Proteogenomic Approaches for Finding Therapeutic Vulnerabilities in Metastatic Breast Tumors Expressing Transcriptionally Active ESR1 Fusions
Abstract
The vast majority (~70%) of breast cancers are driven by the hormone estrogen through direct binding to the estrogen receptor-alpha (ER). When women and occasionally men present with ER-positive cancer, we treat with anti-estrogens (tamoxifen) or estrogen-lowering agents called aromatase inhibitors, collectively called endocrine therapy (ET). Initially favorable clinical response to ET is often observed, but unfortunately ER-positive breast cancers become ET-resistant over time, and this is often associated with lethal tumor spread beyond the breast into vital organs (metastasis). Thus, understanding how ET resistance is acquired is critical. In up to 40% of ER-positive, ET-resistant metastatic breast cancer samples, the sequence of the gene for ER (ESR1) is altered (mutation) in the region of the gene responsible for estrogen binding – the “ligand binding domain” (LBD). These changes result in an ER that is active without estrogen. Fortunately, patients with tumors harboring LBD mutations will likely be treatable with a new generation of improved anti-estrogens. However, for the remaining 60% of patients with ET-resistant disease, we need to discover what genetic changes are driving resistance, study these events biologically, and thus develop new treatments. In 2013 the Ellis laboratory discovered a new resistance mechanism in a metastatic breast cancer sample where the ESR1 gene was fused with another gene, resulting in production of a functional “chimeric” protein (after the Greek term for a mythical animal composed of two creatures). This fused protein, called ESR1-YAP1, contained the front half of ER and the back half of another gene from a transcriptional coactivator called YAP1. Since then, the Ellis lab with other clinical collaborators have identified 21 additional in-frame ESR1 fusions with diverse partner genes. In preliminary data for this grant, we have shown four ESR1 fusions with partner sequences from ARNT2, SOX9, YAP1, and PCDH11X allow breast cancer cells to survive ET treatment and also drive metastasis. Thus, there is a clear clinical need to address the following unanswered questions: 1) What makes an ESR1 chimera pathologically “active” and can we apply “rules” to define a newly identified fusion in the clinic as “active”? 2) Since active ESR1 fusions cannot bind anti-estrogen drugs, can we devise new therapeutics to treat breast cancers driven by these unfortunate events? Our grant thus will address the BRCP overarching challenge to “eliminate the mortality associated with metastatic breast cancer” in the subset of ER-positive, ET-resistant breast cancer patients that express ESR1 fusions. To address our two critical questions, our grant will have three research aims. Aim 1 will address question 1. Here we will engineer breast cancer cell lines expressing up to 30 different ESR1 fusions identified from RNA-sequencing of clinical samples. From these cell lines, we will define an “active ESR1 fusion gene signature” by identifying a common set of genes dysregulated in cells expressing an ESR1 fusion relative to those that are wild-type (WT) (expressing regular ER) cells. Our gene signature will then be validated with additional clinical RNA-sequencing data and then applied to new identified ESR1 fusions in the clinic. We will also test whether active ESR1 fusions confer ET-resistant tumor growth and metastasis to distant organs by transplanting breast cancer cells expressing an ESR1 fusion into mice lacking an immune system (called a xenograft). Aims 2 and 3 will address question 2. In these aims, we will use the breast cancer cell lines expressing ESR1 fusions created in Aim 1 and use a technology called mass spectrometry to identify potential new drug targets. In Aim 2, we will identify proteins that phosphorylate other proteins (called kinases) that are activated in ESR1 fusion cells as compared to WT cells. Kinases are excellent drug targets as small molecule inhibitors can be designed to their A
Document Details
- Document Type
- DoD Grant Award
- Publication Date
- Dec 05, 2021
- Source ID
- W81XWH2110119
Entities
People
- Matthew J Ellis
Organizations
- Baylor College of Medicine
- United States Army