The m(6)A Methyltransferase METTL3 Promotes Translation in Human Cancer Cells

Abstract

METTL3 is an RNA methyltransferase implicated in mRNA biogenesis, decay, and translation control through N(6)-methyladenosine (m(6)A) modification. Here we find that METTL3 promotes translation of certain mRNAs including epidermal growth factor receptor (EGFR) and the Hippo pathway effector TAZ in human cancer cells. In contrast to current models that invoke m(6)A reader proteins downstream of nuclear METTL3, we find METTL3 associates with ribosomes and promotes translation in the cytoplasm. METTL3 depletion inhibits translation, and both wild-type and catalytically inactive METTL3 promote translation when tethered to a reporter mRNA. Mechanistically, METTL3 enhances mRNA translation through an interaction with the translation initiation machinery. METTL3 expression is elevated in lung adenocarcinoma and using both loss- and gain-of-function studies, we find that METTL3 promotes growth, survival, and invasion of human lung cancer cells. Our results uncover an important role of METTL3 in promoting translation of oncogenes in human lung cancer.

Keywords: EGFR; METTL3; N(6)-methyladenosine; cancer; m(6)A; ribosome; translation.

Figure 1. METTL3 regulates protein expression

(A–B) Global profiling of m⁶A in A549 cells. (A) Sequence motif identified from the top 1000 m⁶A peaks. (B) Distribution of m⁶A peaks across all mRNAs. (C) Integrative Genomics Viewer (IGV) plots of m⁶A peaks at individual mRNAs. The y-axis shows sequence read number, blue boxes represent exons, and blue lines represents introns. (D) q.RT-PCR analysis of α-m⁶A IP in A549 cells using indicated PCR primers. (E) q.RT-PCR analysis of FLAG-METTL3 RNA IP in A549 cells with indicated primers. (F) Western blot with indicated antibodies. (G) q.RT-PCR analysis of EGFR m⁶A levels upon depletion of METTL3 in A549 cells. (H, I) Expression of METTL3 and m⁶A targets in the METTL3 knockdown cells. (H) q.RT-PCR analysis of indicated mRNA levels. mRNA was first normalized to β-Actin mRNA. Relative ratio (fold-change) obtained in the presence of shGFP was set to 1. (I) Western blotting with indicated antibodies. All q.RT-PCR data are presented as ±SEM. n=3. **p<0.01, ***p<0.001. See also Figures S1 and S2, and Supplementary Table 1.

Figure 2. METTL3 enhances translation

(A–B) METTL3 knockdown in HeLa cells (A) Western blot using indicated antibodies. (B) q.RT-PCR of indicated mRNAs normalized to β-Actin mRNA. Relative ratio (fold-change) obtained in the presence of shGFP was set to 1. Data are presented as ±SEM. n=3. (C) Western blot analysis of METTL3 in nuclear and cytoplasmic fractions using β-Tubulin (cytoplasmic, Cy) and Fibrillarin (nuclear, Nc) as controls. (D–E) Cytoplasmic extracts from control or METTL3-depleted cells were subjected to sucrose grandient centrifugation. (D) Polysome-fractionated samples analyzed by Western blot using the indicated antibodies and RT-PCR performed with α-[³²P]-dCTP. (E) Relative levels of EGFR or TAZ mRNAs in each ribosome fraction were quantified and normalized to RCN2 mRNA and plotted as a percentage of the total. Data are from three independent polysome-profiling experiments. Error bars = mean ±SEM, n=3.

Figure 3. METTL3 directly promotes translation independently of catalytic activity or downstream reader proteins

(A) Schematic diagram of tethering reporter assay. (B) Western blot analysis of YTHDF1 and YTHDF2 expression in control and siRNA knockdown cells. (C) αFLAG western blot of indicated proteins. (D) Tethering assay to measure translation efficiency of reporter mRNAs. Firefly luciferase (FLuc) activity was measured and normalized to the Renilla luciferase (RLuc) activity. Relative FLuc activity was normalized to the relative FLuc-MS2bs mRNAs. The normalized FLuc activity (translation efficiency) in the presence of MS2 and control siRNA for each set was set to 1. **P<0.01. Error bars = mean ±s.d., n=3. (E) αFLAG western blot of indicated proteins. (F) Tethering assay to measure translation efficiency of reporter mRNAs. (G) Schematic diagram of METTL3 deletion mutants. (H) α-FLAG western blot of indicated proteins. (I) Tethering assay to measure translation efficiency of reporter mRNAs. See also Figure S3.

Figure 4. METTL3 recruits eIF3 to the translation initiation complex

(A–E) Co-IPs of indicated FLAG-tagged proteins analyzed by Western blot using the indicated antibodies. Where indicted lysates were treated with RNase A. (E) Co-IPs performed using lysates collected from either control- or METTL3 siRNA transfected cells. (F) Western blot performed on cell lysates collected from indicated cells transfected with control-, METTL3-, or YTHDF1 siRNA. See also Figure S4.

Figure 5. METTL3 promotes translation by recruiting translation initiation factors

(A) Schematic diagram of tethering reporter assay. (B) α-FLAG western blot of indicated proteins. (C) Tethering assay to measure translation efficiency of reporter mRNAs. FLuc activity was measured and normalized to the RLuc activity. ***P<0.001. Error bars = mean ±s.d., n=3.

Figure 6. METTL3 promotes cancer cell growth, survival, and invasion

(A) Expression of METTL3 and METTL14 in normal tissue (n=58) and lung andenocarcinoma (n=513) from TCGA-LUAD dataset. (B) Western blot analysis of METTL3 expression in normal human fibroblasts and lung adenocarcinoma cell lines. (C–H) Knockdown of METTL3 regulates cellular proliferation, survival and invasion of A549 cells. (C) Westen blot shows stable knockdown of METTL3 by shRNAs. (D) MTS assay of cellular proliferation in A549 cells. (E) Annexin V/PI staining of METTL3 knockdown and control A549 cells by FACS. (F) Quantification of apoptotic cells, numbers represent the sum of early and late apoptotic cells. (G) In vitro cell invasion assay. (H) Quantification of invasive cells. (I–K) METTL3 overexpression regulates cell invasion in IMR-90 cells. (I) Western blot. (J) In vitro cell invasion assay. (K) Quantification of invasive IMR-90 cells. Data are presented as ±SEM. n=3. **p<0.01, ***p<0.001. See also Figure S5.

Figure 7. Model of the role of METTL3 in promoting translation initiation of target mRNAs

AUG, translation initiation codon; CAP, Cap; 20, CBP20; 80, CBP80; STOP, translation stop codon; CH₃, m⁶A; (A)n, poly(A) tail; 40S, 40S ribosomal subunit; 60S, 60S ribosomal subunit.