A Comprehensive Review on Function of miR-15b-5p in Malignant and Non-Malignant Disorders

Discovery and functional characterization of LncRNAs associated with inflammation and macrophage activation

Long noncoding RNAs (lncRNA) are emerging players in regulation of gene expression and cell signaling and their dysregulation has been implicated in a multitude of human diseases. Recent studies from our laboratory revealed that lncRNAs play critical roles in cytokine regulation, inflammation, and metabolism. We demonstrated that lncRNA HOTAIR, which is a well-known regulator of gene silencing, plays critical roles in modulation of cytokines and proinflammatory genes, and glucose metabolism in macrophages during inflammation. In addition, we recently discovered a series of novel lncRNAs that are closely associated with inflammation and macrophage activation. We termed these as long-noncoding inflammation associated RNAs (LinfRNAs). We are currently engaged in the functional characterization of these hLinfRNAs (human LinfRNAs) with a focus on their roles in inflammation, and we are investigating their potential implications in chronic inflammatory human diseases. Here, we have summarized experimental methods that have been utilized for the discovery and functional characterization of lncRNAs in inflammation and macrophage activation.

Topology and Dynamics of Transcriptome (Dys)Regulation

RNA transcripts play a crucial role as witnesses of gene expression health. Identifying disruptive short sequences in RNA transcription and regulation is essential for potentially treating diseases. Let us delve into the mathematical intricacies of these sequences. We have previously devised a mathematical approach for defining a "healthy" sequence. This sequence is characterized by having at most four distinct nucleotides (denoted as nt≤4). It serves as the generator of a group denoted as fp. The desired properties of this sequence are as follows: fp should be close to a free group of rank nt-1, it must be aperiodic, and fp should not have isolated singularities within its SL2(C) character variety (specifically within the corresponding Groebner basis). Now, let us explore the concept of singularities. There are cubic surfaces associated with the character variety of a four-punctured sphere denoted as S24. When we encounter these singularities, we find ourselves dealing with some algebraic solutions of a dynamical second-order differential (and transcendental) equation known as the Painlevé VI Equation. In certain cases, S24 degenerates, in the sense that two punctures collapse, resulting in a "wild" dynamics governed by the Painlevé equations of an index lower than VI. In our paper, we provide examples of these fascinating mathematical structures within the context of miRNAs. Specifically, we find a clear relationship between decorated character varieties of Painlevé equations and the character variety calculated from the seed of oncomirs. These findings should find many applications including cancer research and the investigation of neurodegenative diseases.

Higher Expression of miR-15b-5p with Inclusion of Fresh, Lean Beef as Part of a Healthy Dietary Pattern Is Inversely Associated with Markers of Cardiometabolic Disease Risk

BACKGROUND

Considerable controversy exists surrounding the consumption of red meat and its impacts on cardiometabolic health and if it may further impact risk factors at the molecular level.

OBJECTIVE

The purpose of this study was to examine the acute effects of dietary patterns, varying in red meat quantity, on the expression of circulating microRNAs (miRNAs), which are emerging biomarkers of metabolic dysfunction and chronic disease severity.

METHODS

Secondary analyses were performed on plasma samples collected within a randomized, crossover design study in 16 women with overweight (mean ± standard deviation, age = 33 ± 9.89 y; body mass index = 27.9 ± 1.66 kg/m2). Participants were provided with eucaloric, isonitrogenous diets (15% of daily intake as protein) containing either 2 servings of fresh, lean beef/day (BEEF) or 0 servings of fresh, lean beef/day (PLANT) for 7 d/pattern. Fasting blood samples were collected at the end of each dietary pattern for the assessment of 12 circulating metabolic miRNA expression levels (determined a priori by quantitative reverse transcriptase-polymerase chain reaction), plasma glucose, insulin, interleukin-6, tumor necrosis factor-α, C-reactive protein (CRP), adiponectin, glucagon-like peptide-1, and branched-chain amino acids.

RESULTS

Of the 12 miRNAs, miR-15b-5p expression was higher following BEEF versus PLANT (P = 0.024). Increased miR-15b-5p expression correlated with decreased fasting CRP (r = -0.494; P = 0.086) and insulin concentrations (r = -0.670; P = 0.017). miR-15b-5p was inversely correlated with insulin resistance (r = -0.642; P = 0.024) and β cell function (r = -0.646; P = 0.023) and positively correlated with markers of insulin sensitivity (r = 0.520; P = 0.083). However, the correlations were only observed following BEEF, not PLANT.

CONCLUSIONS

These data indicate that the short-term intake of fresh, lean beef as part of a healthy dietary pattern impacts potential biomarkers of cardiometabolic health that are associated with cardiometabolic risk factors in women with overweight. This study was registered at clinicaltrials.gov as NCT02614729.

Sex differences in neuromuscular and biological determinants of isometric maximal force

AIM

Force expression is characterized by an interplay of biological and molecular determinants that are expected to differentiate males and females in terms of maximal performance. These include muscle characteristics (muscle size, fiber type, contractility), neuromuscular regulation (central and peripheral factors of force expression), and individual genetic factors (miRNAs and gene/protein expression). This research aims to comprehensively assess these physiological variables and their role as determinants of maximal force difference between sexes.

METHODS

Experimental evaluations include neuromuscular components of isometric contraction, intrinsic muscle characteristics (proteins and fiber type), and some biomarkers associated with muscle function (circulating miRNAs and gut microbiome) in 12 young and healthy males and 12 females.

RESULTS

Male strength superiority appears to stem primarily from muscle size while muscle fiber-type distribution plays a crucial role in contractile properties. Moderate-to-strong pooled correlations between these muscle parameters were established with specific circulating miRNAs, as well as muscle and plasma proteins.

CONCLUSION

Muscle size is crucial in explaining the differences in maximal voluntary isometric force generation between males and females with similar fiber type distribution. Potential physiological mechanisms are seen from associations between maximal force, skeletal muscle contractile properties, and biological markers.

Towards the development of a DNA automaton: modular RNA-cleaving deoxyribozyme logic gates regulated by miRNAs

Advancements in DNA computation have unlocked molecular-scale information processing possibilities, utilizing the intrinsic properties of DNA for complex logical operations with transformative applications in biomedicine. DNA computation shows promise in molecular diagnostics, enabling precise and sensitive detection of genetic mutations and disease biomarkers. Moreover, it holds potential for targeted gene regulation, facilitating personalized therapeutic interventions with enhanced efficacy and reduced side effects. Herein, we have developed six DNAzyme-based logic gates able to process YES, AND, and NOT Boolean logic. The novelty of this work lies in their additional functionalization with a common DNA scaffold for increased cooperativity in input recognition. Moreover, we explored hierarchical input binding to multi-input logic gates, which helped gate optimization. Additionally, we developed a new design of an allosteric hairpin switch used to implement NOT logic. All DNA logic gates achieved the desired true-to-false output signal when detecting a panel of miRNAs, known for their important role in malignancy regulation. This is the first example of DNAzyme-based logic gates having all input-recognizing elements integrated in a single DNA nanostructure, which provides new opportunities for building DNA automatons for diagnosis and therapy of human diseases.

Obstructive sleep apnea alters microRNA levels: Effects of continuous positive airway pressure

Background

Obstructive sleep apnea (OSA) has been linked to cytokine-mediated chronic inflammatory states. Continuous positive airway pressure (CPAP) is an established therapy for OSA, but its effects on inflammation remain unclear. A recent study from our group identified soluble cytokine receptors altered in OSA patients and modified by CPAP adherence. However, the upstream regulatory pathways responsible for these shifts in proinflammatory cascades with OSA and CPAP therapy remained unknown. Accordingly, this study mapped OSA and CPAP-modulated soluble cytokine receptors to specific microRNAs and then tested the hypothesis that OSA and CPAP adherence shift cytokine-related microRNA expression profiles.

Study Design

Plasma samples were collected from patients with OSA (n=50) at baseline and approximately 90 days after CPAP initiation and compared to referent control subjects (n=10). Patients with OSA were further divided into cohorts defined by adherence vs nonadherence to CPAP therapy. The microRNAs that mapped to soluble cytokine receptors of interest were subjected to quantitative polymerase chain reaction.

Results

At baseline, increased hsa-miR-15a-5p, hsa-miR-15b-5p, hsa-miR-16-5p, hsa-miR-195-5p, hsa-miR-424-5p, hsa-miR-223-3p, and hsa-miR-223-5p were observed in patients with OSA compared to controls (p<0.05). In CPAP adherent patients (n=22), hsa-miR233-3p and hsa-miR233-5p decreased at follow-up (p<0.05) whereas there was no change in miR levels from baseline in non-adherent CPAP patients (n=28). The miRs hsa-miR233-3p and hsa-miR233-5p mapped to both proinflammatory and innate immunity activation; the inflammasome.

Conclusion

A specific set of microRNAs, including hsa-miR233-3p and hsa-miR233-5p, may serve as a marker of inflammatory responses in patients with OSA, and be used to assess attenuation of inflammasome activation by CPAP.

Oxidative Stress Mediates Epigenetic Modifications and the Expression of miRNAs and Genes Related to Apoptosis in Diabetic Retinopathy Patients

Knowledge on the underlying mechanisms and molecular targets for managing the ocular complications of type 2 diabetes mellitus (T2DM) remains incomplete. Diabetic retinopathy (DR) is a major cause of irreversible visual disability worldwide. By using ophthalmological and molecular-genetic approaches, we gathered specific information to build a data network for deciphering the crosslink of oxidative stress (OS) and apoptosis (AP) processes, as well as to identify potential epigenetic modifications related to noncoding RNAs in the eyes of patients with T2DM. A total of 120 participants were recruited, being classified into two groups: individuals with T2MD (T2MDG, n = 67), divided into a group of individuals with (+DR, n = 49) and without (-DR, n = 18) DR, and a control group (CG, n = 53). Analyses of compiled data reflected significantly higher plasma levels of malondialdehyde (MDA), superoxide dismutase (SOD), and glutathione peroxidase (GPx) and significantly lower total antioxidant capacity (TAC) in the +DR patients compared with the -DR and the CG groups. Furthermore, the plasma caspase-3 (CAS3), highly involved in apoptosis (AP), showed significantly higher values in the +DR group than in the -DR patients. The microRNAs (miR) hsa-miR 10a-5p and hsa-miR 15b-5p, as well as the genes BCL2L2 and TP53 involved in these pathways, were identified in relation to DR clinical changes. Our data suggest an interaction between OS and the above players in DR pathogenesis. Furthermore, potential miRNA-regulated target genes were identified in relation to DR. In this concern, we may raise new diagnostic and therapeutic challenges that hold the potential to significantly improve managing the diabetic eye.

miR-15b-5p transcription mediated by CREB1 protects against inflammation and apoptosis in Parkinson disease models by inhibiting AXIN2 and activating Wnt/β-catenin

Parkinson disease (PD) is a major neurodegenerative disease that greatly undermines people's health and for which effective therapeutic strategies are currently limited. This study dissected the effects of expression changes of AXIN2, a modulator of the Wnt/beta-catenin signaling pathway, the transcription factor CREB1, and of the microRNA miR-15b-5p on apoptosis and the inflammatory response in a PD mouse model in vivo and in a cellular PD model in vitro. The analyses demonstrated low CREB1 and miR-15b-5p expression and high AXIN2 expression in both models. miR-15b-5p overexpression or AXIN2 knockdown alleviated the inflammatory response indicated by decreased levels of TNF-α, IL-6, and IL-1β and apoptosis indicated by decreased levels of cleaved caspase-3 and Bax and elevated Bcl-2. Protection by miR-15b-5p upregulation was counteracted by the simultaneous overexpression of AXIN2. miR-15b-5p targeted AXIN2. CREB1 promoted miR-15b-5p expression, which activated the Wnt/β-catenin pathway by inhibiting AXIN2. Collectively, the data indicate that transcriptional expression of miR-15b-5p can be promoted by CREB1 to inhibit AXIN2 and activate Wnt/β-catenin, thereby reducing the inflammatory response and apoptosis in these PD models. These data suggest the CREB1/miR-15b-5p/AXIN2 axis is a potential therapeutic target in PD patients.

Dysregulation of MicroRNAs in Adult Osteogenesis Imperfecta: The miROI Study

As epigenetic regulators of gene expression, circulating micro-RiboNucleic Acids (miRNAs) have been described in several bone diseases as potential prognostic markers. The aim of our study was to identify circulating miRNAs potentially associated with the severity of osteogenesis imperfecta (OI) in three steps. We have screened by RNA sequencing for the miRNAs that were differentially expressed in sera of a small group of OI patients versus controls and then conducted a validation phase by RT-qPCR analysis of sera of a larger patient population. In the first phase of miROI, we found 79 miRNAs that were significantly differentially expressed. We therefore selected 19 of them as the most relevant. In the second phase, we were able to validate the significant overexpression of 8 miRNAs in the larger OI group. Finally, we looked for a relationship between the level of variation of the validated miRNAs and the clinical characteristics of OI. We found a significant difference in the expression of two microRNAs in those patients with dentinogenesis imperfecta. After reviewing the literature, we found 6 of the 8 miRNAs already known to have a direct action on bone homeostasis. Furthermore, the use of a miRNA-gene interaction prediction model revealed a 100% probability of interaction between 2 of the 8 confirmed miRNAs and COL1A1 and/or COL1A2. This is the first study to establish the miRNA signature in OI, showing a significant modification of miRNA expression potentially involved in the regulation of genes involved in the physiopathology of OI. © 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).

Transcriptional repression of lncRNA and miRNA subsets mediated by LRF during erythropoiesis

Non-coding RNA (ncRNA) species, mainly long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been currently imputed for lesser or greater involvement in human erythropoiesis. These RNA subsets operate within a complex circuit with other epigenetic components and transcription factors (TF) affecting chromatin remodeling during cell differentiation. Lymphoma/leukemia-related (LRF) TF exerts higher occupancy on DNA CpG rich sites and is implicated in several differentiation cell pathways and erythropoiesis among them and also directs the epigenetic regulation of hemoglobin transversion from fetal (HbF) to adult (HbA) form by intervening in the γ-globin gene repression. We intended to investigate LRF activity in the evolving landscape of cells' commitment to the erythroid lineage and specifically during HbF to HbA transversion, to qualify this TF as potential repressor of lncRNAs and miRNAs. Transgenic human erythroleukemia cells, overexpressing LRF and further induced to erythropoiesis, were subjected to expression analysis in high LRF occupancy genetic loci-producing lncRNAs. LRF abundance in genetic loci transcribing for studied lncRNAs was determined by ChIP-Seq data analysis. qPCRs were performed to examine lncRNA expression status. Differentially expressed miRNA pre- and post-erythropoiesis induction were assessed by next-generation sequencing (NGS), and their promoter regions were charted. Expression levels of lncRNAs were correlated with DNA methylation status of flanked CpG islands, and contingent co-regulation of hosted miRNAs was considered. LRF-binding sites were overrepresented in LRF overexpressing cell clones during erythropoiesis induction and exerted a significant suppressive effect towards lncRNAs and miRNA collections. Based on present data interpretation, LRF's multiplied binding capacity across genome is suggested to be transient and associated with higher levels of DNA methylation. KEY MESSAGES: During erythropoiesis, LRF displays extensive occupancy across genetic loci. LRF significantly represses subsets of lncRNAs and miRNAs during erythropoiesis. Promoter region CpG islands' methylation levels affect lncRNA expression. MiRNAs embedded within lncRNA loci show differential regulation of expression.

Circulating miRNAs as biomarkers for diagnosis, surveillance and post-operative follow-up of abdominal aortic aneurysms

OBJECTIVE

To provide a summary of the current state of research in English medical literature on circulating miRNAs, as biomarkers for AAA. Additionally, for the most commonly mentioned circulating miRNAs in the literature, to attempt a documentation of the biological mechanisms underlying their role in AAA development.

METHODS

A literature search was undertaken in the MEDLINE database. Only reports that involved peripheral blood samples (whole blood, plasma, serum) were included. The following terms were used in combination: microrna, mirna, abdominal aortic aneurysm, human, circulating, plasma, serum, endovascular and EVAR.

RESULTS

A total of 25 reports, published from 2012 to 2022 were included with a total of 1259 patients with AAA, predominantly men (N= 1040, 90%). Six of these reports recruited healthy donors who underwent ultrasound screening for AAA as control samples. The majority of studies were undertaken in plasma samples and the most preferred microRNA profiling method was Real - Time quantitative polymerase chain reaction (qRT-PCR). The following nine miRNAs (out of a total of 76) were studied in more than two references: miR-145, miR-24, miR-33, miR-125, let-7, miR-15, miR-191, miR-29 and miR-133.

CONCLUSION

The nine miRNAs described in this study, are implicated in known pathogenetic mechanisms of AAA such as atherosclerosis, vascular smooth muscle cell phenotype switch and apoptosis, vascular inflammation, extracellular matrix degradation and lipid metabolism. Identifying disease-specific miRNAs, in combination with other clinical parameters, as indicators of AAA, is crucial for early diagnosis as well as follow-up of AAAs. For future research on miRNAs as AAA biomarkers, strict case and control group definitions, sample acquisition protocols, and miRNA expression profiling techniques are warranted.

MiR-15b-5p inhibits castration-resistant growth of prostate cancer cells by targeting the muscarinic cholinergic receptor CHRM3

Cholinergic receptor muscarinic 3 (CHRM3)-mediated focal adhesion kinase/YES-associated protein (YAP) signalling is essential for the growth of castration-resistant prostate cancer (CRPC) cells. Here, we evaluated the molecular mechanisms through which CHRM3 overexpression facilitates castration-resistant growth. Small RNA sequencing combined with in silico analyses revealed that CHRM3 was a putative target of miR-15b-5p. Notably, androgen deprivation suppressed miR-15b-5p expression and increased CHRM3 expression. Moreover, miR-15b-5p bound directly to CHRM3 and inhibited YAP activation induced by CHRM3 stimulation. Furthermore, miR-15b-5p abolished the growth of CRPC cells induced by CHRM3 stimulation. We conclude that the miR-15b-5p/CHRM3/YAP signalling axis promotes the castration-resistant growth of prostate cancer.

MiR-15b-5p Expression in the Peripheral Blood: A Potential Diagnostic Biomarker of Autism Spectrum Disorder

BACKGROUND

Autism spectrum disorder (ASD), is a neurodevelopmental disorder that is known to have a high degree of heritability. Diagnosis of ASD is difficult because of the high heterogeneity of the clinical symptoms. MicroRNAs (miRNAs) can potentially be diagnostic biomarkers for ASD, and several studies have shown the relationship between miRNAs and ASD pathogenesis. In this study, we investigated ten miRNA and mRNA expression of target genes in peripheral blood to explore a diagnostic biomarker for ASD.

METHODS

We recruited control and ASD subjects for the discovery cohort (n = 6, each) and replication cohort (n = 20, each). Using qPCR, miRNA and mRNA expression was measured using the SYBR green and probe methods, respectively. In-silico prediction was used for identifying target genes of miRNAs. An in vitro experiment using HEK293 cells was conducted to investigate whether miR-15b-5p modulates the predicted target genes (TGFBR3 and MYBL1).

RESULTS

miR-15b-5p expression indicated an increased trend in the discovery cohort (p = 0.052) and a significant upregulation in the replication cohort (p = 0.021). In-silico analysis revealed that miR-15b-5p is relevant to cell development and Wnt signaling. The decreased trends of TGFBR3 and MYBL expression were the same as in previous RNA-seq data. MiR-15b-5p positively regulated TGFBR3 expression in in vitro experiments.

CONCLUSIONS

Upregulated miR-15b-5p expression may represent a useful diagnostic marker of ASD subjects, and it may regulate TGFBR3 mRNA expression. These findings indicate a new perspective in the understanding of the pathogenesis of ASD.

Emerging roles and mechanisms of miR-206 in human disorders: a comprehensive review

As a member of the miR-1 family, miR-206 is located between IL-17 and PKHD1 genes in human. This miRNA has been shown to be involved in the pathogenic processes in a variety of human disorders including cancers, amyotrophic lateral sclerosis, Alzheimer's disease, atherosclerosis, bronchopulmonary dysplasia, coronary artery disease, chronic obstructive pulmonary disease, epilepsy, nonalcoholic fatty liver disease, Hirschsprung disease, muscular dystrophies, pulmonary arterial hypertension, sepsis and ulcerative colitis. In the current review, we summarize the role of miR-206 in both malignant and non-malignant situations and explain its possible therapeutic implications.

The emerging roles and potential applications of circular RNAs in ovarian cancer: a comprehensive review

Ovarian cancer (OC) is among the most common human malignancies and the first cause of deaths among gynecologic cancers. Early diagnosis can help improving prognosis in those patients, and accordingly exploring novel molecular mechanisms may lead to find therapeutic targets. Circular RNAs (circRNAs) comprise a group of non-coding RNAs in multicellular organisms, which are identified with characteristic circular structure. CircRNAs have been found with substantial functions in regulating gene expression through interacting with RNA-binding proteins, targeting microRNAs, and transcriptional regulation. They have been found to be involved in regulating several critical processes such as cell growth, and death, organ development, signal transduction, and tumorigenesis. Accordingly, circRNAs have been implicated in a number of human diseases including malignancies. They are particularly reported to contribute to several hallmarks of cancer leading to cancer development and progression, although a number also are described with tumor-suppressor function. In OC, circRNAs are linked to regulation of cell growth, invasiveness, metastasis, angiogenesis, and chemoresistance. Notably, clinical studies also have shown potentials in diagnosis, prediction of prognosis, and therapeutic targets for OC. In this review, I have an overview to the putative mechanisms, and functions of circRNAs in regulating OC pathogenesis in addition to their clinical potentials.