The acquisition of oncogenic drivers is a critical feature of cancer progression. For some carcinomas, it is clear that certain genetic drivers occur early in neoplasia and others late. Why these drivers are selected and how these changes alter the neoplasia’s fitness is less understood. Here we use spatially oriented genomic approaches to identify transcriptomic and genetic changes at the single-duct level within precursor neoplasia associated with invasive breast cancer. We study HER2 amplification in ductal carcinoma in situ (DCIS) as an event that can be both quantified and spatially located via fluorescence in situ hybridization (FISH) and immunohistochemistry on fixed paraffin-embedded tissue. By combining the HER2-FISH with the laser capture microdissection (LCM) Smart-3SEQ method, we found that HER2 amplification in DCIS alters the transcriptomic profiles and increases diversity of copy number variations (CNVs). Particularly, interferon signaling pathway is activated by HER2 amplification in DCIS, which may provide a prolonged interferon signaling activation in HER2-positive breast cancer. Multiple subclones of HER2-amplified DCIS with distinct CNV profiles are observed, suggesting that multiple events occurred for the acquisition of HER2 amplification. Notably, DCIS acquires key transcriptomic changes and CNV events prior to HER2 amplification, suggesting that pre-amplified DCIS may create a cellular state primed to gain HER2 amplification for growth advantage. By using genomic methods that are spatially oriented, this study identifies several features that appear to generate insights into neoplastic progression in precancer lesions at a single-duct level.

中文翻译：

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HER2 扩增的乳腺瘤形成过程中的转录组和基因组进化

获得致癌驱动因素是癌症进展的一个关键特征。对于某些癌症，很明显某些遗传驱动因素发生在肿瘤形成的早期，而另一些则发生在晚期。为什么选择这些驱动因素以及这些变化如何改变肿瘤的适应性尚不清楚。在这里，我们使用面向空间的基因组方法来识别与浸润性乳腺癌相关的前体肿瘤内单导管水平的转录组和遗传变化。我们研究了导管原位癌 (DCIS) 中的 HER2 扩增事件，该事件可以通过荧光原位杂交 (FISH) 和固定石蜡包埋组织的免疫组织化学进行量化和空间定位。通过将 HER2-FISH 与激光捕获显微切割 (LCM) Smart-3SEQ 方法相结合，我们发现 DCIS 中的 HER2 扩增改变了转录组谱并增加了拷贝数变异 (CNV) 的多样性。特别是，干扰素信号通路在 DCIS 中被 HER2 扩增激活，这可能在 HER2 阳性乳腺癌中提供延长的干扰素信号激活。观察到具有不同 CNV 特征的 HER2 扩增 DCIS 的多个亚克隆，表明发生了多个事件以获取 HER2 扩增。值得注意的是，DCIS 在 HER2 扩增之前获得了关键的转录组变化和 CNV 事件，这表明预扩增的 DCIS 可能会产生一种细胞状态，以便获得 HER2 扩增以获得生长优势。通过使用空间定向的基因组方法，