However, there has not been an analysis of the regulatory mechanisms of these lncRNAs in all tumors, nor a comprehensive categorization and comparison of these mechanisms. This review aims to uncover whether PTC-related lncRNAs also play an important role in other tumors and to identify a common pattern of action.

Methods

We conducted a statistical analysis of lncRNAs related to PTC that have been reported during the period from Jan 2022 to May 2024 through searching in the Embase, Web of Science, and PubMed databases, focusing on those with greater research value. Using them as the focal points of our study, we compiled data on their different regulatory mechanisms across various malignant tumors, emphasizing key findings.

Key Content and Findings

This comprehensive analysis not only provides valuable insights into potential regulatory mechanisms of these lncRNAs in PTC but also serves as a reference for exploring their broader regulatory networks within cancer. The principal discovery is that lncRNAs associated with PTC can competitively interact with microRNAs (miRNAs). This interaction influences miRNA-targeted messenger RNA (mRNA) and the expression of cancer-related proteins, ultimately facilitating the progression of PTC as well as other malignant tumors.

Conclusions

The lncRNAs associated with PTC exert regulatory functions in other malignancies as well and possess similar regulatory mechanisms. This provides a molecular basis for the future development of relevant targeted therapies.

A therapeutic role for a regulatory glucose transporter1 (Glut1)-associated natural antisense transcript

The mammalian brain relies primarily on glucose for its energy needs. Delivery of this nutrient to the brain is mediated by the glucose transporter-1 (Glut1) protein. Low Glut1 thwarts glucose entry into the brain, causing an energy crisis and, triggering, in one instance, the debilitating neurodevelopmental condition - Glut1 deficiency syndrome (Glut1DS). Current treatments for Glut1DS are sub-optimal, as none address the root cause - low Glut1 - of the condition. Levels of this transporter must respond rapidly to the brain's changing energy requirements. This necessitates fine-tuning its expression. Here we describe a long-noncoding RNA (lncRNA) antisense to Glut1 and show that it is involved in such regulation. Raising levels of the lncRNA had a concordant effect on Glut1 in cultured human cells and transgenic mice; reducing levels elicited the opposite effect. Delivering the lncRNA to Glut1DS model mice via viral vectors induced Glut1 expression, enhancing brain glucose levels to mitigate disease. Direct delivery of such a lncRNA to combat disease has not been reported previously and constitutes a unique therapeutic paradigm. Moreover, considering the importance of maintaining homeostatic Glut1 levels, calibrating transporter expression via the lncRNA could become broadly relevant to the myriad conditions, including Alzheimer's disease, wherein Glut1 concentrations are perturbed.

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.

Advances in RNA therapy for the treatment of autoimmune diseases

Autoimmune diseases (ADs) are a group of complex, chronic conditions characterized by disturbance of immune tolerance, with examples including systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, and psoriasis. These diseases have unclear pathogenesis, and traditional therapeutic approaches remain limited. However, advances in high-throughput histology technology and scientific discoveries have led to the identification of various pathogenic factors contributing to ADs. Coupled with improvements in RNA nucleic acid-based drug synthesis, design, and delivery, RNA-based therapies have been extensively investigated for their potential in treating ADs. This paper reviews the progress in the use of miRNAs, lncRNAs, circRNAs, siRNAs, antisense oligonucleotides (ASOs), aptamers, mRNAs, and other RNA-based therapies in ADs, focusing on their therapeutic potential and application prospects, providing insights for future research and clinical treatment of autoimmune diseases.

Innovative Strategies for Combating Multidrug-Resistant Tuberculosis: Advances in Drug Delivery Systems and Treatment

Multidrug-resistant tuberculosis (MDR-TB) is a significant public health challenge globally, exacerbated by the limited efficacy of existing therapeutic approaches, prolonged treatment duration, and severe side effects. As drug resistance continues to emerge, innovative drug delivery systems and treatment strategies are critical to combating this crisis. This review highlights the molecular mechanisms underlying resistance to drugs in Mycobacterium tuberculosis, such as genetic mutation, efflux pump activity, and biofilm formation, contributing to the persistence and difficulty in eradicating MDR-TB. Current treatment options, including second-line drugs, offer limited effectiveness, prompting the need for innovation of advanced therapies and drug delivery systems. The progression in drug discovery has resulted in the approval of innovative therapeutics, including bedaquiline and delamanid, amongst other promising candidates under investigation. However, overcoming the limitations of traditional drug delivery remains a significant challenge. Nanotechnology has emerged as a promising solution, with nanoparticle-based drug delivery systems offering improved bioavailability and targeted and controlled release delivery, particularly for pulmonary targeting and intracellular delivery to macrophages. Furthermore, the development of inhalable formulations and the potential of nanomedicines to bypass drug resistance mechanisms presents a novel approach to enhancing drug efficacy. Moreover, adjunctive therapies, including immune modulation and host-directed therapies, are being explored to improve treatment outcomes. Immunotherapies, such as cytokine modulation and novel TB vaccines, offer complementary strategies to the use of antibiotics in combating MDR-TB. Personalized medicine approaches, leveraging genomic profiling of both the pathogen and the host, offer promise in optimizing treatment regimens and minimizing drug resistance. This review underscores the importance of multidisciplinary approaches, combining drug discovery, advanced delivery system development, and immune modulation to address the complexities of treating MDR-TB. Continued innovation, global collaboration, and improved diagnostics are essential to developing practical, accessible, and affordable treatments for MDR-TB.

Decoding Salivary ncRNAomes as Novel Biomarkers for Oral Cancer Detection and Prognosis

Oral cancer (OC) ranks among the most prevalent head and neck cancers, becoming the eleventh most common cancer worldwide with ~350,000 new cases and 177,000 fatalities annually. The rising trend in the occurrence of OC among young individuals and women who do not have tobacco habits is escalating rapidly. Surgical procedures, radiation therapy, and chemotherapy are among the most prevalent treatment options for oral cancer. To achieve better therapy and an early detection of the cancer, it is essential to understand the disease's etiology at the molecular level. Saliva, the most prevalent body fluid obtained non-invasively, holds a collection of distinct non-coding RNA pools (ncRNAomes) that can be assessed as biomarkers for identifying oral cancer. Non-coding signatures, which are transcripts lacking a protein-coding function, have been identified as significant in the progression of various cancers, including oral cancer. This review aims to examine the role of various salivary ncRNAs (microRNA, circular RNA, and lncRNA) associated with disease progression and to explore their functions as potential biomarkers for early disease identification to ensure better survival outcomes for oral cancer patients.