- Open Access
Co-modulated behavior and effects of differentially expressed miRNA in colorectal cancer
- Wei-Shone Chen†1,
- Ting-Wen Chen†2, 3,
- Tzu-Hsien Yang4,
- Ling-Yueh Hu5,
- Hung-Wei Pan6,
- Chung-Man Leung7,
- Sung-Chou Li8,
- Meng-Ru Ho9,
- Chih-Wen Shu6,
- Pei-Feng Liu6,
- Shou-Yu Yu6,
- Ya-Ting Tu6,
- Wen-Chang Lin5,
- Tony T Wu10, 11Email author and
- Kuo-Wang Tsai6Email author
© Chen et al.; licensee BioMed Central Ltd. 2013
- Published: 16 October 2013
MicroRNAs (miRNAs) are short noncoding RNAs (approximately 22 nucleotides in length) that play important roles in colorectal cancer (CRC) progression through silencing gene expression. Numerous dysregulated miRNAs simultaneously participate in the process of colon cancer development. However, the detailed mechanisms and biological functions of co-expressed miRNA in colorectal carcinogenesis have yet to be fully elucidated.
The objective of this study was to identify the dysfunctional miRNAs and their target mRNAs using a wet-lab experimental and dry-lab bioinformatics approach. The differentially expressed miRNA candidates were identified from 2 miRNA profiles, and were confirmed in CRC clinical samples using reported target genes of dysfunctional miRNAs to perform functional pathway enrichment analysis. Potential target gene candidates were predicted by an in silico search, and their expression levels between normal and colorectal tumor tissues were further analyzed using real-time polymerase chain reaction (RT-PCR).
We identified 5 miRNAs (miR-18a, miR-31, miR-96, miR-182, and miR-224) and 10 miRNAs (miR-1, miR-9, miR-10b, miR-133a, miR-143, miR-137, miR-147b, miR-196a/b, and miR-342) that were significantly upregulated and downregulated in colon tumors, respectively. Bioinformatics analysis showed that the known targets of these dysregulated miRNAs simultaneously participated in epithelial-to-mesenchymal transition (EMT), cell growth, cell adhesion, and cell cycles. In addition, we identified that several pivotal target gene candidates may be comodulated by dysfunctional miRNAs during colon cancer progression. Finally, 7 candidates were proven to be differentially expressed, and had an anti-correlationship with dysregulated miRNA in 48 CRC samples.
Fifteen dysfunctional miRNAs were engaged in metastasis-associated pathways through comodulating 7 target genes, which were identified by using a multi-step approach. The roles of these candidate genes are worth further exploration in the progression of colon cancer, and could potentially be targets in future therapy.
- colorectal cancer
- pathway enrichment analysis
Colorectal cancer (CRC) is one of the most common types of cancer in humans, and is the third leading cause of cancer-related death worldwide . It is the consequence of a multi-step process caused by different genetic and epigenetic changes in numerous genes. MicroRNAs (miRNAs) are a class of non-protein coding RNA molecules of 18-25 nucleotides that exert their function on the base pairing between the seed region of miRNAs and the 3'-untranslated regions (3'-UTR) of target genes. Based on the degree of the complementary pairing between miRNAs and mRNAs, miRNAs either repress translation or promote the degradation of the mRNAs of target genes . In the past decade, considerable evidence has shown that miRNAs are involved in the pathogenesis of human cancer, including CRC [2–7]. An miRNA profiling is an effective approach for high-throughput identification of dysregulated miRNAs during CRC progression, and numerous dysregulated miRNAs in colon cancer have been identified in previous studies [8–12].
The expression of tumor-suppressive miRNA usually suppresses tumor progression through silencing oncogene expression, and oncogenic miRNA frequently inhibits tumor-suppression gene expression, resulting in accelerating carcinogenesis. In colon cancer, most studies have focused on understanding the biological functions of several individual miRNAs, using both in vitro wet-lab experimental and in silico bioinformatics approaches, which provided invaluable information on miRNA-mRNA interactions. Even though miRNAs have been shown to target at genes involved in crucial steps within the protein interaction network . It's been known that miRNAs usually repressed their target gene expressions slightly and alteration of an individual miRNA is insufficient to cause CRC. Therefore, in this study we are especially interested in the consequence of changes of a group of miRNAs in CRC. For those miRNAs that are changed systematically, the influence from a group of miRNAs is generally complex because of the regulation of an abundance of target genes. To further understand the detailed influences of miRNAs, the concept of miRNA regulatory modules (MRMs) was introduced [14–17]. MRMs are groups of miRNAs and their target genes that are thought to work together as a module, and that have correlated functions or are involved in similar biological processes. In 2005, Yoon and De Micheli suggested a method to identify MRMs that was based on miRNAs and their predicted target genes . Since then, other methods have been proposed to identify modules from miRNA and mRNA expression profiles [14, 15, 17]. These studies have found that MRMs are highly enriched in known sets of biological pathways or GO biological process and shown that these MRMs may potentially serve as a model for understanding phenotype alterations or cancer pathogenesis.
In this study, we identified differentially expressed miRNAs in clinical samples of colon cancer, and then used the known targets for these miRNAs to accomplish the identification of potentially affected pathways. Differ from previous studies which used both miRNA and mRNA profiles to obtain a regulatory modules, we take advantage of pathway information to identified important target genes. Based on these pathways, we selected several potential candidate genes involved in colorectal progression. Our results provide biological evidence to support the hypothesis that miRNAs work as a team to regulate the expression of multiple targets, which leads to the alteration of cellular processes and specific biological pathways.
Clinical samples and RNA extraction
48-paired tumor and adjacent normal mucosa samples, and 8-paired metastatic liver tumor, primary tumor, and adjacent mucosa samples were obtained from CRC patients who underwent surgical operation at the Department of Surgery, Veterans General Hospital in Taipei, Taiwan. Informed consent was obtained from all patients. Among the 8 metastatic liver cancer patients, 2 patients were selected that exhibited metastatic liver tumors, primary tumors, and adjacent mucosa samples for ABI TaqMan low-density miRNA array analysis (Applied Biosystems, Foster City, CA, USA). The total RNA of the fresh tumor and non-tumor specimens was extracted using TRIzol reagent (Invitrogen, USA) according to the manufacturer instructions. In brief, tissue samples were homogenized in a 1 mL TRIzol reagent and mixed with 0.2 mL chloroform to extract protein, and the RNA was then precipitated using 0.5 mL isopropanol. The concentration, purity, and the amount of total RNA were determined using a NanoDrop 1000 spectrophotometer (NanoDrop Technologies Inc., USA).
Stem-loop reverse transcription and real-time polymerase chain reaction
The primers were designed to detect mature miRNAs for stem-loop RT-PCR according to the methods described by Chen et al. . One microgram of total RNA was reverse-transcribed using a stem-loop RT reaction with RT primers and SuperScript III Reverse Transcriptase according to the user manual (Invitrogen, Carlsbad, CA, USA). The reaction was performed under the following incubation conditions: 30 min at 16 °C, followed by 50 cycles of 20 °C for 30 s, 42 °C for 30 s, and 50 °C for 1 s. The enzyme was subsequently inactivated by incubation at 85 °C for 5 min. RT-PCR reactions were performed using an miRNA-specific forward primer and a universal reverse primer, and were conducted at 94 °C for 10 min, followed by 40 cycles of 94 °C for 15 s, and 60 °C for 32 s. Gene expression was detected using a SYBR Green I assay (Applied Biosystems, Foster City, CA, USA), and the expression levels of the miRNAs were normalized to that of U6. The expression levels of the predicted target genes were examined using RT-PCR analysis with a gene-specific primer, and were normalized to S26. The expression levels of the target genes were evaluated between the normal and cancer tissues using a paired t test. The difference was considered to be significant if the P value was less than 0.05. The individual primers used in this study are shown in Additional File 1.
Pathway enrichment analysis
Known targets of the 15 dysregulated miRNAs were used to establish which biological processes or pathways these miRNAs might influence. A list of the known targets of each selected miRNA was identified using the MetaCore database. Both targets for upregulated miRNAs and targets for downregulated miRNAs were used for enrichment analysis using MetaCore. These statistically enriched pathways were further investigated to select candidate genes for further validation experiments.
Selection of target genes for further investigation
After identifying the pathways potentially affected by the differentially expressed miRNAs, further validation was required to determine whether these reported targets were influenced in actual biological samples. Several enriched pathways relating to cancer development were targeted for study, such as cell proliferation, cell cycles, cytoskeleton remodeling, cell adhesion, EMT, and apoptosis. Within those pathways, the previously reported targets were selected for further examination. In addition to the reported miRNA targets, this study attempted to identify other potential targets. Potential miRNA targets were downloaded from TargetScan (Release 6.0: November 2011) . Within the predicted targets, those with a context score greater than -0.2 were removed first because they were predicted to be low-efficacy targets [20, 21]. After a list of high-efficacy targets was obtained, targets that were regulated by more than one differentially expressed miRNA were selected, except for genes targeted by both miR-196a and miR196b. Because miR-196a and miR-196b are in the same family and have the same group of predicted target genes, their target genes were treated as if they were targeted only once. Among those predicted high efficacy and co-regulated targets, 7 of them which were located at pathways that we previously selected, were noteworthy. These targets were further investigated to determine whether their expression patterns were consistent with the expected trends.
Identifying miRNAs differentially expressed in colorectal carcinoma
The top 20 most differential up- and downregulated miRNAs are shown from 2 miRNA profiles.
Dysregulated miRNA coexpression in colon cancer
Biological pathways analysis
Locating potential target genes of dysregulated miRNAs in colon cancer
Target genes of 15 dysregulated miRNA were selected for RT-PCR examination in this study
Expression level in colon cancer#
miR133, miR96, miR182
miR1, miR96, miR182, miR31
For known targets, we selected the 6 most reported targets in the enriched pathways, excluding those that have no predicted target site in TargetScan or were predicted to target only controversial dysregulated miRNAs; that is, we selected 3 groups of known targets. The first 2 target groups have been reported and predicted as only downregulated miRNAs (Group III) or as only upregulated miRNAs (Group IV). The third group of targets reportedly targets either up- or downregulated miRNA and is predicted by both upregulated and downregulated miRNAs (Group V). For these predicted targets, we only considered the targets which were predicted to be targeted by more than one of our selected differentially expressed miRNAs to increase our accuracy. From the predicted targets downloaded from TargetScan, there are 179 predicted targets co-regulated by at least 2 upregulated miRNAs and 172 predicted targes co-regulated by at least 2 downregulated miRNAs. Among those predicted co-regulated targets, we further selected 7 that are involved in the enriched pathways we previously derived from known targets. Within these 7 predicted targets, 3 are potential targets for downregulated miRNAs (Group I), and 4 are potential targets for upregulated miRNAs (Group II). Based on the concepts of co-function and co-modulation, we reasonably reduced our candidate list, which was composed of both reported and predicted potential target genes (Table 2).
Examination of the expression levels of miRNA targets
We also identified 3 cancer-associated genes, GAN13, HBEGF, and PPP2R3A, with significantly decreasing expression levels in colon cancer (Figure 3, Group II). They were selected from predicted target genes of miR-182 and miR-96 in Group II. Among them, PPP2R3A was implicated as a tumor-suppressor gene contributing to cell transformation . However, we do not have a complete understanding of the regulation mechanism of PPP2R3A and its relationship with miRNAs in CRC. In this study, we provided a finding that miR-182 and miR-96 may contribute to silence PPP2R3A expression in CRC. In Group III, we identified 3 putative candidates, Collagen I, Cyclin D1, and Versican, which were significantly upregulated in CRC tissues. Although previous studies have shown that miR-196a directly targeted Collagen I, and miR-143 repressed the expression of Cyclin D1 and Versican [35–39], the regulation mechanism of Collagen I, Cyclin D1, and Versican by miRNAs in CRC is not understood. In addition, we have also identified novel miRNAs candidates, miR-143, miR-1, and miR-9, which have the potential to regulate Collagen I, Cyclin D1, and Versican, respectively (Table 2). In our data, we have observed conflicting results in the expression pattern between the miRNAs and anticipated target genes. These conflicting results may be because one gene is usually regulated by a complex mechanism. In addition, previous systematic genome-wide studies have indicated that the regulation effects of miRNAs may be detectable at the protein-synthesis level, although no significant changes may exist at the mRNA expression level [31, 40].
MiRNAs play either a tumor-suppressive or an oncogenic role depending on their target genes, and may modulate cancer growth, cell cycles, and migration in CRC [5, 22, 23, 41]. In general, multiple miRNAs are simultaneously dysfunctional during carcinogenesis. One miRNA regulates the expression of more than one target, and one gene can be regulated by more than one miRNA. This type of many-to-many relationship complicates the study of relevance between miRNAs and their targets, and results in difficulties in comprehensively investigating the altered expression of a group of miRNAs. It has been proposed that miRNAs work together to regulate their target genes in the regulatory network, which differs from previous MRM identification methods [14–17] that considered the sequence similarity or expression profiles, but not biological pathways. These MRMs are likely to simultaneously involve several biological pathways. MRMs identified in a previous study were shown to be enriched in biological pathways, and that these MRMs are likely to be functionally correlated . In addition, regarding pathways, the predicted targets for differentially expressed miRNAs in cancer cells show a broad range of changes, which provide clues to explain abnormal phenotypical alterations . Together with these studies, our results suggest that, beginning with pathway analysis, one may successfully integrate several crucial targets of dysregulated miRNAs to provide an explanation of cancer development.
Compared with previous studies, most of dysfunctional miRNAs detected in this study had been reported in colorectal cancer [5, 22–24]. However, the biological functions of these miRNAs in CRC remained unclear, particularly for miR-10b, miR-96, miR-133a, miR-147b, miR-196a/b, and miR-342. In this study, a comodulated concept was adopted to reasonably identify the miRNA targets. To locate the modules of these differentially expressed miRNAs that may participate in colon cancer; we constructed miRNA and mRNA relationships by using direct targets. We focused on direct targets because a previous study suggested that the high through-put of mRNA and miRNA expression profiles did not yield more accurate prediction outcomes of the protein product levels  compared to the direct targets. In order to obtain more reliable miRNA-mRNA relationships, we used reported targets instead of predicted targets that were used in previous studies [14, 15, 17, 44]. Accordingly, these targets should improve the accuracy of potentially altered pathways. Numerous metastasis- and cancer-related pathways were enriched. Our results also support the theory of MRMs that these miRNAs target at many targets and work as a module, which leads to abnormalities in cancer development or metastases.
Our approach toward potential miRNA target gene selection, namely the use of co-regulation, the same pathway, and the context score, may also provide biologically reasonable rules for novel miRNA target prediction fields. Although not all of our predicted targets were supported through qPCR, the potential targets selected through these criteria are still convincing. For example, when we prepared this manuscript, Rasheed et al. reported that miR-182 can silence GAN13 protein expression, but cannot alter mRNA levels by targeting its 3'-UTR, which results in inhibiting prostate cancer cell migration and invasion . Their results support our findings in which GNA13 is predicted as a putative novel target of miR-182, and its transcriptional levels have a slight negative correlation with miR-182 expression in clinical samples (Table 2). Although the detailed functions of miR-182 silencing the GNA13 expression in colon cancer requires further investigation, their data helps support the reliability of our strategy of novel target selection.
Through further experimental validation, we learned that certain target mRNA expression levels changed in an unexpected manner. This inconsistency has also been observed in a recent study, in which the expression levels of miRNAs and genes in the same MRM were associated by up to 69% . Although we only retained reported targets and high-efficacy and coregulated predicted targets, several of these exhibited nonsignificant or conflicting expression patterns. One gene is usually regulated by numerous regulatory factors in actual biological systems, and the regulatory effects of miRNAs may be observed at either the mRNA expression level or the protein synthesis level [31, 40]. For example, based merely on miRNA regulation, we expected the expression level of GDNF should be upregulated, but some other factors have already been shown to involve in regulation of GDNF expression in cancers. DNA hypermethylation contributes to the low expression of GDNF in several human cancers [46–48]. Satio et al. also found that the promoter region of GDNF was more highly methylated in active inflamed mucosa than in quiescent mucosa in ulcerative colitis patients . These results could address why GDNF significantly reduced its expression in CRC compared to the adjacent normal tissue. Here, we only focused on investigating the mRNA expression levels of targeted genes because of the scarcity of clinical samples, and budgetary limitations. Although the mRNA expression levels of the targeted genes did not completely fit our expectations because they were under the regulation of the miRNAs, these expression levels coupled with the expression-level changes of the miRNA from the clinical samples are invaluable.
Fifteen dysregulated miRNAs were identified by screening clinical samples. We have successfully examined the major biological functions and signaling pathways of these co-expressed miRNAs, and have provided an approach to reasonably narrow down the target genes of co-expressed miRNAs in colon cancer. Both dysfunctional miRNAs and their comodulating target genes are worth further exploration in the progression of colon cancer, and could potentially be targets in future therapy.
This work was supported by grants from Kaohsiung Veterans General Hospital, Taiwan (VGHKS 102-005 and VGHKS102-074).
Publication of this article was funded by National Science Council, Taiwan (NSC 102-2320-B-010-029).
This article has been published as part of BMC Genomics Volume 14 Supplement 5, 2013: Twelfth International Conference on Bioinformatics (InCoB2013): Computational biology. The full contents of the supplement are available online at http://www.biomedcentral.com/bmcgenomics/supplements/14/S5.
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