Identification of Novel Gene Regulatory Interactions Driving the Immune Evasion Program Through Transcriptional Activation of CD47 in Cancer

鉴定通过癌症中 CD47 转录激活驱动免疫逃避程序的新基因调控相互作用

• 批准号: 10000966
• 负责人: Paola A Betancur
• 金额: $ 19.91万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-01 至 2022-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10000966
• 关键词: Address; Affect; Anti-CD47; Automobile Driving; Binding; Binding Sites; Breast Cancer Cell; CD47 gene; CD47-SIRPα blockade; Cancerous; Cell Line; Cell Surface Proteins; Cells; ChIP-seq; Clinical; Data; Development; Developmental Process; Distal; Eating; Enhancers; Epigenetic Process; Event; Excision; Gene Expression Regulation; Genes; Genetic; Genomic Segment; Genomics; Goals; Hematopoiesis; Hematopoietic; High-Throughput Nucleotide Sequencing; Hormones; Immune Evasion; Immune system; Immunologic Surveillance; Inflammation; Inflammatory; Leukemic Cell; Ligands; Lymphoblastic Leukemia; Malignant Neoplasms; Modification; Molecular; Monoclonal Antibodies; Mutation; NF-kappa B; Nucleic Acid Regulatory Sequences; Outcome; Pathologic; Pathway interactions; Patients; Phagocytes; Phagocytosis; Population; Principal Investigator; Public Health; Publishing; Regulation; Regulator Genes; Research; Research Project Grants; Research Proposals; Sampling; Signal Pathway; Signal Transduction; Solid Neoplasm; T-Lymphocyte; TNF gene; Testing; Transcript; Transcriptional Activation; Up-Regulation; acute T-cell lymphoblastic leukemia cell; base; cancer cell; cancer therapy; cancer type; cell injury; cell type; epigenomics; experimental study; extracellular; immune clearance; improved; leukemia; macrophage; malignant breast neoplasm; neoplastic cell; novel; novel therapeutics; overexpression; prevent; programs; protein expression; receptor; recruit; response; targeted treatment; therapeutic target; therapy design; transcription factor; tumor immunology; tumorigenic; virtual

ABSTRACT: CD47 is a cell surface protein, found virtually in every cell, which interacts with SIRPα on macrophages to inhibit phagocytosis. In cancer cells, CD47 transcript and protein expression is aberrantly upregulated, protecting the cancer cells from being recognized and cleared by macrophages. Blockade of CD47-SIRPα signaling by anti-CD47 or anti-SIRPα monoclonal antibodies (mAbs) enhances macrophage phagocytosis of a variety of cancer types. Due to the clinical implications this information has, it is critical to understand the precise mechanisms and upstream regulators responsible for increasing CD47 expression in cancer cells, to develop novel therapies to target the upstream group of transcription factors, genetic or epigenetic modifications that misregulate CD47 in leukemia and solid tumors, and in this manner, prevent malignant cells from evading immunosurveillance. By performing a genomic cis- regulatory analysis, I found that two distinct super-enhancers (SEs) are associated with CD47 in certain cancer cell types and not in their healthy counterparts. I also found that a set of active constituent enhancers, located within each of the two CD47 SEs, regulate CD47 expression in different cancer cell types: while 1) an upstream CD47 constituent enhancer is active in T-cell lymphoblastic leukemia (T-ALL) cells, 2) a downstream CD47 constituent enhancer is active in breast cancer (hormone-positive subtype), and it responds to induction of the TNF–NFKB1 signaling pathway. In contrast, my preliminary data suggests that CD47 upregulation in leukemia cell lines, is independent of this inflammatory pathway, and is dependent on pathways that are involved in hematopoietic developmental processes. Based on these findings, I hypothesize that: in different cancer types, uniquely formed distal enhancers or super-enhancers (SEs), recruit inputs (transcription factors) from the inflammatory and/or developmental program to dysregulate target genes of immune evasion (e.g, CD47). This proposal aims to investigate other mechanisms (including epigenetic changes and genomic modifications) that alone or in combination with the TNF inflammatory pathway are used particularly by breast cancer cells and leukemia subtypes to initiate an immune evasion response by misregulating CD47. To understand how these mechanisms of regulation are altered in cancer versus healthy cells, the proposed experiments will be carried out mainly in patient-derived solid tumors (specifically breast cancer) and leukemia samples; and the results will be compared with results from healthy donor samples. For this proposal, the following specific aims will be performed: 1) Determine whether unique CD47 super-enhancers (SEs) are formed to respond to inflammatory signaling to misactivate the immune evasion program in hormone-positive breast cancers. 2) Investigate whether CD47 enhancers or SEs are erroneously recruiting inputs (transcription factors) that typically drive hematopoiesis development, to trigger misactivation of CD47 in leukemia cells.

摘要：CD47 是一种细胞表面蛋白，几乎存在于每个细胞中，它与 SIRPα 相互作用 抑制巨噬细胞的吞噬作用。在癌细胞中，CD47 转录本和蛋白质表达异常 上调，保护癌细胞不被巨噬细胞识别和清除。封锁 抗 CD47 或抗 SIRPα 单克隆抗体 (mAb) 的 CD47-SIRPα 信号传导可增强巨噬细胞 多种癌症类型的吞噬作用。由于该信息具有临床意义，因此至关重要 了解导致 CD47 增加的精确机制和上游调控因子 在癌细胞中表达，开发针对上游转录组的新疗法 白血病和实体瘤中 CD47 失调的因素、遗传或表观遗传修饰，以及 通过这种方式，可以防止恶性细胞逃避免疫监视。通过执行基因组顺式 通过监管分析，我发现两种不同的超级增强子 (SE) 与某些癌症中的 CD47 相关 细胞类型而不是健康细胞。我还发现了一组活性成分增强剂，位于 在两个 CD47 SE 中的每一个中，调节不同癌细胞类型中的 CD47 表达：而 1) 上游 CD47 成分增强子在 T 细胞淋巴母细胞白血病 (T-ALL) 细胞中具有活性，2) 下游 CD47 成分增强子在乳腺癌（激素阳性亚型）中具有活性，并且对诱导有反应 TNF-NFKB1 信号通路。相反，我的初步数据表明 CD47 上调 白血病细胞系，独立于该炎症途径，并且依赖于所涉及的途径 在造血发育过程中。基于这些发现，我假设：在不同的癌症中 类型，独特形成的远端增强子或超级增强子（SE），从 炎症和/或发育程序失调免疫逃避的靶基因（例如 CD47）。这 该提案旨在研究其他机制（包括表观遗传变化和基因组修饰） 单独使用或与 TNF 炎症途径组合使用，尤其是乳腺癌细胞使用 白血病亚型通过错误调节 CD47 启动免疫逃避反应。要了解这些如何 癌症与健康细胞的调节机制发生了变化，拟议的实验将进行 主要存在于患者来源的实体瘤（特别是乳腺癌）和白血病样本中；和结果 将与健康捐赠者样本的结果进行比较。对于该提案，将实现以下具体目标 执行： 1) 确定是否形成独特的 CD47 超级增强子 (SE) 来响应 炎症信号传导失活激素阳性乳腺癌的免疫逃避程序。 2) 调查CD47增强子或SE是否错误地招募输入（转录因子） 通常会驱动造血发育，从而引发白血病细胞中 CD47 的错误激活。