Pancreatic intraepithelial neoplasias (PanINs) are the most common precursors of pancreatic cancer, but their small size and inaccessibility in humans make them challenging to study¹. Critically, the number, dimensions and connectivity of human PanINs remain largely unknown, precluding important insights into early cancer development. Here, we provide a microanatomical survey of human PanINs by analysing 46 large samples of grossly normal human pancreas with a machine-learning pipeline for quantitative 3D histological reconstruction at single-cell resolution. To elucidate genetic relationships between and within PanINs, we developed a workflow in which 3D modelling guides multi-region microdissection and targeted and whole-exome sequencing. From these samples, we calculated a mean burden of 13 PanINs per cm³ and extrapolated that the normal intact adult pancreas harbours hundreds of PanINs, almost all with oncogenic KRAS hotspot mutations. We found that most PanINs originate as independent clones with distinct somatic mutation profiles. Some spatially continuous PanINs were found to contain multiple KRAS mutations; computational and in situ analyses demonstrated that different KRAS mutations localize to distinct cell subpopulations within these neoplasms, indicating their polyclonal origins. The extensive multifocality and genetic heterogeneity of PanINs raises important questions about mechanisms that drive precancer initiation and confer differential progression risk in the human pancreas. This detailed 3D genomic mapping of molecular alterations in human PanINs provides an empirical foundation for early detection and rational interception of pancreatic cancer.

胰腺上皮内瘤变 (PanIN) 是胰腺癌最常见的前兆，但其体积小且难以在人体中发现，这使得研究具有挑战性¹。至关重要的是，人类 PanIN 的数量、尺寸和连接性在很大程度上仍然未知，这阻碍了对早期癌症发展的重要见解。在这里，我们通过分析 46 个完全正常的人类胰腺的大样本，利用机器学习管道以单细胞分辨率进行定量 3D 组织学重建，对人类 PanIN 进行了显微解剖学调查。为了阐明 PanIN 之间和内部的遗传关系，我们开发了一个工作流程，其中 3D 建模指导多区域显微切割以及靶向和全外显子组测序。根据这些样本，我们计算出每 cm ³ 13 个 PanIN 的平均负荷，并推断正常完整的成人胰腺含有数百个 PanIN，几乎全部都具有致癌KRAS热点突变。我们发现大多数 PanIN 起源于具有不同体细胞突变谱的独立克隆。一些空间连续的 PanIN 被发现含有多个KRAS突变；计算和原位分析表明，不同的KRAS突变定位于这些肿瘤内不同的细胞亚群，表明它们的多克隆起源。 PanIN 广泛的多灶性和遗传异质性引发了关于驱动人类胰腺癌前发生和赋予不同进展风险的机制的重要问题。这种人类 PanIN 分子改变的详细 3D 基因组图谱为胰腺癌的早期检测和合理拦截提供了经验基础。