Persistent Homology Based Characterization of the Breast Cancer Immune Microenvironment: A Feasibility Study
Persistent Homology Based Characterization of the Breast Cancer Immune Microenvironment: A Feasibility Study
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DOI：
10.4230/lipics.socg.2020.11
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发表时间：
2020
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影响因子：
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通讯作者：
Andrew Aukerman;Mathieu Carrière;Chao Chen;K. Gardner;R. Rabadán;R. Vanguri
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作者：
Andrew Aukerman;Mathieu Carrière;Chao Chen;K. Gardner;R. Rabadán;R. Vanguri
持久同源性是拓扑数据分析的常用工具，其主要描述符持久性图用于计算和编码给定数据集的几何和拓扑。在这篇文章中，我们提出了一种新的应用程序的持久同源性，以表征乳腺癌免疫微环境内的免疫和上皮（肿瘤）细胞的空间排列。更具体地说，定量和稳健的表征是通过计算持久性图表的染色技术（定量多重免疫荧光），使我们能够获得空间坐标和染色强度的个别细胞。将所得持久性图作为癌症亚型的特征性生物标志物和总生存期的预后生物标志物进行评价。对于约700例乳腺癌患者的中位8.5年的临床随访队列，我们表明，这些持久性图优于和补充通常的描述符捕捉空间关系与最近邻分析。这为构建（基于拓扑学的）生物标志物的一般问题提供了新的见解和可能性，这些生物标志物是癌症亚型、总生存期和对治疗的反应的特征和预测。2012年ACM学科分类计算理论→计算几何
Persistent homology is a common tool of topological data analysis, whose main descriptor, the persistence diagram, aims at computing and encoding the geometry and topology of given datasets. In this article, we present a novel application of persistent homology to characterize the spatial arrangement of immune and epithelial (tumor) cells within the breast cancer immune microenvironment. More specifically, quantitative and robust characterizations are built by computing persistence diagrams out of a staining technique (quantitative multiplex immunofluorescence) which allows us to obtain spatial coordinates and stain intensities on individual cells. The resulting persistence diagrams are evaluated as characteristic biomarkers of cancer subtype and prognostic biomarker of overall survival. For a cohort of approximately 700 breast cancer patients with median 8.5-year clinical follow-up, we show that these persistence diagrams outperform and complement the usual descriptors which capture spatial relationships with nearest neighbor analysis. This provides new insights and possibilities on the general problem of building (topology-based) biomarkers that are characteristic and predictive of cancer subtype, overall survival and response to therapy. 2012 ACM Subject Classification Theory of computation → Computational geometry