A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers

Breast cancer (BC) risk for BRCA1 and BRCA2 mutation carriers varies by genetic and familial factors. About 50 common variants have been shown to modify BC risk for mutation carriers. All but three, were identified in general population studies. Other mutation carrier-specific susceptibility variants may exist but studies of mutation carriers have so far been underpowered. We conduct a novel case-only genome-wide association study comparing genotype frequencies between 60,212 general population BC cases and 13,007 cases with BRCA1 or BRCA2 mutations. We identify robust novel associations for 2 variants with BC for BRCA1 and 3 for BRCA2 mutation carriers, P < 10−8, at 5 loci, which are not associated with risk in the general population. They include rs60882887 at 11p11.2 where MADD, SP11 and EIF1, genes previously implicated in BC biology, are predicted as potential targets. These findings will contribute towards customising BC polygenic risk scores for BRCA1 and BRCA2 mutation carriers

Genetics of complex diseases

Approaches to the study of the genetic basis of common complex diseases and their clinical applications are considered. Monogenic Mendelian inheritance in such conditions is infrequent but its elucidation may help to detect pathogenic mechanisms in the more common variety of complex diseases. Involvement by multiple genes in complex diseases usually occurs but the isolation and identification of specific genes so far has been exceptional. The role of common polymorphisms as indicators of disease risk in various studies is discussed

The Biology of the Presenilin Complexes

APP proteolytic processing Alzheimer's Disease (AD) is characterized by the deposition of two kinds of abnormal protein aggregates, senile plaques and neurofibrillary tangles, and by neuronal dysfunction and cell loss in the brain. Senile plaques are primarily composed of extracellular deposits of hydrophobic 37-43 amino acid Aβ peptides. Aβ peptides are derived by successive enzymatic cleavages of the type I membrane protein, β-amyloid precursor protein (APP) (Haass and Selkoe 1993). APP is first cleaved close to the membrane in the extracellular domain by either α-or β-secretase, resulting in a release of soluble APP ectodomains, and residual membrane-tethered C-terminal protein stubs, termed C83 or C99, respectively (The numbers indicate the length of each carboxylterminal fragment). C83 and C99 are substrates for γ-secretase, an activity that generates p3 and Aβ peptides, respectively. γ-Secretase processes substrates at different positions within the membrane domain and thus, both Aβ and p3 have "ragged" termini. Aβ has been best studied in this regard and species between 37 and 43 amino acid residues have been identified. γ-Secretase cleavage of APP also releases the intracellular carboxy-terminal "APP intracellular domain" or "AICD". The function of both Aβ and AICD is the subject of intense investigations. Because Aβ42 is the primary constituent of the amyloid fibrils deposited in the AD brains, and mutations in APP and presenilin enhance the production of this peptide, γ-secretase cleavage of APP is a pivotal step in AD pathogenesis. It is striking that this proteolytic reaction occurs within the highly hydrophobic environment of the membrane. Identification of presenilin Genetic studies in familial AD (FAD) cases have identified disease-linked mutations in three genes that contribute to AD. The first pathogenic mutations in early-onset FAD families were found in the APP gene on chromosome 21 (Chartier-Harlin et al. 1991; Goate et al. 1991; Murrell et al. 1991). However, subsequent studies indicated that mutations in APP account only for a small fraction of FAD cases. Several genetic studies indicated a major locus for FAD on chromosome 14 in early onset autosomal dominant AD, and in 1995, the Presenilin1 (PS1) gene on chromosome 14 (14q24.3) was identified by positional cloning (Sherrington et al. 1995). Shortly thereafter, it was shown that mutations in the closely related PS2 gene on chromosome 1 (1q42.2) could cause FAD as well (Levy-Lahad et al. 1995; Rogaev et al. 1995). Studies in transgenic mice (Borchelt et al. 1996; Duff et al. 1996) and cultured cells (Citron et al. 1997; Scheuner et al. 1996; Tomita et al. 1997) have revealed that expression of FAD-linked PS variants elevates Aβ42/Aβ40 ratios. Moreover, transgenic mice that co-express FAD-mutant PS1 and APP develop amyloid plaques much earlier than age-matched mutant APP mice (Borchelt et al. 1997). Therefore, PS mutations cause a change in the Aβ42/40 ratio, but whether PS is directly involved in γ-secretase processing of APP was unclear. However, in PS-deficient neurons and fibroblasts, APP processing was greatly impaired, leading to the accumulation of the C83 and C99 APP fragments, the direct substrates of γ-secretase, and inhibition of Aβ (and p3) generation (De Strooper et al. 1998; Xia et al. 1998). Thus, PS are directly required for γ-secretase cleavage of APP. Overall, the findings imply that mutations in the substrate (APP) or in the proteolytic machinery (PS) result in similar changes in Aβ42 generation (Scheuner et al. 1996). This provides very strong support for the "amyloid cascade hypothesis". © 2007 Springer Science+Business Media, LLC. All rights reserved

The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer

Breast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PAM, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and pArg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM(-/-) patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM deleterious variants p.Arg658* and p.Arg1931* are risk factors for ER-negative and TNBC subtypes. Overall our data suggest that the effect of truncating variants on breast cancer risk may depend on their position in the gene. Cell sensitivity to olaparib exposure, identifies a possible therapeutic option to treat FANCM-associated tumors.Surgical oncolog