Integrative genomics identifies LMO1 as a neuroblastoma oncogene

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Abstract

Neuroblastoma is a childhood cancer of the sympathetic nervous system that accounts for approximately 10% of all paediatric oncology deaths1,2. To identify genetic risk factors for neuroblastoma, we performed a genome-wide association study (GWAS) on 2,251 patients and 6,097 control subjects of European ancestry from four case series. Here we report a significant association within LIM domain only 1 (LMO1) at 11p15.4 (rs110419, combined P = 5.2 × 10−16, odds ratio of risk allele = 1.34 (95% confidence interval 1.25–1.44)). The signal was enriched in the subset of patients with the most aggressive form of the disease. LMO1 encodes a cysteine-rich transcriptional regulator, and its paralogues (LMO2, LMO3 and LMO4) have each been previously implicated in cancer. In parallel, we analysed genome-wide DNA copy number alterations in 701 primary tumours. We found that the LMO1 locus was aberrant in 12.4% through a duplication event, and that this event was associated with more advanced disease (P < 0.0001) and survival (P = 0.041). The germline single nucleotide polymorphism (SNP) risk alleles and somatic copy number gains were associated with increased LMO1 expression in neuroblastoma cell lines and primary tumours, consistent with a gain-of-function role in tumorigenesis. Short hairpin RNA (shRNA)-mediated depletion of LMO1 inhibited growth of neuroblastoma cells with high LMO1 expression, whereas forced expression of LMO1 in neuroblastoma cells with low LMO1 expression enhanced proliferation. These data show that common polymorphisms at the LMO1 locus are strongly associated with susceptibility to developing neuroblastoma, but also may influence the likelihood of further somatic alterations at this locus, leading to malignant progression.

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Figure 1: Discovery of LMO1 at 11p15.4 as a neuroblastoma susceptibility locus.
Figure 2: LMO1 germline genotypes and somatic copy number gains are associated with mRNA and protein expression.
Figure 3: Genetic manipulation of LMO1 expression in neuroblastoma cell line models influences proliferative phenotype in an expression-specific manner.

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Gene Expression Omnibus

Data deposits

Microarray data are deposited in the GEO database under accession number GSE3960. The genotypic and phenotypic information from this study is deposited in dbGaP (http://www.ncbi.nlm.gov/gap) under accession number phs000124.v2.p1.

References

  1. 1

    Maris, J. M. Recent advances in neuroblastoma. N. Engl. J. Med. 362, 2202–2211 (2010)

  2. 2

    Maris, J. M., Hogarty, M. D., Bagatell, R. & Cohn, S. L. Neuroblastoma. Lancet 369, 2106–2120 (2007)

  3. 3

    Mosse, Y. P. et al. Identification of ALK as a major familial neuroblastoma predisposition gene. Nature 455, 930–935 (2008)

  4. 4

    Janoueix-Lerosey, I. et al. Somatic and germline activating mutations of the ALK kinase receptor in neuroblastoma. Nature 455, 967–970 (2008)

  5. 5

    Chen, Y. et al. Oncogenic mutations of ALK kinase in neuroblastoma. Nature 455, 971–974 (2008)

  6. 6

    George, R. E. et al. Activating mutations in ALK provide a therapeutic target in neuroblastoma. Nature 455, 975–978 (2008)

  7. 7

    Maris, J. M. et al. Chromosome 6p22 locus associated with clinically aggressive neuroblastoma. N. Engl. J. Med. 358, 2585–2593 (2008)

  8. 8

    Capasso, M. et al. Common variations in BARD1 influence susceptibility to high-risk neuroblastoma. Nature Genet. 41, 718–723 (2009)

  9. 9

    Diskin, S. J. et al. Copy number variation at 1q21.1 associated with neuroblastoma. Nature 459, 987–991 (2009)

  10. 10

    Su, A. I. et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl Acad. Sci. USA 101, 6062–6067 (2004)

  11. 11

    Rabbitts, T. H. LMO T-cell translocation oncogenes typify genes activated by chromosomal translocations that alter transcription and developmental processes. Genes Dev. 12, 2651–2657 (1998)

  12. 12

    Rabbitts, T. H. et al. The effect of chromosomal translocations in acute leukemias: the LMO2 paradigm in transcription and development. Cancer Res. 59, 1794s–1798s (1999)

  13. 13

    Fisch, P. et al. T-cell acute lymphoblastic lymphoma induced in transgenic mice by the RBTN1 and RBTN2 LIM-domain genes. Oncogene 7, 2389–2397 (1992)

  14. 14

    Neale, G. A., Rehg, J. E. & Goorha, R. M. Disruption of T-cell differentiation precedes T-cell tumor formation in LMO-2 (rhombotin-2) transgenic mice. Leukemia 11 (suppl. 3). 289–290 (1997)

  15. 15

    Hacein-Bey-Abina, S. et al. LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1. Science 302, 415–419 (2003)

  16. 16

    Sum, E. Y. et al. The LIM domain protein LMO4 interacts with the cofactor CtIP and the tumor suppressor BRCA1 and inhibits BRCA1 activity. J. Biol. Chem. 277, 7849–7856 (2002)

  17. 17

    Visvader, J. E. et al. The LIM domain gene LMO4 inhibits differentiation of mammary epithelial cells in vitro and is overexpressed in breast cancer. Proc. Natl Acad. Sci. USA 98, 14452–14457 (2001)

  18. 18

    Aoyama, M. et al. LMO3 interacts with neuronal transcription factor, HEN2, and acts as an oncogene in neuroblastoma. Cancer Res. 65, 4587–4597 (2005)

  19. 19

    Attiyeh, E. F. et al. Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy. Genome Res. 19, 276–283 (2009)

  20. 20

    Wang, Q. et al. Integrative genomics identifies distinct molecular classes of neuroblastoma and shows that multiple genes are targeted by regional alterations in DNA copy number. Cancer Res. 66, 6050–6062 (2006)

  21. 21

    Peto, R. et al. Design and analysis of randomized clinical trials requiring prolonged observation of each patient. II. analysis and examples. Br. J. Cancer 35, 1–39 (1977)

  22. 22

    Saeki, N. et al. GASDERMIN, suppressed frequently in gastric cancer, is a target of LMO1 in TGF-beta-dependent apoptotic signalling. Oncogene 26, 6488–6498 (2007)

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Acknowledgements

We acknowledge the Children’s Oncology Group for providing most blood and tumour specimens and clinical and outcome data (U10-CA98543 and U10-CA98413) from neuroblastoma patients. We thank G. P. Tonini for providing neuroblastoma DNA samples in the Italian replication cohort. This work was supported in part by National Institutes of Health grant R01-CA124709 (to J.M.M.), the Giulio D’Angio Endowed Chair (J.M.M.), the Alex’s Lemonade Stand Foundation (J.M.M.), the Evan Dunbar Foundation (J.M.M.), the Rally Foundation (J.M.M.), Andrew’s Army Foundation (J.M.M.), the Abramson Family Cancer Research Institute (J.M.M.), a Howard Hughes Medical Institute Research Training Fellowship (K.B.), a fellowship from Associazione Oncologia Pediatrica e Neuroblastoma (M.C.), a Research Development Award from the Cotswold Foundation (H.H.), UL1-RR024134-03 (H.H.) and an Institutional Development Award to the Center for Applied Genomics from the Children’s Hospital of Philadelphia (H.H.).

Author information

H.H. and J.M.M. conceived the study, guided interpretation of results and helped preparation of the manuscript. K.W., H.Z. and C.H. performed SNP association analysis. K.W., S.J.D., E.F.A. and J.J. performed gene expression and copy number analysis. C.W. and K.B. performed PCR validation of gene expression data. C.W., R.W.S., K.B., P.A.M., S.J.D. and K.A.C. performed and/or analysed shRNA transfection and LMO1 overexpression experiments. N.S. and H.S. generated viral construct for human LMO1 complementary DNA. M.C. and A.I. performed the replication study on the Italian case series, and N.R. performed the replication study on the UK case series. P.W.M. and W.B.L. performed outcome and clinical covariate analyses on the Children’s Oncology Group samples. C.H., C.K., E.F., M.G., W.G. and R.C. generated the genotyping data. L.N. and M.D. helped with data analysis. S.F.A.G., Y.P.M., H.L. and M.D. advised on data interpretation. K.W. drafted the manuscript; H.H., J.M.M. and other authors edited it.

Correspondence to Hakon Hakonarson or John M. Maris.

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The authors declare no competing financial interests.

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The file contains Supplementary Materials and Methods, Supplementary Tables 1-14 and Supplementary Figures 1-8 with legends and additional references. (PDF 1614 kb)

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