A variant at 9p21.3 functionally implicates CDKN2B in paediatric B-cell precursor acute lymphoblastic leukaemia aetiology
Eric A Hungate, Sapana R Vora, Eric R Gamazon, Takaya Moriyama, Timothy Best, Imge Hulur, Younghee Lee, Tiffany-Jane Evans, Eva Ellinghaus, Martin Stanulla, Jéremie Rudant, Laurent Orsi, Jacqueline Clavel, Elizabeth Milne, Rodney J Scott, Ching-Hon Pui, Nancy J Cox, Mignon L Loh, Jun J Yang, Andrew D Skol, Kenan Onel, Eric A Hungate, Sapana R Vora, Eric R Gamazon, Takaya Moriyama, Timothy Best, Imge Hulur, Younghee Lee, Tiffany-Jane Evans, Eva Ellinghaus, Martin Stanulla, Jéremie Rudant, Laurent Orsi, Jacqueline Clavel, Elizabeth Milne, Rodney J Scott, Ching-Hon Pui, Nancy J Cox, Mignon L Loh, Jun J Yang, Andrew D Skol, Kenan Onel
Abstract
Paediatric B-cell precursor acute lymphoblastic leukaemia (BCP-ALL) is the most common cancer of childhood, yet little is known about BCP-ALL predisposition. In this study, in 2,187 cases of European ancestry and 5,543 controls, we discover and replicate a locus indexed by rs77728904 at 9p21.3 associated with BCP-ALL susceptibility (Pcombined=3.32 × 10(-15), OR=1.72) and independent from rs3731217, the previously reported ALL-associated variant in this region. Of correlated SNPs tagged by this locus, only rs662463 is significant in African Americans, suggesting it is a plausible causative variant. Functional analysis shows that rs662463 is a cis-eQTL for CDKN2B, with the risk allele associated with lower expression, and suggests that rs662463 influences BCP-ALL risk by regulating CDKN2B expression through CEBPB signalling. Functional analysis of rs3731217 suggests it is associated with BCP-ALL by acting within a splicing regulatory element determining CDKN2A exon 3 usage (P=0.01). These findings provide new insights into the critical role of the CDKN2 locus in BCP-ALL aetiology.
Figures
References
- Mullighan C. G. Molecular genetics of B-precursor acute lymphoblastic leukemia. J. Clin. Invest. 122, 3407–3415 (2012).
- Cazzaniga G. et al.. Developmental origins and impact of BCR-ABL1 fusion and IKZF1 deletions in monozygotic twins with Ph+ acute lymphoblastic leukemia. Blood 118, 5559–5564 (2011).
- van der Weyden L. et al.. Modeling the evolution of ETV6-RUNX1-induced B-cell precursor acute lymphoblastic leukemia in mice. Blood 118, 1041–1051 (2011).
- Enciso-Mora V. et al.. Common genetic variation contributes significantly to the risk of childhood B-cell precursor acute lymphoblastic leukemia. Leukemia 26, 2212–2215 (2012).
- Trevino L. R. et al.. Germline genomic variants associated with childhood acute lymphoblastic leukemia. Nat. Genet. 41, 1001–1005 (2009).
- Papaemmanuil E. et al.. Loci on 7p12.2, 10q21.2 and 14q11.2 are associated with risk of childhood acute lymphoblastic leukemia. Nat. Genet. 41, 1006–1010 (2009).
- Xu H. et al.. Novel susceptibility variants at 10p12.31-12.2 for childhood acute lymphoblastic leukemia in ethnically diverse populations. J. Natl Cancer Inst. 105, 733–742 (2013).
- Sherborne A. L. et al.. Variation in CDKN2A at 9p21.3 influences childhood acute lymphoblastic leukemia risk. Nat. Genet. 42, 492–494 (2010).
- Ellinghaus E. et al.. Identification of germline susceptibility loci in ETV6-RUNX1-rearranged childhood acute lymphoblastic leukemia. Leukemia 26, 902–909 (2012).
- Migliorini G. et al.. Variation at 10p12.2 and 10p14 influences risk of childhood B-cell acute lymphoblastic leukemia and phenotype. Blood 122, 3298–3307 (2013).
- Perez-Andreu V. et al.. Inherited GATA3 variants are associated with Ph-like childhood acute lymphoblastic leukemia and risk of relapse. Nat. Genet. 45, 1494–1498 (2013).
- Orsi L. et al.. Genetic polymorphisms and childhood acute lymphoblastic leukemia: GWAS of the ESCALE study (SFCE). Leukemia 26, 2561–2564 (2012).
- Rudant J. et al.. Childhood acute leukemia, early common infections, and allergy: the ESCALE study. Am. J. Epidemiol. 172, 1015–1027 (2010).
- Borowitz M. J. et al.. Clinical significance of minimal residual disease in childhood acute lymphoblastic leukemia and its relationship to other prognostic factors: a Children's Oncology Group study. Blood 111, 5477–5485 (2008).
- Evans T. J. et al.. Confirmation of childhood acute lymphoblastic leukemia variants, ARID5B and IKZF1, and interaction with parental environmental exposures. PLoS ONE 9, e110255 (2014).
- Akasaka T. et al.. Five members of the CEBP transcription factor family are targeted by recurrent IGH translocations in B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Blood 109, 3451–3461 (2007).
- McVean G. A. et al.. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56–65 (2012).
- Walsh K. M. et al.. Novel childhood ALL susceptibility locus BMI1-PIP4K2A is specifically associated with the hyperdiploid subtype. Blood 121, 4808–4809 (2013).
- Pasmant E. et al.. Characterization of a germ-line deletion, including the entire INK4/ARF locus, in a melanoma-neural system tumor family: identification of ANRIL, an antisense noncoding RNA whose expression coclusters with ARF. Cancer Res. 67, 3963–3969 (2007).
- Nicolae D. L. et al.. Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet. 6, e1000888 (2010).
- Trynka G. et al.. Chromatin marks identify critical cell types for fine mapping complex trait variants. Nat. Genet. 45, 124–130 (2013).
- Lonsdale J. et al.. The Genotype-Tissue Expression (GTEx) project. Nat. Genet. 45, 580–585 (2013).
- Battle A. et al.. Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Res. 24, 14–24 (2014).
- Ward L. D. & Kellis M. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res. 40, D930–D934 (2012).
- Boyle A. P. et al.. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res. 22, 1790–1797 (2012).
- Dunham I. et al.. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
- Wang J. et al.. : a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res. 41, D171–D176 (2013).
- Matys V. et al.. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 34, D108–D110 (2006).
- Lappalainen T. et al.. Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501, 506–511 (2013).
- Stranger B. E. et al.. Patterns of cis regulatory variation in diverse human populations. PLoS Genet. 8, e1002639 (2012).
- Lee Y. et al.. Variants affecting exon skipping contribute to complex traits. PLoS Genet. 8, e1002998 (2012).
- Quelle D. E., Zindy F., Ashmun R. A. & Sherr C. J. Alternative reading frames of the INK4a tumor suppressor gene encode two unrelated proteins capable of inducing cell cycle arrest. Cell 83, 993–1000 (1995).
- Lin Y. C. et al.. Human p16gamma, a novel transcriptional variant of p16(INK4A), coexpresses with p16(INK4A) in cancer cells and inhibits cell-cycle progression. Oncogene 26, 7017–7027 (2007).
- Stott F. J. et al.. The alternative product from the human CDKN2A locus, p14(ARF), participates in a regulatory feedback loop with p53 and MDM2. EMBO J. 17, 5001–5014 (1998).
- Tanguay R. L. & Gallie D. R. Translational efficiency is regulated by the length of the 3′ untranslated region. Mol. Cell. Biol. 16, 146–156 (1996).
- Stranks G. et al.. Deletions and rearrangement of CDKN2 in lymphoid malignancy. Blood 85, 893–901 (1995).
- Mullighan C. G., Williams R. T., Downing J. R. & Sherr C. J. Failure of CDKN2A/B (INK4A/B-ARF)-mediated tumor suppression and resistance to targeted therapy in acute lymphoblastic leukemia induced by BCR-ABL. Genes Dev. 22, 1411–1415 (2008).
- Mullighan C. G. et al.. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 446, 758–764 (2007).
- Ladomery M. Aberrant alternative splicing is another hallmark of cancer. Int. J. Cell Biol. 2013, 463786 (2013).
- Zhang J. & Manley J. L. Misregulation of pre-mRNA alternative splicing in cancer. Cancer Discov. 3, 1228–1237 (2013).
- Loo J. C. et al.. Germline splicing mutations of CDKN2A predispose to melanoma. Oncogene 22, 6387–6394 (2003).
- Harland M., Mistry S., Bishop D. T. & Bishop J. A. A deep intronic mutation in CDKN2A is associated with disease in a subset of melanoma pedigrees. Hum. Mol. Genet. 10, 2679–2686 (2001).
- Winick N. et al.. Delayed intensification (DI) enhances event-free survival (EFS) of children with B-precursor acute lymphoblastic leukemia (ALL) who received intensification therapy with six courses of intravenous methotrexate (MTX): POG 9904/9905: A Children's Oncology Group Study (COG). ASH Annu. Meet. Abs. 110, 583 (2007).
- Manolio T. A. et al.. New models of collaboration in genome-wide association studies: the Genetic Association Information Network. Nat. Genet. 39, 1045–1051 (2007).
- Korn J. M. et al.. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat. Genet. 40, 1253–1260 (2008).
- Ehret G. B. et al.. Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk. Nature 478, 103–109 (2011).
- Metayer C. et al.. The Childhood Leukemia International Consortium. Cancer Epidemiol. 37, 336–347 (2013).
- Krawczak M. et al.. PopGen: population-based recruitment of patients and controls for the analysis of complex genotype-phenotype relationships. Community Genet. 9, 55–61 (2006).
- Purcell S. et al.. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).
- Meyer L. R. et al.. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 41, D64–D69 (2013).
- Price A. L. et al.. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904–909 (2006).
- Howie B. N., Donnelly P. & Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 5, e1000529 (2009).
- Delaneau O., Marchini J. & Zagury J. F. A linear complexity phasing method for thousands of genomes. Nat. Methods 9, 179–181 (2012).
- Marchini J., Howie B., Myers S., McVean G. & Donnelly P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet. 39, 906–913 (2007).
- Willer C. J., Li Y. & Abecasis G. R. METAL: fast and efficient meta-analysis of genomewide association scans. Bioinformatics 26, 2190–2191 (2010).
- Higgins J. P., Thompson S. G., Deeks J. J. & Altman D. G. Measuring inconsistency in meta-analyses. BMJ 327, 557–560 (2003).
- Devlin B. & Roeder K. Genomic control for association studies. Biometrics 55, 997–1004 (1999).
- Pruim R. J. et al.. LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics 26, 2336–2337 (2010).
- Barrett J. C., Fry B., Maller J. & Daly M. J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263–265 (2005).
- Bild D. E. et al.. Multi-ethnic study of atherosclerosis: objectives and design. Am. J. Epidemiol. 156, 871–881 (2002).
- Pritchard J. K., Stephens M. & Donnelly P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).
- Yang J. J. et al.. Ancestry and pharmacogenomics of relapse in acute lymphoblastic leukemia. Nat. Genet. 43, 237–241 (2011).
- Mao X. et al.. A genomewide admixture mapping panel for Hispanic/Latino populations. Am. J. Hum. Genet. 80, 1171–1178 (2007).
- Zeller T. et al.. Genetics and beyond--the transcriptome of human monocytes and disease susceptibility. PLoS ONE 5, e10693 (2010).
- Bernstein B. E. et al.. The NIH Roadmap Epigenomics Mapping Consortium. Nat. Biotechnol. 28, 1045–1048 (2010).
- International HapMap Consortium. et al.. Integrating common and rare genetic variation in diverse human populations. Nature 467, 52–58 (2010).
- Sandelin A., Alkema W., Engstrom P., Wasserman W. W. & Lenhard B. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 32, D91–D94 (2004).
- 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).
- R Development Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. ISBN 3-900051-07-0. (2008).
- Thierry-Mieg D. & Thierry-Mieg J. AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biol. 7 Suppl 1,, S12 1–14 (2006).
Source: PubMed