Abstract
Aggressive NK-cell leukemia (ANKL) is a rare form of NK cell neoplasm that is more prevalent among people from Asia and Central and South America. Patients usually die within days to months, even after receiving prompt therapeutic management. Here we performed the first comprehensive study of ANKL by integrating whole genome, transcriptome and targeted sequencing, cytokine array as well as functional assays. Mutations in the JAK-STAT pathway were identified in 48% (14/29) of ANKL patients, while the extracellular STAT3 stimulator IL10 was elevated by an average of 56-fold (P < 0.0001) in the plasma of all patients examined. Additional frequently mutated genes included TP53 (34%), TET2 (28%), CREBBP (21%) and MLL2 (21%). Patient NK leukemia cells showed prominent activation of STAT3 phosphorylation, MYC expression and transcriptional activities in multiple metabolic pathways. Functionally, STAT3 activation and MYC expression were critical for the proliferation and survival of ANKL cells. STAT signaling regulated the MYC transcription program, and both STAT signaling and MYC transcription were required to maintain the activation of nucleotide synthesis and glycolysis. Collectively, the JAK-STAT pathway represents a major target for genomic alterations and IL10 stimulation in ANKL. This newly discovered JAK/STAT-MYC-biosynthesis axis may provide opportunities for the development of novel therapeutic strategies in treating this subtype of leukemia.
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Acknowledgements
We thank all the faculties and staffs in the Clinical and Laboratory Unit of the Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology for their clinical and technical support; the Core Genomic Facility of Beijing Institute of Genomics, Chinese Academy of Sciences for the construction and sequencing of libraries; Drs Qing Li and Jiguang Wang for critical reading and valuable comments on the manuscript; Dr Kai Fu for providing the cell line YT. This study was supported by the National Natural Science Foundation of China (81570196 to JZ, 81425003 to QW, 81670152 to Liang H, 81600120 to NW, 81300410 to DW, 81500100 to YL and 81400122 to KZ), the National Key Basic Research Program of China (2014CB542001 to QW), the Key Program of the National Natural Science Foundation of China (81230052 to JZ), the Key Research Program of the Chinese Academy of Sciences (Precious Medicine Research in Chinese Population; KJZD-EW-L14-3 to QW), and the National High Technology Research and Development Program of China (863 program; 2012AA02A507 to JZ and 2014AA020532 to Liang H).
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Supplementary information
Supplementary information, Figure S1
Strategies for the integrative analysis of ANKLs. (PDF 401 kb)
Supplementary information, Figure S2
Isolation of granulocytes, leukemia NK cells and normal NK cells. (PDF 387 kb)
Supplementary information, Figure S3
Frequency of somatic SNV of ANKL and 40 additional cancer types. (PDF 493 kb)
Supplementary information, Figure S4
EBV reads number of leukemia NK cells and granulocytes from 8 ANKL patients. (PDF 421 kb)
Supplementary information, Figure S5
KEGG pathway enrichment analysis of protein-altering somatic SNVs. (PDF 438 kb)
Supplementary information, Figure S6
Functional enrichment analysis of genomic alterations with HotNet2. (PDF 373 kb)
Supplementary information, Figure S7
STAT3 and STAT5B mutations identified in ANKL patients. (PDF 541 kb)
Supplementary information, Figure S8
TET2 mutations identified in ANKL patients. (PDF 471 kb)
Supplementary information, Figure S9
Semi-quantitative immunoreactivity histological scores of MYC staining in bone marrow biopsy of ANKL and control samples. (PDF 422 kb)
Supplementary information, Figure S10
Functional enrichment map for MYC-signature genes that were upregulated in ANKLs compared to healthy donors. (PDF 856 kb)
Supplementary information, Figure S11
The effect of IL10 or a STAT3 inhibitor (Stattic) on the apoptosis of ANKL cell lines. (PDF 457 kb)
Supplementary information, Figure S12
The effect of IL10 and the STAT3 inhibitor (Stattic) on the mRNA expression of MYC in ANKL cell lines. (PDF 470 kb)
Supplementary information, Figure S13
The rate of EdU incorporation in JQ1-treated ANKL cell lines. (PDF 404 kb)
Supplementary information, Figure S14
Gene-set enrichment analysis (GSEA) of known MYC and STAT3 signatures. (PDF 523 kb)
Supplementary information, Figure S15
Enrichment of metabolic pathways in primary ANKL leukemia cells and ANKL cell lines. (PDF 480 kb)
Supplementary information, Figure S16
The effect of STAT3 Y640F mutant on the phosphorylation of STAT3 and mRNA expression of MYC target gene. (PDF 583 kb)
Supplementary information, Figure S17
The effect of IL10 on the mRNA expression of MYC and MYC target genes in KHYG-1 cell line transfected with STAT3 Y640F mutant. (PDF 584 kb)
Supplementary information, Figure S18
The effect of IL10 on STAT3 phosphorylation, MYC expressionand the proliferation of STAT3 Y640F-mutant ANKL cell line YT. (PDF 505 kb)
Supplementary information, Figure S19
Quantitative analysis of the Epstein-Barr virus (EBV) load in ANKL patients and healthy donors with whole-transcriptome sequencing (WTS) data. (PDF 351 kb)
Supplementary information, Figure S20
Expression of EBV-encoded small RNAs in primary ANKL leukemia cells. (PDF 400 kb)
Supplementary information, Figure S21
A large gain across MYC and an inter-chromosomal translocation detected by GVC-CNV and GVC-SV in ANKL No.19. (PDF 456 kb)
Supplementary information, Table S1
Patient characteristics of ANKL. (PDF 633 kb)
Supplementary information, Table S2
SNVs identified in ANKL NK leukemia cells. (PDF 412 kb)
Supplementary information, Table S3
CNVs identified in ANKL NK leukemia cells. (PDF 6359 kb)
Supplementary information, Table S4
SVs identified in ANKL NK leukemia cells. (PDF 3596 kb)
Supplementary information, Table S5
AmpliSeq targeted sequencing results of ANKLs. (PDF 630 kb)
Supplementary information, Table S7
H-score of phosphorylated STAT3 and corresponding STAT mutation status of ANKL cases. (PDF 369 kb)
Supplementary information, Table S8
Differentially upregulated genes in ANKL leukemia cells in comparison with normal controls. (PDF 730 kb)
Supplementary information, Table S9
Differentially downregulated genes in ANKL leukemia cells in comparison with normal controls. (PDF 1385 kb)
Supplementary information, Table S10
KEGG pathway enrichment analysis of upregulated genes in ANKL leukemia cells. (PDF 548 kb)
Supplementary information, Table S11
KEGG pathway enrichment analysis of downregulated genes in ANKL leukemia cells. (PDF 398 kb)
Supplementary information, Table S12
IPA metabolic pathways analysis of ANKL and tumors that have known metabolic features. (PDF 1531 kb)
Supplementary information, Table S13
Sequencing depth information of 8 WGS ANKL patients. (PDF 430 kb)
Supplementary information, Table S14
Primers for quantitative RT-PCR (PDF 319 kb)
Supplementary information, Data S1
Materials and methods (PDF 1056 kb)
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Huang, L., Liu, D., Wang, N. et al. Integrated genomic analysis identifies deregulated JAK/STAT-MYC-biosynthesis axis in aggressive NK-cell leukemia. Cell Res 28, 172–186 (2018). https://doi.org/10.1038/cr.2017.146
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DOI: https://doi.org/10.1038/cr.2017.146
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