Fighting aggressive skin cancer becomes possible with AI-designed vaccine approach

Researchers have harnessed the power of artificial intelligence to design a blueprint for building a vaccine that aims to teach the body’s immune system to fight cancer.

“Our current focus is on addressing the growing challenges of melanoma, one of the most aggressive forms of skin cancer,” says Saba Ismail, a Ph.D. student in co-author and pharmacy professor Khaled Barakat’s lab in the Faculty of Pharmacy and Pharmaceutical Sciences and lead author of a paper introducing the vaccine, recently published in Computers in Biology and Medicine. “However, once we finalize this model, we will use it for other cancers as well, not just melanoma.”

Although the vaccine is still in the theoretical phase (not yet tested on actual cells or in humans), it marks “an exciting step in a very long journey to come,” adds Barakat.

The computer model of the vaccine contains multiple neoantigens—markers found on cancer cells that identify them to the immune system as something foreign. The body’s T cells recognize these neoantigens and are triggered to eliminate them. Neoantigen-based vaccines are a promising approach for cancer immunotherapy, the authors note in the paper, but identifying which neoantigens should be targeted for different types of cancer, and in different patients, can be a challenge.

Computer modeling allows for a much faster and more efficient way to narrow down the potential neoantigens to a handful of promising targets. Ismail and Barakat began with 750 neoantigens and, with their model, found eight strong candidates they then combined into the vaccine “construct.”

A vaccine with multiple neoantigens means it will likely have broader efficacy against different types of melanoma cells, explains Ismail, who recently received a Vanier Canada Graduate Scholarship for this research.

“Even if one neoantigen can escape the immune system, others can activate the necessary mechanism.”

In addition to filters that measured antigenicity—the likelihood of provoking a strong immune system response—the researchers applied filters that looked at allergenicity and toxicity to ensure the vaccine won’t cause negative reactions.

The neoantigens in the vaccine are joined together with linkers, which are short amino acid sequences. These linkers create a bit of space between the various neoantigens so that they can’t overlap and interfere with the processes happening at the cellular level, Ismail explains.

“This also enhances the immunogenicity of the overall vaccine construct,” she adds.

Ismail and Barakat also added something called an adjuvant to the vaccine, which is designed to spark an even stronger response from the immune system. Together, the three components—linkers, adjuvant and the eight neoantigens—are primed to fight melanoma cells.

The vaccine has shown promising results in computational testing. Ismail also notes it “has high binding affinity towards immune receptors,” another essential step for triggering the immune system.

The researchers stress that these findings are just the first step, highlighting the need for extensive testing in the lab followed by an eventual clinical trial.

“We hope to build a generalized workflow that would aid in personalized medicine, where the idea is to compare the normal and cancerous cells and quickly identify what neoantigens should be used in vaccine design,” says Barakat, who is a member of the Cancer Research Institute of Northern Alberta and Women and Children’s Health Research Institute.

“The goal is to streamline vaccine development, making it faster, more precise and more tailored to each patient, offering new hope for those battling melanoma and other cancers globally,” adds Ismail.

Researchers have harnessed the power of artificial intelligence to design a blueprint for building a vaccine that aims to teach the body’s immune system to fight cancer.

“Our current focus is on addressing the growing challenges of melanoma, one of the most aggressive forms of skin cancer,” says Saba Ismail, a Ph.D. student in co-author and pharmacy professor Khaled Barakat’s lab in the Faculty of Pharmacy and Pharmaceutical Sciences and lead author of a paper introducing the vaccine, recently published in Computers in Biology and Medicine. “However, once we finalize this model, we will use it for other cancers as well, not just melanoma.”

Although the vaccine is still in the theoretical phase (not yet tested on actual cells or in humans), it marks “an exciting step in a very long journey to come,” adds Barakat.

The computer model of the vaccine contains multiple neoantigens—markers found on cancer cells that identify them to the immune system as something foreign. The body’s T cells recognize these neoantigens and are triggered to eliminate them. Neoantigen-based vaccines are a promising approach for cancer immunotherapy, the authors note in the paper, but identifying which neoantigens should be targeted for different types of cancer, and in different patients, can be a challenge.

Computer modeling allows for a much faster and more efficient way to narrow down the potential neoantigens to a handful of promising targets. Ismail and Barakat began with 750 neoantigens and, with their model, found eight strong candidates they then combined into the vaccine “construct.”

A vaccine with multiple neoantigens means it will likely have broader efficacy against different types of melanoma cells, explains Ismail, who recently received a Vanier Canada Graduate Scholarship for this research.

“Even if one neoantigen can escape the immune system, others can activate the necessary mechanism.”

In addition to filters that measured antigenicity—the likelihood of provoking a strong immune system response—the researchers applied filters that looked at allergenicity and toxicity to ensure the vaccine won’t cause negative reactions.

The neoantigens in the vaccine are joined together with linkers, which are short amino acid sequences. These linkers create a bit of space between the various neoantigens so that they can’t overlap and interfere with the processes happening at the cellular level, Ismail explains.

“This also enhances the immunogenicity of the overall vaccine construct,” she adds.

Ismail and Barakat also added something called an adjuvant to the vaccine, which is designed to spark an even stronger response from the immune system. Together, the three components—linkers, adjuvant and the eight neoantigens—are primed to fight melanoma cells.

The vaccine has shown promising results in computational testing. Ismail also notes it “has high binding affinity towards immune receptors,” another essential step for triggering the immune system.

The researchers stress that these findings are just the first step, highlighting the need for extensive testing in the lab followed by an eventual clinical trial.

“We hope to build a generalized workflow that would aid in personalized medicine, where the idea is to compare the normal and cancerous cells and quickly identify what neoantigens should be used in vaccine design,” says Barakat, who is a member of the Cancer Research Institute of Northern Alberta and Women and Children’s Health Research Institute.

“The goal is to streamline vaccine development, making it faster, more precise and more tailored to each patient, offering new hope for those battling melanoma and other cancers globally,” adds Ismail.