Single-cell lineage tracing of metastatic cancer reveals selection of hybrid EMT states

The underpinnings of cancer metastasis remain poorly understood, in part due to a lack of tools for probing their emergence at high resolution. Here we present macsGESTALT, an inducible CRISPR-Cas9-based lineage recorder with highly efficient single-cell capture of both transcriptional and phylogenetic information. Applying macsGESTALT to a mouse model of metastatic pancreatic cancer, we recover ~380,000 CRISPR target sites and reconstruct dissemination of ~28,000 single cells across multiple metastatic sites. We find cells occupy a continuum of epithelial-to-mesenchymal transition (EMT) states. Metastatic potential peaks in rare, late-hybrid EMT states, which are aggressively selected from a predominately epithelial ancestral pool. The gene signatures of these late-hybrid EMT states are predictive of reduced survival in both human pancreatic and lung cancer patients, highlighting their relevance to clinical disease progression. Finally, we observe evidence for in vivo propagation of S100 family gene expression across clonally distinct metastatic subpopulations.

癌症转移的分子基础仍未被充分阐明，部分原因在于缺乏可高分辨率解析其发生过程的研究工具。本研究报道了macsGESTALT：一种基于诱导型CRISPR-Cas9的谱系记录系统，可高效同时捕获单细胞的转录组与系统发育信息。本研究将macsGESTALT应用于转移性胰腺癌小鼠模型，共获取约38万个CRISPR靶位点，并重构了约2.8万个单细胞在多个转移灶间的播散轨迹。研究发现肿瘤细胞处于上皮间质转化（epithelial-to-mesenchymal transition, EMT）的连续状态谱中。肿瘤转移潜能在罕见的晚期混合EMT状态中达到峰值，这类细胞由以上皮表型为主的祖先细胞群中被显著正向筛选而来。这类晚期混合EMT状态的基因特征可预测人类胰腺癌与肺癌患者的不良预后，凸显其与临床疾病进展的相关性。最后，本研究观察到S100家族基因的表达可在体内跨克隆异质性转移亚群传播的证据。