Scientists Track Cancer cells’ Family Tree via CRISPR to Better Understand Metastasis

In a recent publication in Science, researchers from the University of California, San Francisco (UCSF) used single-cell tracers to map specific sub-populations of cancer cells after they injected them into a mouse model. The tracers allowed them to determine which sub-populations metastasized to other parts of the body and which ones remained in the site of origin. The experiment also revealed that KRT12 suppressed metastasis.

Metastasis is when cancerous cells spread from the primary tumor to other parts of the body. Around 90% of cancer-related deaths are attributed to metastasis. For instance, the 5-year survival rate of a patient with lung cancer is 56% without metastasis; however, once cancer spreads to other organs, it falls to 5%. More research is necessary to further understand the biology and discover new drivers of metastasis.

Tracking Cancer Cells’ Family Tree

To gain more insight into the biology of metastasis, researchers at UCSF created a technique that would allow them to identify and track the family history of each individual cancer cell.

They used human lung adenocarcinoma cells that they raised outside the body (in vitro) and modified them with three components to create a DNA barcode: a DNA Target, a CRISPR-Cas9 molecule, and sgRNA sequences that guide the Cas9 protein specifically to the DNA Target site

After every cut by the CRISPR tool, a unique insertion or deletion is created. This heritable DNA barcode can then be used to differentiate one cell from the other.

What Did They Learn about Metastasis?

The barcoded cancer cells were injected into the mouse lung, and the adenocarcinoma was let to spread to other organs. Following this step, the cells were extracted, and each individual cancer cell was identified using single-cell RNA-sequencing.

From these experiments, the scientists were able to learn three main points:

1. The results showed that there are “families” of cells in which members of multiple generations spread to other organs, other “families” that stay in the site of origin, and some “families” in which only some members spread to other organs.
2. The “families” of cells that were the most abundant outside the body (in vitro) are not necessarily the most abundant in mice. This means there is an interplay between the body and cancer cells that selects for specific “families.”
3. Changes were observed in several genes that were previously associated with metastasis. However, for the first time, it was discovered that the gene KRT12 reduced the cancer cell invasion to other tissues.

This method was able to differentiate between tens of thousands of individual cells and reconstruct family trees. In the future, it can become a powerful tool to determine which “families” of cells do better in specific organs, which “families” survive to therapy, and enhance our understanding of when the changes that lead to metastasis happen. This information can guide the creation of new drugs or change the timing or location for specific therapies.

By Daniel Ojeda, Ph.D.

References

1. https://science.sciencemag.org/content/early/2021/01/21/science.abc1944
2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597235/
3. https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/cancer/art-20044517#:~:text=The%20five%2Dyear%20survival%20rate,%2Dfree%20(achieved%20remission).
4. https://www.nature.com/articles/nbt.4124

Author

Daniel Ojeda