Despite the intimate link between cell organization and function, the principles underlying intracellular organization and the relation between organization, gene expression and phenotype are not well understood. We address this by creating a benchmark for mean cell organization and the natural range of cell-to-cell variation. This benchmark can be used for comparison to other normal or abnormal cell states. To do this, we developed a reproducible microscope imaging pipeline to generate a high quality dataset of 3D, high-resolution images of over 200,000 live cells from 25 isogenic human induced pluripotent stem cell (hiPSC) lines from the Allen Cell Collection. Each line contains one fluorescently tagged protein, created via endogenous CRISPR/Cas9 gene editing, representing a key cellular structure or organelle. We used these images to develop a new multi-part generalizable analysis approach of the locations, amounts, and variation of the 25 cellular structures. Taking an integrated approach, we found that both the extent to which a structure's individual location varied ("stereotypy") and the extent to which the structure localized relative to all the other cellular structures ("concordance") were robust to a wide range of cell shape variation, from flatter to taller, smaller to larger, or less to more polarized cells. We also found that these cellular structures varied greatly in how their volumes scaled with cell and nuclear size. These analyses create a data-driven set of quantitative rules for the locations, amounts, and variation of 25 cellular structures within the hiPSC as a normal baseline for cell organization.

中文翻译：

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人iPS细胞的强大整合细胞内组织：位置，数量和变量

尽管细胞组织和功能之间有着密切的联系，但细胞内组织的基本原理以及组织，基因表达和表型之间的关系仍未得到很好的理解。我们通过为平均细胞组织和细胞间差异的自然范围创建基准来解决此问题。该基准可用于与其他正常或异常细胞状态进行比较。为此，我们开发了可再现的显微镜成像管线，以生成来自Allen Cell Collection的25种等基因人类诱导多能干细胞（hiPSC）系的200,000多个活细胞的3D高分辨率图像的高质量数据集。每个品系包含一个荧光标记的蛋白，该蛋白是通过内源CRISPR / Cas9基因编辑创建的，代表关键的细胞结构或细胞器。我们使用这些图像来开发一种新的多部分可概括的25种细胞结构的位置，数量和变异分析方法。采用综合方法，我们发现结构的单个位置变化的程度（“定型”）和相对于所有其他细胞结构定位的结构的程度（“一致性”）在很宽的范围内都很稳健。细胞形状的变化，从扁平到较高，从小到大，或从小到多极化的细胞。我们还发现，这些细胞结构的体积如何随细胞和核大小的变化而变化很大。这些分析创建了一组数据驱动的定量规则，用于hiPSC中25个细胞结构的位置，数量和变异，作为细胞组织的正常基线。