Robust integrated intracellular organization of the human iPS cell: where, how much, and how variable
Authors: Viana Matheus P. , Chen Jianxu , Knijnenburg Theo A. , Vasan Ritvik , Yan Calysta , Arakaki Joy E. , Bailey Matte , Berry Ben , Borensztejn Antoine , Brown Jackson M. , Carlson Sara , Cass Julie A. , Chaudhuri Basudev , Cordes Metzler Kimberly R. , Coston Mackenzie E. , Crabtree Zach J. , Davidson Steve , DeLizo Colette M. , Dhaka Shailja , Dinh Stephanie Q. , Do Thao P. , Domingus Justin , Donovan-Maiye Rory M. , Foster Tyler J. , Frick Christopher L. , Fujioka Griffin , Fuqua Margaret A. , Gehring Jamie L. , Gerbin Kaytlyn A. , Grancharova Tanya , Gregor Benjamin W. , Harrylock Lisa J. , Haupt Amanda , Hendershott Melissa C. , Hookway Caroline , Horwitz Alan R. , Hughes Chris , Isaac Eric J. , Johnson Gregory R. , Kim Brian , Leonard Andrew N. , Leung Winnie W. , Lucas Jordan J. , Ludmann Susan A. , Lyons Blair M. , Malik Haseeb , McGregor Ryan , Medrash Gabe E. , Meharry Sean L. , Mitcham Kevin , Mueller Irina A. , Murphy-Stevens Timothy L. , Nath Aditya , Nelson Angelique M. , Paleologu Luana , Alexander Popiel T. , Riel-Mehan Megan M. , Roberts Brock , Schaefbauer Lisa M. , Schwarzl Magdalena , Sherman Jamie , Slaton Sylvain , Filip Sluzewski M. , Smith Jacqueline E. , Sul Youngmee , Swain-Bowden Madison J. , Joyce Tang W. , Thirstrup Derek J. , Toloudis Daniel M. , Tucker Andrew P. , Valencia Veronica , Wiegraebe Winfried , Wijeratna Thushara , Yang Ruian , Zaunbrecher Rebecca J. ,   Allen Institute for Cell Science, Johnson Graham T. , Gunawardane Ruwanthi N. , Gaudreault Nathalie , Theriot Julie A. , Rafelski Susanne M. 
Published: December 2020

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 and generalizable analysis approach of the locations, amounts, and variation of these 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.