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Fred Hutch researcher and proteonomics pioneer Amanda Paulovich. (Fred Hutch Photo / Bo Jungmayer)

Genomics, or the study of a person’s genes, has long been seen as an essential part of understanding human health, and particularly learning about and treating cancer. But less flashy — and much less understood — is genomic’s younger cousin, proteomics — the large-scale study of proteins.

Applying the study of proteins to cancer research is the focus of the Applied Proteogenomics Organizational Learning and Outcomes network, part of the Beau Biden Cancer Moonshot and appropriately nicknamed APOLLO.

The Paulovich Laboratory at Seattle’s Fred Hutchinson Cancer Research Center has just been tapped for a key step in that project: developing protein tests that could match patients to the most effective drug to combat their cancer.

Amanda Paulovich, a Fred Hutch researcher and head of the lab taking on the project, said the complexities of cancer mean finding the correct treatment for a patient can be exceedingly difficult.

Cancer drugs work by acting on proteins, which are created and directed by a person’s DNA. Those proteins play key roles in the cancer’s development and vary a great deal between patients, even those with the same kind of cancer.

U.S. Vice President Joe Biden speaking about the Cancer Moonshot at Fred Hutch in March of 2016. (GeekWire photo)

For the past decade, the Clinical Proteomic Tumor Analysis Consortium (CPTAC), which the Paulovich lab is a part of, has worked to make the measurements of these proteins more precise and reliable.

“That’s taught us a lot about cancer biology, but we’re now trying to translate that to a way to predict patient’s responses to therapies,” Paulovich told GeekWire in an interview today. “And while we’ve made a lot of progress on that front, we’re still not able to consistently match the right drug to the right tumor.”

She said doctors are able to make very educated guesses about what treatment to give patients, but when it comes down to it, unknown elements of a patient’s protein makeup could mean the drug doesn’t work as anticipated.

“The reality is when we give patients therapies, even we often aren’t sure if that patient is going to respond to that therapy, and that was really frustrating to me,” Paulovich said.

“Part of that problem was that we had no good ways to measure these proteins, which are where our drugs are acting on the tumor cells. And we’re using 50-year-old technologies to do that, that are wholly inadequate to meet the needs of the proteogenomic community,” she said.

Past research in this area has relied on immunoassay procedures, which can detect only a few proteins at a time.

“By bringing mass spectrometry into the picture and using that as a detector for the proteins, we’re able to look at more proteins in a much easier fashion and be quantitative in a way that hasn’t been possible in the past,” Paulovich said.

She is also hopeful that the APOLLO project and other ongoing research will bring doctors closer to being able to get patients the most effective drugs.

“It’s not going to solve all of the problems, but it’s one of the major steps that needs to be taken in order to get us closer to realizing the true promise of personalized oncology,” she said.

The Beau Biden Cancer Moonshot, created last year by President Obama and spearheaded by former Vice President Joe Biden, is focused on advancing cancer research at almost double the anticipated pace by organizing and funding research collaborations around the country.

Biden visited Fred Hutch last year to discuss the moonshot and the work being done at the institution, saying at the time, “our grandchildren will see changes in the next ten years that took 40 years to get to for us, and 75 and 100 years before that.”

He also emphasized the need to “reinvigorate the country with a sense of, ‘we can do anything.’”

The Moonshot project is named after Biden’s son, who passed away from brain cancer in 2015.

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