PO.TB03.04 · 肿瘤生物学
人类转移性肿瘤细胞的单细胞染色质可及性分析
Single cell chromatin accessibility profiling of human metastatic tumor cells
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
转移是绝大多数癌症死亡的原因，然而使转移性肿瘤细胞（MTC）得以在远处器官中存活、适应和扩增的调控程序仍未被充分理解。脑转移（BrM）尤为致命，其特点是治疗选择有限且对现有治疗存在深度耐药。尽管染色质可及性协调着转录状态和细胞可塑性，但其对转移定植的作用在很大程度上仍未被探索。在此，我们呈现了迄今为止最全面的人类BrM MTC单细胞染色质可及性图谱，涵盖源自多种原发癌的15例转移灶。在免疫细胞去除后，使用10x Genomics单细胞ATAC-seq对细胞核进行分析，并采用Cell Ranger ATAC、Signac和Seurat进行分析，整合了来自已发表BrM数据集的推断基因表达。我们使用Pando重建了基因调控网络（GRN），以将转录因子活性、DNA可及性和下游基因调控联系起来。在49,907个高质量单细胞和147,139个共享可及峰中，我们发现了三种主导性调控组（regulome）：两种与已知的炎症和增殖程序一致，第三种为非增殖性、偏向发育的状态，此前在BrM或任何其他远处转移中均未被表征。我们对这些模块中的关键标志物进行了机制验证，并辅以人类样本中的蛋白水平验证。我们还鉴定出22,242个保守的顺式调控元件（CRE），其中91%映射到已知的人类增强子——然而其对转移适应性的意义此前未知。值得注意的是，我们在与发育和中胚层转录因子相关的非编码区中发现了大量CRE，凸显了支撑转移适应的核心调控构架。这项工作提供了人类BrM顺式调控图景的广泛参考图谱，并揭示了MTC中此前未被认识的发育调控回路，为转移性癌症的治疗靶向提供了新途径。
查看英文原文 English abstract
Metastasis is responsible for the vast majority of cancer deaths, yet the regulatory programs that enable metastatic tumor cells (MTCs) to survive, adapt, and expand in distant organs remain incompletely understood. Brain metastasis (BrM) is particularly lethal, marked by limited therapeutic options and profound resistance to existing treatments. Although chromatin accessibility orchestrates transcriptional states and cellular plasticity, its contribution to metastatic colonization has been largely unexplored.Here, we present the most comprehensive single-cell chromatin accessibility atlas of human BrM MTCs to date, spanning 15 metastases originating from diverse primary carcinomas. Following immune-cell depletion, nuclei were profiled using 10x Genomics single-cell ATAC-seq and analyzed with Cell Ranger ATAC, Signac, and Seurat, integrating inferred gene expression from published BrM datasets. We reconstructed gene regulatory networks (GRNs) with Pando to connect transcription factor activity, DNA accessibility, and downstream gene regulation.Across 49,907 high-quality single cells and 147,139 shared accessible peaks, we uncovered three dominant regulomes: two aligned with known inflammatory and proliferative programs, and a third non-proliferative, developmentally biased state not previously characterized in BrM or any other distant metastasis. We performed mechanistic validation of key markers from these modules, complemented by protein-level validation in human specimens. We also identified 22,242 conserved cis-regulatory elements (CREs), with 91% mapping to known human enhancers-yet with previously unknown implications for metastatic fitness. Notably, we discovered abundant CREs located in non-coding regions linked to developmental and mesodermal transcription factors, highlighting a core regulatory architecture underlying metastatic adaptation. This work provides an expansive reference map of the cis-regulatory landscape of human BrM and reveals previously unappreciated developmental regulatory circuits in MTCs, offering new avenues for therapeutic targeting in metastatic cancer.
利益披露 Disclosure
V. Opazo-Mellado, None..
M. Oviedo, None..
D. Figueroa, None..
C. Perez, None..
L. Hernandez, None..
J. Phillips, None..
J. Roose, None..
H. Gonzalez, None.