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Publications of the Week

Phenomics-Based Quantification of CRISPR-Induced Mosaicism in Zebrafish

By April 8, 2020No Comments

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This week we profile a recent publication in Cell Reports from Dr. Claire Watson (pictured,
right) in the laboratory of Dr. Ronald Kwon (second from right) at UW Medicine.

Can you provide a brief overview of your lab’s current research focus?

Osteoporosis is a disease of bone fragility that affects 1 in 3 women and 1 in 5 men over the age of 50. With advances in genome sequencing, scientists have begun to identify genetic variants–sequences of DNA that vary among individuals–that can protect some individuals from osteoporosis, and make others more susceptible to this disease. However, in most cases, we do not know how these genetic variants affect osteoporosis risk. To help address this barrier, our lab has developed a rapid pipeline for the prediction of human skeletal gene function. We have established methods for gene editing using CRISPR that enable rapid screening and mutation in zebrafish – our model for skeletal research. We have also pioneered new techniques to image zebrafish skeletons. With institutional, NIH, and private support, our lab is conducting one of the largest screens of genes linked to osteoporosis risk performed to date. Our hope is that identifying the genes that underlie osteoporosis risk will lead to clues about how to control bone regeneration, and bring relief to patients in the form of new treatments.

What is the significance of the findings in this publication?

This manuscript provides validation of an approach to rapidly screen zebrafish using first-generation (G0) CRISPR-edited mutants for phenotypes related to human skeletal disease. Despite genetic mosaicism and variability in phenotypic penetrance between and within individual zebrafish, we demonstrate that phenomic analysis, paired with appropriate statistical analyses, can allow for the rapid detection of distributed and variable phenotypes in the zebrafish skeleton. We also characterize the size distribution of mosaic clusters throughout a distributed organ system, which may apply to many somatic, CRISPR-edited, models. Thus, we present an approach to decode spatially variable phenotypes generated during CRISPR-based screens.

What are the next steps for this research?

Building on the approach presented in this manuscript, we have begun screening genes linked to osteoporosis risk in humans using rapid, G0, CRISPR screening in our zebrafish model. Our goal is to screen over 50 new genes in the next few years, and to expand the throughput of the approach to achieve the screening of 100s of genes in the near future. The end goal of the project is to help annotate and predict the likelihood of skeletal function in the several hundred candidate genes identified through human genetic analysis (GWAS and whole genome sequencing) to date.

This work was funded by:

The work in this manuscript was funded through grants from the NIH, the University of Washington, and a John H. Tietze Stem Cell Scientist Award.

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