Elucidating Human Leukemia and T Cell Interactions within the Tumor Microenvironment

项目摘要/摘要 白血病复发仍然是异基因干细胞移植(allo-SCT)成功的主要障碍。 在这里，供者淋巴细胞输注(DLI)寻求修复潜在的移植物抗白血病(GVL)效应，即 提高allo-SCT疗效。然而，推动临床GVL预后的机制仍然知之甚少。 为了应对这一挑战，Bchireddy博士对白血病和 肿瘤微环境(TME)中免疫细胞在DLI应答和治疗期间的多个时间点 抵抗。他之前在DLI期间展示了T细胞耗竭的逆转，这是T细胞功能障碍的一种独特形式 回应。使用高通量单细胞RNA测序(scRNA-seq)，他现在已经确定了两个主要的 耗竭T细胞亚型：终末耗竭(TE)细胞，富含DLI反应前TME，以及 祖细胞耗竭(PE)细胞，在DLI后反应者中持续扩张。虽然这些子集是 在激发PD-1途径抑制物的T细胞衰竭小鼠模型中定义，它们与 人类白血病在免疫治疗反应中的作用及其与致癌途径的关系 先前已阐明。因此，他将测试特定基因调控网络(GRN)(1)的假设。 定义TE和PE子集内和子集之间的异质性，此外，(2)受以下因素影响 白血病衍生突变和基因表达状态。在目标1中，他将确定规则和功能 通过首先将scRNA-seq数据与染色质可及性分布相结合来识别TE和PE子集 GRN，然后从功能上评估每个子集的相对抗白血病效果(和 每个GRN)在体内。在目标2中，他将确定与DLI相关的白血病衍生分子图谱 T/PE T细胞亚群的转归和形态。白血病基因组和scRNA-seq数据将联合分析以 对DLI结局和T/PE T细胞亚群的候选白血病驱动因素进行电子识别， 反过来，在体内进行功能评估。这些结果将确定支配GRN的GRN和致癌途径 这种形状，TE和PE T细胞，揭示了调节癌症免疫的新靶点，并揭示了 移植后TME中支持白血病-免疫相互作用的分子回路。巴奇雷迪医生有 概述了一项五年职业发展计划，以实现他成为一名独立调查员的目标 专注于血液系统恶性肿瘤的免疫治疗。他组建了一个咨询委员会， 国际公认的专家，提供科学/职业指导，并招募符合以下条件的合作者 计算生物学、系统免疫学和功能基因组学专家提供实验 该领域的建议和具体培训。达纳-法伯癌症研究所和麻省理工学院博德研究所 哈佛大学是完成他的科学和职业目标的理想环境，因为他们表现出色 培训独立内科科学家的研究社区和大量记录。

Project Summary/Abstract Leukemic relapse remains the major obstacle to successful allogeneic stem cell transplantation (allo-SCT). Here, donor lymphocyte infusion (DLI) seeks to repair the underlying graft-versus-leukemia (GvL) effect that drives allo-SCT efficacy. However the mechanisms driving clinical GvL outcomes remain poorly understood. To address this challenge, Dr. Bachireddy has performed deep molecular phenotyping of both leukemia and immune cells within the tumor microenvironment (TME) across multiple timepoints during DLI response and resistance. He previously showed reversal of T cell exhaustion, a unique form of T cell dysfunction, during DLI response. Using high-throughput single cell RNA sequencing (scRNA-seq), he has now identified 2 main subtypes of exhausted T cells: terminally exhausted (TE) cells, enriched in pre-DLI responding TMEs, and progenitor exhausted (PE) cells, expanding consistently in responders post-DLI. While these subsets are defined in murine models of T cell exhaustion that motivated inhibitors of the PD-1 pathway, their relevance to human leukemia, roles in immunotherapeutic response, and relationship to oncogenic pathways have not been previously elucidated. Thus, he will test the hypothesis that specific gene regulatory networks (GRNs) (1) define the heterogeneity within and between TE and PE subsets and, moreover, (2) are influenced by leukemic-derived mutations and gene expression states. In Aim 1, he will determine the regulation and function of TE and PE subsets by, first, integrating scRNA-seq data with chromatin accessibility profiles to identify GRNs for each subset and then functionally evaluating the relative anti-leukemic efficacy of each subset (and each GRN) in vivo. In Aim 2, he will identify leukemic-derived molecular profiles that associate with DLI outcome and shape T/PE T cell subsets. Leukemic genomic and scRNA-seq data will be jointly analyzed to perform in silico identification of candidate leukemic drivers of DLI outcome and T/PE T cell subsets, which will, in turn, be functionally evaluated in vivo. These results will identify GRNs that govern, and oncogenic pathways that shape, TE and PE T cells, revealing novel targets for modulating cancer immunity and uncovering the molecular circuitry underpinning leukemic-immune interactions in the post-transplant TME. Dr. Bachireddy has outlined a five-year career development plan to meet his goal of becoming an independent investigator focused on immunotherapy in hematologic malignancies. He has assembled an Advisory Committee of internationally recognized experts to provide scientific/career mentorship and enlisted collaborators who are experts in computational biology, systems immunology, and functional genomics to provide experimental advice and specific training in the field. The Dana-Farber Cancer Institute and Broad Institute of MIT and Harvard are the ideal environments for completion of his scientific and career goals, given their outstanding research communities and substantial records for training independent physician-scientists.