Background
MicroRNAs (miRNAs), a class of single-stranded small RNA with 18–25 nucleotides, are capable of regulating gene expression at the post-transcriptional level by binding the 3′-untranslated region (3′-UTR) of target mRNAs [
1‐
3]. Past researches have proved that miRNAs involve various biological processes, such as cell differentiation, proliferation, and apoptosis [
2,
4,
5]. Moreover, dysregulation of miRNAs is implicated in many types of disease, including cancer and cardiovascular diseases [
6‐
8]. miRNAs are not only in cells, but also present in extracellular fluids, including plasma, serum, urine, saliva and milk [
9‐
11]. For example, more than 500 miRNAs had been detected in the serum or plasma [
12]. Majority of circulating miRNAs cofractionate with protein complexes and circulate in blood in a highly stable form [
13]. More importantly, circulating miRNAs correlate with diagnosis, prognosis and responses to treatment [
14‐
16]. These findings suggest that circulating miRNAs have great potential as biomarkers in monitoring the body’s physiopathology status.
Colorectal cancer (CRC) is the third most common cancer in the world and the second leading cause of cancer-related deaths. It is estimated that over 1.8 million new CRC cases and 881,000 deaths occurred in 2018, which is about 1 in 10 cancer cases and deaths [
17]. If diagnosed at an early stage, the mortality of the disease could be potentially reduced. Unfortunately, most patients have no phenotypic symptoms until later stages [
18]. Moreover, the current established colorectal cancer screening tests in these years, including colonoscopy, fecal occult-blood testing, and stool DNA test have not been well-accepted, because of their invasive and unpleasant nature, high cost or limited sensitivity [
19,
20]. Therefore, more efforts need to be devoted to discovering noninvasive, sensitive and convenient screening test methods, and miRNAs show to be one of the most promising molecular biomarkers for tumor early diagnosis and prediction of prognosis. Up to now, advances in miRNA biomarkers have generated some candidate markers of CRC with potential clinical values [
21‐
23]. However, these published results have not been clinically applicable until today. The possible reasons could be the lack of sensitive and easily applied method in clinic, as well as knowledge about which biomarker(s) are stable and reproducible for clinical use.
Reverse-transcription quantitative real-time PCR (RT-qPCR) method is most frequently used for measuring the expression of miRNAs due to its high sensitivity, specificity and reproducibility [
12,
24,
25]. Currently, RT-qPCR is mainly based on RNA purification and small RNA enrichment. During the procedure, it is unavoidable to loss slight RNA during washing and dissolving steps and it may lead to detection failure. Moreover, it is time-consuming and laborious for processing large numbers of samples, which limits clinical application. We had previously developed an assay that could detect the virus from serum specimen without the need for RNA purification [
26]. In this study, we optimized an effective RT-qPCR assay for directly detecting miRNAs without RNA extraction, named as “Direct S-Poly(T) Plus”. This method relies on a complete denaturation of miRNA-containing protein complexes and endogenous RNase, and it is followed by a single-step, multiple-stage reaction achieving polyadenylation and reverse transcription simultaneously, during which, an elaborately designed RT primer is used. Then, the non-specific amplification of crude cDNA in quantification PCR relies on a high-activity hot-start DNA polymerase of Thermus aquaticus (Taq). With this approach, it is possible to detect miRNAs at minimal cost and time (~ 140 min). 20 μl plasma/serum could be used for approximately 100 miRNAs detection. This approach also affords higher sensitivity compared with the RNA purification-based miRNA assay, including the widely used stem-loop method and our previous method, S-Poly(T) Plus. Finally, by application of the direct S-Poly(T) Plus, seven potential biomarkers were validated from a genome-wide expression profile in plasma of colorectal cancer patients. We hope that this simple but robust protocol will enable potential circulating biomarkers to enter the clinical application very soon.
Materials and methods
Plasma and serum collection
Human blood samples were collected from Shenzhen People’s Hospital (Shenzhen, China) and Cancer Center of Guangzhou Medical University (Guangzhou, China). Plasma was obtained after centrifuging blood (3000
g for 10 min at 4 °C) that has been collected in EDTA-containing tubes; Serum was drawn after centrifuging blood (3000
g for 10 min at 4 °C) that has been kept at room temperature for 1 h and allowed to spontaneously clot. Sera were collected in the absence of anticoagulant. The plasma and sera were divided into aliquots and stored at − 80 °C. The information of participants was detailed in Additional file
1: Table S1.
Plasma/serum preparation for miRNA measurement
To release circulating miRNAs from protein complexes, we mixed 20 μl of serum/plasma with 10 μl of 4× reaction buffer (100 mM Tris–HCl, 300 mM NaCl, 20 mM MgCl2, 2 mM ATP, 1 mM dNTP, pH 8.0), 10 μl RNase-free water, as well as 1 μg of proteinase K (ThermoFisher, Cat. no. 25,530,049). A 20-min incubation at 50 °C was followed by a 5-min enzyme inactivation at 95 °C. The mixture was centrifuged at 13,000g for 5 min at 4 °C to eliminate the protein precipitant, and then the supernatant (crude RNA) was used as the template for polyadenylation and reverse transcription.
RT-qPCR in serum/plasma
The prepared serum/plasma supernatant was directly used as the template in one-step to complete the polyadenylation and reverse transcription (Poly(A)/RT) as in S-Poly(T) Plus protocol [
25]. More specific, 10 μl of reaction mixture contains 0.5–7.5 μl of crude RNA, 1.5 μl of 4× reaction buffer, 1 μl 0.5 μM RT primer, and 1 μl Poly(A)/RT enzyme. Every microliter of Poly(A)/RT enzyme contains 1 units of Poly(A) polymerase (Enzymatics, Beverly, MA, USA) and 100 units of SuperScript III Transcriptase (Invitrogen, WY, USA). The reaction was incubated at 37 °C for 30 min, 42 °C for 30 min, and then 65 °C for 5 min. No-template control and no-reverse transcriptase control were conducted simultaneously.
Eventually, 0.5 μl of Poly(A)/RT products (crude cDNA) was amplified and detected in real-time PCR, and each qPCR (20 μl) contained 5 μl 4× qPCR Buffer, 0.5 unit hot-start Alpha Taq DNA Polymerase, 0.4 μl 10 μM forward primer, 0.4 μl 10 μM universal reverse primer, 0.5 μl 10 μM universal Taqman probe, and 0.2 μl 100× ROX reference dye. The sequence information of universal reverse primer and Taqman probe were detailed in our previous study [
25]. Each reaction was performed in duplicates on ABI StepOnePlus thermal cycler at the following conditions: 95 °C for 5 min, followed by 40 cycles of 95 °C for 10 s and 60 °C for 40 s.
RNA purification-based miRNA assay as a comparison
Extraction of total RNA, polyadenylation, reverse transcription and real-time PCR were performed using S-Poly(T) Plus method, exactly as previously detailed [
25]. The other RNA purification-based miRNA assay was performed with TaqMan microRNA assay kit (Applied Biosystems), according to the manufacturer’s instructions. To make sure of directly proportional of serum/plasma inputs in RNA purification-based method and Direct S-Poly(T) Plus assay, extracted RNA was diluted as need before the next test.
miRNA profiling
A five-step test was designed to identify potential miRNA biomarkers for colorectal cancer, including early-screening, further-screening, training, validation set-1 and validation set-2. First, 485 blood-derived miRNAs were profiled in serum samples of both colorectal cancer and healthy control and this part of the result had been published [
27]. Second, comparing those in healthy cohort, miRNAs in colorectal cancer group differ by more than 1.5-fold changes on outcome were selected and confirmed with Direct S-Poly(T) Plus method. 172 plasma samples from healthy individuals and 172 from colorectal cancer patients were pooled separately and used in the further-screening. Plasma samples were collected from Shenzhen People’s Hospital (Shenzhen, China). In this step, all PCR products were detected by electrophoresis in 3.5% agarose gel, and miRNAs with nonspecific amplification were excluded. Third, miRNAs with more than 1.5-fold changes, Ct values less than 33 and without nonspecific amplification were further validated using small number of individual specimens (38 NC and 38 CRC). Ultimately, miRNAs with significant difference between colorectal cancer group and healthy group were revalidated using each individual of 106 colorectal cancer samples and 106 healthy samples. Also, potential miRNAs were confirmed with serum samples from 36 colorectal cancer patients and 36 patients from Rectum Department but without colorectal cancer. Serum samples were collected from the Cancer Center of Guangzhou Medical University (Guangzhou, China).
Statistics
hsa-miR-93-5p was selected from 485 cancer-related miRNAs as one of the most stable miRNAs in colorectal cancer [
27]. Relative quantities of miRNAs therefore were calculated using the 2
−ΔCt method with hsa-miR-93-5p as an endogenous normalizer. Statistical analysis was submitted to the GraphPad Prism 5. Data were shown as mean ± SE (standard error). Two-tailed Student’s test was used for statistical analysis.
Discussion
The Direct S-Poly(T) Plus quantification protocol described here is simple, efficient and sensitive for measuring circulating miRNAs without RNA extraction. Usually, trizol reagent is formulated for total RNA isolation, however, it is unavoidable to have some of the miRNAs lost due to incomplete protein denaturation or incomplete RNA precipitation and recovery. More importantly, it is very tedious and time-consuming for processing large numbers of samples, which limits its clinical application. Strategies for direct RT-qPCR analysis in the measurement of circulating miRNAs had been proposed in cell lysates [
32], serum [
28] or plasma [
29]. Comparing to these approaches, we have made more efforts to improve the sensitivity of the method in this study. With Direct S-Poly(T) Plus assay, 20 μl plasma could be used for detecting approximately 100 miRNAs (with two duplicate), and it is possible to detect single miRNA with 0.0003 μl initial plasma inputs (Fig.
4), which is much less than that in the reports of Asaga et al. [
28] (0.625 μl) and Zhao et al. [
29] (0.02 μl). The sensitivity of direct S-Poly(T) Plus relies on: first, a complete denaturation of miRNA-containing protein complexes and endogenous RNase. According to the literature, this success may in part reflect the incorporation of tween 20 or proteinase K [
28,
29]. In our study, we discovered that miRNAs were more easily detected in the proteinase K digestion of plasma (Fig.
1b). This result would be explained by that proteinase may be more effective for the digestion of protein complexes, and destroy the RNase-rich environment of plasma/serum for decreasing degradation of miRNA; second, an elaborately designed RT primer, which consists of an oligo(dT)
11 sequence and six miRNA-specific bases, thus provides higher binding strength and thermodynamic stability between miRNA template and RT primer [
12,
25]; Third, a single-step, multiple-stage reaction achieving polyadenylation and reverse transcription simultaneously [
25]; fourth, a high-activity hot-start DNA polymerase Taq for the crude cDNA. Comparing to RNA purification-based assays, the sensitivity of Direct S-Poly(T) Plus assay was 2.7–343-fold higher than that of the widely used stem-loop method, and comparable with the previous version, S-Poly(T) plus method.
The direct identification of circulating miRNAs may impact the development of specific miRNAs as biomarkers. We also made lots of efforts on improving the applicability of Direct S-Poly(T) Plus and the performance of miRNA biomarkers in clinic cases. In previous literature, only several miRNAs were detected to determine the usability and sensitivity of direct RT-qPCR assay [
28,
29]. In our study, hundreds of miRNAs had been tested using Direct S-Poly(T) Plus method and part of results were verified with RNA purification-based method, and then potential biomarkers with high AUC and sensitivity were validated. Besides, data normalization is a challenge for analysis for circulating miRNA, especially in direct RT-qPCR assay. Spiked-in RNAs, such as cel-miR-39, cel-miR-54, and cel-miR-238, could only monitor the efficiency of RNA purification or RT as a class of exogenous references. However, these non-protein-complexes-coated exogenous references were specifically destabilized in Rnase-rich plasma/serum. Suitable endogenous reference genes could be expressed constitutively and the expression levels should not be affected by biological change, disease or treatment. In our previous study, we identified three endogenous references (hsa-miR-93-5p, hsa-miR-25-3p and hsa-miR-106b-5p) out of from 485 blood-derived miRNAs, which could stably express in different cohorts of plasma samples of colorectal cancer and healthy donor [
27]. More interestingly, three miRNAs validated from 485 miRNAs are derived from a single primary transcript, indicting the cluster may be highly conserved in colorectal cancer. In this study, we used one of them, hsa-miR-93-5p as reference, and then seven miRNAs (hsa-miR-423-5p, hsa-miR-451a, hsa-miR-30b-5p, hsa-miR-27b-3p, hsa-miR-199a-3p, hsa-let-7d-3p and hsa-miR-423-5p) were validated as potential biomarkers in colorectal cancer. Importantly, these seven miRNAs could discriminate colorectal cancer stage I from healthy individuals, which generates exciting prospects for early diagnosis and prognosis.
Advances in miRNA biomarkers have generated a large number of disease markers with potential clinical values [
33‐
37]. It was even reported that miRNA expression analyses in plasma samples collected 1–2 years before the onset of lung cancer, at the time of CT detection, resulting in the generation of miRNA signatures with strong predictive potential [
36]. We also have validated 11 miRNA biomarkers of non-small cell lung cancer from genome-wide expression profile, and these miRNAs are reliable in different hospital samples, pooled or individual samples [
38]. However, none of these published results have been applied in clinic until today. The main reason could be lacking a very simple but robust standardized execution of miRNA measurements with clinical application value. Direct S-Poly(T) Plus assay could minimize human and mechanical errors and reduce time and cost. Using this approach, a detection report could be obtained in 2–3 h and only 20 μl plasma is enough for a panel of miRNAs.
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