Search

Fractures continue to be a global economic burden as there are currently no osteoanabolic drugs approved to accelerate fracture healing. In this study, we aimed to develop an osteoanabolic therapy which activates the Wnt/β-catenin pathway, a molecular driver of endochondral ossification. We hypothesize that using an mRNA-based therapeutic encoding β-catenin could promote cartilage to bone transformation formation by activating the canonical Wnt signaling pathway in chondrocytes. To optimize a delivery platform built on recent advancements in liposomal technologies, two FDA-approved ionizable phospholipids, DLin-MC3-DMA (MC3) and SM-102, were used to fabricate unique ionizable lipid nanoparticle (LNP) formulations and then tested for transfection efficacy both in vitro and in a murine tibia fracture model. Using firefly luciferase mRNA as a reporter gene to track and quantify transfection, SM-102 LNPs showed enhanced transfection efficacy in vitro and prolonged transfection, minimal fracture interference and no localized inflammatory response in vivo over MC3 LNPs. The generated β-cateninGOF mRNA encapsulated in SM-102 LNPs (SM-102-β-cateninGOF mRNA) showed bioactivity in vitro through upregulation of downstream canonical Wnt genes, axin2 and runx2. When testing SM-102-β-cateninGOF mRNA therapeutic in a murine tibia fracture model, histomorphometric analysis showed increased bone and decreased cartilage composition with the 45 μg concentration at 2 weeks post-fracture. μCT testing confirmed that SM-102-β-cateninGOF mRNA promoted bone formation in vivo, revealing significantly more bone volume over total volume in the 45 μg group. Thus, we generated a novel mRNA-based therapeutic encoding a β-catenin mRNA and optimized an SM-102-based LNP to maximize transfection efficacy with a localized delivery.

Messenger RNA (mRNA) recruitment to the 40S ribosomal subunit is mediated by eukaryotic initiation factor 4F (eIF4F). This complex includes three subunits: eIF4E (m7G cap-binding protein), eIF4A (DEAD-box helicase), and eIF4G. Mammalian eIF4G is a scaffold that coordinates the activities of eIF4E and eIF4A and provides a bridge to connect the mRNA and 40S ribosomal subunit through its interaction with eIF3. While the roles of many eIF4G binding domains are relatively clear, the precise function of RNA binding by eIF4G remains to be elucidated. In this work, we used an eIF4G-dependent translation assay to reveal that the RNA binding domain (eIF4G-RBD; amino acids 682-720) stimulates translation. This stimulating activity is observed when eIF4G is independently tethered to an internal region of the mRNA, suggesting that the eIF4G-RBD promotes translation by a mechanism that is independent of the m7G cap and mRNA tethering. Using a kinetic helicase assay, we show that the eIF4G-RBD has a minimal effect on eIF4A helicase activity, demonstrating that the eIF4G-RBD is not required to coordinate eIF4F-dependent duplex unwinding. Unexpectedly, native gel electrophoresis and fluorescence polarization assays reveal a previously unidentified direct interaction between eIF4G and the 40S subunit. Using binding assays, our data show that this 40S subunit interaction is separate from the previously characterized interaction between eIF4G and eIF3. Thus, our work reveals how eIF4F can bind to the 40S subunit using eIF3-dependent and eIF3-independent binding domains to promote translation initiation.

A new in vitro system called Rec-Seq sheds light on how mRNA molecules compete for the machinery that translates their genetic sequence into proteins.

We present a plasmonics-enhanced spikey nanorattle-based biosensor for direct surface-enhanced Raman scattering (SERS) detection of mRNA cancer biomarkers. Early detection of cancers such as head and neck squamous cell carcinoma (HNSCC) is critical for improving patient outcomes in regions with limited access to traditional diagnostic methods. Our method targets Keratin 14 (KRT14), a promising diagnostic mRNA biomarker for HNSCC, using a sandwich hybridization approach with magnetic beads and SERS spikey nanorattles (SpNR). We synthesized SpNR with a core-gap-shell structure to enhance SERS signals, achieving a limit of detection of 90 femtomolar. A pilot study using clinical samples demonstrated the efficacy of our biosensor in distinguishing between tissue with positive or negative diagnosis for HNSCC, highlighting its potential for rapid and sensitive cancer diagnostics in low-resource settings. This plasmonic assay offers a promising avenue for portable and high-specificity detection of nucleic acid biomarkers, with implications for early cancer detection and improved patient care, especially in middle and low-resource settings. [ABSTRACT FROM AUTHOR]

The advent of RNA therapy, particularly through the development of mRNA cancer vaccines, has ushered in a new era in the field of oncology. This article provides a concise overview of the key principles, recent advancements, and potential implications of mRNA cancer vaccines as a groundbreaking modality in cancer treatment. mRNA cancer vaccines represent a revolutionary approach to combatting cancer by leveraging the body's innate immune system. These vaccines are designed to deliver specific mRNA sequences encoding cancer-associated antigens, prompting the immune system to recognize and mount a targeted response against malignant cells. This personalized and adaptive nature of mRNA vaccines holds immense potential for addressing the heterogeneity of cancer and tailoring treatments to individual patients. Recent breakthroughs in the development of mRNA vaccines, exemplified by the success of COVID-19 vaccines, have accelerated their application in oncology. The mRNA platform's versatility allows for the rapid adaptation of vaccine candidates to various cancer types, presenting an agile and promising avenue for therapeutic intervention. Clinical trials of mRNA cancer vaccines have demonstrated encouraging results in terms of safety, immunogenicity, and efficacy. Pioneering candidates, such as BioNTech's BNT111 and Moderna's mRNA-4157, have exhibited promising outcomes in targeting melanoma and solid tumors, respectively. These successes underscore the potential of mRNA vaccines to elicit robust and durable anti-cancer immune responses. While the field holds great promise, challenges such as manufacturing complexities and cost considerations need to be addressed for widespread adoption. The development of scalable and cost-effective manufacturing processes, along with ongoing clinical research, will be pivotal in realizing the full potential of mRNA cancer vaccines. Overall, mRNA cancer vaccines represent a cutting-edge therapeutic approach that holds the promise of transforming cancer treatment. As research progresses, addressing challenges and refining manufacturing processes will be crucial in advancing these vaccines from clinical trials to mainstream oncology practice, offering new hope for patients in the fight against cancer. [ABSTRACT FROM AUTHOR]

In recent years, the impact of methylation modifications on Dickkopf-1 (DKK1) in relation to ankylosing spondylitis (AS) has remained elusive. Our objective was to investigate the potential link between DKK1 methylation patterns and transcript levels and AS susceptibility. DNA methylation level of DKK1 was measured in 82 AS and 82 healthy controls (HCs) using targeted bisulfite sequencing. In addition, the transcript level of DKK1 in peripheral blood mononuclear cells from 35 AS patients and 35 HCs was detected using real-time quantitative transcription-polymerase chain reaction. Our study showed that the DKK1 was significantly hypomethylated in AS patients (P < 0.001). The Receiver operating characteristic curve (ROC) showed that DKK1 methylation may be a potential biomarker. The results showed that the difference in DKK1 transcript levels between AS and HCs was not statistically significant. Further analysis showed that DKK1 methylation levels were positively correlated with age and negatively correlated with C-reactive protein levels, neutrophil/lymphocyte ratio (NLR) and platelet/lymphocyte ratio (PLR). The methylation level of DKK1 in PBMC of AS patients was significantly lower than that of HCs, and DKK1 methylation may be associated with susceptibility to AS. In addition, DNA methylation levels of DKK1 were negatively correlated with the level of inflammation in AS patients. [ABSTRACT FROM AUTHOR]

Selenium (Se) is indispensable for the majority of organisms, yet it also possesses toxic properties, with a delicate balance between insufficiency and harmful levels. Some plants can be used for resistance of Se pollution. Here, to identify the Se tolerance and resistance potential of alfalfa, we comprehensively investigated the effects of excessive Na2SeO3 on the physio-biochemical, anatomical, mRNA, and miRNA expression profile alterations. Foliar spraying 500 mg/kg Se significantly reduced the biomass in alfalfa probably by inhibiting photosynthesis (20.2%). Excessive Se breaks the balance of antioxidant system, resulting in an increase of H2O2 and MDA content by 14.2 and 4.3%. Leaf ultra-structure damages subsequently revealed the phytotoxic effects of Se. And at 500 mg/kg, alfalfa synthesized more S-type lignin probably to increase the Se tolerance, but it resulted in lower nutritional quality. Through RNA-seq, we found 2112 Se-responsive differentially expressed genes, including 1322 up-regulated and 790 down-regulated mRNAs, many of which were related to plant hormone signal transduction, redox reaction, S-assimilation, and cell homeostasis. Moreover, we identified 296 known and 258 conserved miRNAs, and predicted 310 novel miRNAs, among which 77 differentially expressed miRNAs were induced by Se. miRNAs play a crucial role in forming Se tolerance in alfalfa under the precise regulation of redox, chlorophyll degradation, photosynthesis, cell wall synthesis, and other related target genes. Our results provided insights into the complex mechanism of the Se stress response in alfalfa. [ABSTRACT FROM AUTHOR]

The article in the journal "Histopathology" by Robers et al. discusses the role of routine diagnostic histopathology in determining the viability of infectious agents in human tissues. The study focuses on hydatid disease pathology, specifically cystic echinococcosis and alveolar echinococcosis infections. The authors explore new morphological aspects of hydatid parasite viability, providing criteria for assessing viability and discussing the implications for treatment decisions. The article also touches on the viability assessment of other infectious agents, such as helminths, bacteria, protozoa, and viruses, highlighting the challenges and uncertainties in determining viability using histopathological techniques. [Extracted from the article]

Background and objectives: Behçet's disease (BD) is an ongoing systemic vasculitis with mouth and genital ulceration and eye, skin, and systemic affection. It has considerable morbidity and mortality, and a high incidence and a higher male-to-female affection characterize Egypt. We aimed to evaluate liver x receptor messenger RNA beta (LXR β) and microRNA-146a (miR-146a) gene expression in Behçet's disease cases in Egypt to relate them with clinicopathological features. Subject and method: Eighty Egyptian individuals were split into two groups for the current study: Forty Behçet's disease cases and forty healthy controls matched by age and gender from the Rheumatology Department at Helwan University Hospital, Egypt. The transformed score, also known as the Behçet's Disease Current Activity Form (BDCAF), was utilized to measure disease activity. To assess the amounts of LXR β and miR-146a serum expression via real-time PCR, a blood sample was obtained. Results: There was a downregulation of both LXR β and miR-146a levels that significantly differed between the BD group and the control group (p = 0.0001 and 0.0001, respectively). There is a noteworthy inverse relationship between the expression level of LXR β and BDCAF Patients Index (r = − 0.79 and p = 0.0001) was found. Regarding miR-146a, it had a reverse correlation with BDCAF Patients Index (r = − 0.89 and p = 0.0001). Conclusion: LXR β and miR-146a were found to be significant non-invasive predictor biomarkers for Behçet's disease and can indicate disease activity. [ABSTRACT FROM AUTHOR]

Simple Summary: Adapting to severe dehydration poses significant challenges for wildlife, particularly for the African clawed frog, Xenopus laevis, which relies on estivation to survive dry seasons. By examining the protein levels of key components in the m6A modification pathway, we found that while most m6A-related proteins responsible for adding, removing, or interpreting m6A marks decreased during dehydration, the total amount of m6A on mRNA increased substantially in the liver and kidneys. This increase may serve as a rapid, reversible way for X. laevis to adjust gene activity and conserve energy under stressful conditions. Although many proteins involved in energy-intensive processes were downregulated, one specific m6A reader protein showed increased levels in the liver, potentially aiding in selective gene expression during dehydration. Our findings suggest that these molecular adjustments help frogs survive prolonged water scarcity, enhancing our understanding of how animals manage extreme environmental stress. The African clawed frog, Xenopus laevis, exhibits remarkable adaptations to survive in its arid habitat, including behavioral and metabolic changes during periods of drought. During extreme dehydration, X. laevis undergoes estivation, a state characterized by increased urea and ammonia levels, depression of the metabolic rate, and tissue hypoxia. To understand the molecular mechanisms underlying these adaptations, we investigated the potential role of N6-methyladenosine (m6A), a widespread mRNA modification, in X. laevis during extreme dehydration. We analyzed the protein levels of key components in the m6A pathway, including writers (METTL3, METTL14, and WTAP), erasers (ALKBH5 and FTO), and readers (SRSF3, YTHDF1, YTHDF2, YTHDF3, and eIF3a), in the liver and kidneys of control frogs and frogs that had lost 35 ± 0.93% of their total body water. The relative protein levels generally decreased or remained unchanged, with the exception of YTHDF3, which depicted a protein level increase in the liver. Notable changes included eIF3a, which was downregulated by 26 ± 8% and 80 ± 8% in the dehydrated liver and kidney tissues, respectively. Additionally, the total m6A increased by 353 ± 30% and 177 ± 17% in dehydrated liver and kidney RNA samples, respectively. This study highlights the importance of epigenetic mechanisms in stress tolerance and provides a foundation for further exploration of the role of epigenetics in dehydration tolerance. [ABSTRACT FROM AUTHOR]

Simple Summary: Geese are seasonal breeding animals, and in the process of ovarian development, they are affected by many factors, among which genetic factors play a crucial role. Histomorphological and transcriptome analysis of goose ovaries at different reproductive stages can effectively screen out differentially expressed genes, miRNAs and pathways in three periods (pre-laying period, egg-laying period and ceased-laying period). We constructed an interactive co-expression network using differentially expressed genes and differentially expressed miRNAs, which can reveal the regulatory mechanism of goose follicle development and egg-laying performance, and provide new insights into the genetic regulation mechanism of goose egg-laying performance. Ovarian development significantly influences the laying performance of geese. In this study, the transcriptome analysis was conducted on the ovarian tissues of Wanxi White Geese during the pre-laying (KL), laying (CL), and ceased-laying period (XL). Short Time-series Expression Miner (STEM) analysis and miRNA–mRNA regulatory network construction were performed to identify the key genes and miRNAs regulating laying traits. Comparative analysis of KL vs. CL, CL vs. XL, and XL vs. KL groups resulted in the identification of 337, 136, and 525 differentially expressed genes (DEGs), and 258, 1131, and 909 differentially expressed miRNAs (DEMs), respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis (p < 0.05) revealed that the main enrichment pathways of DEGs and DEMs at different breeding periods were Neuroactive ligand–receptor interaction, GnRH signaling pathway and Wnt signaling pathway, all associated with ovarian development. According to the three groups of common pathways, four DEGs were screened out, including INHBB, BMP5, PRL, and CGA, along with five DEMs, including let-7-x, miR-124-y, miR-1-y, and miR-10926-z, all of them may affect ovarian development. A miRNA–mRNA regulatory network was constructed through integrated analysis of DEGs and DEMs, revealing nine miRNAs highly associated with ovarian development: miR-101-y, let-7-x, miR-1-x, miR-17-y, miR-103-z, miR-204-x, miR-101-x, miR-301-y, and miR-151-x. The dual-luciferase reporter gene verified the target relationship between WIF1 and miR-204-x, suggesting that these miRNAs may influence ovarian development in Wanxi White Goose by regulating the expression levels of their target genes within ovarian tissue. This study provides a theoretical foundation for analyzing the mechanisms of ovarian development across different breeding periods and accelerating the cultivation of new breeds through post-transcriptional regulation levels. [ABSTRACT FROM AUTHOR]

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive cognitive decline and memory loss. While the precise causes of AD remain unclear, emerging evidence suggests that messenger RNA (mRNA) dysregulation contributes to AD pathology and risk. This study examined exosomal mRNA expression profiles of 15 individuals diagnosed with AD and 15 healthy controls from Barranquilla, Colombia. Utilizing advanced bioinformatics and machine learning (ML) techniques, we identified differentially expressed mRNAs and assessed their predictive power for AD diagnosis and AD age of onset (ADAOO). Our results showed that ENST00000331581 (CADM1) and ENST00000382258 (TNFRSF19) were significantly upregulated in AD patients. Key predictors for AD diagnosis included ENST00000311550 (GABRB3), ENST00000278765 (GGTLC1), ENST00000331581 (CADM1), ENST00000372572 (FOXJ3), and ENST00000636358 (ACY1), achieving > 90% accuracy in both training and testing datasets. For ADAOO, ENST00000340552 (LIMK2) expression correlated with a delay of ~12.6 years, while ENST00000304677 (RNASE6), ENST00000640218 (HNRNPU), ENST00000602017 (PPP5D1), ENST00000224950 (STN1), and ENST00000322088 (PPP2R1A) emerged as the most important predictors. ENST00000304677 (RNASE6) and ENST00000602017 (PPP5D1) showed promising predictive accuracy in unseen data. These findings suggest that mRNA expression profiles may serve as effective biomarkers for AD diagnosis and ADAOO, providing a cost-efficient and minimally invasive tool for early detection and monitoring. Further research is needed to validate these results in larger, diverse cohorts and explore the biological roles of the identified mRNAs in AD pathogenesis. [ABSTRACT FROM AUTHOR]

Antibody–drug conjugates targeting folate receptor alpha (FRα) are a promising treatment for platinum-resistant ovarian cancer (OC) with high FRα expression. Challenges persist in accurately assessing FRα expression levels. Our study aimed to better elucidate FRα gene expression and identify mRNA signatures in OC. We pooled OC gene expression data from 16 public datasets, encompassing 1832 OC and 30 normal ovarian tissues. Additional data included DNA copy number and methylation data from TCGA and protein data from 363 cancer cell lines from the Broad Institute Cancer Cell Line Encyclopedia. FOLR1 mRNA expression was significantly correlated with protein expression in pan-cancer cell lines and ovarian cancer cell lines. FOLR1 expression was higher in OC samples than in normal ovarian tissues (OR = 3.88, p = 6.97 × 10−12). Patients with high FOLR1 expression were more likely to be diagnosed with serous histology, FIGO stage III–IV, and high-grade tumors; however, nearly similar percentages of patients with low FOLR1 expression were also diagnosed with these features. FOLR1 mRNA expression was not correlated with platinum sensitivity or complete surgery, nor with prognosis. However, we identified a 187-gene signature associated with high FOLR1 expression that was significantly associated with improved survival (HR = 0.71, p = 1.18 × 10−6), independently from clinicopathological features. We identified a gene expression signature correlated to high FRα expression and OC prognosis, which may be used to refine therapeutic strategies targeting FRα in OC. These findings warrant validation in larger cohorts. [ABSTRACT FROM AUTHOR]

Post-transcriptional modification of RNA regulates gene expression at multiple levels. ALKBH8 is a tRNA-modifying enzyme that methylates wobble uridines in a subset of tRNAs to modulate translation. Through methylation of tRNA-selenocysteine, ALKBH8 promotes selenoprotein synthesis and regulates redox homeostasis. Pathogenic variants in ALKBH8 have been linked to intellectual disability disorders in the human population, but the role of ALKBH8 in the nervous system is unknown. Through in vivo studies in Drosophila, we show that ALKBH8 controls oxidative stress in the brain to restrain synaptic growth and support learning and memory. ALKBH8 null animals lack wobble uridine methylation and exhibit reduced protein synthesis in the nervous system, including a specific decrease in selenoprotein levels. Either loss of ALKBH8 or independent disruption of selenoprotein synthesis results in ectopic synapse formation. Genetic expression of antioxidant enzymes fully suppresses synaptic overgrowth in ALKBH8 null animals, confirming oxidative stress as the underlying cause of dysregulation. ALKBH8 null animals also exhibit associative memory impairments that are reversed by pharmacological antioxidant treatment. Together, these findings demonstrate the critical role of tRNA wobble uridine modification in redox homeostasis in the developing nervous system and reveal antioxidants as a potential therapy for ALKBH8-associated intellectual disability. [ABSTRACT FROM AUTHOR]

Macrophages are unique immune cells attracting growing attention as a potential candidate for cell‐based therapy for infectious diseases and cancer. Strategies that can reprogramme or gene‐edit macrophages hold potential across a spectrum of acute and chronic conditions. Herein, lipid nanoparticles (LNPs) are developed containing the ionizable lipid SM‐102, helper lipid monoolein which is known for self‐assembly in aqueous solutions into the inverse cubic lyotropic liquid crystalline mesophase, and cholesterol as an mRNA nanocarrier. The immortalized alveolar macrophage cell line (MH‐S cells) is utilized to investigate how cholesterol concentration impacts on mRNA delivery which is further validated using primary mouse alveolar macrophages isolated from the bronchoalveolar compartment and human monocyte derived macrophages. By using high‐throughput synchrotron small angle X‐ray scattering (SAXS), an acidification‐induced non‐ordered to ordered internal nanostructure transition of the formulated LNPs is observed, following the transition sequence of inverse micellar to hexagonal to cubic mesophase in the pH range from 7 to 4. Cholesterol is identified as another crucial component for superior mRNA transfection in macrophages, contributing to nanostructure transition and protein corona variation. Successful ex vivo mRNA transfection is also achieved in primary macrophages, highlighting the prospectivity of reprogramming macrophages as a cell therapy for lung diseases. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are short, nonprotein‐coding RNAs, and their expression is dysregulated in malignant germ cell tumors (GCTs). Here, we investigated the causes and consequences of downregulated miR‐99a‐5p/miR‐100‐5p (functionally identical) and miR‐125b‐5p levels in malignant GCTs regardless of age, site, or subtype. Quantitative RT‐PCR was used to assess miR‐99a‐5p/miR‐100‐5p, miR‐125b‐5p, and associated gene expression in malignant GCT tissues/cell lines [seminoma (Sem), yolk sac tumor (YST), embryonal carcinoma (EC)]. Cells were treated with demethylating 5‐azacytidine and pyrosequencing was performed. Combination miR‐100‐5p/miR‐125b‐5p mimic replenishment was used to treat malignant GCT cells. Global messenger RNA (mRNA) targets of the replenished miRNAs were identified and Metascape used to study pathway effects. We found that expression levels of miR‐99a‐5p/miR‐100‐5p and miR‐125b‐5p, their respective pri‐miRNAs, and associated genes from chromosomes 11 and 21 (chr11/chr21) were downregulated and highly correlated in malignant GCT cells. Treatment with 5‐azacytidine caused upregulation of these miRNAs, with pyrosequencing revealing hypermethylation of their chr11/chr21 loci, likely contributing to miR‐100‐5p/miR‐125b‐5p downregulation. Combination miR‐100‐5p/miR‐125b‐5p mimic replenishment resulted in growth inhibition in Sem/YST cells, with miR‐100‐5p/miR‐125b‐5p mRNA targets enriched in downregulated genes, which were involved in cell cycle (confirmed by flow cytometry) and signaling pathways. Knockdown of the miR‐100‐5p/miR‐125b‐5p target tripartite motif containing 71 (TRIM71kd) recapitulated miR‐100‐5p/miR‐125b‐5p replenishment, with growth inhibition and cell cycle disruption of Sem/YST/EC cells. Further, replenishment led to reduced lin‐28 homolog A (LIN28A) levels and concomitant increases in let‐7 (MIRLET7B) tumor suppressor miRNAs, creating a sustained reversion of cell phenotype. In summary, combination miR‐100‐5p/miR‐125b‐5p mimic replenishment or TRIM71kd caused growth inhibition in malignant GCT cells via cell cycle disruption. Further studies are now warranted, including mimic treatment alongside conventional platinum‐based chemotherapy. [ABSTRACT FROM AUTHOR]

Background: Helicobacter pylori (H. pylori) is a known gastro-intestinal pathogen but implicated in extra-gastric diseases. The relationship between H. pylori infection and type 2 diabetes (T2DM) remains insufficiently elucidated, particularly in terms of molecular mediators such as microRNAs (miRNAs) and messenger RNAs (mRNAs). Objective: We aimed to characterize expression pattern of insulin signalling mRNAs and targeted miRNAs in T2DM patients exposed to H. pylori infection. Methods: We conducted a cross-sectional study among patients diagnosed with type 2 diabetes mellitus and were aged 18 to 60 years. Overnight fasting blood samples were collected and processed for plasma and serum. The plasma samples were used for glucose estimation and the serum used for H. pylori IgG screening. Total RNA was extracted from the serum with commercial kit, and mRNAs and miRNAs quantified by RT-qPCR with specific primers and under predetermined amplification conditions. Clinical data were obtained from medical records of patients. Results: Among 351 patients enrolled, 267 (76.1%) were females, 224 (63.8%) were married, and 79 (22.5%) had tertiary education. Expression level of insulin receptor mRNA was significantly lower in H. pylori positive T2DM patients compared to H. pylori negative (P <.05). There was no evidence of a difference in insulin receptor substrate 1 mRNA level (P >.05). Although not statistically significant, the expression levels of miRNA-222 and miRNA-155 in the patients exposed to H. pylori were higher than that of the unexposed group (P >.05). Conclusions: We found a significantly reduced serum insulin receptor messenger RNA level and higher levels of miRNA-222 and miRNA-155 in H. pylori exposed T2DM patients. The findings suggest a possible role of the infection in insulin signalling alteration in the patients. [ABSTRACT FROM AUTHOR]

Background: The efficacy of mRNA-based vaccines and therapies relies on lipid nanoparticles (LNPs) as carriers to deliver mRNA into cells. The chemical structure of ionizable lipids (ILs) within LNPs is crucial in determining their delivery efficiency. Results: In this study, we synthesized 623 alkyne-bearing ionizable lipids using the A3 coupling reaction and assessed their effectiveness in mRNA delivery. ILs with specific structural features—18-carbon alkyl chains, a cis-double bond, and ethanolamine head groups—demonstrated superior mRNA delivery capabilities. Variations in saturation, double bond placement, and chain length correlated with decreased efficacy. Alkynes positioned adjacent to nitrogen atoms in ILs reduced the acid dissociation constant (pKa) of LNPs, thereby hindering mRNA delivery efficiency. Conversion of alkynes to alkanes significantly enhanced mRNA delivery of ILs both in vitro and in vivo. Moreover, combining optimized ILs with cKK-E12 yields synergistic LNPs that showed markedly augmented mRNA expression levels in vivo. Conclusions: Overall, our study provides insights into the structure–function relationships of ILs, providing a foundation for the rational design of ILs to enhance the efficacy of LNPs in mRNA delivery. [ABSTRACT FROM AUTHOR]

SUMMARY N1‐methyladenosine (m1A) methylation is an essential mechanism of gene regulation known to impact several biological processes in living organisms. However, little is known about the abundance, distribution, and functional significance of mRNA m1A modification during fruit ripening of tomato the main model species for fleshy fruits. Our study shows that m1A modifications are prevalent in tomato mRNA and are detected in lncRNA and circRNA. The distribution of m1A peaks in mRNA segments indicates that m1A is mainly enriched at the start codon and CDS regions. Assessing changes in global RNA methylation during fruit ripening in wild‐type tomatoes and in the ripening‐impaired Nr mutant affected in the ethylene receptor gene (SlETR3) revealed a decrease in the overall methylation levels from mature green (MG) stage to 6 days postbreaker (Br + 6). Nr mutant fruits show significantly lower methylation levels than Ailsa Craig (AC) fruits. Notably, differences in m1A methylation are well correlated to the expression levels of a number of key ripening‐related genes. The integration of RNA‐seq and MeRIP‐seq data suggests a potential positive impact of m1A modifications on gene expression. In comparison to the AC fruits, the hypomethylation and reduced expression of ethylene‐related genes, ACO3, EBF1, and ERF.D6, in the Nr mutants likely underpin the distinct phenotypic traits observed between the two fruit genotypes at the Br6 stage. Overall, our study brings further arguments supporting the potential significance of m1A methylation modifications in fruit ripening, a developmental process that is instrumental to plant reproduction and to fruit sensory and nutritional qualities. [ABSTRACT FROM AUTHOR]

Meat and its derivatives serve as crucial sources of protein, vitamins, minerals, and other essential nutrients for humans. Pork stands as China's primary animal-derived food product consumed widely across diverse dietary structures; evaluating intramuscular fat content becomes pivotal in assessing its quality standards. Nonetheless, the intricate molecular mechanisms governing intramuscular fat deposition remain elusive. Our study utilized sequencing technology to scrutinize longitudinal development stages within Ningxiang pig's longest dorsal muscles aiming to unravel these underlying mechanisms. In three distinct comparisons (30d vs. 90d, 90d vs. 150d and 150d vs. 210d) there were 578, 1,000 and 3,238 differentially expressed mRNA, along with 16, 158 and 85 lncRNAs were identified. STEM analysis unveiled six enriched model profiles for lncRNAs while seven such profiles emerged for mRNAs; notably, multiple shared model profiles existed between both RNA types. Enriched analysis highlighted numerous genes from mRNA profile8 and lncRNA profile7 significantly associated with pathways linked to fat deposition. Weight Gene Co-Expression Network Analysis (WGCNA) revealed that differential expression modules (DMEs) & differential expression lncRNAs primarily clustered within cyan, dark slate blue and pale turquoise modules. Furthermore, target genes PKD2 (MSTRG21592.MTRSG8859 and MTRSG18175), COL5A1 (MTRSG9969 and MTRSG180) and SOX13 (MTRSG21592 and MTRSG9088) as core components all intricately tied into processes related to fat deposition. This study lays the groundwork for deeper exploration into the molecular mechanisms underlying LDM fat deposition traits, and it also presents candidate genes for future molecular marker-assisted breeding. [ABSTRACT FROM AUTHOR]

Background: Eosinophil activation is associated with asthma. Whether air pollution affects the activation of blood eosinophils in patients with asthma remains unknown. In this study, we investigated the correlation between transcriptional activity in eosinophils and air pollutant exposure in patients receiving different levels of Global Initiative for Asthma (GINA) treatment. Methods: We evaluated the expression levels of activation‐ and function‐related genes in eosinophils from patients with GINA 4 or 5 (n = 20), those with GINA 3 (n = 12), and normal individuals (n = 7); the eosinophils were activated with interleukin (IL)−5 or IL‐17. A land use regression model was used to estimate air pollutant exposure. The correlations between mRNA expression, lung function, and air pollutant exposure were investigated. Results: The expression levels of TGFB1, IL7R, and TLR3 were significantly higher for patients with GINA 4 or 5 than for those with GINA 3 or normal individuals. The expression of certain genes, particularly in IL‐17‐activated eosinophils, was correlated with lung function decline in patients with GINA 4 or 5. For patients with GINA 4 or 5, NO2 exposure was correlated with upregulated TGFB1 expression in IL‐5‐activated eosinophils. For patients with GINA 3, O3 exposure was correlated with upregulated CCR5, IL5RA, IL7R, and TGFB1 expression in IL‐17‐activated eosinophils and upregulated IL7R expression in IL‐5‐activated eosinophils. Conclusion: Patients with GINA 4 or 5 may exhibit elevated transcriptional activity in eosinophils; this elevation is correlated with lung function decline. Air pollution may affect eosinophil mRNA expression in patients with asthma. [ABSTRACT FROM AUTHOR]

Nucleic acid medicines are a highly attractive modality that act in a sequence-specific manner on target molecules. To date, 21 such products have been approved by the Food and Drug Administration. However, the development of nucleic acid medicines continues to face various challenges, including tissue and cell targeting as well as intracellular delivery. Numerous research groups are addressing these issues by advancing the development of nucleic acid medicines through nanotechnology. In countries other than Japan (including Europe and the USA), >40 nanotechnology-based nucleic acid medicines have been tested in clinical trials, and 15 clinical trials are ongoing. In Japan, three phase I trials are ongoing, and future results are awaited. The review summarizes the latest research in the nanotechnology of nucleic acid medicines and statuses of clinical trials in Japan, with expectations of further evolutions. [ABSTRACT FROM AUTHOR]

The remit of this review is to give an autobiographical account of our discovery of the role of local protein synthesis in axon guidance. The paper reporting our initial findings was published in 2001. Here, I describe some of the work that led to this publication, the skepticism our findings initially received, and the subsequent exciting years of follow-up work that helped gradually to convince the neuroscience community of the existence and functional importance of local protein synthesis in multiple aspects of axon biology—guidance, branching, synaptogenesis, and maintenance. The journey has been an exhilarating one, taking me into a new field of RNA biology, with many unexpected twists and turns. In retelling it here, I have tried to recall the major influences on my thinking at the time rather than give a comprehensive review, and I apologize for any omissions due to my own ignorance during that era. [ABSTRACT FROM AUTHOR]

Objectives This study investigates the dual role of ALKBH5, an eraser enzyme, in colorectal cancer (CRC), focusing on how N6-methyladenosine (m6A) mutations influence CRC development and progression. Methods We reviewed various studies that highlighted the role of ALKBH5 in colorectal cancer (CRC). This includes the impact of ALKBH5 on tumor cell behavior including immune system interactions, invasion, and proliferation in CRC. We also looked into how ALKBH5 acts as a tumor suppressor under different conditions analyzed clinical data to assess the impact of ALKBH5 expression on outcomes in colorectal cancer patients. Key findings In CRC, ALKBH5 plays a dual role. In certain situations, it inhibits the progression of the tumor, but in other circumstances, it promotes tumor growth and immunosuppression. The interaction with RABA5 plays a role in the development of CRC. Having elevated levels of ALKBH5 has been associated with unfavorable patient outcomes, such as reduced survival rates and more advanced cancer stages. Various factors, including tumor differentiation, TNM stages, and carcinoembryonic antigen (CEA) levels, be linked to ALKBH5 expression. Conclusions ALKBH5 plays a complicated and situation-specific role in colorectal cancer (CRC). Targeting ALKBH5 could result in novel therapy options that balance its tumor-promoting and tumor-fighting properties in CRC. Further research into m6A alterations and ALKBH5 could enhance CRC treatment approaches and patient outcomes. [ABSTRACT FROM AUTHOR]

The human body is a complex network of systems that is harmonized with multiple biological components. To understand these interactions is very challenging. With rapid development of advanced sequencing technologies, massive amounts of data such as mRNA, miRNA are rapidly accumulated. The integrated analysis of mRNA–miRNA has brought an extensive understanding of complex biological systems and pathological mechanisms. MicroRNAs (miRNAs) are small non-coding RNAs that intricately regulate target gene products, resulting in the inhibition of gene expression. While these miRNAs play crucial roles in essential biological processes—ranging from immunity and metabolism to cell death—their specific impacts on diseases remain unknown. Recent studies have been focused on the integration of miRNA and mRNA expression to reveal the underlying biological pathways and mechanisms responsible for disease manifestation. We proposed a novel approach for integrative analysis of miRNA and mRNA expression data and developed MIMR (Integrative Analysis of miRNA and mRNA), a web-based application that leverages the Random Walk with Restart (RWR) algorithm. MIMR incorporates both direct and indirect interactions by utilizing protein–protein interaction (PPI) networks and experimentally validated mRNA–miRNA target interactions. MIMR provides comprehensive results, including novel pathological pathways associated with a specific disease and interactive network diagrams representing the mRNAs and miRNAs. We applied it to Alzheimer and breast cancer data and successfully identified the novel biological pathways related to these diseases. In summary, MIMR will offer a deeper insight into the hidden mechanisms of diseases and identify potential therapeutic strategies through integrated analysis of miRNAs and mRNAs. [ABSTRACT FROM AUTHOR]

In muscle, digoxin inhibits Na+,K+‐ATPase (NKA) whereas acute exercise can increase NKA gene expression, consistent with training‐induced increased NKA content. We investigated whether oral digoxin increased NKA isoform mRNA expression (qPCR) in muscle at rest, during and post‐exercise in 10 healthy adults, who received digoxin (DIG, 0.25 mg per day) or placebo (CON) for 14 days, in a randomised, double‐blind and cross‐over design. Muscle was biopsied at rest, after cycling 20 min (10 min each at 33%, then 67% V̇O2peak${{\dot{V}}_{{{{\mathrm{O}}}_2}{\mathrm{peak}}}}$), then to fatigue at 90% V̇O2peak${{\dot{V}}_{{{{\mathrm{O}}}_2}{\mathrm{peak}}}}$ and 3 h post‐exercise. No differences were found between DIG and CON for NKA α1–3 or β1–3 isoform mRNA. Both α1 (354%, P = 0.001) and β3 mRNA (P = 0.008) were increased 3 h post‐exercise, with α2 and β1–2 mRNA unchanged, whilst α3 mRNA declined at fatigue (−43%, P = 0.045). In resting muscle, total β mRNA (∑(β1+β2+β3)) increased in DIG (60%, P = 0.025) and also when transcripts for each isoform were normalised to CON then either summed (P = 0.030) or pooled (n = 30, P = 0.034). In contrast, total α mRNA (∑(α1+α2+α3), P = 0.348), normalised then summed (P = 0.332), or pooled transcripts (n = 30, P = 0.717) did not differ with DIG. At rest, NKA α1–2 and β1–2 protein abundances were unchanged by DIG. Post‐exercise, α1 and β1–2 proteins were unchanged, but α2 declined at 3 h (19%, P = 0.020). In conclusion, digoxin did not modify gene expression of individual NKA isoforms at rest or with exercise, indicating NKA gene expression was maintained consistent with protein abundances. However, elevated resting muscle total β mRNA with digoxin suggests a possible underlying β gene‐stimulatory effect. Highlights: What is the central question of this study?Na+,K+‐ATPase (NKA) in muscle is important for Na+/K+ homeostasis. We investigated whether the NKA‐inhibitor digoxin stimulates increased NKA gene expression in muscle and exacerbates NKA gene responses to exercise in healthy adults.What is the main finding and its importance?Digoxin did not modify exercise effects on muscle NKA α1–3 and β1–3 gene transcripts, which comprised increased post‐exercise α1 and β3 mRNA and reduced α3 mRNA during exercise. However, in resting muscle, digoxin increased NKA total β isoform mRNA expression. Despite inhibitory‐digoxin or acute exercise stressors, NKA gene regulation in muscle is consistent with the maintenance of NKA protein contents. [ABSTRACT FROM AUTHOR]

During the COVID-19 pandemic, it was important for people to be able to comprehend information about mRNA vaccination. Moderna and Pfizer were two of the largest distributors of mRNA vaccinations, and their websites provided information about how mRNA vaccinations work. Applying the tenets of Fuzzy-trace Theory (FTT), we calculated Gist Inference Scores (GIS) to assess the extent to which texts taken from Moderna and Pfizer websites facilitate gist comprehension. We then rewrote the Moderna and Pfizer texts to increase GIS and tested their ability to facilitate a reader's understanding of how mRNA vaccinations work. We conducted two experiments in which participants read original Moderna and Pfizer texts, a High GIS-version presenting the same content, or control texts on unrelated topics. Findings indicate that the High GIS-version increased comprehension. We conclude that this theory-driven approach can help subject-matter experts better communicate important information, allowing readers to "get the gist" of it. [ABSTRACT FROM AUTHOR]

Messenger RNA (mRNA) vaccines have revolutionized the fight against infectious diseases and are poised to transform other therapeutic areas. Lipid nanoparticles (LNP) represent the most successful delivery system for mRNA. While the mRNA-LNP products currently in clinics are stored as frozen suspensions, there is evidence that freeze-drying mRNA-LNP into dry powders can potentially enable their storage and handling at non-freezing temperatures. Previously, we successfully applied thin-film freeze-drying (TFFD) to transform a polyadenylic acid [poly(A)]-LNP formulation from a liquid suspension to dry powders. The poly(A)-LNP were structurally multilamellar spheres without blebs, but the mRNA vaccines in clinics are comprised of mRNA-LNP that are structurally spheres surrounded by a unilamellar lipid bilayer, with some containing blebs, and it was reported that the presence of blebs increases the sensitivity of mRNA-LNP to freeze-drying-induced stress. In the present study, using an influenza A virus hemagglutinin (HA) mRNA in LNP that were structurally similar to that in the COVID-19 mRNA vaccines currently in clinic, we studied the effect of TFFD on the physical properties, internal structure, as well as immunogenicity of the HA mRNA-LNP vaccine. We concluded that TFFD can be utilized to prepare dry powders of the HA mRNA-LNP, but a sufficient amount of excipients were needed to minimize changes in the physical properties, structure, and immunogenicity of the HA mRNA-LNP vaccine. [Display omitted] • The HA mRNA-LNP vaccine used in this study contained nanoparticles with unilamellar lipid bilayer, some with blebs. • TFFD was used to transform the HA mRNA-LNP vaccine from liquid to dry powders while maintaining its immunogenicity. • Sufficient excipients were needed to minimize the effect of the freeze-drying stress on the HA mRNA-LNP. [ABSTRACT FROM AUTHOR]

Acute respiratory infections are the leading cause of death and illness in children under 5 years old and represent a significant burden in older adults. Primarily caused by viruses infecting the lower respiratory tract, symptoms include cough, congestion, and low‐grade fever, potentially leading to bronchiolitis and pneumonia. Messenger ribonucleic acid (mRNA)‐based vaccines are biopharmaceutical formulations that employ mRNA molecules to induce specific immune responses, facilitating the expression of viral or bacterial antigens and promoting immunization against infectious diseases. Notably, this technology had significant relevance during the COVID‐19 pandemic, as these formulations helped to limit SARS‐CoV‐2 virus infections, hospitalizations, and deaths. Importantly, mRNA vaccines promise to be implemented as new alternatives for fighting other respiratory viruses, such as influenza, human respiratory syncytial virus, and human metapneumovirus. This review article analyzes mRNA‐based vaccines' main contributions, perspectives, challenges, and implications against respiratory viruses. [ABSTRACT FROM AUTHOR]

While there are numerous brain regions that have been shown to play a role in this AUD in humans and animal models, the central nucleus of the amygdala (CeA) has emerged as a critically important locus mediating binge alcohol consumption. In this study, we sought to understand how relative gene expression of key signaling molecules in the CeA changes during different periods of abstinence following bouts of binge drinking. To test this, we performed drinking in the dark (DID) on two separate cohorts of C57BL/6J mice and collected CeA brain tissue at 1 day (acute) and 7 days (protracted) abstinence after DID. We used qRTPCR to evaluate relative gene expression changes of 25 distinct genes of interest related to G protein-coupled receptors (GPCRs), neuropeptides, ion channel subunits, and enzymes that have been previously implicated in AUD. Our findings show that during acute abstinence CeA punches collected from female mice had upregulated relative mRNA expression of the gamma-aminobutyric acid receptor subunit alpha 2 (Gabra2), and the peptidase, angiotensinase c (Prcp). CeA punches from male mice at the same time point in abstinence had upregulated relative mRNA encoding for neuropeptide-related molecules, neuropeptide Y (Npy) and somatostatin (Sst), as well as the neuropeptide Y receptor Y2 (Npyr2), but downregulated Glutamate ionotropic receptor NMDA type subunit 1 (Grin1). After protracted abstinence, CeA punches collected from female mice had increased mRNA expression of corticotropin releasing hormone (Crh) and Npy. CeA punches collected from male mice at the same timepoint had upregulated relative mRNA expression of Npy2r, Npy, and Sst. Our findings support that there are differences in how the CeA of male and female mice respond to binge-alcohol exposure, highlighting the need to understand the implications of such differences in the context of AUD and binge drinking behavior. • There are differences in mRNA of alcohol related targets from the CeA of male and female mice. • There are differences in the time course mRNA of alcohol related targets from the CeA. • Correlations across genes are strongly modulated by sex. [ABSTRACT FROM AUTHOR]

Background: Current L1-based human papillomavirus (HPV) vaccines provide type-specific protection but offer limited cross-protection against non-vaccine HPV types. Therefore, developing a broad-spectrum HPV vaccine is highly desirable. Methods: In this study, we optimized mRNA constructs and developed a multivalent L2-based mRNA vaccine encoding L2 aa 2-130, which includes all known neutralizing epitopes from four prevalent HPV types (HPV-6, -11, -16, and -18). We evaluated its immunogenicity in a mouse model and compared the efficacy of a commercially available mRNA delivery reagent with a custom-synthesized lipid nanoparticle (LNP) formulation. Results: We identified that a construct containing E01 (a 5′-untranslated region) and SL2.7 (a poly(A) polymerase recruitment sequence) significantly increased protein expression. The L2-based mRNA vaccine induced robust and long-lasting humoral immune responses, with significant titers of cross-reactive serum IgG antibodies against L2 epitopes. Notably, the vaccine elicited cross-neutralizing antibodies and conferred cross-protective immunity not only against vaccine-targeted HPV types but also against non-vaccine HPV types, following intravaginal challenge in mice. We also found that LNP delivered mRNA more effectively in vivo. Conclusions: The L2-based mRNA vaccine developed in this study shows significant potential for broad-spectrum protection against multiple HPV types. This approach offers a promising strategy for reducing the global burden of HPV-associated cancers. [ABSTRACT FROM AUTHOR]

Background/Objectives: In post-traumatic stress disorder (PTSD), anxiety-like symptoms are often associated with elevated noradrenaline levels and decreased serotonin. Selective serotonin reuptake inhibitors (SSRIs) are frequently used to treat anxiety, but elevated serotonin has been observed in some anxiety disorders. This study investigates stress-induced anxiety as an immediate effect of chronic stress exposure using the predator stress paradigm. Methods: We examined serotonin levels, serotonin transporter (SERT), and 5-HT3A receptor gene expression in response to stress. The effects of SSRIs (paroxetine, sertraline) and resveratrol on these parameters were also analyzed, alongside co-treatment with resveratrol and sertraline. Results: Chronic stress exposure led to a significant increase in serotonin levels and upregulation of SERT and 5-HT3A receptor expression. SSRIs failed to prevent anxiety or reduce serotonin levels, partly due to suppressed SERT expression. Resveratrol downregulated SERT and 5-HT3A expression less than SSRIs but effectively reduced anxiety and restored serotonin, likely by upregulating MAO-A expression. Co-treatment with resveratrol and sertraline produced the strongest anxiolytic effect. Conclusions: Elevated serotonin and increased expression of SERT and 5-HT3A receptor genes are key factors in stress-related anxiety. Resveratrol and SSRIs target these mechanisms, suggesting potential therapeutic strategies for anxiety disorders. Future research will focus on further elucidating the serotonergic mechanisms involved and identifying new anxiolytic drug targets. [ABSTRACT FROM AUTHOR]

In vitro transcription (IVT) reaction is an RNA polymerase‐catalyzed production of messenger RNA (mRNA) from DNA template, and the unit operation with highest cost of goods in the mRNA drug substance production process. To decrease the cost of mRNA production, reagents should be optimally utilized. Due to the catalytic, multicomponent nature of the IVT reaction, optimization is a multi‐factorial problem, ideally suited to design‐of‐experiment approach for optimization and identification of design space. We derived a data‐driven model of the IVT reaction and explored factors that drive process yield (in g/L), including impact of nucleoside triphosphate (NTP) concentration and Mg:NTP ratio on reaction yield and how to optimize the main cost drivers RNA polymerase and DNA template, while minimizing dsRNA formation, a critical quality attribute in mRNA products. We report a methodological approach to derive an optimum reaction design, with which cost efficiency of the reaction was improved by 44%. We demonstrate the validity of the model on mRNA construct of different lengths. Finally, we maximized the yield of the IVT reaction to 24.9 ± 1.5 g/L in batch, thus doubling the highest ever reported IVT yield. [ABSTRACT FROM AUTHOR]

Objective To observe the effects of atorvastatin calcium on the cell proliferation and migration of human umbilical vein endothelial cells (HUVECs), and to screen the hub mRNA and co-related long non-coding RNA (lncRNA) of atorvastatin calcium on HUVECs. Methods HUVECs in the logarithmic growth phase were divided into the group 1 and group 2. Cells in the group 1 and group 2 were treated with 5 µmol/L atorvastatin calcium and the same amount of PBS for 24 h, respectively. ① Observation of effects of atorvastatin calcium on the cell proliferation and migration of HUVECs: The cell cycle was measured by flow cytometry, the cell proliferation was observed by CCK-8 method, and the cell migration was observed by scratch healing test. ② Screening of hub mRNAs and co-related lncRNAs in HUVECs treated with atorvastatin calcium: illumina platform was used to detect mRNA and lncRNA in cells of the two groups. Differentially expressed mRNAs and lncRNAs with |log2 Fold change| > 1. 5 and P adjusted < 0. 05 were screened using limma package in R Studio software. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were used to analyze the biological functions of differentially expressed mRNAs. The STRING database was used to analyze the protein interaction of differentially expressed mRNAs. The CytoNCA plug-in was used to screen the top 10 hub mRNAs with the highest mediation centrality, and the co-expressed lncRNAs with the hub mRNAs with Pearson correlation coefficient > 0. 99 were screened. Real-time fluorescence quantitative PCR (qPCR) was used to detect the hub mRNA and its coexpressed lncRNA in the two groups. Results Compared with the group 2, the proportion of cells in the G0/G1 phase of the group 1 was higher, the cell proliferation was inhibited, and the cell migration area was smaller after 24 h of culture (all P<0. 05) . Compared with the group 2, there were 1 510 differentially expressed mRNAs and 744 differentially expressed lncRNAs in the group 1; the biological functions of differentially expressed mRNAs involved 294 GO sets and 27 KEGG pathways; there were 10 hub mRNAs and 130 lncRNAs co-expressed with them, including AC017101. 1, AC125257. 1, AC004846. 1, etc. Compared with the group 2, the relative expression levels of HSP90AA1, CDK4, CCND1, PLK1, and PCNA in the group 1 were lower, and the relative expression levels of AC017101. 1, AC125257. 1, AC004846. 1, and AL390719. 1 were higher (all P<0. 05) . Conclusions Atorvastatin calcium can block the HUVECs in the G0/G1 phase and inhibit their proliferation and migration. There are 10 hub mRNAs such as HSP90AA1, CDK4 and CCND1, and 130 co-related lncRNAs such as AC017101. 1, AC125257. 1 and AC004846. 1 in atorvastatin calcium treatment of HUVECs. Atorvastatin calcium may promote the expression of co-related lncrnas such as AC017101. 1, AC125257. 1 and AC004846. 1 and down-regulate the expression of HSP90AA1, CDK4 and CCND1 mRNA in HUVECs. Thus, the cell cycle of HUVECs is arrested and cell proliferation and migration are inhibited. [ABSTRACT FROM AUTHOR]

The addition of non-templated nucleotides at the 3' terminus of RNA is a pervasive and evolutionarily conserved posttranscriptional modification in eukaryotes. Apart from canonical poly(A) polymerases (PAPs), which are responsible for catalyzing polyadenylation of messenger RNAs in the nucleus, a distinct group of non-canonical PAPs (ncPAPs), also known as nucleotidyl transferase proteins (NTPs), mediate the addition of uridine and adenosine or of more intricate combinations of nucleotides. Among these, HEN1 SUPPRESSOR 1 (HESO1) and UTP: RNA URIDYLYLTRANSFERASE (URT1) are the two most extensively studied NTPs responsible for the addition of uridine to the 3' ends of RNAs (RNA uridylation). Recent discoveries have improved our understanding of the functions and mechanisms of uridylation mediated by HESO1 and URT1 in RNA metabolism. Furthermore, more NTPs have been identified to function in the 3' tailing of RNA and not solely through uridylation. Accumulating evidence indicates that RNA tailing plays important roles in plant growth and development, stress responses, and disease resistance. In this review, we examined the latest developments in RNA tailing by NTPs, with a focus on RNA uridylation and metabolism in plants. We also discussed the essential aspects for future research in this field. [ABSTRACT FROM AUTHOR]

Introduction: Extracellular vesicles (EVs) known for their pivotal role in intercellular communication through RNA delivery, hold paramount implications for understanding muscle phenotypic variations in diverse pig breeds. Methods: In this study, we compared the mRNA expression profiles of longissimus dorsi muscles and muscle-derived extracellular vesicles (M-EVs), and also examined the diversity of enriched genes in M-EVs between weaned wild boars and commercial Large White pigs with respect to their numbers and biological functions. Results: The results of the study showed that the variation in the expression profiles of mRNAs between muscles and M-EVs was much greater than the variability between the respective breeds. Meanwhile, the enrichment trend of low-expressed genes (ranked <1,000) was significantly (p-value = 0.05) powerful in M-EVs compared to highly expressed genes in muscles. In addition, M-EVs carried a smaller proportion of coding sequences and a larger proportion of untranslated region sequences compared to muscles. There were 2,110 genes enriched in M-EVs (MEGs) in Large White pigs and 2,322 MEGs in wild boars, with 1,490 MEGs shared interbreeds including cyclin D2 (CCND2), which inhibits myogenic differentiation. Of the 89 KEGG pathways that were significantly enriched (p-value = 0.05) for these MEGs, 13 unique to Large White pigs were mainly related to immunity, 27 unique to wild boars were functionally diverse but included cell fate regulation such as the Notch signaling pathway and the TGF-beta signaling pathway, and 49 were common to both breeds were also functionally complex but partially related to innate immunity, such as the Complement and coagulation cascades and the Fc gamma R-mediated phagocytosis. Discussion: These findings suggest that mRNAs in M-EVs have the potential to serve as indicators of muscle phenotype differences between the two pig breeds, highlighting the need for further exploration into the role of EV-RNAs in pig phenotype formation. [ABSTRACT FROM AUTHOR]

Bone is a three‐dimensional (3D) highly dynamic tissue under constant remodeling. Commonly used tools to investigate bone biology require sample digestion for biomolecule extraction or provide only two‐dimensional (2D) spatial information. There is a need for 3D tools to investigate spatially preserved biomarker expression in osteocytes. In this work, we present a new method, WISH‐BONE, to label osteocyte messenger RNA (mRNA) and protein in whole‐mount mouse bone. For mRNA labeling, we used hybridization chain reaction‐fluorescence in situ hybridization (HCR‐FISH) to label genes of interest in osteocytes. For protein labeling, samples were preserved using an epoxy‐based solution that protects tissue structure and biomolecular components. Then an enzymatic matrix permeabilization step was performed to enable antibody penetration. Immunostaining was used to label various proteins involved in bone homeostasis. We also demonstrate the use of customized fluorescent nanobodies to target and label proteins in the cortical bone (CB). However, the relatively dim signal observed from nanobodies' staining limited detection. mRNA and protein labeling were performed in separate samples. In this study, we share protocols, highlight opportunities, and identify the challenges of this novel 3D labeling method. They are the first protocols for whole‐mount osteocyte 3D labeling of mRNA and protein in mature mouse bones. WISH‐BONE will allow the investigation of molecular signaling in bone cells in their 3D environment and could be applied to various bone‐related fields of research. [ABSTRACT FROM AUTHOR]

The treatment of pancreatic ductal adenocarcinoma (PDAC) is an unmet challenge, with the median overall survival rate remaining less than a year, even with the use of FOLFIRINOX-based therapies. This study analyzed archived macrophage-associated mRNA expression using datasets deposited in the UCSC Xena web platform to compare normal pancreatic tissue and PDAC tumor samples. The TGFB2 gene exhibited low mRNA expression levels in normal tissue, with less than one TPM. In contrast, in tumor tissue, TGFB2 expression levels exhibited a 7.9-fold increase in mRNA expression relative to normal tissue (p < 0.0001). Additionally, components of the type-I interferon signaling pathway exhibited significant upregulation of mRNA levels in tumor tissue, including Interferon alpha/beta receptor 1 (IFNAR1; 3.4-fold increase, p < 0.0001), Interferon regulatory factor 9 (IRF9; 4.2-fold increase, p < 0.0001), Signal transducer and activator of transcription 1 (STAT1; 7.1-fold increase, p < 0.0001), and Interferon Alpha Inducible Protein 27 (IFI27; 66.3-fold increase, p < 0.0001). We also utilized TCGA datasets deposited in cBioportal and KMplotter to relate mRNA expression levels to overall survival outcomes. These increased levels of mRNA expression were found to be prognostically significant, whereby patients with high expression levels of either TGFB2, IRF9, or IFI27 showed median OS times ranging from 16 to 20 months (p < 0.01 compared to 72 months for patients with low levels of expression for both TGFB2 and either IRF9 or IFI27). Examination of the KMplotter database determined the prognostic impact of TGFB2 mRNA expression levels by comparing patients expressing high versus low levels of TGFB2 (50th percentile cut-off) in low macrophage TME. In TME with low macrophage levels, patients with high levels of TGFB2 mRNA exhibited significantly shorter OS outcomes than patients with low TGFB2 mRNA levels (Median OS of 15.3 versus 72.7 months, p < 0.0001). Furthermore, multivariate Cox regression models were applied to control for age at diagnosis. Nine genes exhibited significant increases in hazard ratios for TGFB2 mRNA expression, marker gene mRNA expression, and a significant interaction term between TGFB2 and marker gene expression (mRNA for markers: C1QA, CD74, HLA-DQB1, HLA-DRB1, HLA-F, IFI27, IRF9, LGALS9, MARCO). The results of our study suggest that a combination of pharmacological tools can be used in treating PDAC patients, targeting both TGFB2 and the components of the type-I interferon signaling pathway. The significant statistical interaction between TGFB2 and the nine marker genes suggests that TGFB2 is a negative prognostic indicator at low levels of the IFN-I activated genes and TAM marker expression, including the immune checkpoint LGALS9 (upregulated 16.5-fold in tumor tissue; p < 0.0001). [ABSTRACT FROM AUTHOR]

SUMMARY Gametocidal (Gc) chromosomes have been widely utilized in genetic breeding due to their ability to induce chromosomal breakage and eliminate gametes that lack them. Long noncoding RNAs (lncRNAs) have various functional mechanisms in regulating pollen and anther development; however, their regulatory contributions to Gc action are still unknown. Here, we identified 2824 differentially expressed lncRNAs (DE‐lncRNAs) from the anther tissues of Triticum aestivum cv. Chinese Spring (CS) and Chinese Spring‐Gc 3C chromosome monosomic addition line (CS‐3C) through sequencing. In this study, we predicted 161 target mRNAs for 145 DE‐lncRNAs, including 104 cis‐regulatory, 60 trans‐regulatory, and three both cis‐regulatory and trans‐regulatory manner. Combined with our previous miRNA sequencing data, 241 DE‐lncRNAs functioned as potential endogenous target mimics (eTMs) for 84 differentially expressed microRNAs (DE‐miRNAs, including 12 novel miRNAs). The results of transient transformation in tobacco leaves indicated that L006278 could bind to MTCONS_00006277, which encoded a calcineurin CBL‐interacting protein kinase 19‐like, and suppress its expression. Furthermore, L117735 could function as an eTM for tae‐miR9657b‐3p, and L056972 could function as an eTM for gc‐m2240‐5p. To explore the function of lncRNAs in the process of Gc action, we transformed L006278, an up‐regulated lncRNA in CS‐3C, into rice to analyze its effect on pollen fertility. Overexpression of L006278 led to a reduction in rice pollen fertility. Overall, our findings indicate that lncRNAs can contribute to the regulation of pollen fertility during the process of Gc action by regulating the expression levels of target mRNAs and acting as eTMs for certain key miRNAs. [ABSTRACT FROM AUTHOR]

The post COVID-19 pandemic era has emerged with more efficient vaccines, all based on genetic materials. However, to expand the use of nucleic components as vaccines, a new generation of nanosystems particularly constructed to increase RNA/DNA stability, half-life and facilitate administration are still required. This review highlights novel developments in mRNA and pDNA vaccines formulated into nanostructures exclusively composed by biopolymeric materials. Recent advances suggest that a new generation of vaccines may arise by adapting the structural features of biopolymers with the effectiveness of nucleic acids. The advantages offered by biopolymers, such as increased stability and targeting ability may cause a revolution in the immunization field for offering promptly adaptable and effective formulations for worldwide distribution. Graphical Abstract Article highlights Polymeric biomaterials for nucleic acid delivery in vaccines We review the potential of chitosan, PLL, PEI, PLA and PLGA as mRNA/DNA vaccine systems. Chitosan Chitosan has significant potential for new intranasal vaccine designs. Poly(L-lysine) Vaccines based on PLL still require long, difficult and costly biomaterial modifications for translation. Poly(ethyleneimine) PEI's cytotoxicity may be circumvented by reducing the molar mass and using shorter chains. Poly(lactic acid) & poly(lactide-co-glycolide) PLA or PLGA lack chemical functionalities for optimal nuclei acid anchoring. Conclusion & future perspectives The cationic character causes a balance between nuclei material deliver efficiency and cytotoxicity. [ABSTRACT FROM AUTHOR]

Recent breakthroughs in cancer immunotherapies have emphasized the importance of harnessing the immune system for treating cancer. Vaccines, which have traditionally been used to promote protective immunity against pathogens, are now being explored as a method to target cancer neoantigens. Over the past few years, extensive preclinical research and more than a hundred clinical trials have been dedicated to investigating various approaches to neoantigen discovery and vaccine formulations, encouraging development of personalized medicine. Nucleic acids (DNA and mRNA) have become particularly promising platform for the development of these cancer immunotherapies. This shift towards nucleic acid-based personalized vaccines has been facilitated by advancements in molecular techniques for identifying neoantigens, antigen prediction methodologies, and the development of new vaccine platforms. Generating these personalized vaccines involves a comprehensive pipeline that includes sequencing of patient tumor samples, data analysis for antigen prediction, and tailored vaccine manufacturing. In this review, we will discuss the various shared and personalized antigens used for cancer vaccine development and introduce strategies for identifying neoantigens through the characterization of gene mutation, transcription, translation and post translational modifications associated with oncogenesis. In addition, we will focus on the most up-to-date nucleic acid vaccine platforms, discuss the limitations of cancer vaccines as well as provide potential solutions, and raise key clinical and technical considerations in vaccine development. [ABSTRACT FROM AUTHOR]

Originally devised for cancer control, mRNA vaccines have risen to the forefront of medicine as effective instruments for control of infectious disease, notably their pivotal role in combating the COVID-19 pandemic. This review focuses on fundamental aspects of the development of mRNA vaccines, e.g., tumor antigens, vector design, and precise delivery methodologies, - highlighting key technological advances. The recent, promising success of personalized mRNA vaccines against pancreatic cancer and melanoma illustrates the potential value for other intractable, immunologically resistant, solid tumors, such as glioblastoma, as well as the potential for synergies with a combinatorial, immunotherapeutic approach. The impact and progress in human cancer, including pancreatic cancer, head and neck cancer, bladder cancer are reviewed, as are lessons learned from first-in-human CAR-T cell, DNA and dendritic cell vaccines targeting glioblastoma. Going forward, a roadmap is provided for the transformative potential of mRNA vaccines to advance cancer immunotherapy, with a particular focus on the opportunities and challenges of glioblastoma. The current landscape of glioblastoma immunotherapy and gene therapy is reviewed with an eye to combinatorial approaches harnessing RNA science. Preliminary preclinical and clinical data supports the concept that mRNA vaccines could be a viable, novel approach to prolong survival in patients with glioblastoma. [ABSTRACT FROM AUTHOR]

Vaccines have always been a critical tool in preventing infectious diseases. However, the development of traditional vaccines often takes a long time and may struggle to address the challenge of rapidly mutating viruses. The emergence of mRNA technology has brought revolutionary changes to vaccine development, particularly in rapidly responding to the threat of emerging viruses. The global promotion of mRNA vaccines against severe acute respiratory syndrome coronavirus 2 has demonstrated the importance of mRNA technology. Also, mRNA vaccines targeting viruses such as influenza, respiratory syncytial virus, and Ebola are under development. These vaccines have shown promising preventive effects and safety profiles in clinical trials, although the duration of immune protection is still under evaluation. However, the development of mRNA vaccines also faces many challenges, such as stability, efficacy, and individual differences in immune response. Researchers adopt various strategies to address these challenges. Anyway, mRNA vaccines have shown enormous potential in combating viral diseases. With further development and technological maturity, mRNA vaccines are expected to have a profound impact on public health and vaccine equity. This review discussed the potential of mRNA vaccines to fight against viruses, current progress in clinical trials, challenges faced, and future prospects, providing a comprehensive scientific basis and reference for future research. [ABSTRACT FROM AUTHOR]

The remarkable efficacy of COVID-19 vaccines has established mRNA as a highly promising biomedical technology. However, the adequate application of mRNA therapeutics necessitates additional measures to mitigate the inherent immunogenicity, which is predominantly caused by dsRNA. As a byproduct of the in vitro transcription of mRNA, dsRNA was reported to be originated through several distinct mechanisms, including the extension of 3′ loop-back hairpins, the extension of hybridized abortive transcripts, and promoter-independent transcription. The intricate mechanisms involved pose a dilemma as the reduction in dsRNA results in a concomitant decrease in other critical quality attributes of mRNA. Here, we demonstrate that the promoter binding motifs of T7 RNA polymerase directly impact the production of promoter-independent transcription-based dsRNA. Specifically, the G753A mutation significantly reduces the formation of dsRNA byproducts, which can further combine with modified nucleotides to enhance the effectiveness of dsRNA mitigation and with previously reported high-integrity mutation K389A to minimize side effects. Accordingly, the present study reports a cost-effective approach to synthesize high-purity, less immunostimulatory mRNA by using an engineered T7 RNA polymerase mutant. [ABSTRACT FROM AUTHOR]

Background: Cancer survival prediction is vital in improving patients' prospects and recommending therapies. Understanding the molecular behavior of cancer can be enhanced through the integration of multi-omics data, including mRNA, miRNA, and DNA methylation data. In light of these multi-omics data, we proposed a graph attention network (GAT) model in this study to predict the survival of non-small cell lung cancer (NSCLC). Methods: The different omics data were obtained from The Cancer Genome Atlas (TCGA) and preprocessed and combined into a single dataset using the sample ID. We used the chi-square test to select the most significant features to be used in our model. We used the synthetic minority oversampling technique (SMOTE) to balance the dataset and the concordance index (C-index) to measure the performance of our model on different combinations of omics data. Results: Our model demonstrated superior performance, with the highest value of the C-index obtained when we used both mRNA and miRNA data. This demonstrates that the multi-omics approach could be effective in predicting survival. Further pathway analysis conducted with KEGG showed that our GAT model provided high weights to the features that are associated with the viral entry pathways, such as the Epstein–Barr virus and Influenza A pathways, which are involved in lung cancer development. From our findings, it can be observed that the proposed GAT model leads to a significantly improved prediction of survival by exploiting the strengths of multiple omics datasets and the findings from the enriched pathways. Our GAT model outperforms other state-of-the-art methods that are used for NSCLC prediction. Conclusions: In this study, we developed a new model for the survival prediction of NSCLC using the GAT based on multi-omics data. Our model showed outstanding predictive values, and the KEGG analysis of the selected significant features showed that they were implicated in pivotal biological processes underlying pathways such as Influenza A and the Epstein–Barr virus infection, which are linked to lung cancer progression. [ABSTRACT FROM AUTHOR]

The influence of gene expression on female caste determination in social Hymenoptera is one of the best-characterized examples of developmental polyphenism. We used mRNA-seq to profile differentially expressed genes (DEGs) between workers and queens at four development stages (early larvae: 1-day-old larvae; mid larvae: 5-day-old larvae; late larvae: 9-day-old larvae; and 7-day-old adult bee) of Bombus terrestris. When DEGs of different female castes were compared, it was found that there were more DEGs at the mid larval and adult stages than at other stages. Caste differentiation may be linked to candidate genes such as Vitellogenin, Kr-h1, Dnmt3, Hexamerin, Yellow, and Chymotrypsin-2. Additionally, the gene expression profiles were observed differently among the four development stages. Comparing one stage to the next showed that, more number of DEGs were found in queens than workers. In the investigation of how gene expression affects larval caste determination, WGCNA showed that five modules were closely associated with larval caste determination. The functions of genes were mainly enriched in energy metabolism and energy production within mitochondria, suggesting that the energy requirements during the larval development process varied between caste determination. The current study sheds light on the patterns of gene expression in the female caste of Bombus terrestris, which will be useful for future research on polyphenism through differential gene expressions. [ABSTRACT FROM AUTHOR]

Nuclear messenger RNA (mRNA) export is vital for cell survival under both physiological and stress conditions. To cope with stress, cells block bulk mRNA export while selectively exporting stress-specific mRNAs. Under physiological conditions, nuclear adaptor proteins recruit the mRNA exporter to the mRNA for export. By contrast, during stress conditions, the mRNA exporter is likely directly recruited to stress-specific mRNAs at their transcription sites to facilitate selective mRNA export. In this review, we summarize our current understanding of nuclear mRNA export. Importantly, we explore insights into the mechanisms that block bulk mRNA export and facilitate transcript-specific mRNA export under stress, highlighting the gaps that still need to be filled. Selective mRNA export is crucial for cell survival, especially under stress. Seidler and Sträßer outline how cells block bulk mRNA export while selectively exporting stress-specific mRNAs, shedding light on the mechanisms at play during normal and stress conditions and highlighting key gaps in our understanding of these vital processes. [ABSTRACT FROM AUTHOR]

Aim: To investigate how delayed post‐exercise carbohydrate intake affects muscle glycogen, metabolic‐ and mitochondrial‐related molecular responses, and subsequent high‐intensity interval exercise (HIIE) capacity. Methods: In a double‐blind cross‐over design, nine recreationally active men performed HIIE (10 × 2‐min cycling, ~94% W˙peak) in the fed state, on two occasions. During 0–3 h post‐HIIE, participants drank either carbohydrates ("Immediate Carbohydrate" [IC], providing 2.4 g/kg) or water ("Delayed Carbohydrate" [DC]); total carbohydrate intake over 24 h post‐HIIE was matched (~7 g/kg/d). Skeletal muscle (sampled pre‐HIIE, post‐HIIE, +3 h, +8 h, +24 h) was analyzed for whole‐muscle glycogen and mRNA content, plus signaling proteins in cytoplasmic‐ and nuclear‐enriched fractions. After 24 h, participants repeated the HIIE protocol until failure, to test subsequent HIIE capacity; blood lactate, heart rate, and ratings of perceived effort (RPE) were measured throughout. Results: Muscle glycogen concentrations, and relative changes, were similar between conditions throughout (p > 0.05). Muscle glycogen was reduced from baseline (mean ± SD mmol/kg dm; IC: 409 ± 166; DC: 352 ± 76) at post‐HIIE (IC: 253 ± 96; DC: 214 ± 82), +3 h (IC: 276 ± 62; DC: 269 ± 116) and + 8 h (IC: 321 ± 56; DC: 269 ± 116), returning to near‐baseline by +24 h. Several genes (PGC‐1ɑ, p53) and proteins (p‐ACCSer79, p‐P38 MAPKThr180/Tyr182) elicited typical exercise‐induced changes irrespective of condition. Delaying carbohydrate intake reduced next‐day HIIE capacity (5 ± 3 intervals) and increased RPE (~2 ratings), despite similar physiological responses between conditions. Conclusion: Molecular responses to HIIE (performed in the fed state) were not enhanced by delayed post‐exercise carbohydrate intake. Our findings support immediate post‐exercise refueling if the goal is to maximize next‐day HIIE capacity and recovery time is ≤24 h. [ABSTRACT FROM AUTHOR]

mRNA-based vaccines symbolize a new paradigm shift in personalized medicine for the treatment of infectious and non-infectious diseases. However, the reactogenicity associated with the currently approved formulations limits their applicability in autoinflammatory disorders, such as tumour therapeutics. In this study, we present a delivery system showing controlled immunogenicity and minimal non-specific inflammation, allowing for selective delivery of mRNA to antigen presenting cells (APCs) within the medullary region of the lymph nodes. Our platform offers precise control over the trafficking of nanoparticles within the lymph nodes by optimizing stealth and targeting properties, as well as the subsequent opsonization process. By targeting specific cells, we observed a potent adaptive and humoral immune response, which holds promise for preventive and therapeutic anti-tumoral vaccines. Through spatial programming of nanoparticle distribution, we can promote robust immunization, thus improving and expanding the utilization of mRNA vaccines. This innovative approach signifies a remarkable step forward in the field of targeted nanomedicine. [Display omitted] [ABSTRACT FROM AUTHOR]

Salinity represents a fatal factor affecting the productivity of alfalfa. But the regulation of salinity tolerance via lncRNAs and mRNAs remains largely unclear within alfalfa. For evaluating salinity stress resistance-related lncRNAs and mRNAs within alfalfa, we analyzed root transcriptomics in two alfalfa varieties, GN5 (salinity-tolerant) and GN3 (salinity-sensitive), after treatments with NaCl at 0 and 150 mM. There were altogether 117,677 lncRNAs and 172,986 mRNAs detected, including 1,466 lncRNAs and 2,288 mRNAs with significant differential expression in GN5150/GN50, GN3150/GN30, GN50/GN30, and GN5150/GN3150. As revealed by GO as well as KEGG enrichment, some ionic and osmotic stress-associated genes, such as HPCA1-LRR, PP2C60, PP2C71, CRK1, APX3, HXK2, BAG6, and ARF1, had up-regulated levels in GN5 compared with in GN3. In addition, NaCl treatment markedly decreased CNGC1 expression in GN5. According to co-expressed network analyses, six lncRNAs (TCONS_00113549, TCONS_00399794, TCONS_00297228, TCONS_00004647, TCONS_00033214 and TCONS_00285177) modulated 66 genes including ARF1, BAG6, PP2C71, and CNGC1 in alfalfa roots, suggesting that these nine genes and six lncRNAs probably facilitated the different salinity resistance in GN5 vs. GN3. These results shed more lights on molecular mechanisms underlying genotype difference in salinity tolerance among alfalfas. [ABSTRACT FROM AUTHOR]