Sage Journals: Discover world-class research

Abstract

Natural killer/T-cell lymphoma (NKTCL) is an aggressive malignancy that usually presents in the upper aerodigestive tract. This malignancy shows substantial geographic variability in incidence, and is characterized by Epstein-Barr virus (EBV) infections. Epigenetic aberrations may dysregulate the expression of genes involved in different hallmarks of cancer. A growing body of evidence underscores the importance of epigenetic aberrations in the pathogenesis of NKTCL. Promoter hypermethylation is a common epigenetic mechanism for the inactivation of tumour suppressor genes. Several epigenetically silenced tumour suppressor candidates (e.g. PRDM1, BIM) were identified in this aggressive cancer using locus-specific and genome-wide promoter methylation analyses. Importantly, genes involved in epigenetic modifications were identified to be mutated (e.g. KMT2D) or methylated (e.g. TET2) in NKTCL patients, which may contribute to pathogenesis through global alterations in chromatin states. Cancer-associated microRNAs, some of which are expressed by EBV, and long noncoding RNAs have been observed to be dysregulated in NKTCL. This review focuses on studies investigating epigenetic aberrations in NKTCL to bolster our overall understanding of the role of these abnormalities in disease pathobiology. We also discuss the potential of these epigenetic aberrations to improve diagnosis and prognosis as well as reveal novel targets of therapy for NKTCL.

Keywords

biomarker epigenetics histone modifications NKTCL noncoding RNAs promoter hypermethylation

Introduction

Natural killer/T-cell lymphoma (NKTCL) constitutes approximately 10% of peripheral T-cell lymphomas.¹ The incidence of this rare type of lymphoma is much higher in East Asia as well as in Central and South America compared with the rest of the world.² NKTCLs are characterized by infection with the Epstein Barr Virus (EBV), which may have a causal role in pathogenesis.³ An EBV-encoded gene, LMP1, has been shown to upregulate PD-L1 expression in NK-cell lines, and high serum expression of PD-L1 is associated with poor prognosis and low response to treatment in NKTCLs,⁴ suggesting a role for EBV in immune evasion of NKTCL tumour cells. EBV frequently integrates into NKTCL genomes, and one of these integrations leads to disruption of the host NHEJ1 gene, suggesting a unique means of EBV-induced pathogenesis.⁵ The frequent expression of P-glycoprotein, which is encoded by the MDR1 gene, may be responsible for the chemotherapy resistance observed in NKTCL patients.^6,7 EBV-encoded LMP1 oncoprotein promotes cell cycle progression and inhibits apoptosis via activation of the NFκB pathway or PI3K/AKT pathway.^8,9 Most NKTCLs are of NK-cell origin and usually occur in the nasal and upper aerodigestive tract.¹⁰ Many studies have focussed on genetic alterations to identify dysregulated tumour suppressor genes or oncogenes in these lymphomas.^11–15 However, accumulating evidence suggests that epigenetic aberrations are at least as common and critical as genetic abnormalities in the pathogenesis of NKTCLs.

Epigenetics focusses on the heritable modifications in cellular chromatins that modify the expression of genes in the absence of any change in DNA sequence. Epigenetic events may include histone modifications, promoter-associated CpG island hypermethylations, nucleosome remodelling and regulation with noncoding RNAs (e.g. miRNA, lncRNA). Epigenetic abnormalities are known to play critical roles in carcinogenesis. Indeed, epigenetic aberrations are implicated in regulating a variety of different ‘hallmarks’ of cancer.¹⁶ In the following sections, we will discuss different epigenetic aberrations that drive the tumourigenesis of NKTCL. Moreover, we will focus on the epigenetic aberrations associated with the diagnosis, prognosis and chemotherapy resistance of NKTCLs.

Epigenetically silenced tumour suppressor genes in NKTCL

Promoter regions of many tumour suppressor genes contain CpG islands that are hypermethylated during tumourigenesis.¹⁷ Promoter CpG hypermethylation transcriptionally silences genes through recruitment of histone-modifying enzymes such as histone deacetylases (HDACs), which in turn generate repressive chromatin states.¹⁸ Hypermethylation of promoter-associated CpG islands is a common mechanism for downregulation of tumour suppressor genes in several types of cancers, such as colon cancer and multiple myeloma.^19,20 A number of tumour suppressor gene candidates were found by different research groups to be epigenetically silenced through promoter-associated CpG island hypermethylation in NKTCL tumours by using locus-specific methodologies such as bisulfite sequencing and methylation-specific PCR (MSP). In a previous study, Siu and colleagues evaluated five putative tumour suppressors (i.e. P73, hMLH1, p16, p15, and RARβ) for their promoter methylation status.²¹ They reported that these genes have promoter hypermethylation in a significant fraction of the NKTCL patients, with P73 being the most frequently (94%) methylated gene. However, apart from P73, the methylation analysis was based only on MSP, which provides qualitative information on a limited number of CpG dinucleotides evaluated. p73 has significant amino acid similarity to p53, and it induces apoptosis in a manner similar to p53 when overexpressed in an osteosarcoma cell line.²² It would be interesting to evaluate the frequency of transcriptional silencing of P73 in NKTCL samples and to address whether ectopic p73 inhibits proliferation or induces apoptosis in p73-nonexpressing NK-cell lines. In another study, Ying and colleagues performed comprehensive epigenetic analyses on DLC1 (ARHGAP7) in NKTCLs and other lymphoma types,²³ which revealed aberrant methylation in 77% (34/44) of NKTCL patients. Of note, decitabine (5‑aza‑2’‑deoxycytidine) treatment increased DLC1 transcription in malignant NK-cell lines with epigenetic silencing of DLC1. This gene is known to encode a RhoGAP domain‑containing protein with high sequence homology to rat p122RhoGAP, which is a GTPase‑activating protein that catalyses the conversion of the active GTP‑bound RhoA protein into its inactive GDP‑bound form.²⁴ Given that RAS-mediated transformation involves active RhoA signalling, epigenetic silencing of DLC1 may lead to constitutively active signalling of the RAS signalling pathway in NKTCLs.²⁴ Using similar approaches, another study showed promoter methylation of PCDH10 (protocadherin 10) causing silencing in 100% (4/4) of malignant NK-cell lines and 20% (2/10) of NKTCL patients evaluated.²⁵ However, the functional role of PCDH10 in NKTCL pathogenesis has not yet been elucidated. Wang and colleagues reported promoter CpG methylation-mediated silencing of DLEC1 in 67% (2/3) of NK-cell lines and 75% (6/8) of NKTCL patients.²⁶ The functional consequences of DLEC1 silencing for the development of NKTCL have not been addressed, but its ectopic expression induced G1 cell-cycle arrest and inhibited colony formation in hepatocellular carcinoma cell lines that also have epigenetically silenced DLEC1.²⁷

Using locus-specific methods, previous reports showed epigenetic silencing of DAPK1 and PTPN6 (SHP1) in certain malignant NK-cell lines, findings that were confirmed in NKTCL patients in a subsequent genome-wide study.^28–30 DAPK1, a pro-apoptotic serine/threonine kinase, is a transcriptional target of p53.³¹ It was shown to suppress oncogene-induced transformation by activating the p19ARF/p53-dependent apoptotic checkpoint; however, its functional role as a tumour suppressor has not yet been addressed in NKTCLs. Interestingly, TET2, a hydroxylase catalyzing enzymatic steps towards demethylation of 5-methylcytosines in DNA,³² was identified to be epigenetically silenced due to promoter hypermethylation.³⁰ Recently, recurrent methylation and transcriptional silencing of TET1 in a variety of carcinomas and lymphomas, including NKTCL patients and NK- cell lines, were discovered via epigenomic analyses with MeDIP-chip.³³ Interestingly, reintroduction of TET1 into TET1-silenced carcinoma cell lines inhibited colony formation and restored the transcription of epigenetically silenced tumour suppressor genes (e.g. SLIT2, ZNF382 and HOXA9).³³ A total of 95 epigenetically silenced genes were identified in NKTCL patients and NK-cell lines by integrative analyses of genome-wide promoter methylation and gene expression profiling.³⁰ Based on in silico pathway analyses, most of these genes may have tumour suppressive function, but further studies need to be performed to address those with genuine tumour suppressor function. Given the lack of IDH2 mutations in NKTCL tumours,³⁴ epigenetic silencing or genetic inactivation of TET1 or TET2 may be responsible for promoter hypermethylation of several tumour suppressor genes observed in NKTCLs.

For some tumour suppressor genes, genetic mechanisms have been reported to cooperate with epigenetic mechanisms during transcriptional silencing in NKTCL patients. Three studies reported promoter hypermethylation-mediated silencing of PRDM1 in NKTCL patients as well as NK-cell lines.^35–37 Loss-of-function mutations of PRDM1 are rarely observed in NKTCL patients; however, functional studies performed in vitro and ex vivo characterized PRDM1 as a bona fide tumour suppressor gene deleted or epigenetically silenced in NKTCL patients and NK-cell lines.^36,38 In another study, receptor-type tyrosine-protein phosphatase k (PTPRK) was shown to be transcriptionally downregulated through monoallelic deletion and promoter hypermethylation in NKTCL patients. Restoration of PTPRK expression inhibited the JAK-STAT3 pathway through dephosphorylation of phospho-STAT3^Tyr705. Importantly, ectopic expression of PTPRK inhibited carcinogenesis in malignant NK-cell lines by inhibiting tumour cell growth, invasion, and metastasis.³⁹ HACE1 was also reported to be transcriptionally downregulated through monoallelic deletions and CpG island hypermethylation; however, its role in NKTCL pathogenesis is still not clear, although its re-expression in a HACE1-null NK- cell line induced G2/M cell cycle arrest and apoptosis.⁴⁰ Frequent concomitant epigenetic silencing of CADM1, a stress-responsive tumour suppressor, and its interaction partner DAL-1 was observed in NKTCLs.⁴¹ Further analyses revealed that CADM1 expression may be lost due to locus deletion in NKTCL patients. This interesting study showed a correlation between the methylation of the CADM1 and DAL-1 genes in NKTCL tumours. As these two genes play roles in cell–cell interactions and cell motility, their silencing may promote invasion and metastasis of neoplastic NK cells.⁴¹ Table 1 lists the pathologically and clinically significant cancer-associated genes silenced through promoter hypermethylation in NKTCLs.

Table 1.

Pathologically and clinically significant cancer-associated genes epigenetically silenced in NKTCLs.

Aberrant gene	Functional evidence as a tumour suppressor in NKTCL	Relationship to NKTCL	Reference
ASNS	N.A.^a	Predictive biomarker of asparaginase-based chemotherapy	Küçük³⁰; Li⁴²
BIM1	Reconstitution of its expression induced apoptosis in NK-cell lines.	Silenced pro-apoptotic gene Potential predictive biomarker of chemotherapy	Küçük³⁰
CADM	N.A.	Candidate tumour suppressor	Fu⁴¹
DAL1	N.A.	Candidate tumour suppressor
DAPK1	N.A.	Silenced pro-apoptotic gene	Röhrs²⁸; Küçük³⁰
DLC1	N.A.	Candidate tumour suppressor	Ying²³
DLEC1	N.A.	Candidate tumour suppressor	Wang²⁶
HACE1	Reconstitution of its expression led to G2/M cell cycle arrest and apoptosis in an NK-cell line.	Candidate tumour suppressor	Küçük⁴⁰
PTPN6 (SHP1)	N.A.	Candidate tumour suppressorInhibitor of NK-cell activation	Oka²⁹; Küçük³⁰
PTPRK	Its ectopic expression inhibited cell growth, and reduced invasion of NKTCL cells	Inhibitor of JAK-STAT3 pathway	Chen³⁹
P73	N.A.	Candidate tumour suppressor	Siu²¹; Jost²²
SOCS6	Reconstitution of its expression induced apoptosis, and decreased STAT3 phosphorylation in NK-cell lines.	Candidate tumour suppressorInhibitor of JAK-STAT pathway	Küçük³⁰
TET1	N.A.	Candidate tumour suppressorDNA CpG demethylase	Li³³
TET2	N.A.	Candidate tumour suppressorDNA CpG demethylase	Küçük³⁰

Ectopic expression of ASNS did not decrease cell growth in ASNS-nonexpressing NK cell lines.

ASNS, asparagine synthetase; N.A., not available; NK, natural killer; NKTCL, natural killer/T-cell lymphoma.

Aberrations of epigenetic regulatory genes in NKTCL

Dysregulated expression or mutations of epigenetic regulatory genes may have dramatic consequences in the epigenomic landscape of tumours that may result in altered expression of several oncogenes or tumour suppressor genes.⁴³ Interestingly, recent NGS-based studies revealed somatic mutations in genes regulating the epigenetic landscape, including ARID1A, ASXL3, CREBBP, KMT2D (MLL2), KDM6A, EP300 and TET2 in NKTCL cases,^15,44–47 underscoring the significance of DNA methylation, post-translational modifications of histones and remodelling of chromatin. EP300 is a histone acetyl transferase (HAT) that regulates transcription by modulating chromatin structure, and it acts as a tumour suppressor with loss-of-function mutations in tumours.⁴⁸ Of note, p53 activity can be regulated by EP300-mediated acetylation in response to DNA damage.⁴⁹ Therefore, the genetic aberrations of EP300 may have pleiotropic biological effects on NKTCL, which may involve aberrations in the DNA damage response pathway. Similar to EP300, CREBBP is a histone acetyl transferase, and both can regulate the transcription of distinct or common genes in B cells.⁵⁰ Apart from KDM6A, which was observed to be mutated in an EBV-negative NKTCL patient,⁴⁶ these mutated genes were implicated in driving B-cell lymphomagenesis. For instance, inactivation of CREBBP was shown to promote HDAC3-dependent lymphomas or to cooperate with BCL2 overexpression in the promotion of B-cell lymphoma in mice.^51,52 Another study showed that the histone lysine transferase KMT2D represses B-cell lymphoma development by sustaining a gene expression programme.⁵³ Of significance, FL/DLBCL-associated KMT2D loss-of-function mutations decreased global H3K4 methylation in germinal-centre (GC) B cells in vivo.⁵⁴ Consistent with the role of TET2 in CpG demethylations, TET2-mutated DLBCL patients showed genome-wide alterations in DNA methylations in promoter-associated CpG islands of tumour suppressor genes.⁵⁵

There are few reports available in the literature on the genetic changes in epigenetic-regulatory genes that lead to global changes in the DNA methylation landscape of NKTCL tumours. Gao and colleagues recently reported the presence of TET2 as well as KMT2D mutations in NKTCL patients, where mutated TET2 or KMT2D was significantly associated with poor prognosis.⁴⁷ Considering that loss of expression of these genes was also associated with shorter overall survival of NKTCL patients, it is possible to speculate that these clinically relevant mutations are loss-of-function mutations. Given the epigenomic changes associated with TET2 mutations in DLBCL patients,⁵⁵ it is possible that several tumour suppressors observed to be epigenetically silenced in NKTCLs may be a consequence of genetic or epigenetic inactivation of TET2. Notably, this type of relationship has already been established for a variety of different cancer types, including NKTCL with the TET1 gene, whose methylation-mediated silencing resulted in promoter methylation and transcriptional silencing of tumour suppressors such as PCDH7 and TCF4 in nasopharyngeal carcinoma cells.³³ However, the functional relationship between TET2 or TET1 inactivation and the NKTCL epigenome has not yet been established.

One of the important observations in the epigenomic profile of NKTCL patients is the global hypomethylation observed in genomic locations distal to the promoters.³⁰ It has long been known that global hypomethylation may lead to genomic instability and tumour formation in vivo.⁵⁶ For instance, DNA hypomethylation may contribute to deletions of genomic loci,⁵⁷ which is also frequently observed in NK-cell malignancies.³⁵ Moreover, DNA hypomethylation in retrotransposons may cause reactivation of these genes and translocation to other genomic loci that can dysregulate the expression of cancer-related genes.⁵⁸ The consequence(s) of this global hypomethylation pattern has not been studied yet in NKTCLs; therefore, it would be interesting to investigate whether global hypomethylation promotes genetic alterations contributing to NKTCL pathogenesis.

EZH2 mediates its oncogenic functions as a part of the polycomb repressive complex 2 (PRC2) by methylating histones and generating H3K27me3 repressive marks.⁵⁹ No mutations of EZH2 have been observed in NKTCL patients. However, Yan and colleagues showed that EZH2 is overexpressed in NKTCLs, and its overexpression confers a growth advantage to primary NK cells and NKTCL cell lines independent of its histone methyltransferase activity.⁶⁰ Another report showed that phosphorylation of EZH2 by JAK3 in NKTCL results in dissociation of EZH2 from polycomb repressive complex 2 (PRC2), which may lead to global changes in H3K27me3 histone marks near promoters.⁶¹ In this model, the noncanonical oncogenic functions of EZH2 may, at least in part, be related to its role as a transcriptional activator. Table 2 lists the dysregulated epigenetic regulator genes and describes their relationship to epigenetic changes and NKTCL pathogenesis.

Table 2.

Aberrant epigenetic regulatory genes and their relationship to epigenetic changes and NKTCL pathogenesis.

Aberrant gene	Gene function and aberration	Relationship to NKTCL	Reference
ARID1A	✓ Chromatin remodelling gene✓ A missense mutation	Unknown	Jiang⁴⁴; Choi⁴⁵
ASXL3	✓ Polycomb group protein✓ Mutated	Unknown	Jiang⁴⁴
CREBBP	✓ Histone acetyl transferase✓ Missense mutation	Unknown	Küçük¹⁵
EP300	✓ Histone acetyltransferase✓ Frame-shift or missense mutations	Unknown	Küçük¹⁵
EZH2	✓ Histone methyltransferase✓ Overexpressed	Promotes NK-cell growth independent of histone methyltransferase activity	Yan⁶⁰
KDM6A (UTX)	✓ Histone demethylase specific for H3K27✓ Mutated	Unknown	Tsuyama⁴⁶
KMT2D (MLL2)	✓ Lysine methyltransferase✓ Missense mutations	Unknown	Jiang⁴⁴; Küçük¹⁵; Choi⁴⁵
TET1	✓ DNA CpG demethylase✓ Promoter hypermethylation	Unknown	Li³³
TET2	✓ DNA CpG demethylase✓ Promoter hypermethylation	Unknown	Küçük¹⁵

NKTCL, natural killer/T-cell lymphoma.

Noncoding RNAs in NKTCL pathogenesis

Noncoding RNAs include long or short RNAs that regulate the expression of other genes through a variety of different mechanisms. Among these noncoding RNAs, microRNAs (miRNAs) have been associated with the pathogenesis of many diseases.^62,63 miRNAs are short (~22 nt) noncoding RNAs that inhibit the expression of target genes by inhibiting their translation or promoting transcript degradation.⁶⁴ They have been observed to be dysregulated in several cancer types, such as breast and prostate cancer.^65,66 Like protein-coding genes, miRNAs may promote or suppress carcinogenesis if their expression levels are dysregulated.

miR-155 is an oncogenic miRNA that was shown to be overexpressed and promote lymphomagenesis of diffuse large B-cell lymphoma and anaplastic large-cell lymphoma (ALCL).^67,68 Several independent studies revealed overexpression of mir-155 in NKTCLs.^69–71 miR-155 was shown to promote NK-cell effector functions such as IFNγ production in vivo.⁷² Intriguingly, miR-155 transgenic mice showed increased cell number and enhanced survival of NK cells, which may be due to activation of AKT and ERK pathways.⁷³ These studies in B-cell lymphomas and NK cells, together with the observation that Eμ-miR155 transgenic mice develop high-grade B-cell lymphoma,⁷⁴ suggest that miR-155 may be a highly potent driver of NKTCL. Ng and colleagues investigated the genome-wide profiles of miRNAs in formalin-fixed paraffin embedded tissues and malignant NK-cell lines, where they observed dysregulated miRNAs.⁷⁵ In addition, they showed that ectopic expression of miR-101, miR-26a, miR26b, miR-28-5 and miR-363, which were downregulated in NK lymphoma tumours, reduced the growth of an NK-cell line. However, further studies are required to elucidate the role of these potential tumour suppressor miRNAs in NKTCL pathogenesis. In another study, Paik and colleagues observed epigenetic downregulation of mir-146a in NK-cell lines and formalin-fixed, paraffin-embedded NKTCL tumour samples.⁷⁶ Reconstitution of its expression inhibited proliferation and induced apoptosis, at least in part due to inhibition of the nuclear factor κB (NFκB) signalling pathway by targeting TRAF6.⁷⁶ Liang and colleagues showed that PRDM1 is a direct target of miR-223 in malignant NK cells, which suggests that a variety of mechanisms are responsible for the transcriptional silencing of this tumour suppressor gene.⁷⁷

Some studies have focused on the role of EBV-encoded miRNAs and NKTCL pathogenesis.^78,79 One of these studies showed that an EBV-expressed miRNA (i.e. BART9 miRNA) is overexpressed in two NKTCL cell lines, and it promotes cellular growth by upregulating LMP1, an oncogene encoded by EBV.⁸⁰ Of note, Ma and colleagues observed that an EBV-encoded miRNA, EBV-miR-BHRF1-2, inhibits PRDM1 by targeting its 3’ UTR region in lymphoblastoid cell lines, suggesting an epigenetic mechanism of PRDM1 silencing during EBV⁺ lymphomagenesis.⁸¹ It would be interesting to address whether PRDM1 protein expression is inhibited by EBV-encoded miRNAs in NKTCL patients with detectable PRDM1 transcript expression. Recently, Peng and colleagues investigated the genomic and transcriptomic landscape of EBV in NKTCL patients, which revealed transcriptional dysregulation of EBV-encoded BART miRNAs due to its locus deletion in the EBV genome.⁵

Long-noncoding RNAs (lncRNAs) are functional transcripts longer than 200 nucleotides.⁸² LncRNAs can modulate the expression of genes using mechanisms more diverse than those of miRNAs.⁸³ Like miRNAs, lncRNAs play pivotal roles in different hallmarks (resisting cell death, replicative immortality etc.) of cancer.⁸⁴ Very few studies have been performed on the role of lncRNAs in NKTCL pathogenesis. Among these, the most comprehensive study is the one performed by Baytak and colleagues that reported a whole-transcriptome analysis of NKTCL patients. This study revealed that 166 lncRNAs and 66 lncRNAs were significantly overexpressed and underexpressed in NKTCL patients, respectively, compared with resting and activated primary NK cells.⁷¹ ZFAS1 was one of the overexpressed lncRNAs identified in this study. Interestingly, the genes whose expression positively or negatively correlated with that of ZFAS1 in normal and malignant NK samples were enriched in biological processes (e.g. stabilization of p53, regulation of apoptosis) or signalling pathways (NFκB or WNT signalling) critical to activation or neoplastic transformation of NK cells.⁷¹ Intriguingly, lncRNAs overexpressed and underexpressed in NKTCL patients are associated with pathways or biological processes that play a role in the activation of NK cells. These in silico analyses suggest that ZFAS1 or other dysregulated lncRNAs may regulate NK-cell function as well as tumourigenesis.⁷¹ Another study reported overexpression of the lncRNA MALAT1 in NK- and T-cell lymphoma tumour samples and cell lines.⁸⁵ Of note, high expression levels of components of the polycomb repressive complex 1 (i.e. BMI1) and PRC2 (i.e. EZH2, SUZ12, and EED) were also reported in NKTCL patients, which raised the possibility of the involvement of MALAT1 and PRC proteins in the same signalling pathway.⁸⁶ In support of this possibility, MALAT1 expression was observed to be positively correlated with the expression of PRC1 and PRC2 genes in NKTCL patients.⁸⁵ MALAT1 was shown to interact directly with PRC2 components (i.e. EZH2 and SUZ12) in a T-cell lymphoma line. Despite a lack of direct physical interaction, MALAT1 probably indirectly induces the expression of BMI, a member of the PRC1 complex, through H3K27me3 histone marks.⁸⁵ Overexpressed MALAT1 interacts with the polycomb repressive complex, suggesting that MALAT1 may promote the generation of H3K27me3, thereby repressing certain target genes.⁸⁵ Cancer-associated noncoding RNAs with pathological and biological significance in NKTCL are shown in Table 3.

Table 3.

Cancer-associated miRNAs and lncRNAs dysregulated in NKTCL.

Aberrant noncoding RNA	Epigenetic aberration	Relationship to NKTCL	Reference
BART9	Overexpressed EBV-encoded miRNA	Promotes NK-cell growthUpregulates LMP1	Ramakrishnan⁸⁰
miR-155	Overexpressed miRNA	Promotes NK-cell survivalInduces AKT and ERK pathways	Yamanaka⁶⁹; Zhang⁷⁰; Baytak⁷¹
miR-101, miR-26a, miR26b, miR-28-5, and miR-363	Underexpressed miRNA	Candidate tumour suppressorReduces growth of a malignant NK-cell line	Ng⁷⁵
miR-221	Overexpressed miRNA	Noninvasive diagnostic and prognostic biomarker	Guo⁸⁷
miR-223	Overexpressed miRNA	Targets and downregulates PRDM1 in NKTCL cells	Liang⁷⁷
MALAT1	Upregulated lncRNA	OncogenePrognostic biomarker	Kim⁸⁵
SNHG12	Overexpressed lncRNA	OncogenePrognostic biomarkerPredictive biomarker of chemoresistance	Zhu⁸⁸
ZFAS1	Upregulated lncRNA	Candidate oncogeneRegulator of apoptosis and cell cycle	Baytak⁷¹

miRNA, microRNA; lncRNA, long noncoding RNA; NK, natural killer; NKTCL, natural killer/T-cell lymphoma.

EBV-induced alterations in NKTCL epigenomes

EBV-associated NKTCLs are characterized by a latent stage of infection, which was reported to be associated with promoter methylation-mediated silencing of the two immediate-early (IE) genes, BZLF1 and BRLF1, in EBV.⁸⁹ A number of studies have reported causal relationships between EBV infection and epigenetic aberrations in the host cells of B-cell lymphomas or certain carcinomas.^90–92 Importantly, some of the EBV-encoded proteins are known to epigenetically silence tumour suppressor genes in EBV-associated tumours. For instance, an EBV-encoded oncoprotein, LMP1 (latent membrane protein 1), was reported to upregulate expression of DNA methyl transferases 1, 3a and 3b (i.e. DNMT1, DNMT3A and DNMT3B) in EBV⁺ nasopharyngeal carcinoma cells, which in turn epigenetically silenced E-cadherin.⁹³ Another study showed that DNMT1 was upregulated by LMP2A via phosphorylation of STAT3, which led to promoter methylation-mediated PTEN silencing in gastric carcinoma.⁹⁴ Given that the EBV-encoded EBNA3 gene product is involved in polycomb-mediated repression of the pro-apoptotic BIM gene in B-cell lines,⁹⁵ a variety of different oncoproteins encoded by EBV may be involved in silencing tumour suppressor genes in EBV-infected host cells. Zhao and colleagues reported that EBV-encoded LMP2A-mediated upregulation of DNMT3B resulted in global changes in the epigenomic landscape through promoter hypermethylation of hundreds of genes in EBV⁺ gastric cancer cells.⁹⁶ Having extrapolated the causal relationships between EBV infection and subsequent epigenomic changes such as promoter hypermethylation in a variety of different EBV-infected cell types, Li and colleagues proposed a model for EBV-induced epigenetic pathogenesis in which EBV-encoded oncoproteins (e.g. LMP1, LMP2A) or EBV-encoded miRNAs or lncRNAs modulate the host cell epigenetic machinery, which leads to methylation-mediated silencing of tumour suppressors, thereby promoting malignant transformation.⁹⁷ However, functional studies on the role of EBV-encoded oncoproteins in modulating NK-cell machinery are still quite scarce. Of significance, a recent report showed that EBV genomes isolated from NKTCL patients form distinct clusters when analysed along with other EBV-infected tumours based on phylogenetic analyses.⁵ This observation suggests that the possibility that EBV-induced epigenetic pathogenesis may have characteristics unique to NKTCLs. EBV-encoded miRNAs may promote the development of NKTCL by targeting key cancer-associated genes. One study showed that BART9 miRNA, which is encoded by EBV, leads to increased expression of EBV-encoded LMP1, which in turn promotes proliferation of NKTCL cells.⁸⁰

Diagnostic, prognostic and therapeutic implications of epigenetic aberrations

Several studies have investigated the relationship between epigenetic aberrations and clinical characteristics in NKTCL patients. Chen and colleagues identified PTPRK, a negative regulator of STAT3 signalling, as a bona fide tumour suppressor silenced through the cooperation of genetic and epigenetic mechanisms.³⁹ Importantly, PTPRK promoter methylation was significantly correlated with advanced disease stage and the number of extranodal sites involved in NKTCL patients.³⁹ This study also showed that NKTCL patients treated with the SMILE regimen showed poorer overall survival when their tumours had PTPRK promoter methylation. In another study, EZH2 overexpression was reported to have significant clinical consequences.⁹⁸ Overexpressed EZH2 was associated with advanced disease stage, poorer overall survival and a high proliferation index.⁹⁸ Gao and colleagues recently reported that NKTCL patients with mutations or loss-of-protein expression in KMT2D or TET2 had significantly poorer overall survival,⁴⁷ which suggests that alterations in the epigenomic landscape may be indirectly responsible for the prognostic differences. However, the authors did not address this causal relationship.

Some studies have revealed relationships between miRNA expression and clinical characteristics in NKTCL patients. Paik and colleagues showed that miR-146a expression level is an independent prognostic factor for NKTCL patients.⁷⁶ They further showed that NKTCL patients with low miR146a expression have significantly poorer prognosis compared with those with high miR146a expression.⁷⁶ These findings suggest that miR146a methylation or expression level can potentially be used as prognostic factors. Another clinically significant finding of this study is the increased chemosensitivity observed in malignant NK-cell lines with ectopic miR146a expression, which suggests that it may be a good target of therapy for chemoresistant NKTCL patients. EBV-encoded miRNAs may be clinically relevant for NKTCL patients. Huang and colleagues reported two EBV-encoded miRNAs, mir-BART20-5p and mir-BART8, were associated with disease progression in NKTCL.⁹⁹ miRNA expression profile analyses and qPCR showed elevated levels of expression of miR-BART2-5p, miR-BART7-3p, miR-BART13-3p and miR-BART1-5p in the sera of NKTCL patients, which may have diagnostic value.¹⁰⁰ Moreover, high miR-BART2-5p level in NKTCL patient sera was associated with disease progression and poor prognosis, suggesting it as a potential biomarker for predicting the risk of the disease.¹⁰⁰

There are few reports available on the clinical significance of lncRNAs in NKTCL patients. A recent study by Zhu and colleagues showed that high SNHG12 lncRNA expression was associated with the clinical grade of NKTCL patients.⁸⁸ In vitro manipulation of SNHG12 expression level in malignant NK-cell lines revealed that high SNHG12 expression conferred cisplatin resistance to NKTCL cells.⁸⁸ Of note, SNHG12 overexpression increased P-glycoprotein expression in an NK-cell line, suggesting that this lncRNA may be responsible for the multi-drug resistance observed in NKTCL patients. Another study investigated whether MALAT1 expression in NKTCLs can predict prognosis in NKTCL patients.⁸⁵ There was a trend for poorer survival in the high-MALAT1-expression group, but it was not statistically significant.⁸⁵ As the mentioned study involved a low number of NKTCL patient samples, future studies with larger cohorts are needed to address whether MALAT1 expression can be used as a prognostic marker for NKTCL patients. Interestingly, expression of one of the targets of MALAT1, BMI, showed prognostic value in NKTCL patients.⁸⁶

One of the interesting questions from a clinical point of view would be to transfer the epigenetic knowledge on NKTCLs to routine clinical practice, in particular for disease monitoring. To address whether previously described promoter CpG island methylations can be used for disease monitoring, Siu and colleagues evaluated the promoter methylation status in NKTCL patients of a panel of genes (i.e. p15, p16, p73, hMLH1, RARb) with methylation-specific PCR (MSP) that were previously shown to be hypermethylated in NKTCLs.¹⁰¹ The concordance between MSP and histological evaluation results was quite high, suggesting that MSP may be useful to monitor minimal residual disease and relapse after treatment in NKTCL patients.

Several studies have shown that circulating miRNAs derived from tumour tissues are stable and detectable in serum; therefore, they can potentially be used as noninvasive biomarkers for cancer diagnosis or prognosis.^102–105 Very few studies have investigated the potential of plasma/serum miRNAs as biomarkers in NKTCLs. qPCR-based analyses revealed miR-221 as a potential diagnostic and prognostic biomarker for NKTCL.⁸⁷ Zhang and colleagues observed significantly higher miR-155 levels in the serum of NKTCL patients compared with the levels in healthy individuals.⁷⁰ More importantly, serum miR-155 levels were higher in patients with stable or progressive disease compared with those in partial or complete remission.⁷⁰

Two distinct studies reported an inverse relationship between ASNS (asparagine synthetase) expression level and response to asparaginase-based chemotherapy in NKTCL cell lines and patient samples.^30,42 ASNS expression was shown to be downregulated due to promoter hypermethylation, and there was a very high correlation between ASNS mRNA level and survival of malignant NK-cell lines treated with asparaginase.³⁰ Given that asparaginase-based therapies are currently the most effective therapies against NKTCL and a subset of patients are resistant to these therapies,¹⁰⁶ assessment of ASNS promoter methylation levels of NKTCL tumours may be used as a predictive biomarker for NKTCL patients who are likely to respond to asparaginase-based chemotherapeutic regimens. BCL2L11 (BIM) may also be responsible for chemotherapy resistance in NKTCL patients, as reintroduction of BIM into two BIM-silenced NK-cell lines increased apoptosis after chemotherapy treatment.³⁰ Whether BIM promoter methylation level can be used as a predictive biomarker of chemotherapy resistance requires further investigation in NKTCL patients. Indeed, re-expression of BIM or other epigenetically silenced tumour suppressor genes may provide therapeutic benefit by inhibiting the growth of NKTCL tumours.

Epigenetic control is involved in all hallmarks of tumour development¹⁰⁷; hence, epigenetic drugs may be effective strategies for therapy. The epigenetic regulatory genes identified to be mutated (i.e. ARID1A, ASXL3, CREBBP, EP300, KMT2D) or methylated (i.e. TET1, TET2) may be of therapeutic value. Given that loss of function or loss of expression of TET genes may be responsible for promoter methylation of several tumour suppressors in NKTCLs,³⁰ DNA methyltransferase (DNMT) inhibitors may be useful for restoring the expression of epigenetically silenced tumour suppressors. Indeed, azacitidine showed efficacy in the treatment of myelodysplastic syndromes.¹⁰⁸ However, due to a lack of specificity, DNMT inhibitors may lead to serious side effects owing to increased expression of oncogenes or induction of genomic instability.¹⁰⁹ Similarly, HDAC inhibitors may be an effective therapeutic option for NKTCL patients when they are used in appropriate doses with correct timing to have fewer side effects.¹⁰⁷ However, functional experiments need to be performed in NKTCLs to show the specific effects of mutations or promoter methylations of epigenetic regulatory genes before proceeding with clinical trials targeting these epigenetic aberrations.

Conclusions and future perspectives

Accumulating evidence suggests that a variety of different epigenetic aberrations have biological or clinicopathological significance in NKTCL. However, it seems that our current knowledge on NKTCL epigenetics is just the tip of the iceberg, and future mechanistic studies are needed to elucidate the extent of regulation of chromatin states, especially in the presence of somatic mutations in epigenetic genes. These abnormalities are not only useful for better understanding of the biology of NKTCLs but also may potentially be translated into routine clinical practice as diagnostic, prognostic, or predictive biomarkers.

Footnotes

Author contributions

C.K., J.W., Y.X. and H.Y. searched and critically evaluated the literature related to the topic and wrote the manuscript. C.K. and H.Y. financially supported the study.

Funding

The author(s) disclosed receipt of the following financial support for the research, authorship, and publication of this article: This study was supported by the Young Scientists Award Program of the Turkish Academy of Sciences (TÜBA GEBİP 2017) (C.K.). The research activity in the Hua You laboratory is supported by Guangzhou Medical University. Hua You is supported by the National Natural Science Foundation of China (81911530169, 81903088, 81850410547, 81670180, and 81711540047), Venture and Innovation Support Program for Chongqing Overseas Returnees (cx2019051), and the Beijing Nova Program of the Beijing Municipal Science and Technology Commission (Z171100001117091). YX is sponsored by Natural Science Foundation of Chongqing, China (cstc2019jcyj-msxmX0793).

Conflict of interest statement

The authors declare that there is no conflict of interest.

References

Foss

Zinzani

Vose

, et al. Peripheral T-cell lymphoma. Blood 2011; 117: 6756–6767.

Aozasa

Zaki

MA.

Epidemiology and pathogenesis of nasal NK/T-cell lymphoma: a mini-review. ScientificWorldJournal 2011; 11: 422–428.

Vockerodt

Yap

Shannon-Lowe

, et al. The Epstein-Barr virus and the pathogenesis of lymphoma. J Pathol 2015; 235: 312–322.

Wang

Zhang

, et al. PD-L1 is upregulated by EBV-driven LMP1 through NF-κB pathway and correlates with poor prognosis in natural killer/T-cell lymphoma. J Hematol Oncol 2016; 9: 109.

Peng

Han

Cai

, et al. Genomic and transcriptomic landscapes of Epstein-Barr virus in extranodal natural killer T-cell lymphoma. Leukemia 2019; 33: 1451–1462.

Yamaguchi

Kita

Miwa

, et al. Frequent expression of P-glycoprotein/MDR1 by nasal T-cell lymphoma cells. Cancer 1995; 76: 2351–2356.

Pastan

Gottesman

Multiple-drug resistance in human cancer. New Engl J Med 1987; 316: 1388–1393.

Sun

Zhao

Shi

, et al. LMP1 promotes nasal NK/T-cell lymphoma cell function by eIF4E via NF-κB pathway. Oncol Rep 2015; 34: 3264–3271.

Sun

Zhao

Shi

, et al. LMP-1 induces survivin expression to inhibit cell apoptosis through the NF-κB and PI3K/Akt signaling pathways in nasal NK/T-cell lymphoma. Oncol Rep 2015; 33: 2253–2260.

10.

Tse

Kwong

YL.

How I treat NK/T-cell lymphomas. Blood 2013; 121: 4997–5005.

11.

Hongyo

Syaifudin

, et al. Mutations of the P53 gene in nasal NK/T-cell lymphoma. Lab Invest 2000; 80: 493–499.

12.

Takakuwa

Dong

Nakatsuka

, et al. Frequent mutations of Fas gene in nasal NK/T cell lymphoma. Oncogene 2002; 21: 4702–4705.

13.

Dobashi

Tsuyama

Asaka

, et al. Frequent BCOR aberrations in extranodal NK/T-cell lymphoma, nasal type. Genes Chromosomes Cancer 2016; 55: 460–471.

14.

Koo

Tan

Tang

, et al. Janus kinase 3-activating mutations identified in natural killer/T-cell lymphoma. Cancer Discov 2012; 2: 591–597.

15.

Küçük

Jiang

, et al. Activating mutations of STAT5B and STAT3 in lymphomas derived from γδ-T or NK cells. Nat Commun 2015; 6: 6025.

16.

Flavahan

Gaskell

Bernstein

. Epigenetic plasticity and the hallmarks of cancer. Science 2017; 21; 357: eaal2380.

17.

Jones

Baylin

. The fundamental role of epigenetic events in cancer. Nat Rev Genet 2002; 3: 415–428.

18.

Jones

Veenstra

Wade

, et al. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet 1998; 19: 187–191.

19.

Esteller

Sparks

Toyota

, et al. Analysis of adenomatous polyposis coli promoter hypermethylation in human cancer. Cancer Res 2000; 60: 4366–4371.

20.

Chim

Fung

Cheung

, et al. SOCS1 and SHP1 hypermethylation in multiple myeloma: implications for epigenetic activation of the Jak/STAT pathway. Blood 2004; 103: 4630–4635.

21.

Siu

Chan

Wong

, et al. Specific patterns of gene methylation in natural killer cell lymphomas: P73 is consistently involved. Am J Pathol 2002; 160: 59–66.

22.

Jost

Marin

Kaelin

Jr.

P73 is a simian [correction of human] P53-related protein that can induce apoptosis. Nature 1997; 389: 191–194.

23.

Ying

Murray

, et al. Tumor-specific methylation of the 8p22 tumor suppressor gene DLC1 is an epigenetic biomarker for Hodgkin, nasal NK/T-cell and other types of lymphomas. Epigenetics 2007; 2: 15–21.

24.

Etienne-Manneville

Hall

. Rho GTPases in cell biology. Nature 2002; 420: 629–635.

25.

Ying

Gao

, et al. Frequent epigenetic silencing of protocadherin 10 by methylation in multiple haematologic malignancies. Br J Haematol 2007; 136: 829–832.

26.

Wang

, et al. Epigenetic silencing of the 3p22 tumor suppressor DLEC1 by promoter CpG methylation in non-Hodgkin and Hodgkin lymphomas. J Transl Med 2012; 10: 209.

27.

Qiu

Salto-Tellez

Ross

, et al. The tumor suppressor gene DLEC1 is frequently silenced by DNA methylation in hepatocellular carcinoma and induces G1 arrest in cell cycle. J Hepatol 2008; 48: 433–441.

28.

Röhrs

Romani

Zaborski

, et al. Hypermethylation of death-associated protein kinase 1 differentiates natural killer cell lines from cell lines derived from T-acute lymphoblastic leukemia. Leukemia 2009; 23: 1174–1176.

29.

Oka

Ouchida

Koyama

, et al. Gene silencing of the tyrosine phosphatase SHP1 gene by aberrant methylation in leukemias/lymphomas. Cancer Res 2002; 62: 6390–6394.

30.

Küçük

Jiang

, et al. Global promoter methylation analysis reveals novel candidate tumor suppressor genes in natural killer cell lymphoma. Clin Cancer Res 2015; 21: 1699–1711.

31.

Martoriati

Doumont

Alcalay

, et al. Dapk1, encoding an activator of a p19ARF-p53-mediated apoptotic checkpoint, is a transcription target of p53. Oncogene 2005; 24: 1461–1466.

32.

Huang

Jankowska

, et al. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature 2010; 468: 839–843.

33.

Mao

, et al. Epigenetic inactivation of the cpG demethylase TET1 as a DNA methylation feedback loop in human cancers. Scientific Rep 2016; 6: 26591.

34.

Cairns

Iqbal

Lemonnier

, et al. IDH2 mutations are frequent in angioimmunoblastic T-cell lymphoma. Blood 2012; 119: 1901–1903.

35.

Iqbal

Kucuk

Deleeuw

, et al. Genomic analyses reveal global functional alterations that promote tumor growth and novel tumor suppressor genes in natural killer-cell malignancies. Leukemia 2009; 23: 1139–1151.

36.

Kucuk

Iqbal

, et al. PRDM1 is a tumor suppressor gene in natural killer cell malignancies. Proc Natl Acad Sci USA 2011; 108: 20119–20124.

37.

Zhang

Liang

, et al. Hypermethylation of PRDM1/BLIMP-1 promoter in extranodal NK/T-cell lymphoma, nasal type: an evidence of predominant role in its downregulation. Hematol Oncol 2017; 35: 645–654.

38.

Karube

Nakagawa

Tsuzuki

, et al. Identification of FOXO3 and PRDM1 as tumor-suppressor gene candidates in NK-cell neoplasms by genomic and functional analyses. Blood 2011; 118: 3195–3204.

39.

Chen

Guo

Shen

, et al. Receptor-type tyrosine-protein phosphatase κ directly targets STAT3 activation for tumor suppression in nasal NK/T-cell lymphoma. Blood 2015; 125: 1589–1600.

40.

Küçük

Iqbal

, et al. HACE1 is a tumor suppressor gene candidate in natural killer cell neoplasms. Am J Pathol 2013; 182: 49–55.

41.

Gao

Zhang

, et al. Frequent concomitant epigenetic silencing of the stress-responsive tumor suppressor gene CADM1, and its interacting partner DAL-1 in nasal NK/T-cell lymphoma. Int J Cancer 2009; 124: 1572–1578.

42.

Zhang

, et al. Asparagine synthetase expression and its potential prognostic value in patients with NK/T cell lymphoma. Oncol Rep 2014; 32: 853–859.

43.

Plass

Pfister

Lindroth

, et al. Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer. Nat Rev Genet 2013; 14: 765–780.

44.

Jiang

Yan

, et al. Exome sequencing identifies somatic mutations of DDX3X in natural killer/T-cell lymphoma. Nat Genet 2015; 47: 1061–1066.

45.

Choi

Kim

, et al. Mutational analysis of extranodal NK/T-cell lymphoma using targeted sequencing with a comprehensive cancer panel. Genomics Inform 2016; 14: 78–84.

46.

Tsuyama

Asaka

Dobashi

, et al. Epstein-Barr virus-negative extranodal ‘true’ natural killer-cell lymphoma harbouring a KDM6A mutation. Hematol Oncol 2018; 36: 328–335.

47.

Gao

Zhao

Zhang

, et al. Somatic mutations in KMT2D and TET2 associated with worse prognosis in Epstein-Barr virus-associated T or natural killer-cell lymphoproliferative disorders. Cancer Biol Ther 2019; 20: 1319–1327.

48.

Gayther

Batley

Linger

, et al. Mutations truncating the EP300 acetylase in human cancers. Nat Genet 2000; 24: 300–303.

49.

Grossman

. P300/CBP/p53 interaction and regulation of the p53 response. Eur J Biochem 2001; 268: 2773–2778.

50.

Meyer

Scuoppo

Vlasevska

, et al. Unique and shared epigenetic programs of the CREBBP and EP300 acetyltransferases in germinal center B cells reveal targetable dependencies in lymphoma. Immunity 2019; 51: 535–547.e9.

51.

Jiang

Ortega-Molina

Geng

, et al. Crebbp inactivation promotes the development of HDAC3-dependent lymphomas. Cancer Discov 2017; 7: 38–53.

52.

Garcia-Ramirez

Tadros

Gonzalez-Herrero

, et al. CREBBP loss cooperates with BCL2 overexpression to promote lymphoma in mice. Blood 2017; 129: 2645–2656.

53.

Ortega-Molina

Boss

Canela

, et al. The histone lysine methyltransferase KMT2D sustains a gene expression program that represses B cell lymphoma development. Nat Med 2015; 21: 1199–1208.

54.

Zhang

Dominguez-Sola

Hussein

, et al. Disruption of KMT2D perturbs germinal center B cell development and promotes lymphomagenesis. Nat Med 2015; 21: 1190–1198.

55.

Asmar

Punj

Christensen

, et al. Genome-wide profiling identifies a DNA methylation signature that associates with TET2 mutations in diffuse large B-cell lymphoma. Haematologica 2013; 98: 1912–1920.

56.

Eden

Gaudet

Waghmare

, et al. Chromosomal instability and tumors promoted by DNA hypomethylation. Science 2003; 300: 455.

57.

Chen

Pettersson

Beard

, et al. DNA hypomethylation leads to elevated mutation rates. Nature 1998; 395: 89–93.

58.

Rodriguez-Paredes

Esteller

. Cancer epigenetics reaches mainstream oncology. Nat Med 2011; 17: 330–339.

59.

Simon

Lange

. Roles of the EZH2 histone methyltransferase in cancer epigenetics. Mutat Res 2008; 647: 21–29.

60.

Yan

Tay

, et al. EZH2 overexpression in natural killer/T-cell lymphoma confers growth advantage independently of histone methyltransferase activity. Blood 2013; 121: 4512–4520.

61.

Yan

Lin

, et al. EZH2 phosphorylation by JAK3 mediates a switch to noncanonical function in natural killer/T-cell lymphoma. Blood 2016; 128: 948–958.

62.

Zhang

Deng

, et al. An analysis of human microrna and disease associations. PLoS One 2008; 3: e3420.

63.

Tan

Koo

Kaur

, et al. Micrornas in stroke pathogenesis. Curr Mol Med 2011; 11: 76–92.

64.

Bartel

. Micrornas: genomics, biogenesis, mechanism, and function. Cell 2004; 116: 281–297.

65.

Tavazoie

Alarcon

Oskarsson

, et al. Endogenous human micrornas that suppress breast cancer metastasis. Nature 2008; 451: 147–152.

66.

Shi

Xue

Yang

, et al. An androgen-regulated mirna suppresses BAK1 expression and induces androgen-independent growth of prostate cancer cells. Proc Natl Acad Sci USA 2007; 104: 19983–19988.

67.

Huang

Shen

Liu

, et al. Quantitative proteomics reveals that miR-155 regulates the PI3K-AKT pathway in diffuse large B-cell lymphoma. Am J Pathol 2012; 181: 26–33.

68.

Merkel

Hamacher

Griessl

, et al. Oncogenic role of miR-155 in anaplastic large cell lymphoma lacking the t(2;5) translocation. J Pathol 2015; 236: 445–546.

69.

Yamanaka

Tagawa

Takahashi

, et al. Aberrant overexpression of micrornas activate AKT signaling via down-regulation of tumor suppressors in natural killer-cell lymphoma/leukemia. Blood 2009; 114: 3265–3275.

70.

Zhang

Huang

, et al. Microrna-155 is a potential molecular marker of natural killer/T-cell lymphoma. Oncotarget 2016; 7: 53808–53819.

71.

Baytak

Gong

Akman

, et al. Whole transcriptome analysis reveals dysregulated oncogenic lncRNAs in natural killer/T-cell lymphoma and establishes MIR155HG as a target of PRDM1. Tumour Biol 2017; 39: 1010428317701648.

72.

Trotta

Chen

Ciarlariello

, et al. miR-155 regulates IFN-γ production in natural killer cells. Blood 2012; 119: 3478–3485.

73.

Trotta

Chen

Costinean

, et al. Overexpression of miR-155 causes expansion, arrest in terminal differentiation and functional activation of mouse natural killer cells. Blood 2013; 121: 3126–3134.

74.

Costinean

Zanesi

Pekarsky

, et al. Pre-B cell proliferation and lymphoblastic leukemia/high-grade lymphoma in E(mu)-miR155 transgenic mice. Proc Natl Acad Sci USA 2006; 103: 7024–7029.

75.

Yan

Huang

, et al. Dysregulated micrornas affect pathways and targets of biologic relevance in nasal-type natural killer/T-cell lymphoma. Blood 2011; 118: 4919–4929.

76.

Paik

Jang

Jeon

, et al. MicroRNA-146a downregulates NFκB activity via targeting TRAF6 and functions as a tumor suppressor having strong prognostic implications in NK/T cell lymphoma. Clin Cancer Res 2011; 17: 4761–4771.

77.

Liang

Nong

Zhang

, et al. The downregulation of PRDM1/BLIMP-1 is associated with aberrant expression of miR-223 in extranodal NK/T-cell lymphoma, nasal type. J Exp Clin Cancer Res 2014; 33: 7.

78.

Navari

Etebari

Ibrahimi

, et al. Pathobiologic roles of Epstein-Barr virus-encoded micrornas in human lymphomas. Int J Mol Sci 2018; 19: pii: E1168.

79.

Mei

Zhang

. Non-coding RNAs in natural killer/T-cell lymphoma. Front Oncol 2019; 9: 515.

80.

Ramakrishnan

Donahue

Garcia

, et al. Epstein-Barr virus BART9 miRNA modulates LMP1 levels and affects growth rate of nasal NK T cell lymphomas. PLoS One 2011; 6: e27271.

81.

Nie

Redmond

, et al. EBV-miR-BHRF1-2 targets PRDM1/BLIMP1: potential role in EBV lymphomagenesis. Leukemia 2016; 30: 594–604.

82.

Mercer

Dinger

Mattick

. Long non-coding RNAs: insights into functions. Nat Rev Genet 2009; 10: 155–159.

83.

Wang

Chang

. Molecular mechanisms of long noncoding RNAs. Mol Cell 2011; 43: 904–914.

84.

Schmitt

Chang

. Long noncoding RNAs in cancer pathways. Cancer cell 2016; 29: 452–463.

85.

Kim

Yang

, et al. Association of the long non-coding RNA MALAT1 with the polycomb repressive complex pathway in T and NK cell lymphoma. Oncotarget 2017; 8: 31305–31317.

86.

Kim

Yang

Min

, et al. The role of the polycomb repressive complex pathway in T and NK cell lymphoma: biological and prognostic implications. Tumour Biol 2016; 37: 2037–2047.

87.

Guo

Huang

Guo

, et al. Diagnostic and prognostic value of circulating miR-221 for extranodal natural killer/T-cell lymphoma. Dis Markers 2010; 29: 251–258.

88.

Zhu

Zhang

, et al. c-Myc mediated upregulation of long noncoding RNA SNHG12 regulates proliferation and drug sensitivity in natural killer/T-cell lymphoma. J Cell Biochem 2019; 120: 12628–12637.

89.

Choi

, et al. Methylation profiling of Epstein-Barr virus immediate-early gene promoters, BZLF1 and BRLF1 in tumors of epithelial, NK- and B-cell origins. BMC Cancer 2012; 12: 125.

90.

Leonard

Wei

Anderton

, et al. Epigenetic and transcriptional changes which follow Epstein-Barr virus infection of germinal center B cells and their relevance to the pathogenesis of Hodgkin’s lymphoma. J Virol 2011; 85: 9568–9577.

91.

Ghosh Roy

Robertson

Saha

. Epigenetic impact on EBV associated B-cell lymphomagenesis. Biomolecules 2016; 6: pii: E46.

92.

Nishikawa

Iizasa

Yoshiyama

, et al. The role of epigenetic regulation in Epstein-Barr virus-associated gastric cancer. Int J Mol Sci 2017; 18: pii: E1606.

93.

Tsai

Tse

, et al. The Epstein-Barr virus oncogene product, latent membrane protein 1, induces the downregulation of E-cadherin gene expression via activation of DNA methyltransferases. Proc Natl Acad Sci USA 2002; 99: 10084–10089.

94.

Hino

Uozaki

Murakami

, et al. Activation of DNA methyltransferase 1 by EBV latent membrane protein 2A leads to promoter hypermethylation of PTEN gene in gastric carcinoma. Cancer Res 2009; 69: 2766–2774.

95.

Paschos

Parker

Watanatanasup

, et al. Bim promoter directly targeted by EBNA3C in polycomb-mediated repression by EBV. Nucleic Acids Res 2012; 40: 7233–7246.

96.

Zhao

Liang

Cheung

, et al. Genome-wide identification of Epstein-Barr virus-driven promoter methylation profiles of human genes in gastric cancer cells. Cancer 2013; 119: 304–312.

97.

BBY

Chan

ATC

, et al. Epstein-Barr virus-induced epigenetic pathogenesis of viral-associated lymphoepithelioma-like carcinomas and natural killer/T-cell lymphomas. Pathogens 2018; 7: pii: E63.

98.

Liu

Liang

Huang

, et al. Aberrant differential expression of EZH2 and H3K27ME3 in extranodal NK/T-cell lymphoma, nasal type, is associated with disease progression and prognosis. Hum Pathol 2019; 83: 166–176.

99.

Huang

Lin

. EBV-encoded miR-BART20-5p and miR-BART8 inhibit the IFN-γ-STAT1 pathway associated with disease progression in nasal NK-cell lymphoma. Am J Pathol 2014; 184: 1185–1197.

100.

Komabayashi

Kishibe

Nagato

, et al. Circulating Epstein-Barr virus-encoded micro-RNAs as potential biomarkers for nasal natural killer/T-cell lymphoma. Hematol Oncol 2017; 35: 655–663.

101.

Siu

Chan

Wong

, et al. Aberrant promoter CPG methylation as a molecular marker for disease monitoring in natural killer cell lymphomas. Br J Haematol 2003; 122: 70–77.

102.

Mitchell

Parkin

Kroh

, et al. Circulating micrornas as stable blood-based markers for cancer detection. Proc Natl Acad Sci USA 2008; 105: 10513–10518.

103.

Rabinowits

Gercel-Taylor

Day

, et al. Exosomal microrna: a diagnostic marker for lung cancer. Clin Lung Cancer 2009; 10: 42–46.

104.

Madhavan

Zucknick

Wallwiener

, et al. Circulating mirnas as surrogate markers for circulating tumor cells and prognostic markers in metastatic breast cancer. Clin Cancer Res 2012; 18: 5972–5982.

105.

Cheng

Zhang

Cogdell

, et al. Circulating plasma miR-141 is a novel biomarker for metastatic colon cancer and predicts poor prognosis. PLoS One 2011; 6: e17745.

106.

Jaccard

Gachard

Marin

, et al. Efficacy of l-asparaginase with methotrexate and dexamethasone (aspametdex regimen) in patients with refractory or relapsing extranodal NK/T-cell lymphoma, a phase 2 study. Blood 2011; 117: 1834–1839.

107.

Azad

Zahnow

Rudin

, et al. The future of epigenetic therapy in solid tumours–lessons from the past. Nat Rev Clin Oncol 2013; 10: 256–266.

108.

Silverman

Demakos

Peterson

, et al. Randomized controlled trial of azacitidine in patients with the myelodysplastic syndrome: a study of the cancer and leukemia group B. J Clin Oncol 2002; 20: 2429–2440.

109.

Kelly

De Carvalho

Jones

. Epigenetic modifications as therapeutic targets. Nat Biotechnol 2010; 28: 1069–1078.

Epigenetic aberrations in natural killer/T-cell lymphoma: diagnostic,prognostic and therapeutic implications

Abstract

Keywords

Introduction

Epigenetically silenced tumour suppressor genes in NKTCL

Aberrations of epigenetic regulatory genes in NKTCL

Noncoding RNAs in NKTCL pathogenesis

EBV-induced alterations in NKTCL epigenomes

Diagnostic, prognostic and therapeutic implications of epigenetic aberrations

Conclusions and future perspectives

Footnotes

Author contributions

Funding

Conflict of interest statement

References