Background
Colorectal cancer (CRC) represents the third most frequently occurring cancers on a global scale [
1]. CRC is reportedly heterogeneous accompanied by substantial genetic and phenotypic differences between individuals [
2]. Approximately 90% of CRC cases are affected by adverse events after pharmacological therapy, and the implementation of pharmacogenomics is currently addressed in enhancing drug safety [
3]. Moreover, a great deal of ongoing investigations for identifying molecules involved in the pathophysiology of CRC individualizes therapeutic options in the near future [
4‐
6].
Of note, dysregulation of microRNAs (miRNAs or miRs) has been associated with a wide array of pathological processes due to their abilities to bind to protein-coding mRNAs [
7]. There is a paucity of data highlighting the orchestration of miRNAs on initiation, aggressiveness and metastatic potential of malignancies [
8‐
10]. Interestingly, miR-96 has been widely implicated in the progression and metastatic potential of a plethora of cancers, including cervical [
11], and ovarian [
12] cancers. Although miR-96 is witnessed to link to tumor invasion in addition to cancer cell migration and invasion in CRC [
7,
13], little is well-understood regarding its downstream mechanisms related to the pathophysiological events of CRC.
N6-methyladenosine (m6A) modification has been demonstrated to epitranscriptionally control mammalian gene expression in the multiple biological processes; hence m6A and its mediators are expected to be promising therapeutic targets for human cancers [
14]. Fat mass and obesity-associated (FTO) gene is a well-known m6A eraser that is upregulated in CRC and reported to interact with c-myc proto-oncogene (MYC) to accelerate CRC cell proliferating and migrating capabilities [
15]. AMP-activated protein kinase-alpha2 (AMPKα2), also named PRKAA2, has been stated to be in an inverse correlation with FTO [
16].
Here, we addressed the contribution of miR-96 to CRC progression and demonstrated that miR-96 directly targeted AMPKα2 which inhibits the expression of m6A demethylase FTO. More specifically, FTO can activate MYC by reducing the m6A modification of MYC, whereby leading to cancerogenesis.
Materials and Methods
Clinical sample collection
Sixty patients (42 males and 18 females, aged 35–75 years, with a mean age of 56.70 ± 9.96 years) diagnosed with CRC at The First Affiliated Hospital of Sun Yat-Sen University from August 2017 to August 2019 were enrolled. None of these patients received radiotherapy or chemotherapy prior to operation, and their tumor and paracancerous tissues were preserved in liquid nitrogen for follow-up studies.
Microarray-based gene expression profiling
The key miRNA associated to CRC were determined from the existing literature, and expression of key miRNA was determined based on the microarray dataset GSE38389 retrieved from the GEO database. The differentially expressed genes in CRC were obtained by analyzing TCGA database through GEPIA with the threshold as |logFC > 1|,
p < 0.01. Next, the downstream genes of miRNA were predicted by the databases TargetScan and miRWalk (accessibility < 0.01, au ≥ 0.75). The Venn diagram of the differentially expressed genes and miRNA downstream genes was then plotted. PPI network of the intersected genes was constructed using String, and the PPI network image was drawn using Cytoscape, with the core degree calculated. The genes related to the key genes were predicted by MEM (the first 10,000 with significant co-expression relationship, and 6711 genes left after the removal of duplicates) (
https://biit.cs.ut.ee/mem/index.cgi) and LinkedOmics (the first 2000 with significant correlation degree) (
http://www.linkedomics.org), and subsequently among which the m6A RNA modification-related genes screened. The downstream genes of m6A RNA modification were predicted from the existing literature, and the expression correlation graph was plotted by GEPIA for verification. TCG Aportal (
http://tumorsurvival.org) was used to analyze the relationship between its expression and CRC survival.
Cell culture and transfection
CRC cells SW480 (ZQ0063), SW620 (LZQ0014), HCT-8 (ZQ0331) (Shanghai Zhong Qiao Xin Zhou Biotechnology Co., Ltd., Shanghai, China) and normal intestinal epithelial cells HIEC (American Type Culture Collection [ATCC], Rockville, MD) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) in a 5% CO2 incubator at 37℃. After adherent growth, cells were detached with 0.25% trypsin (Hyclone, South Logan, UT).
Cells were then transfected with the following sequences: negative control (NC) mimic, miR-96 mimic, NC overexpression plasmid (oe-NC), AMPKα2 overexpression plasmid (oe-AMPKα2), FTO overexpression plasmid (oe-FTO), siRNA targeting AMPKα2 (si-AMPKα2), NC shRNA (sh-NC), shRNA targeting FTO (sh-FTO), MYC overexpression plasmid (oe-MYC) singly or in combination. The plasmid pCMV6-AC-GFP for gene overexpression and plasmid pGPU6/Neo for gene silencing were purchased from Fenghui Biotechnology Co., Ltd. (FH1215, Hunan, China) and Shanghai GenePharma Co, Ltd. (Shanghai, China) respectively. The cell transfection was performed with the use of Lipofectamine 2000 reagents (Invitrogen, Carlsbad, CA) (11,668,019, Thermo Fisher Scientific). 4 µg target plasmids and 10 µL Lipofectamine 2000 were diluted in 250 µL Opti-MEM (Gibco) respectively, and then mixed gently. After being allowed to stand for 20 min, the mixture was cultured with the cells in a 5% CO2 incubator at 37℃. After 6 h, the medium was replaced with a complete medium for another 48 h culture.
Reverse transcription quantitative polymerase chain reaction (RT-qPCR)
Total RNA was extracted from tissues or cells by TRIzol reagents (Invitrogen, Carlsbad, CA), and the concentration and purity of the extracted total RNA were detected by a NanoDrop2000 UV microspectrophotometer (1011U, NanoDrop Technologies, Rockland, DE). According to the instructions of TaqMan MicroRNA Assays Reverse Transcription primer (4,427,975, Applied Biosystems, Foster City, CA)/PrimeScript RT reagent Kit (RR047A, Takara, Japan), the RNA was reverse transcribed into cDNA, and primers for miR-96, AMPKα2, FTO, and MYC were designed and synthesized by Takara (Table
1). RT-qPCR was performed on an ABI 7500 instrument (7500, Applied Biosystems, Foster City, CA). The fold changes were calculated using relative quantification (2
−△△CT method) normalized to glyceraldehyde-3-phosphate dehydrogenase (GAPDH) or U6.
Table 1
Primer sequences for RT-qPCR
miR-96 | F: 5’-TTGGGTGAAATATATTGTGCGTCTC-3’ |
R: 5’-AGCCGAAGTGAGCCACTGAA-3’ |
U6 | F: 5’-GCACCGTCAAGGCTGAGAAC-3’ |
R: 5’-AGCCGAAGTGAGCCACTGAA-3’ |
AMPKα2 | F: 5’-GGGACCTGAAACCAGAGAACG-3’ |
R: 5’-ACAGAGGAGGGCATAGAGGATG-3’ |
FTO | F: 5’-TGAAGGTAGCGTGGGACATAGA-3’ |
R: 5’-GGTGAAAAGCCAGCCAGAAC-3’ |
MYC | F: 5’-TTCGGGTAGTGGAAAACCAG-3’ |
R: 5’-AGTAGAAATACGGCTGCACC-3’ |
MYC-m6A | F: 5’-GCATACATCCTGTCCGTCCA-3’ |
R: 5’-GTCGTTTCCGCAACAAGTCCC-3’ |
GAPDH | F: 5’-GCACCGTCAAGGCTGAGAAC-3’ |
R: 5’-TGGTGAAGACGCCAGTGGA-3’ |
Western blot analysis
The total protein was extracted from tissues or cells using radioimmunoprecipitation assay (RIPA) lysis buffer (P0013C, Beyotime, Shanghai, China) containing phenylmethylsulphonyl fluoride (PMSF). The cell lysate was centrifugated to harvest supernatant. Next, 50 µg protein was subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis and transferred to polyvinylidene fluoride membranes by a wet transfer method. The membrane was blocked using 5% skim milk powder at indoor temperature for 1 h and then reacted overnight at 4℃ with the following diluted primary rabbit antibodies (Abcam, Cambridge, UK): AMPKα2 (1:500, ab3760), FTO (1:1500, ab126605), and MYC (1:1000, Ab32072) and CDK2 (1:1000, ab32147), CDK4 (1:500, ab137675), Ki-67 (1:1000, ab16667), PCNA (1:1000, ab18197), Bax (1:1000, Ab199677), and Bcl-2 (1:500, ab59348). The next day, the membrane was washed with Tris-buffered saline Tween-20 (TBST), and re-probed with secondary goat anti-rabbit IgG (H + L) horseradish peroxidase (HRP) (ab97051, 1:2000, Abcam, Cambridge, UK) for 1 h. The immunoreactive bands were visualized using enhanced chemiluminescence reagent (BB-3501, Amersham, UK) and proteins were quantified (normalized to β-actin) using a Bio-Rad image analysis system (Bio-Rad Laboratories, Hercules, CA) and Quantity One v4.6.2 software.
Dual-luciferase reporter assay
Human embryo kidney (HEK) 293T cells were cultured in DMEM containing 10% FBS under 5% CO2 at 37℃. The cDNA fragment of AMPKα2-mutant (Mut) containing miR-96 binding site was inserted into the pmirGLO vector. cDNA fragment of AMPKα2-Mut was synthesized by site-directed mutagenesis and then inserted into pmirGLO vector. The inserted sequence was verified to be correct by sequencing (all the above operations were completed by RIBOBIO, Guangzhou, China). HEK293T cells underwent co-transfection with pmirGLO-AMPKα2-wild type (Wt) or pmirGLO-AMPKα2-Mut recombinant vector and miR-96 mimic or NC mimic for 48 h. The activity of renilla luciferase and firefly luciferase was determined using multi-mode microplate reader (SpectraMax M5, Molecular Devices, Sunnyvale, CA).
Methylated RNA immunoprecipitation (Me-RIP)
Total RNA was isolated from CRC cells by TRIzol method, and mRNA was isolated and purified from the total RNA using PolyATtract® mRNA Isolation Systems (A-Z5300, A&D Technology Corporation, Beijing, China). Antibody to M6A (1:500, ab151230, Abcam, Cambridge, UK) or antibody to IgG (ab109489, 1:100, Abcam, Cambridge, UK) was added to IP buffer (20 mM Tris pH 7.5, 140 mM NaCl, 1% NP-40, 2 mM EDTA) and incubated with protein A/G magnetic beads for 1 h for binding. Then purified mRNA and magnetic bead-antibody complexes were added to IP buffer with ribonuclease inhibitors and protease inhibitors, and incubated overnight at 4℃. Eluent buffer was used to elute RNA, which was then extracted and purified by phenol-chloroform. MYC in the extracted RNA was determined by RT-qPCR using the primer sequences depicted in Table
1.
Photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP)
CRC cells were incubated with 200 mm of 4-thiopyridine (4SU) (Sigma Aldrich) for 14 h and cross-linked with 0.4J/cm2 at 365 nm. After lysis, immunoprecipitation was performed with FTO antibody (5 and 3 mg, respectively) at 4℃, after which the precipitated RNA was labeled with [g-32-p]-ATP, and observed by autoluminescence assay. Protein was removed by detachment using protease K, and RNA was extracted and subjected to RT-qPCR for MYC expression detection.
Cell counting kit-8 (CCK-8) assay
CCK-8 assay kit (CK04, Dojindo, JPN) was utilized to analyze the viability of CRC cells. The cells at logarithmic growth phase, 1 × 104 cells/well, were seeded into 96-well plates for 24 h of pre-culture, followed by 48 h transfection. At 0 h, 24 h, 48 h, 72 h post transfection, 10 µL of CCK-8 reagent was added to each well for reaction at 37℃ for 3 h. After that, absorbance at 450 nm was determined on a microplate reader, and a cell growth curve was drawn.
Flow cytometric analysis
After transfection for 48 h, cells were collected and dispersed into cell suspension with 0.25% trypsin, 1 × 106 cells/mL. As for cell cycle detection, 100 µL cell suspension was incubated with 50 µL PI dye containing RNAase avoiding light exposure for 30 min. Annexin V-fluorescein isothiocyanate (FITC)/propidium iodide (PI) staining was conducted for apoptosis assessment. In short, the cells were stained with 10 µL Annexin V-FITC (ab14085, Abcam, Inc., Cambridge) and 5 µL PI for 15 min devoid of light exposure. The cell cycle and apoptosis were assessed on a flow cytometer (BD Biosciences, FL, Lakes, NJ) at an exciting wavelength of 488 nm.
Scratch test
Cells were seeded overnight into the 6-well plate at a density rate of 2.5 × 104 cells/cm2. After scratches were made using a 200 µL pipette, the cells were cultured with DMEM containing 5% FBS. The images of scratches in each well at 0 and 24 h were captured under an inverted microscope. Three duplicates were set in each group. The width of each scratch was measured using the Image J software and the healing rate was calculated as follows: healing rate = (scratch width at 0 h - scratch width at 24 h)/scratch width at 0 h × 100%.
Transwell assay
A total of 600 mL of DMEM containing 20% FBS was added to the lower chamber of Transwell chamber with polycarbonate membrane(8 µm pore) coated with Matrigel and incubated at 37℃ for 1 h. Cells following 48 h of transfection were resuspended in serum-free DMEM and seeded to the upper chamber at a density of 1 × 106 cells/mL, followed by 24 h of incubation at 37℃ with 5% CO2. Then, Transwell chamber was removed and cells were washed twice with PBS and fixed with 5% glutaraldehyde. Afterwards, 0.1% crystal violet was added to the cells and stained for 5 min. After washing with PBS, the cells remaining on the upper surface were wiped away with a cotton swab. Finally, cells were observed under an inverted fluorescence microscope in five randomly selected visual fields, with mean values obtained.
Nude mouse tumor xenograft model
Twelve specific-pathogen-free female BALB/c nude mice (aged 6 weeks; body weight of 15–18 g) were purchased from Shanghai SLAC Laboratory Animal co. LTD (Shanghai, China). CRC cells SW480 at logarithmic growth phase were prepared into cell suspension with a concentration of about 1 × 107/100 µL, which was then injected into the left axilla of nude mice with a 1 ml syringe to establish a subcutaneous mouse xenograft model. Once the tumor volume reached about 50 mm3, the nude mice were injected with miR-96 antagomir or NC antagomir (10 nmol once every 5 days for 5 weeks). After 5 weeks, the mice were euthanized, after which the subcutaneous transplanted tumor was removed, and weighed. The protein was then extracted from the transplanted tumor tissues for Western blot analysis.
Statistical analysis
SPSS 21.0 statistical software (IBM Corp. Armonk, NY) was utilized for data statistical analysis, with p < 0.05 as a level of statistically significance. Measurement data were expressed as mean ± standard deviation. Data between cancer tissues and paracancerous tissues were compared using paired t-test and data between other two groups were compared using unpaired t-test. Data among multiple groups were assessed by one-way analysis of variance (ANOVA), followed by Tukey’s post hoc tests for multiple comparisons. Time-based multi-comparison was tested by repeated measures ANOVA, with Bonferroni post hoc tests. Enumeration data were analyzed using chi-square test.
Discussion
A minority of the CRC population are affected by the genetic mutations of oncogenes, anti-oncogenes or miRs [
17‐
19]. Microarray profiling has identified a large range of miRNAs dysregulated in human CRC tissues, in contrast to adjacent non-cancerous tissues [
20,
21]. Herein, our study intended to elucidate the functions and mediatory mechanisms of miR-96 in CRC.
In our study, we found miR-96 could augment CRC cell proliferative and invasive capacities, and suppress apoptotic ability by targeting AMPKα2. Consistent with our finding, miR-96 has been documented to be highly expressed in CRC tissues versus normal mucosal tissues [
21], and this upregulation in CRC has also been confirmed in other researchers [
22‐
24]. In addition, miR-96 has been clinically validated to be a circulating biomarker for predicting the overall survival of CRC patients [
25]. Serum miR-96 is also proposed to be an indicator distinguishing chemoresistance in the advanced CRC [
26]. This value may be correlated with the role of miR-96 [
27]. More recently, miR-96 inhibitor could function as a suppressor of cell migration instead of cell invasion that may be affected by the counteraction of cell invasion stimulator Matrigel [
13]. In the present study, we validated the anti-tumor activity exerted by miR-96 antagomir in the nude mouse model.
Emerging evidence demonstrates that miRNAs participate in controlling cancer cell growth, invasiveness and metastatic potential through interacting with the 3’UTR of specific target mRNAs [
28,
29]. In a previous study, miR-96 has been substantiated to contribute to colorectal carcinogenesis
via targeting TP53INP1, FOXO1 and FOXO3a [
30]. AMPKα2 was identified to be a key target of miR-96 and restoration of AMPKα2 could partially reverse the pro-proliferation and anti-apoptosis functions of miR-96. This suggested that miR-96 exerted oncogenic role
via targeting AMPKα2. AMPK is a hub sensor for cellular energy and nutrition. Ablation of AMPK or its deregulation has been observed in cancer and may interact with oncogenic drivers to mediate tumor cell metabolism [
31]. Restored expression of AMPKα2 has been associated with the tumor attenuation in human breast and bladder cancers [
32‐
34].
Further, AMPKα2 was suggested in this study to impede CRC cell proliferative and invasive capacities, while inducing apoptotic ability by repressing FTO. AMPKα2 has been formerly evidenced to repress the expression of FTO [
16]. It was previously demonstrated that FTO could serve as a target gene of miR-1266 and was negatively modulated by miR-1266 in CRC [
35]. MYC, whose deregulation has been found in most cancers including CRC, has a pivotal role to play in the tumorigenesis and carcinogenesis of CRC via the Wnt/β-catenin pathway [
36]. In CRC cells, FTO elevates the expression of MYC by blocking the modification of MYC gene m6A. Consistently, this mechanism has been proposed in another study that FTO mediates m6A modification to accelerate the expression of MYC [
37]. Tang et al. have suggested the interplay between FTO and MYC responsible for the pancreatic cancer cell proliferation [
38]. A recent study demonstrated that FTO could cooperate with MYC for the enhancement of the proliferative and migrative functions of CRC cells [
15]. On the basis of the aforementioned findings demonstrated by our study, we reasoned that miR-96 contributed to tumorigenesis
via the AMPKα2/FTO/m6A/MYC axis.
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