Investigating rare pathogenic mutations of the extended Fanconi Anaemia DNA repair pathway in Acute Myeloid Leukaemia (AML)

Abstract

a significant association of BRCA1/2 variants with Down syndrome and trisomy 21 was also observed (P=0.045). The mutation data were also cross-referenced to the disease databases for FA and breast cancer to determine known disease-causing mutations (D-C mutations). In the adult AML, a significant enrichment was observed for D-C mutations affecting the 19 FANC genes compared to the allfemale healthy control cohort [P=0.018; Odds ratio=3.3 (1.3-8.6)]. Similarly, an overrepresentation of D-C mutations affecting 16 of the FANC genes was observed in the adult AML cohort, compared to that reported in a separate published study of large healthy populations [P=0.002; odds ratio=3.4 (1.7-7.0)]. The mutation data was also compared against cancer and disease databases to determine the presence of disease-causing (D-C) mutations in all 58 genes, and to identify other disease-associated (D-A) variants. This analysis revealed a number of mutations that were present in multiple disease samples, while being absent, or present at low frequency, in the control cohorts. Gene expression profiling was performed for a small set of adult AML (n=57) using microarray. This analysis, comparing gene expression in mutant versus non-mutant AML, revealed differences in gene expression pattern associated with presence of rare variants affecting functional gene subgroups within the FA/BRCA-HRR network. Examination of the individual differentially-expressed genes, and gene set enrichment analysis (GSEA), suggested that there may be potential differences in leukaemic cell of origin for AML carrying rare variants affecting the different functional subgroups of the extended FA/BRCA-HRR network. GSEA also suggested potential up-regulation of gene-sets associated with base excision repair and homologous recombination repair, as well as replicative stress, in samples carrying rare variants affecting the genes encoding the FA core & ID2 proteins. It is speculated that this may be indicative of increased basal replicative stress and DNA damage in the samples carrying these rare variants, with compensatory up-regulation of these repair pathways. Based on the data presented it is hypothesised that rare germline variants affecting the genes in the FA/BRCA-HRR network result in subtle changes to the effectiveness of the FA DNA repair pathway in HSC, with a resultant modest increased pre-disposition to AML. An important question raised by this study relates to the cellular phenotype associated with rare, heterozygous deleterious variants affecting genes in the FA/BRCA-HRR network, and the FANC genes in particular. To investigate this further clonal cell lines were generated from a non-cancer cell line (MCF10A) carrying heterozygous or bi-allelic damaging mutations in FANCL. Changes to DNA repair capacity have been shown in cells with FANCL heterozygous mutations to be statistically different to the wild type cells.