Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration (Hi-C)

Metastatic cancer cells traverse tight junctions that exert forces on their nucleus and the genomic contents within. Cancerous tumors are highly heterogeneous and not all cells within them can achieve such a feat. Here, we investigated what initial genome architecture characteristics favor the constricted migratory ability of cancer cells and which arise only after passage through multiple constrictions. We identified a cell surface protein (ITGB4) whose expression correlates with increased initial constricted migration ability in human melanoma A375 cells. Sorting out this subpopulation allowed us to identify cellular and nuclear features that pre-exist and favor migration, as well as alterations that only appear after cells have passed through constrictions. We identified specific genomic regions that experienced altered genome spatial compartment profiles only after constricted migration. Our study reveals 3D genome structure contributions to both selection and induction mechanisms of cell fate change during cancer metastasis. A375 cells from either the original cell line population (Parental) or a population grown from a single cell (Clone3) were FACS sorted according to expression of Integrin Beta 4 (ITGB4). Cells were then allowed to migrate through 5 rounds of constricted migration. Genome structure was characterized by Hi-C across all populations and migration conditions.转移性肿瘤细胞可穿越紧密连接，此类结构会对其细胞核及内部基因组物质施加机械作用力。实体瘤具有高度异质性，并非所有肿瘤细胞都能完成这一受限迁移过程。本研究旨在探究，哪些初始基因组架构特征能够促进肿瘤细胞的受限迁移能力，又有哪些特征仅在细胞经历多次受限通道穿越后才会产生。我们在人黑色素瘤A375细胞中发现，一种细胞表面蛋白——整合素β4（Integrin Beta 4，ITGB4）——的表达水平与初始受限迁移能力的提升呈显著正相关。通过分选该细胞亚群，我们得以识别出预先存在且利于迁移的细胞及细胞核特征，同时也发现了仅在细胞穿越受限通道后才会出现的细胞改变。我们还鉴定出特定基因组区域，其基因组空间区室化特征仅在受限迁移发生后才会发生改变。本研究揭示了三维（3D）基因组结构在肿瘤转移过程中，对细胞命运改变的筛选与诱导两种机制均具有关键调控作用。本研究中使用的A375细胞分别来源于原始细胞系群体（Parental，亲本细胞群体）以及单细胞扩增的克隆3群体（Clone3）；我们根据整合素β4（Integrin Beta 4，ITGB4）的表达水平，采用荧光激活细胞分选术（FACS）对这些细胞进行了分群。随后，我们让分选得到的细胞完成5轮受限迁移过程。我们通过高通量染色体构象捕获技术（Hi-C）对所有细胞群体及各迁移条件下的基因组结构进行了表征分析。