Cassette exons in neoplastic pro-B-cells: implications for immunotherapy

肿瘤性前 B 细胞中的盒式外显子：对免疫治疗的影响

• 批准号: 10578300
• 负责人: Yoseph Barash
• 金额: $ 42.04万
• 依托单位: CHILDREN'S HOSP OF PHILADELPHIA
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-14 至 2024-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10578300
• 关键词: Ablation; Acute Lymphocytic Leukemia; Adaptive Immune System; Aftercare; Algorithms; Alternative Splicing; Antibodies; Antibody-drug conjugates; Antigen Targeting; Area; B-Cell Acute Lymphoblastic Leukemia; B-Lymphocytes; B-cell precursor acute lymphoblastic leukemia cell; Biochemical; Biological Assay; Bone Marrow; CD19 gene; CD22 gene; CD3 Antigens; CD34 gene; Cell Line; Cell Lineage; Cells; Childhood; Childhood Leukemia; Childhood Precursor B Lymphoblastic Leukemia; Childhood Solid Neoplasm; Cis-Acting Sequence; Code; Data; Data Set; Development; Epitopes; Exons; Extracellular Domain; FDA approved; Future; Genes; Genomics; Goals; Hematologic Neoplasms; Human; Immune Evasion; Immune system; Immunotherapeutic agent; Immunotherapy; Integral Membrane Protein; Introns; Investigation; Malignant Childhood Neoplasm; Malignant Neoplasms; Maps; Membrane Proteins; Missense Mutation; Modality; Mutation; Output; Patients; Peptides; Play; Protein Isoforms; RNA; RNA Splicing; Refractory; Regulation; Relapse; Reporter Genes; Resistance; Response Elements; Reverse engineering; Role; Saint Jude Children' s Research Hospital; Sampling; Source; Specificity; Surface; Surface Antigens; T-Lymphocyte; Testing; Training; Trans-Activators; Transcript; Validation; Variant; Work; Yin-Yang; base; bi-specific T cell engager; biobank; cancer cell; chimeric antigen receptor; chimeric antigen receptor T cells; genetic variant; knock-down; leukemia; neoantigens; neoplastic; novel; overexpression; patient derived xenograft model; predicting response; programs; public health relevance; relapse patients; side effect; success; transcriptome sequencing; tumor; Ablation; Acute Lymphocytic Leukemia; Adaptive Immune System; Aftercare; Algorithms; Alternative Splicing; Antibodies; Antibody-drug conjugates; Antigen Targeting; Area; B-Cell Acute Lymphoblastic Leukemia; B-Lymphocytes; B-cell precursor acute lymphoblastic leukemia cell; Biochemical; Biological Assay; Bone Marrow; CD19 gene; CD22 gene; CD3 Antigens; CD34 gene; Cell Line; Cell Lineage; Cells; Childhood; Childhood Leukemia; Childhood Precursor B Lymphoblastic Leukemia; Childhood Solid Neoplasm; Cis-Acting Sequence; Code; Data; Data Set; Development; Epitopes; Exons; Extracellular Domain; FDA approved; Future; Genes; Genomics; Goals; Hematologic Neoplasms; Human; Immune Evasion; Immune system; Immunotherapeutic agent; Immunotherapy; Integral Membrane Protein; Introns; Investigation; Malignant Childhood Neoplasm; Malignant Neoplasms; Maps; Membrane Proteins; Missense Mutation; Modality; Mutation; Output; Patients; Peptides; Play; Protein Isoforms; RNA; RNA Splicing; Refractory; Regulation; Relapse; Reporter Genes; Resistance; Response Elements; Reverse engineering; Role; Saint Jude Children' s Research Hospital; Sampling; Source; Specificity; Surface; Surface Antigens; T-Lymphocyte; Testing; Training; Trans-Activators; Transcript; Validation; Variant; Work; Yin-Yang; base; bi-specific T cell engager; biobank; cancer cell; chimeric antigen receptor; chimeric antigen receptor T cells; genetic variant; knock-down; leukemia; neoantigens; neoplastic; novel; overexpression; patient derived xenograft model; predicting response; programs; public health relevance; relapse patients; side effect; success; transcriptome sequencing; tumor

PROJECT SUMMARY/ABSTRACT Successful immunotherapies for childhood cancers typically target lineage-, rather than cancer-specific markers, B-cell specific CD19 being the prime example. These successes culminated in the recent FDA approval of bi-specific T-cell engagers and chimeric antigen receptor (CAR)-armed T-cells for B-cell acute lymphoblastic leukemia (B-ALL). However, relapses frequently occur in patients treated with CD19- directed immunotherapies, often due to epitope loss. While strategies based on dual antigen targeting are beginning to emerge, they are still based on targeting canonical B-cell markers, with the unavoidable side effect of total ablation of normal B-cells. The apparent paucity of tumor-specific targets in pediatric cancers (including leukemias) is likely to limit future immunotherapies. We hypothesize that alternative splicing could be both a mechanism of epitope loss and a rich source of a neo-antigens in B-ALL. Indeed, using computational and biochemical approaches, we have identified hundreds of local splicing variations (LSVs), mapping to transmembrane proteins (e.g., CD19 and CD22) with prominent extracellular domains (ectodomains). In fact, in our prior work we described a mechanism of acquired resistance to CART-19 based on selective loss of the CD19 ectodomain, primarily through exon 2 skipping. The two large Aims of this U01 are as follows. Aim 1: To identify programs and determinants of altered splicing of B-ALL cell surface antigens. Our overarching goal is to construct a dedicated “splicing code” for leukemic B-cells. Such a code will predict cis-acting genetic variants as well as trans-acting factors involved in alternative splicing and allow us to identify all alternatively spliced ectodomains. Then in Aim 2, we will investigate the effects of alternative splicing on B-ALL immunotherapy. Using CD22 as just one example, we will determine how truncated protein isoforms confer resistance to CD22-targeting immunotherapeutics, including antibody- drug conjugates such as inotuzumab ozogamicin, which was recently approved by FDA to treat relapsed or refractory B-ALL. We will also raise antibodies against peptides spanning novel exon junctions, generate antibody-drug conjugates, and test their efficacy against B-ALL cell lines and patient-derived xenografts. In summary, this leukemia-based U01 will create new computational and conceptual frameworks, which would be highly synergistic with Pediatric Immunotherapy Discovery & Development Network (PI-DDN) overall goals, including identification of antigenic epitopes that are uniquely expressed on childhood cancers and of cancer cell-intrinsic mechanisms of immune evasion.

项目摘要/摘要 童年癌的成功免疫疗法通常靶向谱系 - 而不是癌症特异性的 标记，B细胞特异性CD19是主要示例。这些成功最终达到了最近的FDA 批准B-Cell急性的双特异性T细胞诱因和嵌合抗原受体（CAR）T-Cells 淋巴细胞白血病（b-all）。但是，用CD19-治疗的患者经常发生复发 定向免疫疗法通常是由于表位损失。而基于双重抗原靶向的策略是 它们开始出现，它们仍然基于针对规范的B细胞标记，而不可避免的一侧 正常B细胞​​总消融的影响。小儿癌中肿瘤特异性靶标的明显缺乏 （包括白血病）可能会限制未来的免疫疗法。我们假设该替代剪接 既可能是表位损失的机制，也可能是B-all中新抗原的丰富来源。确实，使用 计算和生化方法，我们已经确定了数百种本地剪接变化 （LSV），映射到具有突出细胞外域的跨膜蛋白（例如CD19和CD22） （胞外域）。实际上，在我们先前的工作中，我们描述了一种对CART-19的抗药性机制 基于CD19胞外域的选择性损失，主要是通过外显子2跳过。两个大目标 该U01如下。目标1：确定程序并确定B-ALL单元的剪接更改 表面抗原。我们的总体目标是为白血病B细胞构建专门的“剪接代码”。这样的 代码将预测顺式作用遗传变异以及涉及替代剪接的跨性因素 并允许我们识别所有剪接的词汇域。然后在AIM 2中，我们将研究效果 替代剪接B-所有免疫疗法。以CD22为例，我们将确定如何 截短的蛋白质同工型会议对CD22靶向免疫治疗药的耐药性，包括抗体 - 诸如Inotuzumab ozogamicin之类的药物结合物，该毒素最近获得FDA批准以治疗中继或 难治性b-all。我们还将提出针对跨越新外显子连接的宠物的抗体，产生 抗体 - 药物缀合物，并测试其针对B-所有细胞系和患者衍生的Xenographogrictics的效率。在 总而言之，这个基于白血病的U01将创建新的计算和概念框架， 与小儿免疫疗法发现与开发网络（PI-DDN）将是高度协同的 总体目标，包括鉴定在儿童时期唯一表达的抗原表位 癌症和免疫进化的癌细胞中性机制。