Background: An ongoing genome-wide association study (GWAS) in neuroblastoma has identified multiple common and rare variants associated with susceptibility and tumor aggressiveness. Sequencing efforts have also revealed rare germline mutations contributing to tumorigenesis. However, together these still explain only a fraction of the heritability, and additional susceptibility variants/mutations remain to be discovered.
Methods: We performed a GWAS in a discovery cohort of 2,101 neuroblastoma cases and 4,202 controls following genotype imputation using 1000 Genomes Phase I Release 3 data. Significant associations were replicated in three independent cohorts: African American (365 cases; 2,491 controls); United Kingdom (371 cases; 1,122 controls), and Italian (427 cases; 783 controls). In vitro studies were performed in neuroblastoma cell line models following genetic manipulation of candidate genes to assess biological significance. A GWAS annotation tool incorporating functional genomic, transcription factor binding site, and evolutionary conservation data was created to infer putative causal variants.
Results: We refined previously reported susceptibility loci at 6p22 (CASC15), 2q35 (BARD1), 11p15 (LMO1), 6q16-q21 (HACE1, LIN28B), and 17p13 (TP53), and identified two new genome-wide significant associations at 3q25 and 4p16. Both novel associations replicated robustly in independent cohorts (3q25: rs6441201 combined P=1.2x10-11, Odds Ratio 1.23, 95% CI:1.16–1.31; 4p16: rs3796727 combined P=1.26x10-12, Odds Ratio 1.30, 95% CI: 1.21-1.40). The 3q25 signal resides within the arginine/serine-rich coiled-coil 1 (RSRC1) gene and upstream of the myeloid leukemia factor 1 (MLF1) gene. The 4p16 signal maps within the carboxypeptidase Z (CPZ) gene. Increased expression of MLF1 was observed in neuroblastoma cells carrying the rs6441201 risk allele (P = 0.02), and significant growth inhibition was observed upon depletion of MLF1 (P < 0.0001). Putative causal variants were identified at multiple susceptibility loci.
Conclusion: We show that common DNA variation at 4p16 within CPZ and at 3q25 upstream of MLF1 influences neuroblastoma susceptibility. MLF1 likely plays an important role in both initiation and disease progression; ongoing studies will further elucidate the role of this important cancer gene in neuroblastoma.