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Northwestern-Perthera Cancer Pact Indicates Growing Practicality, Potential of Clinical Proteomics

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NEW YORK (GenomeWeb) – Though still wrestling with technical challenges and issues like reproducibility, proteomics is poised in coming years to make a clinical impact similar to that of next-generation sequencing, Francis Giles, associate director for Translational Medicine and Developmental Therapeutics at Northwesten University's Lurie Cancer Center, told ProteoMonitor this week.

Discussing the alliance announced last week between Northwestern and personalized cancer therapy firm Perthera, Giles said that proteomics has matured to the point at which clinicians should begin pursuing integration of such data with data from more established omics methods like NGS.

The Northwestern-Perthera venture aims to assess the utility of combining NGS, proteomic, and phosphoproteomic data as a means of guiding therapy in cancer patients.

Giles noted that he and his Lurie colleagues have done considerable work using NGS to profile patient tumors and guide drug treatment. Now, he said, they are looking to integrate proteomic data, as well.

"We think it's time," he said. "Proteomics seems to us to kind of be where NGS was maybe two years ago. We're still struggling with reproducibility; we're still struggling with all sorts of technical issues; but they are being solved."

"We are seeing much more activity, more money, effort, and resources being put into understanding and analyzing the proteomics of cancer," he said, adding that, "functionally, we are increasingly convinced that proteomic data will be a key next step in personalized medicine."

Founded in 2013 by George Mason University researcher Emanuel Petricoin and venture capitalist Dendy Young, Perthera focuses on facilitating genomic and proteomic analyses of patient tumors. According to Young, the Northwestern agreement offers the company the chance to collect data on and build the case for the sort of integrated molecular analyses it offers.

"The opportunity here is to really demonstrate that multi-omic analysis can add real value to patients," he told ProteoMonitor, noting that "there are a lot of skeptics out there, as there should be."

Since its launch, the McLean, Va.-based firm has obtained genomic and proteomic tumor analyses for roughly 160 patients, Young said. The company is also in the middle of a collaboration with the Pancreatic Cancer Action Network to analyze around 1,000 pancreatic cancer patients.

Partnering with Northwestern on analysis of patients at the Lurie Center, he noted, will give Perthera the opportunity to further expand its pool of data, allowing it to collect information useful to its analyses as well as to potentially demonstrate in a larger cohort the validity of its approach.
"It is going to add a lot of credibility and volume to our database," Young said. "[Our] system allows us to compare what we see in a particular patient's cell structure with everything we've seen before, and we believe that as the number [of patients] rises into the thousands, we'll be able to see some [trends]. We'll be able to say, for instance, 'This patient has the same setup as this patient we saw a year ago, and this is what we recommended, and should we do the same thing now?' Or we can say, 'There is a new drug that targets this structure, and we think that new drug would be a better choice for this patient.'"

Perthera does not perform the molecular analyses itself, but, rather, acts as a concierge service, providing its customers access to molecular profiling assays and then using its Perthera Expert Oncology informatics technology to help generate personalized treatment recommendations. Currently, the company offers patients exome sequencing from Foundation Medicine; genomic, proteomic, and immunohistochemical profiling from Caris Life Sciences; and phosphoproteomic profiling from Theranostics Health, where Petricoin is a co-founder and chairman of the scientific advisory board.

As Petricoin explained to ProteoMonitor in an interview last year Perthera is "a gap-filler" for handling the many steps involved in obtaining and sending out patient tumor samples to molecular profiling firms and returning assay results.

"All of the things you have to do – organize the tumor biopsy, have the tumor sent out to the various companies, get the data back, aggregate that data, bank the tumor – there's really no infrastructure in place for that in the community setting," he said. This, he noted, is despite the fact that roughly 95 percent of tumors are treated in the community setting.

As Young noted, however, while there have been some studies evaluating the effectiveness of multi-omic profiling for guiding cancer therapy – for instance, the Side-Out Foundation's ongoing breast cancer trials -- there is still relatively little data on such approaches.

"You don't prove something with one trial. You have to do multiple trials to do that," he said. "Northwestern wants to run its own trials, and we are very happy to work with them to support that process."

While the areas of focus remain to be determined, the collaboration will likely look at women's cancers like breast, ovarian, and endometrial as well as pediatric cancers, Gilles said.

He noted, as well, that the university is looking to partner with firms beyond Perthera for proteomics work and that, while the proteomic approaches offered through Perthera are all antibody-based, Lurie researchers are also working to integrate mass spec-based proteomics data for guiding cancer treatment.

"Our focus is on how you integrate the data to optimize the therapy," he said. "We have no investment or bias as to the techniques for either the NGS or the proteomics or the phosphoproteomics."

Mass spec-based clinical proteomics "does lag behind [antibody-based approaches]," Gilles said, "but the question is how fast can it catch up? And that is a matter of investment. I don't expect it to remain an antibody-dominated technique for much longer."

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