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Acute Leukemias

Genomic profiling in Down syndrome acute lymphoblastic leukemia identifies histone gene deletions associated with altered methylation profiles

Leukemia volume 25, pages 1555–1563 (2011)Cite this article

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Abstract

Patients with Down syndrome (DS) and acute lymphoblastic leukemia (ALL) have distinct clinical and biological features. Whereas most DS-ALL cases lack the sentinel cytogenetic lesions that guide risk assignment in childhood ALL, JAK2 mutations and CRLF2 overexpression are highly enriched. To further characterize the unique biology of DS-ALL, we performed genome-wide profiling of 58 DS-ALL and 68 non-DS (NDS) ALL cases by DNA copy number, loss of heterozygosity, gene expression and methylation analyses. We report a novel deletion within the 6p22 histone gene cluster as significantly more frequent in DS-ALL, occurring in 11 DS (22%) and only 2 NDS cases (3.1%) (Fisher's exact P=0.002). Homozygous deletions yielded significantly lower histone expression levels, and were associated with higher methylation levels, distinct spatial localization of methylated promoters and enrichment of highly methylated genes for specific pathways and transcription factor-binding motifs. Gene expression profiling demonstrated heterogeneity of DS-ALL cases overall, with supervised analysis defining a 45-transcript signature associated with CRLF2 overexpression. Further characterization of pathways associated with histone deletions may identify opportunities for novel targeted interventions.

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Acknowledgements

We thank Susan Hilsenbeck, Jian Wang, Alexander Yu and Charlotte Ahern for biostatistical support; Daryl Scott for assistance with genomic quantitative PCR; Brandon Ballard for assistance with PCR and data analysis; Emanuela Giarin for assistance with AIEOP sample annotation; Richard Harvey for discussion and sharing preliminary bioinformatic analysis; and the patients and families whose participation made this work possible. This work was supported in part by a Bear Necessities Pediatric Research Foundation Grant; Children's Cancer Research Foundation Grant; National Institutes of Health Pediatric Oncology Clinical Research Training Grant CA90433-06; Gillson Longenbaugh Foundation; Kurt Groten Family Research Scholars' Program (KRR); and the National Cancer Institute (NCI; SPEC U01 CA114762 and Genomics Core of the NYU Cancer Institute P30 CA016087, WLC).

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Author notes

  1. W L Carroll and K R Rabin: These authors contributed equally to this work.

Authors and Affiliations

  1. Division of Pediatric Hematology/Oncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA

    M G Loudin, H-C Eastwood Leung, S Gurusiddappa, S E Plon & K R Rabin

  2. Division of Pediatric Hematology/Oncology, New York University Cancer Institute, New York University School of Medicine, New York, NY, USA

    J Wang, J Meyer, G Condos, D Morrison & W L Carroll

  3. Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, NY, USA

    J Wang

  4. Dan. L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA

    H-C Eastwood Leung

  5. Department of Medicine, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA

    A Tsimelzon

  6. College of Medicine, University of Florida, Gainesville, FL, USA

    M Devidas

  7. Department of Pathology, Ohio State University, Columbus, OH, USA

    N A Heerema

  8. Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA

    A J Carroll

  9. University of Colorado School of Medicine and The Children′s Hospital, Aurora, CO, USA

    S P Hunger

  10. Department of Pediatrics, Laboratory of Pediatric Onco-Hematology, University Hospital of Padova, Padova, Italy

    G Basso

  11. Paediatric Oncology and Haematology Unit ‘Lalla Seràgnoli’, University of Bologna, Bologna, Italy

    A Pession

  12. Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA

    D Bhojwani

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  1. M G Loudin
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  9. M Devidas
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  18. K R Rabin
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Correspondence to K R Rabin.

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Loudin, M., Wang, J., Eastwood Leung, HC. et al. Genomic profiling in Down syndrome acute lymphoblastic leukemia identifies histone gene deletions associated with altered methylation profiles. Leukemia 25, 1555–1563 (2011). https://doi.org/10.1038/leu.2011.128

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