The noncoding RNA revolution-trashing old rules to forge new ones. Cell. 2014;157:77-94. [PMID: 24679528 DOI: 10.1016/j.cell.2014.03.008]

Nucleolar ribosomal RNA synthesis continues in differentiating lens fiber cells until abrupt nuclear degradation required for ocular lens transparency

Cellular differentiation requires highly coordinated action of all three transcriptional systems to produce rRNAs, mRNAs and various 'short' and 'long' non-coding RNAs by RNA Polymerase I, II and III systems, respectively. RNA Polymerase I catalyzes transcription of about 400 copies of mammalian rDNA genes, generating 18S, 5.8S and 28S rRNA molecules. Lens fiber cell differentiation is a unique process to study transcriptional mechanisms of individual crystallin genes as their very high transcriptional outputs are directly comparable only to globin genes in erythrocytes. Importantly, both terminally differentiated lens fiber cells and mammalian erythrocytes degrade their nuclei through different mechanisms. In lens, the generation of the organelle-free zone (OFZ) includes the degradation of mitochondria, endoplasmic reticulum, Golgi apparatus and nuclei. Here, using RNA fluorescence in situ hybridization (FISH), we evaluated nascent rRNA transcription, located in the nucleoli, during the process of mouse lens fiber cell differentiation. Lens fiber cell nuclei undergo morphological changes including chromatin condensation prior to their denucleation. Remarkably, nascent rRNA transcription persists in all nuclei that are in direct proximity of the OFZ. Additionally, changes in both nuclei and nucleoli shape were evaluated via immunofluorescence detection of fibrillarin, nucleolin, UBF and other proteins. These studies demonstrate for the first time that highly condensed lens fiber cell nuclei have the capacity to support nascent rRNA transcription. Thus, we propose that 'late' production of rRNA molecules and consequently of ribosomes increases crystallin protein synthesis machinery within the mature lens fibers.

Curcumin alleviates renal fibrosis in chronic kidney disease by targeting the circ_0008925-related pathway

BACKGROUND

Curcumin has been shown to inhibit renal fibrosis, but whether curcumin mediates renal fibrosis progression by regulating the circular RNA (circRNA)-related pathway remain unclear.

METHODS

TGF-β1 was used to construct renal injury and fibrosis cell model. Cell growth was evaluated by cell counting kit 8 assay, EdU assay and flow cytometry. Fibrosis marker and interleukin 6 signal transducer (IL6ST) protein levels were measured using western bolt analysis. Inflammation factor concentrations were determined by ELISA. Circ_0008925, miR-204-5p and IL6ST expression was assessed by qRT-PCR. Unilateral ureteral obstruction (UUO) mice models were constructed to assess the role of curcumin in vivo.

RESULTS

Curcumin treatment alleviated TGF-β1-induced HK-2 cell apoptosis, inflammation and fibrosis in vitro, as well as relieved renal injury in UUO mice models in vivo. Circ_0008925 was highly expressed in TGF-β1-induced HK-2 cells and its expression was inhibited by curcumin. Circ_0008925 could sponge miR-204-5p to positively regulate IL6ST. The inhibition effect of curcumin on TGF-β1-induced HK-2 cell injury and fibrosis was reversed by circ_0008925 overexpression, miR-204-5p inhibitor or IL6ST upregulation. Besides, circ_0008925 knockdown inhibited TGF-β1-induced HK-2 cell injury and fibrosis by suppressing IL6ST expression.

CONCLUSION

Curcumin relieved renal fibrosis through regulating circ_0008925/miR-204-5p/IL6ST axis.

Identification and functional analysis of wheat lincRNAs in response to Fusarium graminearum infection

Intergenic long non-coding RNAs (lincRNAs) have recently been recognized as pivotal regulators in plant-pathogen interactions. However, the specific regulatory mechanisms of lincRNAs responding to Fusarium graminearum (F. graminearum) infection remain largely unexplored. Here, we performed time-series transcriptome profiling (0, 24, 48, and 72 h post-inoculation) and systematic identification of lincRNAs. A total of 1238 expressed lincRNAs were identified, among which 548 were differentially expressed lincRNAs during the time course of F. graminearum infection. We further predicted cis-regulatory lincRNA-mRNA pairs, comprising 347 lincRNAs and potential 1015 target genes, which were found to be mainly involved in amino acid metabolism and biosynthetic pathways. Moreover, 19 lincRNAs were predicted as putative precursors or endogenous target mimics of miRNAs. Subsequently, we verified that two lincRNAs, MSTRG.6494 and MSTRG.32080, showed strong transcriptional responses to F. graminearum infection by quantitative real-time PCR (qPCR) screening. Silencing MSTRG.6494 reduced the expression level of defense-related genes, resulting in reduced resistance to fungal pathogenicity. Meanwhile, the expression level of the potential target gene ATP synthase subunit beta (TaATP2) was significantly decreased in MSTRG.6494-silenced plants infected with F. graminearum. Overall, we performed the genome-wide identification of lincRNAs and their possible regulatory networks during F. graminearum infection-related process, confirming that MSTRG.6494 participates in wheat resistance to F. graminearum, may be via targeting TaATP2 to enhance defense responses. Our findings provide new insights into the regulatory mechanism of lincRNAs for Fusarium head blight (FHB) resistance, suggesting this mechanism as an essential strategy for protecting wheat from F. graminearum.

Regulation of pancreatic β cells by exosomes from different sources

Diabetes is a chronic metabolic disorder with rising global prevalence, particularly in developed and high-income regions. Central to its pathogenesis is the dysfunction of pancreatic β-cells, alongside impaired glucose and lipid metabolism in peripheral insulin-responsive tissues. Exosomes are nano-sized extracellular vesicles essential for intercellular communication and have emerged as pivotal regulators of metabolic homeostasis. Secreted by virtually all cell types, exosomes encapsulate bioactive cargo that reflects their cellular origin and physiological state, thereby exerting diverse functional effects. Recent evidence highlights the role of exosomes derived from the liver, gut, adipose tissue, skeletal muscle, and mesenchymal stem cells in modulating β-cell proliferation, insulin secretion, and survival. In peripheral tissues exosomes also influence insulin sensitivity by regulating glucose and lipid metabolism, ultimately shaping β-cell responses under hyperglycemic conditions. A more comprehensive understanding of exosome-mediated crosstalk between metabolic organs and pancreatic β-cells could pave the way for the development of exosome-based diagnostic tools and therapeutic strategies aimed at improving early detection, prevention, and treatment of the diabetes.

Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage

Gene gains and losses are a major driver of genome evolution; their precise characterization can provide insights into the origin and diversification of major lineages. Here, we examined gene family evolution of 1154 genomes from nearly all known species in the medically and technologically important yeast subphylum Saccharomycotina. We found that yeast gene family evolution differs from that of plants, animals, and filamentous ascomycetes, and is characterized by smaller overall gene numbers yet larger gene family sizes for a given gene number. Faster-evolving lineages (FELs) in yeasts experienced significantly higher rates of gene losses-commensurate with a narrowing of metabolic niche breadth-but higher speciation rates than their slower-evolving sister lineages (SELs). Gene families most often lost are those involved in mRNA splicing, carbohydrate metabolism, and cell division and are likely associated with intron loss, metabolic breadth, and non-canonical cell cycle processes. Our results highlight the significant role of gene family contractions in the evolution of yeast metabolism, genome function, and speciation, and suggest that gene family evolutionary trajectories have differed markedly across major eukaryotic lineages.

A Dataset Curated for the Assessment of G4s in the LncRNAs Dysregulated in Various Human Cancers

Dysregulated expression of long non-coding RNAs (lncRNAs) in cancer contributes to various hallmarks of the disease, presenting novel opportunities for diagnosis and therapy. G-quadruplexes (G4s) within lncRNAs have gained attention recently; however, their systematic evaluation in cancer biology is yet to be performed. In this work, we have formulated a comprehensive dataset integrating experimentally-validated associations between lncRNAs and cancer, and detailed predictions of their G4-forming potential. The dataset categorizes predicted G4-motifs into anticipated G4 types (2 G, 3 G, and 4 G) and provides information about the subcellular localization of the corresponding lncRNAs. It describes lncRNA-RNA and lncRNA-protein interactions, together with the RNA G4-binding capabilities of these proteins. The dataset facilitates the investigation of G4-mediated lncRNA functions in diverse human cancers and provides distinctive leads about G4-mediated lncRNA-protein interactions.

Non coding RNA biomarkers in pemphigus disease

Pemphigus represents a group of potentially life-threatening autoimmune blistering diseases characterized by the production of pathogenic autoantibodies against desmosomal cadherins, leading to loss of cell adhesion. Early and accurate diagnosis remains critical for optimal management, yet current diagnostic approaches largely rely on invasive biopsies and serological assays that do not always predict disease progression or therapeutic response. In this context, the identification of reliable biomarkers is essential to enhance diagnostic precision, monitor disease activity, and guide treatment strategies. Non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), have emerged as promising biomarker candidates due to their stability in body fluids, tissue- and disease-specific expression patterns, and regulatory functions in immune processes. Increasing evidence suggests that dysregulated ncRNAs play significant roles in the immunopathogenesis of pemphigus, influencing cytokine signaling, immune cell differentiation, and keratinocyte adhesion. Therefore, herein, we summarize current findings on the involvement of specific miRNAs and lncRNAs in pemphigus pathogenesis, their diagnostic and prognostic potential, and the emerging therapeutic opportunities based on modulating ncRNA expression. Additionally, we address the limitations and challenges associated with clinical translation of ncRNA research and highlight future directions that may facilitate the incorporation of ncRNAs into personalized medicine approaches for pemphigus patients.

Machine learning approaches for predicting the small molecule-miRNA associations: a comprehensive review

MicroRNAs (miRNAs) are evolutionarily conserved small regulatory elements that are ubiquitous in cells and are found to be abnormally expressed during the onset and progression of several human diseases. miRNAs are increasingly recognized as potential diagnostic and therapeutic targets that could be inhibited by small molecules (SMs). The knowledge of SM-miRNA associations (SMAs) is sparse, mainly because of the dynamic and less predictable 3D structures of miRNAs that restrict the high-throughput screening of SMs. Toward augmenting the costly and laborious experiments determining the SM-miRNA interactions, machine learning (ML) has emerged as a cost-effective and efficient platform. In this article, various aspects associated with the ML-guided predictions of SMAs are thoroughly reviewed. Firstly, a detailed account of the SMA data resources useful for algorithms training is provided, followed by an elaboration of various feature extraction methods and similarity measures utilized on SMs and miRNAs. Subsequent to a summary of the ML algorithms basics and a brief description of the performance measures, an exhaustive census of all the 32 ML-based SMA prediction methods developed so far is outlined. Distinctive features of these methods have been described by classifying them into six broad categories, namely, classical ML, deep learning, matrix factorization, network propagation, graph learning, and ensemble learning methods. Trend analyses are performed to investigate the patterns in ML algorithms usage and performance achievement in SMA prediction. Outlining key principles behind the up-to-date methodologies and comparing their accomplishments, this review offers valuable insights into critical areas for future research in ML-based SMA prediction.

Unraveling architectural RNAs: Structural and functional blueprints of membraneless organelles and strategies for genome-scale identification

Architectural RNAs (arcRNAs) are long noncoding RNAs that serve as structural scaffolds for membraneless organelles (MLOs), facilitating cellular organization and dynamic responses to stimuli. Acting as blueprints for MLO assembly, arcRNAs recruit specific proteins and nucleic acids to establish and maintain the internal structure of MLOs while coordinating their spatial relationships with other organelles. This organized framework enables precise spatiotemporal regulation, allowing for targeted control of transcription, RNA processing, and cellular responses to stress. Notably, arcRNAs exhibit the "semi-extractable" feature, a property derived from their stable binding to cellular structures, making them partially resistant to conventional RNA extraction methods. This unique feature serves as a useful criterion for identifying novel arcRNAs, providing an opportunity to accelerate research in long noncoding RNAs and deepen our understanding of their functional roles in cellular processes.

From bone marrow mesenchymal stem cells to diseases: the crucial role of m6A methylation in orthopedics

Elucidating the molecular mechanisms underlying orthopedic diseases is crucial for guiding therapeutic strategies and developing innovative interventions. N6-methyladenosine (m6A)-an epitranscriptomic modification-has emerged as a key regulator of cellular fate and tissue homeostasis. Specifically, m6A plays a pivotal role in several RNA biological processes such as precursor RNA splicing, 3'-end processing, nuclear export, translation, and stability. Recent advancements indicate that m6A methylation regulates stem cell proliferation and osteogenic differentiation by modulating various signaling pathways. Extensive research has shown that abnormalities in m6A methylation contribute significantly to the onset and progression of various orthopedic diseases such as osteoporosis (OP), osteoarthritis (OA), rheumatoid arthritis (RA), and bone tumors. This review aims to summarize the key proteases involved in m6A methylation and their functions. The detailed mechanisms by which m6A methylation regulates osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) through direct and indirect ways are also discussed, with a focus on specific molecular pathways. Finally, this review analyzes the roles and mechanisms of m6A modification in the development and progression of multiple orthopedic diseases, offering a comprehensive understanding of the pathophysiology of these conditions and proposing new directions and molecular targets for innovative treatment strategies.

PTPRG-AS1 regulates the KITLG/KIT pathway through the ceRNA axis to promote the malignant progression of gastric cancer and the intervention effect of Compound Kushen injection on it

Gastric cancer (GC) is a common malignant tumor with high mortality, recurrence, and metastasis rates. Compound Kushen injection (CKI) combination chemotherapy has been clinically used for the treatment of GC in China for many years, but its underlying mechanisms of action remain unclear. Recent reports have highlighted the important role of the competing endogenous RNA (ceRNA) mechanism of noncoding RNA (ncRNA) and messenger RNA (mRNA) formation in GC and other tumors. This study aimed to investigate the effects of CKI on GC from the ceRNA perspective. We confirmed the inhibitory effect of CKI on GC in mouse models and cell lines. By examining the GC cell lines sensitive to CKI treatment, we developed the CNScore method to analyze the ceRNA network, revealing that the CKI-GC ceRNA network promotes GC proliferation and metastasis through the PTPRG-AS1/hsa-miR-421/KITLG axis. Finally, we constructed GC cell models with PTPRG-AS1 overexpression or knockdown and GC liver metastasis models and found that PTPRG-AS1 can sponge hsa-miR-421, releasing KITLG and promoting GC proliferation and metastasis through the KITLG/KIT pathway. Taken together, CKI can suppress these malignant phenotypes by regulating the PTPRG-AS1/hsa-miR-421/KITLG axis.

RNA sample optimization for cryo-EM analysis

RNAs play critical roles in most biological processes. Although the three-dimensional (3D) structures of RNAs primarily determine their functions, it remains challenging to experimentally determine these 3D structures due to their conformational heterogeneity and intrinsic dynamics. Cryogenic electron microscopy (cryo-EM) has recently played an emerging role in resolving dynamic conformational changes and understanding structure-function relationships of RNAs including ribozymes, riboswitches and bacterial and viral noncoding RNAs. A variety of methods and pipelines have been developed to facilitate cryo-EM structure determination of challenging RNA targets with small molecular weights at subnanometer to near-atomic resolutions. While a wide range of conditions have been used to prepare RNAs for cryo-EM analysis, correlations between the variables in these conditions and cryo-EM visualizations and reconstructions remain underexplored, which continue to hinder optimizations of RNA samples for high-resolution cryo-EM structure determination. Here we present a protocol that describes rigorous screenings and iterative optimizations of RNA preparation conditions that facilitate cryo-EM structure determination, supplemented by cryo-EM data processing pipelines that resolve RNA dynamics and conformational changes and RNA modeling algorithms that generate atomic coordinates based on moderate- to high-resolution cryo-EM density maps. The current protocol is designed for users with basic skills and experience in RNA biochemistry, cryo-EM and RNA modeling. The expected time to carry out this protocol may range from 3 days to more than 3 weeks, depending on the many variables described in the protocol. For particularly challenging RNA targets, this protocol could also serve as a starting point for further optimizations.

Small RNA and Toll-like receptor interactions: origins and disease mechanisms

Advances in small RNA sequencing have revealed diverse small noncoding RNAs (sncRNAs) beyond microRNAs (miRNAs), derived from transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), small nuclear RNAs (snRNAs), and Y RNAs, carrying distinct RNA modifications. These emerging sncRNAs can function beyond RNA interference (RNAi), adopting aptamer-like roles by interacting with Toll-like receptors 7 and 8 (TLR7 and TLR8) via specific sequences, modifications, and structures. We propose a Sequential Activation Hypothesis where initial abnormal sncRNAs - triggered by infections or stresses - activate TLR7/8, leading to autoantibody production against autoantigens like RNA-binding proteins La and Ro. These autoantibody-antigen complexes further promote secondary immunogenic sncRNA production and repetitive TLR7/8 activation, perpetuating a vicious cycle sustaining autoimmunity. TLR7/8's X chromosome location and sex-biased expression contribute to female-dominant autoimmune diseases. Understanding sncRNA-TLR interactions is essential for designing novel therapeutic strategies.

A guide to the biogenesis and functions of endogenous small non-coding RNAs in animals

Small non-coding RNAs can be categorized into two main classes: structural RNAs and regulatory RNAs. Structural RNAs, which are abundant and ubiquitously expressed, have essential roles in the maturation of pre-mRNAs, modification of rRNAs and the translation of coding transcripts. By contrast, regulatory RNAs are often expressed in a developmental-specific, tissue-specific or cell-type-specific manner and exert precise control over gene expression. Reductions in cost and improvements in the accuracy of high-throughput RNA sequencing have led to the identification of many new small RNA species. In this Review, we provide a broad discussion of the genomic origins, biogenesis and functions of structural small RNAs, including tRNAs, small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), vault RNAs (vtRNAs) and Y RNAs as well as their derived RNA fragments, and of regulatory small RNAs, such as microRNAs (miRNAs), endogenous small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs), in animals.

Porcine jejunal-derived extracellular vesicles participate in the regulation of lipid metabolism

BACKGROUND

Regulating the regional deposition of fat is crucial for improving the carcass characteristics of pigs. The intestine, as an important organ for lipid absorption and homeostasis maintenance, secretes various biological signals that participate in the crosstalk between the intestine and adipose tissue. Extracellular vesicles, as novel extracellular genetic factors that mediate metabolic signal exchange among multiple tissues, have emerged as a hotspot and breakthrough in revealing the mechanisms of physiological homeostasis. However, how extracellular vesicles regulate the intestinal-adipose signaling axis, especially in relation lipid metabolism and deposition is still unclear. Thus, in the current study, intestinal extracellular vesicles from Chinese fat-type piglets of Lantang and typical lean-type piglets of Landrace were isolated and identified, and to reveal the regulatory mechanisms of lipid metabolism via intestinal extracellular vesicles in mediating intestinal-adipose crosstalk.

RESULTS

We isolated and identified intestinal extracellular vesicles from the jejunum of 3-day-old Lantang and Landrace piglets (LT-EVs and LD-EVs) and further investigated their effects on lipid accumulation in porcine primary adipocytes. Compared to LD-EVs, LT-EVs promoted lipid deposition in porcine primary adipocytes, with intestinal-derived miRNAs playing a critical role in the crosstalk between the intestine and adipose tissue. Further analysis of extracellular vesicles-derived miRNA sequencing revealed that miR-30b-5p, enriched in LD-EVs, is involved in the regulation of lipid metabolism. Notably, the enrichment of miR-30b-5p in extracellular vesicles derived from IPEC-J2 cells also influenced lipid metabolism. Mechanistically, the targeted binding of miR-30b-5p and FMO3 may be critical for the extracellular vesicle-mediated regulation of lipid metabolism.

CONCLUSIONS

Our findings suggest that jejunal-derived extracellular vesicles play a critical role in regulating lipid metabolism, and the regulatory effect of extracellular vesicles from obese piglets was higher than that of lean piglets. Furthermore, the different expression of miRNAs, such as miR-30b-5p, in intestinal extracellular vesicles may be the key to determining lipid deposition phenotypes across the two pig breeds.

Targeting Regulatory Noncoding RNAs in Human Cancer: The State of the Art in Clinical Trials

Noncoding RNAs (ncRNAs) are a heterogeneous group of RNA molecules whose classification is mainly based on arbitrary criteria such as the molecule length, secondary structures, and cellular functions. A large fraction of these ncRNAs play a regulatory role regarding messenger RNAs (mRNAs) or other ncRNAs, creating an intracellular network of cross-interactions that allow the fine and complex regulation of gene expression. Altering the balance between these interactions may be sufficient to cause a transition from health to disease and vice versa. This leads to the possibility of intervening in these mechanisms to re-establish health in patients. The regulatory role of ncRNAs is associated with all cancer hallmarks, such as proliferation, apoptosis, invasion, metastasis, and genomic instability. Based on the function performed in carcinogenesis, ncRNAs may behave either as oncogenes or tumor suppressors. However, this distinction is not rigid; some ncRNAs can fall into both classes depending on the tissue considered or the target molecule. Furthermore, some of them are also involved in regulating the response to traditional cancer-therapeutic approaches. In general, the regulation of molecular mechanisms by ncRNAs is very complex and still largely unclear, but it has enormous potential both for the development of new therapies, especially in cases where traditional methods fail, and for their use as novel and more efficient biomarkers. Overall, this review will provide a brief overview of ncRNAs in human cancer biology, with a specific focus on describing the most recent ongoing clinical trials (CT) in which ncRNAs have been tested for their potential as therapeutic agents or evaluated as biomarkers.

Selective deuteration of an RNA:RNA complex for structural analysis using small-angle scattering

The structures of RNA:RNA complexes regulate many biological processes. Despite their importance, protein-free RNA:RNA complexes represent a tiny fraction of experimentally determined structures. Here, we describe a joint small-angle X-ray and neutron scattering (SAXS/SANS) approach to structurally interrogate conformational changes in a model RNA:RNA complex. Using SAXS, we measured the solution structures of the individual RNAs and of the overall RNA:RNA complex. With SANS, we demonstrate, as a proof of principle, that isotope labeling and contrast matching (CM) can be combined to probe the bound state structure of an RNA within a selectively deuterated RNA:RNA complex. Furthermore, we show that experimental scattering data can validate and improve predicted AlphaFold 3 RNA:RNA complex structures to reflect its solution structure. Our work demonstrates that in silico modeling, SAXS, and CM-SANS can be used in concert to directly analyze conformational changes within RNAs when in complex, enhancing our understanding of RNA structure in functional assemblies.

Autoregulation of RPL7B by inhibition of a structural splicing enhancer

Yeast ribosomal protein gene RPL7B is autoregulated by inhibition of splicing. The first intron has a "zipper stem" that brings the 5' splice site near the branch point and serves as an enhancer of splicing that is required for efficient splicing because it has non-consensus branch point sequence of UGCUAAC. The intron also contains an alternative, and mutually exclusive, structure that is conserved across many yeast species. That conserved structure is a binding site for the Rpl7 protein so that when the protein is in excess over what is required for ribosomes, the protein binds to the conserved structure which eliminates the enhancer structure and represses splicing and gene expression.

Plasma-Derived Exosomal i-tRF-LeuCAA as Biomarker for Glioma Diagnosis and Promoter of Epithelial-Mesenchymal Transition via TPM4 Regulation

AIMS

This study aimed to discover plasma-derived exosomal tsRNAs that serve as novel diagnostic biomarkers for glioma and to investigate the mechanism by which tsRNAs regulate glioma development.

METHODS

Differentially expressed tsRNAs in the plasma exosomes of glioma patients were identified using small RNA array sequencing. Bioinformatics analyses were used to predict the biological function of tsRNAs. The changes in the phenotypes of glioma cells treated with a tsRNA mimic and inhibitor were detected. The diagnostic and prognostic characteristics of potential target genes and their related functions in gliomas were further analyzed. The cell and animal experiments were used to analyze the molecular mechanisms.

RESULTS

Among the 453 differentially expressed tsRNAs identified in the plasma-derived exosomes of glioma patients using small RNA sequencing, i-tRF-LeuCAA was associated with the prognosis and molecular diagnostic characteristics of glioma patients and promoted the migration, invasion, and proliferation of glioma cells and inhibited their apoptosis. In addition, TPM4 is a potential target of i-tRF-LeuCAA and is related to epithelial-mesenchymal transition in gliomas.

CONCLUSIONS

i-tRF-LeuCAA could be served as a non-invasive biomarker in the diagnosis and prognosis of glioma. i-tRF-LeuCAA may indirectly regulate TPM4 expression and influence epithelial-mesenchymal transition, which may promote glioma progression.

Flavin adenine dinucleotide (FAD) as a non-canonical RNA cap: Mechanisms, functions, and emerging insights

Flavin adenine dinucleotide (FAD), a versatile metabolic cofactor, is emerging as an important non-canonical RNA cap across various life domains. This review explores FAD's dual role as a coenzyme and an RNA modifier, focusing on its incorporation as a 5' cap structure during transcription initiation and its subsequent implications for RNA metabolism and cellular functions. A comprehensive view of the mechanisms underlying FAD capping and decapping is presented, highlighting key enzymes that play a role in these processes. FAD-capped RNA is shown to play critical roles in viral replication, as demonstrated in the Hepatitis C virus, where FAD capping supports cellular immune evasion. Analytical techniques, including mass spectrometry and innovative sequencing methodologies, have advanced our understanding of the flavin cap, enabling its identification and quantification in different biological systems. This review underscores the significance of FAD-RNA capping as a novel regulatory mechanism, proposes innovative methodologies for its study, and emphasizes its potential therapeutic applications in viral and cellular biology.

LncRNA-miRNA interplay regulate intestinal regeneration in the sea cucumber Apostichopus japonicus

The sea cucumber Apostichopus japonicus, renowned for its remarkable ability to expel and regenerate its internal organs within weeks, serves as a model organism for regeneration research. However, studies on the role of non-coding RNAs, particularly long non-coding RNA (lncRNA), in intestinal regeneration remain limited. In this study, we identified and performed differential expression analysis of lncRNAs in both normal intestines and intestines at 3 days post evisceration (dpe). A total of 2361 lncRNAs were identified, 183 of which were differentially expressed (DE-lncRNAs). The genes targeted by these lncRNAs, either cis- or trans-acting, were involved in oxidative stress, immune response, extracellular matrix remodeling, and energy metabolism during intestinal regeneration. Notably, MSTRG.6200/miR-7847-3p and MSTRG.18440/miR-4220-5p have been confirmed as interacting lncRNA-miRNA pairs. These results suggest that lncRNAs are key regulators of intestinal regeneration in A. japonicus, offering new insights into the underlying mechanisms and potential targets for enhancing regeneration.

fpocketR: A platform for identification and analysis of ligand-binding pockets in RNA

Small molecules that bind specific sites in RNAs hold promise for altering RNA function, manipulating gene expression, and expanding the scope of druggable targets beyond proteins. Identifying binding sites in RNA that can engage ligands with good physicochemical properties remains a significant challenge. fpocketR is a software package for identifying, characterizing, and visualizing ligand-binding sites in RNA. fpocketR was optimized, through comprehensive analysis of currently available RNA-ligand complexes, to identify pockets in RNAs able to bind small molecules possessing favorable properties, generally termed drug-like. Here, we demonstrate use of fpocketR to analyze RNA-ligand interactions and novel pockets in small and large RNAs, to assess ensembles of RNA structure models, and to identify pockets in dynamic RNA systems. fpocketR performs best with RNA structures visualized at high (≤3.5 Å) resolution, but also provides useful information with lower resolution structures and computational models. fpocketR is a powerful, freely available tool for discovery and analysis of ligand-binding pockets in RNA molecules.

Decoding plant thermosensors: mechanism of temperature perception and stress adaption

Global climate change, characterized by increased frequency and intensity of extreme temperature events, poses significant challenges to plant survival and crop productivity. While considerable research has elucidated plant responses to temperature stress, the molecular mechanisms, particularly those involved in temperature sensing, remain incompletely understood. Thermosensors in plants play a crucial role in translating temperature signals into cellular responses, initiating the downstream signaling cascades that govern adaptive processes. This review highlights recent advances in the identification and classification of plant thermosensors, exploring their physiological roles and the biochemical mechanisms by which they sense temperature changes. We also address the challenges in thermosensor discovery and discuss emerging strategies to uncover novel thermosensory mechanisms, with implications for improving plant resilience to temperature stress in the face of a rapidly changing climate.

Deletion of an sRNA primes development in a multicellular bacterium

Small non-coding RNAs (sRNAs) regulate gene expression of many biological processes. During growth, some myxobacteria produce an sRNA-Pxr-that blocks fruiting-body development, an aggregative multicellular process typically triggered by starvation. Deleting the pxr gene allows Myxococcus xanthus to develop despite nutrient availability, but Pxr binding targets and the genes regulated by Pxr remain unknown. Here, after showing that Pxr controls the temporal dynamics of development, we compare the transcriptomes of vegetative M. xanthus cells possessing vs. lacking pxr. Over half of the genes impacted by pxr deletion are linked to development, including known and previously undiscovered critical regulators. Pxr also positively regulates genes associated with general metabolic processes. Our study discovers phenotypic effects of Pxr regulation with ecological importance, identifies the suite of genes this sRNA controls during vegetative growth and reveals a previously unknown developmental regulator. These findings provide insights into the molecular mechanism controlling myxobacterial development.

Improving Aptamer Affinity and Determining Sequence-Activity Relationships via Motif-SELEX

The affinity of nucleic acid aptamers isolated in vitro via Systematic Evolution of Ligands by Exponential Enrichment (SELEX) is often limited because the entire potential sequence space cannot be screened. In this study, we introduce Motif-SELEX, a novel method that enables the optimization of existing underperforming aptamers by generating libraries that broadly represent both the sequence and length variations of the parent sequence. This approach enables the isolation of sequences with improved affinity without the biases and limitations of traditional mutagenesis methods like doped SELEX and error-prone PCR. As a demonstration, we applied Motif-SELEX to a DNA-based morphine aptamer and a 2' fluoro- and methoxy-RNA-based apixaban aptamer, discovering new, better-performing sequences with differing random domain lengths from their parents and up to 10-fold improvements in affinity. These new sequences would be inaccessible to traditional post-SELEX methods. Critically, our analysis of Motif-SELEX pools also enabled us to identify sequence and structural elements crucial for target binding and to predict secondary and tertiary structures for a given aptamer family─even when those structures involve noncanonical nucleotide interactions. We believe that Motif-SELEX offers an effective and generalizable solution for optimizing the structure and binding properties of functional nucleic acid molecules for diverse applications.

Influence of Magnesium Ions and Crowding Agents on Structure and Stability of RNA Aptamers

Aptamers bind to their targets with exceptional affinity and specificity. However, their intracellular application is hampered by the lack of knowledge about the effect of the cellular milieu on the RNA structure/stability. In this study, cellular crowding was mimicked using polyethylene glycol (PEG), and the crucial role of Mg2+ ions in stabilizing the structure of an RNA aptamer was investigated. Increasing the concentration of Mg2+ or PEG increased the thermal stability of the aptamer. The crowding effect lowered the requirement of the Mg2+ ion to form the binding-competent conformer of the aptamer. This suggests that crowding and other factors may compensate for a lower concentration of Mg2+ for proper folding of aptamers inside cells. Selective 2'-hydroxyl acylation and primer extension (SHAPE) probing permitted residue-level analysis of the aptamer. Mg2+ and/or PEG were shown to be involved in increasing the rigidity or flexibility of different regions of the aptamer. Fluorescence correlation spectroscopy showed a significantly low hydrodynamic radius (RH) in the presence of molecular crowders and Mg2+ ions. We believe that the decreased water activity due to crowding may be responsible for reduced RH. Our results show that in a crowded environment, the RNA aptamer was exposed to conformers that were not available to it in simple buffer solutions or solely in the presence of lower concentrations of Mg2+.

o8G-modified circPLCE1 inhibits lung cancer progression via chaperone-mediated autophagy

BACKGROUND

Lung cancer poses a serious threat to human health, but its molecular mechanisms remain unclear. Circular RNAs (circRNAs) are closely associated with tumour progression, and the important role of 8-oxoguanine (o8G) modification in regulating the fate of RNA has been gradually revealed. However, o8G modification of circRNAs has not been reported. We identified circPLCE1, which is significantly downregulated in lung cancer, and further investigated the o8G modification of circPLCE1 and the related mechanism in lung cancer progression.

METHODS

We identified differentially expressed circRNAs by RNA high-throughput sequencing and then conducted methylated RNA immunoprecipitation (MeRIP), immunofluorescence (IF) analysis, crosslinking immunoprecipitation (CLIP) and actinomycin D (ActD) assays to explore circPLCE1 o8G modification. The biological functions of circPLCE1 in vivo and in vitro were clarified via establishing a circPLCE1 silencing/overexpression system. Tagged RNA affinity purification (TRAP), RNA Immunoprecipitation (RIP) and coimmunoprecipitation (Co-IP) assays, and pSIN-PAmCherry-KFERQ-NE reporter gene were used to elucidate the molecular mechanism by which circPLCE1 inhibits lung cancer progression.

RESULTS

This study revealed that reactive oxygen species (ROS) can induce circPLCE1 o8G modification and that AUF1 can mediate a decrease in circPLCE1 stability. We found that circPLCE1 significantly inhibited lung cancer progression in vitro and in vivo and that its expression was associated with tumour stage and prognosis. The molecular mechanism was elucidated: circPLCE1 targets the HSC70 protein, increases its ubiquitination level, regulates ATG5-dependent macroautophagy via the chaperone-mediated autophagy (CMA) pathway, and ultimately inhibits lung cancer progression.

CONCLUSION

o8G-modified circPLCE1 inhibits lung cancer progression through CMA to inhibit macroautophagy and alter cell fate. This study provides not only a new theoretical basis for elucidating the molecular mechanism of lung cancer progression but also potential targets for lung cancer treatment.

LncRNAs Ride the Storm of Epigenetic Marks

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

Comprehensive benchmarking of large language models for RNA secondary structure prediction

In recent years, inspired by the success of large language models (LLMs) for DNA and proteins, several LLMs for RNA have also been developed. These models take massive RNA datasets as inputs and learn, in a self-supervised way, how to represent each RNA base with a semantically rich numerical vector. This is done under the hypothesis that obtaining high-quality RNA representations can enhance data-costly downstream tasks, such as the fundamental RNA secondary structure prediction problem. However, existing RNA-LLM have not been evaluated for this task in a unified experimental setup. Since they are pretrained models, assessment of their generalization capabilities on new structures is a crucial aspect. Nonetheless, this has been just partially addressed in literature. In this work we present a comprehensive experimental and comparative analysis of pretrained RNA-LLM that have been recently proposed. We evaluate the use of these representations for the secondary structure prediction task with a common deep learning architecture. The RNA-LLM were assessed with increasing generalization difficulty on benchmark datasets. Results showed that two LLMs clearly outperform the other models, and revealed significant challenges for generalization in low-homology scenarios. Moreover, in this study we provide curated benchmark datasets of increasing complexity and a unified experimental setup for this scientific endeavor. Source code and curated benchmark datasets with increasing complexity are available in the repository: https://github.com/sinc-lab/rna-llm-folding/.

Chimerism: A whole new perspective in gene regulation

The diversity of molecular entities emerging from a single gene are recognized. Several studies have thus established the cellular role(s) of transcript variants and protein isoforms. A step ahead in challenging the central dogma towards expanding molecular diversity is the identification of fusion genes, chimeric transcripts and chimeric proteins that harbor sequences from more than one gene. The mechanisms for generation of chimeras largely follow similar patterns across all levels of gene regulation but also have interdependence and mutual exclusivity. Whole genome and RNA-seq technologies supported by development of computational algorithms and programs for processing datasets have increasingly enabled the identification of fusion genes and chimeric transcripts, while the discovery of chimeric proteins is as yet more subtle. Earlier thought to be associated with cellular transformation, the contribution of chimeric molecules to normal physiology is also realized and found to influence the expression of their parental genes and regulate cellular pathways. This review offers a collective and comprehensive overview of cellular chimeric entities encompassing the mechanisms involved in their generation, insights on their evolution, functions in gene regulation and their current and novel clinical applications.

Non-coding RNAs as mediators of epithelial to mesenchymal transition in metastatic colorectal cancers

Colorectal cancer (CRC) remains a leading cause of cancer-related mortality globally, necessitating the development of innovative treatment strategies. Recent research has underscored the significant role of non-coding RNAs (ncRNAs) in CRC pathogenesis, offering new avenues for diagnosis and therapy. In this review, we delve into the intricate roles of various ncRNAs, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), in CRC progression, epithelial-mesenchymal transition (EMT), metastasis, and drug resistance. We highlight the interaction of these ncRNAs with and regulation of key signaling pathways, such as Wnt/β-catenin, Notch, JAK-STAT, EGFR, and TGF-β, and the functional relevance of these interactions in CRC progression. Additionally, the review highlights the emerging applications of nanotechnology in enhancing the delivery and efficacy of ncRNA-based therapeutics, which could address existing challenges related to specificity and side effects. Future research directions, including advanced diagnostic tools, targeted therapeutics, strategies to overcome drug resistance, and the integration of personalized medicine approaches are discussed. Integrating nanotechnology with a deeper understanding of CRC biology offers the potential for more effective, targeted, and personalized strategies, though further research is essential to validate these approaches.

Urine exosomal lncRNAs as novel biomarkers for early diagnosis of bladder cancer based on microarray differential expression profiling

PurposeWe aimed to exploit a urine exosomal long non-coding RNAs (lncRNAs) fingerprint to facilitate the early diagnosis of bladder cancer.MethodsMicroarray differential expression profiling of lncRNAs was for the first time employed in urine exosomes from 10 non-muscle-invasive bladder cancer (NMIBC) patients and 10 healthy controls to screen out candidate exosomal lncRNA biomarkers, which were then verified by quantitative real-time polymerase chain reaction in three independent phases including bladder cancer cells, culture fluid and 200 NMIBC participants. Logistic regression was performed to construct a diagnostic model-the diagnostic potency of which was assessed.ResultsThe profile of three exosome-derived lncRNAs (CCDC148-AS1, XLOC_006419, and RP5-1148A21.3) was screened and further verified to be notably over-expressed in NMIBC patients and bladder cancer cell lines, and exhibited area under the receiver-operating characteristic curve values of 0.873, 0.825, and 0.834, respectively, in training, validation, and double-blind validation phases. The profile was superior to urinary cytology in discriminating NMIBC from healthy controls (P < 0.0001). A significant correlation existed between a higher level of CCDC148-AS1 and a higher tumor grade (P < 0.001), and up-regulated CCDC148-AS1 as well as XLOC_006419 were statistically related with tumor node metastasis stage (P = 0.004 and P = 0.031, respectively). These three identified lncRNAs were confirmed to originate from bladder cancer cells and be packaged within exosomes, thus staying sufficiently stable in urine.ConclusionsTumor-originated urine exosomal lncRNAs, as fingerprint in NMIBC, exhibited satisfying clinical significance in early diagnosis of bladder cancer.

Small Nucleolar RNAs and the Brain: Growing Evidence Supporting Their Role in Psychiatric Disorders

Noncoding RNAs comprise most of the transcriptome and represent an emerging area of research. Among them, small nucleolar RNAs (snoRNAs) have emerged as a promising target because they have been associated with the development and evolution of several diseases, including psychiatric disorders. snoRNAs are expressed in the brain, with some showing brain-specific expression that indicates specific roles in brain development, function, and dysfunction. However, the role of snoRNAs in conditions that affect the brain needs further investigation to be better understood. This scoping review summarizes existing literature on studies that have investigated snoRNAs in psychiatry and offers insight into potential pathophysiological mechanisms to be further investigated in future research.

Consistent features observed in structural probing data of eukaryotic RNAs

Understanding RNA structure is crucial for elucidating its regulatory mechanisms. With the recent commercialization of messenger RNA vaccines, the profound impact of RNA structure on stability and translation efficiency has become increasingly evident, underscoring the importance of understanding RNA structure. Chemical probing of RNA has emerged as a powerful technique for investigating RNA structure in living cells. This approach utilizes chemical probes that selectively react with accessible regions of RNA, and by measuring reactivity, the openness and potential of RNA for protein binding or base pairing can be inferred. Extensive experimental data generated using RNA chemical probing have significantly contributed to our understanding of RNA structure in cells. However, it is crucial to acknowledge potential biases in chemical probing data to ensure an accurate interpretation. In this study, we comprehensively analyzed transcriptome-scale RNA chemical probing data in eukaryotes and report common features. Notably, in all experiments, the number of bases modified in probing was small, the bases showing the top 10% reactivity well reflected the known secondary structure, bases with high reactivity were more likely to be exposed to solvent and low reactivity did not reflect solvent exposure, which is important information for the analysis of RNA chemical probing data.

The Role of Non-Coding RNA in Systemic Sclerosis: From Mechanism to Translation

Systemic sclerosis (SSc) is a chronic autoimmune disease characterized by imbalanced immunity, vasculopathy, and excessive fibrosis. The etiology and pathology of this disease remain to be fully elucidated. Genetic predisposition, along with epigenetic modifications are widely considered to significantly affect its development. Among the components of epigenetics, non-coding RNAs (ncRNAs), comprising various types such as microRNA, long ncRNA, circular RNA, and others, play a crucial role. These ncRNAs perform several functions in the development of SSc and can potentially be employed as new targets for its diagnosis and treatment. This review discusses the roles of ncRNAs in the three primary pathological hallmarks-vasculopathy, imbalanced immunity, and excessive fibrosis-of SSc and highlights research progress in the role of RNAs in translational medicine against SSc. The review also provides a comprehensive outline of the key function of ncRNAs in SSc.

Curcumin Inhibits the Development of Pancreatic Cancer by Targeting the circ_0079440/miR-522-3p/EIF4A1 Pathway

Pancreatic cancer (PC) is a common gastrointestinal cancer with high invasiveness and high mortality. Curcumin is a natural polyphenol with anti-tumor activity against different cancers, including PC. Curcumin has been verified to mediate the expression of circular RNAs (circRNAs) to inhibit tumor development. This study aimed to explore the function and regulatory mechanism of curcumin on circ_0079440 in PC. PC cells were treated with different concentrations of curcumin (0, 5, 10 or 15 μM) for 24 h. Gene expression in PC cells and tissues was detected using RT-qPCR. Cell malignant phenotypes were determined by functional assays. The levels of EMT-related proteins were tested using western blot. RNA interaction was determined using RNA pulldown assay, luciferase reporter assay and RIP assay. The results showed that curcumin suppressed cell proliferative, migratory, and invasive capabilities, and weakened epithelial-mesenchymal transition (EMT) in a concentration-dependent way. Circ_0079440 was expressed at a high level in PC and its level was reduced via curcumin administration in PC cells. Rescue assays showed that circ_0079440 overexpression reversed the suppressive effects of curcumin on PC cell malignant phenotypes. Furthermore, in the xenograft mouse models, curcumin treatment inhibited tumor growth and metastasis, and circ_0079440 upregulation reversed the function of curcumin. Additionally, circ_0079440 was revealed to bind to miR-522-3p to upregulate eukaryotic initiation factor 4A1 (EIF4A1) expression in PC cells. EIF4A1 expression was also downregulated by curcumin, and EIF4A1 overexpression abolished the suppressive functions of curcumin. Moreover, EIF4A overexpression or miR-522-3p inhibition counteracted the anti-tumor effects of circ_0079440 depletion on PC development. To sum up, curcumin suppresses PC development by targeting the circ_0079440/miR-522-3p/EIF4A1 pathway, which might provide novel therapeutic targets for treatment of PC.

The lncRNA MIR181A1HG in extracellular vesicles derived from highly metastatic colorectal cancer cells promotes liver metastasis by remodeling the extracellular matrix and recruiting myeloid-derived suppressor cells

BACKGROUND

Colorectal liver metastasis (CRLM) is the main cause of death in colorectal cancer (CRC) patients worldwide. In the initial stage of metastasis, primary tumors provide the necessary conditions for metastasis by shaping the local microenvironment of the target organ, forming "premetastatic niches" (PMNs), and extracellular vesicles (EVs) play important roles in shaping PMNs. Therefore, investigating the EVs involved in the regulation of PMNs and their mechanism is highly valuable for the further understanding of CRLM.

METHODS

Transmission electron microscopy and differential ultracentrifugation were used to verify the existence of exosomes. In vivo and in vitro assays were used to identify the roles of MIR181A1HG in EVs in CRLM. RNA pull-down and dual-luciferase reporter assays were used to clarify the mechanism by which MIR181A1HG in EVs regulated the crosstalk between CRC cells and hepatic stellate cells (HSCs).

RESULTS

We demonstrated that the lncRNA MIR181A1HG was progressively upregulated in tissues, serum EVs from healthy normal controls to CRC and paired liver metastatic groups. Additionally, we verified that HNRNPA2B1 mediated the packaging of MIR181A1HG into CRC cell-derived EVs, which in turn functioned as a ceRNA by sponging miR373-3p to activate HSCs via the TGFβRII/Smad2/3 signaling pathway. Furthermore, activated HSCs could secrete the chemokine CXCL12 to promote CRLM by remodeling the extracellular matrix and recruiting myeloid-derived suppressor cells in the liver, which resulted in liver metastasis.

CONCLUSIONS

MIR181A1HG in EVs from highly metastatic CRC cells promoted CRLM by activating HSCs to form PMNs in the liver, which contributes to the further understanding of the mechanism of CRLM and provides potential predictive markers for CRLM.

Accurate Physics-Based Prediction of Binding Affinities of RNA- and DNA-Targeting Ligands

Accurate prediction of the affinity of ligand binding to nucleic acids represents a formidable challenge for current computational approaches. This limitation has hindered the use of computational methods to develop small-molecule drugs that modulate the activity of nucleic acids, including those associated with anticancer, antiviral, and antibacterial effects. In recent years, significant scientific and technological advances as well as easier access to compute resources have contributed to free-energy perturbation (FEP) becoming one of the most consistently reliable approaches for predicting relative binding affinities of ligands to proteins. Nevertheless, FEP's applicability to nucleic-acid targeting ligands has remained largely undetermined. In this work, we present a systematic assessment of the accuracy of FEP, as implemented in FEP+ software and facilitated by the OPLS4 force field, in predicting relative binding free energies of congeneric series of ligands interacting with a variety of DNA/RNA systems. The study encompassed more than 100 ligands exhibiting diverse binding modes, some partially exposed and others deeply buried. Using a consistent simulation protocol, more than half of the predictions are within 1 kcal/mol of the experimentally measured values. Across the data set, we report a combined average pairwise root-mean-square-error of <1.4 kcal/mol, which falls within one log unit of the experimentally measured dissociation constants. These results suggest that FEP+ has sufficient accuracy to guide the optimization of lead series in drug discovery programs targeting RNA and DNA.

Bidirectional Interplay Among Non-Coding RNAs, the Microbiome, and the Host During Development and Diseases

It is widely known that the dysregulation of non-coding RNAs (ncRNAs) and dysbiosis of the gut microbiome play significant roles in host development and the progression of various diseases. Emerging evidence has highlighted the bidirectional interplay between ncRNAs and the gut microbiome. This article aims to review the current understanding of the molecular mechanisms underlying the crosstalk between ncRNAs, especially microRNA (miRNA), and the gut microbiome in the context of development and diseases, such as colorectal cancer, inflammatory bowel diseases, neurological disorders, obesity, and cardiovascular disease. Ultimately, this review seeks to provide a foundation for exploring the potential roles of ncRNAs and gut microbiome interactions as biomarkers and therapeutic targets for clinical diagnosis and treatment, such as ncRNA mimics, antisense oligonucleotides, and small-molecule compounds, as well as probiotics, prebiotics, and diets.

The role of noncoding RNAs in bacterial immunity

The evolutionary arms race between bacteria and phages has driven the development of diverse anti-phage defense mechanisms. Recent studies have identified noncoding RNAs (ncRNAs) as key players in bacteria-phage conflicts, including CRISPR-Cas, toxin-antitoxin (TA), and reverse transcriptase (RT)-based defenses; however, our understanding of their roles in immunity is still emerging. In this review, we explore the multifaceted roles of ncRNAs in bacterial immunity, offering insights into their contributions to defense and anti-defense mechanisms, their influence on immune regulatory networks, and potential biotechnological applications. Finally, we highlight key outstanding questions in the field to spark future research directions.

A Case-Control Study of the Association Between GSTP1 Gene Polymorphisms (rs1695 and rs1138272) and the Susceptibility to Male Infertility in the Moroccan Population

Background: Infertility affects 10-15% of couples worldwide, with male factors accounting for half of cases. Environmental, behavioral, and genetic problems contribute to spermatogenic failure in 30% of idiopathic male infertility cases. Other factors, such as oxidative stress (OS), cause impaired spermatogenesis, abnormal sperm morphology, and reduced motility, eventually triggering male infertility. In the male reproductive tract, glutathione S-transferase (GST) family antioxidants are essential for preventing OS, detoxification, and DNA damage protection. Methods: GSTP1 isoenzyme, one of GST members, has previously been linked to male infertility, and this case-control study is the first to assess the possible association of GSTP1 gene polymorphisms (rs1695 and rs1138272) with nonobstructive azoospermia and severe oligospermia within 300 patients and 300 controls from the Moroccan population using an allele-specific PCR. The statistical analysis was performed with the R programming language. Results: Genotyping of GSTP1 polymorphisms fitted the Hardy-Weinberg equilibrium in both cases and controls (p > 0.05), but no significant association was found in rs1695 (odds ratio [OR] = 1.238, 95% confidence interval [CI] = 0.855 to 1.794, p = 0.258, power = 0.204) and in rs1138272 (OR = 1.192, 95% CI = 0.852 to 0.1668, p = 0.304, power = 0.176). Likewise, results from haplotype analysis (OR = 1.25, 95% CI = 0.61 to 2.57, p = 0.537) and SNP-SNP interactions (OR = 1.522, 95% CI = 0.838 to 2.762, p = 0.166) demonstrated no correlation with the risk of male infertility. Conclusion: The two SNPs (rs1695 and rs1138272) of the GSTP1 gene loci are not associated with male infertility susceptibility in Moroccan subjects. Yet, future investigations with a larger sample size may conclusively help to confirm this association.

Metabolic resistance to pyrethroids with possible involvement of non-coding ribonucleic acids in Anopheles funestus, the major malaria vector in western Kenya

BACKGROUND

The resurgence of Anopheles funestus, a dominant vector of human malaria in western Kenya was partly attributed to insecticide resistance. However, evidence on the molecular basis of pyrethroid resistance in western Kenya is limited. Here, we reported metabolic resistance mechanisms and demonstrated that multiple non-coding Ribonucleic Acids (ncRNAs) could play a potential role in An. funestus resistance to pyrethroid in western Kenya. Anopheles funestus mosquitoes were sampled using aspiration methods in Bungoma, Teso, Siaya, Port Victoria and Kombewa in western Kenya. The F1 progenies were exposed to deltamethrin (0.05%), permethrin (0.75%), DDT (4%) and pirimiphos-methyl (0.25%) following WHO test guidelines. A synergist assay using piperonyl butoxide (PBO) (4%) was conducted to determine cytochrome P450s' role in pyrethroid resistance. RNA-seq was conducted on a combined pool of specimens that were resistant and unexposed, and the results were compared with those of the FANG susceptible reference strain. This approach aimed to uncover the molecular mechanisms underlying the observed phenotypic pyrethroid resistance.

RESULTS

Pyrethroid resistance was observed in all sites with an average mortality rate (MR) of 57.6%. Port Victoria had the highest level of pyrethroid resistance to permethrin (MR = 53%) and deltamethrin (MR = 11%. Teso had the lowest level of resistance to permethrin (MR = 70%) and deltamethrin (MR = 87%). Resistance to DDT was observed only in Kombewa (MR = 89%) and Port Victoria (MR = 85%). A full susceptibility to P-methyl (0.25%) was observed in all sites. PBO synergist assay revealed high susceptibility (> 98%) to pyrethroids in all the sites except for Port Victoria (MR = 96%). Whole transcriptomic analysis showed that most gene families associated with pyrethroid resistance comprised non-coding RNAs (67%), followed by immunity proteins (10%), cytochrome P450s (6%), cuticular proteins (5%), olfactory proteins (4%), glutathione S-transferases (3%), UDP-glycosyltransferases (2%), ATP-binding cassettes (2%) and carboxylesterases (1%).

CONCLUSION

This study unveils the molecular basis of insecticide resistance in An. funestus in western Kenya, highlighting for the first time the potential role of non-coding RNAs alongside metabolic detoxification in pyrethroid resistance. Targeting non-coding RNAs for intervention development could help in insecticide resistance management.

Functional RNA mining using random high-throughput screening

Functional RNA participates in various life processes in cells. However, there is currently a lack of effective methods to screen for functional RNA. Here, we developed a technology named random high-throughput screening (rHTS). rHTS uses a random library of ∼250-nt synthesized RNA fragments, with high uniformity and abundance. These fragments are circularized into circular RNA by an auto-cyclizing ribozyme to improve their stability. Using rHTS, we successfully screened and identified three RNA fragments contributing significantly to the growth of Escherichia coli, one of which possesses coding potential. Moreover, we found that two noncoding RNAs (ncRNAs) effectively inhibited the growth of E. coli, in vivo rather than in vitro. Subsequently, we applied the rHTS to a coenzyme-dependent screening platform. In this context, two ncRNAs were identified that could effectively promote the conversion from NADPH to NADP+. Exogenous expression of these two ncRNAs was able to increase the conversion rate of glycerol dehydrogenase from glycerol to 1,3-dihydroxyacetone from 18.3% to 21.8% and 23.2%, respectively. These results suggest that rHTS is a powerful technology for functional RNA mining.

Genomic analysis and antibiotic resistance of a multidrug-resistant bacterium isolated from pharmaceutical wastewater treatment plant sludge

Pharmaceutical wastewater treatment plants (PWWTPs) serve as reservoirs for antibiotic-resistant bacteria (ARBs) and antibiotic resistance genes (ARGs). In this study, a multiantibiotic-resistant strain of Acinetobacter lwoffii (named N4) was isolated from the dewatered sludge of a PWWTP. N4 exhibited high resistance to both antibiotics and metals, with minimum inhibitory concentrations (MICs) of chloramphenicol and cefazolin reaching 1024 mg·L-1 and MICs of Cu2+ and Zn2+ reaching 512 mg·L-1. Co-sensitization experiments revealed that when antibiotics are co-existing with heavy metal ions (such as TET and Cd2+, AMP and Cu2+) could enhance the resistance of N4 to them. Whole-genome sequencing of N4 revealed a genome size of 0.37 Mb encoding 3359 genes. Among these, 23 ARGs were identified, including dfrA26, bl2beCTXM, catB3, qnrB, rosB, tlrC, smeD, smeE, mexE, ceoB, oprN, acrB, adeF, ykkC, ksgA and sul2, which confer resistance through mechanisms such as efflux pumps, enzyme modification and target bypass. Additionally, the N4 genome contained 187 genes associated with human disease and 249 virulence factors, underscoring its potential pathogenicity. Overall, this study provides valuable insights into ARBs in PWWTPs and highlights the potential risks posed by multidrug-resistant strains such as N4.

Adipose tissue macrophages-derived exosomal MiR-500a-5p under high glucose promotes adipocytes inflammation by suppressing Nrf2 expression

BACKGROUND

Type 2 diabetes (T2DM) is a chronic metabolic disorder characterized by insulin resistance and chronic inflammation. Adipose tissue macrophages (ATMs), central players in mediating pro-inflammatory responses within adipose tissue, have been shown to influence insulin sensitivity through exosome secretion. While the role of macrophages-derived exosomal miRNA has been studied in various diseases, their pathogenic roles in T2DM, particularly ATMs-derived exosomal miRNA in adipose tissue inflammation, remain underexplored.

OBJECTIVES

This study focuses specifically on T2DM, investigating the role of ATM-derived exosomal miRNAs in adipose tissue inflammation, a critical factor in the pathogenesis of T2DM.

METHODS

ATM were isolated from visceral adipose tissues in patients with or without diabetes. Differentially expressed miRNAs in ATM-derived exosomes were predicted by high-throughput RNA sequencing. The RAW264.7 macrophages and 3T3-L1 preadipocytes was selected as a model system. Quantitative RT-PCR was used to assess miR-500a-5p expression. The direct binding of miR-500a-5p to Nrf2 mRNA 3' UTR was verified by dual luciferase assay.

RESULTS

MiR-500a-5p was also enriched in the exosomes of high-glucose-treated macrophages. Furthermore, these exosomes induced high expression of miR-500a-5p and activation of the NLRP3 inflammasome in adipocytes when co-cultured with them. Additionally, the reduction of miR-500a-5p expression in macrophages by using a miR-500a-5p inhibitor ameliorated the pro-inflammatory properties of the exosomes, and co-culturing these exosomes with adipocytes resulted in decreased expression of NLRP3 inflammasome-associated proteins in adipocytes. In contrast, induction of miR-500a-5p expression led to the opposite results. Moreover, the dual-luciferase assay confirmed that miR-500a-5p directly targeted the 3' UTR of Nrf2 mRNA. Unlike miR-500a-5p, Nrf2 exhibited an anti-inflammatory response.

CONCLUSION

The results indicate that ATM-derived exosomal miR-500a-5p promotes NLRP3 inflammasome activation and adipose tissue inflammation through down-regulation of Nrf2 in adipocytes.

LINC02532 by Mediating miR-541-3p/HMGA1 Axis Exerts a Tumor Promoter in Breast cancer

The newly discovered LINC02532 is abnormally expressed in a variety of cancers and promotes cancer progression. The research proposed to discover the biological and molecular mechanisms of LINC02532 in breast cancer (BCa). In the resected BCa tissue samples and adjacent normal tissues, LINC02532, miR-541-3p, and High Mobility Group A1 (HMGA1) levels were determined. Cell function experiments were carried out on the premise of cell transfection with relevant plasmids. Based on that, the influence of LINC02532, miR-541-3p, and HMGA1 on MCF-7 cell activities (proliferation, migration, invasion, cell cycle, and apoptosis) was determined, as well as on EMT. Additionally, animal experiments were allowed to support cell experimental conclusions on LINC02532. Finally, the mechanistic network of LINC02532, miR-541-3p, and HMGA1 was identified. It was BCa tissues highly expressing LINC02532 and HMGA1, while lowly expressing miR-541-3p. Functionally, LINC02532 depletion repressed the activities and EMT process of MCF-7 cells. Silencing LINC02532 delayed tumor growth in mice. In terms of mechanism, LINC02532 mainly existed in the cytoplasm and could mediate HMGA1 expression by absorbing miR-541-3p. The findings offer new insights into the molecular mechanisms of LINC02532 in BCa and, more importantly, new strategies for the clinical treatment of BCa.

Out-of-Equilibrium ceRNA Crosstalk

Among non-coding RNAs, microRNAs are pivotal post-transcriptional regulators of gene expression in higher eukaryotes. Through a titration-based mechanism of interaction with their target RNAs, microRNAs can mediate a weak but pervasive form of RNA cross-regulation, as different endogenous RNAs can be effectively coupled by competing for microRNA binding (a phenomenon now known as "crosstalk"). Mathematical modeling has been proven of great help in unraveling many features of these competing endogenous RNA (ceRNA) interactions. However, although many studies have been devoted to the steady-state properties of this indirect regulatory layer, little is known about how the information encoded in frequency, amplitude, duration, and other features of regulatory signals can affect the resulting ceRNA crosstalk picture and hence the overall patterns of gene expression. Here, we focus on such dynamical aspects, with a special emphasis on the encoding and decoding of time-dependent signals.

Epigenetically Regulating Non-coding RNAs in Colorectal Cancer: Promises and Potentials

Colorectal cancer (CRC) is a common malignancy with high mortality. Despite advancements in understanding its molecular causes and improved drug therapies, patient survival rates remain low. The main reasons for the high mortality rate are cancer metastasis and the emergence of drug-resistant cancer cell populations. While genetic changes are recognized as the main driver of CRC occurrence and progression, recent studies suggest that epigenetic regulation is a crucial marker in cancer, influencing the interplay between genetics and the environment. Research has shown the significant regulatory roles of non-coding RNAs (ncRNAs) in CRC development. This review explores epigenetically regulated ncRNAs and their functions, aiming to understand key regulatory mechanisms that impact CRC development. Additionally, it discusses the potential use of these ncRNAs in CRC diagnosis, prognosis, and targeted treatments.

NAALADL2-AS2 functions as a competing endogenous RNA to regulate apoptosis and drug resistance in DLBCL

To explore role of NAALADL2-AS2 as ceRNA in DLBCL. Fluorescence in situ hybridization was used to determine location of NAALADL2-AS2 in cells and to verify its expression in DLBCL tissues. The miRNAs interacting with NAALADL2-AS2 and related regulatory genes were identified by small interfering RNA (siRNA) assay, luciferase reporter assay, fluorescent quantitative polymerase chain reaction, western blotting. DLBCL cells transfected with NAALADL2-AS2 siRNA or control siRNA were treated with doxorubicin, rituximab at different concentrations alone or in combination. The growth curves, drug sensitivity changes of cells before and after transfection were detected by MTT assay, ATP-TCA drug sensitivity test. Cell proliferation was detected by BrdU cell proliferation assay, and apoptosis was detected by Annexin V-fluorescein isothiocyanate/propidium iodide staining. The effects and mechanisms of NAALADL2-AS2 on proliferation, apoptosis, drug resistance of DLBCL cells were studied at cellular level. We confirmed expression of NAALADL2-AS2 in both cytoplasm and nuclei of DLBCL cells. Additionally, we observed elevated levels of NAALADL2-AS2 in DLBCL tissues. We discovered that NAALADL2-AS2 functions as ceRNA to inhibit expression of miR-34a, miR-125a, whereas overexpression of NAALADL2-AS2 indirectly upregulates expression of BCL-2. Interfering with NAALADL2-AS2 promoted apoptosis in DLBCL cells, resulting in approximately a 40% increase in sensitivity to doxorubicin and rituximab. In vivo experiments further confirmed that targeting NAALADL2-AS2 effectively suppressed tumor growth, leading to upregulation of miR-34a and miR-125a, downregulation of BCL-2, and enhanced apoptosis in DLBCL cells, which significantly improved their sensitivity to doxorubicin and rituximab by approximately 50%. These results indicate that NAALADL2-AS2/miR-34a, miR-125a/BCL-2 networks hold promise as therapeutic targets for treatment of DLBCL.

Non-Coding RNAs in Breast Cancer: Diagnostic and Therapeutic Implications

Breast cancer (BC) is one of the most prevalent forms of cancer globally, and has recently become the leading cause of cancer-related mortality in women. BC is a heterogeneous disease comprising various histopathological and molecular subtypes with differing levels of malignancy, and each patient has an individual prognosis. Etiology and pathogenesis are complex and involve a considerable number of genetic alterations and dozens of alterations in non-coding RNA expression. Non-coding RNAs are part of an abundant family of single-stranded RNA molecules acting as key regulators in DNA replication, mRNA processing and translation, cell differentiation, growth, and overall genomic stability. In the context of breast cancer, non-coding RNAs are involved in cell cycle control and tumor cell migration and invasion, as well as treatment resistance. Alterations in non-coding RNA expression may contribute to the development and progression of breast cancer, making them promising biomarkers and targets for novel therapeutic approaches. Currently, the use of non-coding RNAs has not yet been applied to routine practice; however, their potential has been very well studied. The present review is a literature overview of current knowledge and its objective is to delineate the function of diverse classes of non-coding RNAs in breast cancer, with a particular emphasis on their potential utility as diagnostic and prognostic markers or as therapeutic targets and tools.