Pediatric non-Down syndrome acute megakaryoblastic leukemia is characterized by distinct genomic subsets with varying outcomes

Nature Genetics

Volumn 49, Issue 3, 2017, Pages 451-456

  De Rooij, Jasmijn D E ^a   Branstetter, Cristyn ^b   Ma, Jing ^b   Li, Yongjin ^b   Walsh, Michael P ^b   Cheng, Jinjun ^b   Obulkasim, Askar ^a   Dang, Jinjun ^b   Easton, John ^b   Verboon, Lonneke J ^a   Mulder, Heather L ^b   Zimmermann, Martin ^c   Koss, Cary ^b   Gupta, Pankaj ^b   Edmonson, Michael ^b   Rusch, Michael ^b   Lim, Joshua Yew Suang ^d   Reinhardt, Katarina ^e   Pigazzi, Martina ^f   Song, Guangchun ^b   Yeoh, Allen Eng Juh ^d,g   Shih, Lee Yung ^h   Liang, Der Cherng ⁱ   Halene, Stephanie ^j   Krause, Diane S ^k   Zhang, Jinghui ^b   Downing, James R ^b   Locatelli, Franco ^l   Reinhardt, Dirk ^e   Van Den Heuvel Eibrink, Marry M ^a,m   Zwaan, C Michel ^a   Fornerod, Maarten ^a   Gruber, Tanja A ^b   more..

^a SOPHIA CHILDREN S HOSPITAL   (Netherlands)

^b ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

^c HANNOVER MEDICAL SCHOOL   (Germany)

^d NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^e UNIVERSITY OF DUISBURG ESSEN   (Germany)

^f UNIVERSITY OF PADOVA   (Italy)

^g NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^h CHANG GUNG UNIVERSITY   (Taiwan)

ⁱ MACKAY MEMORIAL HOSPITAL   (Taiwan)

^j YALE CANCER CENTER   (United States)

^k YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^l UNIVERSITY OF PAVIA   (Italy)

^m the Netherlands The Innovative Therapies for Children with Cancer Consortium   (Netherlands)

more..

Author keywords

[No Author keywords available]

Indexed keywords

COHESIN; E1A ASSOCIATED P300 PROTEIN; HYBRID PROTEIN; RNA; TRANSCRIPTION FACTOR GATA 1; TRANSCRIPTION FACTOR GATA 2; TRANSCRIPTION FACTOR HOXA10; TRANSCRIPTION FACTOR HOXA9; CBFA2T3 PROTEIN, HUMAN; KDM5A PROTEIN, HUMAN; REPRESSOR PROTEIN; RETINOBLASTOMA BINDING PROTEIN 2; TUMOR SUPPRESSOR PROTEIN;

ACUTE MEGAKARYOCYTIC LEUKEMIA; ADULT; ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CHILD; CHILDHOOD LEUKEMIA; COHORT ANALYSIS; DOWN SYNDROME; EPIGENETICS; FEMALE; GENE CLUSTER; GENE EXPRESSION; GENE FUSION; GENE MUTATION; HUMAN; MOUSE; NEXT GENERATION SEQUENCING; NONHUMAN; ONCOGENE; PRIORITY JOURNAL; RNA SEQUENCE; WHOLE EXOME SEQUENCING; ANIMAL; C57BL MOUSE; EXOME; GENE REARRANGEMENT; GENETICS; GENOMICS; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; DOWN SYNDROME; EXOME; FEMALE; GENE REARRANGEMENT; GENOMICS; HUMANS; LEUKEMIA, MEGAKARYOBLASTIC, ACUTE; MICE; MICE, INBRED C57BL; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRESSOR PROTEINS; RETINOBLASTOMA-BINDING PROTEIN 2; RNA; TUMOR SUPPRESSOR PROTEINS;

EID: 85010911803     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3772     Document Type: Article

References (41)

1. Pagano, L. et al. Acute megakaryoblastic leukemia: experience of GIMEMA trials. Leukemia 16, 1622-1626 (2002).
2. Athale, U.H. et al. Biology and outcome of childhood acute megakaryoblastic leukemia: a single institution's experience. Blood 97, 3727-3732 (2001).
3. Barnard, D.R., Alonzo, T.A., Gerbing, R.B., Lange, B. & Woods, W.G. Comparison of childhood myelodysplastic syndrome, AML FAB M6 or M7, CCG 2891: report from the Children's Oncology Group. Pediatr. Blood Cancer 49, 17-22 (2007).
4. Ma, Z. et al. Fusion of two novel genes, RBM15 and MKL1, in the t(1;22)(p13;q13) of acute megakaryoblastic leukemia. Nat. Genet. 28, 220-221 (2001).
5. Gruber, T.A. et al. An Inv(16)(p13.3q24.3)-encoded CBFA2T3-GLIS2 fusion protein defines an aggressive subtype of pediatric acute megakaryoblastic leukemia. Cancer Cell 22, 683-697 (2012).
6. de Rooij, J.D. et al. NUP98/JARID1A is a novel recurrent abnormality in pediatric acute megakaryoblastic leukemia with a distinct HOX gene expression pattern. Leukemia 27, 2280-2288 (2013).
7. Baruchel, A., Daniel, M.T., Schaison, G. & Berger, R. Nonrandom t(1;22)(p12-p13;q13) in acute megakaryocytic malignant proliferation. Cancer Genet. Cytogenet. 54, 239-243 (1991).
8. Mercher, T. et al. Involvement of a human gene related to the Drosophila spen gene in the recurrent t(1;22) translocation of acute megakaryocytic leukemia. Proc. Natl. Acad. Sci. USA 98, 5776-5779 (2001).
9. Radtke, I. et al. Genomic analysis reveals few genetic alterations in pediatric acute myeloid leukemia. Proc. Natl. Acad. Sci. USA 106, 12944-12949 (2009).
10. Dorsam, S.T. et al. The transcriptome of the leukemogenic homeoprotein HOXA9 in human hematopoietic cells. Blood 103, 1676-1684 (2004).
11. Hu, Y.L., Passegué, E., Fong, S., Largman, C. & Lawrence, H.J. Evidence that the Pim1 kinase gene is a direct target of HOXA9. Blood 109, 4732-4738 (2007).
12. Kaushansky, K. et al. Promotion of megakaryocyte progenitor expansion and differentiation by the c-Mpl ligand thrombopoietin. Nature 369, 568-571 (1994).
13. Dastugue, N. et al. Cytogenetic profile of childhood and adult megakaryoblastic leukemia (M7): a study of the Groupe Français de Cytogénétique Hématologique (GFCH). Blood 100, 618-626 (2002).
14. Nimer, S.D., MacGrogan, D., Jhanwar, S. & Alvarez, S. Chromosome 19 abnormalities are commonly seen in AML, M7. Blood 100, 3838 author reply 3838-3839 (2002).
15. Reinhardt, D. et al. GATA1-mutation associated leukemia in children with trisomy 21 mosaic. Klin. Padiatr. 224, 153-155 (2012).
16. Loughran, S.J. et al. The transcription factor Erg is essential for definitive hematopoiesis and the function of adult hematopoietic stem cells. Nat. Immunol. 9, 810-819 (2008).
17. Goyama, S. et al. UBASH3B/Sts-1-CBL axis regulates myeloid proliferation in human preleukemia induced by AML1-ETO. Leukemia 30, 728-739 (2016).
18. Emmrich, S. et al. LincRNAs MONC and MIR100HG act as oncogenes in acute megakaryoblastic leukemia. Mol. Cancer 13, 171 (2014).
19. Malinge, S. et al. Increased dosage of the chromosome 21 ortholog Dyrk1a promotes megakaryoblastic leukemia in a murine model of Down syndrome. J. Clin. Invest. 122, 948-962 (2012).
20. Salek-Ardakani, S. et al. ERG is a megakaryocytic oncogene. Cancer Res. 69, 4665-4673 (2009).
21. Goeman, J.J., van de Geer, S.A., de Kort, F. & van Houwelingen, H.C. A global test for groups of genes: testing association with a clinical outcome. Bioinformatics 20, 93-99 (2004).
22. Andersson, A.K. et al. The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias. Nat. Genet. 47, 330-337 (2015).
23. Yoshida, K. et al. The landscape of somatic mutations in Down syndrome-related myeloid disorders. Nat. Genet. 45, 1293-1299 (2013).
24. Creutzig, U. et al. AML patients with Down syndrome have a high cure rate with AML-BFM therapy with reduced dose intensity. Leukemia 19, 1355-1360 (2005).
25. Inaba, H. et al. Heterogeneous cytogenetic subgroups and outcomes in childhood acute megakaryoblastic leukemia: a retrospective international study. Blood 126, 1575-1584 (2015).
26. Schweitzer, J. et al. Improved outcome of pediatric patients with acute megakaryoblastic leukemia in the AML-BFM 04 trial. Ann. Hematol. 94, 1327-1336 (2015).
27. Kudo, K. et al. Mosaic Down syndrome-associated acute myeloid leukemia does not require high-dose cytarabine treatment for induction and consolidation therapy. Int. J. Hematol. 91, 630-635 (2010).
28. Zhang, J. et al. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature 481, 157-163 (2012).
29. Trapnell, C. et al. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotechnol. 31, 46-53 (2013).
30. Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010).
31. Klusmann, J.H. et al. miR-125b-2 is a potential oncomiR on human chromosome 21 in megakaryoblastic leukemia. Genes Dev. 24, 478-490 (2010).
32. Robinson, M.D., McCarthy, D.J. & Smyth, G.K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
33. Soneoka, Y. et al. A transient three-plasmid expression system for the production of high titer retroviral vectors. Nucleic Acids Res. 23, 628-633 (1995).
34. Mullighan, C.G. et al. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 446, 758-764 (2007).
35. Pounds, S. et al. Reference alignment of SNP microarray signals for copy number analysis of tumors. Bioinformatics 25, 315-321 (2009).
36. Lin, M. et al. dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics 20, 1233-1240 (2004).
37. Olshen, A.B., Venkatraman, E.S., Lucito, R. & Wigler, M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5, 557-572 (2004).
38. McCarroll, S.A. et al. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet. 40, 1166-1174 (2008).
39. Iafrate, A.J. et al. Detection of large-scale variation in the human genome. Nat. Genet. 36, 949-951 (2004).
40. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
41. Koboldt, D.C. et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 22, 568-576 (2012).