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The genomic landscape of core-binding factor acute myeloid leukemias

Abstract

Acute myeloid leukemia (AML) comprises a heterogeneous group of leukemias frequently defined by recurrent cytogenetic abnormalities, including rearrangements involving the core-binding factor (CBF) transcriptional complex. To better understand the genomic landscape of CBF-AMLs, we analyzed both pediatric (n = 87) and adult (n = 78) samples, including cases with RUNX1-RUNX1T1 (n = 85) or CBFB-MYH11 (n = 80) rearrangements, by whole-genome or whole-exome sequencing. In addition to known mutations in the Ras pathway, we identified recurrent stabilizing mutations in CCND2, suggesting a previously unappreciated cooperating pathway in CBF-AML. Outside of signaling alterations, RUNX1-RUNX1T1 and CBFB-MYH11 AMLs demonstrated remarkably different spectra of cooperating mutations, as RUNX1-RUNX1T1 cases harbored recurrent mutations in DHX15 and ZBTB7A, as well as an enrichment of mutations in epigenetic regulators, including ASXL2 and the cohesin complex. This detailed analysis provides insights into the pathogenesis and development of CBF-AML, while highlighting dramatic differences in the landscapes of cooperating mutations for these related AML subtypes.

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Figure 1: Mutational landscape of CBF-AML.
Figure 2: Recurrent mutations in CCND2 and MGA.
Figure 3: DHX15 is recurrently mutated in RUNX1-RUNX1T1 AML.
Figure 4: Mutant allele frequency at diagnosis and relapse in CBF-AMLs.

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Acknowledgements

We thank all the patients and their parents from the St. Jude Children's Research Hospital (USA) and the adult patients and their families from the German-Austrian AML Study Group (AMLSG). We thank the Tissue Resources Laboratory, the Flow Cytometry and Cell Sorting Core, and the Clinical Applications of Core Technology Laboratories of the Hartwell Center for Bioinformatics and Biotechnology of St. Jude Children's Research Hospital. This work was funded by the St. Jude Children's Research Hospital–Washington University Pediatric Cancer Genome Project, the American Lebanese and Syrian Associated Charities of St. Jude Children's Research Hospital and grants from the US National Institutes of Health (P30 CA021765 and K08 HL116605 (J.M.K.)). C.G.M. is a Pew Scholar in Biomedical Sciences and a St. Baldrick's Scholar. J.M.K. holds a Career Award for Medical Scientists from the Burroughs Wellcome Fund. This study was supported in part by grants 01GI9981 and 01KG0605 from the German Bundesministerium für Bildung und Forschung (BMBF), grant 111911 from the Deutsche Krebshilfe and grant DO 704/3-1 from the Deutsche Forschungsgemeinschaft (DFG). K.D., H.D. and L.B. are supported by the Collaborative Research Center SFB 1074 funded by the DFG. L.B. is a Heisenberg Professor of the DFG (BU 1339/8-1).

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Contributions

Z.J.F., A.L.G., J.C., I.R., J.-R.C., A.K.A., J.D., L. Dong, Z.C., R.H. and E.P. contributed to the design of the study and conducted experiments. X. Chen, Y. Liu, G.S., J.M., M.P.W., G.W., M.E., M.R., C.Q., Y. Li, J.W., E.H., H.M., K.B., B.V., D.Y., J.N., J.E., S.S., R.S.F., L.L.F., L. Ding, E.R.M., R.K.W. and J.Z. contributed to the preparation and analysis of the sequencing data. X. Cao and S.B.P. provided statistical support. P.P., R.F.S., L.B., H.D., K.D., C.-H.P. and J.E.R. provided clinical samples and data. Z.J.F., A.L.G. and J.M.K. wrote the manuscript. R.K.W., T.A.G., C.G.M., L.B., J.Z., J.M.K. and J.R.D. contributed to study design and oversaw the study.

Corresponding authors

Correspondence to Lars Bullinger, Jinghui Zhang, Jeffery M Klco or James R Downing.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–24 and Supplementary Note. (PDF 28706 kb)

Supplementary Table 1

Clinicopathological information of 165 CBF-AML samples. (XLSX 22 kb)

Supplementary Table 2

Coding-region SNVs per case of CBF-AML. (XLSX 18 kb)

Supplementary Table 3

Coverage data for WGS cohort. (XLSX 11 kb)

Supplementary Table 4

Coverage data for WES cohort. (XLSX 31 kb)

Supplementary Table 5

Validated WGS sequence mutations for the 17 pediatric CBF-AML discovery cases. (XLSX 78 kb)

Supplementary Table 6

Validated whole-exome sequencing (WES) mutations for recurrency cohort. (XLSX 227 kb)

Supplementary Table 7

Recurrent somatic mutations in discovery and recurrency cohorts. (XLSX 114 kb)

Supplementary Table 8

Discovery cohort CNAs identified by WGS. (XLSX 12 kb)

Supplementary Table 9

Validated structural variants for the 17 pediatric CBF-AML discovery cases. (XLSX 31 kb)

Supplementary Table 10

Rank-ordered list of genes differentially expressed in DHX15 knockdown cells and their enrichment in the Reactome mRNA splicing gene set. (XLSX 13 kb)

Supplementary Table 11

Rank-ordered list of genes differentially expressed in DHX15 knockdown cells and their enrichment in the KEGG ribosome gene set. (XLSX 12 kb)

Supplementary Table 12

GSEA results after DHX15 knockdown. (XLSX 11 kb)

Supplementary Table 13

Spectral counts (SCs) of proteins identified in pulldown experiments with wild-type (Wt) or R222G (Mut) DHX15. (XLSX 61 kb)

Supplementary Table 14

RNA–seq RUNX1-RUNX1T1 upregulated genes. (XLSX 41 kb)

Supplementary Table 15

RNA–seq RUNX1-RUNX1T1 downregulated genes. (XLSX 43 kb)

Supplementary Table 16

GSEA gene list. (XLSX 14 kb)

Supplementary Table 17

Copy number analysis of de novo–relapse pair. (XLSX 56 kb)

Supplementary Table 18

Deep sequencing read counts in diagnosis, germline and relapse trios. (XLSX 47 kb)

Supplementary Table 19

Oligonucleotides used in this study. (XLSX 8 kb)

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Faber, Z., Chen, X., Gedman, A. et al. The genomic landscape of core-binding factor acute myeloid leukemias. Nat Genet 48, 1551–1556 (2016). https://doi.org/10.1038/ng.3709

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