Search Results (8,833)

Complex regional pain syndrome (CRPS) is an idiopathic, highly debilitating chronic disorder with persistent regional pain accompanied by a combination of sensory, motor, and autonomic abnormalities. It is not only difficult to treat but also difficult to study. This scoping review aimed to identify the key clinical and molecular challenges encountered in CRPS research and to examine the assessment tools currently employed. A comprehensive search was conducted across PubMed/Medline, Science Direct, Scopus, Wiley Online Library, and Google Scholar using a combination of free text and MeSH terms related to CRPS, clinical and molecular aspects, neuroinflammation, biomarkers, and research challenges. We analyzed 55 original clinical research papers on CRPS and 17 studies of immunological/biochemical/molecular aspects of CRPS. A significant degree of heterogeneity was observed in the methodologies employed across the reviewed studies. The most frequently reported challenges included difficulties in participant recruitment and controlling confounding factors (reported in 62% of studies), such as the heterogeneity of the patient population, the influence of pain coping strategies and psychological factors, and the impact of sociocultural factors (reported in 62% of studies). Research into diagnostic and prognostic markers for CRPS also faces numerous challenges. Recruiting participants is difficult due to the rarity of the condition, resulting in small sample sizes for studies. In vitro models often fail to replicate the complexity of in vivo inflammation, limiting their applicability. Findings from early CRPS stages may not generalize to chronic CRPS because of differing pathophysiological mechanisms and symptom profiles. Additional obstacles include the disorder’s heterogeneity, difficulties in controlling confounding factors, variability in treatment approaches, and the lack of standardized tools and baseline comparisons. These issues hinder the development of reliable biomarkers and evidence-based treatments. Due to these difficulties, the exact cause of CRPS is still not fully understood, making it difficult to develop effective, specific treatments and conduct targeted research. Full article

Fat deposition represents a crucial feature in the expenditure of physical energy and affects the meat quality of farm animals. It is regulated by multiple genes and regulators. Of them, non-coding RNAs (ncRNAs) play a critical role in modulating the fat deposition process. As well as being an important protein source, farm animals can be used as medical models, so many researchers worldwide have explored their mechanism of fat deposition. This article summarizes the transcription factors, regulatory genes, and signaling pathways involved in the molecular regulation process of fat deposition; outlines the progress of researching the roles of microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs) in fat deposition in common farm animals including pigs, cattle, sheep, ducks, and chickens; and identifies scientific problems in the field that must be further investigated. It has been demonstrated that ncRNAs play a critical role in regulating the fat deposition process and have great potential in improving meat quality traits. Full article

Transcription factors (TFs) and microRNAs (miRNAs) are fundamental regulators of gene expression, cell state, and biological processes. This study investigated whether a small subset of TFs and miRNAs could accurately predict genome-wide gene expression. We analyzed 8895 samples across 31 cancer types from The Cancer Genome Atlas and identified 28 miRNA and 28 TF clusters using unsupervised learning. Medoids of these clusters could differentiate tissues of origin with 92.8% accuracy, demonstrating their biological relevance. We developed Tissue-Agnostic and Tissue-Aware models to predict 20,000 gene expressions using the 56 selected medoid miRNAs and TFs. The Tissue-Aware model attained an $R^2$ of 0.70 by incorporating tissue-specific information. Despite measuring only 1/400th of the transcriptome, the prediction accuracy was comparable to that achieved by the 1000 landmark genes. This suggests the transcriptome has an intrinsically low-dimensional structure that can be captured by a few regulatory molecules. Our approach could enable cheaper transcriptome assays and analysis of low-quality samples. It also provides insights into genes that are heavily regulated by miRNAs/TFs versus alternative mechanisms. However, model transportability was impacted by dataset discrepancies, especially in miRNA distribution. Overall, this study demonstrates the potential of a biology-guided approach for robust transcriptome representation. Full article

Background: Lung cancer is the leading cause of cancer-related mortality globally, with late-stage diagnoses contributing to poor survival rates. While lung cancer screening with low-dose computed tomography (LDCT) has proven effective in reducing mortality among heavy smokers, its limitations, including high false-positive rates and resource intensiveness, restrict widespread use. Liquid biopsy, particularly using microRNA (miRNA) biomarkers, offers a promising adjunct to current screening strategies. This study aimed to evaluate the predictive power of a panel of serum miRNA biomarkers for lung cancer detection. Patients and Methods: A case-control study was conducted at two tertiary hospitals, enrolling 82 lung cancer cases and 123 controls. We performed an extensive literature review to shortlist 25 candidate miRNAs, of which 16 showed a significant two-fold increase in expression compared to the controls. Machine learning techniques, including Random Forest, K-Nearest Neighbors, Neural Networks, and Support Vector Machines, were employed to identify the top six miRNAs. We then evaluated predictive models, incorporating these biomarkers with lung nodule characteristics on LDCT. Results: A prediction model utilising six miRNA biomarkers (mir-196a, mir-1268, mir-130b, mir-1290, mir-106b and mir-1246) alone achieved area under the curve (AUC) values ranging from 0.78 to 0.86, with sensitivities of 70–78% and specificities of 73–85%. Incorporating lung nodule size significantly improved model performance, yielding AUC values between 0.96 and 0.99, with sensitivities of 92–98% and specificities of 93–98%. Conclusions: A prediction model combining serum miRNA biomarkers and nodule size showed high predictive power for lung cancer. Integration of the prediction model into current lung cancer screening protocols may improve patient outcomes. Full article

Background/Objectives: Aortic stenosis (AS) is the most common valvular pathology in the geriatric population and is the primary cause of valve replacement. However, misdiagnoses and delays in treatment are common due to comorbidities, frailty, and sedentary lifestyles among elderly individuals. MicroRNAs (miRNAs) are highly conserved molecular regulators involved in various cellular processes and have gained recognition as reliable biomarkers in cardiovascular diseases. In the present study, we evaluated plasma miRNAs as potential biomarkers for the early diagnosis of AS in the geriatric population to identify early therapeutic strategies. Methods: This prospective, case–control study included 87 individuals over 75 years of age. The participants were divided into AS (n = 58) and control (n = 29) groups. Results: Fifty-four miRNAs were differentially expressed between patients with AS and controls. Among those genes, 29 were upregulated and 25 were downregulated in patients with AS relative to controls. We selected seven candidate genes (miR-185-5p, miR-143-3p, miR-370-3p, let-7d-3p, miR-452-5p, miR-6787-3p, and miR-21-3p) for experimental validation by qRT–PCR. Only miR-143-3p and miR-452-5p were significantly upregulated in the plasma of patients with AS compared with controls. We developed a multiparametric model by combining the two-miRNA signature with echocardiographic parameters (left ventricular ejection fraction, stroke volume, and global longitudinal strain) to increase diagnostic power; this model yielded sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) values of 78.2%, 70.7%, and 0.837, respectively. Conclusions: In clinical practice, the use of a multiparametric model involving this set of miRNAs combined with echocardiographic variables may improve the accuracy of AS diagnosis and risk stratification. Full article

Background and Objectives: This study aimed to determine the relationship between miRNAs and overactive bladder (OAB). We also aimed to reveal the diagnostic properties of miRNAs and their potential to predict responses to therapy. Materials and Methods: The study included 60 patients with OAB as the treatment group and 60 healthy individuals as the control group. The blood levels of 15 miRNAs in both groups were determined using PCR. Also, miRNAs with high diagnostic values were identified with receiver operating characteristic (ROC) curves. Finally, the Turkish-validated OAB questionnaire form was filled out before and after the treatment by the participants in the treatment group. In this way, the relationship between OAB score changes and miRNA levels was examined. Results: The let-7a, let-7c, let-7e, let-7f, and let-7g miRNA molecules in the treatment group were higher, with a high level of significance (p = 0.0001). Additionally, the miR-135b, miR-300, miR-372, miR-373, miR-381, miR-520a, miR-520d, and miR-520e miRNA molecules were found to be statistically higher in the control group (p = 0.0001). In addition, let-7c (area under curve [AUC] = 0.985) and the let-7c + miR-381 combination (area under curve [AUC] = 1) were the highest values in the ROC analysis. Finally, after treatment in the patient group, a significant difference was detected in both miRNAs (let-7f and miR-135b) in patients with clinical improvements of 50% and above in the OAB score. Conclusions: miRNAs may help elucidate the pathophysiology of OAB. They may shed light on diagnosis and evaluation of treatment effectiveness. Full article

The recombinant bovine somatotropin (rbST) is a synthetic hormone developed to mimic the effects of the endogenous growth hormone, also known as bovine somatotropin (bST). Although rbST use in dairy cows is authorized in several countries, it is currently banned in Europe. Different methods for screening and confirmatory detection of rbST were developed, mainly based on LC-MS/MS and immune-enzymatic assays. However, some commercial forms of rbST have above the same amino acid sequence of bST, making it difficult to produce a reliable differentiation of recombinant from endogenous forms. Complementary strategies for indirect detection of rbST can therefore be considered as alternative biomarker-based tools. Untargeted transcriptomics was applied to characterize the microRNAs (miRNA) isolated from milk extracellular vesicles (EVs) in rbST-treated animals, aiming the identification of non-coding biomarkers related to its administration. Sequencing analysis of 63 archive samples collected during previous animal trial allowed for the identification of 35 differentially expressed (DE) miRNAs. A validation study performed by qPCR on a further 70 milk samples from a field survey confirmed the significant upregulation of bta-miR-10167-3p in milk EV from rbST-treated cows. The results obtained suggest the potential use of bta-miR-10167-3p as a non-invasive biomarker to be considered in novel screening strategies, needed to tackle rbST misuse in dairy cows. Full article

Transfection is a fundamental method in biomedical research to study intracellular molecular mechanisms by manipulating target protein expression. Various methods have been developed to deliver nucleic acids into the cells of interest in vitro, with chemical transfection by cationic lipids being the most widely used for RNA interference (RNAi). However, translating these in vitro results into in vivo remains a significant challenge. In this study, we established an ex vivo transfection model using cationic lipids in human whole blood. Three different lipid-based reagents were evaluated regarding toxicity, transfection efficiency, and immunogenicity across leukocyte populations using spectral flow cytometry. CD14⁺ monocytes were identified as the primary population to be transfected by cationic lipids in whole blood. To assess immunogenicity, the monocyte-specific activation markers CD80 and human leukocyte antigen DR isotype (HLA-DR) were analyzed upon transfection. Our results demonstrated that Lipofectamine RNAiMAX outperforms the other two reagents, showing low toxicity and high transfection efficiency in combination with a minimal potential for monocyte activation. Functional knockdown experiments using siRNA targeting CIITA and the microRNA mir-3972 targeting HLA-DRA showed dose-dependent suppression in HLA-DR expression. This study provides the framework for preliminary testing of RNAi in a physiologically relevant ex vivo model, enabling assessment of key endpoints such as toxicity, transfection efficiency, and immune activation potential of gene delivery systems. Full article

(1) Background: MicroRNAs are non-coding RNA sequences that regulate cellular functions by targeting messenger RNAs and inhibiting protein synthesis. Identifying their target sites is vital to understanding their roles. However, it is challenging due to the high cost and time demands of experimental methods and the high false-positive rates of computational approaches. (2) Methods: We introduce a Multi-Input Neural Network (MINN) algorithm that integrates diverse biologically relevant features, including the microRNA duplex structure, substructures, minimum free energy, and base-pairing probabilities. For each feature derived from a microRNA target-site duplex, we create a corresponding image. These images are processed in parallel by the MINN algorithm, allowing it to learn a comprehensive and precise representation of the underlying biological mechanisms. (3) Results: Our method, on an experimentally validated test set, detects target sites with an AUPRC of 0.9373, Precision of 0.8725, and Recall of 0.8703 and outperforms several commonly used computational methods of microRNA target-site predictions. (4) Conclusions: Incorporating diverse biologically explainable features, such as duplex structure, substructures, their MFEs, and binding probabilities, enables our model to perform well on experimentally validated test data. These features, rather than nucleotide sequences, enhance our model to generalize beyond specific sequence contexts and perform well on sequentially distant samples. Full article

Adipose tissue is responsible for fat storage and is an important producer of extracellular vesicles (EVs). The biological content of exosomes, one kind of EV, provides information on aspects such as immunometabolic alterations. This study aimed to compare three plasma exosome isolation methods—using a commercial kit (CK), size exclusion chromatography (SEC), and differential centrifugation (DC)—and select the best one. Individuals categorized by normal and high body fat percentages were used. The DC and CK were proven to be the most advantageous out of the exosome isolation methods, so we suggest these methods for further protein and molecular analyses, respectively. Still, we emphasize the importance of selecting an appropriate methodology depending on the specific research objectives. At the same time, no statistical differences in exosome quality, morphology, total protein, or microRNA concentration were observed between individuals categorized by body fat percentage, so we suggest that the exosomal cargo varies in individuals with normal and high fat percentages. Full article

Osteosarcoma (OS) is the most common primary malignant bone tumor, predominantly affecting children, adolescents, and young adults. Epithelial–mesenchymal transition (EMT), a process in which epithelial cells lose their cell–cell adhesion and gain migratory and invasive properties, has been extensively studied in various carcinomas. However, its role in mesenchymal tumors like osteosarcoma remains less explored. EMT is increasingly recognized as a key factor in the progression of osteosarcoma, contributing to tumor invasion, metastasis, and resistance to chemotherapy. This narrative review aims to provide a comprehensive overview of the molecular mechanisms driving EMT in osteosarcoma, highlighting the involvement of signaling pathways such as TGF-β, transcription factors like Snail, Twist, and Zeb, and the role of microRNAs in modulating EMT. Furthermore, we discuss how EMT correlates with poor prognosis and therapy resistance in osteosarcoma patients, emphasizing the potential of targeting EMT for therapeutic intervention. Recent advancements in understanding EMT in osteosarcoma have opened new avenues for treatment, including EMT inhibitors and combination therapies aimed at overcoming drug resistance. By integrating biological insights with clinical implications, this review underscores the importance of EMT as a critical process in osteosarcoma progression and its potential as a therapeutic target. Full article

Background/Objectives: The aim of the study is to investigate the role of microRNA-17 (miRNA-17), tumor necrosis factor-alpha (TNF-α), and interleukin-6 (IL-6) in the pathogenesis of lumbar degenerative disc disease (LDDD). The goal is to explore how miRNA-17 regulates inflammation and apoptosis within the intervertebral discs, with a particular focus on its involvement in inflammatory pathways via NF-κB signaling. This research seeks to uncover the molecular mechanisms that contribute to LDDD and its associated chronic lower back pain and disability. Methods: A case–control study was conducted, involving 110 patients diagnosed with LDDD and 17 healthy control individuals. Serum levels of miRNA-17, TNF-α, and IL-6 were measured using quantitative real-time PCR and enzyme-linked immunosorbent assays (ELISAs). The patients were further categorized based on the severity of their condition using the Oswestry Disability Index (ODI), which classified them into five subgroups. The correlation between miRNA-17 expression, pro-inflammatory cytokines, and disease severity was analyzed statistically. Results: The results demonstrated a significant downregulation of microRNA-17 in patients with LDDD compared to healthy controls. Inflammatory markers TNF-α and IL-6 were found to be significantly elevated in the patient group. A peak in inflammation and miRNA-17 expression was observed in patients with moderate to severe disability (ODI Grade 3), while inflammation levels decreased in more advanced stages of the disease (ODI Grades 4 and 5), suggesting a possible shift in disease dynamics. Conclusions: This study demonstrates that miRNA-17 plays a regulatory role in inflammation during the progression of LDDD, particularly through the modulation of TNF-α and IL-6 levels. The findings indicate that inflammation is most pronounced in the mid-stages of LDDD, while the later stages are characterized by structural damage rather than ongoing inflammation. These insights could help guide future therapeutic strategies aimed at targeting the molecular mechanisms underlying LDDD, potentially improving patient outcomes. Full article

Background: Platelets are highly enriched in microRNAs (miRNAs), which are genomically encoded 19–25 nucleotide non-coding RNAs that target complementary mRNAs through total or near-total base pairing. MiR-223 is among the most abundant miRNAs in human and murine platelets, but despite ongoing investigations in recent years, miR-223 roles in platelet physiology and its putative roles in high on-treatment platelet reactivity (HTPR) remain controversial, as studies showed varying findings. Objectives: In the current hybrid review/report, we aim to compare studies that investigated miR-223 in platelet function and HTPR. Additionally, we briefly report our own findings on murine miR-223-deficient platelets. Methods: We have thoroughly searched the literature and found three studies that investigated the roles of miR-223 in platelet function by utilizing miR-223 global knockout mice, and three studies that explored the association between miR-223 and residual platelet reactivity by measuring miR-223 levels in platelets of patients treated with clopidogrel for cardiac artery disease. We assessed platelet function in response to different agonists and evaluated P2y12 levels in male and female miR-223-deficient platelets. Results: Integrin activation and α granule secretion were similar between WT and KO platelets in response to all agonists in platelets from both female and male mice, although both genotypes showed elevated thrombin response in females compared to males. Conclusions: In all studies, including ours, taken together, miR-233 appears to play a modest role in platelet function and development of HTPR. Full article

Available interventions for the management of chronic hepatitis B (hepB) exhibit limited efficacy and barriers to vaccination against the hepatitis B virus (HBV) have hampered prophylaxis programmes. Development of potent therapeutics capable of functional cure of chronic hepB thus remains a relevant medical objective. RNA interference (RNAi) can be exploited to effect potent and specific silencing of target genes through the introduction of RNA sequences that mimic the natural activators of the pathway. To achieve a therapeutic effect, artificial primary microRNAs (pri-miRNAs) have been used extensively to target various viruses, including HBV. To date artificial pri-miRNAs have exclusively been produced from DNA expression cassettes. Although this achieves impressive silencing, eventual translation of this platform to the clinic is complicated by the requirement for viral vectors to deliver DNA. Consequently, clinical translation has been slow. Recently, the use of in vitro transcribed RNA, specifically to produce mRNA vaccines at industrial scale, has gained significant interest. We therefore sought to evaluate the feasibility of using in vitro transcribed artificial pri-miRNAs for the inhibition of HBV gene expression. Artificial HBV-targeting pri-miR-31 sequences, which are highly effective when expressed in cells from a DNA template, demonstrated modest silencing of viral replication when incorporated into mRNA that was transcribed in vitro. Off-target effects were also observed. Characterisation revealed that intracellular processing of the artificial pri-miRNAs was inefficient and non-specific effects were caused by stimulation of the interferon response. Nevertheless, optimised nuclear delivery of the artificial pri-miRNAs should improve their processing and achieve better anti-hepB efficacy. Full article

Research exploring involvement of RNA N⁶-methyladenosine (m⁶A) in tomato (Solanum lycopersicum) seed germination remains limited. There is also a lack of direct evidence supporting the interaction among tomato seed germination, microgravity, and m⁶A modification. In this study, Micro-Tom tomatoes are used as the experimental material to conduct tomato genetic transformation, seed germination assay, and m⁶A modification levels identification experiments. During tomato seed germination processes, the m⁶A modification level significantly increases under the mutual influence of various m⁶A methyltransferase subunits and multiple eraser proteins. As a m⁶A reader gene, SlYTP9 expression significantly affects the germination of tomato seeds, with promotion and inhibition in OE (overexpression) and RNAi (RNA interference) transgenic tomato plants, respectively. Microgravity promotes seed germination in the early germination period (0–3 days past germination; 0–3 DPG), but this promoting effect gradually disappears as the seedling grows (8–15 DPG). Further exploration revealed that this promoting effect is correlated with m⁶A modification, manifested as enhanced expression of most m⁶A writer genes; increased expression levels of overall reader genes; altered expression trends of some m⁶A eraser genes, particularly SlALKBH2; and enhanced m⁶A modification levels. The experimental results obtained in this study can provide a theoretical basis and evidence support for elucidating the role of m⁶A in tomato seed germination, as well as for exploring the interactions between seed germination, microgravity, and m⁶A modification. Full article