Abstract PD4-07: Genenomic landscape of breast cancers with FGFR1 amplification and FGFR1/CCND1 co-amplification revealed by targeted capture next generation sequencing
Authors: Gonzalez-Ericsson PI , Estrada MV , Formisano L , Jansen VM , Mayer IA , Rexer BN , Abramson VG , Levy M , Balko JM , Stricker TP , Arteaga CL , Sanders ME 
Published: February 2018

Abstract
Background: FGFR1 amplification (amp) occurs in ˜15% of breast cancers (BC) and associates with poor prognosis and resistance to endocrine therapy. CCND1 regulates cell cycle progression and is amplified in 15-20% of BC. Co-amp of FGFR1 occurs in 30-40% of CCND1amp tumors, suggesting the possibility of oncogene cooperativity. CDK4/6 inhibitors, which block the action of cyclin D1/CDK4 complexes at the G1-to-S transition, are approved for treatment of ER+ BC and FGFR inhibitors are in early phase clinical trials.
Results: Between 11/2013 and 03/2017, 191 BCs from 188 patients with metastatic (M) or refractory locoregional recurrent (RLRR) BC at Vanderbilt (VICC) were profiled by targeted next gen sequencing (Foundation OneTM). These are included within the 2131 publicly available BC sequencing results in GENIE (Foundation OneTM and MSK-IMPACT). Among the GENIE cohort, rates were: FGFR1amp 7% (n=156), CCND1amp 12% (n=261) and CCND1/FGFR1co-amp 3% (n=58). Additional cases showed FGFR1 missense mutations (n=16) and deep deletions (n=5). When the analysis was limited to the VICC cohort allowing restriction to ER+ BC, FGFR1amp (16%) and CCND1amp (23%) rates are similar to rates in primary BC in TCGA (13% FGFR1 [p = 0.44] and 19% CCND1 [p = 0.24]). In GENIE, the most frequent co-mutations in FGFR1amp tumors were TP53 (31%), PIK3CA (21%), GATA3 (13%), CDH1 (11%) and MAP3K1 (10%). However, TP53 and PIK3CA mutations were less common among FGFR1amp tumors than FGFR1non-amp cases (p &lt;0.001). FGFR1amp was associated with 11q13 amp (CCND1, FGF3/4/19) in 35% (p&lt;0.001), 20q.13 amp (GNAS, AURKA) in 27% (p=0.01) and 20q11 amp (SRC) in 15% (p=0.001). ESR1 mutations were enriched among CCND1amp tumors (p&lt;0.001) and ARID1A mutations among FGFR1/CCND1co-amp tumors (p 0.048). Among tumors with FGFR1amp, TP53 mutations were mutually exclusive of ESR1 mutations (p&gt;0.016). Histopathologic correlation on tumors from our institution show a majority of FGFR1 and/or CCND1 amp BC (64%) were ER+/HER2–; 33% of ER+/FGFR1amp tumors were PR–. Distinctive histologic features associated with FGFR1 and/or CCND1 amp were lobular histology (17%) and neuroendocrine differentiation (14%), 0-10%TILs (94%) and high proliferative rate (46%).
Conclusion: FGFR1amp and CCND1amp rates in TCGA are similar to those seen in MBC/LRRBC (GENIE) suggesting FGFR1 can function as both a driver mutation and de novo mechanism of endocrine resistance early in tumorigenesis. Frequent co-amp with CCND1 and lower rates of TP53 and PIK3CAmut also support a driver role for FGFR1amp and FGFR1/CCND1co-amp. The observation of neuroendocrine features in a subset of these tumors suggests lineage plasticity. This may be a consequence of genomic alterations promoting anti-estrogen resistance and is consistent with recently published BC outcome data associating neuroendocrine differentiation with higher grade ER+ tumors, frequent 8p amp, which includes FGFR1, and worse disease-free and overall survival. The frequency of FGFR1amp suggests genotype specific trials with FGFR inhibitors would be highly feasible. Whether FGFR1/CCND1 co-amplified tumors are candidates for treatment with a combination of FGFR and CDK4/6 inhibitors requires further investigation.
Citation Format: Gonzalez-Ericsson PI, Estrada MV, Formisano L, Jansen VM, Mayer IA, Rexer BN, Abramson VG, Levy M, Balko JM, Stricker TP, Arteaga CL, Sanders ME. Genenomic landscape of breast cancers with FGFR1 amplification and FGFR1/CCND1 co-amplification revealed by targeted capture next generation sequencing [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD4-07.