Small and long non-coding RNAs: Past, present, and future

A LncRNA panel within EpCAM-specific exosomes for noninvasive early diagnosing non-small cell lung cancer

BACKGROUND

Plasma tumor-associated exosomes represent a promising source for cancer biomarkers; however, the role of long non-coding RNAs (lncRNAs) within these exosomes is not well-defined in non-small cell lung cancer (NSCLC).

METHODS

We identified a panel of NSCLC-specific lncRNAs within plasma EpCAM-specific exosomes (Epexo) through a comparative analysis of lncRNA profiles between plasma Epexo and lung tissues. The panel's diagnostic value was firstly evaluated in a retrospective cohort of 210 NSCLC patients and 245 healthy controls, and validated in a prospective cohort of 192 patients with pulmonary nodules (nodule size < 3 cm in diameter). The evaluation utilized the area under the ROC curve (AUC) based on a random forest model. For precision, repeat testing was conducted with 31 randomly selected samples. Additionally, 39 paired tissue-plasma samples were employed to assess the concordance of lncRNA expression between tissue and plasma within the same individuals.

RESULTS

The panel, including linc01125, HNF1A-AS1, MIR100HG, linc01160, and ZNRF3-AS1, demonstrated superior capability in distinguishing early-stage NSCLC patients from controls, achieving AUC values of 0.805 and 0.856 in the discovery and validation set, respectively. The panel also showed potential for differentiating adenocarcinoma and squamous cell carcinoma. Repeat sample testing showed a consistency of 90.3% for this panel. The expression levels of MIR100HG and HNF1A-AS1 showed significant correlations between plasma Epexo and cancerous tissues.

CONCLUSIONS

The identified lncRNA panel, consisting of linc01125, HNF1A-AS1, MIR100HG, linc01160, and ZNRF3-AS1, presents a promising diagnostic tool for NSCLC.

CLINICAL TRIAL NUMBER

not applicable.

Navigating thyroid cancer complexity: the emerging role of EV-derived non-coding RNAs

Thyroid cancer (TC), which arises from the epithelial cells of the thyroid gland, is experiencing a significant increase in incidence globally. TC encompasses various subtypes, including papillary, follicular, medullary, and anaplastic thyroid cancers, each with distinct pathological and clinical features. Extracellular vesicles (EVs), are naturally occurring and nanosized lipid bilayers, and can be secreted by almost all cell types. EVs, comprising microvesicles and exosomes, are pivotal in mediating intercellular communication within the tumor microenvironment. Notably, EVs possess unique properties such as stability in circulation and the ability to traverse biological barriers, enhancing their role as carriers of molecular information. EVs carry non-coding RNAs (ncRNAs), including miRNAs, lncRNAs, and circRNAs, which are crucial regulators of gene expression. Recent studies have highlighted the significant role of EV-derived ncRNAs in influencing thyroid cancer progression, metastasis, and immune modulation by mediating intercellular communication within the tumor microenvironment. The expression of EV-derived ncRNAs varies across different stages of thyroid cancer, reflecting potential as biomarkers for diagnosis and targets for therapy. This review delves into the multifaceted roles of EV-ncRNAs in thyroid cancer, emphasizing their impact on tumor growth, metastatic potential, and immune interactions, while also exploring their promising applications in early diagnosis and targeted treatment strategies. Understanding these dynamics is essential for developing innovative interventions to improve patient outcomes in thyroid cancer.

A review of molecular interplay between inflammation and cancer: The role of lncRNAs in pathogenesis and therapeutic potential

The inflammatory microenvironment (IME) has been demonstrated to facilitate the initiation and progression of tumors throughout the inflammatory process. Simultaneously, cancer can initiate or intensify the inflammatory response, thereby promoting tumor progression. This review examines the dual role of long non-coding RNAs (lncRNAs) in the interplay between inflammation and cancer. LncRNA modulate inflammation-induced cancer by influencing the activation of signaling pathways (NF-κB, Wnt/β-catenin, mTOR, etc), microRNA (miRNA) sponging, protein interactions, interactions with immune cells, and encoding short peptides. In contrast, lncRNAs also impact cancer-induced inflammatory processes by regulating cytokine expression, mediating tumor-derived extracellular vesicles (EVs), modulating intracellular reactive oxygen species (ROS) levels, and facilitating metabolic reprogramming. Furthermore, the therapeutic potential of lncRNA and the challenges of clinical translation were explicitly discussed as well. Overall, this review aims to provide a comprehensive and systematic resource for future researchers investigating the impact of lncRNAs on inflammation and cancer.

Zebrafish in neurodevelopmental disorders studies: Genetic models and pathological involvement of microglia

Neurodevelopmental disorders (NDDs) are a group of brain disorders with a neonatal or early childhood onset and are lifelong. Various factors including genetics, and environmental and immune-related risk factors have been associated with NDDs. Given the complex nature of these disorders, multiple animal models have been used to investigate their aetiology and underlying cellular and molecular mechanisms. Recently, zebrafish have attracted great attention as an emerging model for studying NDDs. In addition to their easy maintenance, short developmental cycle, ex utero embryonic evolution, and optical clarity, zebrafish have successfully recapitulated phenotypes seen in human genetic disorders. This review explores the growing role of zebrafish in NDD research, by summarizing recently developed zebrafish genetic models for autism spectrum disorder, schizophrenia, and cerebral palsy. We then explore the potential of zebrafish as a model for studying NDDs linked to immune system dysfunction.

Long noncoding RNA as an emerging regulator of endoderm differentiation: progress and perspectives

Accumulated studies have demonstrated that long noncoding RNAs (lncRNAs) play crucial regulatory roles in diverse biological processes, such as embryonic development and cell differentiation. Comprehensive transcriptome analysis identifies extensive lncRNAs, gradually elucidating their functions across various contexts. Recent studies have highlighted the essential role of lncRNAs in definitive endoderm differentiation, underscoring their importance in early development. In this review, we have analyzed the features of overlapping, proximal, and desert lncRNAs, classified by genomic location, in pluripotent stem cells (PSCs) and the differentiation derivatives. Furthermore, we focus on the endoderm lineage and review the latest advancements in lncRNA identification and their distinct regulatory mechanisms. By consolidating current knowledge, we aim to provide a clearer perspective on how lncRNAs contribute to endoderm differentiation in different manners.

Up-regulated microRNAs in blastocoel fluid of human implanted embryos could control circuits of pluripotency and be related to embryo competence

PURPOSE

The paper aims to investigate the biological role of microRNAs secreted by preimplantation embryo into the blastocoel fluid and to detect a distinctive molecular signature for identifying embryos with the highest implantation potential.

METHODS

We carried on a multicenter retrospective study involving five European IVF centers. We collected 112 blastocoel fluid samples from embryos on day 5 post-fertilization, cultured individually, along with data on blastocyst grade and embryo transfer outcomes. Using a custom TLDA Array, we compared the expression levels of 89 miRNAs between 33 fluids from high-quality implanted embryos and 30 fluids from high-quality not-implanted embryos. Expression differences were assessed using SAM and t-test. Additionally, correlation and function enrichment analysis and network construction were conducted to identify the biological roles of deregulated microRNAs.

RESULTS

We identified six up-regulated microRNAs in the blastocoel fluid from implanted embryos, significantly and positively correlated across all samples (r ≥ 0.7; P ≤ 0.05). They could take part in pluripotency circuits, regulating and being regulated by transcription factors associated with stemness, cell growth, and embryo development. The ROC curve analysis confirmed the potential of these miRNAs as implantation classifiers.

CONCLUSION

The six miRNAs up-regulated in blastocoel fluid from implanted embryos may represent a functional molecular signature for evaluating blastocyst quality and identifying the most competent embryos. Their evaluation associated with non-invasive preimplantation genetic testing, integrating epigenetic and genomic analyses, could enhance implantation grade and allow for identification of the euploid embryo not able to implant.

Tubercidin enhances apoptosis in serum-starved and hypoxic mouse cardiomyocytes by inducing nuclear speckle condensation

Tubercidin, known for its antimicrobial, antiparasitic, and anticancer effects, faces clinical limitations due to adverse effects, especially cardiotoxicity risks for those with ischemic cardiomyopathy. This study aims to clarify the molecular pathways of Tubercidin-induced cardiotoxicity, focusing on nuclear speckles (NSs) disruption in cardiomyocytes under serum deprivation and/or hypoxia. To simulate ischemic cardiomyopathy in vitro, we utilized FMC84 and HL-1 murine cardiomyocyte cell lines, exposing them to conditions of serum limitation and/or hypoxia to evaluate the cardiotoxic impact of Tubercidin and the contributing mechanisms. Apoptosis was quantified using flow cytometry, NSs condensation was visualized via immunofluorescence with an anti-SC35 antibody, and the expression levels of key apoptotic transcripts (RFFL, RIF1, and RNF144B) were analyzed by RT-PCR. Our findings revealed that Tubercidin significantly increased apoptosis in both HL-1 and FMC84 cell lines under conditions mimicking serum deprivation (21% O2 with 1% FBS), hypoxia (1% O2 with 10% FBS), or a combination of both. Furthermore, Tubercidin treatment led to a pronounced enlargement of NSs, as detected by immunofluorescence. Concurrently, we documented significant alterations in the expression of critical apoptotic regulatory genes, implying that Tubercidin may modulate the apoptotic pathway in stressed cardiomyocytes. It is hypothesized that Tubercidin induces NSs condensation, affecting alternative splicing of cell death genes, potentially worsening ischemic cardiomyocytes' damage. Therefore, a cautious clinical use of Tubercidin for ischemic cardiomyopathy patients is advised to reduce cardiotoxicity risks.

miRNA let-7f-5p-encapsulated labial gland MSC-derived EVs ameliorate experimental Sjögren's syndrome by suppressing Th17 cells via targeting RORC/IL-17A signaling axis

Sjögren's syndrome (SS) is an autoimmune disease primarily affecting salivary glands, with xerostomia as a distinct clinical manifestation. This disease also poses a significantly increased risk of lymphoma, severely impacting patients' quality of life. The imbalance between Th17 and Treg cells plays a critical role in SS progression, driving severe immune dysregulation, chronic inflammation, and escalating tissue dysfunction. However, current clinical treatments for SS still remain limited, and it continues to be recognized as a refractory disease. Therefore, the development of novel and effective therapeutic strategies is a pressing demand in clinical research. In recent years, extracellular vesicle (EV) therapy has emerged as a promising approach for autoimmune disease treatment, showing encouraging outcomes in modulating immune balance and alleviating symptoms. EVs carry diverse cargo, among which microRNAs (miRNAs) are highly abundant and play critical roles. These small RNAs are essential for EV-mediated functions, particularly in regulating gene expression and modulating the immune microenvironment. Our research team first isolated labial gland mesenchymal stem cells (LGMSCs) and their derived EVs (LGMSC-EVs), which offer potential therapeutic advantages in SS due to their salivary gland origin. Then we screened and identified the highly enriched miRNA let-7f-5p as a key regulator through miRNA profiling analysis. To achieve better therapeutic outcomes, we transfected exogenous miRNA let-7f-5p into LGMSC-EVs to upregulate its expression, thereby constructing let-7f-5p-encapsulated LGMSC-EVs. These modified EVs were subsequently tested in an experimental SS mouse model to evaluate their therapeutic potential. The upregulation of miRNA let-7f-5p in LGMSC-EVs significantly enhanced their therapeutic effects, resulting in clinical improvements such as increased salivary flow and reduced lymphocytic infiltration. Mechanistically, let-7f-5p-encapsulated LGMSC-EVs suppressed Th17 cells by directly targeting the 3'-untranslated region (3'UTR) of RORC, inhibiting the RORC/IL-17A signaling axis, and reducing IL-17A production, thereby restoring Th17/Treg balance and promoting an anti-inflammatory profile. Collectively, this let-7f-5p-encapsulated LGMSC-EV therapy offers a promising target-driven approach for the treatment of SS, achieving improved clinical outcomes and immune rebalance after modification with miRNA let-7f-5p, which presents new potential for the clinical treatment of SS.

Epigenetic Regulation of Chromatin Functions by MicroRNAs and Long Noncoding RNAs and Implications in Human Diseases

The bulk of RNA produced from the genome of complex organisms consists of a very large number of transcripts lacking protein translational potential and collectively known as noncoding RNAs (ncRNAs). Initially thought to be mere products of spurious transcriptional noise, ncRNAs are now universally recognized as pivotal players in cell regulatory networks across a broad spectrum of biological processes. Owing to their critical regulatory roles, ncRNA dysfunction is closely associated with the etiopathogenesis of various human malignancies, including cancer. As such, ncRNAs represent valuable diagnostic biomarkers as well as potential targets for innovative therapeutic intervention. In this review, we focus on microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), the two most extensively studied classes in the field of ncRNA biology. After outlining key concepts of miRNA and lncRNA biogenesis pathways, we examine their multiple roles in mediating epigenetic regulation of gene expression and chromatin organization. Finally, by providing numerous examples of specific miRNAs and lncRNAs, we discuss how dysregulation of these mechanisms contributes to the onset and/or progression of various human diseases.

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

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

LncRNAs Ride the Storm of Epigenetic Marks

Advancements in genome sequencing technologies have uncovered the multifaceted roles of long non-coding RNAs (lncRNAs) in human cells. Recent discoveries have identified lncRNAs as major players in gene regulatory pathways, highlighting their pivotal role in human cell growth and development. Their dysregulation is implicated in the onset of genetic disorders and age-related diseases, including cancer. Specifically, they have been found to orchestrate molecular mechanisms impacting epigenetics, including DNA methylation and hydroxymethylation, histone modifications, and chromatin remodeling, thereby significantly influencing gene expression. This review provides an overview of the current knowledge on lncRNA-mediated epigenetic regulation of gene expression, emphasizing the biomedical implications of lncRNAs in the development of different types of cancers and genetic diseases.

Plasmonic Biosensors in Cancer-Associated miRNA Detection

Cancer is one of the most lethal diseases and has distinct variants that affect over 60 organs in the human body. The necessity of advanced methodologies for the early diagnosis of cancer has grown over the past decades. Among various biomarkers, microRNAs (miRNAs) have emerged as highly specific and minimally invasive indicators for cancer detection, prognosis, and treatment monitoring. Their stability in biological fluids and their critical role in gene regulation make them valuable targets for diagnostic applications. Plasmonic biosensors have gained massive attention owing to their unique optical properties, such as surface plasmon resonance, making them promising tools for the sensitive and selective analysis of cancer-associated biomarkers. In contrast to previous reviews, this work offers a comprehensive overview of advancements from approximately the past five years, particularly in the detection of cancer-associated miRNAs. It emphasizes emerging plasmonic sensing strategies, integration with novel nanomaterials, and enhanced signal amplification techniques. By focusing on these recent innovations, this review provides new insights into the potential of plasmonic biosensors to improve cancer diagnosis and treatment.

The Unpaved Road of Non-Coding RNA Structure-Function Relationships: Current Knowledge, Available Methodologies, and Future Trends

The genomes from complex eukaryotes are enriched in non-coding genes whose transcription products (non-coding RNAs) are involved in the regulation of genomic output at different levels. Non-coding RNA action is predominantly driven by sequence and structural motifs that interact with specific functional partners. Despite the exponential growth in primary RNA sequence data facilitated by next-generation sequencing studies, the availability of tridimensional RNA data is comparatively more limited. The subjacent reasons for this relative lack of information regarding RNA structure are related to the specific chemical nature of RNA molecules and the limitations of the currently available methods for structural characterization of biomolecules. In this review, we describe and analyze the different structural motifs involved in non-coding RNA function and the wet-lab and computational methods used to characterize their structure-function relationships, highlighting the current need for detailed structural studies to explore the molecular determinants of non-coding RNA function.

Stress-Related LncRNAs and Their Roles in Diabetes and Diabetic Complications

Diabetes mellitus (DM) is a chronic metabolic disorder and one of the most significant global health burdens worldwide. Key pathophysiological mechanisms underlying its onset and associated complications include hyperglycemia-related stresses, such as oxidative stress and endoplasmic reticulum stress (ER stress). Long non-coding RNAs (lncRNAs), defined as RNA transcripts longer than 200 nucleotides and lacking protein-coding capacity, play crucial roles in various biological processes and have emerged as crucial regulators in the pathogenesis of diabetes. This review provides a comprehensive overview of lncRNA biogenesis and its functional roles, emphasizing recent findings that link stress-related lncRNAs to diabetic pathology and complications. Also, we discuss how lncRNAs influence diabetes and its complications by modulating pathways involved in cell death, proliferation, inflammation, and fibrosis, which contribute to pancreatic β cell dysfunction, insulin resistance, diabetic nephropathy, and retinopathy. By analyzing current research, we aim to enhance understanding of lncRNA involvement in diabetes while identifying potential therapeutic targets and guiding future research directions to elucidate the complex mechanisms underlying this pervasive condition.

Bol-miR168a is a key regulator of defense responses to Sclerotinia sclerotiorum in Brassica oleracea

KEY MESSAGE

Overexpressing Bol-miR168a in cabbage reduces resistance to Sclerotinia sclerotiorum, highlighting its role in disease susceptibility regulation. miRNA-mediated post-transcriptional regulation plays a central role in regulating physiological processes, including plant growth and development, hormone signal transduction, and stress response. However, the underlying mechanism and function of microRNA-mediated repression, particularly in relation to conferring resistance to S. sclerotiorum, has not been extensively explored. In this study, Bol-miR168a was isolated from cabbage, and its function was identified in transgenic Arabidopsis and cabbage under S. sclerotiorum infection. The miR168a gene promoter contains multiple hormone response and stress response elements, which can be bound and activated by corresponding transcription factors. Expression of the Bol-miR168a was strongly induced during the first 48 h post-inoculation. The overexpression of Bol-miR168a in transgenic cabbage resulted in enhanced sensitivity to S. sclerotiorum infection, as evidenced by decreased antioxidant enzyme activities, reduced phenylalanine ammonia-lyase (PAL) content, and elevated malondialdehyde (MDA) levels. Consistent with this, Bol-miR168a overexpression in Arabidopsis (Arabidopsis thaliana) promoted plant susceptibility to S. sclerotiorum and led to increased their capacity to detoxify reactive oxygen species (ROS) in the leaves. Furthermore, in Bol-miR168a-overexpressing plants, disease-related genes displayed distinct expression patterns in transgenic Arabidopsis and cabbage, highlighting differential regulatory responses to pathogen infection. Taken together, our results suggest that Bol-miR168a played a negative role in regulating the resistance of cabbage to S. sclerotiorum, providing a basis for further investigating how Bol-miR168a regulates resistance to S. sclerotiorum.

Immuno-oncological Challenges and Chemoresistance in Veterinary Medicine: Probiotics as a New Strategic Tool

Cancer has the highest death rates due to increased immuno-oncological (IO) challenges and chemoresistance caused by gut dysbiosis, whereas administration of probiotics may reverse these responses against anticancer therapies. Recently, immunotherapeutics have extensively been focused for significant advancements in pharmacological drug discovery and clinical outcomes. Mammals have intestinal epithelial cells, mucosal immune cells, and indigenous gut microbiota which may reshape immunotherapeutics efficacy. These include use of T-cell immune checkpoint inhibitors (ICPI), genetically engineered T-cells, tumor vaccines, monoclonal antibodies (mAbs), and anti-B- and T-cell antibodies. Immunotherapeutics for cancer treatment became popular in both veterinary and human health care systems due to their strong inhibitory actions against PD-1 and CTLA-4 to check tumorigenesis. IO issues in animals also need special attention, where caninized mAbs targeting CD-20 and CD-52 have been clinically used in treating canine B-cell and T-cell lymphomas, respectively. Probiotics appeared as strong immunotherapeutics that might be shaping the epigenetics of the organisms specifically in animal breeding practices for desired features, but limited literature regarding the immunomodulatory effects in humans and animals is available. In addition, considering the important role of probiotics in humans and veterinary medicine, a new perspective on the probiotic-mediated modulation of ncRNAs (miRNAs, lncRNAs, circRNAs) is also highlighted and would be a new therapeutic tool. This review provides insight into the cellular processes and pharmacological activities for treating veterinary infectious diseases and covers small drug molecules as ncRNA-modulators in veterinary medicine.

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.

MicroRNA Gets a Mighty Award

Recent advancements in microRNAs (miRNAs) research have revealed their key roles in both normal physiological processes and pathological conditions, leading to potential applications in diagnostics and therapeutics. However, the path forward is fraught with several scientific and technical challenges. This review article briefly explores the milestones of the discovery, biogenesis, functions, and application for clinical diagnostic and therapeutic strategies of miRNAs. The potential challenges and future directions are also discussed to fully harness their capabilities.

From non-coding to coding: The importance of long non-coding RNA translation in de novo gene birth

Recent emerging evidence demonstrates that some long non-coding RNAs (lncRNAs) can indeed be translated into functional polypeptides. These discoveries are pivotal for understanding de novo gene birth, the process by which new genes evolve from previously non-genic regions. In this review, we first introduce key methods, such as Ribo-seq and translation initiation site detection by translation complex analysis, for identifying coding sequences within lncRNAs and highlight examples of functional polypeptides derived from lncRNAs across species. These polypeptides play essential roles in maintaining cellular homeostasis and contribute to pathological processes, including cancer. However, because not all lncRNA-derived polypeptides appear to be functional, these lncRNAs may act as gene reservoirs. We also discuss how lncRNAs change their intracellular localization, how lncRNA-derived polypeptides evade immune surveillance, and how they gradually evolve into typical coding RNAs, providing evidence for the evolutionary model of de novo gene birth.

Noncoding RNAs in sepsis-associated acute liver injury: Roles, mechanisms, and therapeutic applications

Sepsis is a life-threatening syndrome characterized by organ dysfunction caused by a dysregulated host response to infection. Sepsis-associated acute liver injury (SA-ALI) is a frequent and serious complication of sepsis that considerably impacts both short-term and long-term survival outcomes. In intensive care units (ICUs), the mortality rate of patients with SA-ALI remains high, mostly due to the absence of effective early diagnostic markers and suitable therapeutic strategies. Recent studies have demonstrated the importance of non-coding RNAs (ncRNAs) in the development and progression of SA-ALI. This review focuses on the critical roles of ncRNAs, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), in regulating "cytokine storms", oxidative stress, mitochondrial dysfunction, and programmed cell death in SA-ALI, and summarizes the current state and limitations of existing studies on lncRNAs and circRNAs in SA-ALI. By integrating advancements in high-throughput sequencing technologies, this review provides novel insights into the dual potential of ncRNAs as diagnostic biomarkers and therapeutic targets, offers new ideas for SA-ALI diagnosis and treatment research and highlights potential challenges in clinical translation.

mRNA Transcript Variants Expressed in Mammalian Cells

Gene expression or gene regulation studies often assume one gene expresses one mRNA. However, contrary to the conventional idea, a single gene in mammalian cells can express multiple transcript variants translated into several different proteins. The transcript variants are generated through transcription from alternative start sites and alternative post-transcriptional processing of the precursor mRNA (pre-mRNA). In addition, gene mutations and RNA editing further enhance the diversity of the transcript variants. The transcript variants can encode proteins with various domains, expanding the functional repertoire of a single gene. Some transcript variants may not encode proteins but function as non-coding RNAs and regulate gene expression. The expression level of the transcript variants may vary between cell types or within the same cells under different biological conditions. Transcript variants are characteristic of cell differentiation in a particular tissue, and the variants may play a key role in normal development and aging. Studies also reported that some transcript variants may have roles in disease pathogenesis. The biological significances urge studying the complexity of gene expression at the transcript level. This article updates the molecular basis of transcript variants in mammalian cells, including the formation mechanisms and potential roles in host biology. Gaining insight into the transcript variants will not only identify novel mechanisms of gene regulation but also unravel the role of the variants in health and disease.

Long Non-Coding RNA THRIL Promotes Influenza Virus Replication by Inhibiting the Antiviral Innate Immune Response

Long non-coding RNAs (lncRNAs) have been recognized for their crucial roles in the replication processes of various viruses. However, the specific functions and regulatory mechanisms of many lncRNAs in influenza A virus (IAV) pathogenesis remain poorly understood. In this study, we identified lncRNA THRIL and observed a significant reduction in its expression following IAV infection in A549 cells. The treatment of cells with the viral mimic poly (I:C), or with type I and type III interferons, resulted in a substantial decrease in THRIL expression. Furthermore, THRIL overexpression significantly enhanced IAV replication, while its silencing markedly reduced IAV replication. Additionally, IAV infection led to notable reductions in the expression levels of type I and type III interferons in cell lines overexpressing THRIL compared to control groups; conversely, cell lines with THRIL knockdown exhibited significantly higher interferon levels than control groups. Moreover, THRIL was found to inhibit the expression of several critical interferon-stimulated genes (ISGs), which are essential for an effective antiviral response. Notably, our findings demonstrated that THRIL impaired the activation of IRF3, a key transcription factor in the interferon signaling pathway, thereby suppressing host innate immunity. These results highlight THRIL's potential as a therapeutic target for antiviral strategies.

MicroRNA-200c in Cancer Generation, Invasion, and Metastasis

MicroRNA-200c (miR-200c) is increasingly recognized as a crucial small RNA molecule that plays a significant and multifaceted role in the complex processes of tumor development, invasion, and metastasis across various types of cancers. Recent studies have compellingly demonstrated that miR-200c exerts its influence on tumor biology by meticulously regulating a range of critical processes, including cell proliferation, apoptosis, epithelial-mesenchymal transition (EMT), and cell migration, all of which are essential for the progression and aggressiveness of tumors. This comprehensive review aims to summarize the expression characteristics and functional implications of miR-200c across a diverse array of tumor types, delving into its potential utility as both a biomarker for early detection and a therapeutic target in the realm of cancer treatment. By synthesizing current research findings and insights, we aspire to provide valuable information that could significantly enhance early diagnostic capabilities and inform the strategic development of targeted therapy approaches in oncology.

Dual Roles of miR-10a-5p and miR-10b-5p as Tumor Suppressors and Oncogenes in Diverse Cancers

Cancer is a complex genetic disorder characterized by abnormalities in both coding and regulatory non-coding RNAs. microRNAs (miRNAs) are key regulatory non-coding RNAs that modulate cancer development, functioning as both tumor suppressors and oncogenes. miRNAs play critical roles in cancer progression, influencing key processes such as initiation, promotion, and metastasis. They exert their effects by targeting tumor suppressor genes, thereby facilitating cancer progression, while also inhibiting oncogenes to prevent further disease advancement. The miR-10 family, particularly miR-10a-5p and miR-10b-5p (miR-10a/b-5p), is notably involved in cancer progression. Intriguingly, their functions can differ across different cancers, sometimes promoting and at other times suppressing tumor growth depending on the cancer type and target genes. This review explores the dual roles of miR-10a/b-5p as tumor-suppressive miRNAs (TSmiRs) or oncogenic miRNAs (oncomiRs) in various cancers by examining their molecular and cellular mechanisms and their impact on the tumor microenvironment. Furthermore, we discuss the potential of miR-10a/b-5p as therapeutic targets, emphasizing miRNA-based strategies for cancer treatment. The insights discussed in this review aim to advance our understanding of miR-10a/b-5p's roles in tumor biology and their application in developing innovative cancer therapies.

lncRNA CHAF1B-2 contributes to the tumorigenesis of gastric cancer by activating the Wnt/β-catenin pathway

Lnc-CHAF1B-2, a newly discovered long noncoding RNA (lncRNA), plays a significant role in the evolution and prognosis of diverse neoplasms. However, its role in the development of gastric cancer is not yet fully understood. Using bioinformatics analysis of gastric cancer RNA-seq data from The Cancer Genome Atlas (TCGA) database, we investigated the expression of lnc-CHAF1B-2 in gastric carcinoma and its associated molecular signalling pathways. Verification through an array of in vivo and in vitro experiments-namely, EdU incorporation, flow cytometry, trans-well migration and invasion assays, subcutaneous tumour formation in nude mice, and western blot analysis-was conducted. We revealed notable upregulation of lnc-CHAF1B-2 in gastric cancer tissues. Furthermore, a positive correlation was detected between lnc-CHAF1B-2 levels and the occurrence of distant metastases in patients, which was inversely related to their prognostic outlook and survival rates. Moreover, our findings confirmed that lnc-CHAF1B-2 enhanced the proliferation, invasion, and migration of gastric cancer cells while inhibiting apoptosis both in vitro and in vivo. Mechanistically, lnc-CHAF1B-2 promoted the progression of gastric cancer through activating the Wnt/β-catenin signalling pathway. Thus, lnc-CHAF1B-2 and its regulation of the Wnt/β-catenin signalling pathway have emerged as prospective therapeutic targets in gastric cancer management.

LncRNAs chaperoning dynamic protein condensates in cancer cells

In this issue of Molecular Cell, Sun et al. reveal that the long non-coding RNA (lncRNA) DNAJC3-AS1 plays a dual role in maintaining the rRNA processing function of fibrillarin (FBL) in cancer cells. It promotes FBL condensation while preventing abnormal aggregation, offering new therapeutic insights for cancer treatment by targeting lncRNAs involved in the regulation of FBL condensation.

Subcellular Localization Guides eNOS Function

Nitric oxide synthases (NOS) are enzymes responsible for the cellular production of nitric oxide (NO), a highly reactive signaling molecule involved in important physiological and pathological processes. Given its remarkable capacity to diffuse across membranes, NO cannot be stored inside cells and thus requires multiple controlling mechanisms to regulate its biological functions. In particular, the regulation of endothelial nitric oxide synthase (eNOS) activity has been shown to be crucial in vascular homeostasis, primarily affecting cardiovascular disease and other pathophysiological processes of importance for human health. Among other factors, the subcellular localization of eNOS plays an important role in regulating its enzymatic activity and the bioavailability of NO. The aim of this review is to summarize pioneering studies and more recent publications, unveiling some of the factors that influence the subcellular compartmentalization of eNOS and discussing their functional implications in health and disease.