Search Results (602)

Background/Objectives: The KRAS rs61764370 T>G single-nucleotide polymorphism (SNP), located in a let-7 microRNA binding site within the 3′ untranslated region (3′UTR) of the KRAS gene, may modulate tumor aggressiveness by altering post-transcriptional gene regulation. This study evaluated its association with adverse histopathological features in colorectal cancer (CRC). Methods: A preliminary study on 83 CRC patients carrying either the TT (wild-type, n = 64) or TG (heterozygous, n = 19) genotype was analyzed. Clinicopathological variables included patient sex, tumor location, American Joint Committee on Cancer (AJCC) staging system, histological grade, perineural invasion (PNI), and lymphovascular invasion (LVI). A composite “tumor aggressiveness” score was defined based on the presence of Grade 3 differentiation, LVI, and/or PNI. Group comparisons were performed using the Chi-square test or Fisher’s exact test, as appropriate. Results: No statistically significant differences were observed in sex (p = 0.689), tumor location (p = 0.781), or stage at diagnosis (p = 0.812). Poorly differentiated tumors (Grade 3) were present in 20.3% of TT patients and absent in TG carriers (p = 0.06), while low-grade tumors (Grade 1) were more prevalent among TG patients (47.4%) compared to TT (29.7%). The composite high-aggressiveness score was lower in TG (36.8%) than in TT (48.4%), while co-occurrence of PNI and LVI was similar in both groups (~26%). Conclusions: Although no significant associations were identified, TG carriers showed a tendency toward lower-grade, less aggressive tumors. Given the limited sample size, these findings should be interpreted with caution, necessitating larger cohorts in order to validate results. Full article

Background: This study is part of the HEAL ITALIA partnership, funded by the National Recovery and Resilience Plan (PNRR) and the European Union. Heart failure (HF) is a serious health problem, with a reduced density of the β1-adrenergic receptor (β1-AR) in the myocardium as a hallmark. It is unclear whether this downregulation causes dysfunction or represents an epiphenomenon. Recent evidence implicates oxidative stress and mitochondrial signaling, particularly through the 18 kDa translocator protein (TSPO), in the regulation of the β1-AR, with possible modulation by estrogen. Objectives: To determine (1) the role of β1-AR desensitization in the onset and development of HF; (2) whether monocytes can represent a suitable ex vivo model for sex-oriented mechanistic studies in the cardiac field; (3) whether monocytes isolated from peripheral blood of patients can represent a diagnostic and/or therapy response biomarker by monitoring β1-AR density; (4) whether and how the mitochondrial receptor TSPO is involved in the β1-AR dysregulation observed in HF; and (5) whether the mechanisms linked to the onset of HF are regulated in a sex-specific manner through the effect of estrogen and/or the X chromosome on the expression of specific microRNAs. Methods: Using an integrated in vitro-ex vivo-in vivo methodological approach, we will evaluate the density of β1/β2-AR receptors, the downstream signaling (GRK2/β-arrestin), mitochondrial and redox parameters, and miRNA profiles in human monocytes and cardiomyocytes, and in mouse hearts after HF following pressure overload. Conclusions: The goal is to better understand the mechanisms underlying β1-AR desensitization, verify monocytes as peripheral markers of disease progression and response to therapy, and provide potentially useful information for the development of gender-specific therapies for heart failure. Full article

Micronutrients, particularly boron (B), iron (Fe), manganese (Mn), and zinc (Zn), are pivotal for cotton (Gossypium spp.) growth, reproductive success, and fiber quality. However, their critical roles are often overlooked in fertility programs focused primarily on macronutrients. This review synthesizes recent advances in the physiological, molecular, and agronomic understanding of B, Fe, Mn, and Zn in cotton production. The overarching goal is to elucidate their impact on cotton nutrient use efficiency (NUE). Drawing from the peer-reviewed literature, we highlight how these micronutrients regulate essential processes, including photosynthesis, cell wall integrity, hormone signaling, and stress remediation. These processes directly influence root development, boll retention, and fiber quality. As a result, deficiencies in these micronutrients contribute to significant yield gaps even when macronutrients are sufficiently supplied. Key genes, including Boron Transporter 1 (BOR1), Iron-Regulated Transporter 1 (IRT1), Natural Resistance-Associated Macrophage Protein 1 (NRAMP1), Zinc-Regulated Transporter/Iron-Regulated Transporter-like Protein (ZIP), and Gossypium hirsutum Zinc/Iron-regulated transporter-like Protein 3 (GhZIP3), are crucial for mediating micronutrient uptake and homeostasis. These genes can be leveraged in breeding for high-yielding, nutrient-efficient cotton varieties. In addition to molecular hacks, advanced phenotyping technologies, such as unmanned aerial vehicles (UAVs) and single-cell RNA sequencing (scRNA-seq; a technology that measures gene expression at single-cell level, enabling the high-resolution analysis of cellular diversity and the identification of rare cell types), provide novel avenues for identifying nutrient-efficient genotypes and elucidating regulatory networks. Future research directions should include leveraging microRNAs, CRISPR-based gene editing, and precision nutrient management to enhance the use efficiency of B, Fe, Mn, and Zn. These approaches are essential for addressing environmental challenges and closing persistent yield gaps within sustainable cotton production systems. Full article

Background/Objectives: Pacing-induced cardiomyopathy (PiCM) is a recognized complication of chronic right ventricular pacing (RVP), characterized by left ventricular (LV) dysfunction, adverse remodeling, and progression to heart failure. MicroRNAs (miRs) regulate gene expression and play an important role in ventricular remodeling. This study aimed to observe whether dynamic changes in miRs according to a novel peripheral blood mononuclear cell (PBMC)-based approach could serve as early predictive biomarkers of PiCM. Methods: A prospective, single-center cohort study was conducted in adult patients undergoing pacemaker implantation. Clinical characteristics, echocardiographic parameters and expression levels of miR-208b-3p and miR-9 were assessed immediately and 3 months post-pacemaker implantation. PiCM was defined as a ≥10% reduction in LVEF at one year, with no alternative cause. Statistical analyses included correlation testing, ROC curve analysis, and multivariate regression to identify factors associated with PiCM. Results: Among 126 patients, 11.1% developed PiCM. Compared with the non-PiCM group, those who developed PiCM exhibited more pronounced 3-month changes in miR-208b-3p (median Δ₃log miR: +1.3 vs. −0.4, p = 0.013) and miR-9 (median Δ₃log miR: −1.7 vs. +0.21, p = 0.011). In multivariate analyses, Δ₃LV-GLS, Δ₃logmiR-208b-3p, and Δ₃logmiR-9 were associated with a higher likelihood of PiCM. Among PiCM patients, Δ₃logmiR-208b-3p correlated inversely with Δ₃LV-GLS (r = −0.73, p = 0.016), while Δ₃logmiR-9 correlated positively (r = 0.88, p < 0.001). ROC analyses demonstrated good predictive ability for Δ₃LV-GLS (AUC = 0.924), Δ₃log miR-208b-3p (AUC = 0.783), and Δ₃log miR-9 (AUC = 0.835), with no significant differences between curves. Conclusions: Early LV-GLS deterioration and dynamic changes in expression of miR-208b-3p and miR-9 in PBMCs precede overt LV systolic dysfunction. These miRs may serve as early predictive biomarkers for PiCM. Full article

Background: As a newly recognized type of cell death implicated in cancer, ferroptosis plays multiple roles in tumor biology. Here, we sought to construct a prognostic framework for EC on the basis of ferroptosis-related long non-coding RNAs (FerlncRNAs), microRNAs (FermiRNAs), and mRNAs (FRGs) for endometrial cancer (EC). Methods: Transcriptomic profiles of tumors and matched clinical data for 544 EC patients were retrieved from TCGA-UCEC. A prognostic framework was generated through Cox regression, integrating ferroptosis-linked lncRNAs, miRNAs, and mRNAs. EC cases were stratified into groups with high or low predicted risk based on ferroptosis-related gene expression. The model’s prognostic utility was examined through Kaplan–Meier (K–M) analysis and receiver operating characteristic curves. Results: A prognostic model based on 16 RNAs, including 10 FerlncRNAs, 2 FermiRNAs, and 4 FRGs, was developed. Analysis using K–M plots showed that high-risk patients experienced shorter overall survival than their low-risk counterparts (p < 0.001). The model’s area under curve (AUC) values were 0.731, 0.749, and 0.768 at 1-, 3-, and 5-year time points, surpassing those of standard clinical parameters. Furthermore, in an external validation cohort, these signature RNAs were associated with EC prognosis. Conclusions: The novel ferroptosis-related lncRNA–miRNA–mRNA prognostic model provides a basis to assess clinical prognosis in EC patients. Full article

Atherosclerosis is a chronic, multifactorial vascular disease and the leading global cause of cardiovascular morbidity. Its development reflects interconnected disturbances in lipid metabolism, endothelial function, inflammation, smooth muscle cell (SMC) phenotypic switching, and extracellular matrix remodeling. Genetic predisposition, including monogenic disorders such as familial hypercholesterolemia and polygenic risk variants, modulates disease susceptibility by altering lipid homeostasis as well as inflammatory and thrombotic pathways. Epigenetic regulators and noncoding RNAs, such as histone modifications, microRNAs, and long noncoding RNAs, further shape gene expression and link environmental cues to vascular pathology. Endothelial injury promotes lipoprotein retention and oxidation, triggering monocyte recruitment and macrophage-driven foam cell formation, cytokine secretion, and necrotic core development. Persistent inflammation, macrophage heterogeneity, and SMC plasticity collectively drive plaque growth and destabilization. Emerging insights into immune cell metabolism, intracellular signaling networks, and novel regulatory RNAs are expanding therapeutic possibilities beyond lipid-lowering. Current and evolving treatments include statins, proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitors, anti-inflammatory agents targeting interleukin-1 beta (IL-1β) or NOD-, LRR-, and pyrin domain-containing protein 3 (NLRP3), and advanced approaches such as gene editing, siRNA, and nanoparticle-based delivery. Integrating multi-omics, biomarker-guided therapy, and precision medicine promises improved risk stratification and next-generation targeted interventions. This review summarizes recent molecular advances and highlights translational opportunities for enhancing atherosclerosis prevention and treatment. Full article

Early fruit development in tomato is driven by complex gene expression patterns and metabolic reprogramming, a crucial phase that shapes the fruit’s final size and structure. Previous studies using the Micro-Tom model have largely focused on later stages of development, especially ripening, leaving early developmental processes relatively unexplored. To address this knowledge gap, we performed RNA-seq analyses on Micro-Tom fruits harvested at three key developmental stages: 3, 5, and 8 days post-anthesis (DPA). Pairwise differential gene expression analyses revealed that the most extensive transcriptional reprogramming occurs during the transition from 5 to 8 DPA, while comparatively fewer changes were observed between 3 and 5 DPA. K-means clustering of 11,035 stably expressed genes revealed nine distinct expression profiles associated with specific developmental phases, including cell proliferation, transition, and cell expansion. Integrating transcriptomic and metabolomic datasets uncovered coordinated shifts in gene expression and metabolite accumulation, highlighting both conserved regulatory mechanisms and cultivar-specific pathways governing early fruit development. These findings advance our understanding of the molecular regulation of early fruit development in Micro-Tom tomatoes and provide a basis for future efforts to improve fruit quality and yield. Full article

Wheat dwarf virus (WDV) is a major constraint to global wheat production, causing severe yield losses and economic disruption. Understanding the molecular basis of wheat–WDV interactions is essential for developing resistant cultivars. Non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), are key regulators of gene expression and defence. This study identified ncRNAs involved in wheat responses to WDV, including host lncRNAs, miRNAs, and viral small interfering RNAs (siRNAs) targeting WDV genomic regions. High-throughput sequencing revealed extensive ncRNA reprogramming under WDV infection. A total of 437 differentially expressed lncRNAs (DElncRNAs) and 58 miRNAs (DEmiRNAs) were detected. Resistant genotypes displayed more DElncRNAs (204 in Svitava; 163 in Fengyou 3) than the susceptible Akteur (141). In Akteur, 66.7% of DElncRNAs were downregulated, whereas in Svitava, 56.9% were upregulated. Akteur also exhibited more DEmiRNAs (28) than resistant genotypes (15), with predominant downregulation. A co-expression network analysis revealed 391 significant DElncRNA–mRNA interactions mediated by 16 miRNAs. The lncRNA XLOC_058282 was linked to 298 transcripts in resistant genotypes, suggesting a central role in the host defence. Functional annotation showed enrichment in signalling, metabolic, and defence-related pathways. Small RNA profiling identified 1166 differentially expressed sRNAs targeting WDV, including conserved hotspots and 408 genotype-specific sites in Akteur versus Fengyou 3. Infected plants displayed longer sRNAs, a sense-strand bias, and a 5′ uridine preference, but lacked typical 21–24 nt phasing. These findings highlight the central roles of ncRNAs in orchestrating wheat antiviral defence and provide a molecular framework for breeding virus-resistant wheat. Full article

MicroRNAs, pivotal regulators of gene expression and physiology, serve as reliable biomarkers for early cancer diagnosis and therapy. As one of the earliest discovered miRNAs in the human genome, miRNA-21 provides critical information for early cancer diagnosis, drug therapy, and prognosis. In this work, we harness CRISPR as a bridge to integrate target-induced self-priming hairpin isothermal amplification (SIAM) with terminal transferase (TdT) polymerization labeling, constructing a facile, straightforward electrochemical biosensor for sensitive miRNA-21 detection. Unlike conventional single-strand template-based exponential amplification (EXPAR), the SIAM hairpin undergoes target triggered intramolecular conformational change, initiating extension and strand displacement reactions that suppress nonspecific dimer formation and lower background current. Notably, the assay requires only a single probe, enabling unidirectional signal amplification while nonspecific reactions caused by system complexity. The generated SIAM products activate the Cas12a/crRNA complex to trans-cleave PO₄³⁻ modified single-stranded DNAs (ssDNAs); the resulting 3′ hydroxyl ssDNAs are subsequently labeled by TdT, with the assistance of SA-HRP catalyzing hydrogen peroxide, achieving robust signal amplification. Under optimized conditions, the cathodic current exhibits a logarithmic relationship with miRNA concentrations from 20 fM to 5.0 × 10⁸ fM, with a detection limit of 9.2 fM. The biosensor successfully quantified miRNA-21 in commercial serum samples and biological lysates, demonstrating its potential for cancer diagnostics and therapy. Full article

Background: Decitabine efficacy in acute myeloid leukemia (AML) may be enhanced by the pharmacologic upregulation of microRNA miR-29b, a regulator of DNA methyltransferase (DNMT) expression. Bortezomib and sorafenib have been shown preclinically to increase miR-29b levels, providing a biologically informed strategy to sensitize leukemic blasts to DNMT inhibition. Objectives: To evaluate the safety, tolerability, biological activity, and preliminary efficacy of combining bortezomib and sorafenib followed by decitabine in patients with newly diagnosed or relapsed/refractory AML. Methods: This phase I, dose-escalation study enrolled 15 patients (11 untreated, 4 relapsed/refractory) who received fixed-dose bortezomib and sorafenib across three dose levels prior to decitabine. Dose escalation was guided by dose-limiting toxicities (DLTs) and an increase in miR-29b expression. Results: The regimen was generally well tolerated with the most frequent grade ≥3 adverse events of hypertension and febrile neutropenia. At the highest dose level, a ≥2-fold increase in miR-29b expression was observed in two of the six evaluable patients. The overall response rate was 33.3%, with clinical responses observed in both newly diagnosed and relapsed/refractory patients. However, changes in miR-29b expression did not consistently correlate with clinical response. Conclusions: Sequential treatment with bortezomib and sorafenib followed by decitabine is feasible and demonstrates acceptable safety in AML. Although the biologic modulation of miR-29b was variable, this trial provides a proof of concept for pharmacodynamic-guided dose finding in epigenetic therapy combinations. Full article

Background/Objectives: Breast cancer is the most prevalent tumor among women worldwide, with the triple-negative (TNBC) being the most aggressive and therapeutically resistant subtype. It is crucial to investigate new therapeutic targets for the treatment of TNBC. Pentraxin 3 (PTX3), an acute-phase protein, has a complex role in tumor progression, with its expression associated with disease severity. We investigated the role of recombinant human PTX3 (rhPTX3) in modulating microRNA (miRNA) expression and extracellular vesicle (EV) release in TNBC MDA-MB-231 cells. Methods: PTX3 gene expression was evaluated by RT-qPCR. The miRNA expression profile was determined by small RNA Next-Generation Sequencing (NGS). EV release was analyzed by nanoparticle tracking analysis (NTA), flow cytometry, and protein quantification. Results: rhPTX3 treatment significantly increased PTX3 gene expression in MDA-MB-231 cells. Furthermore, rhPTX3 altered the expression profile of 142 miRNAs, with 112 being upregulated and 30 downregulated. These differentially expressed miRNAs were predicted to have 12,894 potential targets, impacting 29 canonical pathways related to carcinogenesis. Key molecules for cancer progression were inhibited (IL6, IL4, CXCL8, CXCR4, CXCL12; ICAM1, CD44 and BCL2), and pro-apoptotic BAD was activated. While rhPTX3-treatment increased total EV release, it specifically reduced the percentage of the CD44+ EV subpopulation. Conclusions: Our data demonstrates that PTX3 modulates the miRNA expression profile and EV release dynamics, particularly by reducing the CD44+ EV population, which points to a tumor-suppressor role in this TNBC context. Given the limited therapeutic avenues for TNBC, our results suggest that PTX3 and its downstream molecular effects represent promising and previously unexplored potential therapeutic targets. Full article

Background: HER2-positive breast cancer patients receiving chemotherapy and targeted therapy (including anthracyclines and trastuzumab) face an elevated risk of cardiotoxicity, which can lead to long-term cardiovascular complications. Identifying predictive biomarkers is essential for early intervention. Circulating microRNAs (miRNAs), known regulators of gene expression and cardiovascular function, have emerged as potential indicators of cardiotoxicity. This study aims to evaluate the differential expression of circulating miRNAs in HER2-positive breast cancer patients undergoing chemotherapy and to assess their prognostic ability for therapy-induced cardiotoxicity using machine learning models. Methods: Forty-seven patients were assessed for cardiac toxicity at baseline and every 3 months, up to 15 months. Blood samples were collected at baseline. MiRNA expression profiling for 84 microRNAs was performed using the miRCURY LNA miRNA PCR Panel. Differential expression was calculated via the 2^−∆∆Ct method. The five most upregulated and five most downregulated miRNAs were further assessed using univariate logistic regression and receiver operating characteristic (ROC) analysis. Five machine learning models (Decision Tree, Random Forest (RF), Support Vector Machine (SVM), Gradient Boosting Machine (GBM), k-Nearest Neighbors (KNN)) were developed to classify cardiotoxicity based on miRNA expression. Results: Forty-five miRNAs showed significant differential expression between cardiac toxic and non-toxic groups. ROC analysis identified hsa-miR-155-5p (AUC 0.76, p = 0.006) and hsa-miR-124-3p (AUC 0.75, p = 0.007) as the strongest predictors. kNN, SVM, and RF models demonstrated high prognostic accuracy. The decision tree model identified hsa-miR-17-5p and hsa-miR-185-5p as key classifiers. SVM and RF highlighted additional miRNAs associated with cardiotoxicity (SVM: hsa-miR-143-3p, hsa-miR-133b, hsa-miR-145-5p, hsa-miR-185-5p, hsa-miR-199a-5p, RF: hsa-miR-185-5p, hsa-miR-145-5p, hsa-miR-17-5p, hsa-miR-144-3p, and hsa-miR-133a-3p). Performance metrics revealed that SVM, kNN, and RF models outperformed the decision tree in overall prognostic accuracy. Pathway enrichment analysis of top-ranked miRNAs demonstrated significant involvement in apoptosis, p53, MAPK, and focal adhesion pathways, all known to be implicated in chemotherapy-induced cardiac stress and remodeling. Conclusions: Circulating miRNAs show promise as biomarkers for predicting cardiotoxicity in breast cancer patients. Machine learning approaches may enhance miRNA-based risk stratification, enabling personalized monitoring and early cardioprotective interventions. Full article

Background: Bone fracture is a partial or complete break in the continuity of a bone, which poses a significant healthcare burden. It is important to discover a novel method to stimulate and speed-up the healing of bone fractures. Aim: This study aimed to investigate the effects and mechanisms of alternating current (AC) in promoting bone fracture healing. Methods: A rabbit bone fracture model was used. X-ray and Micro-CT evaluated fracture healing, while HE staining and immunohistochemistry assessed morphological changes. In vitro, pre-osteoblastic cells were tested with alizarin red S staining and alkaline phosphatase (ALP) activity. RNA-seq analysis explored potential mechanisms. Results: X-ray evaluation showed that alternating current stimulation (ACS) promoted bone formation and shaping by day 14 post-treatment. Micro-CT results revealed significant new bone formation as early as day 3 and day 7 (p < 0.05). HE staining indicated more trabecular bone formation in the ACS group compared to the model group at days 7 and 14. Immunohistochemistry showed higher expression of BMP-2 and VEGF in the ACS group by day 7. In vitro, ACS enhanced osteogenic differentiation, increasing calcified nodule formation and ALP activity. Gene expression analysis demonstrated significant changes in key osteogenic genes, confirmed by multiple immunohistochemical staining. Conclusions: ACS may be a novel method for treating bone fractures more rapidly, significantly relieving the patient’s burden, particularly in the early stages of bone healing. Full article

(1) Background: ‘Chaling’ common wild rice (CLWR), one of the two wild rice populations with the northernmost natural distribution worldwide, exhibits excellent cold tolerance. The role of microRNA (miRNA) in regulating cold tolerance in plants has been reported in some species. However, the miRNA landscape in CLWR remains unexplored. (2) Methods: We assessed cold tolerance in CLWR and the conventional rice variety 9311 at 4 °C, and conducted small RNA sequencing and analysis on eight samples from both CLWR and 9311, before and after cold treatment. (3) Results: All seedlings of CLWR survived after cold treatment and recovery, while all seedlings of 9311 died. After quality control and classification analysis of the small RNA sequences, numerous known and novel microRNAs (miRNAs) were identified. The expression analysis showed 59 differentially expressed miRNAs in CLWR before and after cold treatment, and 19 in 9311, with eight overlapping differentially expressed miRNAs between the two varieties. Target gene prediction for these miRNAs indicated that some predicted target genes, such as CTB4a and GRF4, are key genes involved in regulating cold tolerance in rice. Additionally, CLWR actively mobilizes more miRNAs and their target genes to resist cold stress than 9311. (4) Conclusions: This study offers new insights into the regulatory mechanisms of cold tolerance in CLWR at the miRNA level, providing a wealth of gene (miRNA) resources for genetic breeding research in rice aimed at enhancing cold tolerance. Full article

Recently, studies have increasingly focused on neuropathological and molecular alterations that occur in the early stages of neurodegenerative diseases to understand the primary pathogenesis. This review provides an updated overview of the early pathological and molecular changes in multiple system atrophy (MSA), a neurodegenerative condition characterised by the degeneration of both the striatonigral and olivopontocerebellar systems. In advanced stages of MSA, abnormal α-synuclein accumulates in the cytoplasm and nuclei of oligodendrocytes and neurones. However, in addition to these established pathological hallmarks, previous analyses of preclinical MSA cases have revealed characteristic accumulations of abnormal α-synuclein within and adjacent to the nuclear membrane. Moreover, analyses of cerebrospinal fluid and plasma from patients with MSA within 3 years of disease onset have identified alterations in various proteins and microRNAs linked to neurodegeneration and neuroinflammation. Consistent with these findings, in vitro and in vivo models of early-stage MSA have demonstrated abnormalities in neurodegeneration, neuroinflammation, and mitochondrial function. Collectively, these observations highlight the primary pathogenesis of early-stage MSA. Full article