Image Processing Pipeline to Compute Homologous Recombination Score
Image Processing Pipeline to Compute Homologous Recombination Score
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计算同源重组分数的图像处理管道
DOI：
10.1145/3535694.3535704
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发表时间：
2022
期刊：
影响因子：
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通讯作者：
Kauppi, Liisa
中科院分区：
文献类型：
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作者：
Vundavilli, Haswanth;Tumiati, Manuela;Hautaniemi, Sampsa;Datta, Aniruddha;Kauppi, Liisa
DNA双链断裂（DSB）是真核细胞中常见的损伤，同源重组途径是修复DSB的主要途径之一。然而，能够修复DSB的肿瘤细胞不太可能由于DNA损伤化疗（如铂化合物）引起的损伤而死亡。虽然基于铂的疗法在治疗各种癌症方面是有效的，但它们也会带来严重的副作用，因此理想情况下，铂应该在治疗耐药的可能性较低时使用。HR评分为患者的肿瘤HR能力提供了一种衡量标准，并已被证明可预测其化疗反应和长期生存。从每个患者的免疫荧光显微镜图像手动计算该评分容易出错且耗时。在此，我们提出了一种图像处理管道，该管道将来自落射荧光显微镜的三个发射通道（代表细胞核、S期细胞和HR介导的肿瘤切片修复）的成像数据作为输入，并计算HR评分。我们的开源方法形成了一个理论基础，以开发类似的方法来预测化疗反应和促进治疗决策。
DNA double-strand breaks (DSBs) occur frequently in eukaryotic cells, and the homologous recombination pathway (HR) is one of the major pathways required to repair these breaks. However, tumor cells that are able to repair DSBs are unlikely to die due to damage incurred by DNA damaging chemotherapies, such as platinum compounds. While platinum-based therapies have been effective in treating various cancers, they also carry harsh side effects, and thus ideally platinum should be used when the probability of treatment resistance is low. HR scores provide a measure for patients' tumor's HR capacity and have been shown to predict their chemotherapy response and long-term survival. Calculating this score manually from immunofluorescence microscopy images for each patient is error-prone and time-consuming. Herein, we propose an image processing pipeline that takes as input imaging data from three emission channels (representing nuclei, S-phase cells, and HR-mediated repair in a tumor slice) from an epifluorescence microscope and computes the HR score. Our open-source methodology forms a rationale to develop similar approaches in predicting chemotherapeutic responses and facilitating to make treatment decisions.