Background
Colorectal cancer (CRC) is the third most commonly diagnosed cancer in the world with the second-highest mortality rate [
1]. The stage status of tumors often determine the prognosis of CRC patients. The 5-year survival rate of CRC patients ranges from greater than 90% in patients with stage I disease to slightly greater than 10% in patients with stage IV disease [
2]. Therefore, understanding the mechanisms behind the CRC progression is the key to improving patients’ prognosis.
MicroRNAs (miRNAs) are a class of single-stranded non-coding RNAs with a length of 21–25 nucleotides. miRNAs regulate the expression of approximately 60% of the protein-coding genes [
3]. Aerobic glycolysis, one of the central contributors to cancer progression [
4], help cancer cell meet the energy demand, accumulate glycolytic intermediates for cancer biomass synthesis and create an acidic microenvironment [
5]. Existing studies have proved that microRNAs play an important role in the progression of CRC by regulating key glycolytic genes directly or indirectly [
6,
7]. For example, miR-34a-5p inhibited HK1-mediated glycolysis while the miR-122-PKM2 axis contributed to attenuated glycolysis in CRC [
8,
9]. miR-500a is located within the p11 locus on the X chromosome and plays various roles in cancer. miR-500a is upregulated in prostate cancer and promotes cell proliferation and invasion [
10]. miR-500a promotes cell stemness via different pathways in gastric and liver cancer [
11,
12]. However, miR-500a suppresses cell proliferation, migration and invasion in non-small cell lung cancer [
13]. According to the data of a cohort of 551 CRC patients derived from the cBioportal database, miR-500a has the most significant correlation with prognosis (with the lowest
P value). miR-500a has two arms, miR-500a-5p and miR-500a-3p. miR-500a-5p is downregulated and acts as a tumor suppresser in CRC. miR-500a-5p may attenuate epithelial‑mesenchymal transition through targeting the transforming growth factor‑β signaling pathway [
14] and suppress cell proliferation by targeting the p300/YY1/HDAC2 axis [
15]. However, the role of miR-500a-3p has not been elucidated in CRC.
Cyclin-dependent kinases 6 (CDK6) is known as a classic cell cycle kinase that facilitates the proliferation of cells through the early G1 phase of the cell cycle. CDK6 participates in the process of cancer progression through the kinase-dependent or non-kinase-dependent function [
16]. Recently, the role of CDK6 in metabolic regulation has been reported. Wang et al. found that CDK6 regulates the catalytic activity of two key enzymes in the glycolytic pathway, 6-phosphofructokinase and pyruvate kinase M2 [
17]. Nevertheless, the role of CDK6 in regulating CRC metabolism remains to be revealed.
In the current study, we investigated the effects of miR-500a-3p on the cell proliferation and glycolysis in CRC using patient samples and cell lines and uncovered its potential link to CDK6.
Materials and methods
Patients
From January 2015 to March 2015, 134 continuous CRC specimens and 20 matching adjacent non-tumor specimens obtained from CRC patients at the Zhongshan Hospital, Fudan University were collected. The inclusion criteria were as follows: with histologically confirmed CRC, receiving radical surgery, having complete follow-up. The exclusion criteria were receiving preoperative chemotherapy or radiation, pregnancy or breastfeeding, previous malignancy within 5 years or no written informed consent. The primary tumor ki67 score is the routine pathological evaluation of our center and was evaluated by two experienced pathologists. Patients in the cohort (134 continuous CRC specimens) who received PETCT preoperatively (n = 52) were included to analyze the association between miR-500a-3p expression and the SUV of the primary tumors. The study was authorized by the Ethics Committee of the Zhongshan Hospital, Fudan University. Written informed consent was obtained from each patient.
Collection of TCGA public data and identification of significantly differential expression miRNA
We collected gene expression profiles of 551 COADREAD samples from the TCGA cohort (
http://gdac.broadinstitute.org/). Data including mRNA expression level and miRNA expression level. All the data have been standardized. For miRNAs differential analysis, we calculated the mean expression level of these miRNAs and divided them into high and low expression groups.
The R package DESeq2 (version 1.22.2) was used to calculate the differential expressed t statistics for microarray and RNA sequencing data. We used the univariate Cox proportional hazards model to examine the associations between gene expression and overall survival. MiRNAs with P values less than 0.05 were considered to be statistically significant and included in consensus survival analysis.
Immunohistochemistry staining
The whole cohort which contained 134 continuous CRC specimens were stained with the CDK6 antibody (ab124821, Abcam) and HK2 antibody (2867T, Cell Signaling Technology). The 20 matched adjacent non-tumor specimens were stained with CDK6 antibody (ab124821, Abcam). IHC scores were conducted according to the ratio and intensity of positive-staining areas. The staining areas were scored as follow: 0–25%, score 1; 25–50%, score 2; 50–75%, score 3; and beyond 75%, score 4. The signal intensity was scored on a scale of 0–3: 0-negative, 1-weak, 2-moderate and 3-strong. IHC scores were averaged from two experienced pathologists who scored the IHC staining independently.
Cell lines and culture
Human CRC cell lines [HCT116 (RRID: CVCL_0291) and SW480 (RRID: CVCL_0546)] and normal human colon epithelial cell line NCM460 (RRID: CVCL_0460) were obtained from the National Collection of Authenticated Cell Cultures (Shanghai, China). All human cell lines have been authenticated using STR profiling within the last three years and all experiments were performed with mycoplasma-free cells. These cell lines were maintained in Dulbecco’s Modified Eagle Medium (Logan Utah, HyClone, USA) with 10% fetal bovine serum (FBS; Gibco), 1% penicillin (10 U/mL) and 1% streptomycin (10 μg/mL) in an incubator with the environment of 37 °C and 5% CO2.
Quantitative real-time polymerase chain reaction (qRT-PCR)
RNA was isolated with Trizol reagent. The purity and the concentration of different RNA samples were measured using NanoDrop ND-1000 (Thermo Scientific, USA). Reverse transcription reaction was performed using miRcute miRNA cDNA synthesis Kit (kr211, Tiangen, China) for miRNAs and SuperScript IV VILO cDNA synthesis kit (11756050, Thermo Scientific, USA) for mRNAs. Quantitative RT-PCR (qRT-PCR) was performed using SYBR® Premix Ex Taq™ (Takara) containing mRQ 3′ Primer on an ABI 7500 platform (Applied Biosystems, Carlsbad, CA, USA). The relative quantities of miR-500a-3p in cells were normalized to U6. Beta-actin was used as an internal control for mRNA detection. The primer sequences for miRNA and mRNA detection are listed in Additional file
1: Table S3.
Lentivirus and miRNA transfection
The lentivirus particles overexpressing human miR-500a-3p and CDK6 were purchased from Genomeditech (Shanghai, China). miR-500a-3p mimics were synthesized by Genomeditech (Shanghai, China). The sequences of miR-500a-3p mimic were 5′-AUGCACCUGGGCAAGGAUUCUG-3′. The miRNA oligonucleotides were transfected using Lipofectamine® RNAiMAX™ (50 nmol/L; Invitrogen, CA, USA).
Cell viability assay
At 72 h after lentivirus infection or at 24 h after miRNA transfection, HCT-116 (2500/well) and SW480 (2000/well) cells were plated into 96-well culture plates. Cell viability was measured at 24, 48, 72 and 96 h post-seeding, using the Cell Counting Kit-8 (Dojindo, Kumamoto, Japan) according to the manufacturer’s instructions.
HCT-116 (1500/well) and SW480 (2000/well) cells were seeded in six-well plates after 72 h lentivirus infection. The culture medium was changed every 3 days. After incubating for 2 weeks, colonies were fixed with 4% paraformaldehyde for 15 min and stained with 5% Giemsa for 20 min. The colonies containing at least 50 cells were scored.
Cell cycle analysis
Seventy-two hours after infection, cells were harvested, washed with phosphate-buffered saline (PBS), and fixed in 70% ethanol at 4 °C overnight. After fixation, cells were washed with PBS before suspension in RNase A/propidium iodide solutions (100 mg/mL RNase A and 5 μg/mL propidium iodide). Cells were incubated at room temperature for an hour. Stained cells were analyzed by a FACScan flow cytometer (BD Biosciences, Mountain View, CA, USA).
Cell apoptosis analysis
Cell apoptosis was assessed by annexin V/propidium iodide (BD Biosciences, San Jose, CA, USA). Cells were harvested, washed with PBS, and resuspended in 1× binding buffer at a concentration of 1 × 106 cells/mL. A total of 100 μL solution was transferred to a new tube and added with 5 μL of APC Annexin V and 5 μL of propidium iodide. Cells were incubated at room temperature for 15 min in the dark and then analyzed by a FACScan flow cytometer.
Cell invasion assay
The cell invasion assay was performed in 24-well transwell chambers pre-coated with Matrigel (Corning, NY, USA). HCT-116 cells (105/well). Serum-free medium (200 μL) was placed into the upper chamber, and 600 μL complete medium (with 10% FBS) was filled into the lower chamber. Cells on the inner membrane were removed with a cotton swab after 24 h. The outer membrane was fixed in 4% formaldehyde (in PBS) and stained with 0.5% crystal violet. Cell numbers were counted and averaged in five random fields at a magnification of 100×.
Xenograft tumor assay
BALB/c nude mice (6 weeks old) were purchased from Shanghai SLAC Laboratory animal co. ltd (shanghai, China) and randomly divided into 2 groups (n = 7/6). SW480 (3 × 106) or HCT116 (4 × 106) cells that stably transfected with miR-NC or miR-500a-3p were injected at the back region of BALB/c mice subcutaneously. The volume of tumors was measured twice a week using a vernier caliper with the method of volume = (length × width2)/2. The mice were killed after inoculation for 30 d, and the tumors were weighed. Tumor tissues were subjected to the expression analysis of ki67. The procedures in this study were permitted by the Animal Research Committee of the Zhongshan Hospital, Fudan University.
Luciferase reporter assay
The putative miR-500a-3p binding sequence and the matching mutant binding sequence in the 3′untranslated region (3′UTR) of CDK6 were amplified and inserted into pGL3 luciferase reporter vector (Genomeditech, shanghai, China). SW480 cells were transfected with miR-NC or miR-500a-3p and the above-constructed reporter plasmids. After transfection for 48 h, the luciferase activities in different groups were determined by the dual-luciferase reporter assay system (Promega).
Glucose, lactate and ATP measurement
SW480 and HCT116 cells were cultured with an FBS-free medium and culture medium was collected after 24 h. Glucose Uptake Colorimetric Assay kit (Biovision, Milpitas, California, USA), Lactate Assay Kit (Biovision) and ATP Colorimetric Assay kit (Biovision) were utilized to detect the glucose consumption, the lactate production and ATP in CRC cells according to the manufacturer’s instructions. The glucose, lactate and ATP levels were normalized to total cell protein.
Seahorse analysis
Extracellular acidification rate (ECAR) was detected using a Seahorse XF96 analyzer (Seahorse Biosciences, USA). SW480 cells (105/well) were seeded in a 96-well XF96 microplate (Seahorse Biosciences, USA). Before experiments, cell culture medium was replaced and cells were then incubated with assay medium for 1 h at 37 °C in a CO2-free incubator. ECAR was detected using a sequential injection of 10 mM glucose, 2 mM oligomycin (Sigma-Aldrich) and 50 mM 2-deoxyglucose (2-DG, Sigma-Aldrich). Each cycle of measurement involved mixing (3 min), waiting (2 min), and measuring (3 min) cycles.
Mass spectrometry
The targeted metabolomics analyses were performed using an HPLC system (Agilent 1290, Agilent Technologies) and a mass spectrometer (Agilent 5500, Agilent Technologies). A 10-cm dish of cultured tumor cells was collected, adding 1 mL acetonitrile/methanol water (v, 2:2:1) and storing at − 80℃ after quick freezing in liquid nitrogen. Sample preparation processes were performed in accordance with the above method of parallel preparation of QC samples. MRM transitions representing the metabolites were simultaneously monitored, and the positive/negative polarity switching was used. Data analyses were performed as instructed by Shanghai Applied Protein Technology [
18].
Western-blot
Whole protein extracts were lysed by radioimmunoprecipitation assay (RIPA) buffer (Thermo Fisher Scientific) according to the manufacturer’s protocol. At that time, 30 μg proteins were run on a 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) gel at 100 V for 2 h and transferred to a polyvinylidene fluoride membrane at 80 V for 2 h. Membranes were blocked with 5% bovine serum albumin (BSA) in Tris-buffered saline with Tween-20 (TBST) at room temperature for 1 h. They were then incubated overnight at 4 °C with one of the following primary antibodies: anti-CDK6 (ab124821, Abcam) (1:1000), anti-GLUT1 (ab115730, Abcam) (1:1000) and anti-HK2 (2867T, Cell Signaling Technology) (1:1000) and anti-beta actin (1:1000) from Santa Cruz Biotechnology (Dallas, Texas, USA). After washing with TBST, membranes were incubated with secondary antibodies for 1 h at room temperature and signals were developed using an enhanced chemiluminescence kit (Pierce, Waltham, MA, USA).
Statistical analysis
SPSS (version 22.0, SPSS Inc.) or GraphPad Prism software (version 7.0, USA) were used to analyze the data and generate the graphs. The differences between the miR-500a-3p expression and the clinical characteristics of CRC patients were analyzed using χ2 test. Survival curves were generated using the Kaplan–Meier method and log-rank tests. Univariate and multivariate Cox regression analyses were conducted to identify the independent factors. The correlation among the expression of miR-500a-3p, CDK6 and HK2 was analyzed using Spearman’s correlation test. Student’s t-test or the Mann–Whitney U test was used to calculate the P values between two groups. A value of P < 0.05 was identified as statistically significant. R software 3.5.1 was applied to this study for the statistical analyses. All miRNA expression data were normalized.
Discussion
Both investigating new prognostic biomarkers and uncovering the mechanisms behind the progression of CRC are critical for developing CRC therapies. In the current study, we focused on the role of miR-500a-3p in CRC progression. We found that patients with low miR-500a-3p expression had a worse prognosis and miR-500a-3p may represent an independent prognostic factor for CRC patients. Further in vitro and in vivo experiments showed that miR-500a-3p inhibits CRC cell proliferation and aerobic glycolysis. In addition, we discovered CDK6 as a novel downstream target of miR-500a-3p. These data suggested that miR-500a-3p might serve as a novel prognostic biomarker or therapeutic target of CRC.
Accumulating evidence indicates that miRNAs contribute to CRC progression [
19‐
21]. However, research studies screening miRNAs from the sequencing results of large cohorts were relatively rare. We analyzed miRNAs that are significantly related to the prognosis of CRC from the cBioportal database and found that miR-500 has the most significant correlation with the prognosis of CRC patients. Then we focused on miR-500a-3p which has not been reported in CRC.
Interestingly, both tumor-promoting and—suppressive roles of miR-500a-3p have been revealed. In both hepatocellular and gastric carcinoma, miR-500a-3p served as a tumor promoter via regulating the cancer cell stemness [
11,
12]. While in non-small cell lung cancer, miR-500a-3p acts as a tumor suppressor via downregulating LY6K expression [
22]. The distinct roles of miR-500a-3p might be due to the heterogeneity of tumors and differences of cancer types. In this study, we provide new evidence that miR-500a-3p serves as a tumor suppressor in CRC and more importantly, for the first time, reveal the role of miR-500a-3p on cancer cell metabolism. Specifically, we found that miR-500a-3p downregulated the expression of glycolytic enzymes and inhibited glycolysis. Decreased glycolysis restrains the cellular buildings for rapid cell proliferation [
4], and ultimately contributes to the tumor-suppressive role of miR-500a-3p in CRC.
Previous studies have shown that CDK6 is regulated by several miRNAs, such as miR-29b, miR-211 and miR-497 [
23‐
25]. Our study provided additional evidence to support that CDK6 is regulated by miRNAs. We report that CDK6 is a direct functional target of miR-500a-3p in CRC and found that miR-500a-3p inhibits the transcription of CDK6. In different cancer types, CDK6 may regulate different metabolic enzymes and play distinct roles in glycolysis. Wang et al. found that CDK6 inhibits the glycolytic pathway and re-directs the glycolytic intermediates into the pentose phosphate pathway (PPP) and serine pathways [
17]. Xing et al. proved that CDK6 promotes glycolysis via phosphorylation of the fructose bisphosphate PFK2 (PFKFB3) in breast cancer [
26]. In this study, we found that CDK6 enhanced glycolysis in CRC and HK2 might be a potential downstream target of CDK6.
The inhibition of glycolysis by miR-500a-3p was only partially restored by CDK6 overexpression, indicating other targets might also be involved in miR-500a-3p-mediated regulation of glycolysis. Some reported targets of miR-500a-3p, such as XBP1 and FBXW7, may regulate glycolysis directly or indirectly [
11,
27‐
29]. Further studies may be needed to validate the mechanistic link of miR-500a-3p and these targets in modulating glycolysis in CRC.
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