Microsatellites are short, repetitive segments of DNA, which are dysregulated in mismatch repair-deficient (MMRd) tumors resulting in microsatellite instability (MSI). MSI has been identified in many human cancer types with varying incidence, and microsatellite instability-high (MSI-H) tumors often exhibit increased sensitivity to immune-enhancing therapies such as PD-1/PD-L1 inhibition. Next-generation sequencing (NGS) has permitted advancements in MSI detection, and recent computational advances have enabled characterization of tumor heterogeneity via NGS. However, the evolution and heterogeneity of microsatellite changes in MSI-positive tumors remains poorly described. We determined MSI status in six patients using our previously published algorithm, MANTIS, and inferred subclonal composition and phylogeny with Canopy and SuperFreq. We developed a simulated annealing-based method to characterize microsatellite length distributions in specific subclones and assessed the evolution of MSI in the context of tumor heterogeneity. We identified three to eight tumor subclones per patient, and each subclone exhibited MMRd-associated base substitution signatures. We noted that microsatellites tend to shorten over time, and that MMRd fosters heterogeneity by introducing novel mutations throughout the disease course. Some microsatellites are altered among all subclones in a patient, whereas other loci are only altered in particular subclones corresponding to subclonal phylogenetic relationships. Overall, our results indicate that MMRd is a substantial driver of heterogeneity, leading to both MSI and subclonal divergence. Implications: We leveraged subclonal inference to assess clonal evolution based on somatic mutations and microsatellites, which provides insight into MMRd as a dynamic mutagenic process in MSI-H malignancies.

中文翻译：

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通过多区域肿瘤测序表征微卫星不稳定转移性癌症的克隆进化

微卫星是短的、重复的 DNA 片段，在错配修复缺陷 (MMRd) 肿瘤中失调，导致微卫星不稳定性 (MSI)。MSI 已在多种发病率不同的人类癌症类型中被发现，并且微卫星不稳定性高 (MSI-H) 肿瘤通常表现出对免疫增强疗法（如 PD-1/PD-L1 抑制）更高的敏感性。下一代测序 (NGS) 已经在 MSI 检测方面取得了进步，并且最近的计算进步使通过 NGS 表征肿瘤异质性成为可能。然而，MSI 阳性肿瘤中微卫星变化的演变和异质性仍然很少被描述。我们使用我们之前发布的算法 MANTIS 确定了 6 名患者的 MSI 状态，并使用 Canopy 和 SuperFreq 推断出亚克隆组成和系统发育。我们开发了一种基于模拟退火的方法来表征特定亚克隆中的微卫星长度分布，并评估了肿瘤异质性背景下 MSI 的演变。我们为每位患者鉴定了 3 到 8 个肿瘤亚克隆，每个亚克隆都表现出与 MMRd 相关的碱基替换特征。我们注意到微卫星往往会随着时间的推移而缩短，并且 MMRd 通过在整个疾病过程中引入新的突变来促进异质性。一些微卫星在患者的所有亚克隆中发生改变，而其他基因座仅在与亚克隆系统发育关系相对应的特定亚克隆中发生改变。总体而言，我们的结果表明 MMRd 是异质性的重要驱动因素，导致 MSI 和亚克隆分化。影响：