PO.MCB07.02 · 分子与细胞生物学
乳腺癌模型中三维基因组结构和全转录组基因表达的整合空间多组学分析
Integrated spatial multiomic profiling of 3D genome architecture and transcriptome-wide gene expression in breast cancer models
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
三维基因组组织的破坏深刻影响基因表达，驱动疾病和癌症进展。癌基因扩增、缺失和染色质结构域错误折叠等机制是肿瘤发生的关键因素。然而，全基因组测序（WGS）、RNA-seq和Hi-C等传统方法通常在群体水平评估这些变化，掩盖了细胞间异质性。为以单细胞和空间分辨率剖析这些机制，我们利用PaintScape™系统在单细胞内原位可视化三维基因组结构。然后，我们使用CosMx® 空间分子成像仪（SMI）上的空间多组学检测，将基因组结构变化与在平行样本中测量的基因表达和表型相关联，以生成全面的多模态数据集。使用正常（MCF10a）和癌性（MCF7）乳腺细胞系，PaintScape检测能够高分辨率可视化涉及癌症相关通路（包括细胞周期调控、凋亡和染色质重塑）的染色体区域和基因区域。我们鉴定出细胞类型特异性的结构改变，如易位、染色体外DNA（ecDNA）形成、位点拷贝数变异以及拓扑关联结构域（TAD）边界的移动。平行的CosMx SMI多组学成像揭示了全转录组特征和关键分子标志物的亚细胞定位模式。在暴露于雌激素受体（ER）激动剂雌二醇后，我们观察到ER+ MCF7细胞中MYC、CCND1和E2F1的转录上调，而ER- MCF10a细胞的反应极小。PaintScape分析进一步揭示了远端雌激素应答元件（DERE）在Chr17q和Chr20q附近的空间聚集，而CosMx SMI量化了局部转录激活，凸显了两个平台的互补见解。总之，PaintScape系统和CosMx SMI能够对基因组结构、转录组学和蛋白质组学进行整合的、单细胞的和空间分辨的探究。这种多模态方法揭示了具有不同基因组和表型状态的细胞群体，为阐明三维基因组组织和转录调控如何共同驱动癌症异质性和进展提供了一个强大的框架。
查看英文原文 English abstract
Disruption of 3D genome organization profoundly influences gene expression, driving disease and cancer progression. Mechanisms such as oncogene amplification, deletion, and chromatin domain misfolding are key contributors to tumorigenesis. However, conventional approaches like whole-genome sequencing (WGS), RNA-seq, and Hi-C typically assess these changes at the bulk level, masking cell-to-cell heterogeneity. To dissect these mechanisms with single-cell and spatial resolution, we leverage the PaintScape™ system to visualize 3D genome architecture in situ, within single cells. We then correlate changes in genome structure to gene expression and phenotype measured in parallel samples using a spatial multiomic assay on the CosMx® Spatial Molecular Imager (SMI) to generate a comprehensive multi-modal dataset. Using normal (MCF10a) and cancerous (MCF7) breast cell lines, the PaintScape assay enabled high-resolution visualization of chromosomal territories and gene regions involved in cancer-associated pathways, including cell cycle regulation, apoptosis, and chromatin remodeling. We identified cell type-specific structural alterations such as translocations, extrachromosomal DNA (ecDNA) formation, locus copy number variation and shifts in topologically associating domain (TAD) boundaries. Parallel CosMx SMI multiomic imaging revealed transcriptome-wide signatures and subcellular localization patterns of key molecular markers. Upon exposure to Estradiol, an estrogen receptor (ER) agonist, we observed transcriptional upregulation of MYC, CCND1, and E2F1 in ER+ MCF7 cells, contrasting with minimal response in ER- MCF10a cells. PaintScape profiling further revealed spatial clustering of distant estrogen response elements (DEREs) near Chr17q and Chr20q, while CosMx SMI quantified local transcriptional activation, highlighting complementary insights from the two platforms. Together, the PaintScape system and CosMx SMI enable an integrated, single-cell, and spatially resolved interrogation of genome architecture, transcriptomics, and proteomics. This multi-modal approach uncovers cell populations with distinct genomic and phenotypic states, offering a powerful framework to elucidate how 3D genome organization and transcriptional regulation jointly drive cancer heterogeneity and progression.
利益披露 Disclosure
Y. Cui, None..
H. Nguyen, None..
A. Floris, None..
D. King, None..
S. Tulu, None..
D. Castillo, None..
S. He, None..
S. Chattoraj, None..
J. Dunne, None..
M. Corselli, None..
J. Lyssand, None..
J. M. Beechem, None.