Circulating microRNAs have shown promise as biomarkers for cardiovascular diseases and acute myocardial infarctions. In this study, we describe a protocol for miRNA extraction, reverse transcription, and digital PCR for the absolute quantification of miRNAs in the serum of patients with cardiovascular disease.
Circulating serum microRNAs (miRNAs) have shown promise as biomarkers for the cardiovascular disease and acute myocardial infarction (AMI), being released from the cardiovascular cells into the circulation. Circulating miRNAs are highly stable and can be quantified. The quantitative expression of specific miRNAs can be linked to the pathology, and some miRNAs show high tissue and disease specificity. Finding novel biomarkers for cardiovascular diseases is of importance for medical research. Quite recently, digital polymerase chain reaction (dPCR) has been invented. dPCR, combined with fluorescent hydrolysis probes, enables specific direct absolute quantification. dPCR exhibits superior technical qualities, including a low variability, high linearity, and high sensitivity compared to the quantitative polymerase chain reaction (qPCR). Thus, dPCR is a more accurate and reproducible method for directly quantifying miRNAs, particularly for the use in large multi-center cardiovascular clinical trials. In this publication, we describe how to effectively perform digital PCR in order to assess the absolute copy number in serum samples.
Circulating miRNAs have been identified as promising markers for a number of diseases, including cardiovascular disease1. The miRNAs are small, non-coding single-stranded RNA molecules (approximately 22 nucleotides long) are involved in the post-transcriptional regulation via the alteration of the messenger RNA translation and influencing gene expression2, and are released into the circulation in both physiological and pathological states. The quantitative expression of specific miRNAs can be linked to the pathology, and some miRNAs show high tissue and disease specificity1. In cardiovascular diseases, miRNAs have become attractive candidates as novel biomarkers because they are remarkably stable in the serum and can easily be quantified with the help of PCR methodology3. The potential value of miRNAs as biomarkers for myocardial infarction has been evaluated in small studies, but a validation in large cohorts is lacking2. For example, miR-499 is found highly expressed in the myocardial muscle, and it has been shown to be significantly increased in an AMI4,5,6. Further, it regulates programmed cell death (apoptosis) and the differentiation of cardiomyocytes and is thus involved in several mechanisms following an AMI7. Apart from some small studies reporting a superiority and incremental value of miRNAs for the diagnosis of AMI, the superiority or equality to high-sensitivity cardiac troponins has not yet been proven in large-scale studies2,5,6,8. More prospective studies in large cohorts are, therefore, needed to assess the potential diagnostic value of miRNAs. Additionally, methods of miRNA quantification need to be optimized and standardized using comparable protocols9. Standardized assays may reduce inconsistent results and may help miRNAs to become potential biomarkers for the routine clinical application, as biomarkers need to be quantified in a reproducible way to ensure their clinical applicability.
Recently, dPCR has been introduced as an end-point analysis. It partitions the sample into approximately 20,000 individual reactions10. The dPCR system then utilizes a mathematical Poisson statistical analysis of fluorescent signals (positive and negative reactions), enabling an absolute quantification without a standard curve10. When combining dPCR with fluorescent hydrolysis probes, the highly specific direct absolute quantification of miRNAs is made possible. Digital polymerase chain reaction has shown to exhibit superior technical qualities (including a decreased variability, an increased day-to-day reproducibility, a high degree of linearity, and a high sensitivity) for quantifying miRNA levels in the circulation compared to quantitative real-time PCR10,11. These superior technical qualities might help to mitigate current limitations on using circulating miRNAs as biomarkers and may lead to the establishment of miRNAs as biomarkers in large multi-center cardiovascular clinical trials and as a diagnostic method in general. In a previous study, we recently applied dPCR for the absolute quantification of circulating miRNAs in patients with an AMI and were able to demonstrate superior diagnostic potential compared to the quantification of miRNAs by qPCR12.
In this publication, we want to demonstrate that using dPCR is an accurate and reproducible method for directly quantifying circulating cardiovascular miRNAs. The absolute quantification of miRNA levels in serum, using digital PCR, shows potential for the use in large multi-center cardiovascular clinical trials. In this publication, we describe in detail how to effectively perform digital PCR and how to detect the absolute miRNA copy number in serum.
1. Extraction of miRNA from Plasma/Serum
Note: In order to quantify miRNAs appropriately, the correct microRNA isolation from the plasma/serum is a crucial step. A key thing to keep in mind, especially because different protocols exist, is to adhere to the same workflow while processing the samples. In this protocol, miRNA is extracted from 50 µL of serum. Do not use more than 200 µL as this limit the correct extraction process.
2. Reverse Transcription
Note: Complementary DNA (cDNA) was synthesized using the following 15 µL reverse transcription (RT) protocol (total reaction volume).
3. Droplet Generation and Digital PCR
Note: Digital PCR was performed using the following 40 µL protocol.
4. Droplet Reading and Analyzing
5. Correct Calculations on the Sample
6. Synthetic Oligonucleotide Dilution Series
Digital PCR combined with fluorescent hydrolysis probes enables researchers to directly quantify the absolute amounts of specific miRNAs in copies/µL. As the sample in dPCR is partitioned in approximately 20,000 individual PCR reactions, dPCR does not require technical replicates10. The dPCR system utilizes a mathematical Poisson statistical analysis of fluorescent signals (differing between positive and negative reactions) enabling an absolute quantification without the need for a standard curve10. In order to correctly calculate the concentrations, an acceptable droplet count is needed (>15,000). No template controls ensure the exclusion of considerable nonspecific amplification. All samples included in the analysis are processed using the same volume, method, and PCR protocol to strengthen the validity of the obtained results. The obtained concentrations in dPCR are normalized using a median normalization procedure across all samples analyzed with the synthetic spiked-in C. elegans miR-3913. Normalizing the data to the measured amount of spiked-in C. elegans miR-39 corrects for the sample-to-sample variation in the RNA extraction efficiency and serves as a PCR reaction control, further adding to the validity of the results. There is no established gold standard for normalizing serum miRNAs; however, exogenous controls such as the spiked-in C. elegans miR-39 are an elegant solution for normalization procedures, as endogenous miRNAs are often altered in various disease states9.
The analyzed serum samples were acquired before a percutaneous coronary intervention (PCI), 8 h after a PCI, and 16 h after a PCI, from patients with an acute ST-segment elevation myocardial infarction (STEMI). STEMI patients exhibit severe ischemia and thus qualify for the evaluation of new ischemia biomarkers. To evaluate the kinetics of miR-499 release and the potential use of miR-499 as a biomarker for ischemia in cardiovascular disease, miR-499 was analyzed with dPCR across all patients for the three different time points14.
Figure 1 demonstrates the selection of positive droplets giving the final miRNA concentration calculated by the software. The fraction of positives in a sample determines the concentration of copies/µL as calculated by the commercial dPCR software. The results can also be visualized in a 2D plot and the positives can be manually marked with circles. Concentrations are only considered if they are above the nonspecific amplification of the NTCs.
Figure 2 shows the linearity and goodness-of-fit of a synthetic miRNA oligonucleotide hsa-miR-499-5p dilution series in duplicates. An 8-step dilution series was performed from 2,500 copies/µL to 0 copies/µL. The calculated expected copies/µL as described in Table 5 assume 100% RT and digital PCR efficiency. In this setup, digital PCR demonstrates a high degree of linearity (r2 = 0.99). The limit of detection (LoD = 0.12) and the limit of quantification (LoQ = 0.23) are also presented in Figure 2, showing that even a low miRNA expression can be detected successfully. Thus, dPCR can be used to quantify even low serum levels of circulating miRNAs. The limit of detection (LoD) and the limit of quantification (LoQ) are calculated following the approach of Forootan et al.15 and are defined as LoD = LoB + 1.645 x σlow concentration sample, where the limit of blank (LoB) is calculated as LoB = meanblank + 1.645 x σblank. The LoQ is then estimated running replicate standard curves15. To ensure the reproducible quantification of miRNAs, only miRNA concentrations that lie above both the LoD and the LoQ are considered as a valid exact value.
Figure 3 shows representative results of miR-499 levels of patients with an ST-elevation myocardial infarction (STEMI), n = 16 at each time point. Samples were taken before a percutaneous intervention (PCI) (t = 0), 8 h after a PCI (t = 8), and 16 h after a PCI (t = 16), and the miR-499 levels were compared to miR-499 levels of patients with stable coronary artery disease (CAD, n = 20). The main patient characteristics can be found in Table 6. After the initial release of miR-499 into the serum in the first 8 h following a myocardial infarction, miR-499 levels decrease again after 16 h. A trend in increase can already be seen at the beginning of the STEMI (t = 0), and a significant increase of miR-499 levels compared to patients with CAD can be seen 8 h after the STEMI (t = 8, p <0.01) when comparing miR-499 levels to miR-499 levels of stable CAD patients. The receiver operating curves (ROC) show the possible utility of miR-499 as a novel biomarker to differentiate between patients with CAD and patients with a STEMI [the area under the curve (AUC) = 0.62 for samples taken before a percutaneous intervention (PCI), AUC = 0.75 for samples taken 8 h after a PCI, and AUC = 0.78 for samples taken 16 h after a PCI compared to serum levels of miR-499 in patients with CAD].
Figure 1: Selection of positive droplets in a dilution series performed in duplicates. (A) The threshold is set manually above the negative droplets. (B) The results are visualized in a 2D blot, the positives selected by circling. Please click here to view a larger version of this figure.
Figure 2: Synthetic miR-499 oligonucleotide dilution series. (A) The measurements were performed in duplicate. The data are presented log transformed as absolute copies per µL. Linear regressions and goodness-of-fit (r2-value) are shown. The data are presented as mean ± SEM. (B) This panel shows the limit of detection (LoD) and the limit of quantification (LoQ). Please click here to view a larger version of this figure.
Figure 3: Quantification of circulating serum miR-499-5p in patients with ST-elevation myocardial infarction (n = 16) before percutaneous coronary intervention (PCI), 8 h after PCI, and 16 h after PCI, compared to patients with stable coronary artery disease (n = 20). (A) The circulating serum miR-499-5p is represented as mean with the standard error of the mean with the corresponding p-value calculated by one-way ANOVA followed by a Bonferroni post hoc test (p <0.05 was considered as statistically significant). (B) A receiver operating characteristic curve (ROC) analysis is performed on the data from panel A. The ROC analysis demonstrates the sensitivity and specificity of the biomarker. Further, the corresponding area under the curve (AUC) values are shown. Please click here to view a larger version of this figure.
sample amount | ||||
n = 1 | /well [μl] | |||
nuclease-free water | 4.16 | |||
10x Reverse Transcription buffer | 1.5 | |||
100nM dNTP | 0.15 | |||
RNAse inhibitor | 0.19 | |||
specific RT Primer | 3 | |||
Commercial Reverse Transcriptase Enzyme 50 U/ul | 1 | |||
Master-Mix total | 10 |
Table 1: Reverse Transcription Reagents Mix.
Temperature | Time |
16 °C | 30 mins |
42 °C | 30 mins |
85 °C | 5 mins |
4 °C | ∞ |
Table 2: Thermal Cycling Conditions for Reverse Transcription.
sample amount | ||||
n = 1 | /well [μl] | |||
nuclease-free water | 7.67 | |||
commercial dPCR mix | 10 | |||
20x specific hydrolysis primer/probe | 1 | |||
Master-Mix total | 18.67 |
Table 3: Digital PCR Reagent Mix.
Temperature | Time |
95 °C | 10 mins |
94 °C | 30 secs (x40) |
60 °C | 1 min |
98 °C | 10 mins |
4 °C | ∞ |
Table 4: Thermal Cycling Conditions for digital PCR.
Tube | Transferred synthetic oligonucleotide miR-499 (µL) | Diluent (µL) | miRNA (copies/µL) | Expected Copies/µL in RT | Expected Copies/µL in dPCR |
Original | 6.022 x 1012 | ||||
1 | 10 | 990 | 6.022 x 1010 | ||
2 | 10 | 990 | 6.022 x 108 | ||
3 | 10 | 990 | 6.022 x 106 | ||
4 | 18.7 | 981.3 | 1.128 x 105 | 37600 | 2500 |
5 | 40 | 60 | 4.511 x 104 | 15040 | 1000 |
6 | 50 | 50 | 2.256 x 104 | 7520 | 500 |
7 | 40 | 160 | 4.511 x 103 | 1504 | 100 |
8 | 50 | 50 | 2.256 x 103 | 752 | 50 |
9 | 40 | 160 | 4.511 x 102 | 150.4 | 10 |
10 | 50 | 150 | 1.128 x 102 | 37.6 | 2.5 |
11 | 0 | 50 | 0 | 0 | 0 |
Table 5: Synthetic dilution series for miR-499.
Characteristic | All | Stable CAD Patients (n=20) | STEMI Patients (n= 24) | p-value |
Age | 64.7 ± 11.9 | 66.7 ± 13.1 | 62.2 ± 9.9 | 0.2810 |
Males | 77.8% | 65% | 93.8% | 0.0392 |
DM | 33.3% | 40% | 25% | 0.3428 |
HTN | 61.1% | 60% | 62.5% | 0.8785 |
Dyslipidemia | 38.9% | 65% | 6.3% | 0.0003 |
Smoker | 47.2% | 55% | 37.5% | 0.3796 |
Family history | 25% | 35% | 12.5% | 0.1213 |
Overweight | 58.3% | 55% | 62.5% | 0.6501 |
Serum Creatinine (mg/dL) | 0.94 (0.83 – 1) | 0.98 (0.82 – 1.01) | 0.93 (0.83 – 1) | 0.7255 |
CK Peak (U/I) | 161 (102 – 611) | 126 (81 – 161) | 492 (228 – 3208) | 0.0004 |
cTnT Peak (ng/L) | 322.5 (23.8 -4533) | 18 (7 – 25.3) | 2492 (240 – 5586) | 0.0002 |
LVEF% | 45% (40% – 50%) | 45% (32.5% – 55%) | 45% (45% – 50%) | 0.9596 |
Values are presented as mean ± SD; median value (25th to 75th percentile range) or % | ||||
DM: Diabetes mellitus | ||||
HTN: Hypertension | ||||
CK: Creatine kinase | ||||
cTnT: Cardiac troponin T | ||||
LVEF: Left ventricular ejection fraction |
Table 6: Main patient characteristics.
Digital PCR is a relatively novel end-point method of PCR that allows the direct absolute quantification of nucleic acids within a sample. The method possesses particular advantages, including a decreased variability, an increased day-to-day reproducibility, and a superior sensitivity11,12. Further, due to the partitioning of the sample into approximately 20,000 single reactions and endpoint analyses, dPCR is more robust to interfering substances in PCR compared to quantitative RT-PCR16. These qualities in dPCR make it an attractive alternative to quantitative RT-PCR as a diagnostic tool for quantification. As circulating miRNAs are often present at low serum concentrations, so far, scientists have been challenged to appropriately quantify miRNAs by PCR9. On the other hand, dPCR can appropriately quantify even a low miRNA expression in serum, mitigating the problems observed in low count miRNA quantification17. The ability of dPCR to directly give the counts/µL, even in a very low miRNA expression, thus makes it an attractive diagnostic tool for the cardiovascular research community in miRNA biomarker studies. As the concentration given in counts/µL can be multiplied by the dilution factor used in extraction, RT-reaction, and dPCR, it is possible to achieve the exact number of copies in 1 µL of serum. The workflow presented here can be performed in up to 96 samples on a plate, hence providing a tool for large cardiovascular studies. Although dPCR exhibits several advantages over quantitative RT-PCR, it is not yet routinely applied for the quantification of miRNAs in cardiovascular trials. Further, standardized data normalization procedures are lacking.
In this approach, we demonstrate that dPCR, combined with fluorescent hydrolysis probes, enables the specific direct absolute quantification of circulating miRNAs linked to cardiovascular disease. With this report, we aimed to both demonstrate an optimized protocol for miRNA detection via dPCR and confirm the advantages of dPCR over quantitative RT-PCR.
We confirmed the good linearity dPCR exhibits and the low limits of the detection and quantification of dPCR for quantifying miRNAs. By spiking the sample with a synthetic oligonucleotide, the normalization of the sample is possible, adjusting for extraction efficiency and sample-to-sample variation.
In conclusion, digital PCR, as it exhibits superiority in both technical proficiency and diagnostic potential, is the best current method for miRNA quantification and may further be used for large multi-center cardiovascular miRNA biomarker studies.
The authors have nothing to disclose.
The authors have no acknowledgments.
RNA-Extraction | |||
miRNeasy Serum/Plasma Kit (50) | Qiagen-Sample & Assay Technologies, Hilden, Deutschland | 217184 | Kit for microRNA extraction. Kit contains commercial buffer RWT (called number one in the manuscript) and RPE (called number two in manuscript). |
miRNeasy Serum/Plasma Spike-in-Control; Syn-cel-miR-39 miRNA; 10pmol | Qiagen-Sample & Assay Technologies, Hilden, Deutschland | 219610 | Spike-in for normalisation , Sequence: 5'-UCACCGGGUGUAAAUCAGCUUG-3' |
Reverse Transcription | |||
TaqMan MicroRNA Reverse Transcription Kit (1000 Reactions) | Applied Biosystems, Inc., Foster City, CA, USA | 4366597 | Kit for microRNA reverse transcription |
TaqMan MicroRNA Assays M | Applied Biosystems, Inc., Foster City, CA, USA | 4440887 | Assays used in reverse transcription |
hsa-miR-499 (750 RT/750 PCR rxns) | Applied Biosystems, Inc., Foster City, CA, USA | 4440887 | Assay Number 001352 |
cel-miR-39 (750 RT/750 PCR rxns) | Applied Biosystems, Inc., Foster City, CA, USA | 4440887 | Assay Number 000200 |
PCR Plate, 96-well, segmented, semi-skirted | Thermo Fisher Scientific, Waltham, MA, USA | AB0900 | 96 well plate for reverse transcription |
Microseal ‘B’ seal Seals | Bio-Rad Laboratories, Inc., Hercules, CA, USA | MSB1001 | Foil to ensure proper storage |
C1000 Touch Thermal Cycler | Bio-Rad Laboratories, Inc., Hercules, CA, USA | 1851196 | Cycler used for reverse transcription |
Droplet Digital PCR | |||
100 nmole RNA oligo hsa-miR-499-5p | Integrated DNA Technologies | Custom | Sequence: 5'-phos-UUAAGACUUGCAGUGAUGUUU-3' |
ddPCR Supermix for Probes (No dUTP) | Bio-Rad Laboratories, Inc., Hercules, CA, USA | 1863024 | Supermix used in droplet generation |
TaqMan MicroRNA Assays | Applied Biosystems, Inc., Foster City, CA, USA | 4440887 | Assays used in digital PCR (fluorescent hydrolysis probe) |
hsa-miR-499 (750 RT/750 PCR rxns) | Applied Biosystems, Inc., Foster City, CA, USA | 4440887 | Assay Number 001352, commercial primers |
cel-miR-39 (750 RT/750 PCR rxns) | Applied Biosystems, Inc., Foster City, CA, USA | 4440887 | Assay Number 000200, commercial primers |
DG8 Cartridges and Gaskets | Bio-Rad Laboratories, Inc., Hercules, CA, USA | 1864007 | Cartridge takes up to 8 samples for droplet generation |
DG8 Cartridge Holder | Bio-Rad Laboratories, Inc., Hercules, CA, USA | 1863051 | Holds cartridges in droplet generation |
Droplet Generation Oil for Probes | Bio-Rad Laboratories, Inc., Hercules, CA, USA | 1863005 | Oil used in droplet generation |
ddPCR 96-Well Plates | Bio-Rad Laboratories, Inc., Hercules, CA, USA | 12001925 | 96 well plate for ddPCR |
PCR Plate Heat Seal, foil, pierceable | Bio-Rad Laboratories, Inc., Hercules, CA, USA | 1814040 | Pierceable foil, compatible with droplet reader |
ddPCR Droplet Reader Oil | Bio-Rad Laboratories, Inc., Hercules, CA, USA | 1863004 | Oil used in droplet reading |
QX100 or QX200 Droplet Generator | Bio-Rad Laboratories, Inc., Hercules, CA, USA | 1863002 | Droplet Generator, generates the droplets from sample/oil emulsion |
PX1 PCR Plate Sealer | Bio-Rad Laboratories, Inc., Hercules, CA, USA | 1814000 | Seals the plate before PCR |
C1000 Touch Thermal Cycler | Bio-Rad Laboratories, Inc., Hercules, CA, USA | 1851196 | Cycler used for ddPCR |
QX100 or QX200 Droplet Reader | Bio-Rad Laboratories, Inc., Hercules, CA, USA | 1863003 | Reads PCR-positive and PCR-negative droplets with an optical detector |
ddPCR Buffer Control for Probes | Bio-Rad Laboratories, Inc., Hercules, CA, USA | 1863052 | Blank control and to fill up the remaining wells of 8-well cassette |
Software | |||
QuantaSof Software | Bio-Rad Laboratories, Inc., Hercules, CA, USA | 1864011 | Program for droplet reading |
Prism Windows 5 | GraphPad Software Inc., La Jolla, CA, USA | Program for statistical analysis |