Researchers Use CRISPR To Build A Human Melanoma Model From Scratch

This post was adapted from a Broad Institute post by Allessandra DiCorato.

Over the last two decades, researchers have discovered thousands of genetic mutations in cancer. But understanding how they affect the growth and spread of tumors in the body remains challenging because each patient’s tumor can have many different mutations. 

Now, scientists have used the CRISPR-Cas9 gene-editing system to build cell models of melanoma “from scratch,” allowing them to pinpoint the effects of individual and specific combinations of mutations. The powerful gene-editing method enabled the investigators to introduce specific mutations one at a time in a controlled manner into healthy human skin cells, which then acquired malignant traits.

In a report in Science, the team from Dana-Farber, the Broad Institute of MIT and Harvard, and Harvard Medical School describes how they installed five melanoma mutations, one-by-one and in different combinations, in the genomes of human skin cells. These edited cells grew and multiplied to become tumors that showed hallmarks of melanoma, including rapid growth, heightened ability to invade other tissues, activation of certain gene programs, and specific pigmentation patterns. 

Eran Hodis, MD, PhD, the study’s co-first and co-corresponding author, said this is the first time scientists have made a human cancer model using precisely controlled genetic engineering and starting from fully differentiated, or specialized, cells rather than from stem cells, which are not relevant for every cancer type.

“It’s our hope that this approach will open up opportunities to build similar models across many other cancer types, accelerating the linking of cancer genetics to specific disease features,” says Hodis. He began the study while working toward his PhD at Dana-Farber, the Broad, and Harvard University, and is now an internal medicine resident at Brigham and Women’s Hospital. At the Broad, he was in the laboratory of Aviv Regev, PhD, a computational and systems biologist who is now head of Genentech Research and Early Development. Hodis is scheduled to start a hematology-oncology fellowship at Dana-Farber and Mass General Brigham in July.

Co-first author Elena Torlai Triglia, PhD, explains that connecting an individual tumor’s genetic makeup, or genotype, with a particular trait, or phenotype, can be particularly difficult when studying melanoma.

“The skin is exposed to a lot of external agents, such as UV light, so there are a lot of mutations present in melanoma patients that might not be the ones really driving the disease,” says Torlai Triglia, who worked on the project while a postdoctoral fellow at the Broad in the Regev laboratory. She is currently in the Dana-Farber laboratory of Bradley Bernstein, MD, PhD, of Cancer Biology.

By introducing mutations into healthy human melanocytes — skin cells that produce a pigment called melanin and become cancerous in melanoma — the team could observe the effects of the mutations on a blank slate.

The results not only shed light on key mutations in melanoma, but also suggest a new way to study the role of specific genes in other cancers.

“Having this toolbox enables us to ask what effects mutations have in cells,” says Torlai Triglia. “These questions help us understand how the disease develops and how to target it.”

[Learn more: Melanoma: what it is, how to spot it, and treatment options.]

Making melanoma

To make their melanoma models, the team used Cas9, the CRISPR editing protein, to install mutations in the CDKN2A, BRAF, and TERT genes, which are commonly seen in melanoma. Together, the three mutations caused the cells to behave like cancer, dividing indefinitely. 

Next, the researchers added different combinations of additional melanoma-associated mutations in the genes PTEN, TP53, and APC, resulting in nine different cell models that the team then implanted in mice. The animals developed tumors that showed similar pigmentation and tissue architecture to human tumors. Single-cell RNA sequencing revealed that as more mutations were added, the cells gradually shifted their gene expression programs so that the animal tumor models had similar patterns of gene expression as patient tumors with the same genotype — something the researchers were surprised to observe.

“This would be such an impossible thing for us to mimic if we set out to do that in the lab,” Hodis says. “We’re talking about the coordinated expression of thousands of genes. This is one of the best pieces of evidence we have that the melanomas we built ‘from scratch’ faithfully reflect melanomas that arise in patients.”

Melanomas are notorious for metastasizing early; this spreading beyond the initial site of the tumor is an often-lethal process with an unclear genetic basis. The researchers and their collaborators found that metastasis often occurred in tumors with an APC mutation, suggesting that activation of the pathway controlled by the APC gene, the Wnt pathway, could contribute to the ability of tumors to spread.

Hodis and Torlai Triglia plan to use their method to build more cancer models and study mutations that aren’t well understood. They said their findings underscore the importance of studying interactions between genes in models of disease, and that their approach may help scientists study how tumors become resistant to targeted therapies, which can’t always be explained by a single mutation. 

“Every time we present this work, people have all sorts of amazing ideas on how they could expand on our method,” Torlai Triglia says. “We’re really looking forward to seeing what other people do with it.”