Search Results (3,008)

Background/Aim: Long non-coding RNAs (lncRNAs) such as NEAT1, HULC, and MALAT1, which are expressed in adipose tissue, are known to play a role in regulating adiposity. However, how the plasma expression of these lncRNAs changes in obese patients following rapid adipose tissue loss after sleeve gastrectomy remains unclear. This study aimed to investigate the relationship between plasma NEAT1, HULC, and MALAT1 expression levels and short-term weight loss after sleeve gastrectomy. Materials and Methods: Plasma samples prospectively collected from patient groups were used for total RNA extraction to measure the expression levels of NEAT1, HULC, and MALAT1 both before sleeve gastrectomy and 30 days after the procedure. Additionally, patients were followed for changes in body mass index (BMI) and HbA1C levels over a 12-month period. Associations between lncRNA expression levels and clinical parameters were evaluated. Results: Before sleeve gastrectomy, the expression levels of NEAT1 and HULC were significantly higher in obese patients compared to non-obese individuals (p < 0.0001). Sleeve gastrectomy was associated with decreased expression levels of NEAT1 (p = 0.004) and HULC (p = 0.0027). NEAT1 and HULC expression levels showed significant associations with changes in HbA1C and BMI, respectively (p < 0.05). Conclusions: NEAT1 and HULC expression levels were associated with short-term metabolic and anthropometric changes following sleeve gastrectomy. These findings are exploratory and hypothesis-generating, and further studies with larger cohorts and longer follow-up are needed to determine their potential clinical relevance. Full article

This study aimed to investigate the molecular mechanisms underlying dopaminergic injury induced by gestational and lactational atrazine (ATR) exposure in rat offspring, with a particular focus on non-coding RNA-mediated regulation. Pregnant rats were exposed to ATR during gestation and lactation. Offspring underwent behavioral testing at postnatal day 21 (PND21) and were sacrificed for midbrain tissue collection at PND28. Behavioral alterations, histopathological changes in the substantia nigra, and dopaminergic marker expression were assessed to evaluate ATR-induced neurotoxicity. Whole-transcriptome sequencing was then performed to identify differentially expressed mRNAs, miRNAs, and lncRNAs, followed by co-expression, protein–protein interaction, and competing endogenous RNA (ceRNA) network analyses. Key targets were validated by qRT-PCR. Candidate molecules identified from transcriptomic and ceRNA analyses were further examined in an ATR-induced neurotoxicity model established in RA-differentiated SK-N-SH cells. Dual-luciferase reporter, Ago2-RNA immunoprecipitation, and biotin-labeled RNA pull-down assays were used to examine putative binding relationships and molecular interactions. In addition, lentivirus-mediated Elavl4 overexpression was performed to further evaluate the role of this candidate regulator in ATR-induced Nurr1 downregulation. Gestational and lactational ATR exposure induced significant behavioral abnormalities in rat offspring. These changes were accompanied by histopathological alterations in the substantia nigra, including reduced TH immunoreactivity, as well as abnormal expression of dopaminergic markers, characterized by decreased TH and Nurr1 levels and increased α-syn expression. Together, these findings indicate the presence of dopaminergic injury. Whole-transcriptome analysis further revealed widespread dysregulation of mRNAs, miRNAs, and lncRNAs in ATR-exposed offspring. Subsequent integrative analysis suggested a potential ceRNA regulatory relationship among Elavl4, miR-301a-5p, and Nurr1, which was further supported by qRT-PCR. Dual-luciferase reporter, RIP, and RNA pull-down assays supported direct interactions between miR-301a-5p and both Elavl4 and Nurr1, as well as their association with the Ago2-containing silencing complex. Moreover, Elavl4 overexpression partially reversed ATR-induced Nurr1 downregulation in vitro. Gestational and lactational ATR exposure induced behavioral abnormalities and dopaminergic injury in rat offspring. Whole-transcriptome analysis combined with experimental validation suggests a potential association between the Elavl4/miR-301a-5p/Nurr1 ceRNA axis and ATR-induced dopaminergic injury, providing insight into the post-transcriptional mechanisms underlying developmental neurotoxicity. Full article

Our previous work demonstrated that bovine milk-derived extracellular vesicles (mEVs) could alleviate the inflammatory response of mice colitis, along with hundreds of differentially expressed (DE) mRNAs. This study further analyzed the profiles of non-coding RNAs (ncRNAs) and explored the correlation with DE mRNAs by constructing ceRNA networks. Six-week-old male C57BL/6 mice were fed either a control diet or a diet added with mEVs for 30 days. Then the mice were given dextran sulphate sodium in drinking water for 7 days to induce colitis. A total of 40 miRNAs, 541 lncRNAs and 643 circRNAs exhibited changes in mEVs pretreatment group. Among these DE miRNAs, mEVs pretreatment significantly increased the expressions of miR-122, miR-147, miR-210, miR-1224, miR-148a, and miR-212, which might participate in the inflammatory response of the colitis models. The expression of Tug1 increased after mEVs pretreatment, while Snhg5 and H19 decreased, which might be involved in intestinal barrier restoration. Functional analysis of the DE ncRNAs suggested mEVs might exert protective effects not only through modulation of inflammatory responses but also by enhancing intestinal stem cell function and epithelial regeneration, which were mainly regulated by Wnt and Hippo signaling pathways according to the ceRNA networks. Full article

Circulating long non-coding RNAs (lncRNAs) have emerged as promising non-invasive biomarkers for colorectal cancer (CRC) detection; however, data in Vietnamese populations remain limited. In this study, a total of 218 participants (106 CRC, 80 adenomas, and 32 healthy controls) were included. Relative expression levels and diagnostic performance of three circulating lncRNAs—CCAT1, HOTAIR, and NEAT1—were quantified using RT-qPCR and analyzed by the 2^−ΔΔCt method. Receiver operating characteristic (ROC) curve analysis was performed to assess the diagnostic accuracy of individual lncRNAs and their combinations. CCAT1, HOTAIR, and NEAT1 were significantly upregulated in CRC patients compared with adenoma patients and healthy controls (all p < 0.001). Expression levels were higher in advanced-stage (TNM III–IV) CRC than in early-stage disease. Among individual markers, HOTAIR demonstrated the highest diagnostic accuracy (AUC = 0.918), followed by CCAT1 (AUC = 0.908) and NEAT1 (AUC = 0.890). Combined biomarker models showed improved performance, with the CCAT1 + HOTAIR combination achieving the highest AUC (0.944). Overall, circulating CCAT1, HOTAIR, and NEAT1 demonstrated favorable diagnostic performance in a Vietnamese population and outperformed conventional markers (CEA and CA19-9). These findings support the potential utility of multi-lncRNA panels as non-invasive biomarkers for CRC detection, warranting further validation in larger, independent cohorts. Full article

Long non-coding RNAs (lncRNAs) interact with chromatin and recruit epigenetic complexes to specific genomic loci, yet their relationship with super-enhancers (SEs), key regulatory elements frequently reprogrammed in cancer, remains unexplored. We developed an integrative pipeline that combines RNA–chromatin contact data (RNA-Chrom), histone modification–lncRNA expression correlation profiles (HiMoRNA peaks), and super-enhancer annotations (SEdb 3.0) to map lncRNA–SE regulatory axes. Applying this framework to SNHG1 in HCT116 colorectal cancer cells, we identified 21 SNHG1-reactive super-enhancers (Ψ-SEs) among 184 cancer-specific SEs, at which SNHG1 physical contacts co-occur with SNHG1-correlated histone modifications (HiMoRNA peaks), predominantly H3K4me1 (permutation p = 0.001, fold enrichment = 2.03). Comparison with 4145 lncRNAs demonstrated that epigenetic correlations alone do not distinguish SNHG1; instead, the addition of the contact layer is required to delineate the Ψ-SE set. Differential expression (DESeq2) and co-expression analyses in 471 TCGA-COAD tumor samples identified 12 Ψ-SE target genes (including CDC20, PDP1, and TOP1) consistently upregulated in both HCT116 cells and patient tumors and positively correlated with SNHG1, with the co-expression signal robust to tumor purity correction. The proposed Ψ/Ω classification provides a generalizable framework for prioritizing super-enhancers at which lncRNA–chromatin interactions may shape the local epigenetic environment across cancer types. Full article

The human genome produces a large repertoire of non-coding RNAs (ncRNAs) with important regulatory roles in development, physiology, and most of diseases. Among these, long non-coding RNAs (lncRNAs) have emerged as key modulators of gene expression, chromatin organization, and cellular homeostasis, despite displaying remarkably low primary-sequence conservation across species. This apparent evolutionary paradox questions the limitations of predicting biological function based on conservation, particularly across different biological domains. Here, we examine current evidence on lncRNA evolution, with a focus on their roles in metabolic regulation compared with neurobiological processes. We hypothesize that lncRNAs involved in ancient and conserved pathways such as metabolism may be under stronger evolutionary constraint than those associated with higher-order, species-specific traits, although available data support a more nuanced interpretation. Functional importance often correlates poorly with linear sequence conservation and instead appears to depend on higher-level features, including RNA secondary or tertiary structure, genomic context, regulatory architecture, and interactions with conserved molecular partners. We propose a systematic comparative framework to empirically assess conservation among metabolism- and neuro-associated lncRNAs using phylogenetic, syntenic, structural, and expression-based metrics. Finally, we discuss the therapeutic implications of lncRNA biology, highlighting how a deeper understanding of their evolutionary and mechanistic properties may inform the development of more precise and effective RNA-targeting strategies. Together, these insights underscore the non-coding transcriptome as a critical frontier for both fundamental biology and precision medicine. Full article

LncRNAs, defined as transcripts longer than 200 nucleotides with limited protein-coding potential, have emerged as important regulators of gene expression across multiple levels of cellular regulation. These molecules influence chromatin organization, transcriptional activity, and post-transcriptional processes through diverse interactions with DNA, RNA, and protein complexes. Although initially considered transcriptional byproducts, accumulating evidence now indicates that lncRNAs participate in a wide range of physiological processes and are implicated in numerous human diseases, including cancer, cardiovascular disorders, neurological diseases, and immune related conditions. However, the strength of mechanistic evidence varies substantially across the field, with robust functional validation currently limited to a relatively small number of well-characterized lncRNAs. In many cases, proposed regulatory roles remain supported primarily by expression correlations or limited perturbation studies, highlighting the need for careful evaluation of reproducibility, context dependence, and locus-specific effects. In addition, translating lncRNA discoveries into therapeutic strategies faces several practical challenges, including efficient tissue-specific delivery, subcellular localization constraints, isoform complexity, and potential off-target effects. This review provides an overview of current knowledge on lncRNA classification, biogenesis, and molecular mechanisms, evaluates their roles in human disease, and discusses emerging therapeutic approaches in the context of translational feasibility. By integrating mechanistic insights with current limitations and unresolved questions, we highlight priorities for future research aimed at harnessing lncRNAs for diagnostic and therapeutic applications in precision medicine. Full article

The red cusk-eel (Genypterus chilensis) is an endemic Chilean teleost fish of significant importance to fisheries and aquaculture; however, no reference genome is available for this species. In this study, we present the first hybrid genome assembly of G. chilensis using Nanopore long-reads and Illumina short-reads, integrated with structural and functional annotations from RNA-seq data of the intestine and head kidney. The resulting genome assembly was 439.89 Mb in size, with an N50 of 7.96 Mb, containing 35,029 coding genes. Comparative genomics with G. blacodes revealed high similarity in genome size and completeness. Additionally, 14,681 lncRNAs were annotated, with 641 lncRNAs and 7323 coding genes differentially expressed in a tissue-specific expression pattern. These findings provide a high-quality genomic resource that enhances the understanding of lncRNA regulation and genome structure in the Genypterus genus. This study establishes a foundation for future research on commercial traits, conservation, and the evolution of the Ophidiiformes order. Full article

Background/Objectives: Nuclear receptor corepressors NCOR1 and NCOR2 are key regulators of transcriptional repression, chromatin remodelling, and immunometabolic signalling. While NCOR1 has already been linked to vascular biology, its relevance in abdominal aortic aneurysm (AAA) remains unclear, particularly for NCOR2. This study aimed to investigate the expression, cellular localisation, and molecular interactions of NCOR1/2 in human AAA tissue. Methods: Human AAA samples (elective and ruptured) (n = 45) and non-aneurysmal control aortas (n = 18) were obtained from our Swiss Vascular Biobank. Transcriptomic profiling was performed using ribosomal RNA-depleted RNA sequencing. Differential expression and correlation analyses were performed using DESeq2/EdgeR and Spearman rank correlation with Benjamini–Hochberg correction. Cellular localisation was assessed through immunohistochemistry (IHC). Results: Bulk transcriptomic analyses showed no significant differences in NCOR1 or NCOR2 expression between AAA and controls. IHC revealed that NCOR1 was found in endothelial cells (ECs), smooth muscle cells (SMCs), and inflammatory infiltrates, while NCOR2 was primarily associated with macrophages. Correlation analyses suggest that NCOR1 interacts with various cellular markers, proteolytic enzymes, inflammatory mediators, and epigenetic regulators, including the lncRNA MALAT1. NCOR2 showed distinct associations with remodelling enzymes, TGFB1 signalling, selective epigenetic modifiers, and lncRNA H19. Conclusions: The lack of transcriptional differences in NCOR1 and NCOR2 between AAA and controls does not exclude cell-type-specific regulation or functional relevance. The specific cellular distributions and molecular associations in human AAA imply that NCOR1 and NCOR2 play non-redundant roles in vascular remodelling, inflammation, and epigenetic regulation. Our findings highlight NCOR pathways as potential modulators of AAA pathophysiology and promising targets for future therapies. Full article

Lycoris plants are known for their diverse flower colors, but the molecular mechanisms behind these variations remain unclear. In this study, we first used the CIELAB system to precisely measure flower color. We objectively defined the petals of Lycoris sprengeri as blue-purple (Bp) and compared them with the white petals of Lycoris longituba (W) and the red petals of Lycoris radiata var. pumila (R). Metabolomic analysis showed that specific kaempferol glycosides, including kaempferol-3-O-sophoroside and lonicerin, accumulated significantly in the blue-purple petals. Transcriptomic analysis revealed that genes related to flavonoid biosynthesis were generally more active in the colored petals (Bp and R). However, different expression patterns of key hydroxylase genes created a metabolic split. Specifically, the blue-purple petals showed high expression of LrF3′5′H (directing synthesis toward delphinidin) and LrFLS (promoting kaempferol accumulation), whereas the red petals mainly expressed LrF3′H (leading to cyanidin synthesis). Further investigation identified LrWRKY70 as a core transcription factor highly correlated with these flavonoid pathway genes. Crucially, we discovered a new long non-coding RNA, LncRNA401, located downstream of the LrWRKY70 antisense strand. It showed a strong positive correlation with LrWRKY70. Functional verification through transient overexpression demonstrated that LncRNA401 significantly increased the expression of LrWRKY70. This, in turn, broadly activated downstream flavonoid biosynthesis genes, including LrCHS, LrF3′5′H, LrFLS, and LrDFR. This cascade ultimately promoted the synthesis of anthocyanins and kaempferol derivatives, resulting in the unique blue-purple phenotype. Our results reveal a novel LncRNA401-LrWRKY70 regulatory module. This module plays a key role in metabolic reprogramming for flower color formation in Lycoris, providing important insights into plant secondary metabolism and valuable targets for breeding specific flower colors. Full article

The 5′-proximal region of the citrus tristeza virus (CTV) RNA genome is a hub where several elements involved in different facets of the virus cycle reside, including the sequences driving the production of the viral long non-coding RNA (lncRNA) LMT1. The sequence of this region is one of the most divergent genome areas, allowing for strain differentiation. Beyond its use in assessing viral population diversity, the region provides a valuable model for studying the conservation of RNA structure and function despite sequence variation. Here, we integrated comparative in silico analysis of the LMT1 region from variants of eight CTV strains with selective 2′-hydroxyl acylation, analyzed by primer extension and mutational profiling (SHAPE-MaP) probing of in vitro–generated LMT1 RNAs from two divergent strains, T36 and T68. The predicted consensus structures revealed 19 putative, conserved stem-loops. The SHAPE-MaP reactivity data supported and substantiated the thermodynamics-based predictions for the 15 previously uncharacterized stem-loops and two functional elements identified earlier. The strong structural conservation across strains highlights that the LMT1 RNA structure contributes to its function during CTV infection. These results provide the first experimentally supported structure of this viral lncRNA and lay the foundation for defining how individual RNA motifs influence CTV biology. Full article

Hypertensive nephropathy (HN) is a leading cause of chronic kidney disease and end-stage renal disease worldwide and results from the long-term effects of hypertension on renal structure and function. The pathogenesis of HN is complex and involves haemodynamic disturbances, renal vascular injury, oxidative stress, chronic inflammation, and progressive interstitial fibrosis. In recent years, increasing attention has focused on the role of non-coding RNAs (ncRNAs)—including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs)—as key regulators of gene expression involved in these processes. This review summarises the current understanding of the molecular mechanisms underlying HN, with particular emphasis on the roles of oxidative stress, activation of the renin–angiotensin–aldosterone system, transforming growth factor beta signalling, and inflammatory and fibrogenic pathways. The contribution of dysregulated ncRNAs to endothelial dysfunction, inflammatory responses, apoptosis, angiogenesis, and renal remodelling and fibrosis is also discussed. Particular attention is given to miRNAs and lncRNAs as mediators of disease progression and potential biomarkers, as well as to the emerging role of circRNAs in hypertensive kidney injury, including their involvement in the regulation of redox balance and intercellular communication. Collectively, available evidence indicates that ncRNAs represent a critical link between haemodynamic stimuli and persistent molecular alterations in renal tissue, highlighting their potential as diagnostic markers and therapeutic targets in HN. Full article

Lung cancer remains a leading cause of morbidity and mortality worldwide. This review critically synthesizes recent advances on long non-coding RNAs (lncRNAs) in lung cancer. Unlike previous descriptive compilations, we provide an evidence-based analysis, distinguish preclinical from clinically validated findings (e.g., serum exosomal SNHG15, DLX6-AS1), and highlight recurring mechanistic themes (ceRNA, chromatin remodeling, m⁶A). We discuss inconsistencies in the literature, barriers to clinical translation (such as standardization, sample variability, and validation), and propose a roadmap for clinical integration, including how lncRNA panels could complement existing biomarkers like CYFRA21-1. A transparent literature search strategy is included. Full article

Glioblastoma (GBM) is the most lethal and aggressive primary brain tumor in adults. Despite a standard-of-care regimen involving surgical resection, radiotherapy and temozolomide (TMZ), median overall survival typically hovers between 12 and 15 months. This poor prognosis is driven by profound intratumoral heterogeneity, glioma stem cell populations, and an immunosuppressive microenvironment that collectively fuel resistance to traditional apoptosis-centric therapies. Ferroptosis—a form of regulated cell death driven by iron-dependent phospholipid peroxidation and the collapse of antioxidant defenses—has emerged as a compelling alternative for eliminating therapy-refractory GBM cells. This review examines the molecular machinery of ferroptosis in glioma and explores how an additional regulatory layer, noncoding RNAs (ncRNAs), modulates this process. We highlight key experimentally validated axes where microRNAs, long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs) orchestrate iron handling and antioxidant thresholds. These include sensitizers like miR-147a and circLRFN5, which promote iron overload, and resistors like circCDK14 and TMEM161B-AS1, which act as “ferroptosis brakes”. Furthermore, we discuss how integrative analyses of TCGA and CGGA cohorts have yielded ferroptosis-related lncRNA signatures that robustly predict patient survival. Finally, we outline the clinical potential of these ncRNAs as biomarkers and therapeutic targets while addressing the delivery challenges, such as the blood–brain barrier, that must be overcome to achieve precision, ferroptosis-oriented GBM therapy. Full article

RCC remains a therapeutically challenging malignancy, particularly in its metastatic stage, in which treatment resistance and limited response durability persist despite recent advances in immunotherapy and targeted therapies. Although immune checkpoint inhibitors (ICIs) have significantly improved outcomes for a subset of patients, reliable prognostic and predictive biomarkers to guide therapy selection are still lacking. Current clinical models, such as the International Metastatic RCC Database Consortium (IMDC) risk score, offer only limited insight into the molecular and immunologic complexity of RCC. Emerging molecular biomarkers implicated in resistance mechanisms reflect the underlying heterogeneity of RCC and may inform future therapeutic strategies. Kidney Injury Molecule-1 (KIM-1), a transmembrane protein that is up-regulated in RCC and detectable in circulation, has demonstrated potential as a non-invasive biomarker for diagnosis, prognosis, and treatment monitoring. Liquid-biopsy approaches, including the analysis of circulating tumour DNA (ctDNA), microRNAs (miRNAs), and long non-coding RNAs (lncRNAs), are also gaining traction due to their minimally invasive nature and potential for real-time disease monitoring. This review aims to provide a structured overview of emerging biomarkers in metastatic RCC, critically evaluate their current clinical applicability, and propose a biologically informed framework for their integration into clinical decision-making. In addition, we propose a conceptual IMDC-Plus framework that integrates clinical, biological, and early dynamic markers to improve risk stratification in the era of immunotherapy (IO). Full article