Purpose: BRCA1/2 deficient breast tumors are highly sensitive to poly- ADP-ribose polymerase inhibitors (PARPi). The Fanconi Anemia (FA) associated gene products along with BRCA 1/2 function in a common pathway that regulates the cellular response to DNA damage, suggesting that tumors with dysfunction of any of the components of FA network would be susceptible to PARPi. Understanding the prevalence of such defects in breast tumors using reproducible methodology will help us target these tumors with novel agents and potentially improve outcomes. Hence we sought to assess the prevalence of FA pathway defect in breast tumors by the absence of nuclear FANCD2 (a pivotal protein in the FA/BRCA pathway which is monoubiquitylated in the nucleus in response to DNA damage) repair foci using a novel immunofluorescence method and correlate this with known molecular markers of breast cancer.

Methods: Using primary tumors obtained from the ongoing PARPi clinical trials (NCT01017640 and NCT01251874) and tumor bank, we evaluated 102 breast tumors for the somatic functionality of the FA pathway (FANCD2 foci formation) by the FA Triple Stain Immuno-Fluorescence (FATSI) test performed in a CLIA-certified laboratory using paraffin embedded tissues. The tissue sections are incubated with a primary antibody cocktail of rabbit polyclonal FANCD2 antibody and a monoclonal anti-Ki67 mouse antibody, followed by co-incubation with a secondary antibody (FITC conjugated to anti-rabbit IgG and Alexafluor 594 donkey anti-mouse), mounted on glass slides in a DAPI containing embedding medium and evaluated by a fluorescence microscope. Absence of nuclear FANCD2 formation in 100 proliferating tumor cells was considered positive for FA defect. Hormone receptor (HR) and Her2 status was compared between the groups using Fisher's exact test.

Results: A total of 102 primary breast tumors were analyzed for FANCD2 by FATSI test of which 62 were triple negative (TN), 37 were HR positive and 3 were Her2 positive. Of these, 29 tumors (28%) were positive for FA defect with no significant differences among the molecular subtypes (26% in TN vs 32% in HR + vs 33% in Her2+).

Conclusions: We report a novel methodology to efficiently screen archival FFPE tumors for somatic functional defect of FA DNA repair pathway and demonstrated a high prevalence (one-third) in breast tumors irrespective of molecular subtype. We are currently conducting clinical trials with PARPi including patients with tumors that test positive for FA defect to demonstrate if such tumors are sensitive to PARPi.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr PD10-01.