Background
Globally, breast cancer (BC) is a highly heterogeneous disease with complex molecular bidirectional crosstalk between hormone receptors (HRs) and human epidermal growth factor receptor 2 (HER2) [
1,
2]. Approximately 70% of patients have BC that is HR-positive and HER2-negative (HR+HER2−) [
3]. Although endocrine-based therapies (aromatase inhibitors [AIs] and/or anti-oestrogen treatments with or without ovarian suppression) are the gold standard of treatment of BC and the backbone of adjuvant therapies for these patients with significantly decreased risk of recurrence and death [
4], up to 20% of patients will eventually relapse [
5,
6]. Single-agent chemotherapy is an essential treatment option for endocrine-resistant or treatment-refractory disease [
7]. However, response rates to these therapies are low. Reported progression-free survival (PFS) ranges from 4.0 to 6.3 months with second-line chemotherapy and from 2.4 to 5.5 months with third-line chemotherapy [
8]. Similarly, the association of pathological complete response (pCR) with disease-free survival (DFS) or overall survival (OS) in HR+HER2− BC following neoadjuvant systemic therapy is relatively low compared to that of the other two subtypes of BCs [
9]. Thus, there is an imperative need to further improve our insight into the tumour biology and the tumour cell response to chemotherapy for HR+HER2− BC.
N6-Methyladenosine (m
6A) is the most prevalent messenger RNA (mRNA) modification in eukaryotes and is added to mRNA molecules by the
N6-adenosine methyltransferase complex, which consists of methyltransferase-like 3 (METTL3), methyltransferase-like 14 (METTL14) and Wilms tumour 1-associated protein (WTAP) [
10]. METTL3 and METTL14 are two active methyltransferases that form a heterodimer to catalyse m
6A RNA methylation, while WTAP interacts with this complex and substantially affects mRNA methylation [
11]. Two m
6A demethylases fat mass and obesity-associated (FTO) and AlkB homolog 5 (ALKBH5) have been discovered since 2011, revealing the dynamic nature of m
6A modification [
12]. Some cellular proteins have been found to preferentially bind m
6A-modified RNA, whereas others have been characterized to specifically recognize m
6A-modified mRNA and accelerate the decay of the mRNA [
13]. These results indicated that this chemical modification is common and important in a variety of biological processes.
With the elucidation of the mechanisms involved in m
6A modification, a recent report described the role of the m
6A modification in multiple tumours [
14]. Although studies on the function of m
6A in BC are still in their early stages, there is growing evidence showing that m
6A plays a critical role in many aspects of BC, including tumorigenesis [
15], metastasis [
16], prognosis [
17] and treatment resistance [
18]. Reduced expression of METTL3 promotes metastasis of BC by increasing COL3A1 expression [
19]. Hypoxia stimulates ALKBH5, which stabilizes NANOG mRNA and induces a phenotype associated with BC stem cells (BCSCs) and lung metastasis [
20,
21]. YTHDF3 promotes BC metastasis to the brain by inducing m
6A-enriched gene translation [
16]. Moreover, m
6A modification patterns have therapeutic implications and correlate with drug resistance. HNRNPA2B1 and METTL3 overexpression in MCF-7 cells reduces their sensitivity to 4-hydroxytamoxifen and/or fulvestrant [
22,
23]. In triple-negative BC (TNBC) cells, IGF2BP3 promotes chemoresistance to doxorubicin (DOX) and mitoxantrone by regulating ABCG2 expression [
24]. Therefore, it is possible to determine why HR+HER2− BC is insensitive to chemotherapy treatment by further exploring the role of m
6A modification in this subtype of BC.
In this study, we investigated the potential effect of m6A methylation on the tumour progression and sensitivity of HR+HER2− BC to chemotherapy. Our data revealed that chemotherapy decreased the levels of the m6A modification, which was dependent on METTL3 expression. We demonstrated that METTL3 depletion facilitates HR+HER2− BC progression via its downstream target cyclin-dependent inhibitor kinase 1A (CDKN1A), which mediates epithelial–mesenchymal transition (EMT). In addition, METTL3 reduction inhibits apoptosis by regulating BAX/caspase3/8/9 signalling in an m6A-independent manner. Overall, our results suggested that METTL3 plays a pivotal tumour-suppressor role in the progression of HR+HER2− BC, indicating that METTL3 is a promising biomarker for predicting the efficacy of chemotherapy as well as a potential therapeutic target for reversing chemotherapy resistance in HR+HER2− BC.
Methods
Human BC tissues
Thirteen pairs of primary BC tissues collected before and after treatment were obtained from the Second Xiangya Hospital of Central South University (Hunan, China) from August 2020 to March 2021. All individuals with BC were diagnosed for the first time, only received chemotherapy prior to surgery and had histologically confirmed HR+HER2− BC (Table
1). All patients provided written informed consent, which was conducted in accordance with the Declaration of Helsinki, and this study was reviewed and approved by the Research Ethics Committee of the Second Xiangya Hospital of Central South University.
Table1
Clinicopathologic parameters of 13 HR+HER2− breast cancer patients
Age (years) | |
Median | 52.00 |
Clinical T stage | |
cT1-2 | 6 (46.2) |
cT3-4 | 7 (53.8) |
NAC regimen | |
AC-T/P | 11 (84.6) |
TAC | 2 (15.4) |
NAC cycles | |
≤ 4 | 9 (69.2) |
> 4 | 4 (30.8) |
Residual tumour size | |
≤ 2 cm | 1 (7.7) |
> 2 cm | 12 (92.3) |
Nodal status | |
Neg | 5 (38.5) |
Pos | 8 (61.5) |
Cell culture and chemicals
BC cell lines (MCF-7, T47D and MDA-MB-231) were obtained from the Shanghai Type Culture Collection of the Chinese Academy of Sciences and were grown in DMEM or RPMI 1640 medium (Gibco, Carlsbad, CA, USA) supplemented with 1% penicillin/streptomycin (Shanghai, Beijing, China). All cells in this study were incubated in 37 °C incubators with 5% carbon dioxide and routinely tested for mycoplasma. The chemotherapy drugs (doxorubicin [DOX], paclitaxel [PTX] and cisplatin [
25]) were purchased from Dingguo (Beijing, China). The half-maximal inhibitory concentration (IC50) values of DOX were 1.0 and 0.2 μg/ml for MCF-7 and T47D cells, respectively. The IC50 values of PTX were 0.5 and 0.1 μM for MCF-7 and T47D cells, respectively, and the IC50 value of Cis was 400 nM for MCF-7 and T47D cells (Additional file
1A).
Cell transduction
Stable knockdown and overexpression of METTL3 were achieved with lentiviral-based delivery of short-hairpin RNA (shRNA) and overexpression vectors, respectively. The shRNA sequences were subcloned into a lentiviral expression vector containing GFP by Shanghai Genechem Co., Ltd. (Shanghai, China). Lentiviral transduction was performed according to the manufacturer’s instructions. All constructed vectors were verified by DNA sequencing.
Western blotting
Total proteins from cell lines and tissues were extracted with RIPA buffer and then quantified by BCA analysis. Subsequently, 20 µg of total protein per sample (10 µL per lane) was separated using sodium lauryl sulphate–polyacrylamide gel electrophoresis (10% polyacrylamide gel) before the proteins were transferred to a PVDF membrane. After incubation with primary antibodies overnight, the membranes were then incubated with secondary antibody. Finally, target protein bands were detected using a chemiluminescence system. The antibodies used targeted the following proteins: AKT (Cell Signaling #9272s), Caspase-9 (Proteintech 10380-1-AP), Caspase-3 (Proteintech 66470-2-Ig), Caspase-8 (Proteintech 66093-1-Ig), p-ATK (Cell Signaling #4060), BAX (Proteintech 60267-1-Ig), Vimentin (Proteintech 10366-1-AP), N-cadherin (Proteintech 22018-1-AP), E-cadherin (Proteintech 20874-1-AP), GAPDH (Signalway Antibody #21612) and METTL3 (ABclonal A8370).
Quantitative real-time polymerase chain reaction (qRT-PCR)
Total RNA from cell lines and tissues was isolated using TRIzol reagent (Thermo Fisher Scientific, Beijing, China). A PrimeScript RT kit (Thermo Fisher Scientific, Beijing, China) was used for cDNA synthesis. Real-time quantitative PCR analysis was performed using a SYBR Premix Kit (Abclonal, Wuhan, China). Each sample was run in triplicate, and the expression levels were normalized to those of GAPDH using relative quantitative methods. All PCR primers (Well Biological Science, China) are listed as follows:
-
GAPDH-F: ACAGCCTCAAGATCATCAGC
-
GAPDH-R: GGTCATGAGTCCTTCCACGAT
-
METTL3-F: TTGTCTCCAACCTTCCGTAGT
-
METTL3-R: RCCAGATCAGAGAGGTGGTGTAG
-
CDKN1A-F: CAAGCTCTACCTTCCCACGG
-
CDKN1A-R: TCGACCCTGAGAGTCTCCAG
-
BAX-F: ACTAAAGTGCCCGAGCTGA
-
BAX-R: ACTCCAGCCACAAAGATGGT
Cell proliferation assay
Cell proliferation and cytotoxicity assay kits (Dingguo, Beijing, China) were used to assess cell viability. Cells were seeded into 96-well plates at a density of 1 × 103 cells per well and cultured in an incubator (37 °C with 5% CO2) for 24 h, 48 h and 72 h, after which cell proliferation was examined on a microplate reader by measuring the absorbance at a wavelength of 450 nm. To assess colony formation, cells were seeded into 6-well plates at a density of 1 × 103 cells per well and cultured in an incubator (37 °C with 5% CO2). After 14 days, the cells were fixed and stained with Giemsa stain, modified solution (Sigma), and colonies containing 50 or more cells were counted.
Cell cycle analysis
For cell cycle analysis, cells were seeded in 6-well plates at a density of 2–3 × 105 per well and grown to ~ 70% confluence. Cells were then harvested and suspended in a complete medium. The cell suspension was centrifuged at 1300 rpm at 4 °C, washed once in D-Hanks buffer, counted and resuspended to a density of 3–6 × 106 cells/mL. Ice-cold 70% ethanol was added dropwise to fix the cells, which were then centrifuged, washed once with D-Hanks, stained with 20 μg/mL propidium iodide (Sigma, P4170) in D-Hanks containing 50 μg/mL RNase A (Fermentas, EN0531) for 1 h at room temperature and analysed using flow cytometry.
Transwell migration and invasion assay
For the tumour cell transwell migration and invasion assay, transfected breast cancer cells were seeded in DMEM/1640 without FBS in the upper chamber with or without a Matrigel coating. The lower chamber was filled with DMEM/1640 containing 10% FBS acting as a chemoattractant. After 24 h or 48 h, the cells in the upper chamber were washed away, and the remaining cells were fixed, dyed and photographed.
Wound healing assay
For the wound healing assay, cells were seeded and cultured until a 90% confluent monolayer was formed. Cells were then scratched by a sterile pipette tip and treated as indicated in the text in an FBS-free medium. Cell migration distances into the scratched area were measured in 10 randomly chosen fields under a microscope.
TUNEL assay
A TUNEL kit (Roche) was used according to the manufacturer’s instructions. In brief, cells were fixed with 4% paraformaldehyde, permeated with 0.1% Triton X-100 in PBS, incubated with 50 μL of TUNEL reaction mixture for 1 h at 37 °C and then washed with PBS 3 times. A total of 1000 cells were counted, and the percentage of apoptotic cells was quantified.
In vivo tumour xenograft model
To assess the in vivo effects of METTL3, 4-week-old female BALB/c nude mice were used for tumour formation experiments. The experiments were carried out with the prior approval of the Second Xiangya Hospital of Central South University Committee on Animal Care, and the protocols were performed in accordance with the guidelines for the use of laboratory animals. For the experiments, mice were injected subcutaneously in the axilla with 1 × 10
7 MCF-7 cells with stable expression of relevant plasmids. When the tumour diameter reached approximately 5 mm, nude mice were randomly divided into two groups (six mice per group). Xenografted mice were then administrated with PBS or DOX (5 mg/kg each mouse every 3 days) [
26]. The health of the nude mice and the growth of the tumours were observed every 3 days for 21 days. Mice were killed after 3 weeks, and the tumours were separated, weighed and collected for experiment evaluation.
Immunohistological staining
Fresh tumour tissues were excised from nude mice and fixed with 4% paraformaldehyde. Then, the sections were dehydrated with a graded alcohol series, cleared in xylene, embedded in paraffin and sliced into sections with a microtome at a thickness of approximately 4 µm. After more treatments with xylene and an alcohol gradient, the sections were dewaxed and hydrated. Ki-67 antibody was added and then incubated overnight, and the secondary antibody was incubated for 1 h. Diaminobenzidine (DAB) was used for colour development, and the slides were stained with haematoxylin before they were mounted in neutral resin. With a common microscope, 40× high-definition fields were randomly selected for counting the total number of cells and the number of Ki-67-positive cells (which have brown nuclei).
RNA m6A quantification, methylated RNA immunoprecipitation (MeRIP) and quantitative PCR
The m
6A content of 200 ng of RNA extracted from tissues and cell lines was measured by an EpiQuik m
6A RNA methylation quantification kit (EpigenTek, USA) according to the manufacturer’s instructions. Immunoprecipitation of m
6A-modified BAX and CDKN1A mRNA was performed using a Tiangen MeRIP m
6A Kit (FP313, Tiangen, China) according to the manufacturer’s protocol. m
6A enrichment was analysed by qPCR with specific primers (Well Biological Science, China), and data were normalized to the input. Primer sequences were as follows:
-
BAX-Positive-F: AGGATCGAGCAGGGCGAAT
-
BAX-Positive-R: AGCTGCCACTCGGAAAAAGA
-
BAX-Negative-F: CCGAGTCACTGAAGCGACTG
-
BAX-Negative-R: ACGTGGGCGTCCCAAAGTAG
-
CDKN1A-Positive-F: TCTTCGGCCCAGTGGACA
-
CDKN1A-Positive-R: AGTCGAAGTTCCATCGCTCA
-
CDKN1A-Negative-F: TCCTCATCCCGTGTTCTCCT
-
CDKN1A-Negative-R: ACAAGTGGGGAGGAGGAAGT
Statistical analysis
Experimental data are presented as the mean ± standard deviation (SD) and were analysed using GraphPad Prism 8.0 software. All in vitro results are representative of at least three independent trials. Two-group comparisons were assessed by the Mann–Whitney U test or Student’s t test, and paired t tests were employed for paired BC and corresponding chemo-only BC samples. A two-tailed p value of 0.05 was considered statistically significant.
Discussion
In recent decades, substantial improvements have been made in therapeutic interventions for BC, which have increased the survival and quality of life of patients [
30]. Chemotherapy, as the broadest application of tumour treatment, remains the cornerstone of adjuvant therapy for BC and is widely used in BC patients with high metastatic burden and locally advanced disease [
31]. Nevertheless, recent studies have indicated that the response rate of BC patients with the HR+HER2− subtype to chemotherapy is low [
32]. Hence, the demand for elucidating the mechanism of HR+HER2− BC insensitivity to chemotherapy is crucial. In this study, we first discovered that m
6A modifications and METTL3 expression were inhibited by chemotherapy; thus, we evaluated the function of METTL3 in regulating HR+HER2− BC progression and drug sensitivity. Based on our findings, we revealed that METTL3 plays a protective role in HR+HER2− BC and regulates the CDKN1A/EMT and BAX/caspase3/8/9 axes in an m
6A-dependent manner, which could be novel pathways involved in a potential mechanism of HR+HER2− BC chemoresistance (Fig.
6H).
m
6A modification, one type of RNA epigenetic modification, has been identified on almost all types of RNAs and has been implicated in a variety of cellular processes, including mRNA stability, splicing, location, and translation, RNA–protein interactions and pri-miRNA processes (28–33). An increasing number of studies have addressed the pathological significance of m
6A dysregulation in human diseases, especially in cancers [
33‐
35]. The results of our current study showed that the overall level of m6A modification was significantly downregulated after chemotherapy in HR+/HER2− BC patients, and treatment of MCF-7 and T47D cells with DOX, PTX and Cis also resulted in a decrease in m
6A modifications. However, the levels of m
6A modification were not affected by drug intervention in MDA-MB-231 cells. Therefore, our results suggested that chemotherapy-induced changes in m
6A levels are a biological difference between HR+HER2− BC and TNBC, especially in terms of responsiveness to chemotherapy. Various studies indicate that the m
6A modification affects drug sensitivity by regulating ABC transporters either directly at the transcript level or via upstream signalling pathways [
36]. Recent studies also indicated that the m
6A modification is involved in the maintenance of CSCs in tumours, leading to drug resistance and recurrence [
37]. It has also been shown that m
6A modifications can affect the response of BC to endocrine therapy [
22]. However, there are few studies on the relationship between m
6A and chemotherapy response. Therefore, considering the potential role of the m
6A RNA modification in the development of chemoresistance, it is necessary to illustrate the relationship between these two phenomena.
METTL3, a key component of the
N6-methyltransferase complex, has been reported to play an important role in many tumour types [
38‐
43]. Previous studies reported that METTL3 plays an oncogenic role in acute myeloid leukaemia through diverse downstream targets [
43], whereas other studies suggested that either increased or decreased METTL3 expression could promote the self-renewal and tumorigenicity of glioma stem-like cells, respectively [
42,
44]. Regarding METTL3 in BC, data from the literature have suggested that METTL3 can promote BC progression by targeting Bcl-2, HBXIP or SOX2 [
41,
45,
46] and that METTL3 could promote adriamycin resistance by accelerating pri-miRNA-221-3p maturation [
47] or mediating MALAT1/E2F1/AGR2 axis [
48]. However, our results illustrated that chemotherapy-mediated depletion of METTL3 plays a significant unprotective role in tumour progression and drug tolerance. Reasonable explanations for these contradictory phenomena could be attributed to recognition by different m
6A readers [
49]. We speculated that the m
6A modification and METTL3 expression protect some critical genes from degradation or restrain the role of oncogenes by enhancing their recognition by “readers”. We analysed the differential expression of “readers” in two data sets (GSE87455 and GSE763), and the results showed that only HNRNPA2B1 expression was significantly decreased after chemotherapy in both data sets. We also verified the expression of HNRNPA2B1 in cell lines after DOX intervention (Additional file
4B, C). Current studies have shown that HNRNPA2B1 participates in gene processing and alternative splicing and is a negative regulator of human breast cancer metastasis by maintaining the balance of multiple genes and pathways [
50,
51], and the relationship between HNRNPA2B1 and chemotherapy in breast cancer is not clear. Therefore, we speculated that the downregulation of HNRNPA2B1 caused the dysregulation of CDKN1A and BAX, but the specific mechanism still needs further verification. In summary, the decreased METTL3 expression is secondary to chemotherapy, which is consistent with the clinical medication pattern, and HR+HER2− BC is the only BC subtype to exhibit this expression pattern. Therefore, METTL3 can be used as a biomarker to predict the sensitivity of HR+HER2− BC to chemotherapy and as a novel target for combination therapy to reverse chemotherapy resistance.
Our results further showed that METTL3 regulates the proliferation, apoptosis, migration and drug sensitivity of HR+/HER2− BC through multiple signalling pathways. On the one hand, METTL3 can affect the m
6A modification of BAX mRNA, thereby promoting activation of the pro-apoptotic caspase cascade and (consequently) apoptosis. Apoptosis is an important mechanism to mitigate the uncontrolled growth of tumour cells and is mainly regulated by the Bcl2 protein family [
52]. The Bcl2 protein family can be divided into two categories according to their functions: one plays a pro-apoptotic role and includes BAX and Bak, whereas the other plays an anti-apoptotic role and includes Bcl2. Both pathways promote caspase cascades that eventually lead to cell death [
52]. Our experiment found that METTL3 can promote the expression of BAX and the subsequent activation of caspase3, 8, and 9, leading to apoptosis.
On the other hand, downregulation of METTL3 can regulate CDKN1A expression to affect the EMT process and promote cell proliferation, migration and invasion. CDKN1A is one of the key molecules involved in cell cycle progression and was first identified as a tumour suppressor [
53]. Later, it was found to be involved in pathways related to tumorigenesis and development, such as cell death, DNA replication/repair, gene transcription and cell motility [
54]. It is believed that the role of CDKN1A depends on its cellular localization [
55]. When in the nucleus, CDKN1A functions as a tumour suppressor. However, when CDKN1A is concentrated in the cytoplasm, p53-impaired or p53-deficient cells may acquire carcinogenic properties, which may inhibit apoptosis and promote cell migration and proliferation [
56]. Studies have shown that miR-33b-3p can promote the survival and cisplatin resistance of A549 human lung cancer cells by targeting CDKN1A after DNA damage [
57]. It was also found that miR-520g mediated the resistance of colorectal cancer cells to 5-fluorouracil (5-FU) or oxaliplatin by downregulating CDKN1A expression [
58]. These studies suggest that the presence of CDKN1A protects cancer cells from apoptosis after anti-cancer therapy. Therefore, in this study, the changes in CDKN1A expression were caused by chemical drugs, which may stimulate the translocation of CDKN1A protein from the nucleus to the cytoplasm, thereby activating downstream-related pathways to reduce the sensitivity of cells to chemotherapy drugs; however, the specific mechanism is still unknown. In short, the mechanisms of interaction between cell signalling pathways and epigenetic elements are diverse and complex and merit further exploration and verification.
This study still has some shortcomings, such as the small sample size and lack of follow-up data. The direct intermolecular regulatory mechanism by which METTL3 affects tumour progression and survival was not clarified in detail, and we will be further studied in the future.
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