HSCI scientists develop CRISPR-based tool for lineage tracing

A new mouse model allows scientists to track every cell in the body, from the embryo stage until adulthood. The system, published in the journal Cell, could yield a greater understanding of development, aging, and disease.

“The dream of many developmental biologists for decades is a way to reconstruct every single cell lineage, cell-by-cell, as an embryo develops, or as a tissue is built up,” said Fernando Camargo, Ph.D., who is an HSCI principal faculty member at Boston Children’s Hospital. “We could use this mouse model to follow an organism’s entire development.”

The researchers developed a method called CRISPR array repair lineage tracing, or CARLIN. Using CRISPR gene editing to mark cells with unique “barcodes,” the model reveals both cell lineages — a cell “family tree” — and what genes each cell turns on or off over time.

Live single-cell tracking with barcodes

Previously, scientists could trace only small groups of cells in mice using dyes or fluorescent markers. While molecular tags or barcodes have been used in the past, scientists had to know markers in advance to isolate different cell types. Alternatively, they had to extract cells from the body and manipulate them, potentially changing their properties.

The advent of CRISPR gene editing has enabled researchers to barcode cells without extracting them, and to follow the lineage of thousands of cells at once. Using an inducible form of CRISPR, the new system allows researchers to create up to 44,000 different identifying barcodes at any point in a mouse’s lifespan.

Researchers can then read out the barcodes with another technology called single-cell RNA sequencing. This gives information on thousands of genes that are turned on inside each cell, profiling the cells’ identity and function.

Understanding development, disease, and aging

As a test case, the researchers applied their new system to track blood development in the embryo. They also studied how blood cells are replenished in adult mice after chemotherapy.

Additionally, the researchers believe their system could help reveal what changes happen in cellular lineage trees during disease and aging. Moreover, the system could record responses to environmental stimuli like nutrient intake and exposure to pathogens.

“Being able to create single-cell lineage maps of mammalian tissues is unprecedented,” Camargo said. “Besides its many applications in developmental biology, our model will provide important insight on the cell types and hierarchies that are affected as organisms respond to injury and disease.”

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This story was originally published on the Boston Children’s Hospital website on May 18, 2020.

Source article: Bowling, S., Sritharan, D., et al. (2020). An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells. Cell. DOI: 10.1016/j.cell.2020.04.048

Funding: The study was supported by the Natural Sciences and Engineering Research Council of Canada, EMBO, the National Institutes of Health, the Leukemia and Lymphoma Society, the Howard Hughes Medical Institute, and the Harvard University William F. Milton Fund.