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A R T I C LE I N FO A B S T R A C T
Keywords: Background: Accumulating evidence has indicated that microRNAs play important roles in the initiation and
miR-139 progression of digestive system tumors. However, previous studies suggest that the accuracy of miRNA detection
Digestive system tumors in digestive system tumors was inconsistent.
Bioinformatics Methods: The candidate miRNAs were obtained from The Cancer Genome Atlas (TCGA). Meta-analysis was
Meta-analysis
performed to evaluate the diagnostic value of these miRNAs in digestive system tumors. Furthermore, the po-
tential target genes of the miRNAs were predicted and assessed with functional analysis.
Results: According to TCGA data, miR-139 was a common biomarker of digestive system tumors. It was mark-
edly reduced in tumor tissues as compared with non-cancerous tissues in digestive system tumors. In the meta-
analysis, the pooled diagnostic odds ratio (DOR) and AUC was 57.51 (95% CI: 14.25–232.04) and 0.96 (95% CI:
0.94–0.97), respectively. Furthermore, the overall sensitivity and specificity was 0.89 (95% CI: 0.73–0.96) and
0.91 (95% CI: 0.75–0.97), respectively. The diagnostic value of tissue miR-139 was higher than the diagnostic
value of blood miR-139. In particular, miR-139 was a superior marker for distinguishing colorectal cancer.
Conclusion: miR-139 could be a potential biomarker for diagnosis of digestive system tumors especially color-
ectal cancer.
⁎
Correspondence to: F.B. Wang, Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuchang District, Wuhan 430071, PR China.
⁎⁎
Correspondence to: B.C. Wang, Department of Pathology, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuchang District, Wuhan 430071, PR China.
E-mail addresses: wbcheng2006@126.com (B.-C. Wang), wfb20042002@sina.com (F.-B. Wang).
1
These authors contributed equally to this work.
https://doi.org/10.1016/j.cca.2018.06.006
Received 19 February 2018; Received in revised form 2 June 2018; Accepted 4 June 2018
Available online 05 June 2018
0009-8981/ © 2018 Elsevier B.V. All rights reserved.
Y.-H. Wang et al. Clinica Chimica Acta 485 (2018) 33–41
diseases through data mining from public databases such as The Cancer 2.4. Data extraction and quality assessment
Genome Atlas (TCGA) [19]. Subsequently, it is feasible to use bioin-
formatics analysis to predict dysregulation of miRNAs, potential target Two independent researchers (Yu-Hui Wang and Hong Weng) ex-
genes and signal pathways in various disorders. Therefore, bioinfor- tracted the data from each eligible study for analysis, including the first
matics analysis can be a novel tool to identify crucial miRNAs to direct author, published papers date, country, cancer type, sample size, con-
early diagnosis, prognosis and therapeutic design for cancer patients. It trols, specimens, sensitivity and specificity of the detection. The third
is also powerful for understanding the molecular mechanism of miRNAs reviewer (Jia Ji) joined the discussion to resolve differences.
in cancers [20]. Methodological quality of selected diagnostic studies was assessed by
In our study, a systematic expression profiling analysis was con- the QUADAS-2 (Quality Assessment of Diagnostic Accuracy Studies 2)
ducted based on the gene expression data from TCGA on digestive [22].
system tumors. miR-139, which was differentially expressed between
the tumor tissues and adjacent normal tissues, stood out to be a
common cancer biomarker. To further substantiate the significance of 2.5. Prediction and functional analysis of target genes
miR-139, we performed an integrated meta-analysis to quantitatively
evaluate the effect of miR-139 on the diagnosis of digestive system Target genes of miR-139 were predicted using two prediction da-
tumors. Additionally, bioinformatics analysis was also used to predict tabases including Pictar [23] (Available online: http://pictar.mdc-
the target genes of miR-139 as well as their potential roles in several berlin.de/) and miRDB [24] (Available online: http://www.mirdb.
signal pathways. Furthermore, GO enrichment analysis and KEGG org/), and were further validated in DIANA-TarBase v7.0 [25] data-
analysis of target genes were conducted. Our results suggest that miR- base with strong evidence including luciferase reporter assay, WB and
139 is a potential tumor biomarker for the screening and diagnosis of RT-PCR (Available online: http://diana.imis.athena-innovation.gr/
digestive system tumors. DianaTools/index.php?r=tarbase/index). Only genes that were con-
firmed by all three databases were considered target genes. To com-
2. Materials and methods prehensively study miR-139, GO [26] enrichment analysis and KEGG
[27] analysis were conducted on the target genes using an online tool
2.1. TCGA data downloading and analysis DAVID (https://david.ncifcrf.gov/, version 6.8). P-value < 0.05 was set
as the cut-off criterion.
High throughput miRNA sequencing data in the project LIHC,
PAAD, ESCA, CHOL, STAD, COAD and READ were downloaded from
The Cancer Genome Atlas (TCGA) database. miRNA expression pro- 2.6. Statistical analysis
filing was conducted on 375 liver cancer tissues and 50 normal liver
tissues, 179 pancreatic cancer tissues and 4 normal pancreatic tissues, R package “edgeR” of R language (version 3.2.5) was used to ana-
187 esophageal cancer tissues and 13 normal esophageal tissues, 36 lyze the high-throughput data to determine the differential gene ex-
cholangiocarcinoma tissues and 9 normal bile ducts tissues, 446 sto- pression. Statistical analysis was performed using the STATA software
mach cancer tissues and 45 normal stomach tissues, 619 colorectal 12.0 (Stata Corp, College Station, TX, USA) to calculate two-sided P-
carcinoma tissues and 11 normal colorectal tissues, respectively. values. In the meta-analysis, P-value < 0.05 was considered significant.
Because the sample size of project CHOL is limited, we pooled data We used the bivariate meta-analysis model to estimate the pooled
from project CHOL and LIHC for analysis. The differential miRNA ex- sensitivity, specificity, positive likelihood ratio (PLR), negative like-
pression between each cancer and corresponding normal tissue was lihood ratio (NLR) and diagnostic odd ratio (DOR) with the 95% con-
determined using R package “edgeR” [21]. Benjamini-Hochberg fidence intervals (95% CIs). Meanwhile, we plotted the summary re-
method was used to control the false discovery rate (FDR). Differen- ceiver operator characteristic (SROC) curve and calculated the area
tially expressed miRNAs (DEmiRNAs) were identified using a threshold under the curve (AUC) to evaluate the differential diagnosis power. The
of ︱LogFoldChange︱ > 1.5 and FDR < 0.05. heterogeneity of multiple studies was assessed by the Cochran's Q test
and the inconsistency index (I2) test [28]. P-value > 0.10 and I2
2.2. Literature search strategy value < 50% suggest acceptable heterogeneity, and a fixed effects
model was adopted. In contrast, a random-effects model was adopted to
PubMed, Embase, Web of Science, the Cochrane Library, CNKI and estimate the pooled results. To evaluate the sources of heterogeneity,
Wanfang database were thoroughly searched for studies (in English or we further performed subgroup analysis and meta-regression. Further-
Chinese) related to the role of miR-139 in human digestive system tu- more, the publication bias analysis was conducted using Deeks' test.
mors until May 4, 2018. The keywords used in the search were “cancer”
or “tumor” or “neoplasm” together with “miR-139” or“microRNA-139”
or “miRNA-139” or “hsa-miR-139”. After the search, the published 3. Results
papers were carefully reviewed and additional relevant references were
also included. 3.1. Hsa-miR-139 as a potential biomarker for the diagnosis of digestive
system tumors
2.3. Screening criteria
Following the screening criteria, 183 DEmiRNAs between liver
Published papers were selected based on the following criteria: (1) cancer tissues and normal liver tissues, 6 DEmiRNAs between pan-
studies are about the diagnostic potential of miR-139 for digestive creatic cancer tissues and normal pancreatic tissues, 93 DEmiRNAs
system tumors; (2) cancer cases are confirmed by histological ex- between esophageal cancer tissues and normal esophageal tissues, 190
amination; (3) studies provide diagnostic indices such as sensitivity and DEmiRNAs between stomach cancer tissues and normal stomach tis-
specificity, or sufficient information to calculate. Several published sues, 448 DEmiRNAs between colorectal carcinoma tissues and normal
papers were excluded because: (1) they are unrelated to the role of miR- colorectal tissues were obtained. Among these DEmiRNAs, miR-139
139 in the diagnosis of digestive system tumors; (2) there are no was the only common DEmiRNA in all five digestive system tumors.
available diagnostic test indices; (3) they are not human research; (4) Meanwhile, further analysis of TCGA data indicated that miR-139 was
they are reviews, case reports, meta-analysis and letters; (5) they have markedly reduced in digestive system tumor tissues in comparison with
duplicate references. adjacent non-cancerous tissues (Fig. 1).
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Y.-H. Wang et al. Clinica Chimica Acta 485 (2018) 33–41
Fig. 1. Identification of potential biomarkers for the diagnosis of digestive system tumors with Bioinformatics. A. Venn diagram of differentially expressed miRNAs
between tumor tissues and non-cancerous tissues in 5 digestive system tumors. B. Relative expression of miR-139 in 5 digestive system tumors based on TCGA data.
3.2. Characteristics of eligible studies These papers focus on colorectal cancer (n = 3) and hepatocellular
carcinoma (n = 1) with 223 cases and 182 controls in total. The blood
As shown in Fig. 2, a total of 803 eligible published papers were miR-139 was detected by Quantitative real-time polymerase chain re-
found after the search. After a stringent review, 748 papers were ex- action (qRT-PCR) and TaqMan. Regarding the specimen types, blood
cluded in the step of duplicate removed and title and abstract screening. plasma was studied in three papers while blood serum was studied in
55 articles, which are closely related to miR-139 expression for the one paper. Three studies were done in China [29, 31, 32]. Four pub-
diagnosis of digestive system tumors, were selected and further lished studies and TCGA data, with 2065 cases and 314 controls, were
screened for the eligibility. 51 articles were subsequently excluded due enrolled in our meta-analysis from 2013 to 2017. The general char-
to insufficient information about diagnostic test indices. Eventually, 4 acteristics were presented in Table 1. Consequently, we assessed the
eligible papers were chosen for our present meta-analysis [29–32]. quality of studies along with the QUADAS-2 and showed them in Fig. 3.
35
Y.-H. Wang et al. Clinica Chimica Acta 485 (2018) 33–41
Table 1
Characteristics of diagnostic studies and TCGA sets included in the meta-analysis.
First author Year Country Histology TNM Specimen Methods Case Control Sensitivity Specifcity
stage
Ng 2017 China Colorectal cancer I–IV Serum TaqMan 117 90 0.966 0.978
Yu 2014 China Colorectal cancer I–IV Plasma TaqMan 30 35 0.6 0.857
Li 2014 China Liver cancer I–III Plasma RT-qPCR 31 31 0.806 0.581
Kanaan 2013 America Colorectal cancer I–IV Plasma TaqMan 45 26 0.91 0.57
TCGA-colorectum 2016 America Colorectal cancer I–IV Tissue miRNA-Seq 619 11 0.998 1
TCGA-liver 2016 America Liver cancer I–IV Tissue miRNA-Seq 411 59 0.886 0.983
TCGA-stomach 2016 America Stomach cancer I–IV Tissue miRNA-Seq 446 45 0.866 0.911
TCGA-pancreas 2016 America Pancreatic cancer I–IV Tissue miRNA-Seq 179 4 0.531 0.75
TCGA-esophagus 2016 America Esophageal squamous cell carcinoma I–IV Tissue miRNA-Seq 187 13 0.813 0.923
3.3. Diagnostic accuracy of miR-139 in screening digestive system tumors Ratio (PLR) was 10.19 (95% CI: 3.02–34.45), the Negative Likelihood
Ratio (NLR) was 0.12 (95% CI: 0.04–0.34), and the diagnostic odds
We analyzed the pooled sensitivity and specificity of all eligible ratio (DOR) was 57.51 (95% CI: 14.25–232.04). The area under the
published papers. Because of the significant heterogeneity curve (AUC) was 0.96 (95% CI: 0.94–0.97) according to the corre-
(I2 = 97.57% for sensitivity and I2 = 89.86% for specificity), the sponding overall summary receiver operator characteristic (SROC)
random-effects model was used to calculate the sensitivity and speci- curve (Fig. 5A). These results indicated that the diagnostic accuracy of
ficity. As shown in forest plots (Fig. 4A), the overall sensitivity and miR-139 in screening digestive system tumors was relatively high.
specificity were 0.89 (95% CI: 0.73–0.96) and 0.91 (95% CI:
0.75–0.97), respectively. Additionally, the pooled Positive Likelihood
Fig. 3. Methodological quality of the study on miR-139 for the diagnosis of digestive system tumors.
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Y.-H. Wang et al. Clinica Chimica Acta 485 (2018) 33–41
Fig. 4. Summary estimates of the sensitivity and specificity with forest plots analysis. A. Forest plots for miR-139 in digestive system tumors; B. Forest plots for miR-
139 in colorectal carcinoma; C. Forest plots for miR-139 in tumor tissues; D. Forest plots for miR-139 in blood.
3.4. Diagnostic efficacy of miR-139 in screening colorectal cancer 3.6. Meta-regression analysis
Colorectal cancer was the most commonly diagnosed cancer in the We performed meta-regression to further explore the potential
papers that were used to evaluate the diagnostic efficacy of miR-139. source of heterogeneity (Fig. 6). The meta-regression explored the
Therefore, we further analyzed the significance of miR-139 in distin- characteristics of each study including “Ethnicity (Asian or not)”,
guishing colorectal cancer patients from healthy individuals. The “Control (Healthy control or not)”, “Sample (blood or not)” and
pooled sensitivity and specificity were 0.96 (95% CI: 0.72–1.00) and “Method (miRNA-Seq or not)”. Our result suggested that the control
0.94 (95% CI: 0.62–0.99), respectively, with the significant hetero- covariate was responsible for the heterogeneity in the specificity.
geneity (I2 = 97.52% and 96.5%) (Fig. 4B). The PLR, NLR and DOR
were 16.12 (95% CI: 1.77–146.86), 0.04 (95% CI 0.00–0.39) and
3.7. Publication bias
149.33 (95% CI: 9.22–2418.70), respectively. The AUC for colorectal
cancer was 0.99 (95% CI: 0.97–0.99) (Fig. 5B).
To assess potential publication bias of selected papers, the Deeks'
funnel plot asymmetry test was conducted. No significant publication
bias was found in the pooled analysis (p = 0.18) (Fig. 7), indicating no
3.5. Pooled effect of tissue miR-139 or blood miR-139 on the diagnosis of
significant publication bias in our meta-analysis.
digestive system tumors
The sensitivity and specificity in the tissue group were 0.91 (95% CI: 3.8. Target genes of miR-139 and the functional and pathway enrichment
0.63–0.98) and 0.97 (95% CI: 0.75–1.00), respectively (Fig. 4C). In
addition, the PLR and NLR were 28.7 (95% CI: 2.60–316.8) and 0.09 To provide a precise and deep insight into the role of miR-139 in the
(95% CI: 0.02–0. 50), respectively. The heterogeneity was significant in initiation and progression of digestive system tumors, the target genes
the sensitivity and specificity data (I2 = 99.02 and I2 = 64.13), we used of miR-139 were predicted using miRNA target gene prediction data-
the random-effects model. The DOR was 309 (95% CI, 6.00–16,647). bases. As a result, a total of 30 potential target genes of miR-139 were
The AUC of the corresponding SROC curve was 0.98 (95% CI: found (Table 2).
0.97–0.99), indicating that tissue miR-139 had a relatively high accu- The functional and pathway enrichment analysis of miR-139 was
racy in the diagnosis (Fig. 5C). With regard to the diagnosis using blood performed using the DAVID website (https://david.ncifcrf.gov/, ver-
miR-139, the sensitivity, specificity, PLR, NLR and DOR were 0.87 sion 6.8). The terms of cellular component (CC) and molecular function
(95% CI: 0.68–0.95), 0.82 (95% CI: 0.53–0.95), 4.9 (95% CI: 1.4–16.8), (MF) were nucleus (GO: 0005634) and DNA binding (GO: 0003677),
0.16 (95% CI: 0.05–0.48) and 31 (95% CI: 4–261), respectively respectively. The enriched biological process (BP) term was positive
(Fig. 4D). Moreover, the AUC was 0.92 (95%CI: 0.89–0.94) (Fig. 5D). regulation of translational initiation (GO: 0045948). However, the
KEGG analysis didn't find an enriched signal pathway (Table 3).
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Y.-H. Wang et al. Clinica Chimica Acta 485 (2018) 33–41
Fig. 5. SROC analysis of the diagnostic performance of miR-139. A. SROC curves for miR-139 in digestive system tumors; B. SROC curves for miR-139 in colorectal
carcinoma; C. SROC curves for miR-139 in tumor tissues; D. SROC curves for miR-139 in blood.
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Y.-H. Wang et al. Clinica Chimica Acta 485 (2018) 33–41
Fig. 7. Deeks' funnel plot for the assessment of the publication bias.
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Y.-H. Wang et al. Clinica Chimica Acta 485 (2018) 33–41
Table 2
Targets of miR-139 in data mining.
miRNA Target genes
Table 3
GO functional annotation for the most significantly enriched targeted genes of miR-139.
Type Term Gene
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