Beyond transcription factors-how oncogenic signaling reshapes the epigenetic landscape.pdf

Beyond transcription factors:how oncogenic signaling reshapes the epigenetic landscapeFan Liu1,2,Lan Wang5,6,Fabiana Perna3,and Stephen D.Nimer1,2,4,*1Department of Biochemistry and Molecular Biology,University of Miami,Miller School of Medicine,Miami,FL 331362Sylvester Comprehensive Cancer Center,University of Miami,Miller School of Medicine,Miami,FL 331363Molecular Pharmacology and Chemistry Program,Sloan-Kettering Institute,Memorial Sloan-Kettering Cancer Center,New York,NY 100654Department of Internal Medicine,University of Miami,Miller School of Miami,FL331365Institute of Health Sciences,Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences/School of Medicine,Shanghai Jiao Tong University,Shanghai,China6State Key Laboratory of Medical Genomics,Shanghai Institute of Hematology,Rui Jin Hospital,School of Medicine,Shanghai Jiao Tong University,Shanghai,ChinaAbstractCancer,once thought to be caused largely by genetic alterations,is now considered to be a mixed genetic and epigenetic disease.The epigenetic landscape,which is dictated by covalent DNA and histone modifications,is profoundly altered in transformed cells.These abnormalities may arise due to mutations in or altered expression of chromatin modifiers.Recent reports on the interplay between cellular signaling pathways and chromatin modifications add another layer of complexity to the already complex regulation of the epigenome.In this Review,we discuss these new studies and how the insights they provide can contribute to a better understanding of the molecular pathogenesis of neoplasia.Signal transduction pathways convert environmental stimuli to changes in cell behavior,and are thus central to the control of all biological processes.Not surprisingly,deregulation of these pathways contributes to the development of many diseases,and is particularly important in the context of cancer.Extensive studies over the past decades have identified genetic alterations in components of many signaling pathways involved in cancer,and have also led to the development of therapeutics that can successfully target some of these pathways,most notably the use of tyrosine kinase inhibitors in chronic myeloid leukemia1,HER2(also known as ERBB2)inhibitors in breast cancer2,BRAF inhibitors in melanoma3 and Janus kinase 2(JAK2)inhibitors in myeloproliferative neoplasms4.Corresponding Author:snimermed.miami.edu.Conflict of interestNo Competing Interest.HHS Public AccessAuthor manuscriptNat Rev Cancer.Author manuscript;available in PMC 2017 August 08.Published in final edited form as:Nat Rev Cancer.2016 June;16(6):359372.doi:10.1038/nrc.2016.41.Author ManuscriptAuthor ManuscriptAuthor ManuscriptAuthor ManuscriptCanonical signaling pathways usually involve a cascade of protein phosphorylation events,ultimately resulting in the activation(or inactivation)of transcriptional regulators and changes in target gene expression.The kinases that comprise these pathways are largely cytoplasmic,and are therefore not generally considered to directly affect chromatin structure;yet numerous kinases,including AKT5,6 and JAK27,have been shown to modify histones or proteins that control chromatin structure.Thus,although diagrams typically show these complex signaling pathways ending at transcription factors,they can also directly regulate histone proteins,and histone or DNA modifying enzymes.The N-terminal tails of histones undergo extensive posttranslational modifications,including phosphorylation,acetylation,methylation,ubiquitination and SUMOylation8.These modifications affect chromatin configuration and chromatin-DNA interactions,and subsequently regulate numerous cellular processes,including transcriptional regulation,DNA damage repair,DNA replication,genomic imprinting and X chromosome inactivation.Some histone modifications,such as histone H3-lysine 14 acetylation(H3K14Ac),H3K27Ac and H3K4 trimethylation(H3K4me3),are found at actively transcribed promoters or active enhancers,whereas others,such as H3K9me3 and H3K27me3,are considered to represent repressive marks for transcription(Table 1 summarizes histone modifications and their functions on transcriptional regulation).However,it is the combination of histone modifications and DNA methylation at regulatory regions in the genome,in concert with regulation by non-coding RNAs,that determines whether genes are expressed or not,and at what level.For example,many promoters in embryonic stem cells(ESCs)harbor a specific histone modification pattern that combines the activating histone mark H3K4me3 and the repressive H3K27me3 mark9.These bivalent domains silence the developmental genes in ESCs,while keeping them poised for activation,and provide a key example of how gene expression can be determined by the combined effects of different histone marks on the same promoter.Cancer genetic studies have focused on mutations that contribute to cell transformation,either as gain-of-function or loss-of-function genetic events.In the past few decades,many studies have demonstrated the impact of epigenetic events on cancer development,adding another dimension to our understanding of cancer.Almost 30 years ago,it was discovered that tumor cells had lower levels of genome-wide CpG island methylation compared with their normal counterparts10.This global DNA hypomethylation is thought to contribute to genomic instability,due in part to the activation of transposable elements and loss of genomic imprinting.DNA hypermethylation is also a common feature of cancer,sometimes at the promoter regions of tumor suppressor genes,leading to loss of expression of key gatekeeper genes,such as CDKN2A(cyclin-dependent kinase inhibitor 2A)and BRCA1(breast cancer 1)11,12.Cancer-associated perturbations in histone modifications often occur at individual gene promoters or enhancers in a given cancer,resulting in the improper activation or repression of genes that could contribute to cancer development.However,some common events,such as the global loss of both H4K16ac and H4K20me3 are observed in many types of human cancer13.Unlike the irreversible character of genetic events,epigenetic alterations are potentially reversible.In fact,some epigenetic drugs,most notably some histone deacetylase(HDAC)and DNA methyltransferase(DNMT)inhibitors,Liu et al.Page 2Nat Rev Cancer.Author manuscript;available in PMC 2017 August 08.Author ManuscriptAuthor ManuscriptAuthor ManuscriptAuthor Manuscripthave been approved by the US Food and Drug Administration(FDA)for the treatment of hematological malignancies14.Due to the complex regulation of the human epigenome,the cause of aberrant epigenetic modifications remains difficult to determine for most cancers.Nevertheless,the interplay between upstream signaling pathways and chromatin modifications represents an important molecular mechanism that leads to specific alterations in the cancer epigenome.This Review summarizes recent findings into how such cross talk can contribute to the development of cancer.Regulation of histone phosphorylation by upstream signalling pathwaysHistone phosphorylation is involved in a variety of cellular processes.Phosphorylation of H3S10 and H3S28 is associated with two seemingly paradoxical functions,transcriptional activation and chromosome condensation15,16.Whereas phosphorylation of H3S10 and H3S28 by mitotic kinases such as Aurora kinase B is required for the initiation of chromosome condensation and the onset of mitosis16,phosphorylation at these sites by signal transduction kinases,such as ribosomal S6 kinase 2(RSK2)and mitogen-and stress-activated kinase 1 and 2(MSK1 and 2),promotes the transcriptional activation of immediate early genes,such as FOS,JUN and MYC17,18.Mitotic histone H3 phosphorylation is a highly coordinated spatio-temporal event,initiating at pericentromeric heterochromatin regions at the onset of mitosis,reaching maximal abundance during metaphase,and then decreasing rapidly upon the transition to anaphase.Unlike the global H3 phosphorylation seen during mitosis,interphase H3 phosphorylation occurs rapidly in response to extracellular stimuli,but targets only a small fraction of nucleosomes,thus affecting only the local chromatin structure19.Other signaling kinases,including I-B kinase-(IKK)20,JUN N-terminal kinase(JNK)21 and PIM122,have also been reported to phosphorylate H3 at either S10 or S28 and control gene transcription.IKK,a crucial regulator of nuclear factor-B(NF-B)signaling that controls the stability of IB protein(the inhibitor of NF-B)in the cytoplasm,has been shown to shuttle into the nucleus and phosphorylate H3S10 at NF-B-responsive promoters,thus directly affecting the cytokine-induced expression of NF-B-regulated genes20.Whereas JNK-mediated H3S10 phosphorylation contributes to the differentiation of stem cells into neurons21;PIM1 forms a complex with MYC on MYC-responsive genes,where it phosphorylates H3S10 and facilitates MYC-induced gene expression and cellular transformation22.In addition to cell cycle progression and control of gene transcription,H3S10 phosphorylation by protein kinase C-(PKC)has been shown to play a role in apoptosis-induced chromatin condensation23.The mechanisms by which phosphorylation at these two serine residues in histone H3 affects gene expression and mitosis are still unclear.H3S10 and H3S28 phosphorylation have been shown to recruit the scaffolding protein 14-3-3-and to the promoters of immediate early genes,allowing the transcription initiation machinery to assemble there;the recruitment of 14-3-3 proteins is greatly enhanced when H3K14(on the histone H3 tail)is simultaneously acetylated24,25.Since both H3S10 and H3S28 reside within anARKS sequence motif,Liu et al.Page 3Nat Rev Cancer.Author manuscript;available in PMC 2017 August 08.Author ManuscriptAuthor ManuscriptAuthor ManuscriptAuthor Manuscriptresearchers have speculated that dynamic serine phosphorylation might affect the readout of the more stable methyl marks on the adjacent lysine residues.Indeed,H3S10 phosphorylation has been shown to displace heterochromatin protein 1(HP1)from the adjacent methylated H3K9 residue,impairing its ability to propagate heterochromatin during both transcriptional activation and mitosis26,27.In contrast,phosphorylation of H3S28 not only prevents binding of polycomb-repressive complexes to methylated H3K27,but it also induces a switch from methylation to acetylation at this lysine residue28.We are beginning to learn how aberrant histone phosphorylation contributes to cellular transformation.For example,mutating H3S10 or H3S28 to alanine blocks the epidermal growth factor(EGF)-induced transformation of mouse epidermal cells in culture29,likely due to reduced transactivation of EGF target genes,including Fos and Jun.Similarly,inhibiting MSK1 activity reduces the activation of immediate early genes in response to oncogenic RAS-MAPK signaling,impairing tumor cell growth in soft agar colony assays30.Both of these observations support that phosphorylation of H3S10 and H3S28 are important in tumorigenesis.However,neither report examined the changes in chromatin condensation that occur during mitosis when phosphorylation of H3S10 and H3S28 is inhibited.Another example of crosstalk between histone phosphorylation and lysine methylation was reported in two studies by Metzger and colleagues31,32.They showed that histone H3 is phosphorylated at T6 by PKC1 and at T11 by protein-kinase C-related kinase 1(PRK1;also known as PKN1),two phospholipid-dependent kinases that are involved in cell proliferation and migration and are overexpressed in several human cancers33.These phosphorylation events can be androgen-driven and facilitate the transactivation of androgen receptor(AR)target genes in prostate cancer cell lines.Interestingly,the ability of lysine demethylases,such as lysine-specific histone demethylase 1(LSD1,also known as KDM1A)and Jumonji domain-containing protein 2C(JMJD2C;also known as KDM4C),to remove the methyl marks from H3K4 and H3K9 is affected by H3T6 and H3T11 phosphorylation31,32.H3T6 phosphorylation blocks the demethylation of H3K4me1 and H3K4me2 by LSD1,whereas phosphorylation of H3T11 accelerates the demethylation of H3K9me3 by JMJD2C.Given the positive role of H3K4 methylation and the inhibitory effect of H3K9 methylation on gene expression,these changes to methylation would be expected to promote transcription and enhance the strength of AR-dependent gene expression.In fact,high H3T6 and H3T11 phosphorylation levels correlates with high Gleason scores(and worse prognosis)for prostate cancer patients.In addition,inhibition of PRK1 and PKC1 greatly impairs the in vitro growth of prostate cancer cells,supporting at least one role of histone H3 threonine phosphorylation in promoting AR-dependent transformation31,32.In addition to serine and threonine phosphorylation,histone H3 is also phosphorylated at tyrosine residues by JAK234.JAK2 signaling plays an important role in normal hematopoiesis,as it is downstream of several cytokine receptors.These pathways can be hijacked in cancer through mutations in cytokine receptor genes or in the tyrosine kinase genes themselves.For example,JAK2-V617F,a constitutively activated form of JAK2,is found in more than half of all patients with myeloproliferative neoplasms(MPNs)35.Dawson and colleagues34 found that a substantial proportion of the cellular JAK2 protein is Liu et al.Page 4Nat Rev Cancer.Author manuscript;available in PMC 2017 August 08.Author ManuscriptAuthor ManuscriptAuthor ManuscriptAuthor Manuscriptin the nuclei of hematopoietic cells,where it phosphorylates histone H3Y41(Figure 1).Phosphorylation of H3Y41 excludes HP1 from chromatin,an event linked to the transcriptional activation of at least one JAK2-target gene,LIM domain only 2(LMO2),a gene that is essential for normal hematopoietic development and that has been implicated in leukemogenesis36,37.Direct signaling of JAK2-V617F to chromatin was also shown to mediate ESC self-renewal via regulation of NANOG expression38.Using genome-wide chromatin immunoprecipitation-sequencing(ChIP-seq)technology,the same group identified many more genes that are regulated through phosphorylation of H3Y4139.Furthermore,the detection of H3Y41 phosphorylation in JAK2-deficient gamma-2A cells indicates that tyrosine kinases other than JAK2 are also capable of phosphorylating H3Y4134.Even though histone H3 seems to be the major target of upstream signaling kinases,other histones such as H2B can also be phosphorylated at multiple serine and threonine residues,providing additional mechanisms that can regulate cell behavior.For example,AMP-activated protein kinase(AMPK),a crucial regulator of cell metabolism,controls stress-elevated gene transcription via phosphorylation of H2BS36 in both the promoters and transcribed regions of these genes40.In contrast,phosphorylation of H2BS14 by mammalian STE20-like protein kinase 1(MST1;also known as STK4)is associated