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The MBNL3 splicing factor promotes hepatocellular carcinoma by increasing PXN expression through the alternative splicing of lncRNA-PXN-AS1

Abstract

Understanding the roles of splicing factors and splicing events during tumorigenesis would open new avenues for targeted therapies. Here we identify an oncofetal splicing factor, MBNL3, which promotes tumorigenesis and indicates poor prognosis of hepatocellular carcinoma patients. MBNL3 knockdown almost completely abolishes hepatocellular carcinoma tumorigenesis. Transcriptomic analysis revealed that MBNL3 induces lncRNA-PXN-AS1 exon 4 inclusion. The transcript lacking exon 4 binds to coding sequences of PXN mRNA, causes dissociation of translation elongation factors from PXN mRNA, and thereby inhibits PXN mRNA translation. In contrast, the transcript containing exon 4 preferentially binds to the 3′ untranslated region of PXN mRNA, protects PXN mRNA from microRNA-24–AGO2 complex-induced degradation, and thereby increases PXN expression. Through inducing exon 4 inclusion, MBNL3 upregulates PXN, which mediates the pro-tumorigenic roles of MBNL3. Collectively, these data demonstrate detailed mechanistic links between an oncofetal splicing factor, a splicing event and tumorigenesis, and establish splicing factors and splicing events as potential therapeutic targets.

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Figure 1: MBNL3 expression is increased in HCC, and NANOG, OCT4 and SOX2 upregulate MBNL3 expression.
Figure 2: MBNL3 drives HCC tumorigenesis.
Figure 3: MBNL3 is required for tumorigenesis of HCC cells.
Figure 4: MBNL3 induces transcriptomic change and alternative splicing of lncRNA-PXN-AS1.
Figure 5: PXN-AS1-L and PXN-AS1-S have different effects on PXN mRNA stability.
Figure 6: PXN-AS1-L and PXN-AS1-S have different effects on PXN mRNA translation.
Figure 7: PXN-AS1-L and PXN-AS1-S have opposing effects on tumorigenesis of HCC cells.
Figure 8: The correlation between MBNL3 expression, lncRNA-PXN-AS1 splicing, and PXN expression in HCC tissues.

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Acknowledgements

We thank T. A. Cooper from Baylor College of Medicine, USA, for the gift of the RG6 minigene. This work was supported by grants from the National Key Basic Research Program (973 project) (2015CB554004) from the Ministry of Science and Technology of China, the National Natural Science Foundation of China (Grant No. 81572792, 81330037, 81372240, and 81171937), the Shanghai Sailing Program (15YF1400100), and the Natural Science Foundation of Shanghai (15XD1504500 and 14JC1407800).

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Authors

Contributions

S.-h.S., J.-h.Y. and F.W. designed the experiments. J.-h.Y., X.-n.L., T.-t.W. and W.P. performed the experiments. J.-h.Y., F.W., X.-n.L., T.-t.W., W.P. and Q.-f.T. analysed the data. W.-p.Z. and Q.-f.T. provided clinical specimens. J.-h.Y. wrote the manuscript. S.-h.S. supervised the project and helped with the writing of the manuscript. All authors discussed the results and commented on the manuscript.

Corresponding authors

Correspondence to Fang Wang or Shu-han Sun.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 MBNL3 expression is increased in HCC, and NANOG, OCT4, and SOX2 upregulate MBNL3 expression.

(a) Mbnl3 expression levels during mouse liver development from GSE13149 data. (b) Mbnl3 expression levels during mouse liver development from GSE21224 data. (c) MBNL3 expression levels in human HCC tissues (n = 268 independent samples) and noncancerous hepatic tissues (n = 243 independent samples) from GSE25097 data. P < 0.0001 by Mann–Whitney test. (d) MBNL3 expression levels in human HCC tissues (n = 247 independent samples) and noncancerous hepatic tissues (n = 239 independent samples) from GSE14520 data. P < 0.0001 by Mann–Whitney test. For c and d, the horizontal lines in the box plots represent the medians, the boxes represent the interquartile range, and the whiskers represent the minimum and maximum values. (e) The representative images of MBNL3 IHC staining in HCC tissues and noncancerous hepatic tissues. Scale bar, 50 μm. (f) Western blot analysis of MBNL3 expression in human immortalized, nontransformed liver cell line (QSG-7701), HCC cell lines (SMMC-7721, HCCLM3, MHCC97H, Huh7 and Hep3B), and hepatoblastoma cell line (HepG2). (g) Western blot analysis of NANOG, OCT4, and SOX2 expression in SMMC-7721 cells overexpressing NANOG, OCT4, and SOX2. (h) Western blot analysis of NANOG, OCT4, and SOX2 expression in NANOG, OCT4, and SOX2 depleted SMMC-7721 cells. (i) Western blot analysis of NANOG, OCT4, and SOX2 expression in human immortalized, nontransformed liver cell line (QSG-7701), HCC cell lines (SMMC-7721, HCCLM3, and Huh7), and hepatoblastoma cell line (HepG2). (j) Schematic outlining the predicted binding sites for NANOG, OCT4, and SOX2 in the MBNL3 promoter. (k) ChIP assays in SMMC-7721 cells using anti-NANOG, anti-OCT4, anti-SOX2, or nonspecific IgG. Enrichment was determined relative to input controls. Site N was used as negative control with no binding sites for NANOG, OCT4, and SOX2. Data are mean ± s.d. of n = 3 independent experiments. P < 0.05, P < 0.01, P < 0.001 by Student’s t-test. Source data are available in Supplementary Table 8. Uncropped images of blots are shown in Supplementary Fig. 9.

Supplementary Figure 2 MBNL3 drives HCC tumorigenesis and is required for HCC tumorigenesis.

(ab) Tumors generated by subcutaneous injection with MBNL3 stably overexpressed SMMC-7721 cells into nude mice were stained for Ki67 (a) or TUNEL (b). n = 5 independent samples. Scale bars, 50 μm. (c,d) Tumors generated by subcutaneous injection with MBNL3 stably overexpressed QSG-7701 cells into nude mice were stained for Ki67 (c) or TUNEL (d). n = 4 independent samples. Scale bars, 50 μm. For ad, data are mean ± s.d. P < 0.05, P < 0.01 by Mann–Whitney test. (e) Representative hematoxylin and eosin-stained images of liver tissues isolated from the mice at 28 day after intrasplenic injection with indicated SMMC-7721 cells. Scale bars, 500 μm. (f) The mRNA and protein levels of MBNL3 in MBNL3 stably silenced Huh7 cells. (g,h) Cell proliferations were measured using CCK-8 assays (g) or EdU immunofluorescence staining (h) in MBNL3 stably silenced Huh7 cells. Scale bars, 100 μm. (i) Colony formation assays of MBNL3 stably silenced Huh7 cells. Scale bars, 5 mm. (j) Cell apoptosis was detected by TUNEL staining in MBNL3 stably silenced Huh7 cells. Scale bars, 100 μm. For fj, data are mean ± s.d. of n = 3 independent experiments. P < 0.05, P < 0.01, P < 0.001 by Student’s t-test. (k) Western blot analysis of apoptosis markers in MBNL3 stably silenced Huh7 cells. (l) Effects of MBNL3 knockdown in SMMC-7721 cells on subcutaneous tumor growth. Image of mice 28 days after injection is shown. (m) Effects of another independent shRNA knockdown of MBNL3 in SMMC-7721 cells on subcutaneous tumor growth. Image of mice 35 days after injection is shown. (n) Effects of MBNL3 knockdown in Huh7 cells on subcutaneous tumor growth. Images of mice and tumors 28 days after injection are shown. Scale bars, 1 cm. (o) Representative hematoxylin and eosin-stained images of liver tissues isolated from the mice 28 days after intrasplenic injection with indicated SMMC-7721 cells. Scale bars, 500 μm. Source data are available in Supplementary Table 8. Uncropped images of blots are shown in Supplementary Fig. 9.

Supplementary Figure 3 Depletion of MBNL3 inhibits HCC cells growth in vitro and in vivo.

(ad) The protein levels of MBNL3 in MBNL3 stably depleted MHCC97H (a), HCCLM3 (b), HepG2 (c), or Hep3B (d) cells. (eh) Cell proliferations were measured using CCK-8 assays in MBNL3 stably depleted MHCC97H (e), HCCLM3 (f), HepG2 (g), or Hep3B (h) cells. (il) Cell proliferations were assessed using EdU immunofluorescence staining in MBNL3 stably depleted MHCC97H (i), HCCLM3 (j), HepG2 (k), or Hep3B (l) cells. Scale bars, 100 μm. (m-p) Cell apoptosis was detected by TUNEL staining in MBNL3 stably depleted MHCC97H (m), HCCLM3 (n), HepG2 (o), or Hep3B (p) cells. Scale bars, 100 μm. For e-p, data are mean ± s.d. of n = 3 independent experiments. P < 0.05, P < 0.01, P < 0.001 by Student’s t-test. (qx) Effects of MBNL3 depletion on MHCC97H (qu), HCCLM3 (rv), HepG2 (sw), or Hep3B (tx) cells subcutaneous tumor growth. Tumor volumes were measured every 7 days (qt). The mice were killed at 28 day after injection, and the tumors were excised and weighed (ux). Data are mean ± s.d., n = 8 mice in each group for MHCC97H and HCCLM3 cells, n = 7 mice in each group for HepG2 and Hep3B cells, P < 0.05, P < 0.01, P < 0.001 by Mann–Whitney test.

Supplementary Figure 4 MBNL3 induced alternative splicing of lncRNA-PXN-AS1.

(a) GSEA of gene signatures reported to be associated with poor or good survival in MBNL3 shRNA-2 stably transduced SMMC-7721 cells versus control cells. NES, normalized enrichment score. (b) Inclusion of exon 4 was examined in MBNL1 or MBNL2 overexpressed SMMC-7721 cells by RT-PCR. (c) LncRNA-PXN-AS1 isoforms expression levels was examined in SMMC-7721 cells overexpressing MBNL1 or MBNL2 by real-time qPCR. (d) A schematic showing PXN-AS1 minigene containing exon 4, 250bp of its upstream intron 3, and 302bp of its downstream intron 4. (e) The insert sequence of pre-lncRNA-PXN-AS1. The underlined sequences are exon 4. The previous reported putative MBNL3 binding motif YGCY were highlighted in red. (fg) RT-PCR analysis of PXN-AS1 minigene coexpressed with MBNL3 expressing plasmid (f) or MBNL3 shRNA (g). (h) Binding of MBNL3 with pre-lncRNA-PXN-AS1 was detected by CLIP assays in SMMC-7721 cells exogenously expressing PXN-AS1 minigene with primer pairs complementary to MBNL3 intron 3, exon 4, intron 4, or S100A4 by real-time qPCR. (i) RT-PCR analysis of the effects of MBNL3 overexpression on wild type PXN-AS1 minigene (PXN-AS1-wt), PXN-AS1 minigene with mutation of the predicated MBNL3 binding sites in intron 3, exon 4, or intron 4. (j) Inclusion of exon 4 was examined in human fetal livers and adult livers by RT-PCR. (k) Inclusion of exon 4 was examined in human nontransformed liver cell line and HCC cell lines by RT-PCR. For b,c, and fk, data are mean ± s.d. of n = 3 independent experiments. P < 0.05, P < 0.01 by Student’s t-test. Source data are available in Supplementary Table 8. Uncropped images of gels are shown in Supplementary Fig. 9.

Supplementary Figure 5 Characterization of lncRNA-PXN-AS1 and the different effects of lncRNA-PXN-AS1 isoforms on PXN.

(a) Left; representative images of PCR products from the 5′-RACE or 3′-RACE procedure. The major PCR product is marked by an arrow. Right; sequencing of PCR products revealed the boundary of lncRNA-PXN-AS1 sequences. (b) The nucleotide sequence of full-length PXN-AS1-L and PXN-AS1-S. (c) The levels of PXN-AS1-L and PXN-AS1-S in purified polyadenylated RNAs. β-actin and U6 serve as poly (A) positive and negative control, respectively. (d) The levels of PXN-AS1-L and PXN-AS1-S in purified cytoplasmic or nuclear RNAs. β-actin and U6 serve as cytoplasmic and nuclear control, respectively. (e) Confocal RNA FISH images showed cytoplasmic localization of lncRNA-PXN-AS1. Scale bars, 10 μm. The probe detects both PXN-AS1-L and PXN-AS1-S. (f) PXN protein levels in PXN-AS1-L or PXN-AS1-S overexpressed QSG-7701 cells. (g) AMT crosslinking followed by proximity ligation of interacting RNA and sequencing confirmed the interactions between PXN-AS1-L exon 4 and PXN 3′UTR. (h) miR-24 expression in QSG-7701, SMMC-7721, HCCLM3, Huh7, and HepG2 cells. For c,d,h, data are mean ± s.d. of n = 3 independent experiments. P < 0.05, P < 0.01, P < 0.001 by Student’s t-test. (i) SMMC-7721 cell lysates were incubated with PXN full-length mRNA and biotin-labeled PXN-AS1-L, or PXN-AS1-L and biotin-labeled PXN full-length mRNA; after pull-down, bound proteins were extracted and assessed by western blot, and bound mRNAs were extracted and assessed by real-time qPCR. (j) Polysome profiles from SMMC-7721 cells incubated with harringtonine for 0 s (up) and 180 s (low) before harvest. The absorbance profile in 254 nm is outlined. (k,l) SMMC-7721 cells transiently expressing indicated transcripts of lncRNA-PXN-AS1 were incubated with harringtonine for 0 s and 180 s. Then polysomes in cytoplasmic extracts from these cells were fractionated through sucrose gradients, and the relative distributions of PXN (k) or β-actin (l) mRNAs in gradient fractions were measured by real-time qPCR, and polysomes fractions are shown as percentage of total RNA in the gradient. Source data are available in Supplementary Table 8. Uncropped images of gels and blots are shown in Supplementary Fig. 9.

Supplementary Figure 6 PXN modulates MCL1 and BIM expression, and promotes HCC tumorigenesis.

(a) PXN protein levels in SMMC-7721 cells stably overexpressing PXN. (b) Western blot analysis of MCL1 and BIM protein levels in SMMC-7721 cells stably overexpressing PXN. (cf) Western blot analysis of MCL1 and BIM protein levels in SMMC-7721 (c) or QSG-7701(d) cells stably overexpressing MBNL3, SMMC-7721 (e) or Huh7 (f) cells stably silencing MBNL3. (g) Cell proliferations were measured using CCK-8 assays in SMMC-7721 cells stably overexpressing PXN. (h) Cell proliferations were assessed using EdU immunofluorescence staining in SMMC-7721 cells stably overexpressing PXN. Scale bars, 100 μm. (i) Colony formation assays of SMMC-7721 cells stably overexpressing PXN. Scale bars, 5 mm. (j) Cell apoptosis was detected by TUNEL staining in SMMC-7721 cells stably overexpressing PXN. Scale bars, 100 μm. For g,j, data are mean ± s.d. of n = 3 independent experiments P < 0.05, P < 0.01 by Student’s t-test. (k) Western blot analysis of apoptosis markers in SMMC-7721 cells stably overexpressing PXN. (l,n) Effects of PXN overexpression in SMMC-7721 cells on subcutaneous tumor growth. Tumor volumes were measured every 7 days (l). The mice were killed 21 days after injection, and the tumors were excised and weighed (m,n). Scale bars, 1 cm. Data are mean ± s.d. of n = 10 mice in each group, P < 0.01 by Mann–Whitney test. Source data are available in Supplementary Table 8. Uncropped images of blots are shown in Supplementary Fig. 9.

Supplementary Figure 7 The biologic effects of MBNL3 on HCC cells tumorigenesis are partially medicated by AS of lncRNA-PXN-AS1.

(a) SMMC-7721 cells with stable coexpression of shMBNL3 and PXN-AS1-L were generated. PXN-AS1-L expression levels in indicated cells were confirmed by real-time qPCR. (b) PXN protein levels in indicated SMMC-7721 cells. (c,d) Cell proliferations were measured using CCK-8 assays (c) or EdU immunofluorescence staining (d) in indicated cells. Scale bars, 100 μm. (e) Cell apoptosis was detected by TUNEL staining in indicated cells. Scale bars, 100 μm. (f) Western blot analysis of apoptosis markers in indicated cells. (g,h) PXN-AS1-L partially rescues the effects of MBNL3 depletion on subcutaneous tumor growth. Tumor volumes were measured every 7 days (g). The mice were killed 28 days after injection, and the tumors were excised and weighed (h). Scale bars, 1 cm. (i) SMMC-7721 cells with stable coexpression of MBNL3 and PXN-AS1-S were generated. PXN-AS1-S expression levels in indicated cells were confirmed by real-time qPCR analysis. (j) PXN protein levels in indicated SMMC-7721 cells. (k,l) Cell proliferations were measured using CCK-8 assays (k) or EdU immunofluorescence staining (l) in indicated cells. Scale bars, 100 μm. (m) Cell apoptosis was detected by TUNEL staining in indicated cells. Scale bars, 100 μm. (n) Western blot analysis of apoptosis markers in indicated cells. (o,p) PXN-AS1-S partially rescues the effects of MBNL3 overexpression on subcutaneous tumor growth. Tumor volumes were measured every 7 days (o). The mice were killed 28 days after injection, and the tumors were excised and weighed (p). Scale bars, 1 cm. For a,ce,i and k-m data are mean ± s.d. of n = 3 independent experiments P < 0.05, P < 0.01, P < 0.001 by Student’s t-test. For g,h,o,p, data are mean ± s.d. of n = 8 mice in each group for g,h, and n = 7 mice in each group for o,p P < 0.05, P < 0.01,P < 0.001 by Mann–Whitney test. Source data are available in Supplementary Table 8. Uncropped images of blots are shown in Supplementary Fig. 9.

Supplementary Figure 8 Depletion of PXN abolishes the biological effects of MBNL3 overexpression.

(a) SMMC-7721 cells with stable coexpression of MBNL3/shPXN or controls were generated. The protein levels of PXN in indicated cells were confirmed by western blot. (b) Cell proliferations were measured using CCK-8 assays in indicated SMMC-7721 cells. (c) Cell proliferations were assessed using EdU immunofluorescence staining in indicated SMMC-7721 cells. Scale bars, 100 μm. (d) Colony formation assays of indicated SMMC-7721 cells. Scale bars, 5 mm. (e) Cell apoptosis was detected by TUNEL staining in indicated SMMC-7721 cells. Scale bars, 100 μm. For be, data are mean ± s.d. of n = 3 independent experiments P < 0.05, P < 0.01, P < 0.001 by Student’s t-test. (f) Western blot analysis of apoptosis markers in indicated SMMC-7721 cells. (gi) Depletion of PXN abolishes the effects of MBNL3 overexpression on subcutaneous tumor growth. Tumor volumes were measured every 7 days (g). The mice were killed at 21 day after injection, and the tumors were excised and weighed (hi). Scale bars, 1 cm. Data are mean ± s.d. of n = 8 mice in each group P < 0.001 by Mann–Whitney test. Source data are available in Supplementary Table 8. Uncropped images of blots are shown in Supplementary Fig. 9.

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Yuan, Jh., Liu, Xn., Wang, Tt. et al. The MBNL3 splicing factor promotes hepatocellular carcinoma by increasing PXN expression through the alternative splicing of lncRNA-PXN-AS1. Nat Cell Biol 19, 820–832 (2017). https://doi.org/10.1038/ncb3538

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