Deep in the cells of the human immune system, DNA is constantly being replicated, transcribed and even mutated — but rarely does it change dramatically. Like every other living organism, humans and their genes developed from millions of years of evolutionary pruning.

But to Yale microbiologists, altering the entire genomes of T-cells — the body’s main offensive weapon against diseases such as cancer — is as simple as putting together a Lego set.

In a new study published in the journal Nature Methods on Feb. 25, researchers at the Sidi Chen Lab at Yale have come up with a new way to use the gene-editing technology CRISPR that significantly improves the technology’s efficiency. By allowing scientists to select multiple genes to include in the same CRISPR system, scientists will now be able to edit their samples’ genomes in one go, saving time and money in the process. These findings have considerable promise for engineering T-cells that can fight off cancers such as leukemia and lymphoma.

According to senior author and genetics professor at the School of Medicine Sidi Chen, modularity is the way forward for research in immunotherapy.

“That’s how you make life easy. You want to build an airplane, you want to build a train, you want to build ships, then you plug and play with the modules. What our platform allows you to do is use such a modular system to engineer the T-cells like you’re playing Legos,” he said.

Instead of using CRISPR-Cas9, a similar system of gene editing, Chen said his team used CRISPR-Cpf1. This less common system makes many small cuts into the DNA of the T-cells into which man-made viruses can insert new genes. In addition, scientists can use the cuts to remove multiple genes at the same time.

According to co-author of the study Jonathan Park MED ’22 GRD ’22, the team has not only been able to remove the gene that makes T-cells tired but also insert receptors that can detect cancer.

“Essentially, you can do a lot of modifications in the same effort that it takes to do one,” he said. “Now, the field is opened for T-cell engineering.”

T-cells have receptors on the outside of their cell membranes that allow them to recognize the identities of cells with which they come into contact. If an unwelcome cell is spotted by a T-cell, the immune system will swiftly kill the invader. Since cancerous cells come from the human body, the immune system can have a difficult time differentiating between what is healthy and what is cancerous. By genetically engineering T-cells to have a wide range of receptors that can identify cancer cells, Park said, the immune system can kill them more effectively.

However, Park said that the study’s findings come with limitations. While his team has confirmed the viability of the new method on lab-grown human cell cultures, clinical testing will only occur far in the future. In addition, Park and his co-authors can only program T-cells to attack lymphomas and leukemias — cancers of white blood cells — because the body can only handle being completely depleted of white blood cells.

He added that since T-cells have a hard time distinguishing between healthy and cancerous cells, scientists are wary of using genetically-engineered T-cells on solid tumor cancers because the cells can inadvertently kill too many healthy cells.

Despite the obstacles, Chen said his team’s findings are promising for cancer research as a whole.

“My left hand is trying to build new tools to engineer. My right hand has a magnifying glass to look into the immune cell to see which genes need targeting,” he said. “With both at hand, we should be able to advance our knowledge and tools to develop next-generation immunotherapy and to benefit more patients.”

CRISPR-Cpf1 was first developed in 2015 by researchers at MIT and Harvard.

Matt Kristoffersen | matthew.kristoffsen@yale.edu