New research by scientists at UCSF and UC San Diego involving techniques also deployed to fight COVID-19 has the potential to revolutionize cancer treatment by creating opportunities for more specific treatments, they say – which can be much less harmful than chemotherapy.

The collaborative effort – called the Cancer Cell Map Initiative – found that mapping protein disruptions caused by mutations in DNA, rather than the mutations themselves, is very useful in bringing together different types of carcinogenic mutations. This opens up the possibility of creating precision treatments that can target groups of mutations, rather than just one.

Thursday, the group published Three papers in the journal Science describing how cards work for breast cancer and head and neck cancers.

The research itself does not show a cure for cancer. Rather, it’s a tool that scientists can use to find better treatments, the researchers explained.

And it’s “disease agnostic,” said Nevan Krogan, director of the Quantitative Biosciences Institute at UCSF’s School of Pharmacy and one of the project’s lead authors. This means that it can be used to better understand and treat almost any disease.

Krogan’s laboratory has already used the techniques, who have been in development for cancer research for about 10 years, to understand and work on treatments for infections of SARS-CoV-2 – the virus that causes COVID-19.

“We will revolutionize drug discovery in the future,” he added. “I know this sounds like a big goal, but I really believe it.”

Previous cancer research only looks at DNA mutations that cause cancer, which isn’t always helpful because hundreds of sequences can lead to cancer, said Trey Ideker, co-lead author of the articles and professor at UC San Diego School of Moores Center for Medicine and Cancer.

For example, scientists know that the BRCA gene causes breast cancer, he said, and there are precision treatments for it. But only about 4% of women with breast cancer also have the BRCA gene. This research seeks to understand what the mutation actually does in something like the BRCA gene, so that similar mutations can be dealt with all at once.

“It’s really moving towards a more holistic view,” Ideker said. “Rather than looking at one gene at a time, we are looking at the systems created by those genes.”

He described it as an IKEA manual – the human genome, or DNA sequences, is the first page, showing you the parts of a piece of furniture. CCMI looks to be the next few pages, with the instructions on how the pieces actually fit together.

“We see the disease as a network, not just an individual gene,” Krogan said.

The change “opens a new door for cancer research,” said Dr. Howard Chang, professor of cancer research and genetics at the Stanford School of Medicine.

Chang’s colleagues at Stanford, Ran Cheng and Peter Jackson, agree – writing that protein interaction maps could be “a framework for future analyzes that could drive our understanding of oncogenic transformation and identify therapeutic targets.” in a piece in perspective which coincided with science studies.

“It’s a very powerful hypothesis generation tool,” Chang said. But that still leaves the question of how many of those assumptions about treatments actually come true, he said. He would also like to see how the tool works outside of a lab, which could take some time, depending on advancements in the type of technology used to build these protein sequences.

Ideker and Krogan also noted that this is only a first step and that there is still a lot of work to be done to bring this tool into clinical settings.

Nonetheless, Chang said the papers are an important “building block” in cancer research, and the team working there should “be applauded for their efforts to really systematically address this question” of how mutations affect protein interactions.

Danielle Echeverria is a writer for the San Francisco Chronicle. E-mail: [email protected] Twitter: @DanielleEchev

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