Mitigating off-target effects of small RNAs: conventional approaches, network theory and artificial intelligence

The miR-21-5p/DUSP8/MAPK signaling pathway mediates inflammation and apoptosis in vascular endothelial cells induced by intermittent hypoxia and contributes to the protective effects of N-acetylcysteine

Obstructive sleep apnoea hypopnea syndrome (OSAHS) is a sleep disorder associated with significant cardiovascular complications, characterized by intermittent hypoxia (IH). IH causes endothelial dysfunction, an early event in cardiovascular disease. We investigated the role of dual-specificity phosphatase 8 (DUSP8), a key negative regulator of the mitogen-activated protein kinase (MAPK) signalling pathway, in IH-induced endothelial cell damage, and the therapeutic effects of N-acetylcysteine (NAC) by establishing IH models in human umbilical vein endothelial cells and C57BL/6 mice. DUSP8 and MAPK signalling pathway-related proteins were analysed by western blotting, and DUSP8 mRNA and miR-21-5p expression was assessed by RT-qPCR. Inflammatory cytokines were detected by an enzyme-linked immunosorbent assay, apoptosis-related proteins were analysed by western blotting, and apoptosis was assessed using flow cytometry. IH stimulation induced inflammation and apoptosis in endothelial cells, downregulated DUSP8 expression, and upregulated the phosphorylation of key molecules involved in the MAPK signalling pathway. However, DUSP8 overexpression alleviated IH-induced inflammation and apoptosis in endothelial cells and reduced the phosphorylation of key molecules in the MAPK signalling pathway. Bioinformatic analysis and dual-luciferase reporter assays confirmed that DUSP8 is a direct target of miR-21-5p. DUSP8 overexpression effectively reversed the damage caused by miR-21-5p upregulation under IH conditions. Furthermore, in cell and animal models of IH, NAC demonstrated protective effects against inflammation, apoptosis, and oxidative stress through a mechanism linked to the miR-21-5p/DUSP8/MAPK signalling pathway. Overall, this study elucidated the protective role of DUSP8 against IH-induced endothelial injury and confirmed the potential of NAC as a therapeutic agent for OSAHS-related diseases.

MAT2A Knockdown Enhances Recombinant Protein Expression in Transgenic CHO Cells Through Regulation of Cell Cycle

Chinese hamster ovary (CHO) cells represent the most widely utilized host system for industrial production of high-quality recombinant protein therapeutics. Novel CHO cell line development is achieved through genetic and cellular engineering approaches, effectively addressing limitations such as clonal variation and productivity loss during culture. Previous studies have established that MAT2A inhibition in tumor cells promotes expression of the cyclin-dependent kinase inhibitor p21, inducing antitumor activity. Notably, p21 induction has been shown to enhance recombinant protein expression in CHO cells by triggering cell cycle arrest. In this study, we identified MAT2A as a potential regulatory target, showing significant differential expression in transfected CHO cells with elevated versus diminished recombinant protein production. To investigate this phenomenon, we generated CHO cells with MAT2A knockdown (shMAT2A) and evaluated their recombinant protein output. Results demonstrated that MAT2A silencing enhanced recombiant protein/antibody production by 1.73-/1.70-fold through suppression of CyclinD1, thereby activating p21 and inducing G1 phase arrest. Furthermore, pharmacological inhibition of MAT2A using small molecules increased cell volume, boosted metabolic activity, and improved specific antibody productivity of recombiant protein/antibody production by 1.88-/2.16-fold in transfected CHO cells. These findings advance our understanding of MAT2A-mediated regulatory mechanisms and provide a strategic framework for developing high-efficiency CHO cell expression systems.

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.

Alternative splicing in autism spectrum disorder: Recent insights from mechanisms to therapy

Alternative splicing (AS) is a vital and highly dynamic RNA regulatory mechanism that allows a single gene to generate multiple mRNA and protein isoforms. Dysregulation of AS has been identified as a key contributor to the pathogenesis of autism spectrum disorders (ASD). A comprehensive understanding of aberrant splicing mechanisms and their functional consequences in ASD can help uncover the molecular basis of the disorder and facilitate the development of therapeutic strategies. This review focuses on the major aberrant splicing events and key splicing regulators associated with ASD, highlighting their roles in linking defective splicing to ASD pathogenesis. In addition, a discussion of how emerging technologies, such as long-read sequencing, single-cell sequencing, spatial transcriptomics and CRISPR-Cas systems are offering novel insights into the role and mechanisms of AS in ASD is presented. Finally, the RNA splicing-based therapeutic strategies are evaluated, emphasizing their potential to address unmet clinical needs in ASD treatment.

The Role of Artificial Intelligence in Drug Discovery and Pharmaceutical Development: A Paradigm Shift in the History of Pharmaceutical Industries

In today's world, with an increasing patient population, the need for medications is increasing rapidly. However, the current practice of drug development is time-consuming and requires a lot of investment by the pharmaceutical industries. Currently, it takes around 8-10 years and $3 billion of investment to develop a medication. Pharmaceutical industries and regulatory authorities are continuing to adopt new technologies to improve the efficiency of the drug development process. However, over the decades the pharmaceutical industries were not able to accelerate the drug development process. The pandemic (COVID-19) has taught the pharmaceutical industries and regulatory agencies an expensive lesson showing the need for emergency preparedness by accelerating the drug development process. Over the last few years, the pharmaceutical industries have been collaborating with artificial intelligence (AI) companies to develop algorithms and models that can be implemented at various stages of the drug development process to improve efficiency and reduce the developmental timelines significantly. In recent years, AI-screened drug candidates have entered clinical testing in human subjects which shows the interest of pharmaceutical companies and regulatory agencies. End-end integration of AI within the drug development process will benefit the industries for predicting the pharmacokinetic and pharmacodynamic profiles, toxicity, acceleration of clinical trials, study design, virtual monitoring of subjects, optimization of manufacturing process, analyzing and real-time monitoring of product quality, and regulatory preparedness. This review article discusses in detail the role of AI in various avenues of the pharmaceutical drug development process, its limitations, regulatory and future perspectives.

RNA-based therapies for neurodegenerative disease: Targeting molecular mechanisms for disease modification

Neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD) are characterized by progressive neuronal damage, protein aggregation, and chronic inflammation, leading to cognitive and motor impairments. Despite symptomatic relief from current therapies, disease-modifying treatments targeting the core molecular mechanism are still lacking. RNA-based therapies offer a promising approach to treating neurodegenerative disease by targeting molecular mechanisms such as gene expression, protein synthesis, and neuroinflammation. Therapeutic strategies include Long non-coding RNA (lncRNA), Antisense oligonucleotides (ASOs), RNA interference (RNAi), small interfering RNA (siRNA) and short hairpin RNA (shRNA), messenger RNA (mRNA) therapies, and microRNA (miRNA)-based interventions. These therapies aim to decrease toxic protein accumulation, restore deficient proteins, and modulate inflammatory responses in conditions like AD, PD, and HD. Unlike conventional treatments that primarily manage symptoms, RNA-based therapies have the potential to modify disease progression by addressing its root causes. This review aims to provide a comprehensive overview of current RNA-based therapeutic strategies for neurodegenerative diseases, discussing their mechanism of action, preclinical and clinical advancement. It further explores innovative solutions, including nanocarrier-mediated delivery, chemical modifications to enhance RNA stability, and personalized medicine approaches guided by genetic profiling that are being developed to overcome these barriers. This review also underscores the therapeutic opportunities and current limitations of RNA-based interventions, highlighting their potential to transform the future of neurodegenerative disease management.

Molecular mechanisms of lncRNA NEAT1 in the pathogenesis of liver-related diseases, with special focus on therapeutic approaches

Liver diseases are a major worldwide health concern, with high rates of dysfunction and mortality. In recent years, a variety of lncRNAs have been studied and discovered to be engaged in numerous cellular-level regulatory mechanisms as competing endogenous RNAs (ceRNAs), which play a significant role in the development of liver-related diseases. A class of RNA molecules known as lncRNAs, which are over 200 nucleotides long, do not translate into proteins. Nuclear Enriched Abundant Transcript 1 (NEAT1) is a type of lncRNA that has a critical function in paraspeckles formation and stability. NEAT1 levels are consistently found to be higher than normal in a number of different types of diseases, as well as patients who have high levels of NEAT1 expression often have a poor prognosis. The significance and mode of action of NEAT1 in liver illnesses, such as nonalcoholic fatty liver disease (NAFLD), alcohol-related liver disease (ALD), liver fibrosis/cirrhosis, hepatocellular carcinoma (HCC), viral hepatitis, and liver injury, are becoming more widely known. In this review, we highlighted significant recent studies concerning the various roles of lncRNA NEAT1 in hepatic diseases. As well as, we reviewed novel therapeutic potential of lncRNAs in several liver-related diseases.

SNHG family lncRNAs: Key players in the breast cancer progression and immune cell's modulation

Breast cancer, a highly prevalent form of cancer worldwide, has observed a steady increase in its prevalence over the past few decades. This rise can be attributed to the complex nature of the disease, characterized by its heterogeneity, ability to metastasize, and resistance to various treatment. In the field of cancer research, long non-coding RNAs (lncRNAs) are of special interest, which play an important role in the development and progression of various tumors, including breast cancer. LncRNAs affect the tumor microenvironment by attracting diverse immunosuppressive factors and controlling the differentiation of immune cells, often referred to as myeloid and lymphoid cells, which contributes to immune escape of tumor cells. Among the lncRNA families, the small nucleolar RNA host gene (SNHG) family has been found to be dysregulated in breast cancer. These SNHGs have been implicated in crucial cellular processes such as cell proliferation, invasion, migration, resistance to therapies, apoptosis, as well as immune cell regulation and differentiation. Consequently, they have great potential as diagnostic and prognostic biomarkers as well as potential therapeutic targets for breast cancer. In this comprehensive review, we aim to summarize the recent advances in the study of SNHGs in breast cancer pathogenesis and their role in regulating the activity of immune cells in the tumor microenvironment through affecting SNHGs/miRNA/mRNA pathways, with the aim of providing new insights into the treatment of breast cancer.

Critical analysis of descriptive microRNA data in the translational research on cardioprotection and cardiac repair: lost in the complexity of bioinformatics

The unsuccessful translation of cardiac regeneration and cardioprotection from animal experiments to clinical applications in humans has raised the question of whether microRNA bioinformatics can narrow the gap between animal and human research outputs. We reviewed the literature for the period between 2000 and 2024 and found 178 microRNAs involved in cardioprotection and cardiac regeneration. On analyzing the orthologs and annotations, as well as downstream regulation, we observed species-specific differences in the diverse regulation of the microRNAs and related genes and transcriptomes, the influence of the experimental setting on the microRNA-guided biological responses, and database-specific bioinformatics results. We concluded that, in addition to reducing the number of in vivo experiments, following the 3R animal experiment rules, the bioinformatics approach allows the prediction of several currently unknown interactions between pathways, coding and non-coding genes, proteins, and downstream regulatory elements. However, a comprehensive analysis of the miRNA-mRNA-protein networks needs a profound bioinformatics and mathematical education and training to appropriately design an experimental study, select the right bioinformatics tool with programming language skills and understand and display the bioinformatics output of the results to translate the research data into clinical practice. In addition, using in-silico approaches, a risk of deviating from the in vivo processes exists, with adverse consequences on the translational research.

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.

EDITORIAL for BJP themed issue "noncoding RNA therapeutics"

LINKED ARTICLES

This article is part of a themed issue Non-coding RNA Therapeutics. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v182.2/issuetoc.

Advances in the roles and mechanisms of mesenchymal stem cell derived microRNAs on periodontal tissue regeneration

Periodontitis is one of the most prevalent oral diseases leading to tooth loss in adults, and is characterized by the destruction of periodontal supporting structures. Traditional therapies for periodontitis cannot achieve ideal regeneration of the periodontal tissue. Mesenchymal stem cells (MSCs) represent a promising approach to periodontal tissue regeneration. Recently, the prominent role of MSCs in this context has been attributed to microRNAs (miRNAs), which participate in post-transcriptional regulation and are crucial for various physiological and pathological processes. Additionally, they function as indispensable elements in extracellular vesicles, which protect them from degradation. In periodontitis, MSCs-derived miRNAs play a pivotal role in cellular proliferation and differentiation, angiogenesis of periodontal tissues, regulating autophagy, providing anti-apoptotic effects, and mediating the inflammatory microenvironment. As a cell-free strategy, their small size and ability to target related sets of genes and regulate signaling networks predispose miRNAs to become ideal candidates for periodontal tissue regeneration. This review aims to introduce and summarize the potential functions and mechanisms of MSCs-derived miRNAs in periodontal tissue repair and regeneration.