Researchers combine CRISPR gene editing technology with drug discovery to understand why cancer treatment works

According to the American Cancer Society, 11,000 people would die of acute myeloid leukemia (AML) in 2019. Cancer begins in the bone marrow. There, mutated genes do not prevent blood cells from replicating again and again and again, by developing tumors.

Chemotherapy helps two out of three patients achieve remission. And recently, drug developers have devised a new attack, aimed at targeting the patient's defective genes, retrieving diverted cells, and stopping growth. But this type of drug development can cause more errors in testing and can take years to go from the lab to the patient.

Now, in an article published in Nature Chemical BiologyBrian Liau, an assistant professor of chemistry and chemical biology at Harvard University, explains why some LMA drugs only work from time to time. With his new technique, Liau and his team expose more intimate details about the drug-body relationship and, in doing so, refute previous assumptions about the functioning of AML drugs.

The drug-body relationship

To test a new drug, the developers manipulate the small molecules of their product, moving them to see how the changes affect the effectiveness of the drug.

To study the functioning of LMA drugs, the Liau group followed the same process. But, as a good mediator, they also tracked down the next verse: what was happening, they wanted to know, if we handled rather the protein target?

"As chemists, we have the ability to make almost anything," says Liau. "Now, we have the unprecedented ability to systematically change the structure of proteins directly into cells."

For their first mediation, the Liau group focused on a specific subtype of LMA, whose mutated genes cause a change in the so-called epigenetic state of a blood cell. Epigenetic changes, in which chemical labels land on genes and activate or deactivate them, result from environmental triggers: what you eat, your volume of physical activity and sleep and your place of residence can have an impact on your epigenome.

In the AML, mutated genes are enough to trigger epigenetic change and reprogram cells to grow in an uncontrollable way. As enzymes often regulate the conversation between genes and their host cells, new drugs target these proteins, hoping to reverse their dysfunction. For AML, this enzymatic target is called LSD1 (histone demethylase 1 specific for lysine).

Until now, drugs targeting LDS1 only work sometimes. Thus, Liau and his team decided to discover what makes the protein so slippery.

Exploit weakness

Proteins, like bicycles, have essential and non-essential parts (or domains). Without handlebars, the machine continues to move. without wheels, it stops. Thus, the Liau group sought the "wheels" of LSD1 which, once dismantled, would stop the protein and the disease.

To do this, the team used a technique called CRISPR-scanning. The CRISPR gene editing tool can perform precise cuts in the genetic code (DNA). Thus, the Liau group used this tool to simultaneously perform systematic but random slices in many genes relevant to AML.

Then, when the cell intervenes to repair the cut, small scars can form in the genome. These scars produce different types of mutant genes, and the mutant genes produce mutant proteins. One mutant loses the handlebars, another the pedal and finally, one loses its wheels. Even though the first two proteins have lost some parts, their cancer cells remain. But the last is immobilized; growth stops.

Through their systematic approach, the Liau group can rank the weaknesses of LSD1 that drug developers can exploit. A well-designed medicine can behave like a pebble in a gear: a simple but effective way to hinder the device.

Bosses and holes

Some mutations may strengthen rather than weaken: The protein could acquire a new set of impermeable wheels to drugs.

To determine which mutations might affect the effectiveness of the drug, the Liau group examines the interactions between a drug and each mutant (a technique called CRISPR-suppressor scanning). Once again, some mutants die while others persist in continuing their malignant growth. Developers can use this information to tweak their medication and subvert the new defenses of the protein.

"Maybe I add something on the drug, like making it bigger or adding a lump," says Liau. "Or maybe I add something to the protein, like a hole, if the hole-hole is complete, we can unravel that information with the methodology."

Using the CRISPR-suppressor scan, her group explored how bumps and holes could affect the relationship between mutant LMA LSD1 and drugs under development to treat cancer. What they found was surprised.

Drugs targeting LSD1 stop the enzymatic function of the protein. However, this function is not as essential to cancer growth as previously thought. The Liau group discovered that drugs could interrupt communication between LSD1 and a transcription factor (GFI1B).

Although the drugs worked because they (sometimes) disrupted both actions, the Liau group's new technique showed that the LSD1-GFI1B relationship is the most critical for the survival of AML. Their discovery could also explain why some LMA subtypes rely so heavily on LSD1. With this new information, drug developers can focus their efforts, accelerate drug development and produce more targeted treatment.

Next, Liau and his team plan to study more bumps and holes on LSD1, the darker corners of the protein and other cancer-related proteins. Previously, according to Liau, "It was not understood nor understood why some cancers were sensitive to LSD1 inhibitors". Now, his technique could reveal new, more powerful sensitivities, leading to more effective and efficient cancer treatments.