Breast cancer and the role of low penetrance alleles: a focus on ATM gene

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1 Modena novembre 2010 Breast cancer and the role of low penetrance alleles: a focus on ATM gene Dr. Laura La Paglia

2 Breast Cancer genetic Other BC susceptibility genes TP53 PTEN STK11 CHEK2 BRCA1 and BRCA2 ATM SPORADIC

3 Ataxia Telangiectasia Autosomal recessive disorder Inesorable and gradual cerebellar cortical atrophy Telangiectases in the eyes, facial skin, with variable appearance Thymic degeneration Immune deficiency Recurrent sinopulmonary infections Extreme predisposition to lymphoreticular malignancies Chromosomal instability Acute sensitivity to ionizing radiation A-T carriers - cancer-prone to different type of malignancies mainly leukaemia and lymphomas Some evidences link ATM mutational status with an increased Breast Cancer risk.

4 ATM cloned in 1995 Chromosomic localization: 11q exons, 62 coding mrna 13Kb prot 370kDal no mutational hot spot (http/chromium.liacs.nl/lovd/.) ATM gene ATM protein Substrate binding Ser-367 Ser-1893 Ser-1981 P Leucine Zipper Proline rich P P FAT domain ATP binding site Catalytic site PIK3- domain FATCH domain PTS1 domain

5 ATM-mediated DNA damage response Ser1981

6 ATM and lymphoid neoplasies Taylor et al reported that A-T patients are at high risk of T-cell acute lymphocytic leukaemia (T-ALL) and more especially to prolymphocytic leukaemia (T-PLL). A.M. Taylor et al, Blood 87 (1996), Different works report that about 40-46% of T-PLL exhibit alterations of both ATM alleles. M.A. Haidar et al, Cancer 88 (2000), F. Gumy-Pause et al, Leukemia 18 (2004), Somatic inactivation of the ATM gene have been reported also in T-PLL and B-CLL occurring in patients without A-T. Vorechovsky analysis on tumor DNA from T-PLL pts shows a high frequency of ATM mutations, most missense mutations. Vorechovsky et al, Nat Genet 17 (1997), S. Stilgenbauer et al, Nat Med 3 (1997), Stankovic s series of T-PLL pts shows 18% of ATM mut carriers T. Stankovic, P et al, Lancet 353 (1999), In a nordic study of relatives of A-T children, an increased standardized incidence ratio (SIR) of 37 (95% CI: 13 to 80) was observed for leukaemias and NHL. J.H. Olsen et al, J Natl Cancer Inst 93 (2001),

7 ATM heterozigosity and Breast Cancer Swift 1987 Fitzgerald 1997 Chen 1998 Htz female relatives of AT 2 to 5 fold increase in risk of BC Thompson 1999 Renwick 2006 Key predictor of this hypothesis: Htz for ATM mutations is more common among BC individuals than the general population Renwick strategy: Case-control strategy Genomic screening from all cases and controls through the 62 coding exons and all splice junctions Index cases from families with at least 3 BC Pre-screening for BRCA1/2 mutations and LGR Combining truncating, splicing, RR of BC of 2.37 (95% C.I.= , P = ) and missense variants ATM mutations that cause AT are BC susceptibility alleles

8 Patients selection Unrelated Pts BRCA1 and BRCA2 mutation negative Index Cases with BC onset before the age of 36 Index Cases with family history of BC and/or OC family history of BC was defined as follows: 1) at least 1 with invasive BC before the age of 41 2) 1 with OC or BC at any age, or 3 first or second degree relatives from the same lineage with invasive BC or OC at any age, including the index case At least one first or second degree relative with leukaemia or lymphoma, and this relative belonging to the branch of the family in which breast cancers were segregating. Written informed consent for breast cancer genetic studies was obtained from each woman at the family cancer clinic.

9 ATM genetic screening by DS and EMMA 68 Sicilian pts 122 French pts Negatively tested for BRCA1/2 mut

10 ATM germline variants and their characteristics in our series of BC pts with a family history of BC and haemat. malignancies 28 different monoallelic sequence variants identified in 35 of 122 BC women screened for ATM gene mutation in French population : 1. 1 Non-sense mut missense mut 3. 2 silent mut 4. 7 intronic variants No LGR detected 22 Htz polymorphisms detected (NCBI SNP database) 2 different monoallelic sequence variants identified in 2 of 68 BC women screened for ATM gene mutation in Italian population : 2 missense mut No LGR detected 5 Htz polymorphisms detected (NCBI SNP database)

11 Criteria proposed to assess the clinical significance of missense mutations The biological function of the 20 missense mutations was unknown. We proposed 5 criteria to assess the significance of their functional effect: A carrier frequency less than 1% in a series of controls Identification of the missense mut in an A-T child carrying no more than one deleterious ATM mut Localization in an ATM protein domain known to be functionally important (PI3K, FAT) The relevance of the AA change and AA species conservation analysed by the A-GVGD algorithm Putative splice effect by using in silico splice site score prediction models The criteria are listed in order of increasing relevance with respect to a putative deleterious effect

12 ATM germline variants and their characteristics in our series of BC pts with a family history of BC and haemat. malignancies 1. n. 1 Non sense mutation 2. n. 1 Splicing mutation 3. n. 20 missense mutations 4. n. 2 silent mut 5. n. 7 intronic variants 1. 6 likely deleterious UV 3. 2 likely neutral

13 Results 2/68 (2.9%) Italian BC patients (independently of their family history of haematological diseases) presented a mutation in ATM gene. Interestingly, the percentage of ATM mutations in French BC patients with a family history of both BC and haematological malignancy was 6.56% (95% CI: ), a higher frequency compared to that observed in the general population ( %).

14 CONCLUSIONS Although a trend towards an increased frequency of ATM carriers in BC families + haemat. diseases observed, it was not different from that observed in a population of familial BC women not selected for haemat. malignancy (frequency of ATM carriers was 2.90%, a value situated in the confidence interval of our study ( )). Althow the RR of hemat diseases in ATM heterozigotes reported by Olsen s study was SIR 37, the absolute risk remains low, as the incidence of hemat malignancies in the general population is low Larger studies are needed to indicate that ATM polymorphisms and mutations can have an important effect on breast cancer risk.