Clonal Therapy for Pediatric T-cell Acute Lymphoblastic Leukemia

项目摘要/摘要 儿童T细胞急性淋巴细胞性白血病(PT-ALL)，治疗选择有限，历史上 与B细胞ALL相比，化疗的治疗结果较差。尽管取得了进步 在我们对PT-ALL病因的认识上，这种疾病的总体存活率并不显著 改进了。患有复发T-ALL的儿童存活率很低，仅为25%，而长期存活的儿童则有 与他们接受的根治化疗相关的疾病负担增加。因此，小说有针对性 联合治疗是非常必要的。基于群体的基因组和转录组研究 揭示了PT-ALL的白血病间多样性。然而，人们对白血病内克隆知之甚少。 PT的异质性-所有已知的导致耐药和疾病复发的因素。例如，它 这些稀有克隆的分子和细胞特征如何才能使它们在治疗中存活仍然是个谜 因为其他主要的克隆人被淘汰了。T-ALL出现在动态的发育过程中，并保持 它们细胞起源的特征。然而，目前尚不清楚T细胞的发育如何有助于克隆 PT-ALL的异质性。此外，癌细胞和正常细胞之间的细胞间通讯是否在 肿瘤微环境对疾病复发的影响尚不清楚。使用批量系统药理学和 单细胞系统生物学方法，我们发现了与T细胞相关的白血病异质性 单细胞成熟度和药物敏感性。因此，我们假设通过靶向信号转导进行克隆治疗 T细胞分化产生的克隆亚群中的网络将最大限度地减少复发/难治性疾病和 改善PT-ALL的结果。我们在圣犹大的团队处于独特的地位，可以应对这些挑战，利用 在系统生物学、所有药物基因组学和T细胞开发方面拥有丰富的专业知识。具体地说，在这个 建议，我们将确定T细胞的发展如何有助于PT-ALL的白血病内异质性 (目标1)。我们将通过原始样本的单细胞分析将PT-ALL中的克隆映射到T细胞成熟阶段 和发育正常的T细胞。我们将确定驱动克隆异质性的克隆特定隐藏驱动因素 以及对药物的敏感性。接下来，我们将确定针对多个克隆中的信号驱动程序的药物组合 (目标2)。我们将把大宗系统药理学与单细胞隐藏驱动程序分析相结合，以不偏不倚地 预测协同药物组合，并通过药物筛选进行验证。我们将使用患者派生的 为活体验证保留克隆复杂性的异种移植物。我们还将调查TME重新编程是如何 在PT-ALL中调整克隆选择和治疗(目标3)。我们将重建肿瘤和TME 来自scRNA-seq数据的通信网络，并阐明克隆选择的分子机制 PT-ALL治疗。综上所述，该项目将在内部解决尚未回答的基本问题 白血病克隆性，并提供一种新的克隆治疗方法，消除多个克隆，包括 这有助于疾病复发，从而改善T-ALL儿童的预后。

PROJECT SUMMARY / ABSTRACT Pediatric T-cell acute lymphoblastic leukemia (pT-ALL), with limited treatment options, has been historically associated with inferior treatment outcomes with chemotherapy, compared to B-cell ALL. Despite the advances made in our understanding of the etiology of pT-ALL, the overall survival of this disease has not significantly improved. Children with recurrent T-ALL have a dismal survival rate of < 25%, and long-term survivors have an increased burden of disease associated with the curative chemotherapies they received. Therefore, novel targeted therapeutics in combinations are much needed. Population-based genomic and transcriptomic studies have revealed the inter-leukemia diversity of pT-ALL. However, very little is known about intra-leukemia clonal heterogeneity in pT-ALL that were known to contribute to drug resistance and disease recurrence. For example, it remains mysterious what molecular and cellular features of the rare clones have to allow them to survive treatment as other major clones are eliminated. T-ALL arises during the dynamic developmental processes and retains hallmarks of their cellular origins. However, it remains unclear how T-cell development contributes to clonal heterogeneity of pT-ALL. Moreover, whether cell–cell communications between cancer cells and normal cells in the tumor microenvironment contribute to disease recurrence is unclear. Using bulk systems pharmacology and single-cell systems biology approaches, we discovered the leukemia heterogeneity associated with T-cell maturation and drug sensitivity in single cells. Therefore, we hypothesize that clonal therapy by targeting signaling networks in clonal subpopulations arising from T-cell differentiation will minimize relapsed/refractory diseases and improve outcomes for pT-ALL. Our team at St. Jude is uniquely positioned to tackle these challenges, capitalizing on vast expertise in systems biology, ALL pharmacogenomics, and T-cell development. Specifically, in this proposal, we will determine how T-cell development contributes to the intra-leukemia heterogeneity in pT-ALL (Aim 1). We will map clones in pT-ALL to T-cell maturation stages by single-cell analyses of primary samples and normal developmental T cells. We will identify clone-specific hidden drivers that drive clonal heterogeneity and drug sensitivity. Next, we will identify drug combinations that target signaling drivers in multiple clones (Aim 2). We will integrate bulk systems pharmacology with single-cell hidden-driver analyses to unbiasedly predict synergistic drug combinations and validate them by drug screening. We will use patient-derived xenografts that retain clonal complexity for in vivo validation. We will also investigate how TME reprograming modulates clone selection with treatment in pT-ALL (Aim 3). We will reconstruct the tumor and TME communication network from scRNA-seq data and elucidate the molecular mechanisms of clonal selection with treatment in pT-ALL. Taken together, this project will address fundamental unanswered questions in intra- leukemia clonality and provide a new clonal therapy approach that eliminates multiple clones, including those that contribute to disease recurrence, thereby, improves the outcomes for children with T-ALL.