Optimized Collection Protocol for Plasma MicroRNA Measurement in Patients with Cardiovascular Disease

Key methodological challenges in detecting circulating miRNAs in different biofluids

The technological advancement in diagnostic techniques has immensely improved the capability of predicting disease progression. Yet, there is a great interest in developing newer biomarkers that can enhance disease risk prediction thereby minimising the associated morbidity and mortality. Circulating miRNAs, a non-coding RNA molecule, are critical regulators in the pathophysiology of various complex multifactorial diseases. In recent years, circulating miRNAs have been enormously studied and are considered as an emerging biomarker due to their easy accessibility, stability, and detection by sequence-specific amplification methods. However, there is a distinct lack of consensus regarding the preanalytical factors such as preferred sample selection, methodological aspects, etc that may independently or together influence the detection of circulating miRNAs resulting in erroneous expression profiles. Therefore, the present review makes an attempt to highlight the various pre-analytical and analytical factors that can potentially influence the circulating miRNA levels. Literature on circulating miRNA's stability, processing and quantitation in different biofluids along with the effect of various controllable and uncontrollable factors influencing circulating miRNA expression have been summarised in the current review.

Multiple cancer type classification by small RNA expression profiles with plasma samples from multiple facilities

Liquid biopsy is expected to be a promising cancer screening method because of its low invasiveness and the possibility of detecting multiple types in a single test. In the last decade, many studies on cancer detection using small RNAs in blood have been reported. To put small RNA tests into practical use as a multiple cancer type screening test, it is necessary to develop a method that can be applied to multiple facilities. We collected samples of eight cancer types and healthy controls from 20 facilities to evaluate the performance of cancer type classification. A total of 2,475 cancer samples and 496 healthy control samples were collected using a standardized protocol. After obtaining a small RNA expression profile, we constructed a classification model and evaluated its performance. First, we investigated the classification performance using samples from five single facilities. Each model showed areas under the receiver curve (AUC) ranging from 0.67 to 0.89. Second, we performed principal component analysis (PCA) to examine the characteristics of the facilities. The degree of hemolysis and the data acquisition period affected the expression profiles. Finally, we constructed the classification model by reducing the influence of these factors, and its performance had an AUC of 0.76. The results reveal that small RNA can be used for the classification of cancer types in samples from a single facility. However, interfacility biases will affect the classification of samples from multiple facilities. These findings will provide important insights to improve the performance of multiple cancer type classifications using small RNA expression profiles acquired from multiple facilities.

Whole Blood Holding Time Prior to Plasma Processing Alters microRNA Expression Profile

MicroRNAs (miRNAs) can exhibit aberrant expression under different physiological and pathological conditions. Therefore, differentially expressed circulating miRNAs have been a focus of biomarker discovery research. However, the use of circulating miRNAs comes with challenges which may hinder the reliability for their clinical application. These include varied sample collection protocols, storage times/conditions, sample processing and analysis methods. This study focused on examining the effect of whole blood holding time on the stability of plasma miRNA expression profiles. Whole blood samples were collected from healthy pregnant women and were held at 4°C for 30 min, 2 h, 6 h or 24 h prior to processing for plasma isolation. Plasma RNA was extracted and the expression of 179 miRNAs were analyzed. Unsupervised principal component analysis demonstrated that whole blood holding time was a major source of variation in miRNA expression profiles with 53 of 179 miRNAs showing significant changes in expression. Levels of specific miRNAs previously reported to be associated with pregnancy-associated complications such as hsa-miR-150-5p, hsa-miR-191-5p, and hsa-miR-29a-3p, as well as commonly used endogenous miRNA controls, hsa-miR-16-5p, hsa-miR-25-3p, and hsa-miR-223-3p were significantly altered with increase in blood holding time. Current protocols for plasma-based miRNA profiling for diagnostics describe major differences in whole blood holding periods ranging from immediately after collection to 26 h after. Our results demonstrate holding time can have dramatic effects on analytical reliability and reproducibility. This highlights the importance of standardization of blood holding time prior to processing for plasma in order to minimize introduction of non-biological variance in miRNA profiles.

Pre-Analytical Modification of Serum miRNAs: Diagnostic Reliability of Serum miRNAs in Hemolytic Diseases

Circulating microRNAs (miRNAs) are useful biomarkers of hemolysis. Since blood cells are the main origins of circulating miRNAs, we evaluated blood cell-related pre-analytical modification of the miRNA signatures during blood drawing and serum processing. The levels of miRNA before and after ex vivo blood drawing were analyzed with the reverse transcriptase-based polymerase chain reaction method. Furthermore, the changes of miRNA signatures caused by different time-lag between blood drawing and serum preparation by 24 h were evaluated. Finally, we compared the miRNA levels between leftover samples and samples of hemolytic diseases. Blood drawing procedure induced increments of red blood cell (RBC)-related miRNAs (miR-451a, miR-486) about 2-fold. One hour standing of blood samples before serum separation induced almost the same increases in RBC-related miRNAs. To test the clinical usefulness of miR-451a as a biomarker of hemolytic diseases, we analyzed miRNAs of samples from 10 normal subjects, 30 leftover samples in the clinical laboratory, and 20 samples from patients with hemolytic diseases. Serum miR-451a significantly increased in patients with hemolytic anemia more than the levels of pre-analytical modification. In conclusion, the pre-analytical modification of serum miRNAs did not disturb the usefulness of RBC-derived miRNAs as biomarkers of hemolytic diseases.

Circulating microRNAs as Diagnostic Markers in Primary Aldosteronism

Simple Summary

Many patients remain at increased risk of primary aldosteronism (PA) and its consequences due to the difficulty of accurate diagnosis. MicroRNAs circulating in the bloodstream are emerging as biomarkers for disease, particularly specific forms of cancer. In this review article, we argue that they may also have a role in the diagnosis of PA, if observed changes in the microRNA profile of PA tissue are reflected in circulating microRNAs, which can be sampled and analysed readily in a clinical setting. However, for various practical reasons, studies of potential diagnostic circulating microRNAs have often proved difficult to reproduce consistently. We describe these problems and how they might be overcome using, as an example, our design of the circulating microRNA arm of the ongoing ENS@T-HT project, which is intended to confirm whether circulating microRNAs can serve as biomarkers for PA.

Abstract

Primary aldosteronism (PA) is a common and highly treatable condition, usually resulting from adrenocortical tumorous growth or hyperplasia. PA is currently underdiagnosed owing to its complex and protracted diagnostic procedures. A simplified biomarker-based test would be highly valuable in reducing cardiovascular morbidity and mortality. Circulating microRNAs are emerging as potential biomarkers for a number of conditions due to their stability and accessibility. PA is known to alter microRNA expression in adrenocortical tissue; if these changes or their effects are mirrored in the circulating miRNA profile, then this could be exploited by a diagnostic test. However, the reproducibility of studies to identify biomarker-circulating microRNAs has proved difficult for other conditions due to a series of technical challenges. Therefore, any studies seeking to definitively identify circulating microRNA biomarkers of PA must address this in their design. To this end, we are currently conducting the circulating microRNA arm of the ongoing ENS@T-HT study. In this review article, we present evidence to support the utility of circulating microRNAs as PA biomarkers, describe the practical challenges to this approach and, using ENS@T-HT as an example, discuss how these might be overcome.

An Ex Vivo and In Silico Study Providing Insights into the Interplay of Circulating miRNAs Level, Platelet Reactivity and Thrombin Generation: Looking beyond Traditional Pharmacogenetics

Platelet reactivity (PR), a key pharmacodynamic (PD) component of the action of antiplatelet drugs in cardiovascular disease (CVD) patients, is highly variable. PR is associated with occurrence or recurrence of thrombotic and bleeding events, but this association is modulated by several factors. Conventional pharmacogenetics explains a minor part of this PR variability, and among determinants of PR, circulating microRNAs (miRNAs) have been the focus of attention during these last years as biomarkers to predict PR and clinical outcomes in CVD. This being said, the impact of miRNAs on platelet function and the mechanisms behind it are largely unknown. The level of a set of candidate miRNAs including miR-126-3p, miR-150-5p, miR-204-5p and miR-223-3p was quantified in plasma samples of stable CVD patients and correlated with PR as assessed by light-transmission aggregometry and in vivo thrombin generation markers. Finally, miRNA target networks were built based on genes involved in platelet function. We show that all candidate miRNAs were associated with platelet aggregation, while only miR-126-3p and miR-223-3p were positively correlated with in vivo thrombin generation markers. In silico analysis identified putative miRNA targets involved in platelet function regulation. Circulating miRNAs were associated with different aspects of platelet reactivity, including platelet aggregation and platelet-supported thrombin generation. This paves the way to a personalized antithrombotic treatment according to miRNA profile in CVD patients.

A critical approach for successful use of circulating microRNAs as biomarkers in cardiovascular diseases: the case of hypertrophic cardiomyopathy

MicroRNAs (miRNAs) are small noncoding RNA molecules that act as major regulators of gene expression at the post-transcriptional level. As the potential applications of miRNAs in the diagnosis and treatment of human diseases have become more evident, many studies of hypertrophic cardiomyopathy (HCM) have focused on the systemic identification and quantification of miRNAs in biofluids and myocardial tissues. HCM is a hereditary cardiomyopathy caused by mutations in genes encoding proteins of the sarcomere. Despite overall improvements in survival, progression to heart failure, stroke, and sudden cardiac death remain prominent features of living with HCM. Several miRNAs have been shown to be promising biomarkers of HCM; however, there are many challenges to ensuring the validity, consistency, and reproducibility of these biomarkers for clinical use. In particular, miRNA testing may be limited by pre-analytical and analytical caveats, making our interpretation of results challenging. Such factors that may affect miRNA testing include sample type selection, hemolysis, platelet activation, and renal dysfunction. Therefore, researchers should be careful when developing appropriate standards for the design of miRNA profiling studies in order to ensure that all results provided are both accurate and reliable. In this review, we discuss the application of miRNAs as biomarkers for HCM.

Practical Procedures for Improving Detection of Circulating miRNAs in Cardiovascular Diseases

Hemolysis has been known to affect the measurement of circulating biomarkers. In this study, clinically applicable procedures for microRNA (miRNA) detection in serum samples of acute myocardial infarction patients were established. The 89 samples from patients admitted to the coronary care unit were collected. These samples obtained from heparin-treated and untreated patients were subjected to heparinase digestion prior to miRNA measurements by multiplex RT-qPCR. The good reproducibility of miRNA detection after heparinase digestion (average R2 = 0.97) indicated that this method can be used routinely for samples regardless of heparin medication. Additionally, the degree of hemolysis in these samples was highly related to the hemoglobin absorbance at 414 nm. Based on the hemoglobin absorbance, five hemolysis-associated miRNAs were identified in our data normalized with respect to both the spike-in control and the RNA amount in a given sample. Using these calibration procedures, miRNAs can be accurately quantified and identified for clinical samples. Graphical Abstract The practical procedures for miRNA detection in serum samples from the coronary care unit were established, and five hemolysis-associated miRNAs were accurately clarified through serial normalization.

Circulating MicroRNAs in Duchenne Muscular Dystrophy

OBJECTIVE

The diagnosis of Duchenne Muscular Dystrophy (DMD) currently depends on non-specific measures such as Creatine kinase (CK) levels. MicroRNAs (miRNAs) are a class of small, endogenous RNAs of 21-25 nucleotides, that are important regulators for numerous physiological and pathological processes. The aim of the current study is to assess the potential of miRNAs as non-invasive biomarker for the diagnosis of DMD and for identifying carriers.

PATIENTS AND METHODS

Thirty healthy subjects and 29 families with one member diagnosed with DMD were enrolled in the study. Peripheral blood samples were collected from all subjects where microRNAs were extracted from plasma followed by the quantification of miR-499, miR-103a-3p, miR-103a-5p, miR-206, miR-208a, miR-223 and miR-191-5p. MLPA and NGS were carried out as a gold standard technique to identify the mutations in the participants.

RESULTS

Our data revealed that miR-499 was significantly upregulated in all DMD patients, and true carriers (mothers), while 78 % of potential carriers (sisters) exhibited high levels of this miRNA. Similarly, miR-103a-3p showed an increase in the patients' families although to a lesser extent. On the other hand, miR-206 and miR-191-5p were significantly downregulated in the majority of the DMD patients and the tested female family members. MicroRNA miR-103a-5p and miR-208a followed a comparable trend in patients and mothers.

CONCLUSIONS

Ourresults suggest that the plasma levels of miRNAs have the capability to diagnose DMD patients and more importantly, miRNAs can be used to identify female carriers.

MicroRNA Isolation by Trizol-Based Method and Its Stability in Stored Serum and cDNA Derivatives

MicroRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression at the post-transcriptional level. Since aberrant expression of miRNAs has been proposed as usage for blood-based biomarkers, hence reliable techniques for miRNA isolation as well as stability of miRNAs in various stored conditions needs to be explored. This present study aimed to investigate the efficacy of the Trizol-based isolation technique and the stability of miRNAs in stored serum and cDNA derivatives. Total RNA, including miRNAs, was isolated from human serum and a comparison of the efficiency of the Trizol^®LS reagent isolation method against the miRNeasy^®mini kit was conducted. Expression of RNU6, miR-145, and miR-20a was determined by quantitative real-time polymerase chain reaction (qRT-PCR). We showed that Trizol^®LS isolation yielded significantly lower RNA concentrations than that of the miRNeasy^®mini kit by approximately 35%. Purity of the isolated RNAs by both methods was similar. RNU6, miR-145, and miR-20a degraded at room temperature, but all genes were stable at 4ºC, -20ºC and -80ºC for a 72-hrs period, in both serum and cDNA storage conditions. In the stored cDNA derivatives, we observed the stability of RNU6, miR-145, and miR-20a for 3 months at -20ºC, and all genes also resisted 4 repeated freeze-thaw cycles at -20ºC. In conclusion, the Trizol-based method is efficient as well as economical to use for quantification of circulating miRNAs. In addition, we proposed that the storage of miRNA-derived cDNAs may be an alternative choice to avoid the stability effect.

A circulating miRNA signature for early diagnosis of acute kidney injury following acute myocardial infarction

Background

Acute kidney injury (AKI) is a common complication of acute myocardial infarction (AMI), and is associated with adverse outcomes. The study aimed to identify a miRNA signature for the early diagnosis of post-AMI AKI.

Methods

A total of 108 patients admitted to a coronary care unit (CCU) were divided into four subgroups: AMI⁻AKI⁻, AMI⁺AKI⁻, AMI⁺AKI⁺, and AMI⁻AKI⁺. Thirty-six miRNA candidates were selected based on an extensive literature review. Real-time quantitative RT-PCR analysis was used to determine the expression levels of these miRNAs in the serum collected on the day of CCU admittance. TargetScan 7.1 and miRDB databases were used for target prediction and Metacore 6.13 was used for pathway analysis.

Results

Through a stepwise selection based on abundance, hemolytic effect and differential expression between four groups, 9 miRNAs were found to have significantly differential expression levels as potential biomarkers for post-AMI AKI specifically. Noticeably, the expression levels of miR-24, miR-23a and miR-145 were significantly down-regulated in AMI⁺AKI⁺ patients compared to those in AMI⁺AKI⁻ patients. Combination of the three miRNAs as a panel showed the best performance in the early detection of AKI following AMI (AUC = 0.853, sensitivity 95.65%), compared to the analysis of serum neutrophil gelatinase-associated lipocalin (AUC = 0.735, sensitivity 63.16%). Furthermore, bioinformatic analysis indicated that these three miRNAs regulate the transforming growth factor beta signaling pathway and involve in apoptosis and fibrosis in AKI.

Conclusions

For the first time, this study identify a unique circulating miRNA signature (miR-24-3p, miR-23a-3p, miR-145-5p) that can potentially early detect AKI following AMI and may be involved in renal injury and fibrosis in post-AMI AKI pathogenesis.

Electronic supplementary material

The online version of this article (10.1186/s12967-019-1890-7) contains supplementary material, which is available to authorized users.

Study Design and qPCR Data Analysis Guidelines for Reliable Circulating miRNA Biomarker Experiments: A Review

BACKGROUND

In the past decade, the search for circulating microRNA (miRNA) biomarkers has yielded numerous associations between miRNAs and different types of disease. However, many of these relations could not be replicated in subsequent studies under similar experimental conditions. Although this lack of replicability may be explained by the variation in experimental design and analysis methods, guidelines on the most appropriate design and analysis methods to study circulating miRNAs are scarce.

CONTENT

miRNA biomarker experiments generally consist of a discovery phase and a validation phase. In the discovery phase, typically hundreds of miRNAs are measured in parallel to identify candidate biomarkers. Because of the costs of such high-throughput experiments, the number of individuals included in those studies is often too small, which can easily lead to false positives and false negatives. In the validation phase, a small number of identified biomarker candidates are measured in a large cohort of cases and controls, generally by quantitative PCR (qPCR). Although qPCR is a sensitive method to measure miRNAs in the circulation, experimental design and qPCR data analysis remain challenging. Omitting some crucial steps in the design and analysis of the qPCR experiment or performing them incorrectly can cause serious biases, ultimately leading to false conclusions.

SUMMARY

In this review, we aim to expose and discuss the most common sources of interstudy variation in miRNA research from a methodological point of view and to provide guidelines on how to perform these steps correctly to increase replicability of studies on circulating miRNAs.

Circulating MicroRNAs as Potential Biomarkers of Atrial Fibrillation

Atrial fibrillation (AF) is the most common supraventricular arrhythmia in the population. MicroRNAs (small endogenous noncoding RNAs) are attractive candidates as biomarkers for AF, especially considering that miRNAs are stable and are detected within easily accessible biofluids such as blood. In this review, we selected twelve studies (2012 to 2016) that were classified according to the sample type. We aimed to provide an overview of the role of circulating miRNAs in AF and to discuss the variability of the results, seeking to improve the perspective of the use of miRNAs as potential noninvasive biomarkers for this heart disease.