Colorectal cancer (CRC) ranks fifth on the list of worldwide cancers in terms of morbidity and mortality,1 thus being a serious threat to human health and life. Currently, surgery combined with chemotherapy is the preferred treatment option for patients with CRC due to its high efficiency.2 The diversification of methods for early diagnosis and the development of new drugs have significantly improved the survival rate of patients with this type of cancer. However, it has been reported that the 5-year relative survival rate is only 68%, thereby there is still a need for the development of new therapeutic approaches that may improve these outcomes.3 Furthermore, it is also important to highlight that some patients with CRC who undergo surgical resection may experience a recurrence of the disease.4
Circular RNAs (circRNAs), an important group of regulatory non-coding RNAs, are characterized by a closed circular structure and their roles have been investigated extensively in many diseases, especially in cancer.5,6 Recent studies have revealed that circRNAs such as circSPARC, circRHOBTB3, and Circ3823 can act as promoters or suppressors to regulate growth, metastasis, and angiogenesis of CRC cells.7–9 In this regard, Liang Chen et al.10 proposed that circ-MALAT1 could promote the self-renewal of cancer stem cells (CSC) in hepatocellular carcinoma (HCC), suggesting a carcinogenic potential for this circRNA. Moreover, our results showed that circ-MALAT1 level was higher in tissues of patients with CRC, and therefore we investigated if circ-MALAT1 could play a role in the progression of this disease.
MicroRNAs (miRNAs) are another important class of regulatory non-coding RNAs of ∼22 nts in length, and their roles in disease have been studied extensively in the past decade.11 In CRC, for example, miR-4463 acts as an oncogene by promoting the progression of CRC via regulation of the PPP1R12B gene.12 It has also been proposed that upregulation of miR-582-5p expression could inhibit migration and chemotherapy drug resistance of CRC cells.13 Conversely, several studies have suggested that miR-506-3p expression is remarkably lower in CRC cells than in normal cells, suggesting a role as a tumor suppressor in the progression of CRC.14,15 Our preliminary results indicate that miR-506-3p level was decreased in CRC tissues. Additionally, we also observed that miR-506-3p overexpression inhibited cell proliferation of CRC cells. Consequently, we considered that the roles of miR-506-3p in the progression of CRC deserve further investigation.
KAT6B is a major histone acetyltransferase involved in the regulation of many cancers, including glioma and gastric cancer.16,17 For instance, Yingzi Liu et al. showed that KAT6B level is increased in clinical glioma tissues and promotes the acetylation of STAT3, accelerating the development of glioma via the mechanism of ferroptosis.17 In addition, abnormal expression of STAT3 has been shown to be involved in cell proliferation and EMT of CRC cells.18 Our bioinformatic gene expression analysis showed that KAT6B is upregulated in colorectal adenocarcinoma compared with normal tissue, therefore suggesting that this chromatin-remodeling enzyme could play a role in CRC tumorigenesis, a prediction that needs to be tested in future studies.
Moreover, results obtained by bioinformatic analysis and experimental validation showed that circ-MALAT1 binds to miR-506-3p and KAT6B is located downstream of miR-506-3p. Based on this information, we propose a model in which circ-MALAT1 facilitates proliferation, migration, and EMT of CRC cells through the regulation of the miR-506-3p/KAT6B axis. We expect that the findings in this study will provide new insights into the development of diagnostic markers and therapeutic targets for CRC.
METHODS Clinical tissue collectionA total of 30 patients with CRC who underwent surgical treatment at the First Hospital of Changsha were enrolled in this study. CRC tumor tissues and adjacent normal tissues were collected and stored in a refrigerator at −80°C. The present protocol was approved by the Ethics Committee of the First Hospital of Changsha (ethics number: 2022-29) and conducted strictly in accordance with the Declaration of Helsinki. Signed informed consent was provided by the enrolled participants. Table 1 summarizes the clinical pathological information of patients included in this study.
TABLE 1 Clinical characteristics of CRC patients with high and circ-MALAT1 risk scores.
Case (n) | MALAT1 | p | ||
Low-risk (n = 15) | High-risk (n = 15) | |||
Age | 0.4621 | |||
≥Mean | 17 | 7 | 10 | |
<Mean | 13 | 8 | 5 | |
FIGO stage | 0.0253 | |||
I–II | 17 | 5 | 12 | |
III–IV | 13 | 10 | 3 | |
Histological type | 0.7152 | |||
I | 16 | 9 | 7 | |
II–III | 14 | 6 | 8 | |
Residual tumor (cm) | 0.0092 | |||
<1 cm | 14 | 11 | 3 | |
≥1 cm | 16 | 4 | 12 | |
Histology | 0.048 | |||
Mucinous | 8 | 1 | 7 | |
Setous | 7 | 3 | 4 | |
Endometrioid | 4 | 3 | 1 | |
Clear cell | 11 | 8 | 3 | |
Lymphatic metastasis | 0.0078 | |||
No | 18 | 13 | 5 | |
Yes | 12 | 2 | 10 | |
Ascites | 0.2451 | |||
No | 10 | 3 | 7 | |
Yes | 20 | 12 | 8 |
Human colonic epithelial cells (NCM460) and CRC cell lines (SW480, SW620, HT29) were purchased from Shanghai Cell Bank (Chinese Academy of Sciences, China). CRC cell lines (HCT116, LS513, SW837) were acquired from ATCC (USA). All cells were maintained in RPMI 1640 medium (Thermo Fisher Scientific, USA), and supplemented with 10% FBS (Thermo Fisher Scientific) and 1% antibiotics (Beyotime, China). The conditions of the cell incubator were 5% CO2 and 37°C.
Cell transfectionA plasmid vector expressing the short hairpin RNA targeting circ-MALAT1 (sh-circ-MALAT1), miR-506-3p mimics/inhibitor, overexpression vector of KAT6B (oe-KAT6B), and circ-MALAT1 (oe-circ-MALAT1) as well as negative control groups (i.e., sh-NC, mimics/inhibitor NC, oe-NC) were purchased from GenePharma (Shanghai, China). LS513 and SW837 cells were seeded into 96-well plates and incubated overnight. Afterward, cells were subjected to plasmids as described above or sequence transfection using Lipofectamine™ 3000 (Invitrogen, USA), according to the manufacturer's instructions.
qRT-PCR analysisTotal RNA was collected from clinical tissues and cultured cells using TRIzol reagent (Beyotime, Shanghai, China). The cDNA synthesis was performed using Script Reverse Transcription Reagent Kit (TaKaRa, China). The SYBR Premix Ex Taq II Kit (TaKaRa) was used for quantitative PCR (qPCR). The forward (F) and reverse (R) primer sequences were as follows:
Circ-MALAT1 (F): 5'-GGACTACAGAGCCCCGAATT-3′;
Circ-MALAT1 (R): 5'-CCCTGCGTCATGGATTTCAAG-3′;
miR-506-3p (F): 5'-GCCACCACCATCAGCCATAC-3′;
miR-506-3p (R): 5'-GCACATTACTCTACTCAGAAGGG-3′;
KAT6B (F): 5'-GGAAGAGCGTCATCTTGGAG-3′;
KAT6B (R): 5'-GCTTTTCCATGTGGCTCAAT-3′;
U6 (F), 5'-CTCGCTTCGGCAGCACA-3′;
U6 (R), 5'-AACGCTTCACGAATTTGCGT-3′;
GAPDH (F), 5'-TGGAAGGACTCATGACCACA-3′;
GAPDH (R), 5'-TTCAGCTCAGGGATGACCTT-3′.
The relative changes in gene expression were calculated using the 2−ΔΔCt formula. The reference genes GAPDH and U6 were used to normalize gene expression levels.
Western blotTotal proteins were extracted from cells with RIPA lysis buffer (Beyotime). The BCA Assay Kit (Beyotime) was used to determine the concentration of proteins according to the manufacturer's instructions. Proteins were separated with SDS-PAGE on 10% gels and then transferred onto polyvinylidene difluoride (PVDF) membranes. After blocking with skimmed milk (5%), the PVDF membranes were incubated overnight at 4°C with primary antibodies KAT6B (ab191994, 1:500, abcam, Britain), N-cadherin (ab245117, 1:1000), E-cadherin (ab231303, 1:1000), snail (ab216347, 1:1000), vimentin (ab137321, 1:2000), STAT3 (ab68153, 1:2000), H3K23ac (ab177275, 1:1000), Lamin B1 (ab16048, 1:5000), and β-actin (ab6276, 1:5000) and then with HRP-conjugated secondary antibodies (1:5000, ASPEN) for 1 h. An enhanced chemiluminescence (ECL) kit (Thermo Fisher Scientific) was used to visualize the bands. Densitometry analysis was determined by the Image J software.
MTT assayLS513 and SW837 cells were seeded at 1 × 103 cells/well in 96-well plates and then cultured for 12, 24, 48, 60, and 72 h. Cells were incubated with MTT solution (20 μL) for 4 h, and the absorbance was determined by a microplate reader (Thermo Fisher Scientific) at a wavelength of 490 nm.
Clone formation assayLS513 and SW837 cells were seeded at 1 × 103 cells/well in 6-well plates. After a period of incubation of 2 weeks, absolute methanol was used to fix cells and 0.1% crystalized violet (Sigma-Aldrich, USA) was used to stain cells. Finally, the number of cloned cells was counted.
Wound-healing assayLS513 and SW837 cells were seeded at 1 × 104 cells/well in six-well plates. When an 80%–90% confluence was reached, the cells were scratched with sterile 200 μL pipet tips in a straight line, and serum-free medium was then used to culture these cells for 24 h. The scratch widths were measured at 0 and 24 h.
Dual-luciferase reporter assayThe StarBase software was employed to predict the binding sites among circ-MALAT1, miR-506-3p, and KAT6B. The binding sites of circ-MALAT1 or KAT6B with miR-506-3p were cloned into pGL6 vectors (Beyotime) for constructing reporter vectors with wild-type (WT) circ-MALAT1 (WT-circ-MALAT1), mutant type (MUT) circ-MALAT1 (MUT-circ-MALAT1), WT-KAT6B, and MUT-KAT6B. MiR-506-3p mimics in combination with circ-MALAT1 (WT/MUT) or KAT6B (WT/MUT) were transfected into LS513 and SW837 cells using lipofectamine 3000 (Invitrogen). The luciferase activity was evaluated using the dual-luciferase reporter assay system (Promega, USA).
Statistical analysisAll data were presented as mean ± standard deviation. Statistically significant differences between groups were assessed by the Student's t-test using the GraphPad Prism 6 software (
We first detected the relative abundance of circ-MALAT1, miR-506-3p, and KAT6B in CRC tumor tissues and adjacent normal tissues. We found that the levels of circ-MALAT1 and KAT6B were significantly higher in CRC tumor tissues compared to the adjacent normal tissues while miR-506-3p expression was significantly lower (Figure 1A). Pearson's correlation analysis showed a negative correlation between the levels of circ-MALAT1 and miR-506-3p and a positive correlation between circ-MALAT1 and KAT6B (Figure 1B). In addition, circ-MALAT1, miR-506-3p, and KAT6B levels were also measured in six CRC cell lines (i.e., LS513, HT29, HCT116, SW837, SW480, and SW620 cells). We observed that circ-MALAT1 and KAT6B levels were significantly higher while miR-506-3p expression was markedly lower in all CRC cell lines compared to normal NCM460 colorectal cells (Figure 1C). Furthermore, western blot analysis showed that the protein level of KAT6B was significantly high in CRC cells (Figure 1D). Taken together, these results suggest that circ-MALAT1, miR-506-3p, and KAT6B are abnormally expressed in CRC cells.
FIGURE 1. Relative gene expression levels of circ-MALAT1, KAT6B, and miR-506-3p in CRC cells. (A) qRT-PCR was performed to examine the relative abundance of circ-MALAT1, miR-506-3p, and KAT6B in CRC and adjacent normal tissues. (B) The correlation analyses among MALAT1, miR-506-3p, and KAT6B were conducted using Pearson's correlation coefficient. (C) qRT-PCR was used to examine the relative abundance of circ-MALAT1, miR-506-3p, and KAT6B in NCM460, LS513, HT29, HCT116, SW837, SW480, and SW620 cells. (D) Western blot was used to measure the protein level of KAT6B in NCM460, LS513, HT29, HCT116, SW837, SW480, and SW620 cells. N = 3, *p [less than] 0.05, **p [less than] 0.01, and ***p [less than] 0.001.
Since abnormal expression of target genes in this study was most evident in LS513 and SW837 cells, these cell lines were used in further studies. To explore the effects of circ-MALAT1 on cell proliferation, migration, and EMT in CRC cells, we knocked down and overexpressed circ-MALAT1 in CRC cells by transfecting sh-circ-MALAT1 and oe-circMALAT1, respectively (Figure 2A). We observed that knockdown of circ-MALAT1 dramatically suppressed cell proliferation and migration, while its overexpression showed opposite effects. These findings were confirmed using MTT, clone formation, and wound-healing assays (Figure 2B–D). Moreover, we found that E-cadherin level was increased in circ-MALAT1-silenced LS513 and SW837 cells, while N-cadherin, vimentin, and snail levels were decreased in these cells. Conversely, overexpression of circ-MALAT1 showed opposite effects (Figure 2E).
FIGURE 2. Circ-MALAT1 knockdown suppressed cell proliferation, migration, and EMT process of CRC cells. LS513 and SW837 cells were subjected to transfection with sh-NC, sh-circ MALAT1, oe-NC, and oe-circ-MALAT1. (A) qRT-PCR analysis was used to verify knockdown and overexpression of circ-MALAT1. (B,C) MTT and clone formation assays were performed to investigate cell proliferation. (D) Wound-healing assay was used to assess cell migration. (E) Western blot measured E-cadherin, N-cadherin, vimentin, and snail levels. N = 3, *p [less than] 0.05, **p [less than] 0.01, and ***p [less than] 0.001.
Bioinformatics analysis using the StarBase software predicted that circ-MALAT1 has binding sites with miR-506-3p, and KAT6B is a target of miR-506-3p. These predictions were experimentally tested using the luciferase activity assay (Figure 3A,B). Moreover, we also observed that downregulation of circ-MALAT1 significantly increased miR-506-3p level and inhibited KAT6B expression in LS513 and SW837 cells (Figure 3C,D).
FIGURE 3. Circ-MALAT1 promoted the KAT6B level via sponging miR-506-3p. (A) StarBase software and luciferase activity were performed to predict and validate the interaction between circ-MALAT1 and miR-506-3. (B) LS513 and SW837 cells were subjected to transfection with sh-NC or sh-circ-MALAT1. (C) qRT-PCR was used to determine the level of miR-506-3p. (D) Western blot was performed to investigate the protein level of KAT6B. N = 3, *p [less than] 0.05, **p [less than] 0.01, and ***p [less than] 0.001.
To unravel the role of miR-506-3p in regulating the progression of CRC and metastasis, miR-506-3p mimics and KAT6B were transfected into LS513 and SW837 cells. MiR-506-3p mimics apparently suppressed KAT6B expression; however, we observed that the upregulation of KAT6B decreased the inhibitory effects induced by miR-506-3p (Figure 4A,B). We also observed that miR-506-3p mimics suppressed the protein level of STAT3 and inhibited the enrichment of histone H3 lysine 23 acetylation (H3K23ac), and these effects were subsequently reversed by KAT6B sufficiency (Figure 4B). Interestingly, miR-506-3p mimics suppressed cell growth and migration in LS513 and SW837 cells, while these effects were abolished by KAT6B sufficiency (Figure 4C–E). Furthermore, we also found that miR-506-3p mimics suppressed EMT by regulating proteins associated with this cancer hallmark (Figure 4F). Taken together, these findings suggest that miR-506-3p suppresses KAT6B activity and consequently also acetylation of the STAT3 gene, inhibiting cell proliferation, migration, and EMT of CRC cells.
FIGURE 4. Upregulation of miR-506-3p and STAT3 acetylation in CRC cells. MiR-506-3p and KAT6B were simultaneously upregulated in LS513 and SW837 cells. (A) qRT-PCR was used to determine the relative gene expression levels of 506-3p and KAT6B. (B) Western blot was performed to measure the protein levels of KAT6B, STAT3, and H3K23ac. (C,D) MTT assay and clone formation investigated cell proliferation. (E) Wound-healing assay was used to assess cell migration. (F) Western blot was performed to measure E-cadherin, N-cadherin, vimentin, and snail levels. N = 3, *p [less than] 0.05, **p [less than] 0.01, and ***p [less than] 0.001.
We explored whether the miR-506-3p/KAT6B axis is regulated by circ-MALAT1 during cell proliferation and metastasis of CRC cells. For such a purpose, miR-506-3p inhibitor or oe-KAT6B vector was introduced into circ-MALAT1-silenced LS513 and SW837 line cells. Transfection of sh-circ-MALAT1 significantly decreased circ-MALAT1 and KAT6B levels while increasing miR-506-3p expression. However, miR-506-3p depletion compromised circ-MALAT1 knockdown-mediated changes in miR-506-3p and KAT6B. In addition, KAT6B overexpression only restored circ-MALAT1 knockdown-reduced KAT6B level (Figure 5A,E). Moreover, transfection of miR-506-3p inhibitor or KAT6B sufficiency abolished cell proliferation, migration, and EMT induced by MALAT1 knockdown (Figure 5B–E). Collectively, these results suggest that circ-MALAT1 is able to induce cell growth and EMT of CRC cells through the regulation of the miR-506-3p/KAT6B axis.
FIGURE 5. Circ-MALAT1 accelerates cell proliferation, migration, and EMT in CRC cells by regulating the miR-506-3p/KAT6B axis. LS513 and SW837 cells transfected with sh-circ-MALAT1 were subjected to miR-506-3p inhibitor or oe-KAT6B transfection. (A) qRT-PCR determination of circ-MALAT1, 506-3p and KAT6B levels. (B,C) MTT and clone formation assays were performed to investigate cell proliferation. (D) Wound-healing assay was used to assess cell migration. (E) Western blot was performed to measure protein levels of KAT6B, E-cadherin, N-cadherin, vimentin, and snail. N = 3, *p [less than] 0.05, **p [less than] 0.01, and ***p [less than] 0.001.
CRC is a severe disease that causes a high number of deaths worldwide every year.19 A substantial body of evidence has shown that the indefinite cell proliferation, the ability of cell migration, and the onset of EMT are major factors leading to the rapid progress of CRC.20,21 In consequence, several studies have proposed that suppression of these cancer hallmarks could provide effective therapeutic strategies for treating CRC.22,23 In this work, we found that knockdown of circ-MALAT1 inhibited cell proliferation, migration, and EMT of CRC cells through the modulation of the miR-506-3p/KAT6B pathway.
A growing body of evidence has shown an association between regulatory circRNAs and CRC.5 For example, it has been shown that circ_0085315 induces cell growth and metastasis via the miR-1200/MAP3K1 axis.24 In line with these findings, it has also been reported that hsa_circ_0006732 accelerates cell proliferation, invasion, and EMT through the modulation of the miR-127-5p/RAB3D pathway.25 Before discussing some results of this study, it is worth mentioning that the association between circ-MALAT1 and CRC has not been studied yet. A previous study proposed that circ-MALAT1 contributes to the self-renewal of CSC in HCC,10 suggesting that this circRNA may be involved in tumorigenesis and metastatic potential of cancer cells. In this study, we found that the level of circ-MALAT1 was abnormally high in tissues of patients with CRC and CRC cell lines, thereby suggesting that circ-MALAT1 might play an important role in the progression of this type of cancer. Furthermore, we suggest that the overexpression of circ-MALAT1 might promote cell proliferation, migration, and EMT of CRC cells, an observation supported by the fact that knockdown of circ-MALAT1 led to opposite results.
It is well known that circRNAs can interact with miRNAs to regulate diverse physiological and pathological processes including cancer.26 Here, we found that circ-MALAT1 has a binding site for miR-506-3p, and this interaction was validated by the dual-luciferase reporter assay. We found that knockdown of circ-MALAT1 induced upregulation of miR-506-3p. In consequence, our model suggests that circ-MALAT1 regulates the miR-506-3p/KAT6B axis by sponging miR-506-3p. The effects of miR-506-3p on carcinogenesis have been studied extensively in many types of cancers including, among others, glioma, non-small-cell lung cancer, ovarian cancer, and CRC.14,27–29 A previous study showed that the level of miR-506-3p decreased in tissues of patients with CRC and CRC line cells, while miR-506-3p sufficiency could inhibit the progression of CRC by suppressing cell proliferation and invasion while promoting apoptosis.14 Liao et al. suggested that miR-506-3p might act as a radio-sensitive biomarker for CRC.30 In line with this, our results showed a significant decrease in the level of miR-506-3p in tissues of patients with CRC and CRC cell lines. Moreover, overexpression of miR-506-3p suppressed cell proliferation, migration, and EMT of CRC cells. Furthermore, the miR-506-3p inhibitor reversed the suppression induced by knockdown of circ-MALAT1.
KAT6B is a major histone acetyltransferase epigenetic enzyme and mutations in the encoding gene could be responsible for various disease states.31,32 A substantial number of studies have suggested that KAT6B may contribute to the development of malignant tumors (e.g., glioma and tongue squamous cell carcinoma).17,33 In this study, the level of KAT6B was significantly high in the tissues of patients with CRC and CRC cell lines. Moreover, it is well known that miRNAs target the 3′ untranslated region (3'UTR) region of mRNAs to regulate gene expression.34 For instance, it has been shown that miR-1538 targets DNMT3A methyltransferase gene transcript to block cell proliferation of CRC cells.35 Here, we identified KAT6B as a downstream target negatively regulated by miR-506-3p, an observation supported by both dual-luciferase reporter assay and qRT-PCR. Furthermore, rescue experiments showed that upregulation of KAT6B reversed the suppression of cell proliferation, migration, and EMT induced by miR-506-3p. In this regard, it is also important to highlight that a previous study suggested that KAT6B positively regulates the transcriptional activity of the STAT3 gene through its acetylation.17 Our results revealed that an increased miR-506-3p level inhibits the expression of STAT3 by promoting the recruitment of H3K23ac, while overexpression of KAT6B is able to reverse this phenotype. In addition, circRNAs could indirectly regulate downstream target genes by sponging miRNAs. For example, circIFNGR2 increased the level of KRAS by sponging miR-30b, thereby inducing cell proliferation and migration of CRC cells and cetuximab resistance.36 In this study, we observed that knockdown of circ-MALAT1 decreased KAT6B expression at both mRNA and protein levels. Overexpression of KAT6B restored proliferation, migration, and EMT phenotypes induced by circ-MALAT1 knockdown.
In conclusion, we propose that knockdown of circ-MALAT1 suppresses cell proliferation, migration, and EMT of CRC cells by altering the regulatory mechanism of the miR-506-3p/KAT6B axis. This model provides a new potential target for the development of therapies against CRC, a prediction we expect to test experimentally in the near future.
CONFLICT OF INTEREST STATEMENTThe authors declare no conflicts of interest.
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Abstract
Colorectal cancer (CRC) is a prevalent malignant tumor of the digestive tract. Circular RNAs may play important roles in the progression of CRC. In this study, we investigated the roles and mechanisms of action of circ-MALAT1 in CRC. Gene expression and protein abundance were determined using qRT-PCR and western blot, respectively. Cell proliferation and migration were assessed by MTT, clone formation, and wound-healing assays. The interactions among the long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (circ-MALAT1), miR-506-3p, and lysine acetyltransferase 6B (KAT6B) were predicted using the StarBase software and confirmed by the luciferase activity assay. Circ-MALAT1 and KAT6B were upregulated, while miR-506-3p was downregulated in CRC cells. We validated that knocking down of circ-MALAT1 suppressed proliferation, migration, and epithelial–mesenchymal transition (EMT) of CRC cells, and these effects were abolished by miR-506-3p downregulation or KAT6B sufficiency. Our study suggests that circ-MALAT1 could sponge miR-506-3p to regulate the expression of KAT6B. Moreover, KAT6B sufficiency could neutralize miR-506-3p-dependent growth arrest, migration, and EMT. Circ-MALAT1 promotes cell proliferation, migration, and EMT of CRC cells via the miR-506-3p/KAT6B axis, thereby acting as a novel potential therapeutic target for the treatment of colorectal cancer.
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