Leveraging the TCR Repertoire to identify target neoantigens in FLT3-ITD positive Acute Myeloid Leukemia

利用 TCR 库识别 FLT3-ITD 阳性急性髓系白血病的目标新抗原

• 批准号: 10618925
• 负责人: Houda Alachkar
• 金额: $ 35.18万
• 依托单位: UNIVERSITY OF SOUTHERN CALIFORNIA
• 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 2026-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10618925
• 关键词: Acute Myelocytic Leukemia; Acute leukemia; Advanced Development; Affect; Algorithms; Allogenic; Antigen Presentation; Antigens; Binding; Cell Therapy; Cell physiology; Cell surface; Cells; Characteristics; Clinical; Clonal Expansion; Clone Cells; Data; Development; Diagnosis; Diagnostic; Disease remission; Experimental Models; FDA approved; FLT3 gene; FLT3 inhibitor; Genomics; Hematopoietic Stem Cell Transplantation; Immune; Immunogenomics; Immunophenotyping; Immunotherapy; In Vitro; Investigation; Leukemic Cell; Life; Longitudinal cohort study; Major Histocompatibility Complex; Mediating; Mutation; Normal Cell; Outcome; Patients; Peptides; Population; Prognosis; Proportional Hazards Models; Prospective, cohort study; RNA; Receptor Protein-Tyrosine Kinases; Regimen; Regulatory T-Lymphocyte; Relapse; Research; Risk; Sampling; Somatic Mutation; Structure; Surface; T cell receptor repertoire sequencing; T cell response; T-Cell Receptor; T-Lymphocyte; T-cell receptor repertoire; Technology; Testing; Therapeutic; Time; Transplant Recipients; Validation; antigen-specific T cells; chemotherapy; cohort; curative treatments; cytotoxic; disorder risk; engineered T cells; exome sequencing; graft vs host disease; graft vs leukemia effect; high risk; individual variation; kinase inhibitor; knowledge of results; leukemia; machine learning method; mouse model; neoantigens; next generation sequencing; novel; personalized medicine; post-transplant; pre-clinical; predict clinical outcome; prediction algorithm; predictive modeling; predictive tools; prospective; prototype; receptor; receptor binding; relapse risk; success; targeted treatment; therapeutic target; transcriptomics; transplantation therapy

Abstract Allogeneic hematopoietic stem cell transplantation (HSCT) is the only curative treatment for patients with high- risk acute myeloid leukemia (AML). However, HSCT is affected by graft-versus-host disease (GvHD) and graft- versus-leukemia (GvL) effects, both are mediated by donor T lymphocytes and significantly impact treatment success and thus overall outcome. AML patients commonly harbor FLT3/internal tandem duplication (FLT3-ITD), a mutation in the receptor tyrosine kinase FLT3 that is associated with poor prognosis. FLT3 targeted therapies have proven clinical benefit particularly when used in combinational approaches. Midostaurin (a kinase inhibitor) was recently approved for pre-transplant patients with FLT3-ITD in combination with standard therapy. In addition to their direct leukemia suppressive effects, FLT3 inhibitors activate leukemia antigen-specific T-cell responses. T-cell receptors (TCRs) are proteins expressed on the surface of T cells that recognize antigens presented by MHC molecules. We recently characterized the TCR repertoire in patients who underwent matched donor or haplo-cord HSCT. We demonstrated that GvHD and relapse (exclusive of each other) are associated with lower TCR repertoire diversity and expansion of certain T-cell clones. Our data suggest that individual variations in the immune repertoire significantly impact the clinical outcome in AML patients and underscore the need for comprehensive quantitative, functional, and mechanistic analyses of the TCR repertoire in a large cohort of AML patients. Here, we hypothesize: 1) TCR repertoire (diversity, clonal expansion, and V-segment utilization) affects clinical outcome (GvHD or relapse) and can therefore be used to identify GvL- and GvHD- associated clones; 2) Somatic mutations in leukemic cells (e.g., FLT3-ITD) affect the TCR repertoire and subsequent expansion of specific T-cell clones; and 3) FLT3 inhibitors (e.g., midostaurin) modulate the TCR repertoire and function and enhance GvL effects in patients undergoing HSCT. We will conduct a prospective longitudinal cohort study characterizing the TCR repertoire and mutational landscape of leukemia cells in ~250 patients (~ 60–80 with FLT3-ITD). GvHD or relapse will be predicted using a proportional hazards model for competing risks based on TCR repertoire characteristics. TCR sequences and somatic mutations will be analyzed using a structure based prediction algorithms we developed to predict candidate leukemia neoantigens and associated TCR clones. Neoantigens will be validated using in vitro and murine models. Finally, functional analyses will examine the effect of midostaurin on TCR repertoire and function. Our findings will establish the TCR repertoire as a useful tool for predicting clinical outcomes of HSCT and identify responsible TCR clones. The identification of TCR clones associated with the GvL effect against FLT3-ITD+ cells will facilitate the development of engineered T cells expressing GvL-associated TCR clones. Modifying the TCR repertoire composition via therapies targeting specific somatic mutations will facilitate development of optimized combinational therapeutic approaches, such as the addition of targeted therapy to post-transplant regimens.

摘要 异基因造血干细胞移植（HSCT）是治疗高血压患者的唯一有效方法。 急性髓细胞白血病（AML）然而，HSCT受移植物抗宿主病（GvHD）和移植物抗宿主病（GVHD）的影响。 抗白血病（GvL）效应，两者均由供体T淋巴细胞介导，并显著影响治疗 取得成功，从而取得整体成果。AML患者通常携带FLT 3/内部串联重复（FLT 3-ITD）， 受体酪氨酸激酶FLT 3的一种突变，与不良预后相关。FLT 3靶向治疗 已经证明了临床益处，特别是当用于组合方法时。米多替林（一种激酶抑制剂） 最近被批准用于移植前FLT 3-ITD患者联合标准治疗。此外 FLT 3抑制剂激活白血病抗原特异性T细胞应答，这与其直接的白血病抑制作用有关。 T细胞受体（TCR）是在T细胞表面上表达的蛋白质，其识别由T细胞呈递的抗原。 MHC分子。最近，我们对接受匹配供体或 HSCT。我们证明了GvHD和复发（相互排斥）与较低的 某些T细胞克隆的TCR库多样性和扩增。我们的数据表明， 免疫库显著影响AML患者的临床结果， 在一个大的TCR库进行全面的定量，功能和机制分析， AML患者队列。在此，我们假设：1）TCR库（多样性、克隆扩增和V-区段） 利用）影响临床结果（GvHD或复发），因此可用于鉴定GvL-和GvHD-。 相关克隆; 2）白血病细胞中的体细胞突变（例如，FLT 3-ITD）影响TCR库， 特异性T细胞克隆的随后扩增;和3）FLT 3抑制剂（例如，米多替林）调节TCR 库和功能，并增强GvL的影响，接受HSCT的患者。我们将进行前瞻性的 一项纵向队列研究，描述了~250例白血病细胞的TCR库和突变景观 患者（约60-80例FLT 3-ITD患者）。将使用比例风险模型预测GvHD或复发， 基于TCR库特征的竞争风险。TCR序列和体细胞突变将是 使用我们开发的基于结构的预测算法进行分析，以预测候选白血病新抗原 和相关的TCR克隆。将使用体外和鼠模型验证新抗原。最后，功能 分析将检测米多替林对TCR库和功能的影响。我们的调查结果将确定 TCR库作为预测HSCT临床结局和鉴定负责任TCR克隆的有用工具。 与针对FLT 3-ITD+细胞的GvL效应相关的TCR克隆的鉴定将促进对FLT 3-ITD+细胞的免疫应答。 表达GvL相关TCR克隆的工程化T细胞的开发。修饰TCR库 通过靶向特定体细胞突变的治疗组合物将促进优化的 联合治疗方法，如在移植后方案中加入靶向治疗。

项目成果

pyTCR: A comprehensive and scalable solution for TCR-Seq data analysis to facilitate reproducibility and rigor of immunogenomics research.

• DOI: 10.3389/fimmu.2022.954078
• 发表时间: 2022
• 期刊: FRONTIERS IN IMMUNOLOGY
• 影响因子: 7.3
• 作者: Peng, Kerui;Moore, Jaden;Vahed, Mohammad;Brito, Jaqueline;Kao, Guoyun;Burkhardt, Amanda M.;Alachkar, Houda;Mangul, Serghei
• 通讯作者: Mangul, Serghei

Response to 'comment on rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing' by Davydov A.N.; Bolotin D.A.; Poslavsky S. V. and Chudakov D.M.

对davydov A.N.的T细胞受体库库分析方法的严格基准测试方法的评论的回应； Bolotin D.A。； Poslavsky S. V.和Chudakov D.M.

• DOI: 10.1093/bib/bbad355
• 发表时间: 2023-09-22
• 期刊: Briefings in bioinformatics
• 影响因子: 9.5