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: 10199597
• 负责人: Eneda Toska
• 金额: $ 24.97万
• 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/10199597
• 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; 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.

项目概要 大约 70% 的乳腺癌表达雌激素受体 (ER)，通常采用内分泌治疗 治疗。尽管从几种类型的内分泌治疗中获得了临床益处，但出现了 所有患有转移性疾病的患者最终都会对这些药物产生耐药性。我们已测序 2,752 个 ER 阳性乳腺癌样本，其中包含内分泌反应的详细临床信息 可以进行治疗。这些分析还表明内分泌治疗的出现之间存在相关性 耐药性以及染色质重塑 ARID1A 中存在失活突变。与此同时，我们 对 MCF7 ER 阳性乳腺癌细胞进行了全表观基因组 CRISPR 敲除筛选 已确定 ARID1A 是最重要的候选基因，其丢失会导致对选择性 ER 的抵抗 降解剂 (SERD) 氟维司群，随后失去额外的 SWI/SNF 亚基，即 SMARCB1， SMARCE1。当我们询问内部患者队列时，我们发现 ARID1A 缺失在 转移情况并与 SERD（例如氟维司群）耐药性相关。这些发现表明 ARID1A 在介导内分泌治疗耐药中发挥重要作用。从机制上讲，我们发布的和 初步数据表明，ARID1A 的缺失会导致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 细胞身份。这伴随着细胞系模型中基础（ER-）标记物表达的增加和 含有 ARID1A 失活突变的患者样本。在本提案中，我们将寻求定义 ARID1A作为乳腺癌细胞内分泌治疗抵抗介质的机制基础 ARID1A 突变乳腺癌患者的细胞系、患者来源的异种移植物和样本，以及 确定 ARID1A 缺失如何导致乳腺癌从管腔程序转分化为基础程序 和正常细胞。我们将利用激素治疗难治性患者的样本进行 RNA 测序 ARID1A 为野生型或无效的乳腺癌。然后我们将调查该事件的影响 ARID1A 的敲除会影响 SWI/SNF 复合物的染色质募集以及 SWI/SNF 复合物的结合 SWI/SNF 复合体位于显性转录因子上，调节基因表达程序，对 乳腺癌的细胞分化状态。最后，我们将研究 Arid1a 缺失对乳腺的影响 利用乳腺上皮特异性条件 Arid1a 无效小鼠模型进行形态发生 发育正常的乳腺癌和乳腺癌 3D 类器官。我们的结果将揭示 ARID1A 在决定细胞命运/谱系中的作用以及 ARID1A 和 SWI/SNF 复合物如何在细胞命运/谱系中发挥因果作用 限制对内分泌治疗的敏感性。