microRNA-guided diagnostics in clinical samples

Identifying X-chromosome variants associated with age-related macular degeneration

PURPOSE

In genome-wide association studies (GWAS), X chromosome (ChrX) variants are often not investigated. Sex-specific effects and ChrX-specific quality control (QC) are needed to examine these effects. Previous GWAS identified 52 autosomal variants associated with age-related macular degeneration (AMD) via the International AMD Genomics Consortium (IAMDGC), but did not analyze ChrX. Therefore¸ our goal was to investigate ChrX variants for association with AMD.

METHODS

We genotyped 29 629 non-Hispanic White (NHW) individuals (M/F:10404/18865; AMD12,087/14723) via a custom chip and imputed after ChrX-specific QC (XWAS 3.0) using the Michigan Imputation Server. Imputation generated 1 221 623 variants on ChrX. Age, informative PCs, and subphenotypes were covariates for logistic association analyses with Fisher's correction. Gene/pathway analyses were performed with VEGAS, GSEASNP, ICSNPathway, DAVID, and mirPath.

RESULTS

Logistic association on NHW individuals with sex correction identified variants in/near the genes SLITRK4, ARHGAP6, FGF13 and DMD associated with AMD (P < 1 × 10-6,Fisher's combined-corrected). Association testing of the subphenotypes of choroidal neovascularization and geographic atrophy (GA), identified variants in DMD associated with GA (P < 1 × 10-6, Fisher's combined-corrected). Via gene-based analysis with VEGAS, several genes were associated with AMD (P < 0.05, both truncated tail strength/truncated product P) including SLITRK4 and BHLHB9. Pathway analysis using GSEASNP and DAVID identified genes associated with nervous system development (FDR: P:0.02), and blood coagulation (FDR: P:0.03). Variants in the region of a microRNA (miR) were associated with AMD (P < 0.05, truncated tail strength/truncated product P). Via DIANA mirPath analysis, downstream targets of miRs showed association with brain disorders and fatty acid elongation (P < 0.05). A long noncoding RNA on ChrX near the DMD locus was also associated with AMD (P = 4 × 10-7). Epistatic analysis (t-statistic) for a quantitative trait of AMD vs control including covariates found a suggestive association in the XG gene (P = 2 × 10^-5).

CONCLUSIONS

Analysis of ChrX variation identifies several potential new locifor AMD risk and these variants nominate novel AMD pathways. Further analysis is needed to refine these results and to understand their biological significance and relationship with AMD development in worldwide populations.

Exploring the underlying molecular mechanisms of acute myocardial infarction after SARS-CoV-2 infection

An increase in acute myocardial infarction (AMI)-related deaths has been reported during the COVID-19 pandemic. Despite evidence suggesting the association between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and AMI, the underlying mechanisms remain unclear. Here, we integrated mRNA and microRNA expression profiles related to SARS-CoV-2 infection and AMI from public databases. We then performed transcriptomic analysis using bioinformatics and systems biology approaches to explore the potential molecular mechanisms of SARS-CoV-2 infection affects AMI. First, twenty-one common differentially expressed genes (DEGs) were identified from SARS-CoV-2 infection and AMI patients in endothelial cells datasets and then we performed functional analysis to predict the roles of these DEGs. The functional analysis emphasized that the endothelial cell response to cytokine stimulus due to excessive inflammation was essential in these two diseases. Importantly, the tumor necrosis factor and interleukin-17 signaling pathways appeared to be integral factors in this mechanism. Interestingly, most of these common genes were also upregulated in transcriptomic datasets of SARS-CoV-2-infected cardiomyocytes, suggesting that these genes may be shared in cardiac- and vascular-related injuries. We subsequently built a protein-protein interaction network and extracted hub genes and essential modules from this network. At the transcriptional and post-transcriptional levels, regulatory networks with common DEGs were also constructed, and some key regulator signatures were further identified and validated. In summary, our research revealed that a highly activated inflammatory response in patients with COVID-19 might be a crucial factor for susceptibility to AMI and we identified some candidate genes and regulators that could be used as biomarkers or potential therapeutic targets.

The Present and Future Landscapes of Molecular Diagnostics

Nucleic acid testing is the cornerstone of modern molecular diagnostics. This review describes the current status and future directions of molecular diagnostics, focusing on four major techniques: polymerase chain reaction (PCR), next-generation sequencing (NGS), isothermal amplification methods such as recombinase polymerase amplification (RPA) and loop-mediated isothermal amplification (LAMP), and clustered regularly interspaced short palindromic repeats (CRISPR)-based detection methods. We explore the advantages and limitations of each technique, describe how each overlaps with or complements other techniques, and examine current clinical offerings. This review provides a broad perspective into the landscape of molecular diagnostics and highlights potential future directions in this rapidly evolving field.

Analysis of potential microRNA biomarkers for multiple sclerosis

Multiple sclerosis (MS) is a chronic demyelinating autoimmune neurodegenerative disorder for which no specific blood biomarker is available. MicroRNAs (miRNAs) have been investigated for their diagnostic potential in MS. However, MS-associated miRNAs are rarely replicated in different MS populations, thus impeding their use in clinical testing. Here, we evaluated the fold expression of seven reported MS miRNAs associated with MS incidence and clinical characteristics in 76 MS patients and 75 healthy control plasma samples. We found miR-23a-3p to be upregulated in relapsing-remitting MS (RRMS), while miR-326 was downregulated. MiR-150-5p and -320a-3p were significantly downregulated in secondary progressive MS (SPMS) patients compared to RRMS. High disability was associated with low miR-320a-3p, whereas low BDNF levels were associated with upregulation of miR-150-5p and downregulation of miR-326 expression in the total cohort. MiR-23a-3p and miR-326 showed significant diagnostic sensitivity, specificity, and accuracy for RRMS diagnosis. In addition, miR-150-5p and miR-320a-3p had comparable significant diagnostic test performance metrics distinguishing SPMS from RRMS. Therefore, there is potential for including miR-23a-3p and miR-326 in an RRMS diagnostic miRNA panel. Moreover, we have shown that miR-150-5p and miR-320a-3p could be novel RRMS conversion to SPMS biomarkers. The use of these miRNAs in MS diagnosis and prognosis warrants further investigation.

Principles and Limitations of miRNA Purification and Analysis in Whole Blood Collected during Ablation Procedure from Patients with Atrial Fibrillation

Background: MicroRNA (miRNA) have the potential to be non-invasive and attractive biomarkers for a vast number of diseases and clinical conditions; however, a reliable analysis of miRNA expression in blood samples meets a number of methodological challenges. In this report, we presented and discussed, specifically, the principles and limitations of miRNA purification and analysis in blood plasma samples collected from the left atrium during an ablation procedure on patients with atrial fibrillation (AF). Materials and Methods: Consecutive patients hospitalized in the First Department of Cardiology for pulmonary vein ablation were included in this study (11 with diagnosed paroxysmal AF, 14 with persistent AF, and 5 without AF hospitalized for left-sided WPW ablation-control group). Whole blood samples were collected from the left atrium after transseptal puncture during the ablation procedure of AF patients. Analysis of the set of miRNA molecules was performed in blood plasma samples using the MIHS-113ZF-12 kit and miScript microRNA PCR Array Human Cardiovascular Disease. Results: The miRNS concentrations were in the following ranges: paroxysmal AF: 7-23.1 ng/µL; persistent AF: 4.9-66.8 ng/µL; controls: 6.3-10.6 ng/µL. The low A260/280 ratio indicated the protein contamination and the low A260/A230 absorbance ratio suggested the contamination by hydrocarbons. Spectrophotometric measurements also indicated low concentration of nucleic acids (<10 ng/µL). Further steps of analysis revealed that the concentration of cDNA after the Real-Time PCR (using the PAXgene RNA Blood kit) reaction was higher (148.8 ng/µL vs. 68.4 ng/µL) and the obtained absorbance ratios (A260/A280 = 2.24 and A260/A230 = 2.23) indicated adequate RNA purity. Conclusions: Although developments in miRNA sequencing and isolation technology have improved, detection of plasma-based miRNA, low RNA content, and sequencing bias introduced during library preparation remain challenging in patients with AF. The measurement of the quantity and quality of the RNA obtained is crucial for the interpretation of an efficient RNA isolation.

Discerning the Prospects of miRNAs as a Multi-Target Therapeutic and Diagnostic for Alzheimer's Disease

Although over the last few decades, numerous attempts have been made to halt Alzheimer's disease (AD) progression and mitigate its symptoms, only a few have been proven beneficial. Most medications available, still only cater to the symptoms of the disease rather than fixing the cause at the root level. A novel approach involving the use of miRNAs, which work on the principle of gene silencing, is being explored by scientists. Naturally present miRNAs in the biological system help to regulate various genes than may be implicated in AD-like BACE-1 and APP. One miRNA thus, holds the power to keep a check on several genes, conferring it the ability to be used as a multi-target therapeutic. With aging and the onset of diseased pathology, dysregulation of these miRNAs is observed. This flawed miRNA expression is responsible for the unusual buildup of amyloid proteins, fibrillation of tau proteins in the brain, neuronal death and other hallmarks leading to AD. The use of miRNA mimics and miRNA inhibitors provides an attractive perspective for fixing the upregulation and downregulation of miRNAs that led to abnormal cellular activities. Furthermore, the detection of miRNAs in the CSF and serum of diseased patients might be considered an earlier biomarker for the disease. While most of the therapies designed around AD have not succeeded completely, the targeting of dysregulated miRNAs in AD patients might give a new direction to scholars to develop an effective treatment for Alzheimer's disease.

Highly sensitive and facile microRNA detection based on target triggered exponential rolling-circle amplification coupling with CRISPR/Cas12a

MicroRNAs (miRNAs) play a crucial role in the regulation of gene expression and have been implicated in many diseases. Herein, we develop a target triggered exponential rolling-circle amplification coupling with CRISPR/Cas12a (T-ERCA/Cas12a) system, which can achieve the ultrasensitive detection with simple operation and no annealing procedure. In this assay, T-ERCA combines the exponential amplification with rolling-circle amplification by introducing a dumb-bell probe with two enzyme recognition sites. miRNA-155 targets are activators that trigger exponential rolling circle amplification to produce large amounts of ssDNA, which is then recognized by CRISPR/Cas12a for further amplification. Compared with single EXPAR or RCA combined with CRISPR/Cas12a, this assay shows higher amplification efficiency. Therefore, benefiting from the excellent amplification effect of T-ERCA and the high recognition specificity of CRISPR/Cas12a, the proposed strategy shows a wide detection range from 1 fM to 5 nM with a LOD (limit of detection) down to 0.31 fM. Moreover, it shows good application ability for assessing miRNA levels in different cells, indicating that the T-ERCA/Cas12a may provide a new guidance for molecular diagnosis and clinical practical application.

Comparison of Oncogenes, Tumor Suppressors, and MicroRNAs Between Schizophrenia and Glioma: The Balance of Power

The risk of cancer in schizophrenia has been controversial. Confounders of the issue are cigarette smoking in schizophrenia, and antiproliferative effects of antipsychotic medications. The author has previously suggested comparison of a specific cancer like glioma to schizophrenia might help determine a more accurate relationship between cancer and schizophrenia. To accomplish this goal, the author performed three comparisons of data; the first a comparison of conventional tumor suppressors and oncogenes between schizophrenia and cancer including glioma. This comparison determined schizophrenia has both tumor-suppressive and tumor-promoting characteristics. A second, larger comparison between brain-expressed microRNAs in schizophrenia with their expression in glioma was then performed. This identified a core carcinogenic group of miRNAs in schizophrenia offset by a larger group of tumor-suppressive miRNAs. This proposed "balance of power" between oncogenes and tumor suppressors could cause neuroinflammation. This was assessed by a third comparison between schizophrenia, glioma and inflammation in asbestos-related lung cancer and mesothelioma (ALRCM). This revealed that schizophrenia shares more oncogenic similarity to ALRCM than glioma.

Critical Considerations for Investigating MicroRNAs during Tumorigenesis: A Case Study in Conceptual and Contextual Nuances of miR-211-5p in Melanoma

MicroRNAs are non-coding RNAs fundamental to metazoan development and disease. Although the aberrant regulation of microRNAs during mammalian tumorigenesis is well established, investigations into the contributions of individual microRNAs are wrought with conflicting observations. The underlying cause of these inconsistencies is often attributed to context-specific functions of microRNAs. We propose that consideration of both context-specific factors, as well as underappreciated fundamental concepts of microRNA biology, will permit a more harmonious interpretation of ostensibly diverging data. We discuss the theory that the biological function of microRNAs is to confer robustness to specific cell states. Through this lens, we then consider the role of miR-211-5p in melanoma progression. Using literature review and meta-analyses, we demonstrate how a deep understating of domain-specific contexts is critical for moving toward a concordant understanding of miR-211-5p and other microRNAs in cancer biology.

Identification of Appropriate Endogenous Controls for Circulating miRNA Quantification in Working Dogs under Physiological Stress Conditions

Cell-free miRNAs, called circulating miRNAs (cmiRNAs), can act in a paracrine manner by facilitating a diversity of signaling mechanisms between cells. Real-time qPCR is the most accepted method for quantifying miRNA expression levels. The use of stable miRNA endogenous control (EC) for qPCR data normalization allows an accurate cross-sample gene expression comparison. The appropriate selection of EC is a crucial step because qPCR data can change drastically when normalization is performed using an unstable versus a stable EC. To find EC cmiRNA with stable expression in search and rescue (SAR) working dogs, we explored the serum miRNome by Next-Generation Sequencing (NGS) at T0 (resting state) and T1 immediately after SAR performance (state of physiologically recovered stress). The cmiRNAs selected in the NGS circulating miRNome as probable ECs were validated by qPCR, and miRNA stability was evaluated using the Delta Ct, BestKeeper, NormFinder, and GeNorm algorithms. Finally, RefFinder was used to rank the stability orders at both T0 and T1 by establishing miR-320 and miR-191 as the best-circulating ECs. We are confident that this study not only provides a helpful result in itself but also an experimental design for selecting the best endogenous controls to normalize gene expression for genes beyond circulating miRNAs.

Diagnostic and Therapeutic Roles of the "Omics" in Hypoxic-Ischemic Encephalopathy in Neonates

Perinatal asphyxia and neonatal encephalopathy remain major causes of neonatal mortality, despite the improved availability of diagnostic and therapeutic tools, contributing to neurological and intellectual disabilities worldwide. An approach using a combination of clinical data, neuroimaging, and biochemical parameters is the current strategy towards the improved diagnosis and prognosis of the outcome in neonatal hypoxic-ischemic encephalopathy (HIE) using bioengineering methods. Traditional biomarkers are of little use in this multifactorial and variable phenotype-presenting clinical condition. Novel systems of biology-based "omics" approaches (genomics, transcriptome proteomics, and metabolomics) may help to identify biomarkers associated with brain and other tissue injuries, predicting the disease severity in HIE. Biomarker studies using omics technologies will likely be a key feature of future neuroprotective treatment methods and will help to assess the successful treatment and long-term efficacy of the intervention. This article reviews the roles of different omics as biomarkers of HIE and outlines the existing knowledge of our current understanding of the clinical use of different omics molecules as novel neonatal brain injury biomarkers, which may lead to improved interventions related to the diagnostic and therapeutic aspects of HIE.

miRNA in Molecular Diagnostics

MicroRNAs are a class of small non-coding RNA molecules that regulate gene expression on post-transcriptional level. Their biogenesis consists of a complex series of sequential processes, and they regulate expression of many genes involved in all cellular processes. Their function is essential for maintaining the homeostasis of a single cell; therefore, their aberrant expression contributes to development and progression of many diseases, especially malignant tumors and viral infections. Moreover, they can be associated with certain states of a specific disease, obtained in the least invasive manner for patients and analyzed with basic molecular methods used in clinical laboratories. Because of this, they have a promising potential to become very useful biomarkers and potential tools in personalized medicine approaches. In this review, miRNAs biogenesis, significance in cancer and infectious diseases, and current available test and methods for their detection are summarized.

Unique circulating microRNA profiles in epidemic Kaposi's sarcoma

Background

Human herpesvirus 8 (HHV-8) causes Kaposi's sarcoma (KS). Kaposi sarcoma in HIV/AIDS patients is referred to as epidemic KS and is the most common HIV-related malignancy worldwide. The lack of a diagnostic assay to detect latent and early-stage disease has increased disease morbidity and mortality. Serum miRNAs have previously been used as potential biomarkers of normal physiology and disease. In the current study, we profiled unique serum miRNAs in patients with epidemic KS to generate baseline data to aid in developing a miRNA-based noninvasive biomarker assay for epidemic KS.

Methods

This was a comparative cross-sectional study involving 27 patients with epidemic KS and 27 HIV-positive adults with no prior diagnosis or clinical manifestation of KS. DNA and RNA were isolated from blood and serum collected from study participants. Nested PCR for circulating HHV-8 DNA was performed on the isolated DNA, whereas miRNA library preparation and sequencing for circulating miRNA were performed on the RNA samples. The miRge2 pipeline and EdgeR were used to analyse the sequencing data.

Results

Fifteen out of the 27 epidemic KS-positive subjects (55.6%) tested positive for HHV-8 DNA, whereas only 3 (11.1%) out of the 27 HIV-positive, KS-negative subjects tested positive for HHV-8 DNA. Additionally, we found a unique miRNA expression signature in 49 circulating miRNAs in epidemic KS subjects compared to subjects with no epidemic KS, with 41 miRNAs upregulated and 8 miRNAs downregulated. Subjects with latent KS infection had a differential upregulation of circulating miR-193a compared to HIV-positive, KS-negative subjects for whom circulating HHV-8 DNA was not detected. Further analysis of serum from epidemic KS patients revealed a miRNA signature according to KS tumor status and time since first HIV diagnosis.

Conclusions

This study reveals unique circulating miRNA profiles in the serum of patients with epidemic KS versus HIV-infected subjects with no KS, as well as in subjects with latent KS. Many of the dysregulated miRNAs in epidemic KS patients were previously reported to have crucial roles in KS infection and latency, highlighting their promising roles as potential biomarkers of latent or active KS infection.

Review on combining surface-enhanced Raman spectroscopy and electrochemistry for analytical applications

The discovery of surface enhanced Raman scattering (SERS) from an electrochemical (EC)-SERS experiment is known as a historic breakthrough. Five decades have passed and Raman spectroelectrochemistry (SEC) has developed into a common characterization tool that provides information about the electrode-electrolyte interface. Recently, this technique has been successfully explored for analytical purposes. EC was found to highly improve the performances of SERS sensors, providing, among others, controlled adsorption of analytes and increased reproducibility. In this review, we highlight the potential of EC-SERS sensors to be implemented for point-of-need (PON) analyses as miniaturized devices, and their ability to revolutionize fields like quality control, diagnosis or environmental and food safety. Important developments have been achieved in Raman spectroelectrochemistry, which now represents a promising alternative to conventional analytical methods and interests more and more researchers. The studies included in this review open endless possibilities for real-life EC-SERS analytical applications.

Cardiovascular signatures of COVID-19 predict mortality and identify barrier stabilizing therapies

Background

Endothelial cell (EC) activation, endotheliitis, vascular permeability, and thrombosis have been observed in patients with severe coronavirus disease 2019 (COVID-19), indicating that the vasculature is affected during the acute stages of SARS-CoV-2 infection. It remains unknown whether circulating vascular markers are sufficient to predict clinical outcomes, are unique to COVID-19, and if vascular permeability can be therapeutically targeted.

Methods

Prospectively evaluating the prevalence of circulating inflammatory, cardiac, and EC activation markers as well as developing a microRNA atlas in 241 unvaccinated patients with suspected SARS-CoV-2 infection allowed for prognostic value assessment using a Random Forest model machine learning approach. Subsequent ex vivo experiments assessed EC permeability responses to patient plasma and were used to uncover modulated gene regulatory networks from which rational therapeutic design was inferred.

Findings

Multiple inflammatory and EC activation biomarkers were associated with mortality in COVID-19 patients and in severity-matched SARS-CoV-2-negative patients, while dysregulation of specific microRNAs at presentation was specific for poor COVID-19-related outcomes and revealed disease-relevant pathways. Integrating the datasets using a machine learning approach further enhanced clinical risk prediction for in-hospital mortality. Exposure of ECs to COVID-19 patient plasma resulted in severity-specific gene expression responses and EC barrier dysfunction, which was ameliorated using angiopoietin-1 mimetic or recombinant Slit2-N.

Interpretation

Integration of multi-omics data identified microRNA and vascular biomarkers prognostic of in-hospital mortality in COVID-19 patients and revealed that vascular stabilizing therapies should be explored as a treatment for endothelial dysfunction in COVID-19, and other severe diseases where endothelial dysfunction has a central role in pathogenesis.

Funding Information

This work was directly supported by grant funding from the Ted Rogers Center for Heart Research, Toronto, Ontario, Canada and the Peter Munk Cardiac Center, Toronto, Ontario, Canada.

Extracellular circulating miRNAs as stress-related signature to search and rescue dogs

Our research explores serum extracellular circulating miRNAs (ecmiRNAs) involved in dog stress response immediately after the search and rescue (SAR) of missing people. The experimental plan considers four arduous SAR simulations. The SAR dogs are trained by the Alpine School of the Military Force of Guardia di Finanza (Passo Rolle, Italy). The First SAR Trial analyzed dog serum samples at rest time (T0), and immediately after SAR performance (T1) using the miRNome-wide screening next-generation sequencing (NGS). T1 versus T0 NGS results revealed a different expression level of let-7a and let-7f. Subsequently, in a large sample size including: 1st (n = 6), 2nd (n = 6), 3rd (n = 6), and 4th (n = 4) trials, let-7a and let-7f were validated by qPCR. Bioinformatics analysis with TarBase (v.8) and the Diana-mirPath (v.3) revealed a functional role of let-7a and let-7f in the p53 pathway to restore cellular homeostasis. Let-7a and let-7f, highly expressed at T1, could stop MDMs-p53 inhibition inducing the p53 increase in level. In addition, let-7a and let-7f, via p53 post-transcriptional regulation, buffers p53 transcription spikes. During SAR stress, the possibility of p53 preconditioning could explain the phenomenon of "stress hardening" where the tolerance of particular stress increases after preconditioning.

Plasma miRNA profile at COVID-19 onset predicts severity status and mortality

BACKGROUND

MicroRNAs (miRNAs) have a crucial role in regulating immune response against infectious diseases, showing changes early in disease onset and before the detection of the pathogen. Thus, we aimed to analyze the plasma miRNA profile at COVID-19 onset to identify miRNAs as early prognostic biomarkers of severity and survival.

METHODS AND RESULTS

Plasma miRNome of 96 COVID-19 patients that developed asymptomatic/mild, moderate and severe disease was sequenced together with a group of healthy controls. Plasma immune-related biomarkers were also assessed. COVID-19 patients showed 200 significant differentially expressed (SDE) miRNAs concerning healthy controls, with upregulated putative targets of SARS-CoV-2, and inflammatory miRNAs. Among COVID-19 patients, 75 SDE miRNAs were observed in asymptomatic/mild compared to symptomatic patients, which were involved in platelet aggregation and cytokine pathways, among others. Moreover, 137 SDE miRNAs were identified between severe and moderate patients, where miRNAs targeting the SARS CoV-2 genome were the most strongly disrupted. Finally, we constructed a mortality predictive risk score (miRNA-MRS) with ten miRNAs. Patients with higher values had a higher risk of 90-days mortality (hazard ratio=4.60; p-value<0.001). Besides, the discriminant power of miRNA-MRS was significantly higher than the observed for age and gender (AUROC=0.970 vs. 0.881; p=0.042).

CONCLUSIONS

SARS-CoV-2 infection deeply disturbs the plasma miRNome from an early stage of COVID-19, making miRNAs highly valuable as early predictors of severity and mortality.

Circulating Plasma MicroRNA in Patients With Active Acromegaly

CONTEXT

Excessive production of growth hormone causes marked multiorgan changes in patients with acromegaly, which may involve epigenetic mechanisms.

OBJECTIVE

To evaluate differences in circulating microRNAs (miRNAs) associated with chronic growth hormone overproduction in adults.

DESIGN AND SETTING

A cross-sectional case-control study was conducted at a tertiary medical center.

PARTICIPANTS

We enrolled 12 consecutive patients with acromegaly along with 12 age- and sex-matched controls in the discovery phase of the study and then extended this cohort to 47 patients with acromegaly and 28 healthy controls for the validation study.

MAIN OUTCOME MEASURES

Plasma miRNAs were quantified by next-generation sequencing (NGS) in the discovery phase. Levels of selected miRNAs were validated on extended cohorts using reverse transcription quantitative polymerase chain reaction (RT-qPCR), compared between groups, and correlated with clinical parameters.

RESULTS

Based on NGS data, we selected 3 plasma miRNAs downregulated in patients with acromegaly compared to healthy controls: miR-4446-3p -1.317 (P = 0.001), miR-215-5p -3.040 (P = 0.005), and miR-342-5p -1.875 (P = 0.013) without multiplicity correction for all 3 miRNAs. These results were confirmed by RT-qPCR in the validation phase for 2 miRNAs out of 3: miR-4446-3p (P < 0.001, Padjusted < 0.001), area under the receiver-operator curve (AUC) 0.862 (95% CI 0.723-0.936; P < 0.001) and miR-215-5p (P < 0.001, Padjusted < 0.001), AUC 0.829 (95% CI 0.698-0.907; P < 0.001) to differentiate patients with acromegaly from healthy controls.

CONCLUSIONS

In a 2-phase experiment using 2 different techniques we found and validated the downregulation of plasma miR-4446-3p and miR-215-5p in patients with acromegaly compared to healthy subjects, which makes them promising biomarkers for further research.

Topology preserving stratification of tissue neoplasticity using Deep Neural Maps and microRNA signatures

Background

Accurate cancer classification is essential for correct treatment selection and better prognostication. microRNAs (miRNAs) are small RNA molecules that negatively regulate gene expression, and their dyresgulation is a common disease mechanism in many cancers. Through a clearer understanding of miRNA dysregulation in cancer, improved mechanistic knowledge and better treatments can be sought.

Results

We present a topology-preserving deep learning framework to study miRNA dysregulation in cancer. Our study comprises miRNA expression profiles from 3685 cancer and non-cancer tissue samples and hierarchical annotations on organ and neoplasticity status. Using unsupervised learning, a two-dimensional topological map is trained to cluster similar tissue samples. Labelled samples are used after training to identify clustering accuracy in terms of tissue-of-origin and neoplasticity status. In addition, an approach using activation gradients is developed to determine the attention of the networks to miRNAs that drive the clustering. Using this deep learning framework, we classify the neoplasticity status of held-out test samples with an accuracy of 91.07%, the tissue-of-origin with 86.36%, and combined neoplasticity status and tissue-of-origin with an accuracy of 84.28%. The topological maps display the ability of miRNAs to recognize tissue types and neoplasticity status. Importantly, when our approach identifies samples that do not cluster well with their respective classes, activation gradients provide further insight in cancer subtypes or grades.

Conclusions

An unsupervised deep learning approach is developed for cancer classification and interpretation. This work provides an intuitive approach for understanding molecular properties of cancer and has significant potential for cancer classification and treatment selection.

Ratiometric Detection of microRNA Using Hybridization Chain Reaction and Fluorogenic Silver Nanoclusters

miRNA (miR)-155 is a potential biomarker for breast cancers. We aimed at developing a nanosensor for miR-155 detection by integrating hybridization chain reaction (HCR) and silver nanoclusters (AgNCs). HCR serves as an enzyme-free and isothermal amplification method, whereas AgNCs provide a built-in fluorogenic detection probe that could simplify the downstream analysis. The two components were integrated by adding a nucleation sequence of AgNCs to the hairpin of HCR. The working principle was based on the influence of microenvironment towards the hosted AgNCs, whereby unfolding of hairpin upon HCR has manipulated the distance between the hosted AgNCs and cytosine-rich toehold region of hairpin. As such, the dominant emission of AgNCs changed from red to yellow in the absence and presence of miR-155, enabling a ratiometric measurement of miR with high sensitivity. The limit of detection (LOD) of our HCR-AgNCs nanosensor is 1.13 fM in buffered solution. We have also tested the assay in diluted serum samples, with comparable LOD of 1.58 fM obtained. This shows the great promise of our HCR-AgNCs nanosensor for clinical application.

A critical appraisal of the circulating levels of differentially expressed microRNA in endometriosis†

Endometriosis is a common gynecological condition characterized by estrogen dependence, chronic pelvic pain, infertility, and diagnostic delay of between 5.4 and 12 years. Despite extensive study, no biomarker, either alone or in combination with other markers, has proven superior to laparoscopy for the diagnosis of endometriosis. Recent studies report that circulating levels of differentially expressed microRNA (miRNA) in women with endometriosis compared with controls are potential diagnostic tools. However, the lack of replication and absence of validated differential expression in novel study populations have led some to question the diagnostic value of miRNA. To elucidate potential reasons for the lack of replication of study results and explore future directions to enhance replicability of circulating miRNA results, we carried out an electronic search of the miRNA literature published between 2000 and 2020. Eighteen studies were identified in which 63 different miRNAs were differentially expressed in the circulation of women with endometriosis compared with controls. However, the differential expressions of only 14 miRNAs were duplicated in one or more studies. While individual miRNAs lacked diagnostic value, miRNA panels yielded sensitivity and specificity equal to or better than laparoscopy in five studies. Important differences in study design, sample processing, and analytical methods were identified rendering direct comparisons across studies problematic and could account for the lack of reproducibility of study results. We conclude that while the results of miRNA studies to date are encouraging, refinements to study design and analytical methods should enhance the reliability of circulating miRNA for the diagnosis of endometriosis.

Tumor-Educated Platelet miR-18a-3p as a Novel Liquid-Biopsy Biomarker for Early Diagnosis and Chemotherapy Efficacy Monitoring in Nasopharyngeal Carcinoma

Aims

To evaluate the value of tumor-educated platelet (TEP) miR-18a-3p in the early diagnosis and chemotherapy efficacy monitoring of nasopharyngeal carcinoma (NPC).

Methods

Expression levels of miR-18a-3p in platelets and plasma were detected by relative quantitative real-time PCR in NPC patients (n=54) and normal subjects (n=36). Diagnostic values of TEP miR-18a-3p for NPC was assessed by receiver operating characteristic (ROC) curve analysis. Follow up study was carried out to observe the dynamic changes of TEP miR-18a-3p with chemotherapy on 3 NPC patients.

Results

The expression levels of TEP miR-18a-3p in NPC patients were significantly higher than that in healthy controls (p < 0.0001). ROC curve analysis showed that the area under the curve (AUC) value was 0.841, the sensitivity and specificity for the diagnosis of NPC were 87% and 72.7%. No correlation was found between expression levels of TEP miR-18a-3p and patients’ clinical parameters and their NPC tumor-node-metastasis (TNM) stage. The positive rate of TEP miR-18a-3p and EBV DNA for NPC diagnosis were 85.4% and 66.7%. TEP miR-18a-3p expression were down-regulated after 77.8% (7 of 9) of chemotherapy, and in 66.7% (2 of 3) patients, TEP miR-18a-3p levels decreased after 3 cycles of chemotherapy.

Conclusion

The expression levels of TEP miR-18a-3p are upregulated in NPC and have a high probability to downregulated after chemotherapy, indicating a significant clinical value. TEP miR-18a-3p might serve as a novel type of liquid-biopsy biomarker for early diagnosis and chemotherapy efficacy monitoring in NPC.

MicroRNAs Patterns as Potential Tools for Diagnostic and Prognostic Follow-Up in Cancer Survivorship

Advances in screening methods and pharmacological treatments are increasing the life expectancy of cancer patients. During recent decades, the community of long-term disease-free cancer survivors (LCS) has grown exponentially, raising the issues related to cancer follow-up. Cancer relapse and other cancer-related diseases, as well as lifestyle, influence cancer survival. Recently, the regulatory role of microRNAs (miRNAs) in gene expression and their involvement in human diseases, including cancer, has been identified. Extracellular circulating miRNAs (ECmiRNAs) have been found in biological fluids and specific ECmiRNAs have been associated with cancer development and progression or with a therapy response. Here, we focus on the pivotal role of ECmiRNAs as biomarkers in cancer diagnosis and prognosis. Then, we discuss the relevance of ECmiRNAs expression in cancer survivors for the identification of specific ECmiRNAs profiles as potential tools to assess cancer outcome and to control LCS follow-up.

MDA-CF: Predicting MiRNA-Disease associations based on a cascade forest model by fusing multi-source information

MicroRNAs (miRNAs) are significant regulators in various biological processes. They may become promising biomarkers or therapeutic targets, which provide a new perspective in diagnosis and treatment of multiple diseases. Since the experimental methods are always costly and resource-consuming, prediction of disease-related miRNAs using computational methods is in great need. In this study, we developed MDA-CF to identify underlying miRNA-disease associations based on a cascade forest model. In this method, multi-source information was integrated to represent miRNAs and diseases comprehensively, and the autoencoder was utilized for dimension reduction to obtain the optimal feature space. The cascade forest model was then employed for miRNA-disease association prediction. As a result, the average AUC of MDA-CF was 0.9464 on HMDD v3.2 in five-fold cross-validation. Compared with previous computational methods, MDA-CF performed better on HMDD v2.0 with an average AUC of 0.9258. Moreover, MDA-CF was implemented to investigate colon neoplasm, breast neoplasm, and gastric neoplasm, and 100%, 86%, 88% of the top 50 potential miRNAs were validated by authoritative databases. In conclusion, MDA-CF appears to be a reliable method to uncover disease-associated miRNAs. The source code of MDA-CF is available at https://github.com/a1622108/MDA-CF.

MicroRNA profiling in Chinese children with Henoch-Schonlein purpura and association between selected microRNAs and inflammatory biomarkers

AIM

This study aimed to profile the microRNA levels in Chinese Henoch-Schonlein purpura (HSP) children and to explore their association with inflammatory factors and T helper 17 (Th17)/regulatory T (Treg).

METHODS

Forty-five HSP children and 27 healthy controls were enrolled in this study, and microRNA levels were profiled with a microRNA microarray. The levels of selected microRNAs were determined by quantitative real-time PCR, and the levels of serum IgA, interleukin-6, interleukin-10 and interleukin-17A were detected by enzyme-linked immunosorbent assay. Additionally, Th17 and Treg cells were analysed by flow cytometry.

RESULTS

There were 9 up-regulated and 27 down-regulated microRNAs in the PBMCs of Chinese HSP children. Among them, miR-1-3p, miR-19b-1-5p and miR-29b-1-5p were up-regulated, while miR-483-5p and miR-1246 were down-regulated. Additionally, these selected microRNAs could differentiate HSP patients from healthy controls. Interestingly, miR-29b-1-5p was correlated with IgA, miR-19b-1-5p, miR-483-5p and miR-1246 were correlated with interleukin-6, while miR-1-3p and miR-1246 were correlated with Th17/Treg.

CONCLUSION

This study reveals that the altered microRNAs could differentiate HSP from the healthy, and were associated with inflammatory factors or Th17/Treg. It is indicated that alteration in these microRNAs may contribute to the HSP pathogenesis and may become therapeutic targets or diagnostic biomarkers for HSP.

Focus on MicroRNAs as Biomarker in Pediatric Diseases

BACKGROUND

MiRNAs are a class of small non-coding RNAs that are involved in the post-transcriptional regulation of gene expression. MiRNAs are considered a class of epigenetic biomarkers. These biomarkers can investigate disease at different stages: diagnosis, therapy or clinical follow-up.

OBJECTIVE

The aim of this paper is to highlight the innovative use of miRNAs in several childhood diseases.

METHODS

We conducted a literature review to search the usage of miRNAs in pediatric clinical routine or experimental trials.

RESULTS

We found a possible key role of miRNAs in different pediatric illnesses (metabolic alterations, coagulation defects, cancer).

CONCLUSION

The modest literature production denotes that further investigation is needed to assess and validate the promising role of miRNAs as non-invasive biomarkers in pediatric disorders.

Epigenetic silencing of miR564 contributes to the leukemogenesis of t(8;21) acute myeloid leukemia

The AML1-ETO oncoprotein, which results from t(8;21) translocation, is considered an initial event of t(8;21) acute myeloid leukemia (AML). However, the precise mechanisms of the oncogenic activity of AML1-ETO is yet to be fully determined. The present study demonstrates that AML1-ETO triggers the heterochromatic silencing of microRNA-564 (miR564) by binding at the AML1 binding site along the miR564 promoter region and recruiting chromatin-remodeling enzymes. Suppression of miR564 enhances the oncogenic activity of the AML1-ETO oncoprotein by directly inhibiting the expression of CCND1 and the DNMT3A genes. Ectopic expression of miR564 can induce retardation of G1/S transition, reperform differentiation, promote apoptosis, as well as inhibit the proliferation and colony formation of AML1-ETO+ leukemia cells in vitro. Enhanced miR564 levels can significantly inhibit the tumor proliferation of t(8;21)AML in vivo. We first identify an unexpected and important epigenetic circuitry of AML1-ETO/miR564/CCND1/DNMT3A that contributes to the leukemogenesis in vitro/vivo of AML1-ETO+ leukemia, indicating that miR564 enhancement could provide a potential therapeutic method for AML1-ETO+ leukemia.

An integrated workflow for biomarker development using microRNAs in extracellular vesicles for cancer precision medicine

EV-miRNAs are microRNA (miRNA) molecules encapsulated in extracellular vesicles (EVs), which play crucial roles in tumor pathogenesis, progression, and metastasis. Recent studies about EV-miRNAs have gained novel insights into cancer biology and have demonstrated a great potential to develop novel liquid biopsy assays for various applications. Notably, compared to conventional liquid biomarkers, EV-miRNAs are more advantageous in representing host-cell molecular architecture and exhibiting higher stability and specificity. Despite various available techniques for EV-miRNA separation, concentration, profiling, and data analysis, a standardized approach for EV-miRNA biomarker development is yet lacking. In this review, we performed a substantial literature review and distilled an integrated workflow encompassing important steps for EV-miRNA biomarker development, including sample collection and EV isolation, EV-miRNA extraction and quantification, high-throughput data preprocessing, biomarker prioritization and model construction, functional analysis, as well as validation. With the rapid growth of "big data", we highlight the importance of efficient mining of high-throughput data for the discovery of EV-miRNA biomarkers and integrating multiple independent datasets for in silico and experimental validations to increase the robustness and reproducibility. Furthermore, as an efficient strategy in systems biology, network inference provides insights into the regulatory mechanisms and can be used to select functionally important EV-miRNAs to refine the biomarker candidates. Despite the encouraging development in the field, a number of challenges still hinder the clinical translation. We finally summarize several common challenges in various biomarker studies and discuss potential opportunities emerging in the related fields.

Non-Coding RNAs in Cancer Diagnosis and Therapy: Focus on Lung Cancer

Over the last several decades, clinical evaluation and treatment of lung cancers have largely improved with the classification of genetic drivers of the disease, such as EGFR, ALK, and ROS1. There are numerous regulatory factors that exert cellular control over key oncogenic pathways involved in lung cancers. In particular, non-coding RNAs (ncRNAs) have a diversity of regulatory roles in lung cancers such that they have been shown to be involved in inducing proliferation, suppressing apoptotic pathways, increasing metastatic potential of cancer cells, and acquiring drug resistance. The dysregulation of various ncRNAs in human cancers has prompted preclinical studies examining the therapeutic potential of restoring and/or inhibiting these ncRNAs. Furthermore, ncRNAs demonstrate tissue-specific expression in addition to high stability within biological fluids. This makes them excellent candidates as cancer biomarkers. This review aims to discuss the relevance of ncRNAs in cancer pathology, diagnosis, and therapy, with a focus on lung cancer.

Ionic matrices for matrix-assisted laser desorption/ionization mass spectrometry analysis of microRNA biomarkers

The use of ionic matrices (IMs) was evaluated as an alternative to conventional matrices to analyze microRNAs (miRNAs) by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). 2, 4, 6-Trihydroxyacetophenone (THAP), 6-aza-2-thiothymine (ATT) and 3-hydroxypicolinic acid (3-HPA) and their IMs with pyridine (PYR) and butylamine (BA) were studied to analyze a standard mixture of miRNAs: miR-21, let-7g and iso-miR-16. Among all the studied matrices, ATT-PYR at 75 mg/mL in acetonitrile (MeCN):H₂O (50:50, v/v) was selected as the optimal. Furthermore, addition of ammonium citrate dibasic (AC) as signal enhancer was mandatory to obtain an appropriate miRNA detection. ATT-PYR provided the best sensitivity, with limit of detection (LOD) up to 5 nM (equivalent to 1 fmol in the spot) and excellent spot-to-spot repeatability due to the improved homogeneity of the spots compared to the conventional matrices. The applicability of the established method to direct, multiplex and untargeted analysis of miRNAs in serum samples was also investigated.

Potential role of ACE2-related microRNAs in COVID-19-associated nephropathy

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is responsible for coronavirus disease (COVID-19), potentially have severe kidney adverse effects. This organ expressed angiotensin-converting enzyme 2 (ACE2), the transmembrane protein which facilitate the entering of the virus into the cell. Therefore, early detection of the kidney manifestations of COVID-19 is crucial. Previous studies showed ACE2 role in various indications of this disease, especially in kidney effects. The MicroRNAs (miRNAs) in this organ affected ACE2 expression. Therefore, this review aims at summarizing the literature of a novel miRNA-based therapy and its potential applications in COVID-19-associated nephropathy. Furthermore, previous studies were analyzed for the kidney manifestations of COVID-19 and the miRNAs role that were published on the online databases, namely MEDLINE (PubMed) and Scopus. Several miRNAs, particularly miR-18 (which was upregulated in nephropathy), played a crucial role in ACE2 expression. Therefore, the antimiR-18 roles were summarized in various primate models that aided in developing the therapy for ACE2 related diseases.

Classifying Lung Neuroendocrine Neoplasms through MicroRNA Sequence Data Mining

Lung neuroendocrine neoplasms (NENs) can be challenging to classify due to subtle histologic differences between pathological types. MicroRNAs (miRNAs) are small RNA molecules that are valuable markers in many neoplastic diseases. To evaluate miRNAs as classificatory markers for lung NENs, we generated comprehensive miRNA expression profiles from 14 typical carcinoid (TC), 15 atypical carcinoid (AC), 11 small cell lung carcinoma (SCLC), and 15 large cell neuroendocrine carcinoma (LCNEC) samples, through barcoded small RNA sequencing. Following sequence annotation and data preprocessing, we randomly assigned these profiles to discovery and validation sets. Through high expression analyses, we found that miR-21 and -375 are abundant in all lung NENs, and that miR-21/miR-375 expression ratios are significantly lower in carcinoids (TC and AC) than in neuroendocrine carcinomas (NECs; SCLC and LCNEC). Subsequently, we ranked and selected miRNAs for use in miRNA-based classification, to discriminate carcinoids from NECs. Using miR-18a and -155 expression, our classifier discriminated these groups in discovery and validation sets, with 93% and 100% accuracy. We also identified miR-17, -103, and -127, and miR-301a, -106b, and -25, as candidate markers for discriminating TC from AC, and SCLC from LCNEC, respectively. However, these promising findings require external validation due to sample size.

Characterizing and classifying neuroendocrine neoplasms through microRNA sequencing and data mining

Neuroendocrine neoplasms (NENs) are clinically diverse and incompletely characterized cancers that are challenging to classify. MicroRNAs (miRNAs) are small regulatory RNAs that can be used to classify cancers. Recently, a morphology-based classification framework for evaluating NENs from different anatomical sites was proposed by experts, with the requirement of improved molecular data integration. Here, we compiled 378 miRNA expression profiles to examine NEN classification through comprehensive miRNA profiling and data mining. Following data preprocessing, our final study cohort included 221 NEN and 114 non-NEN samples, representing 15 NEN pathological types and 5 site-matched non-NEN control groups. Unsupervised hierarchical clustering of miRNA expression profiles clearly separated NENs from non-NENs. Comparative analyses showed that miR-375 and miR-7 expression is substantially higher in NEN cases than non-NEN controls. Correlation analyses showed that NENs from diverse anatomical sites have convergent miRNA expression programs, likely reflecting morphological and functional similarities. Using machine learning approaches, we identified 17 miRNAs to discriminate 15 NEN pathological types and subsequently constructed a multilayer classifier, correctly identifying 217 (98%) of 221 samples and overturning one histological diagnosis. Through our research, we have identified common and type-specific miRNA tissue markers and constructed an accurate miRNA-based classifier, advancing our understanding of NEN diversity.

Single-Measurement Multiplexed Quantification of MicroRNAs from Human Tissue Using Catalytic Hairpin Assembly and Förster Resonance Energy Transfer

Absolute quantification of microRNAs (miRNAs) or other nucleic acid biomarkers is an important requirement for molecular and clinical biosensing. Emerging technologies with beneficial features concerning simplicity and multiplexing present an attractive route for advancing diagnostic tools toward rapid and low-cost bioanalysis. However, the actual translation into the clinic by miRNA quantification in human samples is often missing. Here, we show that implementing time-gated Förster resonance energy transfer (TG-FRET) into a catalytic hairpin assembly (CHA) can be used for the simultaneous quantification of two miRNAs with a single measurement from total RNA extracts of human tissues. A single terbium-dye FRET pair was conjugated at two specific distances within target-specific CHA hairpin probes, such that each miRNA resulted in distinct amplified photoluminescence (PL) decays that could be distinguished and quantified by TG PL intensity detection. Enzyme-free amplification in a separation-free assay format and the absence of autofluorescence background allowed for simple, specific, and sensitive detection of miR-21 and miR-20a with limits of detection down to 1.8 pM (250 amol). Reliable duplexed quantification of both miRNAs at low picomolar concentrations was confirmed by analyzing total RNA extracts from different colon and rectum tissues with single- and dual-target CHA-TG-FRET and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) for comparison. These simple and multiplexed nucleic acid biomarker assays present a capable method for clinical diagnostics and biomolecular research.

Autophagy regulation by microRNAs: Novel insights into osteosarcoma therapy

Osteosarcoma (OS) is a kind of primary bone cancer that is considered as the leading cause of children death. Surgery and chemotherapy are considered as common treatment approaches for OS; the rate of survival for patients is almost 60-70%. Besides the used therapeutic approaches, it seems that there is a crucial need to launch new treatments for OS. In this regard, more understanding about cellular and molecular pathways involved in OS can contribute to recovery and develop new therapeutic platforms. Autophagy is a cellular machinery that digests and degrades dysfunctional proteins and organelles, so it can regulate the cell proliferation and survival. Most of the time, OS cells use autophagy to increase their survival and proliferation and to gain the ability to resist chemotherapy. Although, there are several controversial evidences on how OS cells use autophagy. A variety of cellular and molecular pathways, that is, microRNAs (miRNAs) can modulate autophagy. MiRNAs are some endogenous, approximately 22 nucleotide RNAs that have an important role in posttranscriptional regulation of mRNAs by targeting them. There are many evidences that the various miRNA expressions in OS cells are dysregulated, so it can propel a normal cell to cancerous one by influencing the cell survival, apoptosis, and autophagy, and eventually increased chemoresitance. Hence, miRNAs can be considered as new biomarkers for OS diagnosis, and according to the role of autophagy in OS progression, miRNAs can use inhibiting or promoting autophagy agents. The present review summarizes the effects of aberrant expression of miRNAs in OS diagnosis and treatment with focus on their roles in autophagy.

RNA-Based Therapeutics: From Antisense Oligonucleotides to miRNAs

The first therapeutic nucleic acid, a DNA oligonucleotide, was approved for clinical use in 1998. Twenty years later, in 2018, the first therapeutic RNA-based oligonucleotide was United States Food and Drug Administration (FDA) approved. This promises to be a rapidly expanding market, as many emerging biopharmaceutical companies are developing RNA interference (RNAi)-based, and RNA-based antisense oligonucleotide therapies. However, miRNA therapeutics are noticeably absent. miRNAs are regulatory RNAs that regulate gene expression. In disease states, the expression of many miRNAs is measurably altered. The potential of miRNAs as therapies and therapeutic targets has long been discussed and in the context of a wide variety of infections and diseases. Despite the great number of studies identifying miRNAs as potential therapeutic targets, only a handful of miRNA-targeting drugs (mimics or inhibitors) have entered clinical trials. In this review, we will discuss whether the investment in finding potential miRNA therapeutic targets has yielded feasible and practicable results, the benefits and obstacles of miRNAs as therapeutic targets, and the potential future of the field.

A Novel Risk Stratification System for Thyroid Nodules With Indeterminate Cytology-A Pilot Cohort Study

Background: Thyroid ultrasound (US), fine needle aspiration biopsy (FNAB), and molecular testing have been widely used to stratify the risk of malignancy in thyroid nodules. The goal of this study was to investigate a novel diagnostic approach for cytologically indeterminate thyroid nodules (ITN) based upon a combination of US features and genetic alterations. Methods: We performed a pilot cohort study of patients with ITN (Bethesda III/IV), who underwent surgical treatment. Based on standardized sonographic patterns established by the American Thyroid Association (ATA), each ITN received an US score (X_US), ranging between 0 and 0.9 according to its risk of thyroid cancer (TC). DNA and RNA were extracted from pathologic material, available for all patients, and subjected to Oncomine™ Comprehensive Assay v2 (OCAv2) next-generation sequencing. Each genetic alteration was annotated based on its strength of association with TC and its sum served as the genomic classifier score (X_GC). The total risk score (TRS) was the sum of X_US and X_GC. ROC curves were generated to assess the diagnostic accuracy of X_US, X_GC, and TRS. Results: The study cohort consisted of 50 patients (39 females and 11 males), aged 47.5 ± 14.8 years. Three patients were excluded due to molecular testing failure. Among the remaining 47 patients, 28 (59.6%) were diagnosed with TC. BRAFV600E was the most common mutation in papillary TC, PAX8-PPARG fusion was present in NIFTP, pathogenic variants of SLX4, ATM, and NRAS were found in Hürthle cell TC and RET mutations in medullary TC. The diagnostic accuracy of X_GC and TRS was significantly higher compared with X_US (88 vs. 62.5%, p < 0.001; 85.2 vs. 62.5%, p < 0.001, respectively). However, this increased accuracy was due to significantly better sensitivity (80.7 vs. 34.6%, p < 0.001; 84.6 vs. 34.6%, p < 0.001, respectively) without improved specificity (94.7 vs. 90%, p = 0.55; 85.7 vs. 90%, p = 0.63, respectively). Conclusion: Molecular testing might not be necessary in ITN with high-risk US pattern (X_US = 0.9), as specificity of TC diagnosis based on Xus alone is sufficient and not improved with molecular testing. OCAv2 is useful in guiding the management of ITN with low-to-intermediate risk US features (X_US < 0.9), as it increases the accuracy of TC diagnosis.

Implications of exosomes as diagnostic and therapeutic strategies in cancer

Exosomes offer a new perspective on the biology of cancer with both diagnostic and therapeutic concepts. Due to the cell-to-cell association, exosomes are involved in the progression, metastasis, and therapeutic efficacy of the tumor. They can be isolated from blood and other body fluids to determine the disease progression in the body, including cancer growth. In addition to being reservoirs of biochemical markers of cancer, exomes can be designed to restore tumor immunity. Tumor exosomes interact with different cells in the tumor microenvironment to confer beneficial modulations, responsible for stromal activity, angiogenesis, increased vascular permeability, and immune evasion. Exosomes also contribute to the metastasis with the aim of epithelial transmission to the mesenchyme and the formation of premetastatic niches. Moreover, exosomes protect cells against the cytotoxic effects of chemotherapeutic drugs and prevent the transmission of chemotherapy resistance to adjacent cells. Therefore, exosomes are essential for many fatal cancer agents, and understanding their origins and role in cancer is important. In this article, we attempted to clarify the potential of exosomes for the application in cancer diagnosis and therapy.

Advanced liquid biopsy technologies for circulating biomarker detection

Liquid biopsy is a new diagnostic concept that provides important information for monitoring and identifying tumor genomes in body fluid samples. Detection of tumor origin biomolecules like circulating tumor cells (CTCs), circulating tumor specific nucleic acids (circulating tumor DNA (ctDNA), circulating tumor RNA (ctRNA), microRNAs (miRNAs), long non-coding RNAs (lnRNAs)), exosomes, autoantibodies in blood, saliva, stool, urine, etc. enables cancer screening, early stage diagnosis and evaluation of therapy response through minimally invasive means. From reliance on painful and hazardous tissue biopsies or imaging depending on sophisticated equipment, cancer management schemes are witnessing a rapid evolution towards minimally invasive yet highly sensitive liquid biopsy-based tools. Clinical application of liquid biopsy is already paving the way for precision theranostics and personalized medicine. This is achieved especially by enabling repeated sampling, which in turn provides a more comprehensive molecular profile of tumors. On the other hand, integration with novel miniaturized platforms, engineered nanomaterials, as well as electrochemical detection has led to the development of low-cost and simple platforms suited for point-of-care applications. Herein, we provide a comprehensive overview of the biogenesis, significance and potential role of four widely known biomarkers (CTCs, ctDNA, miRNA and exosomes) in cancer diagnostics and therapeutics. Furthermore, we provide a detailed discussion of the inherent biological and technical challenges associated with currently available methods and the possible pathways to overcome these challenges. The recent advances in the application of a wide range of nanomaterials in detecting these biomarkers are also highlighted.

MicroRNA‑186‑5p mediates osteoblastic differentiation and cell viability by targeting CXCL13 in non‑traumatic osteonecrosis

MicroRNAs (miRs) serve varying and important roles in the pathogenesis of non‑traumatic osteonecrosis (ON). However, the role miR‑186‑5p serves in the pathogenesis of osteonecrosis remains unknown and the clinical outcome of ON is still uncertain. The aim of the present study was to determine the expression characteristics, biological function and molecular mechanisms of miR‑186‑5p, which is associated with cancer development and progression, in osteoblastic differentiation and cell viability. The results of the present study showed that the expression levels of miR‑186‑5p were significantly higher in clinical non‑traumatic ON compared with osteoarthritis samples (P=0.0001). An inverse association was observed between miR‑186‑5p and CXCL13 expression levels. Furthermore, miR‑186‑5p inhibited phosphatidylinositol 3 kinase (PI3K)/protein kinase B (AKT) signaling, downregulated osteoblast‑specific markers and reduced the viability and differentiation of human mesenchymal stem cells from bone marrow (HMSC‑bm) through targeting CXCL13. Increasing expression of CXCL13 in HMSC‑bm cells partially restored miR‑186‑5p‑mediated inhibition. In conclusion, abrogation of PI3K/AKT signaling triggered by miR‑186‑5p/CXCL13 may contribute to ON pathogenesis. These results highlight the possible clinical value of miR‑186‑5p in treatment for non‑traumatic ON.

The Missing Link: How Exosomes and miRNAs can Help in Bridging Psychiatry and Molecular Biology in the Context of Depression, Bipolar Disorder and Schizophrenia

MicroRNAs (miRNAs) only recently have been recognized as promising molecules for both fundamental and clinical neuroscience. We provide a literature review of miRNA biomarker studies in three most prominent psychiatric disorders (depression, bipolar disorder and schizophrenia) with the particular focus on depression due to its social and healthcare importance. Our search resulted in 191 unique miRNAs across 35 human studies measuring miRNA levels in blood, serum or plasma. 30 miRNAs replicated in more than one study. Most miRNAs targeted neuroplasticity and neurodevelopment pathways. Various limitations do not allow us to make firm conclusions on clinical potential of studied miRNAs. Based on our results we discuss the rationale for future research investigations of exosomal mechanisms to overcome methodological caveats both in studying etiology and pathogenesis, and providing an objective back-up for clinical decisions.

Milk MicroRNAs in Health and Disease

MicroRNAs are small noncoding RNAs responsible for regulating 40% to 60% of gene expression at the posttranscriptional level. The discovery of circulating microRNAs in several biological fluids opened the path for their study as biomarkers and long-range cell-to-cell communication mediators. Their transfer between individuals in the case of blood transfusion, for example, and their high enrichment in milk have sparked the interest for microRNA transfer through diet, especially from mothers to infants during breastfeeding. The extension of such paradigm led to the study of milk microRNAs in the case of cow or goat milk consumption in adults. Here we provide a comprehensive critical review of the key findings surrounding milk microRNAs in human, cow, and goat milk among other species. We discuss the data on their biological properties, their use as disease biomarkers, their transfer between individuals or species, and their putative or verified functions in health and disease of infants and adult consumers. This work is based on all the literature available and integrates all the results, theories, debates, and validation studies available so far on milk microRNAs and related areas of investigations. We critically discuss the limitations and outline future aspects and avenues to explore in this rapidly growing field of research that could impact public health through infant milk formulations or new therapies. We hope that this comprehensive review of the literature will provide insight for all teams investigating milk RNAs' biological activities and help ensure the quality of future reports.

Evaluating gastroenteropancreatic neuroendocrine tumors through microRNA sequencing

Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) can be challenging to evaluate histologically. MicroRNAs (miRNAs) are small RNA molecules that often are excellent biomarkers due to their abundance, cell-type and disease stage specificity and stability. To evaluate miRNAs as adjunct tissue markers for classifying and grading well-differentiated GEP-NETs, we generated and compared miRNA expression profiles from four pathological types of GEP-NETs. Using quantitative barcoded small RNA sequencing and state-of-the-art sequence annotation, we generated comprehensive miRNA expression profiles from archived pancreatic, ileal, appendiceal and rectal NETs. Following data preprocessing, we randomly assigned sample profiles to discovery (80%) and validation (20%) sets prior to data mining using machine-learning techniques. High expression analyses indicated that miR-375 was the most abundant individual miRNA and miRNA cistron in all samples. Leveraging prior knowledge that GEP-NET behavior is influenced by embryonic derivation, we developed a dual-layer hierarchical classifier for differentiating GEP-NET types. In the first layer, our classifier discriminated midgut (ileum, appendix) from non-midgut (rectum, pancreas) NETs based on miR-615 and -92b expression. In the second layer, our classifier discriminated ileal from appendiceal NETs based on miR-125b, -192 and -149 expression, and rectal from pancreatic NETs based on miR-429 and -487b expression. Our classifier achieved overall accuracies of 98.5% and 94.4% in discovery and validation sets, respectively. We also found provisional evidence that low- and intermediate-grade pancreatic NETs can be discriminated based on miR-328 expression. GEP-NETs can be reliably classified and potentially graded using a limited panel of miRNA markers, complementing morphological and immunohistochemistry-based approaches to histologic evaluation.

Advanced microRNA-based cancer diagnostics using amplified time-gated FRET

MicroRNAs (miRNAs) play an important role in cellular functions and in the development and progression of cancer. Precise quantification of endogenous miRNAs from different clinical patient and control samples combined with a one-to-one comparison to standard technologies is a challenging but necessary endeavor that is largely neglected by many emerging fluorescence technologies. Here, we present a simple, precise, sensitive, and specific ratiometric assay for absolute quantification of miRNAs. Isothermally amplified time-gated Förster resonance energy transfer (TG-FRET) between Tb donors and dye acceptors resulted in miRNA assays with single-nucleotide variant specificity and detection limits down to 4.2 ± 0.5 attomoles. Quantification of miR-21 from human tissues and plasma samples revealed the relevance for breast and ovarian cancer diagnostics. Analysis of miR-132 and miR-146a from acute monocytic leukemia cells (THP-1) demonstrated the broad applicability to different miRNAs and other types of clinical samples. Direct comparison to the gold standard RT-qPCR showed advantages of amplified TG-FRET concerning precision and specificity when quantifying low concentrations of miRNAs as required for diagnostic applications. Our results demonstrate that a careful implementation of rolling circle amplification and TG-FRET into one straightforward nucleic acid detection method can significantly advance the possibilities of miRNA-based cancer diagnostics and research.

Intracellular MicroRNA Quantification in Intact Cells: A Novel Strategy based on Reduced Graphene Oxide Based Fluorescence Quenching

Nanomaterials have been proposed as key components in biosensing, imaging, and drug-delivery since they offer distinctive advantages over conventional approaches. The unique chemical and physical properties of graphene make it possible to functionalize and develop protein transducers, therapeutic delivery vehicles, and microbial diagnostics. In this study we evaluate reduced graphene oxide (rGO) as a potential nanomaterial for quantification of microRNAs including their structural differentiation in vitro in solution and inside intact cells. Our results provide evidence for the potential use of graphene nanomaterials as a platform for developing devices that can be used for microRNA quantitation as biomarkers for clinical applications.