epigenomes Review Epigenetic Regulation of EMT (Epithelial to Mesenchymal Transition) and Tumor Aggressiveness: A View on Paradoxical Roles of KDM6B and EZH2 Camille Lachat 1, Michaël Boyer-Guittaut 1,2, Paul Peixoto 1,3,† and Eric Hervouet 1,2,3,†,* 1 Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, INSERM, EFS BFC, UMR1098, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France; [email protected] (C.L.); [email protected] (M.B.-G.); [email protected] (P.P.) 2 DImaCell Platform, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France 3 EPIGENEXP Platform, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France * Correspondence: [email protected]; Tel.: +33-81666542 † These authors contributed equally to this work. Received: 3 December 2018; Accepted: 17 December 2018; Published: 20 December 2018 Abstract: EMT (epithelial to mesenchymal transition) is a plastic phenomenon involved in metastasis formation. Its plasticity is conferred in a great part by its epigenetic regulation. It has been reported that the trimethylation of lysine 27 histone H3 (H3K27me3) was a master regulator of EMT through two antagonist enzymes that regulate this mark, the methyltransferase EZH2 (enhancer of zeste homolog 2) and the lysine demethylase KDM6B (lysine femethylase 6B). Here we report that EZH2 and KDM6B are overexpressed in numerous cancers and involved in the aggressive phenotype and EMT in various cell lines by regulating a specific subset of genes. The first paradoxical role of these enzymes is that they are antagonistic, but both involved in cancer aggressiveness and EMT. The second paradoxical role of EZH2 and KDM6B during EMT and cancer aggressiveness is that they are also inactivated or under-expressed in some cancer types and linked to epithelial phenotypes in other cancer cell lines. We also report that new cancer therapeutic strategies are targeting KDM6B and EZH2, but the specificity of these treatments may be increased by learning more about the mechanisms of action of these enzymes and their specific partners or target genes in different cancer types. Keywords: cancer; EMT; metastasis; epigenetics; KDM6B; EZH2; H3K27 1. Introduction 1.1. Epithelial to Mesenchymal Transition (EMT) Epithelial to mesenchymal transition (EMT) is a phenomenon that leads epithelial cells to gradually acquire a mesenchymal phenotype. This process is associated with a loss of expression of specific epithelial proteins called “epithelial markers,” such as E-CADHERIN (coded by CDH1 gene), CLAUDIN, or OCCLUDIN, and a gain of expression of other proteins called “mesenchymal markers,” such as VIMENTIN or N-CADHERIN. At least three distinct types of EMT have been reported so far, even if they present highly similar mechanisms: (i) type I is implicated in embryo formation and organ development; (ii) type II is involved in wound healing, regeneration of tissues, and in organ fibrosis; and (iii) type III is implicated in cancer development and aggressiveness. The latter also plays a role in tumor escape, impairing the formation of the immune synapse or leading to the overexpression of the immune checkpoint inhibitor PD-L1 (programmed death ligand 1) [1–3], and in metastasis formation [4,5]. Indeed, in type III EMT, tumor cells have been shown to present a loss of expression of adhesion proteins [6], to secrete various metalloproteases, such as MMP9 or ADAM19 [7], leading to Epigenomes 2019, 3, 1; doi:10.3390/epigenomes3010001 www.mdpi.com/journal/epigenomes Epigenomes 2018, 4, x 2 of 22 the overexpression of the immune checkpoint inhibitor PD-L1 (programmed death ligand 1) [1–3], and in metastasis formation [4,5]. Indeed, in type III EMT, tumor cells have been shown to present a loss of expression of adhesion proteins [6], to secrete various metalloproteases, such as MMP9 or ADAM19 [7], leading to the digestion of the extracellular matrix and then to the escape of the primary Epigenomestumor2019 and, 3 ,the 1 migration through the blood or lymphatic circulation [4,5]. 2 of 21 All the changes occurring during EMT at the morphological, functional, or molecular levels can be reversed to return to the original epithelial phenotype. This phenomenon is called mesenchymal the digestionto epithelial of thetransition extracellular (MET) [8,9]. matrix Through and then this to process, the escape circulating of the primarycancer cells tumor can invade and the another migration throughorgan, the leading blood orto lymphaticthe formation circulation and growth [4,5]. of a secondary tumor called metastasis (Figure 1). However,All the changes the definition occurring of EMT during remains EMT complex at the morphological,since there is not functional,only one EMT or but molecular a multitude levels of can be reversedintermediate to return states to presenting the original different epithelial expressions phenotype. of epithelial This phenomenon and mesenchymal is called markers. mesenchymal This to epithelialplasticity transition has been described (MET) [8 to,9 ].be Through mainly linked this process, to the epigenetic circulating regulation cancer of cells EMT, can which invade is itself another organ,a highly leading plastic to the and formation reversible and process, growth as ofdescribed a secondary below. tumor called metastasis (Figure1). However, Type III EMT can be induced by various intra- or extra-cellular factors or stress. It has been the definition of EMT remains complex since there is not only one EMT but a multitude of intermediate described that EMT-activating transcription factors (EMT-ATFs), such as SNAIL, TWIST, and ZEB states presenting different expressions of epithelial and mesenchymal markers. This plasticity has been (zinc finger E-box-binding homeobox) families, are main regulators of EMT [10]. These EMT-ATFs are describedactivated to bevia mainly hypoxia, linked cytokines to the (TGF epigeneticβ, TNFα), regulationgrowth factors of EMT,(EGF), whichor by cellular is itself signaling a highly pathways plastic and reversible(WNT, process, HEDGEHOG, as described NF-κB, below.and NOTCH), and their activation leads to EMT induction [11]. FigureFigure 1. Roles 1. Roles of EMT of EMT in thein the formation formation of of metastases. metastases. Epithelial Epithelial cells, cells, expressing expressing epithelial epithelial markers, markers, can undergocan undergo EMT andEMT progressively and progressively acquire acquire a mesenchymal a mesenchymal phenotype phenotype characterized characterized by the by expression the of mesenchymalexpression of markers. mesenchymal EMT markers. is reversible EMTand is revers the oppositeible and the transition opposite is transition called MET is called (mesenchymal MET to epithelial(mesenchymal transition). to epithelial EMT and transi METtion). are EMT involved and MET in theare emergenceinvolved in ofthe metastases emergence byof metastases allowing cells to migrateby allowing to the cells blood to ormigrate lymphatic to the circulation blood or lymp andhatic then circulation invade another and then organ invade to generate another organ a secondary to generate a secondary tumor called metastasis. tumor called metastasis. 1.2. Epigenetic Regulation of EMT Type III EMT can be induced by various intra- or extra-cellular factors or stress. It has been describedThe that word EMT-activating “epigenetics” transcriptionwas used for the factors first time (EMT-ATFs), in 1942 by such Conrad as SNAIL,Hal Waddington, TWIST, andwho ZEB (zincused finger the E-box-binding term of “epigenotype” homeobox) to describe families, the are different main regulators phenomena of which EMT [are10]. involved These EMT-ATFs in the are activatedimplementation via hypoxia, of a phenotype cytokines from (TGF aβ genotype,, TNFα), growthand “epigenetics” factors (EGF), for studies or by cellularrelated to signaling the pathwaysunderstanding (WNT, HEDGEHOG, of this phenomenon NF-κB, [12]. and This NOTCH), definition and has their been activation widely modified leads to since EMT the induction 1940s to [11]. lead to the one currently used now: “Epigenetics is the study of the regulation of gene expression, 1.2. Epigeneticwithout DNA Regulation nucleotide of EMT sequence alteration, and linked to hereditary transmission.” This field includes the study of non-coding RNA (miRNA, lncRNA, etc.), which can bind DNA or mRNA and influenceThe word gene “epigenetics” transcription, was DNA used methylation for the first (methylation time in 1942of cytosines by Conrad in CpG Hal regions Waddington, leading to who usedthe the repression term of “epigenotype”of transcription) toand describe histone post-translational the different phenomena modifications which (Table are 1). involved Plasticity inof the implementationepigenetic regulation of a phenotype is conferred from by athe genotype, reversible andcharacter “epigenetics” of the corresponding for studies biochemical related to the understandingreactions. Indeed, of this DNA phenomenon methylatio [n,12 histone]. This definitionpost-translational has been mo widelydifications, modified and non-coding since the RNA 1940s to leadexpression to the one can currently be reversed used according now: “Epigenetics to the cell pathophysiological is the study of the context. regulation Moreover, of gene epigenetic expression, without DNA nucleotide sequence alteration, and linked to hereditary transmission.” This field includes the study of non-coding RNA (miRNA, lncRNA, etc.), which can bind DNA or mRNA and influence gene transcription, DNA methylation