Acquired FGFR and FGF alterations confer resistance to estrogen receptor (ER) targeted therapy in ER+ metastatic breast cancer

Abstract

55Beyond acquired mutations in the estrogen receptor (ER), mechanisms of resistance to 56 ER-directed therapies in ER+ breast cancer have not been clearly defined. We conducted 57 a genome-scale functional screen spanning 10,135 genes to investigate genes whose 58 overexpression confer resistance to selective estrogen receptor degraders. Pathway 59 analysis of candidate resistance genes demonstrated that the FGFR, ERBB, insulin 60 receptor, and MAPK pathways represented key modalities of resistance. In parallel, we 61 performed whole exome sequencing in paired pre-treatment and post-resistance biopsies 62 from 60 patients with ER+ metastatic breast cancer who had developed resistance to ER-63 targeted therapy. The FGFR pathway was altered via FGFR1, FGFR2, or FGF3 64 amplifications or FGFR2 mutations in 24 (40%) of the post-resistance biopsies. In 12 of 65 the 24 post-resistance tumors exhibiting FGFR/FGF alterations, these alterations were not 66 detected in the corresponding pre-treatment tumors, suggesting that they were acquired or 67 enriched under the selective pressure of ER-directed therapy. In vitro experiments in ER+ 68 breast cancer cells confirmed that FGFR/FGF alterations led to fulvestrant resistance as 69 well as cross-resistance to the CDK4/6 inhibitor palbociclib. RNA sequencing of resistant 70 cell lines treated with different drug combinations demonstrated that FGFR/FGF induced 71 resistance through ER reprogramming and activation of the MAPK pathway. The 72 resistance phenotypes were reversed by FGFR inhibitors, a MEK inhibitor, and/or a 73 SHP2 inhibitor, suggesting potential treatment strategies. The detection of targetable, 74 clonally acquired genetic alterations in the FGFR pathway in metastatic tumor biopsies 75 highlights the value of serial tumor testing to dissect mechanisms of resistance in human 76 breast cancer and its potential application in directing clinical management. 77 78 [4][5][6][7], acquired activating mutations in ERBB2 (HER2) [11, 12], loss of function of NF1 96[13], and other alterations in MAPK pathway genes [14]. Additional mechanisms remain 97 to be identified. 98 99 Gain-of-function screens have played a pivotal role in identification of resistance 100 mechanisms to targeted therapies in various cancer types [15-17]. In breast cancer, 101 5 several functional screen studies identified IGF1R, KRAS and ESR1 as mechanisms of 102 resistance to tamoxifen and/or estrogen deprivation [18-20]. However, genome-scale 103 functional screens for SERD resistance have not been reported. 104 105 We conducted a genome-scale gain-of-function screen in ER+ breast cancer cells 106 spanning 17,255 overexpressed lentiviral open reading frames (ORFs) to investigate 107 genes whose overexpression was sufficient to confer resistance to the SERDs fulvestrant 108 and GDC-0810 [21]. In parallel, we sought to identify endocrine resistance mechanisms 109 of clinical significance through genomic profiling of paired pre-treatment and post-110 treatment tumor samples from 60 patients with ER+ me...

The genomic landscape of intrinsic and acquired resistance to cyclin-dependent kinase 4/6 inhibitors in patients with hormone receptor positive metastatic breast cancer

“…This effort confirmed previous reports implicating rare events in RB1 while also revealing novel mediators of resistance including AKT1, RAS family oncogenes, AURKA, CCNE2, and ER loss. Prior work from our group and others identified mutational events in ERBB2 25 and the FGFR pathway 24, 26, 36 in driving resistance. In vitro experiments confirm that AKT1, KRAS G12D, AURKA, and CCNE2 confer resistance to CDK4/6i.…”

“…Prior work from our group and others implicating FGFR pathway and ERBB2 activation in CDK4/6i resistance have been reported elsewhere. 24–26…”

“…Prior work from our laboratory has implicated alterations in ERBB2 and FGFR2 in mediating resistance to CDK4/6i in vitro and in patients. 24, 25 In addition, amplification of FGFR1 , identified via sequencing of ctDNA from MONALEESA-2 (ribociclib and anti-estrogen in the first-line metastatic setting), correlated with reduced PFS and activation of FGFR1 provoked resistance in vitro. 26…”

Fibroblast growth factor receptor facilitates recurrence of minimal residual disease following trastuzumab emtansine therapy

“…Previous studies from our lab and others suggest that FGFR can act as an bypass mechanism to facilitate resistance to ErbB kinase inhibitors (17,18,20,38). Furthermore, FGFR signaling has also been identified as a mechanism of resistance to endocrine therapies in breast and prostate cancer (19,39). Therefore, FGFR appears to constitute a critical node in acquisition of drug resistance.…”

“…FGFR1 can also undergo gene amplification and translocation, and elevated expression of FGFR1 is associated with decreased clinical outcomes of breast cancer patients (14) (15,16). Work from our lab and others suggest that upregulation of FGFRs and FGF ligands can serve as resistance mechanisms for tumor cells that were originally sensitive to ErbB and endocrine-targeted therapies (16)(17)(18)(19)(20). In addition to enhanced expression of the receptor, our recent studies demonstrate that the processes involved in EMT work en masse to support FGFR signaling through diminution of E-cadherin and enhanced interaction with integrins (21).…”