Transcriptional Reprogramming Differentiates Active from Inactive ESR1 Fusions in Endocrine Therapy-Refractory Metastatic Breast Cancer

Abstract

Genomic analysis has recently identified multiple ESR1 gene translocations in estrogen receptor alpha–positive (ERα+) metastatic breast cancer (MBC) that encode chimeric proteins whereby the ESR1 ligand binding domain (LBD) is replaced by C-terminal sequences from many different gene partners. Here we functionally screened 15 ESR1 fusions and identified 10 that promoted estradiol-independent cell growth, motility, invasion, epithelial-to-mesenchymal transition, and resistance to fulvestrant. RNA sequencing identified a gene expression pattern specific to functionally active ESR1 gene fusions that was subsequently reduced to a diagnostic 24-gene signature. This signature was further examined in 20 ERα+ patient-derived xenografts and in 55 ERα+ MBC samples. The 24-gene signature successfully identified cases harboring ESR1 gene fusions and also accurately diagnosed the presence of activating ESR1 LBD point mutations. Therefore, the 24-gene signature represents an efficient approach to screening samples for the presence of diverse somatic ESR1 mutations and translocations that drive endocrine treatment failure in MBC. Significance: This study identifies a gene signature diagnostic for functional ESR1 fusions that drive poor outcome in advanced breast cancer, which could also help guide precision medicine approaches in patients harboring ESR1 mutations.

ESR1 fusions and therapeutic resistance in metastatic breast cancer

“…The loss of a functional LBD suggests a clear pathological impact, leading to complete resistance to the activity of current ER antagonists, which all bind to the LBD. As expected, several ESR1-e6>fusions (ESR1-e6>YAP1, ESR1-e6>PCDH11X, ESR1-e6>SOX9 and ESR1-e6>ARNT2-e18) remained stably expressed in the presence of fulvestrant and promoted ET-resistant growth of T-47D and MCF7 cells ( 80 , 81 ). In contrast, the expression of ER mutant constructs that lack the LBD had decreased transcriptional activity, suggesting that the presence of the 3’ partner is essential for the ER fusion activity ( 80 , 81 , 84 ).…”

“…Although Li and colleagues conducted limited functional studies, overexpression of ESR1-e6>YAP1 in ER+ breast cancer cells conferred estradiol-independent growth in their study ( Table 1 ). Lei and colleagues ( 80 ) and Gou and colleagues ( 81 ) provided additional mechanistic data for the ESR1-e6>YAP1 fusion and described its functional properties in driving estrogen-independent growth, constitutive expression of ER target genes, and anti-estrogen resistance. Several years later, two additional ESR1 fusions, ESR1-e2 fusion with the acidic residue methyltransferase 1 gene, C6orf211/ARMT1 (ESR1-e2>C6orf211/ARMT1) and ESR1-e6 fusion with a-kinase anchoring protein 12 gene, AKAP12 (ESR1-e6>AKAP12) were identified in AI resistant breast cancer by Giltnane and colleagues ( Table 1 ) ( 82 ) with no functional data available ( Table 1 ).…”

“…Several years later, two additional ESR1 fusions, ESR1-e2 fusion with the acidic residue methyltransferase 1 gene, C6orf211/ARMT1 (ESR1-e2>C6orf211/ARMT1) and ESR1-e6 fusion with a-kinase anchoring protein 12 gene, AKAP12 (ESR1-e6>AKAP12) were identified in AI resistant breast cancer by Giltnane and colleagues ( Table 1 ) ( 82 ) with no functional data available ( Table 1 ). Using whole genome sequencing, Robinson and colleagues ( 83 ) identified three additional ESR1 fusions ( Table 1 ) including fusionsaryl hydrocarbon receptor nuclear translator 2 gene, ARNT2 (ESR1-e6>ARNT2-e18); protein-L-isoaspartate O-methyltransferase gene, PCMT1 (ESR1-e6>PCMT1); AT-rich interaction domain 1B gene, ARID1B (ESR1-e6>ARID1B), but the functional properties of these fusions were investigated only later on by Gou and colleagues ( 81 ). Hartmaier and colleagues also described the expression of ESR1-e6>AKAP12 in ER+ MBC and identified several novel ESR1 fusions ( 84 ).…”

“…Seven additional ESR1-e6>fusions ( Table 1 ) were identified by Priestley and colleagues in ER+ MBC, including aqryl hydrocarbon receptor nuclear translocator 2, ARNT2 (ESR1-e6>ARNT2); LIM domain containing preferred translocation partner in lipoma, LPP (ESR1-e6>LPP); nuclear receptor coactivator 1, NCOA1 (ESR1-e6>NCOA1); transcription factor 12, TFC12 (ESR1-e6>TCF12); clathrin interactor 1, CLINT1 (ESR1-e6>CLINT1); glutamate receptor interacting protein 1, GRIP1 (ESR1-e6>GRIP1) and trinucleotide repeat containing adaptor 6B, TNRC6B (ESR1-e6>TNRC6B). Functional characterization of these fusions were investigated by Gou and colleagues ( 81 , 85 ) ( Table 1 ). Except ESR1-e6>TCF12, all ESR1-e6>fusions promoted estrogen-independent growth.…”

“…Structural studies have revealed that this structure is distinct from the ESR1-e6>fusions identified from ET resistant MBC. Despite the diversity among the ESR1-e6>fusions, they share a common structure whereby the first 6 exons of ESR1 (ESR1-e6) are preserved, retaining the hormone-independent transactivation domain (TAD) as well as the DNA-binding domain of ER whereas the LBD is lost and replaced with a functional domain of the 3’ fusion partner ( Figure 1 ) ( 76 , 81 , 84 ). This structure is strongly associated with estrogen independent growth and ET resistant metastatic ER+ breast tumors.…”