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Sandra Pankow: The Cystic Fibrosis Interactome

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Recommended by: John Yates, Scripps Research Institute

With the amount of time Scripps Research Institute scientist Sandra Pankow spent around proteomics, it was bound to eventually rub off.

Pankow didn't do proteomics during her PhD studies at the Swiss Federal Institute of Technology Zurich, but her lab was right next to that of Ruedi Aebersold. Likewise, during a stint at Harvard University, Pankow's husband, fellow Scripps researcher Casimir Bamberger, worked next door to phosphoproteomics expert Steven Gygi, giving Pankow another high profile, if indirect, taste of the field.

Such contact, she says, showed her the sort of work proteomics could make possible. "I thought, 'Wow, that's the right technology to drive biological discovery forward!'" she says.

And so Pankow moved to John Yates' proteomics lab at Scripps, where she is currently a research associate studying protein-protein interactions involved in cystic fibrosis.

"I'm interested in trying to understand genetic diseases from a systems biology point of view," she says. "I've found that proteomics is the ideal tool for this because it gives the researcher the possibility to investigate thousands of proteins at the same time rather than just having to guess which one or two you should look at."

During her time in the Yates lab, Pankow has worked on developing a new technique for large-scale profiling of protein-protein interactions called co-purifying protein identification technology, or CoPIT. The method uses co-purification of proteins followed by mass spectrometry analysis and bioinformatic processing to identify not just primary protein-protein interactions, but second-degree and third-degree interactors as well.

With it, Pankow says, "we've reached about 30-fold to 100-fold higher sensitivity than previous methods. We're now able to profile an interactome to near completeness."

Paper of note

Using the method, Pankow has been studying interactome changes associated with mutations to the CFTR gene linked to cystic fibrosis. She and her colleagues have finished a paper detailing this work that, she says, they plan to submit for publication.

"It took a lot of time to develop [the techniques] in that paper – the experimental part, the statistical analysis, the computational part," Pankow says, noting that she expects this will be her most significant publication to date.

Looking ahead

She says one thing interactome studies would benefit from is greater multiplexing ability. "One drawback of the current technology is that you can only analyze one sample at a time," she says. "What I would love to see would be the ability to parallelize — to be able to acquire data on 96 samples at a time, for example."

Pankow also notes that improving mass spec technology will mean advances for the field. "When I started it was the norm to identify 2,000 or 3,000 proteins from whole cell lysate," she says. "Now it's up to about 5,000 or 6,000."

And the Nobel goes to…

As for what she'd hope to win the Nobel Prize for, Pankow says she is "hoping to help find a cure for cystic fibrosis, certainly."

"We can show that the disease is the consequence of the derailment of whole network of proteins involved in processing the CFTR protein," she adds. "And we would like to see our results being used as a basis to try to find new therapies."

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