Abstract：
Extensive intratumoral heterogeneity (ITH) is believed to contribute to therapeutic failure and tumor recurrence, as treatment-resistant cell clones can survive and expand. However, little is known about ITH in triple-negative breast cancer (TNBC) because of the limited number of single-cell sequencing studies on TNBC. In this study, we explored ITH in TNBC by evaluating gene expression-derived and imaging-derived multi-region differences within the same tumor. We obtained tissue specimens from 10 TNBC patients and conducted RNA sequencing analysis of 2-4 regions per tumor. We developed a novel analysis framework to dissect and characterize different types of variability: between-patients (inter-tumoral heterogeneity), between-patients across regions (inter-tumoral and region heterogeneity), and within-patient, between-regions (regional intratumoral heterogeneity). We performed a Bayesian changepoint analysis to assess and classify regional variability as low (convergent) versus high (divergent) within each patient feature (TNBC and PAM50 subtypes, immune, stroma, tumor counts and tumor infiltrating lymphocytes). Gene expression signatures were categorized into three types of variability: between-patients (108 genes), between-patients across regions (183 genes), and within-patients, between-regions (778 genes). Based on the between-patient gene signature, we identified two distinct patient clusters that differed in menopausal status. Significant intratumoral divergence was observed for PAM50 classification, tumor cell counts, and tumor-infiltrating T cell abundance. Other features examined showed a representation of both divergent and convergent results. Lymph node stage was significantly associated with divergent tumors. Our results show extensive intertumoral heterogeneity and regional ITH in gene expression and image-derived features in TNBC. Our findings also raise concerns regarding gene expression based TNBC subtyping. Future studies are warranted to elucidate the role of regional heterogeneity in TNBC as a driver of treatment resistance.
摘要：
广泛的肿瘤内异质性（ITH）被认为是导致治疗失败和肿瘤复发的原因。作为治疗抗性细胞克隆可以存活和扩大。然而,由于对三阴性乳腺癌(TNBC)的单细胞测序研究数量有限,因此对ITH在三阴性乳腺癌(TNBC)中的应用知之甚少.在这项研究中,我们通过评估同一肿瘤内基因表达来源和成像来源的多区域差异来探索TNBC中的ITH。我们从10名TNBC患者获得组织标本，并对每个肿瘤2-4个区域进行RNA测序分析。我们开发了一个新的分析框架来剖析和表征不同类型的变异性：患者之间（肿瘤间异质性），跨区域的患者之间(肿瘤间和区域异质性)，在病人内部，区域间(区域肿瘤内异质性)。我们进行了贝叶斯变化点分析，以评估和分类每个患者特征（TNBC和PAM50亚型，免疫，基质,肿瘤计数和肿瘤浸润淋巴细胞)。基因表达特征分为三种类型的变异性：患者之间（108个基因），跨区域的患者之间（183个基因），和患者内部，区域间（778个基因）。基于患者间的基因签名,我们确定了两个不同的绝经状态不同的患者群.对于PAM50分类，观察到显著的肿瘤内分歧，肿瘤细胞计数，和肿瘤浸润性T细胞丰度。检查的其他特征显示了发散和收敛结果的表示。淋巴结分期与发散性肿瘤显著相关。我们的结果显示了TNBC中基因表达和图像来源特征的广泛的肿瘤间异质性和区域ITH。我们的发现还引起了关于基于基因表达的TNBC亚型的关注。未来的研究有必要阐明区域异质性在TNBC中作为治疗抵抗驱动因素的作用。
