Quantifying Multiscale Competitive Landscapes of Clonal Diversity in Glioblastoma

摘要 胶质母细胞瘤(GBM)在肿瘤内表现出明显的分子异质性，有助于治疗 抵抗力和生存能力差。具体地说，每个肿瘤包括多个分子上不同的亚群。 具有不同的治疗敏感性。这种异质性不仅预示着抗药性的先天存在 分子亚群，以及相邻亚群之间的通信，从而进一步 调节肿瘤的致瘤性和抗药性。事实上，带有EGFRvIII突变的少数肿瘤亚群已经 已被证明通过野生型EGFR增强大多数亚群，以增加肿瘤生长，细胞存活率， 以及抗药性。这种类型的协作性对改进GBM治疗具有明显的意义。还没有 与其他类型的肿瘤相比，基底膜中的相互作用仍未得到充分研究。 研究分子不同亚群之间相互作用的一个重要障碍是 组织取样在GBM中的挑战。特别是，对比增强磁共振成像(CE-MRI)是外科手术的常规指导 MRI增强核心的活检和切除，但未能解决不同的亚群 周围无强化的实质(所谓的“肿瘤周围的脑”或BAT)。这些未切除的残留物 BAT中的亚群是肿瘤复发的主要贡献者，它们可以表现出不同的 与加强活检相比，治疗靶点(和相互作用)。为了解决组织的局限性 取样，成像技术可以帮助定量描述肿瘤的整体特征，包括未切除的肿瘤 蝙蝠区域。我们小组使用了多参数磁共振成像和图像引导活检来开发和验证 肿瘤内基因组异质性的机器学习(ML)模型，特别关注BAT区。 在目标1中，我们是否将收集和分子描述一大套图像记录的立体定向活检组织 以量化分子不同亚群的多样性以及他们的 整个蝙蝠区都有表型利基。我们将在活检水平上评估局部异质性，并 在序列MRI上共同定位区域模式和复发率。在目标2中，我们将使用这些活组织检查和 空间匹配的MRI指标，以完善我们现有的ML预测模型。我们将使用这些ML模型来联合 定位分子不同亚群(及其表型生态位)的空间模式，以量化其 区域复发的风险。在目标3中，我们将从功能上验证在 使用患者来源的异种移植(PDX)模型的目标1和2。我们还将在人类身上验证这些相互作用 GBM使用来自同一患者的原发和复发肿瘤的空间匹配活检组织的子集。 这项建议利用了我们在图像引导组织分析和基于MRI的计算方面的独特专业知识 研究分子不同亚群多样性和竞争格局演变的模型 在人类GBM中。这项工作将有助于在未来的有针对性的临床药物试验中对患者进行风险分层，还应该 促进新的战略(例如，适应性治疗)，以利用亚群的相互依赖来获得治疗益处。

ABSTRACT Glioblastoma (GBM) exhibits profound intratumoral molecular heterogeneity that contributes to treatment resistance and poor survival. Specifically, each tumor comprises multiple molecularly-distinct subpopulations with different treatment sensitivities. This heterogeneity not only portends the pre-existence of resistant molecular subpopulations, but also the communications between neighboring subpopulations that further modulate tumorigenicity and resistance. In fact, a minority tumor subpopulation with EGFRvIII mutation has been shown to potentiate a majority subpopulation with wild-type EGFR to increase tumor growth, cell survival, and drug resistance. This type of cooperativity presents clear implications for improving GBM treatment. Yet compared to other tumor types, the interactions in GBM remain critically understudied. A significant barrier to studying the interactions between molecularly-distinct subpopulations is the challenge of tissue sampling in GBM. In particular, contrast-enhanced MRI (CE-MRI) routinely guides surgical biopsy and resection of the MRI enhancing core, but fails to address the diverse subpopulations of the surrounding non-enhancing parenchyma (so called “brain around tumor” or BAT). These unresected residual subpopulations in BAT represent the main contributors to tumor recurrence, which can exhibit different therapeutic targets (and interactions) compared with enhancing biopsies. To address the limitations of tissue sampling, imaging techniques can help quantitatively characterize tumors in their entirety, including unresected BAT regions. Our group has used multi-parametric MRI and image-guided biopsies to develop and validate machine-learning (ML) models of intratumoral genomic heterogeneity, with particular focus on the BAT zone. In Aim 1, will we collect and molecularly profile a large set of image-recorded stereotactic biopsies in primary GBM patients to quantify the diversity of molecularly-distinct subpopulations, as well as their phenotypic niches, throughout the BAT zone. We will assess local heterogeneity at the biopsy level and also co-localize regional patterns and rates of recurrence on serial MRI. In Aim 2, we will use these biopsies and spatially matched MRI metrics to refine our existing ML predictive models. We will use these ML models to co- localize spatial patterns of molecularly-distinct subpopulations (and their phenotypic niches) to quantify their risk of regional recurrence. In Aim 3, we will functionally validate the subpopulation interactions observed in Aims 1 and 2 using patient derived xenograft (PDX) models. We will also validate these interactions in human GBM using a subset of spatially matched biopsies from primary and recurrent tumors in the same patients. This proposal leverages our unique expertise in image-guided tissue analysis and MRI-based computational modeling to study the diversity of molecularly-distinct subpopulations and the evolving competitive landscapes in human GBM. This work will help risk stratify patients in future targeted clinical drug trials and should also facilitate new strategies (e.g., adaptive therapy) to exploit subpopulation co-dependency for therapeutic benefit.