Gene regulation by long non-coding RNAs and its biological functions

Identification of differentially expressed non-coding RNAs in the plasma of women with preterm birth

This study aimed to identify differentially expressed non-coding RNAs (ncRNAs) associated with preterm birth (PTB) and determine biological pathways being influenced in the context of PTB. We processed cell-free RNA sequencing data and identified seventeen differentially expressed (DE) ncRNAs that could be involved in the onset of PTB. Per the validation via customized RT-qPCR, the recorded variations in expressions of eleven ncRNAs were concordant with the in-silico analyses. The results of this study provide insights into the role of DE ncRNAs and their impact on pregnancy-related biological pathways that could lead to PTB. Further studies are required to elucidate the precise mechanisms by which these DE ncRNAs contribute to adverse pregnancy outcomes (APOs) and their potential as diagnostic biomarkers.

LncRNA SNHG1: A novel biomarker and therapeutic target in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality globally. Increasing evidence suggests that long non-coding RNAs play a critical role in cancer development, with the small nucleolar RNA host gene family being a key participant in multiple types of carcinogenesis, including HCC. Small nucleolar RNA host gene 1 (SNHG1) is a significant member of the SNHG family. SNHG1 expression consistently increases in various HCC-associated processes, such as cell proliferation, apoptosis, angiogenesis, migration, invasion, and treatment resistance. Higher SNHG1 expression levels predict worse prognosis by positively correlating with clinicopathological features, including larger tumour size, poor differentiation, and advanced stages in patients with HCC. Nevertheless, the precise role of SNHG1 in the initiation and progression of HCC remains unclear. Therefore, this review aims to summarise the current investigations on the pathogenesis of SNHG1 in HCC, highlighting its potential as a molecular marker for early prediction and prognostic assessment. As a multifunctional modulator, SNHG1 is extensively involved in molecular signalling pathways in HCC progression and is valuable for therapeutic targeting.

Urinary exosomal lnc-TAF12-2:1 promotes bladder cancer progression through the miR-7847-3p/ASB12 regulatory axis

Exosomes encompass a great deal of valuable biological information and play a critical role in tumor development. However, the mechanism of exosomal lncRNAs remains poorly elucidated in bladder cancer (BCa). In this study, we identified exosomal lnc-TAF12-2:1 as a novel biomarker in BCa diagnosis and aimed to investigate the underlying biological function. Dual luciferase reporter assay, RNA immunoprecipitation (RIP), RNA pulldown assays, and xenograft mouse model were used to verify the competitive endogenous RNA mechanism of lnc-TAF12-2:1. We found exosomal lnc-TAF12-2:1 up-regulated in urinary exosomes, tumor tissues of patients, and BCa cells. Down-regulation of lnc-TAF12-2:1 impaired BCa cell proliferation and migration, and promoted cell cycle arrest at the G0/G1 phase and cell apoptosis. The opposite effects were also observed when lnc-TAF12-2:1 was overexpressed. lnc-TAF12-2:1 was transferred by intercellular exosomes to modulate malignant biological behavior. Mechanistically, lnc-TAF12-2:1 packaged in the exosomes relieved the miRNA-mediated silence effect on ASB12 via serving as a sponger of miR-7847-3p to accelerate progression in BCa. ASB12 was also first proved as an oncogene to promote cell proliferation and migration and depress cell cycle arrest and cell apoptosis in our data. In conclusion, exosomal lnc-TAF12-2:1, located in the cytoplasm of BCa, might act as a competitive endogenous RNA to competitively bind to miR-7847-3p, and then be involved in miR-7847-3p/ASB12 regulatory axis to promote tumorigenesis, which provided a deeper insight into the molecular mechanism of BCa.

A novel cinnamic acid derivative for hepatocellular carcinoma therapy by degrading METTL16 protein

The RNA methyltransferase methyltransferaselike protein 16 (METTL16) is upregulated in a large proportion of hepatocellular carcinoma (HCC), and its high expression is associated with poor clinical outcomes. METTL16 deletion inhibits HCC growth in vitro and in vivo. Referencing the structure of cinnamic acid, here we designed and synthesized a novel series of small molecular compounds, and found through bioactivity screening that compound 15a effectively reduced METTL16 level and modulated oncogenic PI3K/AKT pathway signaling. Compound 15a inhibited the proliferation and migration of HepG2 cells, and induced apoptosis in vitro. Furthermore, compound 15a significantly inhibited the growth of patient-derived HCC xenografts in nude mice with greater efficacy than the multi-kinase inhibitor lenvatinib. The promising efficacy and good biosafety profile of compound 15a enables us to further develop this compound for treating patients with HCC and possibly other cancers in clinic.

Long noncoding RNA TUG1 promotes chondrosarcoma progression and M2 polarization

The long non-coding RNA taurine up-regulated gene 1 (TUG1) has been reported to be involved in various cancers, but its role in chondrosarcoma (CHS) remains a mystery. This research aimed to examine the function of TUG1 in CHS. We found that TUG1 expression was elevated in CHS. Functional assays demonstrated that TUG1 had a crucial role in the CHS cell progression. Mechanistically, TUG1 recruited ALYREF to maintain the stabilization of enhancer of zest homolog 2 (EZH2) mRNA and expression of H3K27me3, repressing the transcription of the tumor-suppressor gene CPEB1. Additionally, exosomal TUG1 enhanced the polarization of M2 tumor-associated macrophages, which increased the proliferation and metastasis of CHS. Taken together, this study revealed the oncogenic role of TUG1 in CHS and its interactions with the downstream regulatory axis, offering novel insights into the tumorigenic mechanism of CHS.

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

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

An inflammation-associated lncRNA induces neuronal damage via mitochondrial dysfunction

Immune disease-associated non-coding SNPs, which often locate in tissue-specific regulatory elements, are emerging as key factors in gene regulation. Among these elements, long non-coding RNAs (lncRNAs) participate in many cellular processes, and their characteristics make these molecules appealing therapeutic targets. In this study, we have studied lncRNA LOC339803 in the context of neuronal cells, which is located in autoimmunity-associated region 2p15 and recently described to have a proinflammatory role in intestinal disorders. Using human brain samples and a wide variety of in vitro techniques, we have showed a differential function of this lncRNA in neuronal cells. We have further demonstrated the role of LOC339803 in maintaining hexokinase 2 (HK2) levels and thus mitochondrial integrity, partially explaining the implication of the lncRNA in multiple sclerosis (MS) pathogenesis. Our results show the importance of cell-type-specific studies in the case of regulatory lncRNAs. We present LOC339803 as a candidate for further studies as a mitochondrial dysfunction marker or possible therapeutic target in neurodegeneration.

Identification of long non-coding RNAs and their multiple regulation mechanism in shell deposition of pearl oyster

Biomineralization to fabricate diverse morphology shell is typical character of bivalve species and ectopic calcification to form is the production of defense. Long non-coding RNAs (LncRNAs) plays critical roles in multiple cellular biological processes in invertebrate and vertebrate. However, LncRNAs remain poorly understood about expression and regulation roles in bivalve biomineralization studies. In this research, we systematically identified lncRNAs that functioned in differentiated mantle regions for fabricating two phenotypes of CaCO3 crystal shell, along with pearl sac depositing pearls for ectopic calcification by CaCO3. A total of 48,555 non-coding transcripts were obtained. 229 differentially expressed lncRNAs in mantle tissue as well as 401 differentially expressed lncRNAs in the comparison of mantle center to pearl sac were identified. By cis- and trans-regulation ways, these DELs could be involved in provisioning and metabolism such as chitin, glycosaminoglycan, ECM/shell matrix protein, Ca2+ and HCO3- offering, and also affecting related signaling pathways. In addition, lncRNAs were found to crosstalk with miRNAs not only as primary competing endogenous RNAs but as the primary miRNAs. Our studies provided insight into non-coding RNA regulation of epigenetic regulation in biomineralization in bivalve species.

RNA signaling in medicinal plants: An overlooked mechanism for phytochemical regulation

Background/objective

Medicinal plants are invaluable sources of bioactive phytochemicals critical for global health. This mini review explores the role of RNA signaling in regulating phytochemical production in medicinal plants, highlighting its potential for optimizing their therapeutic potential.

Methods

This mini review integrates insights from recent studies published in Scopus and Web of Science (2019-2025) on RNA-mediated signaling, including small RNAs (sRNAs), long non-coding RNAs (lncRNAs), and messenger RNAs (mRNAs).

Results

RNA signaling is revealed as a pivotal mechanism in secondary metabolite regulation, mediating stress-induced compound synthesis and environmental interactions. Notable findings include the role of siRNAs in activating alkaloid pathways and lncRNAs in regulating phenolic compound biosynthesis. RNA-directed DNA methylation and systemic RNA signaling further highlight its versatility in phytochemical regulation.

Conclusion

RNA signaling enhances medicinal plant research, unlocking therapeutic potential through bioactive compound production. The study calls for focused research to bridge knowledge gaps and translate laboratory findings into field applications.

Non-coding RNA RMRP governs RAB31-dependent MMP secretion, enhancing ovarian cancer invasion

Non-coding RNAs (ncRNAs) are frequently dysregulated in various cancers and have been implicated in the etiology and progression of cancer. Ovarian cancer, the most fatal gynecological cancer, has a poor prognosis and a high patient fatality rate due to metastases. In this study, we classified patients with ovarian cancer into three groups based on their ncRNA expression levels. Notably, an ncRNA transcribed by RNA polymerase III, RNA component of mitochondrial RNA processing endoribonuclease (RMRP), is highly expressed in a group with a poor prognosis. Functional assays using SKOV3 and HeyA8 human ovarian cancer cell lines revealed that while RMRP modulation had no significant effect on cell viability, it markedly enhanced cell invasion. Knockdown and ectopic expression experiments demonstrated that RMRP promotes the secretion of matrix metalloproteinase (MMP)-2 and -9, thereby facilitating ovarian cancer cell invasiveness. Transcriptomic analysis further revealed a positive correlation between RMRP expression and genes involved in cellular localization, including RAB31, a member of the Ras-related protein family. Notably, RAB31 knockdown abrogated the pro-invasive effects of RMRP, identifying it as a key downstream effector in SKOV3 and HeyA8 cells. In addition, MechRNA analysis identified RAB31 as a putative RMRP-interacting transcript. These findings establish RMRP as a critical regulator of RAB31-dependent MMP secretion and ovarian cancer cell invasion. Moreover, our results suggest that RMRP could serve as a promising prognostic biomarker for ovarian cancer.

Exploring the role of exosomal and non-exosomal non-coding RNAs in Kawasaki disease: Implications for diagnosis and therapeutic strategies against coronary artery aneurysms

Kawasaki disease (KD) is an acute vasculitis primarily affecting children, with a potential risk of developing coronary artery aneurysms (CAAs) and cardiovascular complications. The emergence of non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), has provided insights into Kawasaki disease pathogenesis and opened new avenues for diagnosis and therapeutic intervention. Furthermore, polymorphism analysis of ncRNA genes offers significant insights into genetic predisposition to Kawasaki disease, facilitating tailored treatment approaches and risk assessment to improve patient outcomes. Exosomal ncRNAs, which are ncRNAs encapsulated within extracellular vesicles, have garnered significant attention as potential biomarkers for Kawasaki disease and CAA due to their stability and accessibility in biological fluids. This review comprehensively discusses the biogenesis, components, and potential of exosomal and non-exosomal ncRNAs in Kawasaki disease diagnosis and prognosis prediction. It also highlights the roles of non-exosomal ncRNAs, such as miRNAs, lncRNAs, and circRNAs, in Kawasaki disease pathogenesis and their implications as therapeutic targets. Additionally, the review explores the current diagnostic and therapeutic approaches for Kawasaki disease and emphasizes the need for further research to validate these ncRNA-based biomarkers in diverse populations and clinical settings.

The role of lncRNAs in sepsis-induced acute lung injury: Molecular mechanisms and therapeutic potential

Sepsis, a life-threatening syndrome, results from a dysregulated immune and hemostatic response, contributing to acute lung injury (ALI) and its progression into acute respiratory distress syndrome (ARDS). The development of septic ALI is complex, involving excessive inflammatory mediator production that damages endothelial and epithelial cells, leading to vascular leakage, edema, and vasodilation-key factors in ALI pathogenesis. Long noncoding RNAs (lncRNAs), over 200 nucleotides in length, play critical roles in various biological processes, including sepsis regulation. They exhibit both promotive and inhibitory effects, influencing sepsis progression and resolution. Despite their significance, comprehensive reviews detailing lncRNA involvement in sepsis-induced ALI remain limited. This review aims to address this gap by summarizing the diverse functions of lncRNAs in septic ALI, emphasizing their potential in diagnosis and treatment. Furthermore, we will explore the molecular mechanisms underlying lncRNA involvement, particularly their miRNA-dependent regulatory pathways. Understanding these interactions may provide novel insights into therapeutic strategies for sepsis-induced ALI.

Identification of a cuproptosis‑related prognostic biomarker and therapeutic target in ovarian cancer

Ovarian cancer (OV) constitutes a significant hazard to the health of women and has low survival and high recurrence rates. Cuproptosis is a newly reported form of copper-dependent regulatory cell death. The present study identified cuproptosis-related long non-coding (lnc)RNAs in OV, highlighting their potential application as prognostic biomarkers and therapeutic targets. The RNA-sequencing data and clinical records of patients with OV were sourced from The Cancer Genome Atlas. Cuproptosis-related lncRNAs were filtered for their prognostic value using univariate and multivariate Cox regression, and least absolute shrinkage selection operator regression. Then, a risk model was formulated using these cuproptosis-related lncRNAs based on correlation coefficients. The risk model was calculated using the following formula: Risk = (0.687927022 × RP11-552D4.1) - (0.659783022 × AP001372.2) - (0.652465319 × RP11-505K9.1) - (1.627006889 × LINC00996). The predictive potential and clinical values of this risk model were identified through survival status, Kaplan-Meier survival curves, immune function, receiver operating characteristic curves, calibration curves, C-index and principal component analysis. Subsequently, the effects of LINC00996 (the lncRNA with the highest correlation coefficient in the risk model) on proliferation, metastasis and sensitivity to cuproptosis were assessed in OV cells. Finally, intracellular location of LINC00996 and the relative regulatory mechanism were predicted. In conclusion, the present study constructed a prognostic risk model based on lncRNAs associated with cuproptosis in OV, which can stratify risk and predict prognosis, and explored the regulatory mechanism of LINC00996 in cuproptosis.

Long non-coding RNAs in bipolar disorder

Bipolar disorder is characterized by alternating episodes of mania or hypomania and depression, encompassing various forms such as cyclothymia, bipolar I disorder, and bipolar II disorder. Manic periods present with increased energy and decreased sleep, whereas depressive episodes involve poor energy and extended sleep duration. Despite the availability of treatments, approximately 30% of patients with bipolar disorder are drug resistant and require alternative strategies. Recent research highlights the role of long noncoding RNAs (lncRNAs) as potential biomarkers for bipolar disorder, aiding in distinguishing it from other mood disorders and improving diagnostic accuracy. LncRNAs such as GAS5 and FOXD3-AS1 are downregulated in bipolar disorder patients, suggesting their utility as diagnostic tools. LncRNAs regulate gene expression through interactions with DNA, RNA, and proteins, influencing various biological processes. Studies have identified several lncRNAs linked to bipolar disorder, including lincRNA-p21, lincRNA-ROR, and lincRNA-PINT. These findings underscore the potential of lncRNAs as biomarkers and therapeutic targets, facilitating more personalized treatment strategies. This review explores the diagnostic and therapeutic potential of lncRNAs in bipolar disorder, aiming to enhance the current understanding and management of this condition.

YTHDF1-targeting nanoassembly reverses tumoral immune evasion through epigenetics and cell cycle modulation

YTHDF1, as a key m6A reader protein, is believed to be one of the key mechanisms leading to tumor cell immune evasion and resistance via promoting MHC-I degradation. We explore therapeutic strategies that combine iron metabolism regulation with epigenetic regulation. Here, a nanoassembly that integrates Deferasirox (DFX, an FDA-approved iron chelator) and YTHDF1 siRNA (known as PPD/siYTHDF1) has been developed, which jointly promotes cell cycle arrest in tumor cells by interfering with iron metabolism and knocking down YTHDF1 protein. At the same time, YTHDF1 deficiency inhibits the mRNA translation of lysosome-related proteins, upregulates MHC-I molecule expression (2.5-fold), reduces the degradation of internalized antigens, enhances T cell-mediated immune response, and ultimately restores tumor immune surveillance and triggers powerful anti-tumor immune efficacy. After treatment, CD8+ T cells in the tumor site increased by 2.2-fold, and effector memory T cells in the spleen increased by 2.1-fold. It demonstrates a highly effective anti-tumor effect in breast cancer treatment, as well as in postoperative anti-recurrence and anti-metastasis models.

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

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

Gene regulation technologies for gene and cell therapy

Gene therapy stands at the forefront of medical innovation, offering unique potential to treat the underlying causes of genetic disorders and broadly enable regenerative medicine. However, unregulated production of therapeutic genes can lead to decreased clinical utility due to various complications. Thus, many technologies for controlled gene expression are under development, including regulated transgenes, modulation of endogenous genes to leverage native biological regulation, mapping and repurposing of transcriptional regulatory networks, and engineered systems that dynamically react to cell state changes. Transformative therapies enabled by advances in tissue-specific promoters, inducible systems, and targeted delivery have already entered clinical testing and demonstrated significantly improved specificity and efficacy. This review highlights next-generation technologies under development to expand the reach of gene therapies by enabling precise modulation of gene expression. These technologies, including epigenome editing, antisense oligonucleotides, RNA editing, transcription factor-mediated reprogramming, and synthetic genetic circuits, have the potential to provide powerful control over cellular functions. Despite these remarkable achievements, challenges remain in optimizing delivery, minimizing off-target effects, and addressing regulatory hurdles. However, the ongoing integration of biological insights with engineering innovations promises to expand the potential for gene therapy, offering hope for treating not only rare genetic disorders but also complex multifactorial diseases.

New dimensions in the molecular genetics of insect chemoreception

Chemoreception is the foundation of olfaction and taste, which in insects underlie the detection of humans to whom they spread disease and crops that they ravage. Recent advances have provided clear and in some cases surprising new insights into the molecular genetics of chemoreception. We describe mechanisms that govern the choice of a single Odorant receptor gene by an olfactory receptor neuron in Drosophila. We highlight genetic and epigenetic mechanisms by which chemoreceptor expression can be modulated. Exitrons, RNA editing, and pseudo-pseudogenes in chemosensory systems are described. We summarize key insights from the recent structural determinations of odorant and taste receptors. Finally, new molecular components of chemosensory systems, including long noncoding RNAs, are described.

Transcriptional stochasticity reveals multiple mechanisms of long non-coding RNA regulation at the Xist-Tsix locus

Long noncoding RNAs (LncRNAs) are increasingly recognized as being involved in human physiology and diseases, but there is a lack of mechanistic understanding for the majority of lncRNAs. We comparatively test proposed mechanisms of antisense lncRNA regulation at the X-chromosome Inactivation (XCI) locus. We find that due to stochasticity in transcription, different mechanisms based on the act of transcription regulate Xist and Tsix at different levels of nascent transcription. At medium levels, RNA polymerases transcribe Xist and Tsix on each strand at the same transcription site and deposit significant amounts of the histone mark H3K36me3, which inhibits Xist. At high levels of nascent transcription, many RNA polymerases transcribe Xist or Tsix resulting in transcriptional interference. Therefore, lncRNA expression variability is not just a quirk of transcription but an important aspect of regulation that allows multiple mechanisms to be employed by the same gene locus within the same cell population.

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.

Cryo-EM reveals mechanisms of natural RNA multivalency

Homo-oligomerization of biological macromolecules leads to functional assemblies that are critical to understanding various cellular processes. However, RNA quaternary structures have rarely been reported. Comparative genomics analysis has identified RNA families containing hundreds of sequences that adopt conserved secondary structures and likely fold into complex three-dimensional structures. In this study, we used cryo-electron microscopy (cryo-EM) to determine structures from four RNA families, including ARRPOF and OLE forming dimers and ROOL and GOLLD forming hexameric, octameric, and dodecameric nanostructures, at 2.6- to 4.6-angstrom resolutions. These homo-oligomeric assemblies reveal a plethora of structural motifs that contribute to RNA multivalency, including kissing-loop, palindromic base-pairing, A-stacking, metal ion coordination, pseudoknot, and minor-groove interactions. These results provide the molecular basis of intermolecular interactions driving RNA multivalency with potential functional relevance.

Identification of lncRNA biomarkers for keloid diagnosis and functional characterization of CPEB2-AS1

BACKGROUND

Keloids are pathological scars marked by excessive tissue growth, and their diagnosis currently depends on clinical observation, lacking objective biomarkers. Although the regulatory role of long non-coding RNAs (lncRNAs) in various diseases has drawn attention, their function in keloids remains unclear.

METHODS

This study employed high-throughput sequencing, bioinformatics analysis and machine learning algorithms to identify differentially expressed lncRNAs in keloid tissues and to construct a diagnostic model. The relationship between these lncRNAs and immune responses, as well as gene expression regulation, was explored through immune signature analysis and co-expression networks. The role of CPEB2-AS1 in keloids was investigated through expression validation, pan-cancer analysis and functional experiments.

RESULTS

Four key differentially expressed lncRNAs were identified, enabling the development of an effective diagnostic model that distinguishes keloid tissues from healthy controls. Immune signature analysis revealed a positive correlation between CPEB2-AS1 and immune cell activity. Co-expression networks and functional enrichment analysis suggested that these lncRNAs may regulate RNA processing and nucleic acid binding. Expression validation and pan-cancer analysis confirmed their abnormal expression in keloids. Functional experiments demonstrated that CPEB2-AS1 significantly influences cell proliferation, migration, invasion and apoptosis.

CONCLUSION

This study identifies new molecular markers for the early diagnosis of keloids and highlights the potential role of CPEB2-AS1 in keloid progression, offering insights for future therapeutic strategies.

Improving IL12 immunotherapy in glioblastoma by targeting the long noncoding RNA INCR1

PURPOSE

The potent antitumor effects of interleukin 12 (IL12) gene therapy in glioblastoma (GBM) are significantly attenuated by the highly immunosuppressive microenvironment and the upregulation of the PD-1/PD-L1 immune checkpoint. However, combining IL12 gene therapy with PD-1/PD-L1 inhibitors failed to improve efficacy. This study aims to assess the effects of silencing the immunosuppressive long noncoding RNA INCR1 when combined with IL12 therapy.

METHODS

RNAscope in situ hybridization was performed to analyze INCR1 and PD-L1 expression in tumor tissues from GBM patients pre- and post-IL12 gene therapy. Quantitative PCR was used to analyze immunosuppressive gene expression in patient-derived GBM cells co-cultured with immune cells stimulated with IL12. The effects of INCR1 and PD-L1 silencing on the expression of immunosuppressive genes were evaluated by RNA sequencing. 3D-cytotoxicity assays were performed to assess the activity of immune cells against GBM tumor cells.

RESULTS

INCR1 and PD-L1 expression was upregulated in tumor tissue from GBM patients treated with IL12 gene therapy compared to the tumor tissue of the same patients before the IL12 treatment. Co-culture of patient-derived GBM cells with IL12-stimulated immune cells increased the expression of several immunosuppressive genes. Knocking down INCR1 was more effective than silencing PD-L1 in reducing the expression of multiple immunosuppressive genes. INCR1 silencing improved IL12-mediated immune cell antitumor activity compared to monoclonal antibodies targeting the PD-1/PD-L1 immune checkpoint signaling.

CONCLUSION

INCR1 silencing affects more immune evasive pathways than PD-L1. Targeting INCR1 may represent a valid approach to improve the efficacy of IL12 therapy in GBM.

Tumor-derived exosomal LINC01812 induces M2 macrophage polarization to promote perineural invasion in cholangiocarcinoma

M2 macrophages play a critical role in the tumor microenvironment of invasive solid tumors. They are closely associated with perineural invasion (PNI) and are often linked to poor prognosis. In this context, tumor-derived exosomes serve as important mediators of intercellular communication. However, the relationship between tumor cell-induced M2 macrophages and PNI in cholangiocarcinoma remains unexplored. In this study, we utilized multiplex immunofluorescence and transcriptomic sequencing to demonstrate the upregulation of LINC01812 in cholangiocarcinoma tissues and its positive correlation with M2 macrophage infiltration. Exosomal lncRNA sequencing, exosome uptake experiments, RNA pull-down assays, and mass spectrometry analysis demonstrated that macrophages can internalize exosomal LINC01812 and promote the M2 phenotype in cholangiocarcinoma cells. Additionally, Transwell and in vitro cocultures with the dorsal root ganglia confirmed that the tumor microenvironment significantly enhances the nerve infiltration of cholangiocarcinoma cells via M2 macrophages. The findings of this study indicate that exosomes containing LINC01812 derived from cholangiocarcinoma can induce M2 macrophage polarization and facilitate nerve infiltration, thereby providing new potential therapeutic targets for managing PNI in cholangiocarcinoma.

A novel lncRNA ABCE1-5 regulates pulmonary fibrosis by targeting KRT14

Idiopathic pulmonary fibrosis (IPF) is a progressive and degenerative interstitial lung disease characterized by complex etiology, unclear pathogenesis, and high mortality. Long noncoding RNAs (lncRNAs) have been identified as key regulators in modulating the initiation, maintenance, and progression of pulmonary fibrosis. However, the precise pathological mechanisms through which lncRNAs are involved in IPF remain limited and require further elucidation. A novel lncABCE1-5 was identified as significantly decreased by an ncRNA microarray analysis in our eight IPF lung samples compared with three donor tissues and validated by quantitative real-time polymerase chain reaction (qRT-PCR) analysis in clinical lung samples. To investigate the biological function of ABCE1-5, we performed loss- and gain-of-function experiments in vitro and in vivo. LncABCE1-5 silencing promoted A549 cell migration and A549 and bronchial epithelial cell line (BEAS-2B) cell apoptosis while enhancing the expression of proteins associated with extracellular matrix deposition, whereas overexpression of ABCE1-5 partially attenuated transforming growth factor-beta (TGF-β)-induced fibrogenesis. Forced ABCE1-5 expression by intratracheal injection of adeno-associated virus 6 revealing the antifibrotic effect of ABCE1-5 in bleomycin (BLM)-treated mice. Mechanistically, RNA pull-down (RPD)-mass spectrometry and RNA immunoprecipitation assay demonstrated that ABCE1-5 directly binds to keratin14 (krt14) sequences, potentially impeding its expression by perturbing mRNA stability. Furthermore, decreased ABCE1-5 levels can promote krt14 expression and enhance the phosphorylation of both mTOR and Akt; overexpression of ABCE1-5 in BLM mouse lung tissue significantly attenuated the elevated levels of p-mTOR and p-AKT. Knockdown of krt14 reversed the activation of mTOR signaling mediated by ABCE1-5 silencing. Collectively, the downregulation of ABCE1-5 mediated krt14 activation, thereby activating mTOR/AKT signaling, to facilitate pulmonary fibrosis progression in IPF.NEW & NOTEWORTHY In the present study, our data first reveal that a novel lncRNA ABCE1-5 could inhibit pulmonary fibrosis through interacting with krt14 and negative regulation of its expression, and indicated ABCE1-5 also regulates the phosphorylation of mTOR and Akt, thus acting on extracellular matrix remodeling in lung fibrosis procession. These results suggest that novel molecules within the ABCE1-5-krt14-mTOR axis may serve as potential candidates for clinical application in IPF.

LncRNA-DANCR Promotes ESCC Progression and Function as ceRNA to Regulate DDIT3 Expression by Sponging microRNA-3193

Long non-coding RNAs (lncRNAs) have emerged as crucial regulators of cancer development and progression. Among them, Differentiation Antagonizing Non-Protein Coding RNA (DANCR) has been implicated in various malignancies, including esophageal squamous cell carcinoma (ESCC). This study explores the clinical characteristics, prognostic implications, functional roles, and molecular mechanisms of DANCR in ESCC. Our results demonstrate that DANCR is highly expressed in ESCC, and acts as an oncogene in ESCC both in vitro and in vivo. Through bioinformatics analysis and experimental validation, we revealed that DANCR promotes ESCC progression by sponging miR-3193 and regulating its target gene DDIT3 expression. These findings highlight the critical role of DANCR in the development of ESCC and suggest its potential as a prognostic predictor and drug therapeutic target.

The Potential of RNA Therapeutics in Treating Cardiovascular Disease

Despite significant advances in cardiology over the past few decades, cardiovascular diseases (CVDs) remain the leading cause of global mortality and morbidity. This underscores the need for novel therapeutic interventions that go beyond symptom management to address the underlying causal mechanisms of CVDs. RNA-based therapeutics represent a new class of drugs capable of regulating specific genetic and molecular pathways, positioning them as strong candidates for targeting the root causes of a wide range of diseases. Moreover, owing to the vast diversity in RNA form and function, these molecules can be utilized to induce changes at different levels of gene expression regulation, making them suitable for a broad array of medical applications, even within a single disease context. Several RNA-based therapies are currently being investigated for their potential to address various CVD pathologies. These include treatments aimed at promoting cardiac revascularization and regeneration, preventing cardiomyocyte apoptosis, reducing harmful circulating cholesterols and fats, lowering blood pressure, reversing cardiac fibrosis and remodeling, and correcting the genetic basis of inherited CVDs. In this review, we discuss the current landscape of RNA therapeutics for CVDs, with an emphasis on their classifications, modes of action, advancements in delivery strategies and considerations for their implementation, as well as CVD targets with proven therapeutic potential.

Roles of non-coding RNAs and exosomal non-coding RNAs, particularly microRNAs, long non-coding RNAs, and circular RNAs, in pathogenic mechanisms behind chronic pain: A review

Chronic pain is a significant public health concern that diminishes patients' quality of life and imposes considerable socioeconomic costs. Effective pharmacological treatments for ongoing pain are limited. Recent studies have indicated that various models of chronic pain-such as neuropathic pain, inflammatory pain, and pain associated with cancer-have abnormal levels of long noncoding RNAs (lncRNAs). Research has explored how these abnormal lncRNAs influence the activation of inflammatory cytokines, microRNAs, and other related molecules, which are crucial to the development of chronic pain. These findings suggest that these lncRNAs are vital in chronic pain mechanisms within the spinal cord and dorsal root ganglion following nerve injury. Additionally, exosomes, which can traverse the blood-brain barrier, are considered carriers of noncoding RNAs (ncRNAs) from neurons to systemic circulation. This study aims to summarize the existing knowledge on ncRNAs and exosomal ncRNAs in the context of chronic pain, highlighting potential biomarkers for diagnosis, regulatory roles in disease progression, therapeutic strategies, and clinical implications.

Single-cell and bulk RNA-sequence identify an immune-derived lncRNA-mRNA signature for predicting clinical outcomes and immunotherapeutic response of prostate cancer

Immunotherapy has limited effectiveness in prostate cancer (PCa), often classified as a "cold tumor" due to immune-related long non-coding RNAs (lncRNAs) and mRNAs. We developed and validated a consensus immune-related lncRNA and mRNA signature (ILMS) to enhance immunotherapy efficacy for PCa patients. By analyzing seven independent datasets, including our own, we confirmed that ILMS is a robust predictor of biochemical recurrence (BCR). Compared to 70 other published signatures, ILMS showed the highest ability to anticipate PCa prognosis. Single-cell analysis indicated that ILMS-high patients had abundant immune cell infiltration, suggesting a favorable response to immunotherapy. Additionally, ILMS was positively associated with immune checkpoints LAG3, TIM3, and TIGIT, identifying patients likely to benefit from immunotherapy. This model will be further validated and refined in subsequent studies.

LncRNA SERPINB9P1 Mitigates Cerebral Injury Induced by Oxygen‒Glucose Deprivation/Reoxygenation by Interacting with HSPA2

Dysregulation of long non-coding RNAs (lncRNAs) is implicated in the pathophysiology of ischemic stroke (IS). However, the molecular mechanism of the lncRNA SERPINB9P1 in IS remains unclear. Our study aimed to explore the role and molecular mechanism of the lncRNA SERPINB9P1 in IS. This study revealed downregulation of the lncRNA SERPINB9P1 in the peripheral blood of IS patients, which was corroborated by the GSE140275 dataset. Furthermore, high lncRNA SERPINB9P1 expression was associated with lower National Institutes of Health Stroke Scale (NIHSS) scores and favorable outcome. Clinically, lncRNA SERPINB9P1 expression was correlated with inflammation and coagulation parameters in IS patients. Furthermore, lncRNA SERPINB9P1 silencing inhibited cell viability, induced apoptosis and inflammatory response under oxygen-glucose deprivation/reperfusion ; however, these effects were reversed upon its overexpression. Additionally, Chromatin Isolation by RNA Purification and mass spectrometry (CHIRP-MS) and western blot confirmed that the lncRNA SERPINB9P1 was involved in the pathological process of IS through binding to heat shock protein 2 (HSPA2). HSPA2 was upregulated in IS patients, and its protein interaction network was significantly enriched in IS-related pathways. In conclusion, the lncRNA SERPINB9P1 may ameliorate neurological injury in IS patients by interacting with the HSPA2 protein and engaging in IS-related pathways, providing new insights into treatment strategies for IS.

Glucose metabolism is controlled by non-coding RNAs in autoimmune diseases; a glimpse into immune system dysregulation

The immune system accidentally targets the body's tissues, causing inflammation and tissue damage, the root causes of autoimmune illnesses. In recent studies, non-coding RNAs have been shown to significantly control gene expression and metabolic pathways linked to autoimmune diseases. This review investigates the effects of non-coding RNA on glucose metabolism, a route frequently dysregulated in autoimmune illnesses such as multiple sclerosis, rheumatoid arthritis, systemic lupus erythematosus, and diabetes. We review how non-coding RNA affects immune cell activity modulation, glucose absorption, glycolysis, and other metabolic processes critical to immune function. We also investigate the possibility of using non-coding RNA-mediated metabolic pathway targeting as a new therapeutic approach to treat autoimmune disorders. By clarifying the complex interplay of non-coding RNA, glucose metabolism, and immune dysregulation, this study endeavors to enhance comprehension of autoimmune etiology and facilitate the creation of focused therapies.

MAMDC2-AS1 Induces Cuproptosis in Relapsed and Refractory Multiple Myeloma

BACKGROUND

Multiple myeloma is a malignant disorder involving the uncontrolled proliferation of plasma cells in the bone marrow. Prognosis remains poor for individuals with relapsed and refractory multiple myeloma (RRMM), and the underlying mechanisms are yet to be fully understood.

METHODS

We collected bone marrow RNA-Seq data from a total of 557 patients with MM from the GEO database (GSE24080) for further analysis, dividing them into relapsed/refractory and control groups. Additionally, we collected bone marrow samples from 57 MM patients to validate the performed RNA-Seq data analysis.

RESULTS

RNA-Seq analysis of patients with RRMM revealed a significant upregulation of genes associated with cuproptosis. Using the LASSO Cox regression method, several long noncoding RNAs (lncRNAs) were identified that influence copper-induced cell death. Based on these lncRNAs, patients were stratified into high-risk and low-risk groups. The high-risk group exhibited a significantly worse overall survival (OS) compared to the low-risk group, with a p-value of less than 0.001. Our statistical analysis, incorporating LASSO Cox regression, indicated that among these lncRNAs, MAMDC2-AS1 was particularly noteworthy due to its strong correlation with OS (p-value < 0.01). Further validation using qPCR and survival analysis established MAMDC2-AS1 as a strong predictor of prognosis in MM. This finding suggests that MAMDC2-AS1 can serve as a potential independent biomarker for RRMM. The qPCR data validated the RNA-Seq findings and uncovered the significance of MAMDC2-AS1 in the prognosis of this disease.

CONCLUSION

MAMDC2-AS1 plays a significant role in RRMM. Promisingly, Bortezomib, Bosutinib, Crizotinib, and DMOG have demonstrated promising efficacy in addressing advanced cases.

The role of lncRNAs in AKI and CKD: Molecular mechanisms, biomarkers, and potential therapeutic targets

Exosomes, a type of extracellular vesicle, are commonly found in different body fluids and are rich in nucleic acids (circRNA, lncRNAs, miRNAs, mRNAs, tRNAs, etc.), proteins, and lipids. They are involved in intercellular communication. lncRNAs are responsible for the modulation of gene expression, thus affecting the pathological process of kidney injury. This review summarizes the latest knowledge on the roles of exosome lncRNAs and circulating lncRNAs in the pathogenesis, biomarker discovery, and treatment of chronic kidney disease, renal fibrosis, and acute kidney injury, providing an overview of novel regulatory approaches and lncRNA delivery systems.

Mechanisms of Impaired Wound Healing in Type 2 Diabetes: The Role of Epigenetic Factors

Despite decades of research, impaired extremity wound healing in type 2 diabetes remains a significant driver of patient morbidity, mortality, and health care costs. Advances in surgical and medical therapies, including the advent of endovascular interventions for peripheral artery disease and topical therapies developed to promote wound healing, have not reduced the frequency of lower leg amputations for nonhealing wounds in type 2 diabetes. This brief report is aimed at reviewing the roles of various cell types in tissue repair and summarizing the known dysfunctions of these cell types in diabetic foot ulcers. Recent advances in our understanding of the epigenetic regulation in immune cells identified to be altered in type 2 diabetes are summarized, and particular attention is paid to the developing research defining the epigenetic regulation of structural cells, including keratinocytes, fibroblasts, and endothelial cells. Gaps in knowledge are highlighted, and potential future directions are suggested based on the current state of the field.

Long non-coding RNAs in schizophrenia

Long noncoding RNAs (lncRNAs) have emerged as critical regulators of the pathogenesis of schizophrenia, a complex neuropsychiatric disorder influenced by genetic and environmental factors. These transcripts modulate gene expression through diverse mechanisms, including chromatin remodeling, transcriptional regulation, and posttranscriptional modifications. Recent studies have demonstrated significant alterations in lncRNA expression profiles in both the peripheral blood and brain tissues of schizophrenia patients, highlighting their potential as biomarkers and therapeutic targets. Dysregulated lncRNAs such as Gomafu, DISC-2, BDNF-AS, MEG3, and TUG1 have been linked to neurodevelopmental processes, inflammatory responses, and key synaptic plasticity pathways implicated in schizophrenia. Furthermore, antipsychotic treatments have been shown to influence lncRNA expression, which is correlated with symptom improvement. Sex-specific and age-related differences in lncRNA regulation further underscore their complexity and relevance to schizophrenia pathophysiology. This review consolidates current knowledge on the role of lncRNAs in schizophrenia, emphasizing their diagnostic potential.

Portrayal of the complex molecular landscape of multidrug resistance in gastric cancer: Unveiling the potential targets

Gastric cancer (GC) is an aggressive malignancy among all Gastrointestinal cancer (GIC) types. Worldwide, among all cancer types, gastric cancer incidence and related mortality remain in fifth position. Multidrug resistance (MDR) in GC presents a major challenge to chemotherapy, and it significantly affects patient survival. A better understanding of the dynamic interaction of cellular factors contributing to MDR phenotype, e.g., the presence and expression of variants of MDR-related genes, including various drug-detoxifying and drug-efflux transporters, and expression of regulatory ncRNAs affecting the expression of MDR-related genes, is required to comprehend the molecular mechanisms for MDR development in GCs. This review article provides a holistic discussion of the cellular factors involved in the MDR development in GC cells, i.e., their roles and cross-talk between specific molecules that give rise to drug-sensitive and drug-resistant phenotypes. Moreover, the pharmacological perspective of drug resistance and the underlying biological processes that allow the escape of GC cells from the cytotoxic effects of drugs have also been discussed. Additionally, this review article provides an in-depth discussion on most potential candidates that can serve as MDR biomarkers in GIC cancer and the growing research interest in non-coding RNAs (ncRNAs) in GC. Notably, the miRNAs, circRNAs, and lncRNAs are not only emerging as crucial prognostic biomarkers of MDR in gastric cancers but also as potential targets for personalized medicine to combat the MDR challenge in GC patients.

LncRNA HITT inhibits autophagy by attenuating ATG12-ATG5-ATG16L1 complex formation

Dysregulated autophagy has been implicated in the pathogenesis of numerous diseases, including cancer. Despite extensive research on the underlying mechanisms of autophagy, the involvement of long non-coding RNAs (lncRNAs) remains poorly understood. Here, we demonstrate that a previously identified lncRNA, HITT (HIF-1α inhibitor at the translation level), is closely associated with biological processes such as autophagy through unbiased bioinformatic analysis. Subsequent studies demonstrate that HITT is increased by several autophagic stimuli, including PI-103, a potent inhibitor of PI3K and mTOR. This is caused by a reduction in the binding between HITT and AGO2, resulting in a reduction in the activity of miR-205 towards HITT degradation. Increased HITT then binds to a key autophagy protein, Autophagy-related 5 (ATG5), and inhibits autophagosome formation by preventing the formation of the ATG12-ATG5-ATG16L1 complex. This results in HITT sensitizing PI-103-mediated cell death both in vitro and in vivo in nude mice by attenuating protective autophagy. The data presented herein demonstrate that HITT is a newly identified RNA regulator of autophagy and that it can be used to sensitize the colon cancer response to cell death by blocking the protective autophagy.

Non-coding RNAs in adipose-derived stem cell exosomes: Mechanisms, therapeutic potential, and challenges in wound healing

The treatment of complex wounds presents a significant clinical challenge due to the limited availability of standardized therapeutic options. Adipose-derived stem cell exosomes (ADSC-Exos) are promising for their capabilities to enhance angiogenesis, mitigate oxidative stress, modulate inflammatory pathways, support skin cell regeneration, and promote epithelialization. These exosomes deliver non-coding RNAs, including microRNAs, long non-coding RNAs, and circular RNAs, which facilitate collagen remodeling, reduce scar formation, and expedite wound healing. This study reviews the mechanisms, therapeutic roles, and challenges of non-coding RNA-loaded ADSC-Exos in wound healing and identifies critical directions for future research. It aims to provide insights for researchers into the potential mechanisms and clinical applications of ADSC-Exos non-coding RNAs in wound healing.

From non-coding RNAs to cancer regulators: The fascinating world of micropeptides

Micropeptides are commonly identified as peptides encoded by non-coding RNAs (ncRNAs). In the short open reading frame (sORF) of ncRNAs, there is a base sequence encoding functional micropeptides, which is of great significance in the biological field. Recently, micropeptides regulate diverse processes, including mitochondrial metabolism, calcium transport, mRNA splicing, signal transduction, myocyte fusion, and cellular senescence, regulating the homeostasis of the internal environment and cancer's incidence and progression. Especially, the study of micropeptides in cancer about the potential regulatory mechanism will be conducive to further understanding of the process of cancer initiation and development. More and more research shows micropeptides have been confirmed to play an essential role in the emergence of multiple kinds of cancers, including Breast cancer, Colon cancer, Colorectal cancer, Glioma, Glioblastoma, and Liver cancer. This review presents a comprehensive synthesis of the latest advancements in our understanding of the biological roles of micropeptides in cancer cells, with a particular focus on the regulatory networks involving micropeptides in oncogenesis. The new mode of action of micropeptides provides innovative ideas for cancer diagnosis and treatment. Moreover, we explored the significant capacity of micropeptides as diagnostic biomarkers and targets for anti-cancer therapies in cancer clinical settings, highlighting their role in the development of innovative micropeptide-based diagnostic tools and anti-cancer therapeutics.

Drought stress memory in maize: understanding and harnessing the past for future resilience

Maize (Zea mays L.), a cornerstone of global food security, faces significant challenges due to drought stress, which disrupts its growth, development, and productivity. This review synthesizes advances in our understanding of drought stress memory, a mechanism that enables maize to "remember" prior drought exposure through transcriptional, epigenetic, and physiological pathways. Key regulators, including transcription factors (ZmEREB24 and ZmNF-YC12) and epigenetic modifications (DNA methylation and histone acetylation), orchestrate stress-responsive pathways that ensure rapid adaptation to recurrent drought events. Complementing these molecular mechanisms, physiological adaptations, such as optimized root and leaf architecture, enhanced water-use efficiency, and antioxidant defenses, further strengthen drought tolerance. Practical applications, including molecular priming techniques (e.g., osmopriming, hydropriming, nanoparticles) and advanced genetic tools (CRISPR/Cas9, GWAS), promise scalable solutions for breeding drought-resilient maize varieties. Despite this progress, challenges remain, including genotype-specific variability, scalability, and trade-offs between resilience and yield. This review provides a roadmap for integrating laboratory discoveries with field-level practices, bridging molecular and agronomic innovations to address climate variability and ensure sustainable maize production and global food security.

LncRNA JINR1 regulates miR-216b-5p/GRP78 and miR-1-3p/DDX5 axis to promote JEV infection and cell death

Japanese encephalitis virus (JEV) infection in the central nervous system (CNS) leads to neuroinflammation and neuronal cell death. Several long non-coding RNAs (lncRNAs) are differentially expressed during viral infection and regulate multiple aspects of viral pathogenesis. Previously, we have shown that JEV/West Nile virus (WNV) infection promotes JEV-induced non-coding RNA 1 (JINR1) expression in SH-SY5Y cells, and it interacts with RNA-binding motif protein 10 (RBM10) to enhance cell death and viral replication. In this study, we show that JEV or WNV infection of the SH-SY5Y cells inhibits the expression of microRNAs (miRNAs) miR-216b-5p and miR-1-3p. These miRNAs bind to the JEV/WNV genome, and their overexpression during JEV/WNV infection reduces viral replication and cell death. Depleting JINR1 or RBM10 during viral infection prevents the downregulation of miR-216b-5p and miR-1-3p. In addition, JINR1 or RBM10 knockdown during JEV/WNV infection enhances the binding of RNA Pol II and H3K4me3 at the promoters of miR-216b-5p and miR-1-3p. JINR1 or RBM10 depletion also prevents the binding of H3K27me3 at the promoters of these miRNAs, suggesting that JINR1 and RBM10 are involved in their transcription repression. Interestingly, JINR1 also acts as a competing endogenous RNA (ceRNA) that directly binds to miR-216b-5p and miR-1-3p, resulting in the upregulation of their targets glucose-regulated protein 78 (GRP78) and DEAD-Box Helicase 5 (DDX5), respectively, which are involved in regulating viral replication. Our findings suggest that JINR1 uses multiple mechanisms to promote JEV and WNV infection in neuronal cells.

IMPORTANCE

Infection of the central nervous system (CNS) by Japanese encephalitis virus (JEV) or West Nile virus (WNV) leads to neuroinflammation and neuronal cell death. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) regulate viral infection by regulating the expression of host genes. However, knowledge about the interplay between lncRNAs and miRNAs during JEN/WNV infection is limited. We show that JEV/WNV infection inhibits the expression of anti-viral host miRNAs miR-216b-5p and miR-1-3p. These miRNAs inhibit the JEV and WNV replication by directly binding with their genome. JINR1 and its interacting protein, RBM10, inhibit the transcription of miR-216b-5p and miR-1-3p. Interestingly, JINR1 also binds and sequesters miR-216b-5p and miR-1-3p, resulting in upregulation of their targets GRP78 and DDX5, respectively, which promote viral infection. Our findings suggest that lncRNA JINR1 is a potential target for developing anti-virals against JEV/WNV infection.

Mechanisms and progress of LncRNAs in prostate cancer development and diagnostic therapy

Prostate cancer (PCa) is a leading cause of cancer-related morbidity and mortality in men worldwide. Despite advancements in diagnosis and treatment, challenges such as late-stage detection, therapeutic resistance, and the complexity of castration-resistant prostate cancer (CRPC) persist. Long non-coding RNAs (LncRNAs) play critical roles in PCa progression through epigenetic regulation, transcriptional and post-transcriptional modulation, and immune response regulation. This review highlights the molecular mechanisms by which LncRNAs influence PCa development, treatment resistance, and immune regulation, emphasizing their potential as biomarkers and therapeutic targets. We also discuss future research directions to advance precision medicine in PCa.

A Pyroptosis-Related LncRNA Signature for Predicting Prognosis, Immune Features and Drug Sensitivity in Ovarian Cancer

Background

Multiple studies have suggested that lncRNAs and pyroptosis play important roles in ovarian cancer (OC). However, the function of pyroptosis-related lncRNAs (PRLs) in OC is not fully understood.

Methods

Clinical information and RNA-seq data of OC patients (n = 379) were collected from TCGA database. Pearson correlation analysis and univariate Cox analysis were performed to identify prognostic PRLs, respectively. LASSO-COX regression was utilized to construct a prognostic PRLs signature. Kaplan-Meier (K-M) curve analyses and receiver operating characteristics (ROC) were used to evaluate the prognostic prediction of the signature. The association between risk score and tumor microenvironment infiltration, immunotherapy response and chemotherapy sensitivity were also analyzed. In addition, the function of TYMSOS on OC and pyroptosis was experimentally confirmed in cell lines.

Results

Firstly, 32 prognostic PRLs were identified, and a novel prognostic PRLs signature was constructed and validated. Surprisingly, the prognostic PRLs signature could solidly predict the clinical outcome of patients with OC and patients with high-risk score shown a short overall survival. GSEA results suggested that the RPLs were mainly enriched in the inflammatory response pathway, p53 pathway, TGF-β signaling and TNFα signaling. Besides, our results demonstrated that the risk score was significantly associated with patients with immune infiltration, immunotherapy response and the sensitivity of veliparib and metformin. Furthermore, the oncogene effect of TYMSOS on OC by inhibiting pyroptosis was verified by experiments.

Conclusion

This study found that the prognostic PRLs signature may serve as an efficient biomarker in predicting the prognosis, tumor microenvironment infiltration, and sensitivity of chemotherapeutic agents. TYMSOS is a potential biomarker in OC, and it might promote tumor progression by inhibiting pyroptosis.

PSMA3-AS1: a promising LncRNA as a diagnostic and prognostic biomarker in human cancers

Long non-coding RNAs (lncRNAs) have shown increasing potential as biomarkers and therapeutic targets in cancer. Among them, PSMA3-AS1 has garnered significant attention due to its dysregulated expression in various human malignancies and its involvement in key oncogenic processes. This review offers a comprehensive analysis of PSMA3-AS1, including its expression patterns, molecular mechanisms, and clinical significance across different cancer types. It explores its abnormal expression levels, correlation with clinicopathological characteristics, and roles in promoting cell proliferation, invasion, migration, and epithelial-mesenchymal transition (EMT). The review delves into the molecular pathways through which PSMA3-AS1 exerts its functions, particularly its interactions with microRNAs. Highlighting its strong potential as both a diagnostic and prognostic biomarker, the study underscores the need for further clinical research to fully harness its therapeutic implications. Ultimately, this review aims to consolidate current knowledge on PSMA3-AS1 in human cancers and encourage continued exploration into its utility in innovative diagnostic and therapeutic approaches.

Biomolecules Interacting with Long Noncoding RNAs

This review explores the complex interactions between long noncoding RNAs (lncRNAs) and other biomolecules, highlighting their pivotal roles in gene regulation and cellular function. LncRNAs, defined as RNA transcripts exceeding 200 nucleotides without encoding proteins, are involved in diverse biological processes, from embryogenesis to pathogenesis. They interact with DNA through mechanisms like triplex structure formation, influencing chromatin organization and gene expression. LncRNAs also modulate RNA-mediated processes, including mRNA stability, translational control, and splicing regulation. Their versatility stems from their forming of complex structures that enable interactions with various biomolecules. This review synthesizes current knowledge on lncRNA functions, discusses emerging roles in development and disease, and evaluates potential applications in diagnostics and therapeutics. By examining lncRNA interactions, it provides insights into the intricate regulatory networks governing cellular processes, underscoring the importance of lncRNAs in molecular biology. Unlike the majority of previous reviews that primarily focused on individual aspects of lncRNA biology, this comprehensive review uniquely integrates structural, functional, and mechanistic perspectives on lncRNA interactions across diverse biomolecules. Additionally, this review critically evaluates cutting-edge methodologies for studying lncRNA interactions, bridges fundamental molecular mechanisms with potential clinical applications, and highlights their potential.

Potential Correlation Between Molecular Biomarkers and Oxidative Stress in Traumatic Brain Injury

Diagnosing traumatic brain injury (TBI) remains challenging due to an incomplete understanding of its neuropathological mechanisms. TBI is recognised as a complex condition involving both primary and secondary injuries. Although oxidative stress is a non-specific molecular phenomenon observed in various neuropathological conditions, it plays a crucial role in brain injury response and recovery. Due to these aspects, we aimed to evaluate the interaction between some known TBI molecular biomarkers and oxidative stress in providing evidence for its possible relevance in clinical diagnosis and outcome prediction. We found that while many of the currently validated molecular biomarkers interact with oxidative pathways, their patterns of variation could assist the diagnosis, prognosis, and outcomes prediction in TBI cases.

JNK kinase promotes inflammatory responses by inducing the expression of the inflammatory amplifier TREM1 during influenza a virus infection

Since the twentieth century, four influenza pandemics caused by IAV have killed millions of people worldwide. IAV infection could induce acute lung injury mediated by cytokine storms, which is an essential cause of death in critically ill patients. Consequently, it is crucial to explore the regulators and regulatory mechanisms of cytokine storms, which may provide potential drug targets and expand our understanding of acute lung injury. Previous studies have shown that JNK kinase is essential in promoting inflammatory responses during viral infections. In this study, we demonstrated that JNK kinase could regulate the IAV-induced cytokine storms by affecting the expression of pro-inflammatory and anti-inflammatory factors. Further studies revealed that inhibition of JNK kinase activity significantly downregulated the expression of the inflammatory amplifier TREM1. Besides, TREM1 knockdown could significantly inhibit the expression of pro-inflammatory factors. Furthermore, SP600125 is a specific inhibitor of JNK kinase. The results show that TREM1 overexpression reversed the effect of SP600125 treatment on the expression of pro-inflammatory factors. Together, we found that JNK kinase could activate the inflammatory amplifier TREM1 to promote inflammatory responses during influenza A virus infection. These findings may provide some inspiration for subsequent researchers to explore the regulatory mechanisms of cytokine storms induced by emerging viral infections.

A nuclear RNA degradation code is recognized by PAXT for eukaryotic transcriptome surveillance

The RNA exosome plays critical roles in eukaryotic RNA degradation, but how it specifically recognizes its targets remains unclear. The poly(A) tail exosome targeting (PAXT) connection is a nuclear adaptor that recruits the exosome to polyadenylated RNAs, especially transcripts polyadenylated at intronic poly(A) sites. Here, we show that PAXT-mediated RNA degradation is induced by the combination of a 5' splice site (ss) and a poly(A) junction (PAJ) but not by either sequence alone. These sequences are bound by U1 small nuclear ribonucleoprotein particle (snRNP) and cleavage/polyadenylation factors, which, in turn, cooperatively recruit PAXT. As the 5' ss-PAJ combination is typically absent on correctly processed RNAs, it functions as a "nuclear RNA degradation code" (NRDC). Importantly, disease-associated single nucleotide polymorphisms that create novel 5' ss in 3' untranslated regions can induce aberrant mRNA degradation via the NRDC mechanism. Together, our study identified the first NRDC, revealed its recognition mechanism, and characterized its role in human diseases.

scPRINT: pre-training on 50 million cells allows robust gene network predictions

A cell is governed by the interaction of myriads of macromolecules. Inferring such a network of interactions has remained an elusive milestone in cellular biology. Building on recent advances in large foundation models and their ability to learn without supervision, we present scPRINT, a large cell model for the inference of gene networks pre-trained on more than 50 million cells from the cellxgene database. Using innovative pretraining tasks and model architecture, scPRINT pushes large transformer models towards more interpretability and usability when uncovering the complex biology of the cell. Based on our atlas-level benchmarks, scPRINT demonstrates superior performance in gene network inference to the state of the art, as well as competitive zero-shot abilities in denoising, batch effect correction, and cell label prediction. On an atlas of benign prostatic hyperplasia, scPRINT highlights the profound connections between ion exchange, senescence, and chronic inflammation.

Small-molecule RNA ligands: a patent review (2018-2024)

INTRODUCTION

Targeting three-dimensional RNA structures with traditional drug-like small molecules is gaining wide attention in both the academia and the pharmaceutical industries, due to their good oral bioavailability, cheap production cost, and the possibility of fine-tuning ADMET properties, which represent a powerful alternative to the current RNA-targeted therapies, including ASO and siRNA. As RNAs are involved in nearly all the physiological and pathological processes, small molecules RNA ligands can have a plethora of different therapeutic applications, spanning from cancer to infectious and neurological diseases.

AREAS COVERED

This review describes patents concerning small molecules RNA ligands published within January 2018 and October 2024, searched through Espacenet, Patentscope, and Google Patents databases.

EXPERT OPINION

The number of patents that has been released in the last few years demonstrates the relevance of targeting RNA structures for the development of next generation chemotherapeutic agents and antiviral/antibacterial drugs, even though this field is still in its infancy and many issues still need to be resolved, in particular related to selectivity. An emerging approach to considerably limiting side effects is presented by RIBOTAC derivatives, as promoting a selective RNase-L mediated RNA degradation allows to significantly reduce the dose of the compound.