Target prediction and validation of microRNAs expressed from FSHR and aromatase genes in human ovarian granulosa cells

DUSP8-attenuated ERK1/2 signaling mediates lipogenesis and steroidogenesis in chicken granulosa cells

The lipogenesis and steroidogenesis of granulosa cells are crucial during follicular development, yet it remains unclear whether dual-specificity phosphatase 8 (DUSP8) is involved. In this study, the specific role of DUSP8 in lipogenesis and steroidogenesis was investigated through culturing chicken granulosa cells in vitro. The results revealed that the expression levels of adipogenic genes were elevated after DUSP8 overexpression and reduced after knockdown. The same was observed for lipid deposition in granulosa cells. Meanwhile, the steroidogenic gene expression and progesterone synthesis were promoted after DUSP8 overexpression and inhibited after knockdown. In addition, we also found that DUSP8 blocked the phosphorylation of extracellular regulatory kinase 1/2 (ERK1/2). Based on the previous results that activated ERK1/2 signaling inhibited lipid deposition and progesterone synthesis in chicken granulosa cells, we demonstrated that DUSP8 promoted lipid deposition and progesterone synthesis through mediating the ERK1/2 signaling pathway. The results will improve our understanding of the molecular regulatory mechanisms regarding lipid metabolism and progesterone synthesis in chicken granulosa cells.

Rocket-miR, a translational launchpad for miRNA-based antimicrobial drug development

IMPORTANCE

Antimicrobial-resistant infections contribute to millions of deaths worldwide every year. In particular, the group of bacteria collectively known as ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter sp.) pathogens are of considerable medical concern due to their virulence and exceptional ability to develop antibiotic resistance. New kinds of antimicrobial therapies are urgently needed to treat patients for whom existing antibiotics are ineffective. The Rocket-miR application predicts targets of human miRNAs in bacterial and fungal pathogens, rapidly identifying candidate miRNA-based antimicrobials. The application's target audience are microbiologists that have the laboratory resources to test the application's predictions. The Rocket-miR application currently supports 24 recognized human pathogens that are relevant to numerous diseases including cystic fibrosis, chronic obstructive pulmonary disease (COPD), urinary tract infections, and pneumonia. Furthermore, the application code was designed to be easily extendible to other human pathogens that commonly cause hospital-acquired infections.

Genome-Wide Association Study of Egg Production Traits in Shuanglian Chickens Using Whole Genome Sequencing

Egg production is the most important economic trait in laying hens. To identify molecular markers and candidate genes associated with egg production traits, such as age at first egg (AFE), weight at first egg (WFE), egg weight (EW), egg number (EN), and maximum consecutive egg laying days (MCD), a genome-wide analysis by whole genome sequencing was performed in Shuanglian chickens. Through whole genome sequencing and quality control, a total of 11,006,178 SNPs were obtained for further analysis. Heritability estimates ranged from moderate to high for EW (0.897) and MCD (0.632), and from low to moderate (0.193~0.379) for AFE, WFE, and EN. The GWAS results showed 11 genome-wide significant SNPs and 23 suggestive significant SNPs were identified to be associated with EN, MCD, WFE, and EW. Linkage disequilibrium analysis revealed twenty-seven SNPs associated with EN were located in a 0.57 Mb region on GGA10, and clustered into five blocks. Through functional annotation, three candidate genes NEO1, ADPGK, and CYP11A1, were identified to be associated with EN, while the S1PR4, LDB2, and GRM8 genes was linked to MCD, WFE, and EW, respectively. These findings may help us to better understand the molecular mechanisms underlying egg production traits in chickens and contribute to genetic improvement of these traits.

MiR-223-3p attenuates radiation-induced inflammatory response and inhibits the activation of NLRP3 inflammasome in macrophages

Macrophage pyroptosis plays an important role in the development of radiation-induced cell and tissue damage, leading to acute lung injury. However, the underlying mechanisms of NOD-like receptor thermal protein domain-associated protein 3 (NLRP3)-mediated macrophage pyroptosis and the regulatory factors involved in radiation-induced pyroptosis are unclear. In this study, the expression of the NLRP3 inflammasome and pyroptosis-associated factors in murine macrophage cell lines was investigated after ionizing radiation. High-throughput RNA sequencing was performed to identify and characterize miRNAs and mRNA transcripts associated with NLRP3-mediated cell death. Our results demonstrated that cleaved-caspase-1 (p10) and N-terminal domain of gasdermin-D (GSDMD-N) were upregulated, and the number of NLRP3 inflammasomes and pyroptotic cells increased in murine macrophage cell lines after irradiation (8 Gy). Comparativeprofiling of 300miRNAs revealed that 41 miRNAsexhibited significantly different expression after 8 Gy of irradiation. Granulocyte-specific microRNA-223-3p (miR-223-3p) is a negative regulator of NLRP3. In vitro experiments revealed that the expression of miR-223-3p was significantly altered by irradiation. Moreover, miR-223-3p decreased the expression of NLRP3 and proinflammatory factors, resulting in reduced pyroptosis in irradiated murine macrophages. Subsequently, in vivo experiments revealed the efficacy of miR-223-3p supplementation in ameliorating alveolar macrophage (AM) pyroptosis, attenuating the infiltration of inflammatory monocytes, and significantly alleviating the severity of acute radiation-induced lung injury (ARILI). Our findings suggest that the miR-223-3p/NLRP3/caspase-1 axis is involved in radiation-induced AM pyroptosis and ARILI.

MicroRNAs as Targets for Cancer Diagnosis: Interests and Limitations

MicroRNAs are small RNAs with ability to attach to the large number of RNA that regulate gene expression on post-transcriptional level via inhibition or degradation of specific mRNAs. MiRNAs in cells are the primary regulators of functions such as cell growth, differentiation, and apoptosis and considerably influence cell function. The expression levels of microRNAs change in human diseases, including cancer. These changes highlight their essential role in cancer pathogenesis. Ubiquitous irregular expression profiles of miRNAs have been detected in various human cancers using genome-wide identification techniques, which are emerging as novel diagnostic and prognostic cancer biomarkers of high specificity and sensitivity. The measurable miRNAs with enhanced stability in blood, tissues, and other body fluids provide a comprehensive source of miRNA-dependent biomarkers for human cancers. The leading role of miRNAs as potential biomarkers in human cancers is discussed in this article. In addition, the interests and difficulties of miRNAs as biomarkers have been explored.

The diagnostic significance of the ZNF gene family in pancreatic cancer: a bioinformatics and experimental study

Background: Pancreatic adenocarcinoma (PAAD) is among the most devastating of all cancers with a poor survival rate. Therefore, we established a zinc finger (ZNF) protein-based prognostic prediction model for PAAD patients. Methods: The RNA-seq data for PAAD were downloaded from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. Differentially expressed ZNF protein genes (DE-ZNFs) in PAAD and normal control tissues were screened using the "lemma" package in R. An optimal risk model and an independent prognostic value were established by univariate and multivariate Cox regression analyses. Survival analyses were performed to assess the prognostic ability of the model. Results: We constructed a ZNF family genes-related risk score model that is based on the 10 DE-ZNFs (ZNF185, PRKCI, RTP4, SERTAD2, DEF8, ZMAT1, SP110, U2AF1L4, CXXC1, and RMND5B). The risk score was found to be a significant independent prognostic factor for PAAD patients. Seven significantly differentially expressed immune cells were identified between the high- and low-risk patients. Then, based on the prognostic genes, we constructed a ceRNA regulatory network that includes 5 prognostic genes, 7 miRNAs and 35 lncRNAs. Expression analysis showed ZNF185, PRKCI and RTP4 were significantly upregulated, while ZMAT1 and CXXC1 were significantly downregulated in the PAAD samples in all TCGA - PAAD, GSE28735 and GSE15471 datasets. Moreover, the upregulation of RTP4, SERTAD2, and SP110 were verified by the cell experiments. Conclusion: We established and validated a novel, Zinc finger protein family - related prognostic risk model for patients with PAAD, that has the potential to inform patient management.

MicroRNA miR-125b can suppress ovarian granulosa cell functions: Interrelationships with FSH

This study aimed to evaluate the involvement of miR-125b and its interrelationship with follicle-stimulating hormone (FSH) in the control of basic ovarian granulosa cell functions. The effect of miR-125b mimics on basic functions of porcine ovarian granulosa cells cultured with and without FSH, and the effect of FSH on the expression of endogenous miR-125b was examined. Expression levels of miR-125b, viability, proliferation (accumulation of PCNA and cyclin B1), apoptosis (accumulation of bax and caspase 3), the accumulation of FSH receptors (FSHR), steroid hormones, insulin-like growth factor I (IGF-I), oxytocin, and prostaglandin E2 release were analysed by reverse transcription-quantitative polymerase chain reaction, Trypan blue exclusion test, quantitative immunocytochemistry, and ELISA. Transfection of cells with miR-125b mimics inhibited cell viability, proliferation, apoptosis, the occurrence of FSHR, progesterone, testosterone, estradiol, and oxytocin release but stimulated prostaglandin E2 output. FSH promoted cell viability, proliferation, steroid hormones, IGF-I, oxytocin, and prostaglandin E2 output and reduced the expression of miR-125b and apoptosis. Furthermore, miR-125b mimics supported the effect of FSH on the release of estradiol, IGF-I, and prostaglandin E2, and inverted FSH influence on cell viability, proliferation, apoptosis, progesterone, and testosterone output. FSH supported both inhibitory and stimulatory action of miR-125b on ovarian cell functions. Present observations indicate that: miR-125b can be involved in the control of basic ovarian functions and that miR-125b and FSH are antagonists in their actions on ovarian cell functions. The ability of FSH to reduce miR-125b expression and the ability of miR-125b mimics to decrease the occurrence of FSHR and to modify FSH effects indicate the existence of the self-inhibiting FSH-miR-125b axis and that miR-125b can mediate the actions of FSH on ovarian cells.

Innovative approaches in transforming microRNAs into therapeutic tools

MicroRNA (miRNA) is regarded as a prominent genetic regulator, as it can fine-tune an entire biological pathway by targeting multiple target genes. This characteristic makes miRNAs promising therapeutic tools to reinstate cell functions that are disrupted as a consequence of diseases. Currently, miRNA replacement by miRNA mimics and miRNA inhibition by anti-miRNA oligonucleotides are the main approaches to utilizing miRNA molecules for therapeutic purposes. Nevertheless, miRNA-based therapeutics are hampered by major issues such as off-target effects, immunogenicity, and uncertain delivery platforms. Over the past few decades, several innovative approaches have been established to minimize off-target effects, reduce immunostimulation, and provide efficient transfer to the target cells in which these molecules exert their function. Recent achievements have led to the testing of miRNA-based drugs in clinical trials, and these molecules may become next-generation therapeutics for medical intervention. Despite the achievement of exciting milestones, the dosage of miRNA administration remains unclear, and ways to address this issue are proposed. Elucidating the current status of the main factors of therapeutic miRNA would allow further developments and innovations to achieve safe therapeutic tools. This article is categorized under: RNA in Disease and Development > RNA in Disease Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action.

mintRULS: Prediction of miRNA–mRNA Target Site Interactions Using Regularized Least Square Method

Identification of miRNA–mRNA interactions is critical to understand the new paradigms in gene regulation. Existing methods show suboptimal performance owing to inappropriate feature selection and limited integration of intuitive biological features of both miRNAs and mRNAs. The present regularized least square-based method, mintRULS, employs features of miRNAs and their target sites using pairwise similarity metrics based on free energy, sequence and repeat identities, and target site accessibility to predict miRNA-target site interactions. We hypothesized that miRNAs sharing similar structural and functional features are more likely to target the same mRNA, and conversely, mRNAs with similar features can be targeted by the same miRNA. Our prediction model achieved an impressive AUC of 0.93 and 0.92 in LOOCV and LmiTOCV settings, respectively. In comparison, other popular tools such as miRDB, TargetScan, MBSTAR, RPmirDIP, and STarMir scored AUCs at 0.73, 0.77, 0.55, 0.84, and 0.67, respectively, in LOOCV setting. Similarly, mintRULS outperformed other methods using metrics such as accuracy, sensitivity, specificity, and MCC. Our method also demonstrated high accuracy when validated against experimentally derived data from condition- and cell-specific studies and expression studies of miRNAs and target genes, both in human and mouse.

Downregulation of hsa-miR-4328 and target gene prediction in Acute Promyelocytic Leukemia

Introduction: Acute promyelocytic leukemia (APL) is defined by the PML-RARA fusion gene. APL treatment can have significant side effects, therefore the development of optimal therapeutic options is crucial. Although the study of miRNAs is still in its infancy, it has been shown that these molecules are involved in the pathogenesis of neoplasms by modulating the expression of target genes. miRNAs can be considered possible biomarkers in APL and can be used as therapeutic targets or as markers for the therapeutic response.

Objectives: The purpose of this study was to determine whether differentially expressed putative miRNAs that have RARA as a target gene could be considered reliable biomarkers for APL.

Methods: Using bioinformatics tools, a panel of 6 miRNAs with possible tropism for the RARA gene was selected from miRDB. We evaluated their expression levels in samples from patients with APL (n=20) or from healthy subjects without mutations in genes associated with leukemia or myeloproliferative diseases (n=21).

Results: All 6 putative miRNAs were identified using electrophoresis (hsamir-4299, hsa-mir-4328, hsa-mir-7851-3p, hsa-mir-6827-5p, hsa-mir-6867-5p, hsa-mir-939-5p). Of the six miRNAs, hsa-mir-4328 is deeply downregulated in subjects diagnosed with APL compared to healthy subjects, whereas hsa-mir-4299 and hsa-mir-7851-3p show small differences in expression between the two study groups, but without statistical significance. Our results suggest that hsa-mir-4328 may have a role in the pathogenesis of APL and may represent a new biomarker for this type of leukemia. Key Words: miRNA, APL, leukemia, bioinformatics.

A bioinformatic approach of targeting SARS-CoV-2 replication by silencing a conserved alternative reserve of the orf8 gene using host miRNAs

The causative agent of the COVID-19 pandemic, the SARS-CoV-2 virus has yielded multiple relevant mutations, many of which have branched into major variants. The Omicron variant has a huge similarity with the original viral strain (first COVID-19 strain from Wuhan). Among different genes, the highly variable orf8 gene is responsible for crucial host interactions and has undergone multiple mutations and indels. The sequence of the orf8 gene of the Omicron variant is, however, identical with the gene sequence of the wild type. orf8 modulates the host immunity making it easier for the virus to conceal itself and remain undetected. Variants seem to be deleting this gene without affecting the viral replication. While analyzing, we came across the conserved orf7a gene in the viral genome which exhibits a partial sequence homology as well as functional similarity with the SARS-CoV-2 orf8. Hence, we have proposed here in our hypothesis that, orf7a might be an alternative reserve of orf8 present in the virus which was compensating for the lost gene. A computational approach was adopted where we screened various miRNAs targeted against the orf8 gene. These miRNAs were then docked onto the orf8 mRNA sequences. The same set of miRNAs was then used to check for their binding affinity with the orf7a reference mRNA. Results showed that miRNAs targeting the orf8 had favorable shape complementarity and successfully docked with the orf7a gene as well. These findings provide a basis for developing new therapeutic approaches where both orf8 and orf7a can be targeted simultaneously.

Effects of transcranial magnetic stimulation on neurobiological changes in Alzheimer's disease (Review)

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by cognitive decline and brain neuronal loss. A pioneering field of research in AD is brain stimulation via electromagnetic fields (EMFs), which may produce clinical benefits. Noninvasive brain stimulation techniques, such as transcranial magnetic stimulation (TMS), have been developed to treat neurological and psychiatric disorders. The purpose of the present review is to identify neurobiological changes, including inflammatory, neurodegenerative, apoptotic, neuroprotective and genetic changes, which are associated with repetitive TMS (rTMS) treatment in patients with AD. Furthermore, it aims to evaluate the effect of TMS treatment in patients with AD and to identify the associated mechanisms. The present review highlights the changes in inflammatory and apoptotic mechanisms, mitochondrial enzymatic activities, and modulation of gene expression (microRNA expression profiles) associated with rTMS or sham procedures. At the molecular level, it has been suggested that EMFs generated by TMS may affect the cell redox status and amyloidogenic processes. TMS may also modulate gene expression by acting on both transcriptional and post‑transcriptional regulatory mechanisms. TMS may increase brain cortical excitability, induce specific potentiation phenomena, and promote synaptic plasticity and recovery of impaired functions; thus, it may re‑establish cognitive performance in patients with AD.

MicroRNA Profile Alterations in Parathyroid Carcinoma: Latest Updates and Perspectives

Simple Summary

Despite the considerable development of diagnostic tools, distinguishing between benign and malignant parathyroid tumors poses a significant diagnostic challenge. Epigenetic regulations, including noncoding microRNAs (miRNAs), have recently emerged as a new and promising source of biomarkers. MiRNAs are post-transcriptional regulators of gene expression. These tissue-specific molecules are known to be deregulated between cancer and normal cells. This review delineates changes in miRNA expression in parathyroid carcinoma (PC), advancing our understanding of PC tumorigenesis and emphasizing, at the same time, that miRNAs can be further exploited for diagnostic and therapeutic purposes.

Abstract

Parathyroid tumors are a genetically heterogenous group with a significant variability in clinical features. Due to a lack of specific signs and symptoms and uncertain histopathological criteria, parathyroid carcinomas (PCs) are challenging to diagnose, both before and after surgery. There is a great interest in searching for accurate molecular biomarkers for early detection, disease monitoring, and clinical management. Due to improvements in molecular pathology, the latest studies have reported that PC tumorigenesis is strongly linked to the epigenetic regulation of gene expression. MicroRNA (miRNA) profiling may serve as a helpful adjunct in distinguishing parathyroid adenoma (PAd) from PC and provide further insight into regulatory pathways involved in PTH release and parathyroid tumorigenesis. So far, only a few studies have attempted to show the miRNA signature for PC, and very few overlaps could be found between these relatively similar studies. A global miRNA downregulation was detected in PC compared with normal glands among differentially expressed miRNAs. This review summarizes changes in miRNA expression in PC and discusses the future research directions in this area.

The importance of establishing genetic phase in clinical medicine

Haplotyping or determination of genetic phase has always played a pivotal role in MHC (HLA studies) both in helping to understand inheritance patterns in diseases such as type 1 diabetes (T1D) and in ensuring better matching in transplantation scenarios such as haematopoietic stem cell transplantation (HSCT), using donors genetically related to the patient. In recent years the need to establish genetic phase in a number of clinical scenarios has become apparent. These include: Genetic phasing for hematopoietic stem cell transplants using unrelated donors, where the HLA haplotypes are not known but where haplotype-matched recipients fare better clinically than allele matched, but haplotype mismatched patients. The use of checkpoint inhibitors is one of the most innovative and exciting developments in cancer treatment in years. An example is the use of the monoclonal ipilimumab to block the CTLA-4 receptor which is known to contain polymorphic sites. Until the phase of these polymorphisms is known it will not be possible to determine how effectively this monoclonal will perform in individual patients. The role of miRNA single strand molecules and their effect on gene expression. Thousands of non-coding genes have been identified and have been shown to be polymorphic, as have their target genes. Genetic phasing of polymorphism both in the miRNA source genes and their targets is clearly a fertile area of research In areas such a drug metabolism where the polymorphic family of CYP genes is responsible for the metabolism of the majority of prescription drugs, determining phase of SNPs is critical to understanding drug metabolism and efficacy. In multigenic disease studies combinations of single nucleotide polymorphisms (SNPs) in participating genes require accurate phasing in order to fully appreciate their role in the disease process. In addition, the level of expression of genes (point 3) is also important in understanding disease processes at the functional level. This review outlines the techniques that are currently available for approximating phase and discusses the clinical relevance of establishing genetic phase in areas of clinical medicine outlined in points 1-3.

Hsa-mir-548 family expression in human reproductive tissues

BACKGROUND

Hsa-miR-548ba expressed in ovarian granulosa cells targets PTEN and LIFR, which are essential for ovarian follicle activation and growth. The expression pattern of hsa-miR-548ba correlates with its host gene follicle-stimulating hormone receptor (FSHR), and FSH has a positive influence on hsa-miR-548ba expression. However, hsa-miR-548ba is a member of a large hsa-mir-548 family with potentially overlapping targets. The current study aims to investigate the co-expression of hsa-mir-548 family members in FSHR-positive reproductive tissues and to explore the potential co-regulation of pathways.

RESULTS

For the above-described analysis, small RNA sequencing data from public data repositories were used. Sequencing results revealed that hsa-miR-548ba was expressed at the highest level in the ovarian granulosa cells and uterine myometrial samples together with another twelve and one hsa-miR-548 family members, respectively. Pathway enrichment analysis of microRNA targets in the ovarian samples revealed the hsa-miR-548ba and hsa-miR-548b-5p co-regulation of RAB geranylgeranylation in mural granulosa cells. Moreover, other hsa-mir-548 family members co-regulate pathways essential for ovarian functions (PIP3 activates AKT signalling and signalling by ERBB4). In addition to hsa-miR-548ba, hsa-miR-548o-3p is expressed in the myometrium, which separately targets the peroxisome proliferator-activated receptor alpha (PPARA) pathway.

CONCLUSION

This study reveals that hsa-mir-548 family members are expressed in variable combinations in the reproductive tract, where they potentially fulfil different regulatory roles. The results provide a reference for further studies of the hsa-mir-548 family role in the reproductive tract.

miRNAs as Regulators of the Early Local Response to Burn Injuries

In burn injuries, risk factors and limitations to treatment success are difficult to assess clinically. However, local cellular responses are characterized by specific gene-expression patterns. MicroRNAs (miRNAs) are single-stranded, non-coding RNAs that regulate mRNA expression on a posttranscriptional level. Secreted through exosome-like vesicles (ELV), miRNAs are intracellular signalers and epigenetic regulators. To date, their role in the regulation of the early burn response remains unclear. Here, we identified 43 miRNAs as potential regulators of the early burn response through the bioinformatics analysis of an existing dataset. We used an established human ex vivo skin model of a deep partial-thickness burn to characterize ELVs and miRNAs in dermal interstitial fluid (dISF). Moreover, we identified miR-497-5p as stably downregulated in tissue and dISF in the early phase after a burn injury. MiR-218-5p and miR-212-3p were downregulated in dISF, but not in tissue. Target genes of the miRNAs were mainly upregulated in tissue post-burn. The altered levels of miRNAs in dISF of thermally injured skin mark them as new biomarker candidates for burn injuries. To our knowledge, this is the first study to report miRNAs altered in the dISF in the early phase of deep partial-thickness burns.