Abstract
Hematopoietic malignancies, including multiple myeloma, are associated with characteristic mutations and genetic instabilities that drive malignant transformation. On the other hand, tumor formation is also associated with drastic epigenetic aberrations, which can impact the genetic sequence. Therefore, the question arises if malignant transformation is primarily caused by genetic or epigenetic events. The tight connection of these processes becomes obvious by the fact that in several malignancies, as well as in age-related clonal hematopoiesis, mutations are particularly observed in epigenetic writers such as DNMT3A and TET2. On the other hand, specific epigenetic aberrations, so-called “epimutations,” can mimic genomic mutations. In contrast to the genetic sequence, which remains relatively stable throughout life, the epigenome notoriously undergoes drastic changes in normal hematopoietic development and aging. It is conceivable that such epigenetic reorganization, e.g., in 3D chromatin conformation, paves the way for secondary chromosomal instabilities, which then result in tumor-specific genomic changes that further trigger disease progression. This scenario might explain the occurrence of tumor-specific mutations particularly in the elderly. Taken together, the causality dilemma is difficult to solve because genetic and epigenetic aberrations are interlinked during disease development. A better understanding of how the chromatin structure or 3D nuclear organization can evoke specific mutations might provide new perspectives for prevention, early diagnostics, and targeted therapy.
Malignancies Are Caused by Genomic Aberrations
Genomic instabilities are a hallmark of cancer (Negrini et al., 2010). Already more than a century ago the causal relationship of chromosomal aberrations and dysfunctional mitosis was suggested (; ), and such research gained significant momentum within the last 20 years with the advent of sequencing technology. For example, in multiple myeloma the relevant genomic aberrations include site-specific mutations, translocations, and gains or losses of parts or whole chromosomes (Morgan et al., 2012; Robiou du Pont et al., 2017). Some of these aberrations have been shown to be of prognostic relevance, such as deletion in 17p13, translocations between chromosome 4 and chromosome 14, or insertions in 1q21, which are rather associated with worse outcome (; Neben et al., 2013).
So far, the reasons for the initial genomic instabilities are largely unclear, but it is generally assumed that they simply arise in a stochastic manner. Some passenger mutations may have neutral effects, while others clearly give rise to proliferative advantage, thereby further increasing the risk of malignant transition (). This process can be accelerated by dysfunctional DNA repair systems as well as impaired chromosome duplication and segregation during mitosis (; Vargas-Rondon et al., 2017). Furthermore, inhibition of DNA damage response pathway allows cells to proliferate beyond senescence (). Improper chromosome segregation can be caused by telomere shortening, and this may result in chromosome breaks or fusions (; ). There is evidence that the order of genomic events is relevant for tumor progression: Initial chromosome translocations can lead to secondary mutations in genes for DNA replication, repair, or genomic stability, which drastically increase occurrence of tertiary genetic aberrations during further development of the disease (Morgan et al., 2012; van Nieuwenhuijzen et al., 2018). In breast cancer, breast cancer 1 (BRCA1) mutations often occur after tumor protein 53 (TP53) mutations (Martins et al., 2012), because an initial BRCA1 mutation leads to a cell cycle arrest, which is not in favor of tumor progression (). Similarly, the clinical image of myeloproliferative neoplasms was demonstrated to be dependent on the mutation order of ten-eleven translocation 2 (TET2) versus janus kinase 2 (JAK2): A JAK2 initial mutation increased the likelihood of presenting with polycythemia vera (as compared to essential thrombocythemia), with an increased risk of thrombosis and an increased sensitivity of JAK2-mutant progenitors to ruxolitinib in vitro (Ortmann et al., 2015). Taken together, genetic alterations, particularly the mutation order, directly impact the regulation of proliferation, apoptosis, and malignant transformation.
Epigenetic Alterations in Cancer and Clonal Hematopoiesis
In contrast to genomic changes, epigenetic aberrations do not involve alterations in the DNA sequence. Dynamic modification of DNA and DNA binding proteins plays a crucial role in the regulation of gene expression, chromatin accessibility, and nuclear architecture (; ; ). Epigenetic marks comprise, for example, DNA methylation and posttranslational modifications of the N-terminal histone tails, such as acetylation, methylation, ubiquitylation, sumoylation, and phosphorylation (). DNA methylation usually occurs at the fifth carbon atom of a cytosine, particularly in the context of cytosine-guanine (CG) dinucleotides, also referred to as a “CpG site” (). This process is mediated by DNA methyltransferases (DNMTs), which either maintain existing methylation patterns upon replication (e.g., DNMT1) or create de novo patterns (e.g., DNMT3A and DNMT3B) (Okano et al., 1999; Schermelleh et al., 2007). On the other hand, DNA methylation marks can be indirectly removed by TET enzymes, which oxidize 5-methylcytosine into 5-hydroxymethylcytosine. This modification is then either passively depleted upon DNA replication or actively reverted to cytosine by iterative oxidation and thymine DNA glycosylase (TDG)-mediated base excision repair ().
Cancer cells often reveal genome-wide hypomethylation, which may result from mutations in DNMTs or TETs (; Russler-Germain et al., 2014). At the same time, tumor-suppressor genes can be silenced by site-specific hypermethylation at promoter regions (). For example, hypermethylation in TP53, cyclin-dependent kinase 4 inhibitor B (CDKN2B), glutathione peroxidase 3 (GPX3), retinol binding protein 1 (RBP1), secreted protein acidic and cysteine rich (SPARC), and transforming growth factor beta induced (TGFBI) was shown to be associated with the transition from the pre-leukemic phase monoclonal gammopathy of undetermined significance (MGUS) to multiple myeloma (; ). Furthermore, hypermethylation in multiple myeloma was shown to be enriched in intronic regions associated with B-cell specific enhancer regions ().
So-called “epimutations” resemble specific epigenetic aberrations that mimic genomic mutations, albeit there is no change in the nucleotide sequence. It has been suggested that such epimutations can contribute in a similar way to malignant transformation as genetic mutations (Peltomaki, 2012; ). We have previously demonstrated that acute myeloid leukemia (AML) patients frequently display aberrant hypermethylation in DNMT3A, which is rather mutually exclusive with genomic mutations in this gene (). Mutations as well as epimutations in DNMT3A seem to be associated with poor prognosis in AML (). Both modifications, mutations and epimutations, may affect alternative splicing of DNMT3A (), which is important, because the distinct DNMT3A variants have different effects on the DNA methylation pattern (). In a recent study, we have demonstrated that knockdown and overexpression of specific transcripts of DNMT3A has complementary effects on the DNA methylation pattern, gene expression, and differentiation of hematopoietic progenitor cells—thus, alternative splicing of DNMT3A has characteristic epigenetic and functional effects ().
Clonal hematopoiesis of indeterminate potential (CHIP) is frequently observed in healthy elderly individuals () and may progress into myeloid and lymphoid malignancies (; The Cancer Genome Atlas Research Network, 2013). Notably, the mutations that predominantly occur in clonal hematopoiesis are located in the genes DNMT3A and TET2 (; Xie et al., 2014). These two genes resemble more than 90% of all mutated genes in CHIP (). Overall, mutations in DNMT3A are most frequent, whereas TET2 mutations arise predominantly in older individuals (). Furthermore, mutations in DNMT3A and TET2 are frequently observed in AML () and to a lesser degree also in multiple myeloma (). These findings support the notion that modulation of DNA methylation patterns plays a central role in initiation of clonal outgrowth and that mutations in epigenetic writers are early key events in the pathogenesis of hematopoietic malignancies (; Shlush et al., 2014).
Usually, clones with mutated driver genes have a competitive advantage over their non-mutated counterparts (). In mice it has been demonstrated that hematopoietic stem cells (HSCs) with loss of Dnmt3a reveal enhanced self-renewal and repopulation potential, even after 12 rounds of transplantation, far exceeding that of normal HSCs (). Mutated HSCs may thus outcompete their native counterparts. While some studies report impaired hematopoiesis (; ), others did not find any significant impact on proliferation or cytopenic effects of either TET2 or DNMT3A mutations in CHIP and found only minor reductions in neutrophils upon TET2 mutation (). Compared to other driver mutations, DNMT3A and TET2 confer a lower risk of progression to AML, but additional mutations, as shown for example for Npm1 in mice, can drive CHIP to overt malignant transformation, and such genetic changes make diseases detectable years before diagnosis (; ). In general, a higher number of mutations and higher variant allele frequencies have a higher risk of AML progression (). Population dynamics studies in healthy individuals indicated that there are hundreds of thousands of stem cells in the body contributing to hematopoiesis, which divide every 2 to 20 months and on average gain 1.2 mutations per division (). Therefore, branching sub-clones would be expected over many years during clonal evolution of disease progression.
The relevance of epigenetic writers for clonal hematopoiesis and malignant transformation lays the ground for therapeutic regimen that directly impact the epigenetic landscape. Many novel treatment strategies have been developed for multiple myeloma in the past years (), and epigenetic regulators resemble promising targets due to the reversibility of epigenetic marks (). Particularly class I and II histone deacetylase (HDAC) inhibitors (such as Varionostat, Panobinostat, and Romidepsin) showed antitumor effects or induced apoptosis via the caspase proteolytic pathway (Mimura et al., 2015; ). Another promising epigenetic target is the histone methyltransferase enhancer of zeste homolog 2 (EZH2). Inhibition of EZH2 in multiple myeloma cells in vitro caused global reduction in H3K27me3 with an antitumor effect in a murine xenograft model (). DNA demethylating agents, such as 5-azacytidine, are less extensively studied in multiple myeloma as compared to AML. However, there is some evidence that a decrease in global DNA methylation has some anti-myeloma activity, particularly for therapy-resistant cells (; ), and some studies developed biomarkers to estimate the sensitivity of primary myeloma cells for DNMT inhibitors (Moreaux et al., 2012).
Epigenetic Modifications Can Elicit Genomic Instabilities
Heterochromatin, which is usually highly methylated to maintain its condensed structure, as well as lamina-associated domains, almost never contains actively transcribed genes (van Steensel and Belmont, 2017). The chromatin structure is tightly associated with DNA methylation, since specific enzymes that contain a methyl-CpG-binding domain (MBDs) are able to read CpG methylation and recruit chromatin remodelers, such as HDACs (). Global hypomethylation, which is observed in various types of cancer, may conversely result in loss of heterochromatin and thereby favor gene rearrangements or chromosomal translocations, due to more frequent homologous recombination events (Zhou and Robertson, 2016). Furthermore, global depletion of DNA methylation may affect binding of CCCTC-binding factor (CTCF), which regulates chromatin architecture by mediating distal chromosome interactions (Wang et al., 2012). Chromatin accessibility is additionally controlled by histone modifications (), and cancer cells particularly display a global loss of histone acetylation and overexpression of histone methyltransferases, such as EZH2 (; Sharma et al., 2010). Overexpression of EZH2 has been associated with aberrant mitosis and genetic instability in benign mammary epithelial cells and hinders DNA repair through impairment of RAD51 recombinase repair foci formation at sites of DNA breaks (Zeidler et al., 2005; ).
DNA methylation not only alters chromatin architecture but also influences genomic integrity by stabilizing transposable elements. Hypomethylation in cancer may therefore result in repeat element-directed recombination (Zhou and Robertson, 2016). Treatment of lung cell lines with 5-aza-2′-deoxycytidine activated the expression of retrotransposons, such as long interspersed nuclear element 1 (LINE-1) and Alu elements (). In addition, hypomethylation of CpG islands can activate nearby oncogenes (). On the other hand, focal hypermethylation can indirectly impact genomic stability by silencing of genes that are relevant for genomic integrity () or DNA repair (; Peng et al., 2006). For example, failure of O6-methylguanine repair, e.g., due to hypermethylation in the promotor of the O6-methylguanine-DNA methyltransferase (MGMT), results in conversion of G:C to A:T (). Last but not least, the cytosine methylation itself can act as an endogenous mutagen, because spontaneous deamination of 5-methylcytosine results in conversion to thymine facilitating point mutations, as observed for most hot-spot mutations in TP53 (Rideout et al., 1990). In fact, it was demonstrated that the occurrence of such methylation-induced point mutations largely differs between cancer types, probably because of varying efficiency of DNA repair mechanisms in those tissues (Sjoblom et al., 2006). Thus, epigenetic modifications play a crucial role for stabilizing genome integrity, and their dysregulation may facilitate genomic instability (Figure 1).
Figure 1
Do Age-Related Epigenetic Changes Trigger Tumorigenesis?
There is a growing perception that aging of the organism is reflected by drastic changes in the epigenetic makeup. Upon aging, there is a global loss of DNA methylation, especially at repetitive elements and transposons, which is also seen in cancer cells (). Nucleosome occupancy decreases with age (), and there is a general decrease in constitutive heterochromatin, which is reflected by a decline of the repressive histone mark H3K9me3 and heterochromatin protein 1 (HP1) (Stewart et al., 2005). Perhaps the most astonishing age-related epigenetic modification is the finding that a large proportion of CpG sites have highly reproducible DNA methylation changes (Weidner and Wagner, 2014). Age-associated DNA methylation changes can be observed across diverse cell types and tissues (). Due to the high reproducibility, age-associated DNA methylation changes can be used to reliably predict the donor age—known as the “epigenetic clock” (; ; Weidner et al., 2014). Notably, the rate of epigenetic aging has been linked to life expectancy, indicating that age-associated DNA methylation can also reflect biological aging (; ; Zhang et al., 2017). It is also striking that age-associated DNA methylation patterns are entirely reset upon reprogramming into induced pluripotent stem cells (; Weidner et al., 2014). However, when it comes to cancer tissue the age predictors fail. In most malignancies the epigenetic clocks are apparently accelerated, whereas they are decelerated in others (). This might be attributed to the fact that tumor tissue recapitulates the epigenetic makeup of the tumor initiating cell, whereas age prediction of healthy tissue is based on a cross section of many cells of the normally developing organism. In fact, there is evidence that age-associated DNA methylation patterns are patient-specific and can be used to track clonal growth ().
Aging is one of the most relevant risk factors for many types of cancers. Notably, the incidence of cancer diagnosis peaks at different ages for different types of cancer—usually above the age of 50, while, for example, testicular cancer occurs more frequently in younger adults (). The reason for this age specificity is not yet fully understood. As indicated above, aging and malignant transformation are to some extent reflected by similar changes in chromatin structure. It is hence conceivable that age-associated epigenetic modifications trigger malignant transformation (Wagner et al., 2015). In fact, epigenetic clocks in cancer, albeit not related to the donor age, correlate with clinical parameters and overall survival in several types of cancer, indicating that regulation of DNA methylation patterns in age-associated CpGs is relevant for cancer development (). Changes in chromatin conformation, which occur commonly at specific ages, might therefore favor tumor-initiating mutations or translocations.
Future Perspectives
There is clear evidence that genetic as well as epigenetic aberrations contribute to tumor development—the question is as follows: What comes first? Traditionally, the focus is on tumor-specific mutations, which can be easily tracked throughout disease development. On the other hand, malignant transformation is associated with profound epigenetic shifts, which directly impact chromatin conformation and can thereby impact the genetic sequence, as well. A better understanding of how specific epigenetic alterations might favor occurrence of specific genomic lesions will be important. It might then be possible to address such changes for disease prevention, early diagnosis, or directed therapy. A bottleneck for this research is, however, that the available tumor tissue at the time of diagnosis already reflects genome-wide epigenetic aberrations, which makes it difficult to identify the most relevant epigenetic alterations in early stages of malignancy.
Funding
This work was supported by the Else Kröner-Fresenius-Stiftung (2014_A193), by the Interdisciplinary Center for Clinical Research within the faculty of Medicine at the RWTH Aachen University (O1-3), by the Deutsche Forschungsgemeinschaft (DFG; WA1706/8-1 and WA1706/11-1), by Deutsche Krebshilfe (TRACK-AML), and by the Bundesministerium für Bildung und Forschung (VIP+ Epi-Blood-Count).
Statements
Author contributions
All authors contributed to writing of this manuscript and reviewed and approved the final version.
Conflict of interest
WW is cofounder of Cygenia GmbH (www.cygenia.com), which can provide service for Epigenetic Senescence Signatures and Epigenetic Aging Signatures to other scientists.
The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
References
1
AbelsonS.CollordG.NgS. W. K.WeissbrodO.Mendelson CohenN.NiemeyerE.et al. (2018). Prediction of acute myeloid leukaemia risk in healthy individuals. Nature559, 400–404. doi: 10.1038/s41586-018-0317-6
2
AgirreX.CastellanoG.PascualM.HeathS.KulisM.SeguraV.et al. (2015). Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers. Genome Res.25, 478–487. doi: 10.1101/gr.180240.114
3
AlzrigatM.ParragaA. A.Jernberg-WiklundH. (2018). Epigenetics in multiple myeloma: from mechanisms to therapy. Semin. Cancer Biol.51, 101–115. doi: 10.1016/j.semcancer.2017.09.007
4
ArtandiS. E.ChangS.LeeS. L.AlsonS.GottliebG. J.ChinL.et al. (2000). Telomere dysfunction promotes non-reciprocal translocations and epithelial cancers in mice. Nature406, 641–645. doi: 10.1038/35020592
5
AshworthA.LordC. J.Reis-FilhoJ. S. (2011). Genetic interactions in cancer progression and treatment. Cell145, 30–38. doi: 10.1016/j.cell.2011.03.020
6
BaylinS. B. (2005). DNA methylation and gene silencing in cancer. Nat. Clin. Pract. Oncol.2Suppl 1, S4–11. doi: 10.1038/ncponc0354
7
BirdA. (2002). DNA methylation patterns and epigenetic memory. Genes Dev.16, 6–21. doi: 10.1101/gad.947102
8
BochkisI. M.PrzybylskiD.ChenJ.RegevA. (2014). Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver. Cell Rep.9, 996–1006. doi: 10.1016/j.celrep.2014.09.048
9
BockerM. T.HellwigI.BreilingA.EcksteinV.HoA. D.LykoF. (2011). Genome-wide promoter DNA methylation dynamics of human hematopoietic progenitor cells during differentiation and aging. Blood117, e182–e189. doi: 10.1182/blood-2011-01-331926
10
BollatiV.SchwartzJ.WrightR.LitonjuaA.TarantiniL.SuhH.et al. (2009). Decline in genomic DNA methylation through aging in a cohort of elderly subjects. Mech. Ageing Dev.130, 234–239. doi: 10.1016/j.mad.2008.12.003
11
BoveriT. (1914). Zur Frage der Entstehung maligner Tumoren. Gustav Fischer VerlagJena.
12
BowmanR. L.BusqueL.LevineR. L. (2018). Clonal hematopoiesis and evolution to hematopoietic malignancies. Cell Stem Cell22, 157–170. doi: 10.1016/j.stem.2018.01.011
13
BožićT.FrobelJ.RaicA.TicconiF.KuoC.-C.Heilmann-HeimbachS.et al. (2018). Variants of DNMT3A cause transcript-specific DNA methylation patterns and affect hematopoiesis. Life Sci. Alliance1, e201800153. doi: 10.26508/lsa.201800153
14
BrandesJ. C.Van EngelandM.WoutersK. A.WeijenbergM. P.HermanJ. G. (2005). CHFR promoter hypermethylation in colon cancer correlates with the microsatellite instability phenotype. Carcinogenesis26, 1152–1156. doi: 10.1093/carcin/bgi058
15
BuscarletM.ProvostS.ZadaY. F.BarhdadiA.BourgoinV.LepineG.et al. (2017). DNMT3A and TET2 dominate clonal hematopoiesis and demonstrate benign phenotypes and different genetic predispositions. Blood130, 753–762. doi: 10.1182/blood-2017-04-777029
16
Corces-ZimmermanM. R.HongW. J.WeissmanI. L.MedeirosB. C.MajetiR. (2014). Preleukemic mutations in human acute myeloid leukemia affect epigenetic regulators and persist in remission. Proc. Natl. Acad. Sci. U. S. A.111, 2548–2553. doi: 10.1073/pnas.1324297111
17
DaskalosA.NikolaidisG.XinarianosG.SavvariP.CassidyA.ZakopoulouR.et al. (2009). Hypomethylation of retrotransposable elements correlates with genomic instability in non-small cell lung cancer. Int. J. Cancer124, 81–87. doi: 10.1002/ijc.23849
18
de MagalhaesJ. P. (2013). How ageing processes influence cancer. Nat. Rev. Cancer13, 357–365. doi: 10.1038/nrc3497
19
DifilippantonioM. J.ZhuJ.ChenH. T.MeffreE.NussenzweigM. C.MaxE. E.et al. (2000). DNA repair protein Ku80 suppresses chromosomal aberrations and malignant transformation. Nature404, 510–514. doi: 10.1038/35006670
20
Dupere-RicherD.LichtJ. D. (2017). Epigenetic regulatory mutations and epigenetic therapy for multiple myeloma. Curr. Opin Hematol.24, 336–344. doi: 10.1097/MOH.0000000000000358
21
EipelM.BozicT.MiesA.BeierF.JostE.BrummendorfT. H.et al. (2019). Tracking of myeloid malignancies by targeted analysis of successive DNA methylation at neighboring CG dinucleotides. Haematologica104, e349–e351. doi: 10.3324/haematol.2018.209734
22
EspadaJ.EstellerM. (2007). Epigenetic control of nuclear architecture. Cell Mol. Life Sci.64, 449–457. doi: 10.1007/s00018-007-6358-x
23
EstellerM.ToyotaM.Sanchez-CespedesM.CapellaG.PeinadoM. A.WatkinsD. N.et al. (2000). Inactivation of the DNA repair gene O6-methylguanine-DNA methyltransferase by promoter hypermethylation is associated with G to A mutations in K-ras in colorectal tumorigenesis. Cancer Res.60, 2368–2371.
24
FeinbergA. P.TyckoB. (2004). The history of cancer epigenetics. Nat. Rev. Cancer4, 143–153. doi: 10.1038/nrc1279
25
FonsecaR.BergsagelP. L.DrachJ.ShaughnessyJ.GutierrezN.StewartA. K.et al. (2009). International Myeloma Working Group molecular classification of multiple myeloma: spotlight review. Leukemia23, 2210–2221. doi: 10.1038/leu.2009.174
26
FragaM. F.BallestarE.Villar-GareaA.Boix-ChornetM.EspadaJ.SchottaG.et al. (2005). Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nat. Genet.37, 391–400. doi: 10.1038/ng1531
27
FrobelJ.HemedaH.LenzM.AbagnaleG.JoussenS.DeneckeB.et al. (2014). Epigenetic rejuvenation of mesenchymal stromal cells derived from induced pluripotent stem cells. Stem Cell Rep.3, 414–422. doi: 10.1016/j.stemcr.2014.07.003
28
GenoveseG.KahlerA. K.HandsakerR. E.LindbergJ.RoseS. A.BakhoumS. F.et al. (2014). Clonal hematopoiesis and blood-cancer risk inferred from blood DNA sequence. N. Engl. J. Med.371, 2477–2487. doi: 10.1056/NEJMoa1409405
29
GonzalezM. E.DuprieM. L.KruegerH.MerajverS. D.VenturaA. C.ToyK. A.et al. (2011). Histone methyltransferase EZH2 induces Akt-dependent genomic instability and BRCA1 inhibition in breast cancer. Cancer Res.71, 2360–2370. doi: 10.1158/0008-5472.CAN-10-1933
30
GreenbergR. A. (2005). Telomeres, crisis and cancer. Curr. Mol. Med.5, 213–218. doi: 10.2174/1566524053586590
31
GrossmannV.HaferlachC.WeissmannS.RollerA.SchindelaS.PoetzingerF.et al. (2013). The molecular profile of adult T-cell acute lymphoblastic leukemia: mutations in RUNX1 and DNMT3A are associated with poor prognosis in T-ALL. Genes Chromosomes Cancer52, 410–422. doi: 10.1002/gcc.22039
32
HannumG.GuinneyJ.ZhaoL.ZhangL.HughesG.SaddaS.et al. (2013). Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol. Cell49, 359–367. doi: 10.1016/j.molcel.2012.10.016
33
HansemannD. (1890). Ueber asymmetrische Zelltheilung in Epithelkrebsen und deren biologische Bedeutung. D. Archiv. für pathologische Anatomie119, 299. doi: 10.1007/BF01882039
34
HellmanA.ChessA. (2007). Gene body-specific methylation on the active X chromosome. Science315, 1141–1143. doi: 10.1126/science.1136352
35
HernandoH.GelatoK. A.LescheR.BeckmannG.KoehrS.OttoS.et al. (2016). EZH2 inhibition blocks multiple myeloma cell growth through upregulation of epithelial tumor suppressor genes. Mol. Cancer Ther.15, 287–298. doi: 10.1158/1535-7163.MCT-15-0486
36
HodgeD. R.PengB.CherryJ. C.HurtE. M.FoxS. D.KelleyJ. A.et al. (2005). Interleukin 6 supports the maintenance of p53 tumor suppressor gene promoter methylation. Cancer Res.65, 4673–4682. doi: 10.1158/0008-5472.CAN-04-3589
37
HorvathS. (2013). DNA methylation age of human tissues and cell types. Genome Biol.14, R115. doi: 10.1186/gb-2013-14-10-r115
38
HyattS.JonesR. E.HeppelN. H.GrimsteadJ. W.FeganC.JacksonG. H.et al. (2017). Telomere length is a critical determinant for survival in multiple myeloma. Br. J. Haematol.178, 94–98. doi: 10.1111/bjh.14643
39
JeongM.ParkH. J.CelikH.OstranderE. L.ReyesJ. M.GuzmanA.et al. (2018). Loss of Dnmt3a immortalizes hematopoietic stem cells in vivo. Cell Rep.23, 1–10. doi: 10.1016/j.celrep.2018.03.025
40
JonesP. A.BaylinS. B. (2002). The fundamental role of epigenetic events in cancer. Nat. Rev. Genet.3, 415–428. doi: 10.1038/nrg816
41
JostE.LinQ.WeidnerC. I.WilopS.HoffmannM.WalendaT.et al. (2014). Epimutations mimic genomic mutations of DNMT3A in acute myeloid leukemia. Leukemia28, 1227–1234. doi: 10.1038/leu.2013.362
42
KaasinenE.KuisminO.RajamakiK.RistolainenH.AavikkoM.KondelinJ.et al. (2019). Impact of constitutional TET2 haploinsufficiency on molecular and clinical phenotype in humans. Nat. Commun.10, 1252. doi: 10.1038/s41467-019-09198-7
43
KaiserM. F.JohnsonD. C.WuP.WalkerB. A.BrioliA.MirabellaF.et al. (2013). Global methylation analysis identifies prognostically important epigenetically inactivated tumor suppressor genes in multiple myeloma. Blood122, 219–226. doi: 10.1182/blood-2013-03-487884
44
KhongT.SharkeyJ.SpencerA. (2008). The effect of azacitidine on interleukin-6 signaling and nuclear factor-kappaB activation and its in vitro and in vivo activity against multiple myeloma. Haematologica93, 860–869. doi: 10.3324/haematol.12261
45
KiziltepeT.HideshimaT.CatleyL.RajeN.YasuiH.ShiraishiN.et al. (2007). 5-Azacytidine, a DNA methyltransferase inhibitor, induces ATR-mediated DNA double-strand break responses, apoptosis, and synergistic cytotoxicity with doxorubicin and bortezomib against multiple myeloma cells. Mol. Cancer Ther.6, 1718–1727. doi: 10.1158/1535-7163.MCT-07-0010
46
KoM.HuangY.JankowskaA. M.PapeU. J.TahilianiM.BandukwalaH. S.et al. (2010). Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature468, 839–843. doi: 10.1038/nature09586
47
KochC. M.WagnerW. (2011). Epigenetic-aging-signature to determine age in different tissues. Aging (Albany NY)3, 1018–1027. doi: 10.18632/aging.100395
48
KohliR. M.ZhangY. (2013). TET enzymes, TDG and the dynamics of DNA demethylation. Nature502, 472–479. doi: 10.1038/nature12750
49
KouzaridesT. (2007). Chromatin modifications and their function. Cell128, 693–705. doi: 10.1016/j.cell.2007.02.005
50
Lee-SixH.ObroN. F.ShepherdM. S.GrossmannS.DawsonK.BelmonteM.et al. (2018). Population dynamics of normal human blood inferred from somatic mutations. Nature561, 473–478. doi: 10.1038/s41586-018-0497-0
51
LeyT. J.DingL.WalterM. J.MclellanM. D.LamprechtT.LarsonD. E.et al. (2010). DNMT3A mutations in acute myeloid leukemia. N. Engl. J. Med.363, 2424–2433. doi: 10.1056/NEJMoa1005143
52
LinQ.WagnerW. (2015). Epigenetic aging signatures are coherently modified in cancer. PLoS Genet.11, e1005334. doi: 10.1371/journal.pgen.1005334
53
LinQ.WeidnerC. I.CostaI. G.MarioniR. E.FerreiraM. R.DearyI. J.et al. (2016). DNA methylation levels at individual age-associated CpG sites can be indicative for life expectancy. Aging (Albany NY)8, 394–401. doi: 10.18632/aging.100908
54
LobergM. A.BellR. K.GoodwinL. O.EudyE.MilesL. A.SanmiguelJ. M.et al. (2019). Sequentially inducible mouse models reveal that Npm1 mutation causes malignant transformation of Dnmt3a-mutant clonal hematopoiesis. Leukemia33, 1635–1649. doi: 10.1038/s41375-018-0368-6
55
LudwigH.BeksacM.BladeJ.BoccadoroM.CavenaghJ.CavoM.et al. (2010). Current multiple myeloma treatment strategies with novel agents: a European perspective. Oncologist15, 6–25. doi: 10.1634/theoncologist.2009-0203
56
MarioniR. E.ShahS.McraeA. F.ChenB. H.ColicinoE.HarrisS. E.et al. (2015). DNA methylation age of blood predicts all-cause mortality in later life. Genome Biol.16, 25. doi: 10.1186/s13059-015-0584-6
57
MartinsF. C.DeS.AlmendroV.GonenM.ParkS. Y.BlumJ. L.et al. (2012). Evolutionary pathways in BRCA1-associated breast tumors. Cancer Discov.2, 503–511. doi: 10.1158/2159-8290.CD-11-0325
58
MimuraN.HideshimaT.AndersonK. C. (2015). Novel therapeutic strategies for multiple myeloma. Exp. Hematol.43, 732–741. doi: 10.1016/j.exphem.2015.04.010
59
MoreauxJ.RemeT.LeonardW.VeyruneJ. L.RequirandG.GoldschmidtH.et al. (2012). Development of gene expression-based score to predict sensitivity of multiple myeloma cells to DNA methylation inhibitors. Mol. Cancer Ther.11, 2685–2692. doi: 10.1158/1535-7163.MCT-12-0721
60
MorganG. J.WalkerB. A.DaviesF. E. (2012). The genetic architecture of multiple myeloma. Nat. Rev. Cancer12, 335–348. doi: 10.1038/nrc3257
61
NebenK.JauchA.HielscherT.HillengassJ.LehnersN.SeckingerA.et al. (2013). Progression in smoldering myeloma is independently determined by the chromosomal abnormalities del(17p), t(4;14), gain 1q, hyperdiploidy, and tumor load. J. Clin. Oncol.31, 4325–4332. doi: 10.1200/JCO.2012.48.4923
62
NegriniS.GorgoulisV. G.HalazonetisT. D. (2010). Genomic instability—an evolving hallmark of cancer. Nat. Rev. Mol. Cell Biol.11, 220–228. doi: 10.1038/nrm2858
63
OkanoM.BellD. W.HaberD. A.LiE. (1999). DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell99, 247–257. doi: 10.1016/S0092-8674(00)81656-6
64
OrtmannC. A.KentD. G.NangaliaJ.SilberY.WedgeD. C.GrinfeldJ.et al. (2015). Effect of mutation order on myeloproliferative neoplasms. N. Engl. J. Med.372, 601–612. doi: 10.1056/NEJMoa1412098
65
PeltomakiP. (2012). Mutations and epimutations in the origin of cancer. Exp. Cell Res.318, 299–310. doi: 10.1016/j.yexcr.2011.12.001
66
PengB.HurtE. M.HodgeD. R.ThomasS. B.FarrarW. L. (2006). DNA hypermethylation and partial gene silencing of human thymine-DNA glycosylase in multiple myeloma cell lines. Epigenetics1, 138–145. doi: 10.4161/epi.1.3.2938
67
RideoutW. M.CoetzeeG. A.OlumiA. F.JonesP. A. (1990). 5-Methylcytosine as an endogenous mutagen in the human LDL receptor and p53 genes. Science249, 1288–1290. doi: 10.1126/science.1697983
68
Robiou du PontS.CleynenA.FontanC.AttalM.MunshiN.CorreJ.et al. (2017). Genomics of multiple myeloma. J. Clin. Oncol.35, 963–967. doi: 10.1200/JCO.2016.70.6705
69
Russler-GermainD. A.SpencerD. H.YoungM. A.LamprechtT. L.MillerC. A.FultonR.et al. (2014). The R882H DNMT3A mutation associated with AML dominantly inhibits wild-type DNMT3A by blocking its ability to form active tetramers. Cancer Cell25, 442–454. doi: 10.1016/j.ccr.2014.02.010
70
SchermellehL.HaemmerA.SpadaF.RosingN.MeilingerD.RothbauerU.et al. (2007). Dynamics of Dnmt1 interaction with the replication machinery and its role in postreplicative maintenance of DNA methylation. Nucleic Acids Res.35, 4301–4312. doi: 10.1093/nar/gkm432
71
SharmaS.KellyT. K.JonesP. A. (2010). Epigenetics in cancer. Carcinogenesis31, 27–36. doi: 10.1093/carcin/bgp220
72
ShlushL. I.ZandiS.MitchellA.ChenW. C.BrandweinJ. M.GuptaV.et al. (2014). Identification of pre-leukaemic haematopoietic stem cells in acute leukaemia. Nature506, 328–333. doi: 10.1038/nature13038
73
SjoblomT.JonesS.WoodL. D.ParsonsD. W.LinJ.BarberT. D.et al. (2006). The consensus coding sequences of human breast and colorectal cancers. Science314, 268–274. doi: 10.1126/science.1133427
74
StewartM. D.LiJ.WongJ. (2005). Relationship between histone H3 lysine 9 methylation, transcription repression, and heterochromatin protein 1 recruitment. Mol. Cell Biol.25, 2525–2538. doi: 10.1128/MCB.25.7.2525-2538.2005
75
The Cancer Genome Atlas Research Network (2013). Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N. Engl. J. Med.368, 2059–2074. doi: 10.1056/NEJMoa1301689
76
van NieuwenhuijzenN.SpaanI.RaymakersR.PeperzakV. (2018). From MGUS to multiple myeloma, a paradigm for clonal evolution of premalignant cells. Cancer Res.78, 2449–2456. doi: 10.1158/0008-5472.CAN-17-3115
77
van SteenselB.BelmontA. S. (2017). Lamina-associated domains: links with chromosome architecture, heterochromatin, and gene repression. Cell169, 780–791. doi: 10.1016/j.cell.2017.04.022
78
Vargas-RondonN.VillegasV. E.Rondon-LagosM. (2017). The role of chromosomal instability in cancer and therapeutic responses. Cancers (Basel)10, 4. doi: 10.3390/cancers10010004
79
WagnerW.WeidnerC. I.LinQ. (2015). Do age-associated DNA methylation changes increase the risk of malignant transformation? Bioessays37, 20–24. doi: 10.1002/bies.201400063
80
WangH.MauranoM. T.QuH.VarleyK. E.GertzJ.PauliF.et al. (2012). Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res.22, 1680–1688. doi: 10.1101/gr.136101.111
81
WeidnerC. I.LinQ.KochC. M.EiseleL.BeierF.ZieglerP.et al. (2014). Aging of blood can be tracked by DNA methylation changes at just three CpG sites. Genome Biol.15, R24. doi: 10.1186/gb-2014-15-2-r24
82
WeidnerC. I.WagnerW. (2014). The epigenetic tracks of aging. Biol Chem395, 1307–1314. doi: 10.1515/hsz-2014-0180
83
XieM.LuC.WangJ.MclellanM. D.JohnsonK. J.WendlM. C.et al. (2014). Age-related mutations associated with clonal hematopoietic expansion and malignancies. Nat. Med.20, 1472–1478. doi: 10.1038/nm.3733
84
ZeidlerM.VaramballyS.CaoQ.ChinnaiyanA. M.FergusonD. O.MerajverS. D.et al. (2005). The Polycomb group protein EZH2 impairs DNA repair in breast epithelial cells. Neoplasia7, 1011–1019. doi: 10.1593/neo.05472
85
ZhangY.HapalaJ.BrennerH.WagnerW. (2017). Individual CpG sites that are associated with age and life expectancy become hypomethylated upon aging. Clin Epigenetics9, 9. doi: 10.1186/s13148-017-0315-9
86
ZhouD.RobertsonK. D. (2016). “Role of DNA methylation in genome stability,” in Genome stability. Eds. KovalchukI.KovalchukO. (University of Lethbridge, Lethbridge, AB, Canada: Elsevier Inc.), 409–424. doi: 10.1016/B978-0-12-803309-8.00024-0
Summary
Keywords
clonal hematopoiesis, multiple myeloma, epigenetics, epimutation, DNA methylation, aging
Citation
Cypris O, Božić T and Wagner W (2019) Chicken or Egg: Is Clonal Hematopoiesis Primarily Caused by Genetic or Epigenetic Aberrations?. Front. Genet. 10:785. doi: 10.3389/fgene.2019.00785
Received
26 February 2019
Accepted
24 July 2019
Published
10 September 2019
Volume
10 - 2019
Edited by
Dirk Hose, Heidelberg University Hospital, Germany
Reviewed by
Julia A. Horsfield, University of Otago, New Zealand; Jun Zhong, National Cancer Institute (NCI), United States
Updates
Copyright
© 2019 Cypris, Božić and Wagner.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Wolfgang Wagner, wwagner@ukaachen.de
†These authors have contributed equally to this work.
This article was submitted to Cancer Genetics, a section of the journal Frontiers in Genetics
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