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Updated: Aug 2, 2025

Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis
Published on: June 27, 2020
Kinome Reprogramming Is a Targetable Vulnerability in ESR1 Fusion-Driven Breast Cancer
Xuxu Gou1,2,3, Beom-Jun Kim1,4, Meenakshi Anurag1,4
1Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas.
Abstract:
Transcriptionally active ESR1 fusions (ESR1-TAF) are a potent cause of breast cancer endocrine therapy (ET) resistance. ESR1-TAFs are not directly druggable because the C-terminal estrogen/anti-estrogen-binding domain is replaced with translocated in-frame partner gene sequences that confer constitutive transactivation. To discover alternative treatments, a mass spectrometry (MS)-based kinase inhibitor pulldown assay (KIPA) was deployed to identify druggable kinases that are upregulated by diverse ESR1-TAFs. Subsequent explorations of drug sensitivity validated RET kinase as a common therapeutic vulnerability despite remarkable ESR1-TAF C-terminal sequence and structural diversity. Organoids and xenografts from a pan-ET-resistant patient-derived xenograft model that harbors the ESR1-e6>YAP1 TAF were concordantly inhibited by the selective RET inhibitor pralsetinib to a similar extent as the CDK4/6 inhibitor palbociclib. Together, these findings provide preclinical rationale for clinical evaluation of RET inhibition for the treatment of ESR1-TAF-driven ET-resistant breast cancer.
Significance:
Kinome analysis of ESR1 translocated and mutated breast tumors using drug bead-based mass spectrometry followed by drug-sensitivity studies nominates RET as a therapeutic target. See related commentary by Wu and Subbiah, p. 3159.
Insights
Targeting RET kinase offers a new treatment strategy for endocrine therapy-resistant breast cancer. This approach addresses resistance caused by estrogen receptor 1 (ESR1) fusions by inhibiting upregulated RET kinase.
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- Transcriptionally active ESR1 fusions (ESR1-TAFs) drive endocrine therapy (ET) resistance in breast cancer.
- ESR1-TAFs are inherently undruggable due to altered C-terminal domains, necessitating alternative therapeutic strategies.
Purpose of the Study:
- To identify druggable kinases upregulated by ESR1-TAFs.
- To evaluate RET kinase as a potential therapeutic target for ESR1-TAF-driven breast cancer.
Main Methods:
- Utilized mass spectrometry-based kinase inhibitor pulldown assay (KIPA) to screen for kinases associated with ESR1-TAFs.
- Conducted drug sensitivity studies using organoids and xenografts from patient-derived models.
Main Results:
- Identified RET kinase as a common vulnerability across diverse ESR1-TAFs.
- Demonstrated that the selective RET inhibitor pralsetinib effectively inhibited tumor growth in preclinical models, comparable to CDK4/6 inhibitors.
Conclusions:
- RET kinase inhibition presents a promising therapeutic avenue for patients with ESR1-TAF-driven endocrine therapy-resistant breast cancer.
- These findings support the clinical investigation of RET inhibitors for this patient population.
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