Genome-Wide Association Study Identifies Novel Risk Variants in BCL11A-PAPOLG for TCF3-PBX1 Acute Lymphoblastic Leukemia

Introduction

Acute lymphoblastic leukemia (ALL) is the most common malignancy in children. Germline genetic variations contribute to ALL pathogenesis, with particular importance in inherited susceptibility. TCF3-PBX1 fusion defines a common molecular subtype, occurring in ~5% of children with B-ALL. The inherited basis and molecular etiology of TCF3-PBX1 ALL are incompletely understood. To this end, we conducted a genome-wide association study (GWAS) of TCF3-PBX1 ALL to identify and explore functional effects of germline genetic variants related to susceptibility to this ALL subtype.

Methods

The ALL cases investigated in this GWAS comprised 2,529 children from frontline ALL studies – COG P9904/P9905/P9906, and St Jude Total Therapy XIIIB and XV. ALL cases included 122 children with TCF3-PBX1 ALL and 2,407 with other subtypes. 5,518 unrelated non-ALL subjects were used as controls. Patients of genetically defined European ancestry formed the GWAS discovery cohort, with subjects of non-European ancestry as the replication cohort. Genotype at each single nucleotide polymorphism (SNP) was compared between cases and controls to determine association with ALL subtype, using a logistic regression model. We also performed functional annotation studies of risk loci using ATAC-seq, to explore potential regulatory elements within identified risk loci.

Results

In the discovery GWAS (40 cases with TCF3-PBX1 ALL and 2,057 non-ALL controls), we imputed SNP genotypes genome-wide and examined 7,528,340 variants for association with TCF3-PBX1 ALL, using an additive logistic regression model with population substructure included as covariates. A single locus in the intergenic region between the BCL11A and PAPOLG genes at 2p16.1 was identified above the genome-wide significance threshold (Figure 1A) (rs2665658, odds ratio [OR] = 4.00, 95% confidence interval [CI] = [2.47-6.49], P=1.88×10^-8). This SNP was also validated in the replication cohort (82 cases with TCF3-PBX1 ALL and 3461 non-ALL controls): OR = 1.82 [1.31-2.53], P=3.85 ×10^-4, particularly in African Americans (OR = 2.21 [1.27-3.86], P=0.0052).

In parallel, we evaluated the association of SNP genotype with TCF3-PBX1 fusion positivity within ALL cases of European ancestry, by comparing allele frequency in TCF3-PBX1 ALL (N=40) vs. ALL without TCF3-PBX1 fusion (N=1,454). The BCL11A-PAPOLG locus was once again the only genome-wide significant hit and confirmed in the replication cohort. Compared to non-ALL controls, the risk allele at this SNP was only over-represented in TCF3-PBX1 ALL but not in any other ALL subtypes (Figure 1B). The 2p16.1 association peak was confined to the intergenic region between BCL11A and PAPOLG genes (Figure 1C).

Examining chromatin accessibility inferred from the ATAC-seq of different human hematopoietic cells and of a panel of human ALL cell lines, we observed multiple open chromatin regions unique to ALL leukemic cells, among which we identified a prominent ATAC-seq peak specific to TCF3-PBX1 ALL and absent in other ALL subtypes (Figure 1D). In fact, this open chromatin region is also marked by H3K27ac and juxtaposes with the ALL risk variants rs356994 and rs356995, suggesting possible effects of these genetic variations on enhancer activity (Figure 1D).

Conclusion

In this study, we performed the first TCF3-PBX1 susceptibility GWAS and identified a novel genome-wide significant risk locus encompassing the BCL11A and PAPOLG genes on chromosome 2p16.1. This discovery highlights a single causal variant with subtype-specific effect, and is deposited in a regulatory DNA element uniquely activated in ALL cells with TCF3-PBX1 fusion.