Cell catalog combines live imaging with GFP markers for important cell structures

cell catalog
Segmentation of mitochondria. Image: Allen Institute

Ruwanthi Gunawardane leads the charge to build a collection of human induced pluripotent stem (hiPS) cell lines with proteins tagged to specific organelles. As the Director of Stem Cells and Gene Editing at the Allen Institute for Cell Science, she says she hopes her work will allow researchers around the world to better understand basic cell biology as well as help build platforms to model disease and test drugs.

The hiPS cell lines, which are described in detail in the Cell Catalog on the Allen Institute website, were each generated using CRISPR/Cas9 genome editing, tagging ~25 organelle-specific endogenous proteins with a green fluorescent protein marker. The protocol is described in a paper published in the August 15, 2017, issue of Molecular Biology of the Cell,1 was also the subject of a talk at the 2018 ASCB|EMBO Meeting, and is presented in detail at Allencell.org.

An organelle based catalog

“The Cell Catalog is very much organelle based,” she said. “We didn’t want to study all the genes because that is too complex. We have taken the question ‘how do cells work’ and made it more tractable,” she says, by identifying the protein most closely associated with each of the major cell structures and focusing the team’s efforts around that. The proteins tagged include alpha tubulin, beta-actin, desmoplakin, fibrillarin, tight junction protein ZO1, Tom20, and lamin B1.

Gunawardane says the cell lines create benchmarks for how normal cells should behave so that researchers can answer questions about what happens when things go awry. By using a ribonuclear protein approach to tag the organelle-related proteins, Gunawardane says she and her colleagues minimized the exposure of the cell to the Cas9 plasmid, which is a common problem with CRISPR.

“We did not want to expose the cells to anything unusual for too long because we wanted to see normal cell processes,” she said.

The hiPS cells derived for the cell lines all come from the skin cells of healthy donors. She says they can and are being used to develop many different types of cell tissues including organoids for “disease-in-a-dish” experiments. Tight quality control is maintained as hundreds of clones are screened for errors to preserve the specimens with the highest genetic integrity.

Live 3D imaging 

Another feature that sets the Allen Institute Cell Catalog apart is that each cell type is 3D live imaged. By live imaging the cells “we can look at the ‘landmarks’ and ‘highways’ of the cells,” she said. “This is going to tell us much more about how a cell works than by looking at individual proteins.”

Gunawardane said the next steps will be turning each line into cardiomyocytes.

“We are interested in learning how cells decide to become a certain cell type and then live imaging the process of differentiation through maturity to witness the transcriptional and morphological changes. We also want to know how the genome is changing by marking proteins in the nucleus… which genes are turned off and on.”


1Roberts B, Haupt A, Tucker A, Grancharova T, Arakaki J, Fuqua MA, Nelson A, Hookway C, Ludmann SA, Mueller IA, Yang R, Horwitz R, Rafelski SM, Gunawardane RN (2017). Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization. Mol. Biol. Cell 28, 2854–2874.

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Mary Spiro is ASCB's Science Writer and Social Media Manager.