Jones, Calley J.

Abstract Breast cancer is the most common female malignancy in the U.S. and the leading cause of cancer-related deaths in women worldwide. Nearly 80% of breast tumors express estrogen receptor alpha (ERα) which drives tumor progression. While endocrine therapies and CDK4/6 inhibitors have increased overall survival, many patients experience recurrence of metastatic disease that is largely refractory to additional lines of endocrine therapy. Metastatic disease remains incurable, highlighting the need for alternative treatment approaches. Through a genome-wide CRISPR knockout screen, we identified Lemur Tail Kinase 2 (LMTK2) as the top hit exhibiting synthetic lethality in the presence of the endocrine therapy, endoxifen, in both endocrine-sensitive and -resistant cell line models. Using publicly available patient tumor databases we identified LMTK2 copy number gain/amplification in 67% of ERα+ human metastatic breast tumors, while only 1% of primary tumors harbored these genomic alterations. Elevated LMTK2 expression in early-stage primary breast tumors was associated with worse recurrence-free survival and overall survival. We discovered that LMTK2 mRNA and protein levels were substantially elevated in nearly all cell-line and patient-derived models of endocrine and CDK4/6i resistance. Utilizing siRNAs and dox-inducible shRNA expressing cell lines, we found that knockdown of LMTK2 enhanced the efficacy of multiple endocrine therapies in treatment naïve models and resensitized resistant models to their respective treatment. LMTK2 overexpression was found to be sufficient for conferring resistance to all standard of care therapies tested including endocrine agents, CDK4/6i, and PI3K inhibitors. RNAseq and global proteomics of LMTK2 overexpressing and knockout models revealed the PI3K/AKT pathway and estrogen signaling as highly regulated pathways by LMTK2. Confirmatory western blot studies demonstrated that LMTK2 overexpression results in dramatic increases in AKT and ERα phosphorylation and activity, while knockout of LMTK2 diminishes these effects. Attempts to completely ablate LMTK2 in endocrine/CDK4/6i-resistant models via CRISPR were not successful, and continuous siRNA or shRNA-mediated knockdown was lethal in resistant cell lines, confirming its essentiality in this setting. In summary we have uncovered LMTK2 as a novel mediator of endocrine/CDK4/6i resistance that is mechanistically linked to the PI3K/AKT pathway among others. Genetic manipulation of LMTK2 has validated it as an ideal therapeutic target for both advanced and newly diagnosed forms of ERα+ breast cancer. Citation Format: Anna Detry, Sofia Marigliano, Jenna Heinen, Adam Bass, Calley Jones, Rajeev Muthyala, Matthew Goetz, John Hawse. LMTK2: A novel driver of endocrine resistance in ERα+ breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 443.

Abstract Breast cancer is the most common female malignancy in the U.S. and the leading cause of cancer-related deaths in women worldwide. Nearly 80% of breast tumors express estrogen receptor alpha (ERα) which drives tumor progression. While CDK4/6 inhibitors in combination with endocrine therapy improve overall survival in the metastatic setting and disease-free survival in the adjuvant setting, many patients eventually relapse/progress with resistant forms of disease. In the post-CDK4/6 inhibitor setting, second line endocrine therapy responses are limited, highlighting the need for alternative treatment approaches. Through a genome-wide CRISPR knockout screen, we identified Lemur Tail Kinase 2 (LMTK2) as the top hit exhibiting synthetic lethality in the presence of the tamoxifen metabolite, endoxifen, in both endocrine-sensitive and -resistant cell line models. We further studied multiple other endocrine resistant models and identified that LMTK2 mRNA and protein expression were both increased in ERα cell lines resistant to estrogen deprivation, tamoxifen, fulvestrant, abemaciclib and palbociclib, as well as in endocrine resistant patient derived models. We then studied LMTK2 in patient samples and identified copy number gain/amplification in 67% of ERα+ human metastatic breast tumors, while only 1% of primary tumors harbored these genomic alterations. From a prognostic standpoint, elevated tumoral LMTK2 expression was associated with worse recurrence-free survival and overall survival in early-stage breast cancer. Through proteomic studies, we identified the MET-PI3K-AKT pathway as overactivated in LMTK2 overexpressing cells. Unlike activating PIK3CA mutations that drive AKT signaling, LMTK2 was found to employ an alternative mechanism to activate AKT signaling by inhibiting PP1α, an AKT-inhibitory phosphatase. Further, LMTK2 overexpression was sufficient to drive endocrine and CDK4/6 inhibitor resistance in vitro and resulted in dramatic increases in AKT and ERα phosphorylation and activity. While knockout of LMTK2 in treatment naïve ERα+ breast cancer cells neither altered AKT/ERα phosphorylation/activity nor endocrine/CDK4/6 inhibitor responsiveness, attempts to knockout LMTK2 in endocrine/CDK4/6 inhibitor-resistant models failed, further confirming its essentiality in this setting. In summary we have uncovered LMTK2 as a novel biomarker of endocrine/CDK4/6 inhibitor resistance that is mechanistically linked to the AKT pathway. LMTK2 may be a novel drug target for the effective treatment of resistant and advanced forms of ERα+ breast cancer. Citation Format: A. M. Detry, S. Marigliano, J. Heinen, A. Bass, C. Jones, R. S. Muthyala, M. P. Goetz, J. R. Hawse. Lmtk2: a novel driver of endocrine resistance in ER+ breast cancer [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS2-11-01.

Abstract Background:. Poor patient outcomes in triple negative breast cancer (TNBC) largely stem from a lack of understanding of therapeutic vulnerabilities and an insufficient armamentarium of effective drugs. The standard of care for most early stage TNBC patients continues to be (neo)adjuvant chemotherapy and radiation. Identifying additional therapeutic options for this subset of patients represents a major unmet need. We and others demonstrated that estrogen receptor beta (ERβ) is expressed in about 20% of TN tumors. Prior research has shown that ligand-mediated activation of ERβ decreases proliferation, invasion, and migration in TNBC cell lines. In vivo, ERβ suppresses the growth of cell line xenograft models and prevents the development of metastatic lesions in a ligand dependent manner. Mechanistically, we found that ERβ repurposes EZH2 to suppress oncogenic NFκB signaling and that pharmacologic inhibition of EZH2 diminishes ERβ function and its anti-cancer effects. This research has led to an ongoing clinical trial (NCT03941730) assessing the efficacy of estradiol in ERβ+ TNBC patients with chemorefractory disease. As with all therapies, patients will exhibit de novo and acquired resistance and therefore we sought to understand the mechanisms of resistance to ERβ targeted therapies. Methods:. Using multiple models of ERβ positive TNBC, we developed ERβ resistant cell lines through chronic exposure to estradiol and the ERβ specific agonist LY500307 over a period of 8 months. We employed RNA sequencing to characterize the transcriptomic changes which occurred following ERβ resistance. We profiled XIST expression across multiple publicly available datasets, including TCGA, Metabric, BEAUTY, and GTEx. XIST expression was also modulated using CRISPR/Cas9 to assess subsequent effects on TNBC cell biology, ERβ function, and response to ERβ targeted therapies. Results:. Our resistant cell line models of ERβ positive TNBC maintained ERβ expression, but were no longer growth inhibited by ERβ agonists. RNAseq revealed substantial differences comparing the transcriptome of resistant versus sensitive cell lines, of which the most increased transcript in the resistant setting was the lncRNA XIST. XIST is best known for its role in X-chromosome inactivation through recruitment and association with the PRC2 complex, and thus EZH2. However, little is known about its functions in breast cancer. We therefore assessed the expression levels of XIST in breast tumors and cell lines. XIST expression was highly variable in breast cancer, was found in a proportion of all breast cancer sub-types and did not correlate with ERβ status. However, XIST expression was up-regulated in ERβ expressing cell lines following long term estrogen treatment. No effects on XIST expression were identified in multiple ERα positive models following estrogen, SERM/SERD treatment, or estrogen deprivation. Furthermore, upregulation of XIST was not associated with resistance to Paclitaxel or Doxorubicin, suggesting XIST is not a part of a broad resistance phenotype. Strikingly, CRISPR mediated knockout of XIST in ERβ resistant cells completely re-sensitized cells to ERβ targeted therapies suggesting that XIST expression is a critical component of ERβ resistance. Conclusions:. ERβ represents a relevant therapeutic target that is being tested in clinical trials. Using multiple in vitro models, we provide evidence that XIST expression is sufficient to induce resistance to. ERβ targeted therapies in TNBC and may therefore represent a relevant biomarker for patient stratification. Further strategies to suppress XIST expression may elicit anti-cancer effects on their own and may resensitize a sub-set of ERβ resistant tumors to ERβ agonists. Citation Format: Michael J Emch, Kirsten GM Aspros, Elizabeth S Bruinsma, Krishna R Kalari, Calley J Jones, Brandon W Simone, Matthew P Goetz, John R Hawse. The lncRNA XIST mediates sensitivity to ERβ targeted therapies in triple negative breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P4-02-09.

Abstract Despite the availability of drugs that target ERα-positive breast cancer, resistance commonly occurs, resulting in relapse, metastasis, and death. Tamoxifen remains the most commonly-prescribed endocrine therapy worldwide, and “tamoxifen resistance” has been extensively studied. However, little consideration has been given to the role of endoxifen, the most abundant active tamoxifen metabolite detected in patients, in driving resistance mechanisms. Endoxifen functions differently from the parent drug and other primary metabolites, including 4-hydroxy-tamoxifen (4HT). Many studies have shown that patients who extensively metabolize tamoxifen into endoxifen have superior outcomes relative to patients who do not, supporting a primary role for endoxifen in driving tamoxifen responses. Therefore, “tamoxifen resistance” may be better modeled by “endoxifen resistance” for some patients. Here, we report the development of novel endoxifen-resistant breast cancer cell lines and have extensively compared these models to 4HT and fulvestrant (ICI)-resistant models. Endoxifen-resistant cells were phenotypically and molecularly distinct from 4HT-resistant cells and more closely resembled ICI-resistant cells overall. Specifically, endoxifen resistance was associated with ERα and PR loss, estrogen insensitivity, unique gene signatures, and striking resistance to most FDA-approved second- and third-line therapies. Given these findings, and the importance of endoxifen in the efficacy of tamoxifen therapy, our data indicate that endoxifen-resistant models may be more clinically relevant than existing models and suggest that a better understanding of endoxifen resistance could substantially improve patient care. Implications: Here we report on the development and characterization of the first endoxifen-resistant models and demonstrate that endoxifen resistance may better model tamoxifen resistance in a subset of patients.

Abstract Despite the availability of effective drugs that target ERα-positive breast cancer, ERα-positive disease still accounts for more breast cancer related deaths than any other subtype. Relapse in these patients is largely due to the development of resistance to anti-estrogen therapies such as tamoxifen. While tamoxifen and its resistance mechanisms have been extensively studied, relatively little is known about its active metabolite endoxifen. Our group has provided evidence that endoxifen is a potent and clinically relevant metabolite of tamoxifen. Therefore, characterization of endoxifen resistance mechanisms may be crucial to understanding tamoxifen resistance. We have developed novel endoxifen resistant MCF7 and T47D cell lines through chronic exposure to endoxifen over a period of 12-24 months. Using these models and their respective controls, we compared global gene expression profiles of endoxifen resistant cells to tamoxifen resistant cells and found marked differences between the two models. We subjected endoxifen resistant cells to a genome-wide, CRISPR-mediated knockout screen to identify genes involved in mediating endoxifen resistance. Subsequent analyses revealed that disruption of genes regulated by the glucocorticoid receptor (GR) enhanced cells’ ability to survive and proliferate in the presence of endoxifen, suggesting that GR signaling blocks growth of resistant cells. We provide evidence that GR activation via dexamethasone significantly inhibits the proliferation rates of endoxifen resistant cells by 50-60%, with little to no inhibitory effects in endoxifen sensitive models. Follow-up studies suggested that alpha zinc-glycoprotein 1 (AZGP1), a secreted lipolytic enzyme induced by GR, plays a role in mediating this phenotype. AZGP1 RNA and protein are highly expressed in normal breast tissue, but corresponding levels are lower in ERα-positive breast malignancies. In these tumors, low AZGP1 expression correlates with worse prognosis. Additionally, high expression of AZGP1 is associated with improved outcomes in patients with prostate, pancreatic, gastric and breast cancer. AZGP1 is expressed in endocrine sensitive MCF7 and T47D cells, but is silenced in endoxifen resistant models at the mRNA and protein level. Further, treatment of resistant cells with conditioned medium containing AZGP1 resulted in significant inhibition of cell proliferation and migration, and antibody-mediated depletion of AZGP1 from conditioned medium completely reversed these effects. While there are no reports regarding the molecular functions of AZGP1 in cancer we provide evidence that AZGP1 directly inhibits oncogenic signaling in endocrine resistant breast cancer through interaction with, and inhibition of, β6 integrin. Through the analysis of endoxifen resistant breast cancer cells, we have identified novel roles for GR, AZGP1 and β6 integrin in the development and progression of endocrine resistant breast cancer. We demonstrate that activation of GR may elicit therapeutic benefit in endocrine resistant breast cancer, specifically in tumors expressing AZGP1 and β6 integrin. Further, AZGP1 and β6 integrin may represent novel prognostic and/or predictive biomarkers in endocrine resistant disease. Citation Format: Calley J. Jones, Santiago Acero Bedoya, Anna V. Mykytyn, Matthew P. Goetz, John R. Hawse. Glucocorticoid receptor signaling elicits anti-cancer effects in endocrine resistant breast cancer via induction of AZGP1 [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-04-16.