Wiping DNA Methylation: Wip1 Regulates Genomic Fluidity on Cancer
Authors: Martin Muñoz-Lopez, Pedro P. Medina, Jose L. Garcia-Perez
Journal: Cancer Cell (2013)

Wip1 phosphatase plays an important role in cancer by inactivating p53 and INK4a/ARF pathways. In this issue of Cancer Cell, Filipponi and colleagues further connect the oncogenic role of Wip1 with heterochromatin dynamics, transposable element expression, and a mutation-prone environment that may enhance heterogeneity and ultimately contribute to tumor evolution. Wip1 phosphatase plays an important role in cancer by inactivating p53 and INK4a/ARF pathways. In this issue of Cancer Cell, Filipponi and colleagues further connect the oncogenic role of Wip1 with heterochromatin dynamics, transposable element expression, and a mutation-prone environment that may enhance heterogeneity and ultimately contribute to tumor evolution. The protein phosphatase Mg/Mn dependent 1D (PPM1D), also known as wild-type p53-induced phosphatase 1 (Wip1), plays an important role in cancer by promoting the termination of the DNA damage response pathway and cell cycle progression. In concordance with this oncogenic activity, Wip1/PPM1D is often overexpressed in breast tumors and other types of human tumors. In this issue of Cancer Cell, Filipponi et al., 2013Filipponi D. Muller J. Emelyanov A. Bulavin D.V. Cancer Cell. 2013; 24 (this issue): 528-541Abstract Full Text Full Text PDF PubMed Scopus (50) Google Scholar reveal a new role for Wip1: connecting heterochromatin dynamics, transposable element (TE) expression, and, ultimately, genomic fluidity in cancer. TE-derived sequences comprise more than half of the human genome, and the activity of currently active TEs continues to generate genomic fluidity in our genome (Beck et al., 2011Beck C.R. Garcia-Perez J.L. Badge R.M. Moran J.V. Annu. Rev. Genomics Hum. Genet. 2011; 12: 187-215Crossref PubMed Scopus (371) Google Scholar). In the human genome, long interspersed element class-1 (LINE-1 or L1) is the only active autonomous TE. LINE-1s comprise 20% of the human genome, although only 80–100 L1s remain retrotranspositionally active (Beck et al., 2011Beck C.R. Garcia-Perez J.L. Badge R.M. Moran J.V. Annu. Rev. Genomics Hum. Genet. 2011; 12: 187-215Crossref PubMed Scopus (371) Google Scholar). Additionally, two nonautonomous retrotransposons, Alu and SVA (comprising 10% and <1% of our genome, respectively), can mediate their mobilization using the LINE-1-encoded enzymatic machinery (reviewed in Beck et al., 2011Beck C.R. Garcia-Perez J.L. Badge R.M. Moran J.V. Annu. Rev. Genomics Hum. Genet. 2011; 12: 187-215Crossref PubMed Scopus (371) Google Scholar). These three non-LTR retrotransposons move in our genome by a “copy and paste” mechanism using an intermediate RNA. Active LINE-1 s are 6-kb-long elements containing a 5′ untranslated region (UTR) with internal promoter activity, two ORFs encoding protein products required for retrotransposition, and end in a short 3′UTR with a poly(A) tail. As “mobile” DNA, new LINE-1 insertions can be mutagenic by a myriad of mechanisms, leading to gene inactivation and/or gene deregulation processes. Thus, the host has evolved multiple mechanisms aimed to reduce the mutagenic load generated by LINE-1 s. Controlling LINE-1 transcription is the most effective manner to control TE activity, because it will abolish mobilization of not only LINE-1, but also Alu and SVA. Notably, the 5′UTR of mammalian LINE-1 s contains a canonical CpG island that serves to regulate its expression by DNA-methylation (Yoder et al., 1997Yoder J.A. Walsh C.P. Bestor T.H. Trends Genet. 1997; 13: 335-340Abstract Full Text PDF PubMed Scopus (1512) Google Scholar). Somatic tissues and germ cells efficiently silence LINE-1 expression by DNA methylation, avoiding accumulation of LINE-1 insertions. However, the LINE-1 promoter is hypomethylated during embryogenesis (leading to the accumulation of new LINE-1 s that will be transmitted to newborns) and in several types of tumors. Indeed, recent studies have demonstrated that selected TEs are active in lung, colorectal, prostate, ovarian, myeloma, glioblastoma, and hepatic tumors (Iskow et al., 2010Iskow R.C. McCabe M.T. Mills R.E. Torene S. Pittard W.S. Neuwald A.F. Van Meir E.G. Vertino P.M. Devine S.E. Cell. 2010; 141: 1253-1261Abstract Full Text Full Text PDF PubMed Scopus (424) Google Scholar, Lee et al., 2012Lee E. Iskow R. Yang L. Gokcumen O. Haseley P. Luquette 3rd, L.J. Lohr J.G. Harris C.C. Ding L. Wilson R.K. et al.Cancer Genome Atlas Research NetworkScience. 2012; 337: 967-971Crossref PubMed Scopus (511) Google Scholar, Shukla et al., 2013Shukla R. Upton K.R. Muñoz-Lopez M. Gerhardt D.J. Fisher M.E. Nguyen T. Brennan P.M. Baillie J.K. Collino A. Ghisletti S. et al.Cell. 2013; 153: 101-111Abstract Full Text Full Text PDF PubMed Scopus (273) Google Scholar, Solyom et al., 2012Solyom S. Ewing A.D. Rahrmann E.P. Doucet T. Nelson H.H. Burns M.B. Harris R.S. Sigmon D.F. Casella A. Erlanger B. et al.Genome Res. 2012; 22: 2328-2338Crossref PubMed Scopus (191) Google Scholar). These data indicate that, on top of other forms of cellular stress, cancer cells can be impacted by potentially mutagenic new TE insertions. DNA damage response (DDR) is often deregulated in cancer, leading to genomic instability. Wip1 is a DDR regulator in the germline. Additionally, the Wip1/PPM1D gene is often amplified in human cancers, whereas genomic depletion in mouse models suggests that Wip1 may act as a tumor regulator. Interestingly, Filipponi et al., 2013Filipponi D. Muller J. Emelyanov A. Bulavin D.V. Cancer Cell. 2013; 24 (this issue): 528-541Abstract Full Text Full Text PDF PubMed Scopus (50) Google Scholar now demonstrate that Wip1 maintains the epigenetic homeostasis of TEs associated to heterochromatin (including active LINE-1s), providing a mechanistic link between DNA-methylation and LINE-1 expression in the germline and in cancer. In a mouse knockout (KO) model for Wip1, Filipponi et al., 2013Filipponi D. Muller J. Emelyanov A. Bulavin D.V. Cancer Cell. 2013; 24 (this issue): 528-541Abstract Full Text Full Text PDF PubMed Scopus (50) Google Scholar confirmed that Wip1 deletion results in attenuated spermatogenesis. Surprisingly, Wip1 deletion also results in increases of heterochromatin centers in germ cells and a concomitant reduction in the expression levels of LINE-1 and intracisternal A-type particle endogenous retrovirus mRNAs. Whether fewer TE insertions accumulate in these mice remains to be determined. Importantly, Wip1 might be the first positive regulator of LINE-1 expression and retrotransposition. Further experiments revealed that depletion of Wip1 in human cancer cell lines results in increased levels of repressive histone marks on LINE-1 promoters and reduced levels of expression. Furthermore, depletion of Wip1 in human cancer and mouse germ cells led to reduced DNA-methylation levels in LINE-1 (and endogenous retroviruses) promoters. Consistently, increased LINE-1 mRNA expression levels (and reciprocal changes in histone marks and DNA methylation) were detected upon Wip1 overexpression in cancer cells. Altogether, these data indicate that Wip1 participates in controlling the homeostasis of TE epigenetic regulation. Consistent with previous reports, Filipponi et al., 2013Filipponi D. Muller J. Emelyanov A. Bulavin D.V. Cancer Cell. 2013; 24 (this issue): 528-541Abstract Full Text Full Text PDF PubMed Scopus (50) Google Scholar confirmed that the ATM-dependent signaling pathway is constitutively activated upon Wip1/PPM1D deletion, resulting in the activation of the downstream effector BRCA1. Additional data demonstrates that BRCA1 interacts with the DNA methyltransferase DNMT3B through HP1 binding, forming a BRCA1-HP1-DNMT3B complex that modulates the LINE-1 promoter DNA-methylation (Figure 1). These data strongly suggest that BRCA-1 is involved in DNA-methylation in an ATM-dependent manner. In the germline, depletion of the DNMT3L results in global reduction of retrotransposon DNA methylation and significant increases in retrotransposon mRNA levels (Bourc’his and Bestor, 2004Bourc’his D. Bestor T.H. Nature. 2004; 431: 96-99Crossref PubMed Scopus (891) Google Scholar). It has been suggested that meiotic failure of DNMT3L-KO mice is a result of retrotransposons overexpression and deregulated retrotransposition. Thus, it is likely that a balance between BRCA1-HP1-DNMT3B and DNMT3L complexes on TE DNA methylation allows normal meiosis to succeed in germ cells, regulating a physiological level of TE expression and retrotransposition. Furthermore, elegant genetic experiments demonstrate that defects in spermatogenesis in Wip1-KO mice can be rescued by the deletion of a single ATM allele, suggesting that ATM is required to establish DNA methylation upon Wip1/PPM1D depletion. Interestingly, previous studies have demonstrated that ATM depletion results in increased levels of engineered LINE-1 retrotransposition in a mouse model and human cell lines (primary and transformed) (Coufal et al., 2011Coufal N.G. Garcia-Perez J.L. Peng G.E. Marchetto M.C. Muotri A.R. Mu Y. Carson C.T. Macia A. Moran J.V. Gage F.H. Proc. Natl. Acad. Sci. USA. 2011; 108: 20382-20387Crossref PubMed Scopus (175) Google Scholar). These data reveal that there is complex regulation of LINE-1 expression and retrotransposition involving ATM-signaling and Wip1 pathways (Figure 1). In human cancer cell lines, Wip1 overexpression correlate with increased levels of LINE-1 mRNAs, including mRNA derived from potentially active elements. Filipponi et al., 2013Filipponi D. Muller J. Emelyanov A. Bulavin D.V. Cancer Cell. 2013; 24 (this issue): 528-541Abstract Full Text Full Text PDF PubMed Scopus (50) Google Scholar further examined whether alterations in Wip1/PPM1D expression, heterochromatin dynamics, and DNA methylation correlate with genomic fluidity observed in breast cancer samples. Indeed, cytidine deaminases are involved in generating point mutations in an epigenetically dependent manner. Activation-induced cytidine deaminase (AID) removes the amino group from a cytosine base and turns it into uracil (which is recognized as a thymine). This deamination may lead to mutation if not corrected by DNA repair. Notably, AID is enriched in TE sequences in a Wip1-dependent manner. Consistent with this, breast cancer samples with an increased copy number of Wip1/PPM1D contain more C-to-T mutations, likely mediated by differential AID binding in a Wip1-dependent manner (Figure 1). Additionally, the accumulation of the AID mutations is also favored, because Wip1 overexpression inhibits base excision repair. Interestingly, a strong correlation was observed between the expression level of the APOBEC3B cytidine deaminase, AID, Wip1, and overall C-to-T substitution load. APOBEC3B has been recently shown to generate genomic editing in cancer genomes (Burns et al., 2013Burns M.B. Lackey L. Carpenter M.A. Rathore A. Land A.M. Leonard B. Refsland E.W. Kotandeniya D. Tretyakova N. Nikas J.B. et al.Nature. 2013; 494: 366-370Crossref PubMed Scopus (592) Google Scholar), consistent with the findings reported by Filipponi et al., 2013Filipponi D. Muller J. Emelyanov A. Bulavin D.V. Cancer Cell. 2013; 24 (this issue): 528-541Abstract Full Text Full Text PDF PubMed Scopus (50) Google Scholar. Intriguingly, several APOBEC cytidine deaminases are known to efficiently inhibit LINE-1-engineered and Alu-engineered retrotransposition by an elusive mechanism (Beck et al., 2011Beck C.R. Garcia-Perez J.L. Badge R.M. Moran J.V. Annu. Rev. Genomics Hum. Genet. 2011; 12: 187-215Crossref PubMed Scopus (371) Google Scholar). Thus, it is tempting to speculate that a balance between AID, APOBECs, and Wip1 might regulate the load of somatic retrotransposition observed in different human cancers. Future experiments are required to determine to what extent Wip1 modulate the somatic load of LINE-1 retrotransposition in cancer. In conclusion, DNA hypomethylation in Wip1/PPM1D-overexpressing tumors may promote genomic fluidity by the accumulation of mutations induced by TE transposition and AID deamination (Figure 1). These data also reveal how the regulation and the impact of retrotransposition in cancer development might be more complex than previously anticipated. We thank Dr. Sara R. Heras (GENYO) for helpful discussions and critically reading the manuscript. M.M.-L. is supported by PeS-FEDER-PI-0224-2011. P.P.M.’s work is funded by PeS-FEDER-PI-0903-2012, the Ministry of Economy (SAF-2012-37252), EU-MarieCurie (CIG-321926), CEI-BIOTIC (20F12.6), and Deutsche José Carreras Leukämie-Stiftung. J.L.G.-P. is supported by CICE-FEDER-P09-CTS-4980, FIS-FEDER-PI11/01489, the Howard Hughes Medical Institute (IECS-55007420), and the European Research Council (ERC Consolidator Grant EPIPLURIRETRO-309433). We apologize to the colleagues whose work could not be cited. Wip1 Controls Global Heterochromatin Silencing via ATM/BRCA1-Dependent DNA MethylationFilipponi et al.Cancer CellOctober 14, 2013In BriefWip1 phosphatase is emerging as an important regulator of tumorigenesis, but no unifying mechanistic network has been proposed. We found that Wip1 plays a key role in the transcriptional regulation of heterochromatin-associated DNA sequences. Wip1 was required for epigenetic remodeling of repetitive DNA elements through regulation of BRCA1 interaction with HP1, the recruitment of DNA methyltransferases, and subsequent DNA methylation. Attenuation of ATM, in turn, reversed heterochromatin methylation. Full-Text PDF Open Archive