For those who pooh-pooh the impact that proteomics may have on biology and drug discovery, scientists at Caprion Pharmaceuticals may have a rebuttal. Last week in the journal Cell, researchers from Caprion and their collaborators published data supporting an earlier finding — obtained using the large scale identification of proteins by mass spectrometry — that provides a new explanation for how the body fights infectious diseases, and represents one of most significant examples to date of how proteomics can lead to new insights into biology, and by extension, disease.
Earlier this year, when groups from Cellzome and MDS Proteomics published side-by-side reports detailing their explorations of protein-protein interactions in yeast, researchers in the field held up the reports as evidence of the potential power of proteomics for understanding cellular circuitry in humans. The Cell paper, published in the July 12 issue, shows that Caprion’s organelle-centric approach to proteomics may hold similar promise for deciphering human biology.
In their study, Caprion scientists, joined by their collaborators at the University of Montreal, McGill University, and the National Institute for Allergies and Infectious Diseases in Hamilton, Mont., used electron microscopy to visualize fluorescently-tagged proteins, Western blotting, and other cell biology experiments to study the location and enrichment of certain proteins found in the phagosome, an organelle responsible for engulfing and eliminating foreign particles. They found that certain proteins from the endoplasmic reticulum (ER) turned up in the phagosome — a discovery that contradicts the textbook explanation for phagocytosis, or the process by which phagosomes form, said Michel Desjardins, a Caprion scientist and pathology and cell biology researcher at the University of Montreal.
Desjardins said he and his team initially made this discovery using Caprion’s proteomics technology, which the company terms CellCarta, and published the results in the Journal of Cell Biology in January, 2001. In that earlier paper, Desjardins and his colleagues identified over 140 proteins from 2D gels containing fractionated samples of phagosome organelles, and attempted to identify the proteins using Bruker MALDI-TOF and Micromass Q-TOF mass spectrometers.
“We were surprised to see that ER proteins were there,” he said. “Our first reflex was that [the sample] was contaminated, although there was not very much evidence [that was the case].”
So they went back to the bench to see if their initial findings had been too astounding to be true. Instead, these follow-up experiments in the Cell paper corroborated the earlier evidence obtained by the researchers using CellCarta. “We were able to demonstrate that the ER proteins were not in fact contaminants, but enriched in the phagosome,” Desjardins said.
In addition to challenging the accepted view of phagocytosis, Desjardins said the results may have implications for how to fight diseases such as salmonella, chlamydia, and tuberculosis, which researchers have associated with the phagosome. Because these pathogens are able to survive in the human body when approached by phagosomes, Desjardins and his colleagues hope their findings may lead to a way to drive the organisms toward more lethal tools of the immune system, such as neutrophils.
“The Cell paper indicates that [Caprion’s] CellCarta approach is going to lead to new understandings of complex biological systems,” said Desjardins. “If you make searches in the literature, you’ll realize that so far in the field of proteomics there’s not been any really outstanding contributions published in a journal like Cell.”
Desjardins isn’t the only researcher to see the results as important. Both Nature and Nature Cell Biology have included commentary on the paper in forthcoming issues, and Desjardins has been invited to present his results at the Fifth Siena Meeting on Functional Proteomics, to be held in Siena, Italy, in September.