Abstract PS16-06: Identification of pathogenic FGFR1, FGFR2, and FGFR3 alterations in cell-free DNA (cfDNA) from patients with metastatic breast cancer
Authors: Taylor Mary Love , Mayro Benjamin , Drusbosky Leylah , Batchelder Robin , Marcom P. Kelly , Anders Carey , Force Jeremy 
Published: February 2021

Background: FGFR alterations are a known mechanism of resistance against breast cancer systemic therapies with higher FGFR RNA expression in breast cancer brain metastases compared to their primary tumors. While the genomic characterization of FGFR alterations has occurred from bulk breast tumors, the frequency and type of FGFR alterations in metastatic breast cancer (MBC) have not been fully characterized from cfDNA. The purpose of this study was to identify the incidence of FGFR1, FGFR2, and FGFR3 genomic alterations in cfDNA from patients with MBC and elucidate which FGFR alterations may increase FGFR kinase activity or may function as mechanisms of resistance against the FDA approved FGFR inhibitor, erdafitinib.

Methods: We queried 16,053 reports from Guardant Health between June 2015 - October 2019 to identify the incidence of FGFR1, FGFR2, and FGFR3 alterations detected in cfDNA from MBC. We classified each alteration type into the following categories: copy number variation (CNV), fusion, indel, or single nucleotide variant (SNV). Focus was placed on characterizing FGFR1, FGFR2, and FGFR3 SNVs. We compared known activating mutations in EGFR, ERBB2, and BRAF with homologous regions in FGFR1, FGFR2, and FGFR3. In silico modeling with PyRx was used to dock erdafitinib onto FGFR1 (PDB 4V05), FGFR2 (PDB 5B7V), and FGFR3 (PDB 6LVM) kinases. Three-dimensional in silico analyses with ChimeraX was utilized to further determine which alterations may increase FGFR1, FGFR2, and FGFR3 kinase activity or may induce resistance against erdafitinib.

Results: The incidence of nonsynonymous alterations occurring in FGFR1, 2213 (13.8%); FGFR2, 1017 (6.3%); and FGFR3, 144 (0.9%) were identified in the Guardant Health MBC database. FGFR1, FGFR2, and FGFR3 alterations are detailed in Table 1. We identified 40 (9.15%) and 167 (38.2%), 55 (7.2%) and 310 (40.4%), and 31 (27.4%) and 32 (28.3%) mutations occurring in the transmembrane/juxtamembrane and kinase domains of FGFR1, FGFR2, and FGFR3, respectively. Hotspot mutations were observed at R54C/S/G/R and N546K/D/S in FGFR1, D304N and N549K/D/S in FGFR2, and at S408/F/C/L/Y in FGFR3. We aligned FGFR1, FGFR2, and FGFR3 with homologous kinases and found 12 unique samples with mutations in our FGFR1 dataset corresponded to known activating mutations in EGFR and ERBB2; 18 samples with mutations in our FGFR2 dataset corresponded to known activating mutations in EGFR, ERBB2, and BRAF; and 1 mutation in our FGFR3 dataset corresponded to a known activating mutation in ERBB2. FGFR1 mutations C488S, V492M, M535I, L569V and FGFR2 mutations L550V, E565A, Y566N, S568C, G570R, G685E are postulated to induce resistance against erdafitinib.

Conclusions: We found that 21% of MBC in this dataset harbor FGFR genomic alterations detected from cfDNA. Novel somatic alterations in FGFR1, FGFR2, and FGFR3 were identified from Guardant Health that were not detected in the public domain. A portion of FGFR SNVs occurred at known homologous kinase activating mutations in EGFR, ERBB2, and BRAF suggesting these specific FGFR mutations may increase FGFR kinase activity and might be actionable therapeutic targets in breast cancers harboring these mutations. Three dimensional analyses of the FGFR protein tyrosine kinase further illustrate which specific alterations may increase FGFR kinase activity or induce resistance against erdafitinib.

Table 1. Incidence and type of FGFR alterations in Guardant Health MBC databaseGeneCNV (%)Fusion (%)Indel (%)SNV (%)FGFR11770 (80%)-6 (0.3%)437 (19.7%)FGFR2224 (22%)15 (1.5%)11 (1.1%)767 (75.4%)FGFR3-24 (16.7%)7 (4.9%)113 (78.4%)

Citation Format: Mary Love Taylor, Benjamin Mayro, Leylah Drusbosky, Robin Batchelder, P. Kelly Marcom, Carey Anders, Jeremy Force. Identification of pathogenic FGFR1, FGFR2, and FGFR3 alterations in cell-free DNA (cfDNA) from patients with metastatic breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS16-06.