Chromosomal aberrations are a hallmark of acute lymphoblastic leukaemia (ALL) but alone fail to induce leukaemia. To identify cooperating oncogenic lesions, we performed a genome-wide analysis of leukaemic cells from 242 paediatric ALL patients using high-resolution, single-nucleotide polymorphism arrays and genomic DNA sequencing. Our analyses revealed deletion, amplification, point mutation and structural rearrangement in genes encoding principal regulators of B lymphocyte development and differentiation in 40% of B-progenitor ALL cases. The PAX5 gene was the most frequent target of somatic mutation, being altered in 31.7% of cases. The identified PAX5 mutations resulted in reduced levels of PAX5 protein or the generation of hypomorphic alleles. Deletions were also detected in TCF3 (also known as E2A), EBF1, LEF1, IKZF1 (IKAROS) and IKZF3 (AIOLOS). These findings suggest that direct disruption of pathways controlling B-cell development and differentiation contributes to B-progenitor ALL pathogenesis. Moreover, these data demonstrate the power of high-resolution, genome-wide approaches to identify new molecular lesions in cancer.
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Greaves, M. F. & Wiemels, J. Origins of chromosome translocations in childhood leukaemia. Nature Rev. Cancer 3, 639–649 (2003)
Peters, U. R. et al. Aberrant FHIT mRNA transcripts are present in malignant and normal haematopoiesis, but absence of FHIT protein is restricted to leukaemia. Oncogene 18, 79–85 (1999)
Jackson, A. et al. Deletion of 6q16-q21 in human lymphoid malignancies: a mapping and deletion analysis. Cancer Res. 60, 2775–2779 (2000)
Okuda, T. et al. Frequent deletion of p16INK4a/MTS1 and p15INK4b/MTS2 in pediatric acute lymphoblastic leukemia. Blood 85, 2321–2330 (1995)
Raynaud, S. et al. The 12;21 translocation involving TEL and deletion of the other TEL allele: two frequently associated alterations found in childhood acute lymphoblastic leukemia. Blood 87, 2891–2899 (1996)
Raimondi, S. C. et al. Acute lymphoblastic leukemias with deletion of 11q23 or a novel inversion (11)(p13q23) lack MLL gene rearrangements and have favorable clinical features. Blood 86, 1881–1886 (1995)
Heerema, N. A. et al. Abnormalities of chromosome bands 13q12 to 13q14 in childhood acute lymphoblastic leukemia. J. Clin. Oncol. 18, 3837–3844 (2000)
Cave, H. et al. Deletion of chromosomal region 13q14.3 in childhood acute lymphoblastic leukemia. Leukemia 15, 371–376 (2001)
Lin, H. & Grosschedl, R. Failure of B-cell differentiation in mice lacking the transcription factor EBF. Nature 376, 263–267 (1995)
Ehrich, M. et al. Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc. Natl Acad. Sci. USA 102, 15785–15790 (2005)
Nutt, S. L., Heavey, B., Rolink, A. G. & Busslinger, M. Commitment to the B-lymphoid lineage depends on the transcription factor Pax5. Nature 401, 556–562 (1999)
Busslinger, M. Transcriptional control of early B cell development. Annu. Rev. Immunol. 22, 55–79 (2004)
Ying, H., Healy, J. I., Goodnow, C. C. & Parnes, J. R. Regulation of mouse CD72 gene expression during B lymphocyte development. J. Immunol. 161, 4760–4767 (1998)
Cazzaniga, G. et al. The paired box domain gene PAX5 is fused to ETV6/TEL in an acute lymphoblastic leukemia case. Cancer Res. 61, 4666–4670 (2001)
Strehl, S., Konig, M., Dworzak, M. N., Kalwak, K. & Haas, O. A. PAX5/ETV6 fusion defines cytogenetic entity dic(9;12)(p13;p13). Leukemia 17, 1121–1123 (2003)
Bohlander, S. K. ETV6: a versatile player in leukemogenesis. Semin. Cancer Biol. 15, 162–174 (2005)
Wlodarska, I. et al. FOXP1, a gene highly expressed in a subset of diffuse large B-cell lymphoma, is recurrently targeted by genomic aberrations. Leukemia 19, 1299–1305 (2005)
Bond, H. M. et al. Early hematopoietic zinc finger protein (EHZF), the human homolog to mouse Evi3, is highly expressed in primitive human hematopoietic cells. Blood 103, 2062–2070 (2004)
Hu, H. et al. Foxp1 is an essential transcriptional regulator of B cell development. Nature Immunol. 7, 819–826 (2006)
Warming, S. et al. Evi3, a common retroviral integration site in murine B-cell lymphoma, encodes an EBFAZ-related Kruppel-like zinc finger protein. Blood 101, 1934–1940 (2003)
Garvie, C. W., Hagman, J. & Wolberger, C. Structural studies of Ets-1/Pax5 complex formation on DNA. Mol. Cell 8, 1267–1276 (2001)
Czerny, T. & Busslinger, M. DNA-binding and transactivation properties of Pax-6: three amino acids in the paired domain are responsible for the different sequence recognition of Pax-6 and BSAP (Pax-5). Mol. Cell. Biol. 15, 2858–2871 (1995)
Maier, H., Colbert, J., Fitzsimmons, D., Clark, D. R. & Hagman, J. Activation of the early B-cell-specific mb-1 (Ig-alpha) gene by Pax-5 is dependent on an unmethylated Ets binding site. Mol. Cell. Biol. 23, 1946–1960 (2003)
Nutt, S. L., Morrison, A. M., Dorfler, P., Rolink, A. & Busslinger, M. Identification of BSAP (Pax-5) target genes in early B-cell development by loss- and gain-of-function experiments. EMBO J. 17, 2319–2333 (1998)
Ross, M. E. et al. Classification of pediatric acute lymphoblastic leukemia by gene expression profiling. Blood 102, 2951–2959 (2003)
Martoriati, A. et al. dapk1, encoding an activator of a p19ARF-p53-mediated apoptotic checkpoint, is a transcription target of p53. Oncogene 24, 1461–1466 (2005)
Conte, N. et al. Carcinogenesis and translational controls: TACC1 is down-regulated in human cancers and associates with mRNA regulators. Oncogene 21, 5619–5630 (2002)
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005)
Georgopoulos, K. et al. The Ikaros gene is required for the development of all lymphoid lineages. Cell 79, 143–156 (1994)
O’Riordan, M. & Grosschedl, R. Coordinate regulation of B cell differentiation by the transcription factors EBF and E2A. Immunity 11, 21–31 (1999)
Winandy, S., Wu, P. & Georgopoulos, K. A dominant mutation in the Ikaros gene leads to rapid development of leukemia and lymphoma. Cell 83, 289–299 (1995)
Nutt, S. L. et al. Independent regulation of the two Pax5 alleles during B-cell development. Nature Genet. 21, 390–395 (1999)
Robson, E. J., He, S. J. & Eccles, M. R. A. PANorama of PAX genes in cancer and development. Nature Rev. Cancer 6, 52–62 (2006)
Busslinger, M., Klix, N., Pfeffer, P., Graninger, P. G. & Kozmik, Z. Deregulation of PAX-5 by translocation of the Eμ enhancer of the IgH locus adjacent to two alternative PAX-5 promoters in a diffuse large-cell lymphoma. Proc. Natl Acad. Sci. USA 93, 6129–6134 (1996)
Matsuzaki, H. et al. Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nature Methods 1, 109–111 (2004)
Lin, M. et al. dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics 20, 1233–1240 (2004)
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)
McCarroll, S. A. et al. Common deletion polymorphisms in the human genome. Nature Genet. 38, 86–92 (2006)
We thank Z. Cai and L. King for technical assistance; B. Schulman for modelling of PAX5 mutations; M. Roussel, M. Busslinger and J. Hagman for providing reagents; the Tumor Processing Laboratory of SJCRH for providing tumour samples; and C. Li for discussions and modifications of dChipSNP. This work was supported by grants from the National Cancer Institute (to J.R.D. and W.E.E.), the National Institute of General Medical Sciences (to M.V.R.), the National Health and Medical Research Council (Australia) (to C.G.M.), the Royal Australasian College of Physicians (to C.G.M.), the Haematology Society of Australia and New Zealand (to C.G.M), and the American Lebanese and Syrian Associated Charities (ALSAC) of SJCRH.
Author Contributions J.R.D. designed and supervised experiments. C.G.M, S.G., I.R, C.B.M., E.C.-S., J.D.D and K.G. performed experiments. S.A.S. collected and managed clinical samples and data. C.G.M., S.G., J.M., S.B.P. and X.S. analysed data. S.B.P. developed software for DNA copy number analysis. C.-H.P., M.V.R. and W.E.E. provided patient samples. C.G.M. and J.R.D. wrote the manuscript. All authors discussed the results and commented on the manuscript.
The primary SNP microarray data have been deposited in NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Series accession number GSE5511. The data are also available at http://www.stjuderesearch.org/data/ALL-SNP1/. Sequences of the PAX5 fusion transcripts have been deposited in GenBank with accessions DQ841178 (PAX5–ETV6), DQ845346 (PAX5–FOXP1) and DQ845345 (PAX5–ZNF521).
Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.
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