Elucidating the role of the SWI/SNF complex in mediating hormone therapy resistance in breast cancer

阐明 SWI/SNF 复合物在介导乳腺癌激素治疗耐药中的作用

• 批准号: 10410445
• 负责人: Eneda Toska
• 金额: $ 18.84万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-06-01 至 2023-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10410445
• 关键词: 3-Dimensional; ARID1A gene; ATAC-seq; Affect; Alleles; Aromatase Inhibitors; Basal Cell; Binding; Binding Sites; Biological Assay; Breast; Breast Cancer Cell; Breast Cancer cell line; Candidate Disease Gene; Cell Line; Cell Lineage; Cells; Chromatin; Chromatin Remodeling Factor; Clinical; Clustered Regularly Interspaced Short Palindromic Repeats; Complex; Data; Disease; Endocrine; Epigenetic Process; Estrogen Receptors; Estrogen receptor positive; Estrogens; Fulvestrant; Gene Expression; Genes; Genetic Transcription; Growth; Hormonal; Human; In Vitro; Individual; Knock-out; Knockout Mice; Laboratory Study; Light; Loss of Heterozygosity; MCF7 cell; Mammary Neoplasms; Mammary gland; Mediating; Mediator of activation protein; Metastatic breast cancer; Modeling; Mus; Mutate; Mutation; Neoplasm Metastasis; Normal Cell; Organoids; Patients; Phenotype; Play; Pre-Clinical Model; Publishing; Receptor Cell; Refractory; Resistance; Role; SMARCB1 gene; SMARCE1 gene; SWI/SNF Family Complex; Sampling; Series; Testing; Transcriptional Regulation; Transgenic Mice; behavior change; chromatin remodeling; cohort; epigenome; experimental study; genome analysis; genome-wide; hormone therapy; in vivo; inhibitor therapy; loss of function; malignant breast neoplasm; mammary; mammary epithelium; mammary gland development; mouse model; mutant; neoplastic cell; patient derived xenograft model; patient population; programs; recruit; resistance mechanism; response; therapy resistant; transcription factor; transcriptome sequencing; transdifferentiation; tumor

PROJECT SUMMARY Approximately 70% of breast cancers express estrogen receptor (ER) and are treated typically with endocrine therapy. Despite the clinical benefit obtained from several types of endocrine therapies, emergence of resistance to these agents eventually develops in all patients with metastatic disease. We have sequenced 2,752 ER-positive breast cancer samples for which detailed clinical information on response to endocrine therapy is available. These analyses have also shown a correlation between emergence of endocrine therapy resistance and the presence of inactivating mutations in the chromatin remodeler ARID1A. In parallel, we have performed an epigenome-wide CRISPR knockout screen on MCF7 ER-positive breast cancer cells and have identified ARID1A to be the top candidate gene whose loss results in resistance to the Selective ER Degrader (SERD) fulvestrant followed by the loss of additional SWI/SNF subunits, namely SMARCB1, SMARCE1. When we interrogated our internal patient cohort, we found that ARID1A loss is enriched in the metastatic setting and correlates with resistance to SERDs (e.g. fulvestrant). These findings indicate an important role for ARID1A in mediating resistance to endocrine therapy. Mechanistically, our published and preliminary data demonstrate that loss of ARID1A leads to widespread changes in the chromatin landscape of breast cancer cells, resulting in loss of motifs for TFs involved in ER-dependent transcription and luminal (ER+) cell identity. This was accompanied by increase expression of basal (ER-) markers in cell line models and patient samples harboring ARID1A inactivating mutations. In this proposal, we will seek to define the mechanistic basis by which ARID1A acts as a mediator of resistance to endocrine therapy in breast cancer cell lines, patient-derived xenografts and samples from patients with ARID1A mutant breast cancers, and to determine how ARID1A loss results in trans-differentiation from a luminal to a basal program in breast cancers and normal cells. We will perform RNA-seq utilizing samples from patients with hormone therapy-refractory breast cancers that are either wild-type or null for ARID1A. We will then investigate the impact that the knockout of ARID1A has on chromatin recruitment of the SWI/SNF complex and on the binding of the SWI/SNF complex at dominant transcription factors that regulate gene expression programs critical for the cellular differentiation state in breast cancer. Finally, we will study the effects of Arid1a loss in mammary-gland morphogenesis utilizing a mammary epithelium-specific conditional Arid1a null mouse model we have developed and normal mammary and breast cancer 3D organoids. Our results will shed light on the role of ARID1A in determining cell fate/lineage and how ARID1A and the SWI/SNF complex plays a causative role in limiting the sensitivity to endocrine therapy.

项目摘要 大约70%的乳腺癌表达雌激素受体（ER），通常用内分泌治疗。 疗法尽管从几种类型的内分泌疗法中获得了临床益处，但 对这些药物的耐药性最终在所有转移性疾病患者中产生。我们已经测序了 2，752例ER阳性乳腺癌样本，其详细临床信息涉及内分泌治疗的反应 治疗是可行的。这些分析也显示了内分泌治疗的出现与 耐药性和染色质重塑ARID 1A中存在失活突变。同时，我们 对MCF 7 ER阳性乳腺癌细胞进行了表观基因组范围的CRISPR敲除筛选， 已经鉴定出ARID 1A是最重要的候选基因，其缺失导致对选择性ER的抗性 降解剂（SERD）氟维司群，随后丢失额外的SWI/SNF亚基，即SMARCB 1， SMARCE1.当我们询问我们的内部患者队列时，我们发现ARID 1A缺失在 转移性环境，并与SERD（如氟维司群）耐药性相关。这些发现表明， ARID 1A在介导对内分泌疗法的抗性中的重要作用。从机制上讲，我们的出版和 初步数据表明，ARID 1A的丢失导致了细胞染色质景观的广泛变化， 乳腺癌细胞，导致参与ER依赖性转录和管腔（ER+）的TF基序丢失 细胞识别这伴随着细胞系模型中基础（ER-）标志物表达的增加， 携带ARID 1A失活突变的患者样品。在本建议中，我们将力求界定 ARID 1A作为乳腺癌细胞内分泌治疗抵抗介质的机制基础 细胞系、患者来源的异种移植物和来自ARID 1A突变乳腺癌患者的样品，以及 确定ARID 1A缺失如何导致乳腺癌从管腔到基底程序的转分化 正常细胞。我们将利用来自激素治疗难治性患者的样本进行RNA-seq。 野生型或ARID 1A无效的乳腺癌。然后我们将调查 ARID 1A的敲除对SWI/SNF复合物的染色质募集和对 SWI/SNF复合物在调节基因表达程序的显性转录因子中的作用， 乳腺癌的细胞分化状态。最后，我们将研究乳腺中Arid 1a缺失的影响。 形态发生利用乳腺上皮特异性条件Arid 1a无效小鼠模型，我们有 发达和正常的乳腺癌和乳腺癌3D类器官。我们的研究结果将阐明 ARID 1A在决定细胞命运/谱系中的作用以及ARID 1A和SWI/SNF复合物如何在 限制了对内分泌治疗的敏感性。