The Fanconi Pathway in Pediatric T-Cell Acute Lymphoblastic Leukemia

BRCA2 (also known as FANCD1), a core component of the Fanconi pathway, suppresses transformation of immature T-cell progenitors in mice. However, whether the Fanconi pathway contributes to human T-cell acute lymphoblastic leukemia (T-ALL) pathogenesis is unknown. Using targeted exon sequencing of childhood T-ALL diagnostic specimens, we found heterozygous mutations of Fanconi pathway genes in 23% of 40 cases analyzed. Array comparative genomic hybridization (CGH) analysis revealed that an additional 15% of these cases harbored large heterozygous deletions involving Fanconi pathway genes. The majority of these mutations appear to be somatic although in 2 of 8 available remission samples, the mutations were present, suggestive that these mutations are likely to be germline. Fanconi genes are typically considered two-hit tumor suppressors, where breast or ovarian cancers arising in heterozygous carriers often lose activity of the wild-type allele, leading to genomic instability. However, T-ALL cases with heterozygous Fanconi mutations lacked evidence of increased genomic instability based on array CGH analysis, were not hypersensitive to the PARP inhibitor olaparib, and did not demonstrate increased radial chromosome formation in response to mitomycin C (MMC), indicating that these cases retained activity of the wild-type allele. Complementation studies of Fanconi mutant cells revealed that most of the identified Fanconi mutations encoded pathogenic alleles, as evidenced by their impaired ability to rescue Fanconi-deficient cells from mitomycin C-induced radial chromosome formation and cytotoxicity. Treatment of a patient-derived xenograft sample harboring a heterozygous BRCA2 mutation with mitomycin C revealed that these cells had an intermediate increase in sensitivity to mitomycin C-induced cytotoxicity compared to Fanconi wild-type T-ALLs, suggesting that Fanconi haploinsufficiency is pathogenic in T-ALL. Together, these findings implicate a tumor suppressor role for Fanconi pathway haploinsufficiency in childhood T-ALL.