The Genomics and Molecular Biology of Natural Killer/T-Cell Lymphoma: Opportunities for Translation
Abstract
:1. Introduction
2. Insights from Gene Expression Profiling
2.1. Classification
2.2. Deregulated Single Genes
2.2.1. Survivin
2.2.2. AURKA
2.2.3. C-MYC
2.2.4. EZH2
2.2.5. RUNX3
2.3. Deregulated Signaling Pathways
2.3.1. JAK/STAT
2.3.2. PDGF pathway
2.3.3. NOTCH-1
2.3.4. NF-κB
2.3.5. Other Signaling Pathways
3. Insights from Copy Number Analysis
3.1. Copy Number Loss (Potential Tumor Suppressor Genes)
3.1.1. PRDM1
3.1.2. HACE1
3.1.3. PTPRK
3.1.4. Other Candidate Genes in the Commonly Deleted 6q21 Region
3.2. Other Chromosomal Gains and Losses
4. Insights from Genome Wide Association Studies
5. Insights from Mutational Profiling
5.1. JAK/STAT Pathway Associated Genes
5.2. Epigenetic Regulators
5.3. DDX3X
5.4. TP53 and Pro-Apoptotic Genes
5.5. ECSIT
5.6. Pro-Survival Signaling Pathways
6. Epigenetic Dysregulation in ENKTL
6.1. Dysregulated Promoter Methylation
6.2. MicroRNA deregulation in ENKTL
6.3. Mechanisms of microRNA Dysregulation in ENKTL
7. Potential Immunotherapeutic Targets in ENKTL
8. Opportunities for Translation
8.1. Refining Diagnosis
8.2. Risk Stratification
8.3. Conclusions, Promising Therapeutic Targets and Future Directions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Gene | Reported Frequency | No. of Positive Cases (Total No. of Cases Tested) | Overall Frequency (%) |
---|---|---|---|
ARID1A | 6 | 6 (105) | 5.7 |
ASXL3 | 4 | 4 (105) | 3.8 |
BCOR | 6–32 | 20 (147) | 13.6 |
b-catenin | 16–30 | 41 (179) | 22.9 |
BIRC3 | 3 | 3 (88) | 3.4 |
BAK | 25.9 | 7 (27) | 25.9 |
CHPF2 | 4 | 4 (105) | 3.8 |
C-KIT | 5–52 | 30 (170) | 18.8 |
CMPK1 | 2 | 2 (88) | 2.3 |
DDX3X | 8–50 | 33 (283) | 11.7 |
ECSIT | 19 | 17 (88) | 19.3 |
EP300 | 4–6 | 7 (156) | 4.5 |
FAT4 | 2–8 | 4 (113) | 3.5 |
FAS | 4 | 3 (76) | 3.9 |
IKBKB | 2 | 2 (88) | 2.3 |
IL6R | 6 | 2(34) | 5.9 |
JAK1 | 2-8 | 3 (90) | 3.3 |
JAK3 | 5-35 | 36 (227) | 13 |
KRAS | 3–25 | 11 (251) | 4.4 |
MLL2 | 2–18 | 14(190) | 7.4 |
MLL3 | 12 | 3 (25) | 12 |
MSH3 | 2 | 2 (88) | 2.3 |
M6PR | 2 | 2 (88) | 2.3 |
MIR17HG | 8 | 2 (25) | 8 |
MSN | 9 | 9 (105) | 8.6 |
MGAM | 4 | 4 (105) | 3.8 |
MGA | 9 | 9 (105) | 8.6 |
NRAS | 2–25 | 6 (227) | 2.6 |
NOTCH2 | 2–25 | 3 (153) | 2 |
STAT1 | 4 | 1 (25) | 4 |
STAT3 | 1–26 | 30 (387) | 8.3 |
STAT5B | 2–6 | 8 (244) | 3.3 |
STAT6 | 4 | 1 (25) | 4 |
TP53 | 4–63 | 139 (611) | 22.7 |
TET2 | 8 | 2 (25) | 8 |
WDR66 | 2 | 2 (88) | 2.3 |
MicroRNA | Evidence Supporting Their Biological Significance | References |
---|---|---|
MicroRNAs underexpressed in ENKTL | ||
miR-146a | Overexpression of mir-146a suppressed cell proliferation, induced apoptosis, and enhanced chemosensitivity by inhibiting the NF-kB pathway via targeted downregulation of TRAF6. ENKTL patients with low miRNA-146a expression had higher frequency of non-response to chemotherapy. | Paik et al. 2011 [97] |
miR-150 | MiR-150 is expressed at lower levels in both ENKTL cell lines and tumor tissue compared to normal NK cells. Its aberrant downregulation induced continuous activation of the PI3K–AKT pathway, leading to telomerase activation and immortalization of cancer cells. | Watanabe et al. 2011 [105] |
miR-26 and miR-101 | Downregulation of miR-26a and miR-101 resulted in upregulation of their target Enhancer of Zeste Homolog 2 (EZH2) in ENKTL tumor tissue and cell lines. | Yan et al. 2013 [34] |
miR-223 | MiR-223 targets PRDM1, a potential tumor suppressor gene in ENKTL: (i) miR-223 and PRDM1 exhibited inverse patterns of expression in ENKTL tissues and cell lines; (ii) PRDM1 was identified as a direct target gene of miR-223 by luciferase assays; (iii) ectopic expression of miR-223 led to downregulation of the PRDM1 protein in vitro whereas a decrease in miR-223 restored the level of PRDM1 protein. | Liang et al. 2014 [61] |
miR-142-3p and miR-205 | miR-142-3p and miR-205 are downregulated in ENKTL compared with normal thymic tissue. Mir-142-3p targets the proinflammatory cytokine interleukin 1 alpha (IL1A) and mir-205 targets the oncogene BCL6 in vitro. | Motsch et al. 2012 [102] |
miR-10, miR-342-3p | Expression of miR-10a and miR-342-3p, which are downregulated in ENTKL tissues, is inversely correlated with protein expression of their predicted target gene, T-lymphoma invasion and metastasis inducing factor 1 (TIAM1). | Huang et al. 2016 [106] |
MicroRNAs overexpressed in ENKTL | ||
miR-155 and miR-21 | MiR-21 and miR-155 are over-expressed in ENKTL samples and cell lines. Mir-21 downregulates phosphatase and tensin homolog (PTEN) and programmed cell death 4 (PDCD4), whilst mir-155 directly targets SHIP1 in ENTKL cell lines. Both PTEN and SHIP1 are involved in the AKT signaling pathway. | Yamanaka et al. 2009 [103] |
EBV-encoded microRNAs | ||
BART9 | BART9 shows a pro-proliferative effect in two ENKTL cell lines (SNK6 and SNT16) that is mediated, at least in part by upregulation of LMP-1 levels. | Ramakrishnan etal. 2011 [107] |
Therapeutic Targets or Signaling Pathway | Clinical Significance for Therapeutics | Reference |
---|---|---|
JAK-3 | JAK-3 inhibition is shown to have potent anti-tumor activity in pre-clinical models. Clinical trials evaluating JAK inhibitors in ENKTL are in progress. | Sim et al. 2017 [77] Narisimagi et al. 2017 [79] |
STAT-3 | STAT-3 mutant ENKTL are sensitive to STAT-3 inhibition in vitro. | Sim et al. 2017 [77] |
NF-kB | NF-kB upregulation is an important event in ENKTL pathogenesis. Bortezomib is being evaluated in early phase clinical trials. | Tang et al. 2016 [49] |
CD38 | CD38 is upregulated in ENKTL. Daratumumab has good in vitro efficacy and one case report documenting complete response. | Mustafa et al. 2017 [124] Hari et al. 2016 [125] |
PD-1 | PD-L1 is upregulated in ENKTL. Early clinical trials show potent single agent activity of anti PD-1 therapy in relapsed, refractory ENKTL. | Kwong et al. 2017 [116] |
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De Mel, S.; Soon, G.S.-T.; Mok, Y.; Chung, T.-H.; Jeyasekharan, A.D.; Chng, W.-J.; Ng, S.-B. The Genomics and Molecular Biology of Natural Killer/T-Cell Lymphoma: Opportunities for Translation. Int. J. Mol. Sci. 2018, 19, 1931. https://doi.org/10.3390/ijms19071931
De Mel S, Soon GS-T, Mok Y, Chung T-H, Jeyasekharan AD, Chng W-J, Ng S-B. The Genomics and Molecular Biology of Natural Killer/T-Cell Lymphoma: Opportunities for Translation. International Journal of Molecular Sciences. 2018; 19(7):1931. https://doi.org/10.3390/ijms19071931
Chicago/Turabian StyleDe Mel, Sanjay, Gwyneth Shook-Ting Soon, Yingting Mok, Tae-Hoon Chung, Anand D. Jeyasekharan, Wee-Joo Chng, and Siok-Bian Ng. 2018. "The Genomics and Molecular Biology of Natural Killer/T-Cell Lymphoma: Opportunities for Translation" International Journal of Molecular Sciences 19, no. 7: 1931. https://doi.org/10.3390/ijms19071931
APA StyleDe Mel, S., Soon, G. S. -T., Mok, Y., Chung, T. -H., Jeyasekharan, A. D., Chng, W. -J., & Ng, S. -B. (2018). The Genomics and Molecular Biology of Natural Killer/T-Cell Lymphoma: Opportunities for Translation. International Journal of Molecular Sciences, 19(7), 1931. https://doi.org/10.3390/ijms19071931