Background
Colon cancer is the third most common cancer with high cancer-related deaths worldwide [
1]. Currently, recurrence and metastasis are the principal causes of death, despite improvements in the multidisciplinary and comprehensive treatment based on surgical operation of colon cancer [
2]. In spite of the in-depth studies of the molecular mechanisms underlying colon cancer for the last decades, chemoresistance remains a crucial challenge for the treatment of colon cancer.
MicroRNAs (miRNAs) are a class of short, non-coding RNAs [
3]. miRNAs bind to the 3′-untranslated regions (UTR) of partially complementary target messenger RNAs (mRNAs) by base pairing mode, thereby suppressing the expression of downstream target genes [
4,
5]. More than 30% of mRNAs are regulated by miRNAs, which can act as tumor suppressor genes or oncogenes, depending on the microenvironment within the cell and the specific downstream target genes they regulate [
6]. Therefore, deregulation of miRNA expression influences many biological functions of tumors such as angiogenesis, differentiation, cell proliferation, and apoptosis [
7]. As a disease with extremely complex molecular mechanisms, many deregulated miRNAs have been implicated in the pathogenesis of colon cancer [
8,
9].
The powerful data analysis and search capabilities of Ingenuity Pathways Analysis (IPA) contribute to the understanding of existing data, target discovery, and validation as well as analysis of biological networks [
10]. The application of IPA software has been widely used in cancer research, and its powerful database makes it easier to identify potential biomarkers for cancer diagnosis and therapy [
11,
12]. Although many miRNAs have been confirmed as biomarkers in colon cancer in a number of studies, limited experimental research has been performed by using IPA to better understand the miRNA/mRNA network of colon cancer.
In this study, we found that miR-19b-3p was significantly upregulated in colon cancer using IPA. To figure out its role in colon cancer, we performed the current study to evaluate the associations of miR-19b-3p dysregulation with colon cancer progression in vitro and in vivo, and further investigate its relationship with prognosis of colon cancer patients.
Methods
IPA database is used for analyze and understand the complex biological and chemical systems in life science research. IPA provides exploratory investigation of genes, proteins, and biological functions, creating customized pathways or molecular interaction networks focused on drug targets and identifying potential biomarkers. The microRNA Target Filter associates microRNAs from a dataset with experimentally observed mRNA targets which is used to overlay microRNA data onto networks and pathways, to add molecules to networks, and to compare molecules from different experimental observations. In this study, we used IPA 9.0 to screen miRNAs specifically expressed in colon cancer to better understand the biology around potential mRNA targets/diseases and to identify the most biologically relevant targets.
The latest release of the miRTarBase database (
http://mirtarbase.mbc.nctu.edu.tw/) was used to collect experimentally validated target genes of miRNAs, which were screened by IPA. The miRNA-gene regulatory network was based on the interactions of miRNAs and predicted target genes. Functional annotations of the predicted target genes of these miRNAs were obtained from R annotation packages. Function enrichment analyses were performed by Fisher’s exact test.
P-values were adjusted for the multiple testing corrections by R function “p.adjust”. We chose functional terms whose adjusted
P-value was smaller than 0.05 as significantly enriched functions.
Patients and tissue samples
A total of 211 tissue samples from colon cancer patients with pathologically confirmed diagnosis were obtained immediately after surgery and frozen at −80 °C in liquid nitrogen before being deposited in the Anal-Colorectal Surgery Department, General Hospital of Ningxia Medical University. For each case, paired tumor and distal mucosae were collected. All patients provided informed consent and the study was approved by the institutional review boards of General Hospital of Ningxia Medical University. The pathologic verification of diagnosis and staging is summarized according to the National Comprehensive Cancer Network (NCCN) Practice guidelines. The follow-up of this cohort ended on July 14, 2014 and the median duration of follow-up was 59 (range, 12–83) months. Disease-free survival (DFS) and overall survival (OS) rates were defined as the interval from the initial surgery to clinically or radiologically proven recurrence/metastasis and death, respectively.
Cell culture and transfection
The human colon cancer cell lines, SW620, LoVo, HCT 116, SW480, Caco-2, HT-29, RKO, DLD1, and human normal colonic epithelial cells, NCM460, were obtained from the Type Culture Collection of the Chinese Academy of Sciences (Shanghai, China). Hsa-miR-193a-3p inhibitor and negative control were purchased from Biomics Biotech (Biomics Biotech, Nantong, China). Their sequences were as follows: miR-19b-3p inhibitors, 5′ -UCAGUUUUGCAUGGAUUUGCACA-3′; negative control, 5′ -CAGUACUUUUGUGUAGUACAA-3′. The coding sequence of miR-19b-3p inhibitors or negative control was cloned into pCDH-CMV lentivectors (SBI, Mountain View, CA, USA) by BioLink Biotechnology (Shanghai, China). To package the construct, 293 T cells were co-transfected with both pPackH1 packaging plasmid mix (SBI, Mountain View, CA, USA) and the lentivectors. Then the virus particles were collected 48 h later. For transfection, cells were plated in 6-well plates at a density of 2 × 105 cells/well and cultured until they reached 80% confluence. Then RKO and SW480 cells were infected with viruses.
RNA extraction and quantitative real-time PCR
Total RNA, including miRNAs, was isolated from clinical tissue specimens and cell lines using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. The first strand cDNA was synthesized with the RevertAid First Strand cDNA Synthesis Kit (MBI Fermentas, Vilnius, Lithuania) using 1 μg of total RNA as the template. miRNAs were prepared with the High-Specificity miRNA qRT-PCR Detection Kit (Stratagene, Santa Clara, CA, USA) and U6 was used as an endogenous control. The relative miR-19b-3p level was calculated from this eq. 2
-ΔCT[ΔCT = Ct (miR-19b-3p) - Ct (control)]. Real-time PCR of SMAD4 and miRNAs was carried out using ViiA™ 7 system (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s instructions.
GAPDH was used as endogenous control to normalize the expression of
SMAD4. The qRT-PCR primers are shown in Additional file
1: Table S1.
Cell proliferation and invasion
Cell Counting Kit-8 (CCK8) assays (Dojindo, Kumamoto, Japan) were used to evaluate the cell proliferation ability according to the manufacturer’s protocol. The invasion assays were implemented by using the transwell system. The pore size of invasion chambers is 8.0 μm coated with matrigel (Millipore, Billerica, MA, USA). The colon cancer cells were suspended after being transfected for 48 h, and then seeded in the upper chambers of 24-well transwell plates with serum and calcium-free solution supplemented with 0.2% BSA. The lower chamber was filled with 500 μL of medium containing 10% FBS. Cells were incubated for 24 h at 37 °C with 5% CO2. Next, a cotton swab was used to wipe off the matrigel and cells remaining in the upper chambers. Cells that migrated to the lower chambers were fixed with methanol for 20 min and then stained with 1% crystal violet for 10 min. The number of migrated cells was counted under a light microscope with a 200× magnification. Five fields were randomly selected on each membrane.
Cell viability and apoptosis
The Annexin V-PE and 7-AAD (BD Biosciences, San Jose, CA, USA) double staining method was used to examine cell viability. The frequency of apoptosis was measured using the BD FACSCalibur™ Flow Cytometer (BD Biosciences, San Jose, CA, USA) according to the manufacturer’s instructions. Before assessing the chemosensitivity of colon cancer cells to oxaliplatin, the optimal drug concentration of oxaliplatin inducing cell death was determined on untransfected cells. Cells were treated with oxaliplatin (MedChem express, Monmouth Junction, NJ, USA) at a final concentration of 50 μg/mL for 24 h. The percentage of oxaliplatin-treated and untreated apoptotic cells was calculated according to the number of cells positive or negative for Annexin V-PE and 7-AAD. Results are presented as the percentage of total cells that were living cells (Ann−/7-AAD-), early apoptotic cells (Ann+/7-AAD-), late apoptotic cells, and dead cells (Ann+/7-AAD +).
Western blot
Western blot was performed to assess SMAD4 expression in miR-19b-3p inhibitor and negative control transfected cells and tumors induced in SCID mice. SMAD4 was detected with anti-SMAD4 (Abcam, Cambridge, UK) at a 1:5000 dilution. The level of SMAD4 was normalized to the level of β-actin protein, which was detected by using anti-β-actin (Abcam, Cambridge, UK) at a 1:2000 dilution. Then horseradish peroxidase (HRP)-tagged anti-rabbit or anti-mouse immunoglobulin (Abgent, San Diego, CA, USA), at a dilution of 1:2000, was used to detect the primary antibody. Enhanced chemiluminescence reagent (Merck Millipore, Temecula, CA, USA) was applied to reveal the protein bands. The Image J software (National Institutes of Health, Bethesda, MD, USA) was used to quantify the band intensity. To further explore the effects of the interactions between miR-19b-3p and several mRNA at the protein level, a series of western blot analyses was performed following the aforementioned experimental protocols. Primary antibodies included PRKACB, ATM, CREB3L2, EGLN3, JUN, NR3C1, WEE1, RASSF1 and TGFBR2 (Abcam, Cambridge, UK).
Tumorigenesis
Twenty 6- to 8-week-old SCID mice were obtained from the Shanghai Jiaotong University and maintained in specific pathogen-free (SPF) conditions. Approximately 5 × 106 SW480 cells transfected with miR-19b-3p inhibitor or a negative control were injected subcutaneously into the opposite flanks of each mouse. Tumors grew in all animals and the tumors size was measured at 4, 8, 12, 16, and 21 days. All nude mice were euthanized by cervical dislocation at day 21 and their tumors were harvested, weighed, and photographed. All procedures followed the Shanghai Jiao tong University Affiliated Shanghai General Hospital Animal Care guidelines.
Plasmid constructs and luciferase reporter assays
Dual-Luciferase reporter assays (Promega, Madison, WI, USA) were used following the manufacturer’s instructions. The putative miR-19b-3p complementary site in the 3′-UTR of SMAD4 mRNA (NM_005395; 3′-UTR: 1352–1358) or its mutant sequence were cloned into the pmirGLO luciferase reporter vector. The novel combined plasmid was named pmirGLO-SMAD4 3′’-UTR-wt (wild type). A mutation of the 3′-UTR of SMAD4 was created by using a site-directed mutagenesis kit (Thermo Fisher Scientific, Waltham, Massachusetts, USA) and designated as pmirGLO-SMAD4 3′-UTR-mut (mutant). SW480 cells were plated at 4000 cells per well in 100 μL DMEM in a 96-well microplate (BD Biosciences, USA). Twenty-four hours after plating, cells were co-transfected with 0.5 μg of pmirGLO-SMAD4 3′-UTR-wt or pmirGLO-SMAD4 3′-UTR-mut, 0.01 μg of the pMirGLO-Vector (Promega, Madison, WI, USA), 50 nM miR-19b-3p mimics (Mimics), and miRNA mimics Negative Control (NC) using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA). The firefly and Renilla luciferase activities were measured 24 h after transfection.
In situ hybridization (ISH) and immunohistochemistry on tissue microarray
The tissue microarray (TMA) including 120 pairs of colon cancer and corresponding normal mucosa was obtained from Outdo Biotech (Shanghai, China). The TMA slides were dewaxed by xylene for 15 min twice. After being dehydrated by immersion in 100% ethanol for 5 min, the slides were air-dried and then incubated with pepsin at 37 °C for 15 min. Then the slides were fixed in 4% paraformaldehyde, dehydrated in 90% ethanol, and incubated with the digoxigenin-labeled probe (Exiqon, Denmark) complementary to miR-19b-3p at 37 °C overnight, according to the manufacturer’s instructions. The slides were washed twice with 2× Saline-Sodium Citrate Bufferat room temperature, and incubated with mouse anti-digoxigenin monoclonal antibody according to the manufacturer’s protocol. miR-19b-3p expression in the TMA was assessed by 2 independent pathologists. The proportion of positively stained tumor cells was graded as follows: 0 (no positive cells), 1 (<10% positive cells), 2 (10–50% positive cells), 3 (>50% positive cells). The intensity of the staining was recorded on a scale of 0 (no staining), 1 (weak staining), 2 (moderate staining), and 3 (strong staining). The staining index (SI) was defined as the proportion of positively stained tumor cells × staining intensity.
To further confirm that SMAD4 is the target of miR-19b-3p, we detected SMAD4 protein expression levels by immunohistochemistry on the same location of the TMA. The scoring systems were similar to those used for ISH.
Statistics
Statistical analyses were performed using the SPSS statistical software program version 20 (SPSS Inc., Chicago, IL, USA). Student’s t-test was applied to compare two groups of quantitative data. The χ2 test or Fisher’s exact test for enumeration data was used to analyze the relationship between miR-19b-3p and clinicopathological features. Kaplan-Meier method was used to analyze the survival rates, and the differences between the survival curves were examined by the log-rank test. Univariate and multivariate survival analyses were performed using Cox proportional hazards models. P < 0.05 was considered statistically significant.
Discussion
Colon cancer is initiated by aberrant processing of genetic information due to genetic changes involving tumor suppressor genes and oncogenes, or altered epigenetic mechanisms manifested in global or local changes of chromatin structure [
15]. Despite the continuous development of novel tumor targeting therapeutics, chemoresistance remains a challenge for the treatment of colon cancer [
16]. At present, researchers have made great progress in the area of chemoresistance-associated miRNAs in colon cancer. However, the identification of novel miRNAs is still pivotal in colon cancer therapy [
17,
18].
Our research used the IPA database to identify miRNAs specifically expressed in colon cancer. The 7 upregulated miRNAs were selected for further study, including miR-19b-3p, miR-155-5p, miR-17-5p, miR-183-5p, miR-25-3p, miR-21-5p, and miR-196a-5p. Several of them are associated with various human cancers. For example, miR-155-5p is deregulated in colorectal cancer, osteosarcoma, and triple-negative breast cancer [
19‐
21]. Functional annotations of the predicted target genes of these miRNAs were obtained from R annotation packages, including GO biological process. Genes in enriched functional terms were used to construct a miRNA-target network. In this network diagram, many genes were closely related with colon cancer progression such as
PTEN, STAT3, FOXO1, and
SMAD4 [
22‐
25]. The biological function analysis of the predicted target genes based on IPA and GO annotation enabled us to comprehensively understand their functional roles in colon cancer progression. The predicted target genes were significantly involved in many biologic processes relevant to cancer such as apoptosis, cell proliferation, and cell cycle arrest. These bioinformatics analyses suggested that the predicted target genes may control broad biological functions associated with colon cancer. miR-19b-3p was identified as the pivotal oncogenic component of the miR-17-92 cluster of miRNAs because of its role in promoting sustained cell survival and recognized as an onco-miR in some types of cells and tissues [
26,
27]. Upregulated miR-19b-3p plays a critical role in the tumorigenesis of Em-Myc-driven B-cell lymphomas [
28]. We found that high expression of miR-19b-3p in colon cancer tissues was significantly associated not only with tumorhistologic grade, but also with AJCC stage. Furthermore, Kaplan-Meier and univariate Cox proportional hazard regression analyses indicated that patients with high miR-19b-3p expression displayed a lower five-year OS and DFS. Multivariate analyses indicated that miR-19b-3p expression in colon cancer was an independent prognostic factor of survival. We also observed that miR-19b-3p downregulation had no effect on invasion, but correlated with reduced cell proliferation and decreased oxaliplatin-based chemoresistance. The proliferation ability is associated with tumor size and the invasion ability is correlated with distant metastasis. In other words, miR-19b-3p does not act as an enhancer of cancer metastasis, but of tumorigenesis in vitro. We speculate that this may be because of the complex tumor microenvironment in vivo. Recent molecular and cellular biology studies indicated that tumor growth and metastasis are not only determined by cancer cells, but are also affected by various stromal cells [
29]. During metastasis, tumor cells need to go through a series of complex steps, during which they continually adapt to different microenvironments [
30]. Thus, a stable in vivo model of colon cancer metastasis will be necessary to further understand the underlying mechanisms in our future study.
In this study, we demonstrated that
SMAD4 is the direct target of miR-19b-3p in colon cancer. As an important mediator of the TGF-β signaling pathway, SMAD4 plays an important role in suppressing tumor progression and promoting apoptosis of tumor cells [
23]. Reduced expression of SMAD4 is associated with attenuated sensitivity to chemotherapy and poor prognosis of patients with colon cancer in several clinical studies [
23,
31]. The inverse relationship between miR-19b-3p and SMAD4 in colon cancer cell lines and tumor samples was investigated in our study. Importantly, since SMAD4 is targeted by this miRNA, we showed that the proliferation ability and resistance to oxaliplatin-based chemotherapy is reversed by the transfection of SMAD4 shRNA.