Noncoding RNA therapeutics - challenges and potential solutions

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.

Harnessing RNA therapeutics: novel approaches and emerging strategies for cardiovascular disease management

RNA therapeutics are emerging as a promising approach for cardiovascular diseases (CVDs) management, offering targeted gene regulation through modalities like mRNA, siRNA, and miRNA. In recent years, researchers have conducted a lot of research on the application of RNA therapeutics technology in the treatment of CVDs. Despite hurdles in off-target effects and immune responses, the clinical trial outcomes are encouraging. This review synthesizes the current progress in RNA therapeutics for CVDs, examining their mechanisms, advantages, and challenges in delivery and safety. We highlight the potential of personalized medicine, combination artificial intelligence (AI) and bioinformatics in advancing RNA therapeutics. The future of RNA therapeutics in CVDs is poised for significant impact, necessitating continued research and interdisciplinary collaboration to optimize these treatments and ensure patient safety and efficacy.

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

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

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

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

miR-27a-5p, miR-21-5p, miR-1246 and miR-4508: a candidate microRNA signature in the protection and regulation of viral infection in mild COVID-19

MicroRNAs (miRNAs) are gene regulators essential for cell homeostasis, their alteration is related to a pathological state, including infectious diseases like COVID-19. Identifying an altered profile of circulating miRNAs in mild COVID-19 may enhance our knowledge of the pathogenesis of SARS-CoV-2 and the range of clinical phenotypes. In the present study, a miRNA screening was performed by Next Generation Sequencing (NGS), and the expression levels of 13 resulting miRNAs were validated through RT-qPCR in the serum of 40 mild cases compared to 29 non-infected individuals. An in-silico analysis was performed to detect target genes and their related pathways. From the validated miRNAs, miR-1246 (p < 0.001), miR-423-5p (p < 0.001), miR-21-5p (p = 0.005), miR-146a-5p (p < 0.001), miR-4508 (p = 0.001), miR-629-5p (p < 0.001), and miR-210-3p (p = 0.002) were found downregulated in infected individuals. Only miR-27a-5p was overexpressed in subjects with COVID-19 (p = 0.013) and associated with SARS-CoV-2 infection (p = 0.010). The KEGG pathways and GO analysis revealed that the differentially expressed miRNAs were related to viral processes or immunological pathways: miR-27a-5p acts on the TGF-beta pathway; miR-21-5p targets SMAD7, which is associated with the inflammatory response in the lung; miR-1246 acts on p53 pathway; and miR-4508 acts on ICAM2. In conclusion, the most relevant miRNAs, miR-27a-5p and miR-21-5p, were differently expressed in mild forms of COVID-19. The higher expression of miR-27a-5p observed in mild COVID-19 cases may suggest a protective effect against severe forms of the disease. Reduced expression of miR-21-5p may prevent pulmonary inflammation and the progression of fibrosis. The downregulation of miR-1246 and miR-4508 in mild COVID-19 cases may conduct the correct control of the infection. Moreover, miR-423-5p might be a suitable biomarker in the early stages of SARS-CoV-2 infection.

Single-Cell Transcriptomic Approaches for Decoding Non-Coding RNA Mechanisms in Colorectal Cancer

Non-coding RNAs (ncRNAs) play crucial roles in colorectal cancer (CRC) development and progression. Recent developments in single-cell transcriptome profiling methods have revealed surprising levels of expression variability among seemingly homogeneous cells, suggesting the existence of many more cell types than previously estimated. This review synthesizes recent advances in ncRNA research in CRC, emphasizing single-cell bioinformatics approaches for their analysis. We explore computational methods and tools used for ncRNA identification, characterization, and functional prediction in CRC, with a focus on single-cell RNA sequencing (scRNA-seq) data. The review highlights key bioinformatics strategies, including sequence-based and structure-based approaches, machine learning applications, and multi-omics data integration. We discuss how these computational techniques can be applied to analyze differential expression, perform functional enrichment, and construct regulatory networks involving ncRNAs in CRC. Additionally, we examine the role of bioinformatics in leveraging ncRNAs as diagnostic and prognostic biomarkers for CRC. We also discuss recent scRNA-seq studies revealing ncRNA heterogeneity in CRC. This review aims to provide a comprehensive overview of the current state of single-cell bioinformatics in ncRNA CRC research and outline future directions in this rapidly evolving field, emphasizing the integration of computational approaches with experimental validation to advance our understanding of ncRNA biology in CRC.

Landscape of small nucleic acid therapeutics: moving from the bench to the clinic as next-generation medicines

The ability of small nucleic acids to modulate gene expression via a range of processes has been widely explored. Compared with conventional treatments, small nucleic acid therapeutics have the potential to achieve long-lasting or even curative effects via gene editing. As a result of recent technological advances, efficient small nucleic acid delivery for therapeutic and biomedical applications has been achieved, accelerating their clinical translation. Here, we review the increasing number of small nucleic acid therapeutic classes and the most common chemical modifications and delivery platforms. We also discuss the key advances in the design, development and therapeutic application of each delivery platform. Furthermore, this review presents comprehensive profiles of currently approved small nucleic acid drugs, including 11 antisense oligonucleotides (ASOs), 2 aptamers and 6 siRNA drugs, summarizing their modifications, disease-specific mechanisms of action and delivery strategies. Other candidates whose clinical trial status has been recorded and updated are also discussed. We also consider strategic issues such as important safety considerations, novel vectors and hurdles for translating academic breakthroughs to the clinic. Small nucleic acid therapeutics have produced favorable results in clinical trials and have the potential to address previously "undruggable" targets, suggesting that they could be useful for guiding the development of additional clinical candidates.

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

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

LncRNAs Orchestrating Neuroinflammation: A Comprehensive Review

CNS diseases account for a major part of the comorbidity and mortality of the human population; moreover, neuroinflammation has become an indication for different CNS diseases, for instance, Parkinson's and Alzheimer's disease. Microglia and astrocytes are the two main glial cells that can be found in the CNS. Each of these plays an important role in mediating immune responses like inflammation. There are many studies suggesting the role of LncRNAs in mediating neuroinflammation. Indeed, LncRNAs orchestrate neuroinflammation through various mechanisms, namely miRNA sponge, and transcriptional activation/inhibition. In addition, LncRNAs regulate different downstream pathways like NF-κB, and PI3K/AKT. In this study, we gathered the existing studies regarding the mechanisms of action of LncRNAs in the pathogenesis of different CNS diseases like neurodegenerative diseases and traumatic injuries through regulating neuroinflammation. We aim to elaborate on the regulatory roles of LncRNAs in neuroinflammation and bring a more profound understanding of the etiology of CNS diseases in terms of neuroinflammation.

In vivo vectorization and delivery systems for gene therapies and RNA-based therapeutics in oncology

Gene and RNA-based therapeutics represent a promising frontier in oncology, enabling targeted modulation of tumor-associated genes and proteins. This review explores the latest advances in payload vectorization and delivery systems developed for in vivo cancer treatments. We discuss viral and non-viral organic particles, including lipid based nanoparticles and polymeric structures, for the effective transport of plasmids, siRNA, and self-amplifying RNA therapeutics. Their physicochemical properties, strategies to overcome intracellular barriers, and innovations in cell-based carriers and engineered extracellular vesicles are highlighted. Moreover, we consider oncolytic viruses, novel viral capsid modifications, and approaches that refine tumor targeting and immunomodulation. Ongoing clinical trials and regulatory frameworks guide future directions and emphasize the need for safe, scalable production. The potential convergence of these systems with combination therapies paves the way toward personalized cancer medicine.

Identifying colorectal cancer-specific vulnerabilities in the Wnt-driven long non-coding transcriptome

BACKGROUND

Aberrant Wnt pathway activation is a key driver of colorectal cancer (CRC) and is essential to sustain tumour growth and progression. Although the downstream protein-coding target genes of the Wnt cascade are well known, the long non-coding transcriptome has not yet been fully resolved.

OBJECTIVE

In this study, we aim to comprehensively reveal the Wnt-regulated long non-coding transcriptome and exploit essential molecules as novel therapeutic targets.

DESIGN

We used global run-on sequencing to define β-catenin-regulated long non-coding RNAs (lncRNAs) in CRC. CRISPRi dropout screens were subsequently used to establish the functional relevance of a subset of these lncRNAs for long-term expansion of CRC.

RESULTS

We uncovered that LINC02418 is essential for cancer cell clonogenic outgrowth. Mechanistically, LINC02418 regulates MYC expression levels to promote CRC stem cell functionality and prevent terminal differentiation. Furthermore, we developed effective small interfering RNA (siRNA)-based therapeutics to target LINC02418 RNA in vivo.

CONCLUSION

We propose that cancer-specific Wnt-regulated lncRNAs provide novel therapeutic opportunities to interfere with the Wnt pathway, which has so far defied effective pharmacological inhibition.

Catalytic Hybrid Lipid Nanoparticles Potentiate Circle RNA-Based Cytokine Immunotherapy

Cytokine therapeutics in cancer immunotherapy are greatly limited by their short half-time, serious toxicity, and frequent administration, which can possibly be addressed by ribonucleic acid (RNA) technology through the expression of targeting cytokines in situ. However, the intracellular translation of RNA remains restricted due to the generation of excessive reactive oxygen species (ROS) and overconsumption of adenosine triphosphate (ATP) within the transfected cells. Herein, hybrid lipid nanoparticles (Mn-LNPs) are developed by incorporating small-sized trimanganese tetraoxide nanoparticles within conventional lipid nanoparticles, showing the ability to generate oxygen, eliminate ROS, and boost intracellular ATP, thus greatly enhancing the translation efficiency. This hybrid platform is employed to encapsulate interleukin 12 (IL-12)-encoding circular RNA (Mn-LNPs@RNAIL-12) for tumor immunotherapy, exhibiting unparalleled advantages in the proliferation of cytotoxic T cells and stimulation of antitumor immunity. Moreover, the antitumor efficacy of Mn-LNPs@RNAIL-12 is further strengthened by synergizing with immune checkpoint blockade therapy to achieve durable and potent antitumor performances.

Deciphering the epigenetic role of long non-coding RNAs in mood disorders: Focus on human brain studies

Epigenetics plays a central role in neuropsychiatric disorders, contributing significantly to their complexity and manifestation. Major depressive disorder (MDD) and bipolar disorder (BD) have profound impact on mood, affect and cognition. Emerging evidence suggests that epigenetic modification of genes plays a pivotal role in the pathogenesis of both MDD and BD. Long non-coding RNAs (lncRNA) constitute a heterogeneous class of transcripts and have emerged as crucial regulators of epigenetic processes, offering promising insights into the pathophysiology of various diseases. Despite their limited coding potential, lncRNAs are known to play a critical role in achieving global transcriptomic regulation in a spatiotemporal fashion, especially in complex tissue like the brain. This review aims to discuss the specific dysregulation of lncRNAs so far observed in the brains of MDD and BD patients and understand their mechanistic contributions to the disease pathogenesis. KEY POINTS: Brain-centric lncRNAs regulate gene networks, and their disruption is linked to MDD. In MDD, altered lncRNAs disrupt gene regulation by changing chromatin looping or modifying chromatin accessibility. These changes lead to neuronal dysfunction, affecting neural circuitry and synaptic plasticity. The result is impaired brain function, contributing to the symptoms of MDD.

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.

Emerging mechanisms and therapeutics in inflammatory muscle diseases

Idiopathic inflammatory myopathies (IIMs), or myositis, are rare diseases marked by immune-driven muscle damage and complications like skin lesions and interstitial lung disease (ILD). Despite advances, challenges in diagnosis and treatment persist, particularly in inclusion body myositis (IBM), where no effective therapy exists. Recent breakthroughs, including transcriptomics and insights into antibody-mediated immunity and interferon (IFN) signaling, have clarified IIM pathophysiology and spurred the development of new therapies, such as chimeric antigen receptor (CAR) T cells and Janus kinase (JAK) inhibitors. We explore the latest findings on the mechanisms underlying adult-onset IIMs, emphasizing IBM pathobiology and its unique immune and degenerative pathways, such as a selective type 2 myofiber damage and severe cell stress. Finally, we highlight the recent advances in transcriptomics, single-cell analysis, and machine learning in transforming IIM research by improving diagnostic accuracy, uncovering therapeutic targets, and supporting the development of personalized treatment strategies.

Competing endogenous RNAs network and therapeutic implications: New horizons in disease research

Different diseases may arise from the dysregulation of non-coding RNAs (ncRNAs), which regulation is necessary for maintaining cellular homeostasis. ncRNAs are regulated by transcriptional, post-transcriptional, translational and post-translational processes. Post-transcriptional regulation of gene expression is carried out by microRNAs (miRNAs), a class of small ncRNA molecules, which can identify their target sites by a brief nucleotide sequence, known as the miRNA response element (MRE), present on the miRNA seed sequence and the target transcript. This binding between miRNAs and targets can regulate the gene expression through inhibition of translation or degradation of target messenger RNA (mRNA). The transcripts that share MREs can be involved in competition for the central miRNA pool, which could have an indirect impact on each other's regulation. This competition network is called competing endogenous RNAs network (ceRNET). Many ncRNAs, including circular RNA, pseudogene, and long non-coding RNA, as well as mRNA, a coding RNA transcript, make up ceRNET. These components play a crucial role in post-transcriptional regulation and are involved in the diagnosis and treatment of many pathological disorders. The mechanism of ceRNET and its essential components, as well as their therapeutic implications in different diseases such as cancer, diabetes mellitus, neurological, cardiovascular, hepatic and respiratory disorders were covered in this review.

Harnessing the potential of long non-coding RNAs in the pathophysiology of Alzheimer's disease

Alzheimer's disease (AD), a diverse neurodegenerative disease, is the leading cause of dementia, accounting for 60-80 % of all cases. The pathophysiology of Alzheimer's disease is unknown, and there is no cure at this time. Recent developments in transcriptome-wide profiling have led to the identification of a number of non-coding RNAs (ncRNAs). Among these, long non-coding RNAs (lncRNAs)-long transcripts that don't seem to be able to code for proteins-have drawn attention because they function as regulatory agents in a variety of biological processes. Recent research suggests that lncRNAs play a role in the pathogenesis of Alzheimer's disease by modulating tau hyperphosphorylation, amyloid production, synaptic impairment, neuroinflammation, mitochondrial dysfunction, and oxidative stress, though their precise effects on the disorder are unknown. The biology and modes of action of the best-characterized lncRNAs in AD will be outlined here, with an emphasis on their possible involvement in the pathophysiology of the disease. As lncRNAs may offer prospective prognostic/diagnostic biomarkers and therapeutic targets for the treatment of AD, a greater comprehension of the molecular processes and the intricate network of interactions in which they are implicated could pave the way for future research.

LINC00525 promotes cell proliferation and collagen expression through feedforward regulation of TGF-β signaling in hypertrophic scar fibroblasts

The etiology of hypertrophic scar formation continues to elude researchers, despite advancements in the understanding of skin scarring. Several long non-coding RNAs (lncRNAs) have been implicated in the pathogenesis of hypertrophic scars, yet the role and molecular mechanisms of LINC00525 in this process remain unclear. This study demonstrates that LINC00525 enhances cell proliferation and collagen expression through knockdown and overexpression techniques. Further analysis, including nuclear and cytoplasmic localization studies, RNA pull-down assays, bioinformatics predictions, and PCR validation, reveals that LINC00525 interacts with miR-29a-5p. The downregulation of LINC00525 enhances the expression of miR-29a-5p and suppresses the TGF-β/Smad signaling pathway. Additionally, TGF-β1 induces the upregulation of LINC00525. Collectively, these findings indicate that LINC00525 operates through a feedforward mechanism to regulate TGF-β signaling in hypertrophic scar fibroblasts. This research offers novel insights for the prevention and treatment of scars.

m7G-modified mt-tRF3b-LeuTAA regulates mitophagy and metabolic reprogramming via SUMOylation of SIRT3 in chondrocytes

N7-methylguanosine (m7G) modification is one of the most prevalent RNA modifications, and methyltransferase-like protein-1 (METTL1) is a key component of the m7G methyltransferase complex. METTL1-catalyzed m7G as a new RNA modification pathway that regulates RNA structure, biogenesis, and cell migration. Increasing evidence indicates that m7G modification has been implicated in the pathophysiological process of osteoarthritis (OA). However, the underlying molecular mechanisms of m7G modification remains incompletely elucidated during the progression of OA. Here we found that METTL1 and m7G levels were markedly increased in OA chondrocytes. In addition, METTL1-mediated m7G modification upregulated mt-tRF3b-LeuTAA expression to exacerbate chondrocyte degeneration. Mechanistically, mt-tRF3b-LeuTAA decreased the SUMO-specific protease 1 (SENP1) protein expression and upregulated the level of sirtuin 3 (SIRT3) SUMOylation to inhibit PTEN induced kinase 1 (PINK1)/Parkin-mediated mitochondrial mitophagy. Intra-articular injection of PMC-tRF3b-LeuTAA inhibitor (Polyamidoamine-polyethylene glycol surface-modified with Minimal self-peptides and Chondrocyte-affinity peptides, PMC) attenuated destabilization of the medial meniscus (DMM) mouse cartilage degeneration in vivo. Our study demonstrates that METTL1/m7G/mt-tRF3b-LeuTAA axis accelerate cartilage degradation by inhibiting mitophagy and promoting mitochondrial dysfunction through SIRT3 SUMOylation, and suggest that targeting METTL1 and its downstream signaling axis could be a promising therapeutic target for OA treatment.

Multifaceted roles of insulin‑like growth factor 2 mRNA binding protein 2 in human cancer (Review)

Insulin‑like growth factor 2 mRNA binding protein 2 (IGF2BP2) is an RNA binding protein that functions as an N6‑methyladenosine reader. It regulates various biological processes in human cancers by affecting the stability and expression of target RNA transcripts, including coding RNAs and non‑coding RNAs (ncRNAs). Numerous studies have shown that IGF2BP2 expression is aberrantly increased in various types of cancer and plays multifaceted roles in the development and progression of human cancers. In the present review, the clinical importance of IGF2BP2 is summarized and its involvement in the regulation of biological processes, including proliferation, metastasis, chemoresistance, metabolism, tumor immunity, stemness and cell death, in human cancers is discussed. The chemical compounds that have been developed as IGF2BP2 inhibitors are also detailed. As ncRNAs are now important potential therapeutic agents for cancer treatment, the microRNAs that have been reported to directly target and inhibit IGF2BP2 expression in cancers are also described. In summary, by reviewing the latest literature, the present study aimed to highlight the clinical importance and physiological functions of IGF2BP2 in human cancer, with a focus on the great potential of IGF2BP2 as a target for inhibitor development. The present review may inspire new ideas for future studies on IGF2BP2, which may serve as a specific therapeutic target in cancer.

Advancements in genetic research and RNA therapy strategies for amyotrophic lateral sclerosis (ALS): current progress and future prospects

This review explores the intricate landscape of neurodegenerative disease research, focusing on Amyotrophic Lateral Sclerosis (ALS) and the intersection of genetics and RNA biology to investigate the causative pathogenetic basis of this fatal disease. ALS is a severe neurodegenerative disease characterized by the progressive loss of motor neurons, leading to muscle weakness and paralysis. Despite significant research advances, the exact cause of ALS remains largely unknown. Thanks to the application of next-generation sequencing (NGS) approaches, it was possible to highlight the fundamental role of rare variants with large effect sizes and involvement of portions of non-coding RNA, providing valuable information on risk prediction, diagnosis, and treatment of age-related diseases, such as ALS. Genetic research has provided valuable insights into the pathophysiology of ALS, leading to the development of targeted therapies such as antisense oligonucleotides (ASOs). Regulatory agencies in several countries are evaluating the commercialization of Qalsody (Tofersen) for SOD1-associated ALS, highlighting the potential of gene-targeted therapies. Furthermore, the emerging significance of microRNAs (miRNAs) and long RNAs are of great interest. MiRNAs have emerged as promising biomarkers for diagnosing ALS and monitoring disease progression. Understanding the role of lncRNAs in the pathogenesis of ALS opens new avenues for therapeutic intervention. However, challenges remain in delivering RNA-based therapeutics to the central nervous system. Advances in genetic screening and personalized medicine hold promise for improving the management of ALS. Ongoing clinical trials use genomic approaches for patient stratification and drug targeting. Further research into the role of non-coding RNAs in the pathogenesis of ALS and their potential as therapeutic targets is crucial to the development of effective treatments for this devastating disease.

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

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

The Relevance of the Accurate Annotation of Micro and Long Non-Coding RNA Interactions for the Development of Therapies

A large fraction of the human genome is transcribed in RNA molecules that do not encode for proteins but that do have a crucial role in regulating almost every level of gene expression and, thus, define the specific phenotype of each cell. These non-coding RNAs include well-characterized microRNAs and thousands of less-defined longer transcripts, named long non-coding RNAs. Both types markedly affect the onset and the progression of numerous pathologies, ranging from cancer to vascular and neuro-degenerative diseases. In recent years, a substantial effort has been made to design drugs targeting ncRNAs, and promising advancements have been produced from micro-RNA mimics and inhibitors. Each ncRNA controls several targets, and the overall effect of its inhibition or overexpression depends on the function of the set of genes it regulates. Therefore, in selecting the most appropriate target, and predicting the final outcome of ncRNA-based therapies, it is crucial to have and utilize detailed and accurate knowledge of their functional interactions. In this review, I recapitulate the principal resources which collect information on microRNA and lncRNA networks, focusing on the non-homogeneity of the data that result from disparate approaches. I highlight the role of RNA identifiers and interaction evidence standardization in helping the user to filter and integrate data derived from different databases in a reliable functional web of regulative relations.

Comparative Transcriptional Analysis of Long Noncoding RNAs in Oxidative Stress and Inflammation Induced by Potassium Permanganate and Lipopolysaccharide in Rat Uterine Tissues

Potassium permanganate (KMnO4) is a commercially available antiseptic used in bovine intrauterine lavage to manage postpartum infections. Lipopolysaccharides (LPS) are well-studied for their ability to induce inflammation and oxidative stress. While KMnO4 is known to cause significant irritation, oxidative stress, and toxicity in uterine tissues, its transcriptional impact and potential for inducing similar molecular damage as LPS have not been fully explored. In this study, we induced oxidative stress in the uterine tissues of Sprague-Dawley (SD) rats using KMnO4 and compared the transcriptional profiles with those treated with LPS. We focused on the differential expression of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) related to oxidative stress, toxicity, and inflammation. RNA sequencing revealed 1125 differentially expressed mRNAs in the KMnO4-treated group and 989 in the LPS-treated group. Additionally, 1649 lncRNAs were differentially expressed in the KMnO4 group compared with 1383 in the LPS group. Gene ontology (GO) and KEGG enrichment analyses showed that 78 pathways were significantly enriched in the KMnO4 group, while 80 pathways were enriched in the LPS group, with 50 pathways shared between the two. This study offers critical insights into the transcriptional profiles associated with KMnO4 exposure and its similarities to LPS-induced damage.

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

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

Muscle Matters: Transforming Amyotrophic Lateral Sclerosis Diagnostics with Next-Gen Biosensors and Smart Detection

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder that primarily targets the motor system, causing patients' speech and swallowing ability to rapidly deteriorate. Although ALS is usually classified into familial and sporadic forms, diagnosing it can be extremely difficult due to the absence of definitive biomarkers, often resulting in delays in diagnosis. Current diagnostic practices rely heavily on clinical assessments that indicate damage to both upper motor neurons (UMNs) and lower motor neurons (LMNs). This includes comprehensive physical examinations, electromyography (EMG) to assess neuromuscular function, and the exclusion of other similar conditions such as cervical spondylotic myelopathy, multifocal motor neuropathy, and Kennedy's disease through appropriate diagnostic procedures. The urgent need for specific biomarkers is critical for timely diagnosis and therapeutic advancements in ALS management. While many recent developments in research have not yet translated into direct patient benefits, the recognition of ALS as a complex disease is beginning to influence clinical practice significantly. Optimal management strategies emphasize on symptom control and improving the quality of life for patients within a holistic healthcare framework. This review provides a comprehensive overview of ALS, delving into its pathophysiology, clinical symptoms, and the latest advancements in detection methods that utilize traditional approaches, innovative biosensors, and smart diagnostic technologies. It discusses various treatment options available for ALS while exploring future developments that may enhance patient screening and improve clinical outcomes. By integrating assessments into the underlying mechanisms of the disease with cutting-edge diagnostic approaches, this review aims to contribute meaningfully to ongoing efforts to optimize ALS management and therapeutic strategies, ultimately improving patient care and outcomes.

The liver-specific long noncoding RNA FAM99B inhibits ribosome biogenesis and cancer progression through cleavage of dead-box Helicase 21

Emerging evidence has demonstrated that long noncoding RNAs (lncRNAs) are promising targets or agents for the treatment of human cancers. Most liver-specific lncRNAs exhibit loss of expression and act as tumor suppressors in liver cancer. Modulating the expression of these liver-specific lncRNAs is a potential approach for lncRNA-based gene therapy for hepatocellular carcinoma (HCC). Here, we report that the expression of the liver-specific lncRNA FAM99B is significantly decreased in HCC tissues and that FAM99B suppresses HCC cell proliferation and metastasis both in vitro and in vivo. FAM99B promotes the nuclear export of DDX21 through XPO1, leading to further cleavage of DDX21 by caspase3/6 in the cytoplasm. FAM99B inhibits ribosome biogenesis by inhibiting ribosomal RNA (rRNA) processing and RPS29/RPL38 transcription, thereby reducing global protein synthesis through downregulation of DDX21 in HCC cells. Interestingly, the FAM99B65-146 truncation exhibits tumor-suppressive effects in vivo and in vitro. Moreover, GalNAc-conjugated FAM99B65-146 inhibits the growth and metastasis of orthotopic HCC xenografts, providing a new strategy for the treatment of HCC. This is the first report of the use of a lncRNA as an agent rather than a target in tumor treatment. Graphical illustration of the mechanism of FAM99B in HCC.

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.

Role of exercise on ncRNAs and exosomal ncRNAs in preventing neurodegenerative diseases: a narrative review

Engaging in activity has proven to have beneficial effects on different facets of well-being, such as conditions related to the deterioration of the nervous system. Non-coding RNAs (ncRNAs) and exosomal ncRNAs associated with vesicles have been recognized as influencers of gene expression and cell signaling, potentially contributing to the positive impact of physical activity on neurodegenerative conditions. It is hypothesized that exercise-induced changes in ncRNA expression may regulate key processes involved in neuroprotection, including neuroinflammation, oxidative stress, protein aggregation, and synaptic function. Exercise has shown promise in preventing neurodegenerative diseases (NDs), and ncRNAs and exosomal ncRNAs are emerging as potential mediators of these benefits. In review, we explored how ncRNAs and exosomal ncRNAs play a role in enhancing the impacts of activity on neurodegenerative disorders for future treatments. Research studies, both preclinical and clinical, that have documented the use of various exercises and their effects on ncRNAs and exosomal ncRNAs for the treatment of NDs have been compiled and enlisted from the PubMed database, spanning the time period from the year 2000 up to the current time. Studies show that manipulating specific ncRNAs or harnessing exercise-induced changes in ncRNA expression and exosomal cargo could potentially be utilized as therapeutic strategies for preventing or treating NDs. In conclusion, studies suggest that various exercise modalities, including aerobic, resistance, and high-intensity interval training, can modulate the expression of ncRNAs and exosomal ncRNAs in the context of NDs. The altered ncRNA profiles may contribute to the neuroprotective and therapeutic effects observed with exercise interventions. However, more research is needed to fully understand the underlying mechanisms and to further explore the potential of exercise-induced ncRNA signatures as biomarkers and therapeutic targets for neurodegenerative disorders.

Novel lncRNA LncMSTRG.11341.25 Promotes Osteogenic Differentiation of Human Bone Marrow Stem Cells via the miR-939-5p/PAX8 Axis

Human bone marrow stem cells (hBMSCs) play an important role during the fracture healing phase. Previous clinical studies by our research group found that fracture healing time was obviously delayed in patients who underwent splenectomy, for combined traumatic fractures and splenic rupture, which is most likely related to the dysregulation of immune inflammatory function of the body after splenectomy. A large number of studies have reported that the inflammatory factor interleukin-1β plays an important role in the multi-directional differentiation ability and immune regulation of BMSC, but its specific regulatory mechanism needs to be further studied. Recently, long noncoding RNAs (lncRNAs) have attracted remarkable attention owing to their close relationship with stem cell osteogenesis and potential role in various bone diseases. In this study, we explored the molecular mechanism of a novel lncRNA, LncMSTRG.11341.25 (LncMSTRG25), in terms of its effects on osteogenic differentiation of hBMSCs. Our results reveal significant up-regulation of LncMSTRG25, osteogenic differentiation markers during the osteogenic differentiation of hBMSCs, and decreased expression of miR-939-5p with an increase in differentiation time. LncMSTRG25 knockdown significantly inhibited the osteogenic ability of hBMSCs. When we knocked down PAX8 alone, we found that the osteogenic ability of hBMSCs was also significantly reduced. The interaction between LncMSTRG25 and PAX8 was verified using the RNA immunoprecipitation assay, RNA pull-down assays, silver staining, and the dual-luciferase reporter. The results show that LncMSTRG25 can function as a sponge to adsorb miR-939-5p, inducing the osteogenic differentiation of hBMSCs by activating PAX8. These findings deepen our understanding of the regulatory role of lncRNA-miRNA-mRNA networks in the immune microenvironment of bone marrow, and highlight the important role played by the spleen as an immune organ in fracture healing.

RMST: a long noncoding RNA involved in cancer and disease

Long non-coding RNA rhabdomyosarcoma 2-associated transcript (RMST) is a crucial regulator in various biological processes, particularly in neurogenesis and cancer progression. This review summarizes current knowledge on structure, expression patterns and functional roles across different organs and diseases of RMST. RMST exhibits tissue-specific expression, notably in brain tissues and vascular endothelial cells, and plays a significant role in neuronal differentiation through interaction with SRY-box 2. In cancer, RMST predominantly functions as a tumour suppressor, with context-dependent roles observed across different cancer types. RMST is also implicated in neurological disorders, cardiovascular diseases and Hirschsprung's disease. Mechanistically, RMST acts as a competing endogenous RNA and a transcriptional regulator, interacting with various microRNAs and proteins to modulate gene expression. The potential of RMST as a biomarker and therapeutic target is increasingly recognized, particularly in atherosclerosis and cancer. While current findings are promising, further research is needed to fully elucidate the functions and translate these insights into clinical applications of RMST. This review underscores the significance of RMST in cellular processes and disease pathogenesis, highlighting its potential as a novel target for diagnostic and therapeutic interventions.

MicroRNA signatures in neuroplasticity, neuroinflammation and neurotransmission in association with depression

Depression is a multifactorial disorder that occurs mainly on account of the dysregulation of neuroplasticity, neurotransmission and neuroinflammation in the brain. In addition to environmental /lifestyle factors, the pathogenesis of disease has been associated with genetic and epigenetic factors that affect the reprogramming of normal brain function. MicroRNA (miRNAs), a type of non-coding RNAs, are emerging as significant players that play a vital role in the regulation of gene expression and have been extensively explored in neurodegenerative disorders. Recent studies have also shown the role of gut microbiota that forms a complex bidirectional network with gut brain axis, impacting neuroinflammation in case of Parkinson's disease and depression. Translating targeted miRNA-based therapies for the treatment of neurological disorders including depression, into clinical practice remains challenging due to the ineffective delivery of the therapeutic molecules and off-target effects of the specific miRNAs. This review provides significant insights into how miRNAs are emerging as vital players in the development of depression, especially the ones involved in three important processes including neuroplasticity, neurotransmission and neuroinflammation. In this review, the current status of miRNAs as biomarkers for therapeutic interventions in the case of depression has been discussed along with an overview of future perspectives, like use of nanotechnology and gene editing, keeping in view other multifactorial disorders where such interventions by mimics and inhibitors have already reached clinical trials. The challenges for targeting the specific miRNAs for therapeutic outcomes have also been highlighted.

Molecular Mechanisms and Therapeutic Implications of Long Non-coding RNAs in Cutaneous Biology and Disease

Human skin is the largest organ of the human body and accounts for approximately fifteen percent of the total bodyweight. Its main physiological role is to protect the body against a wide range of environmental factors including pathogens, ultraviolet light, and injury. Importantly, the skin can regenerate and heal upon injury in large part by the differentiation of keratinocytes. Not surprisingly, dysregulation of cutaneous differentiation and self-renewal can result in a variety of skin-related pathologies, including autoimmune disease and cancer. Increasing evidence supports the premise that long non-coding RNAs (lncRNAs) act as critical mediators of gene expression and regulate important biological processes within the skin. Notably, dysregulation of lncRNAs has been shown to influence diverse physiological and pathological consequences. More recently, numerous reports have revealed new mechanistic insight on the role that lncRNAs play in skin homeostasis as well as their contribution to the pathogenesis of skin-related disorders. Here, we review the biological functions of cutaneous lncRNAs and their impact on skin homeostasis. We also describe the fundamental roles of lncRNAs in the pathogenesis of skin-related disorders, including fibrotic, autoimmune, and malignant diseases. Lastly, we will highlight how a better understanding of lncRNAs at the molecular level may reveal novel therapeutic approaches for the improvement of cutaneous disorders.

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.

Therapeutic application of circular RNA aptamers in a mouse model of psoriasis

Efforts to advance RNA aptamers as a new therapeutic modality have been limited by their susceptibility to degradation and immunogenicity. In a previous study, we demonstrated synthesized short double-stranded region-containing circular RNAs (ds-cRNAs) with minimal immunogenicity targeted to dsRNA-activated protein kinase R (PKR). Here we test the therapeutic potential of ds-cRNAs in a mouse model of imiquimod-induced psoriasis. We find that genetic supplementation of ds-cRNAs leads to inhibition of PKR, resulting in alleviation of downstream interferon-α and dsRNA signals and attenuation of psoriasis phenotypes. Delivery of ds-cRNAs by lipid nanoparticles to the spleen attenuates PKR activity in examined splenocytes, resulting in reduced epidermal thickness. These findings suggest that ds-cRNAs represent a promising approach to mitigate excessive PKR activation for therapeutic purposes.

The role of lncRNAs in the interplay of signaling pathways and epigenetic mechanisms in glioma

Gliomas, highly aggressive tumors of the central nervous system, present overwhelming challenges due to their heterogeneity and therapeutic resistance. Glioblastoma multiforme (GBM), the most malignant form, underscores this clinical urgency due to dismal prognosis despite aggressive treatment regimens. Recent advances in cancer research revealed signaling pathways and epigenetic mechanisms that intricately govern glioma progression, offering multifaceted targets for therapeutic intervention. This review explores the dynamic interplay between signaling events and epigenetic regulation in the context of glioma, with a particular focus on the crucial roles played by non-coding RNAs (ncRNAs). Through direct and indirect epigenetic targeting, ncRNAs emerge as key regulators shaping the molecular landscape of glioblastoma across its various stages. By dissecting these intricate regulatory networks, novel and patient-tailored therapeutic strategies could be devised to improve patient outcomes with this devastating disease.

Exosomes and non-coding RNAs: Exploring their roles in human myocardial dysfunction

Myocardial dysfunction, characterized by impaired cardiac muscle function, arises from diverse etiologies, including coronary artery disease, myocardial infarction, cardiomyopathies, hypertension, and valvular heart disease. Recent advancements have highlighted the roles of exosomes and non-coding RNAs in the pathophysiology of myocardial dysfunction. Exosomes are small extracellular vesicles released by cardiac and other cells that facilitate intercellular communication through their molecular cargo, including ncRNAs. ncRNAs are known to play critical roles in gene regulation through diverse mechanisms, impacting oxidative stress, fibrosis, and other factors associated with myocardial dysfunction. Dysregulation of these molecules correlates with disease progression, presenting opportunities for therapeutic interventions. This review explores the mechanistic interplay between exosomes and ncRNAs, underscoring their potential as biomarkers and therapeutic agents in myocardial dysfunction. Emerging evidence supports the use of engineered exosomes and modified ncRNAs to enhance cardiac repair by targeting signaling pathways associated with fibrosis, apoptosis, and angiogenesis. Despite promising preclinical results, delivery, stability, and immunogenicity challenges remain. Further research is needed to optimize clinical translation. Understanding these intricate mechanisms may drive the development of innovative strategies for diagnosing and treating myocardial dysfunction, ultimately improving patient outcomes.

It is Time to Revisit miRNA Therapeutics

The recent Nobel Prizes awarded to Ambros and Ruvkun have refocused attention on microRNAs (miRNAs). The importance of miRNAs for basic science has always been clear, but the application to therapy has lagged behind. This delay has been made even more apparent by the accelerating pace of successful programs using duplex RNAs and antisense oligonucleotides to target mRNA. Why has progress been slow? A clear understanding of how miRNAs function in mammalian cells is obscured by the fact that miRNAs can exert their effects through multiple complex mechanisms. This gap in our knowledge has complicated progress in drug discovery. Better insights into the mechanism of miRNAs, more rigorous definitions of miRNAs, and more powerful tools for establishing the physical contacts necessary for miRNA action are now available. These advances lead to a central question for nucleic acid therapy-can miRNAs be productive targets for drug discovery and development?

Non-coding RNAs in urinary bladder cancer microenvironment: Diagnostic, therapeutic, and prognostic perspective

Urinary bladder cancer (UBC) is the ninth most common cancer worldwide. Despite the reliance of UBC therapy on definite pathological grading and classifications, the clinical response among patients varies widely. The molecular basis of this type of cancer appeals to considerable research; hence, new diagnostic and therapeutic options are introduced. Convenient keywords were searched in Google Scholar, PubMed, the Egyptian Knowledge Bank (EKB), and Web of Science. The recent era of UBC research is concerned with non-coding RNAs (ncRNAs), predominantly, microRNAs (miRNAs) and long non-coding RNA (lncRNAs). In addition, snoRNAs, PIWI-interacting RNAs, mitochondrial RNAs, circular, and Schistosoma haematobium-related ncRNAs appeared to contribute to the pathogenesis of the UBC. This review underscored the recently studied ncRNAs and their importance in the pathogenesis of UBC. Besides, we introduced the prospectives regarding their diagnostic, therapeutic, and prognostic significance in UBC clinical settings. Conclusion. Oncogenic and oncosuppressor ncRNAs' definite balances and interaction within the TME of UBC are key players in the fate of the tumor. Thus, profiling ncRNA in-depth inspects the TME of the UBC for better clinical insights.

Glycolysis regulated exosomal LINC01214 inhibited CD8+ T cell function and induced anti-PD1 resistance in melanoma via modulating miR-4492/PPP1R11 axis

Background

Long non-coding RNAs (lncRNAs) can be incorporated into exosomes to mediate the intercellular communication, regulating the occurrence, development, and immunosuppression of cancers. T cell dysfunction has been a hallmark of many cancers, including melanoma, which enables cancer cells escape from host immune surveillance. However, the molecular mechanism of exosome-transmitted lncRNAs in CD8+ T cell dysfunction in melanoma remains largely unclear.

Method

The expression of circulating LINC01214 (cirLINC01214) was detected by quantitative real-time polymerase chain reaction (RT-qPCR). Exosomes were isolation from the culture medium and plasma of melanoma patients via ultracentrifugation and characterized by transmission electronic microscopy. The regulation of exosomal LINC01214 on CD8+ T cell function was determined by ELISA. The molecular mechanism of exosomal LINC01214 in CD8+ T cells were assessed by the RNA immunoprecipitation and pull-down assay. A mouse model with reconstituted human immune system was used to explore the role of exosomal LINC01214 in the resistance to anti-PD1 therapy.

Results

LINC01214 was highly expressed in melanoma tissues compared with matched adjacent normal tissues. Increased levels of circulating LINC01214 (cirLINC01214) was observed in melanoma patient plasma and correlated with poor PD-1 immunotherapy response. The cirLINC01214 was predominantly released by melanoma cells in an exosome manner. Melanoma cell-derived exosomal LINC01214 inhibits the production of IFN-γ, TNF-α, Granzyme-B and Perforin by CD8+ T cells. Further mechanism study found that cirLINC01214 delivered by exosomes suppressed CD8+ T cell function by up-regulating the expression of Protein Phosphatase 1 Regulatory Inhibitor Subunit 11 (PPP1R11) through sponging miR-4492. CirLINC01214 conferred resistance to PD-1 immunotherapy in melanoma xenograft mouse model. Melanoma patients with poor prognosis after PD-1 treatment carried high levels of exosomal LINC01214. Additionally, the secretion of exosomal cirLINC01214 was enhanced by the Warburg effect, which was consistent with the reprogrammed glucose metabolism of melanoma.

Conclusions

Our results demonstrated that exosomal LINC01214 released by melanoma cells promoted immunotherapy resistance by inducing CD8+ T cell dysfunction via the miR-4492/PPP1R11 regulatory loop. Targeting cirLINC01214 might be a potential therapeutic strategy to enhance the outcome of immunotherapy in melanoma.

Leveraging epigenetic alterations in pancreatic ductal adenocarcinoma for clinical applications

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy characterized by late detection and poor prognosis. Recent research highlights the pivotal role of epigenetic alterations in driving PDAC development and progression. These changes, in conjunction with genetic mutations, contribute to the intricate molecular landscape of the disease. Specific modifications in DNA methylation, histone marks, and non-coding RNAs are emerging as robust predictors of disease progression and patient survival, offering the potential for more precise prognostic tools compared to conventional clinical staging. Moreover, the detection of epigenetic alterations in blood and other non-invasive samples holds promise for earlier diagnosis and improved management of PDAC. This review comprehensively summarises current epigenetic research in PDAC and identifies persisting challenges. These include the complex nature of epigenetic profiles, tumour heterogeneity, limited access to early-stage samples, and the need for highly sensitive liquid biopsy technologies. Addressing these challenges requires the standardisation of methodologies, integration of multi-omics data, and leveraging advanced computational tools such as machine learning and artificial intelligence. While resource-intensive, these efforts are essential for unravelling the functional consequences of epigenetic changes and translating this knowledge into clinical applications. By overcoming these hurdles, epigenetic research has the potential to revolutionise the management of PDAC and improve patient outcomes.

miRNAs, piRNAs, and lncRNAs: A triad of non-coding RNAs regulating the neurovascular unit in diabetic retinopathy and their therapeutic potentials

Diabetic Retinopathy (DR), a leading complication of diabetes mellitus, has long been considered as a microvascular disease of the retina. However, recent evidence suggests that DR is a neurovascular disease, characterized by the degeneration of retinal neural tissue and microvascular abnormalities encompassing ischemia, neovascularization, and blood-retinal barrier breakdown, ultimately leading to blindness. The intricate relationship between the retina and vascular cells constitutes a neurovascular unit, a multi-cellular framework of retinal neurons, glial cells, immune cells, and vascular cells, which facilitates neurovascular coupling, linking neuronal activity to blood flow. These interconnections between the neurovascular components get compromised due to hyperglycemia and are further associated with the progression of DR early on in the disease. As a result, therapeutic approaches are needed to avert the advancement of DR by acting at its initial stage to delay or prevent the pathogenesis. Non-coding RNAs (ncRNAs) such as microRNAs, piwi-interacting RNAs, and long non-coding RNAs regulate various cellular components in the neurovascular unit. These ncRNAs are key regulators of neurodegeneration, apoptosis, inflammation, and oxidative stress in DR. In this review, research related to alterations in the expression of ncRNAs and, correspondingly, their effect on the disintegration of the neurovascular coupling will be discussed briefly to understand the potential of ncRNAs as therapeutic targets for treating this debilitating disease.

Long noncoding RNA GDIL acts as a scaffold for CHAC1 and XRN2 to promote platinum resistance of colorectal cancer through inhibition of glutathione degradation

Acquired resistance poses a significant obstacle to the effectiveness of platinum-based treatment for cancers. As the most abundant antioxidant, glutathione (GSH) enables cancer cell survival and chemoresistance, by scavenging excessive reactive oxygen species (ROS) induced by platinum. Therapeutic strategy targeting GSH synthesis has been developed, however, failed to produce desirable effects in preventing cancer progression. Thus, uncovering mechanisms of rewired GSH metabolism may aid in the development of additional therapeutic strategies to overcome or delay resistance. Here, we identify upregulation of long noncoding RNA (lncRNA) GDIL (GSH Degradation Inhibiting LncRNA) in platinum resistant colorectal cancer (CRC) and ovarian cancer cells compared with parental ones. High expression of GDIL in resistant CRC is associated with poor survival and hyposensitivity to chemotherapy. We demonstrate that GDIL boosted GSH levels and enhances clearance of ROS induced by platinum. Metabolomic and metabolic flux analysis further reveals that GDIL promotes GSH accumulation by inhibiting GSH degradation. This is attributed by downregulation of CHAC1, an enzyme that specifically degrades intracellular GSH. Mechanistically, GDIL binds and re-localizes the nuclear protein XRN2 to the cytoplasm, where GDIL further serve as a scaffold for XRN2 to identify and degrade CHAC1 mRNA. Suppression of GDIL with selective antisense oligonucleotide, restored drug sensitivity in platinum resistant cell lines and delayed drug resistance in cell line- and patient-derived xenografts. Thus, lncRNA GDIL is a novel target to promote GSH degradation and augment platinum therapy.

Recent advances in surface functionalization of cardiovascular stents

Cardiovascular diseases (CVD) are the leading global threat to human health. The clinical application of vascular stents improved the survival rates and quality of life for patients with cardiovascular diseases. However, despite the benefits stents bring to patients, there are still notable complications such as thrombosis and in-stent restenosis (ISR). Surface modification techniques represent an effective strategy to enhance the clinical efficacy of vascular stents and reduce complications. This paper reviews the development strategies of vascular stents based on surface functional coating technologies aimed at addressing the limitations in clinical application, including the inhibition of intimal hyperplasia, promotion of re-endothelialization. These strategies have improved endothelial repair and inhibited vascular remodeling, thereby promoting vascular healing post-stent implantation. However, the pathological microenvironment of target vessels and the lipid plaques are key pathological factors in the development of atherosclerosis (AS) and impaired vascular repair after percutaneous coronary intervention (PCI). Therefore, restoring normal physiological environment and removing the plaques are also treatment focuses after PCI for promoting vascular repair. Unfortunately, research in this area is limited. This paper reviews the advancements in vascular stents based on surface engineering technologies over the past decade, providing guidance for the development of stents.