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First Human Cell Secretome Published

06/07/2012
Megan Scudellari

A whopping 15% of the proteins encoded by the human genome contribute to cell secretion.

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For almost 20 years, Jeremy Simpson, Professor of Cell Biology at University College Dublin in Ireland, has studied secretion, the fundamental process by which cells move materials—hormones, enzymes, signaling molecules, and more—out of the cell.

During most of that time, “we only ever chipped away at finding odd molecules here or there,” said Simpson. But in the last five years, the technology became available to examine cell secretion in a truly systematic way. Two genome-wide studies in Drosophila, in 2006 and 2010, identified numerous secretion genes, but approximately 40% of these genes had no equivalent in the human genome, leaving the human secretome largely a mystery (1, 2). So, Simpson and colleagues set out to perform the first genome-wide analysis of secretion in human cells.

Human cells treated with small interfering RNAs (siRNA) and immunostained for two markers of the early secretory pathway: the COPI vesicular coat complex and the Golgi apparatus. In siRNA-treated cells, both complexes become fragmented. Source: Jeremy Simpson, UCD





The results of that analysis, more than five years in the making, are finally here. Published online June 3 in Nature Cell Biology, Simpson and colleagues systematically knocked down each of the 22,000 genes in the human genome using RNA interference (RNAi) screens, and observed how the loss of each gene affected the secretion of a fluorescently labeled viral protein (3). They examined more than 8 million individual cells from more than 700,000 microscopy images to identify 3,629 proteins—15% of the human genome—that appear to be involved in secretion. With additional experiments, they narrowed the list to 554 proteins that had the strongest effects on secretion.

The team then analyzed those 554 proteins to see which play a role in the early steps in secretion, which occurs at the endoplasmic reticulum (ER), where secretory proteins are synthesized, and the Golgi complex, which modifies those proteins. By fluorescently labeling the proteins and immunostaining the ER, Golgi, and transport carriers that move between the two compartments, the researchers identified a subset of 143 proteins that appear to be involved in the early stages of secretion.

“That implies the other approximately 350 maybe act later in the pathway,” said Simpson. Of the proteins identified in the screen, some were known to be involved in secretion, others were proteins not previously linked with secretion, and still others were molecules that had never before been characterized. “Those are the most interesting ones,” said Simpson, “but they’re also the most challenging.”

A total of 59 known core secretion machinery proteins were identified in the screen, but surprisingly the screen also identified many proteins involved in signaling from the cell surface and the organization of the cytoskeleton. This implies that human cells have a sophisticated signaling and feedback system between the ER and Golgi and the cell surface, allowing them to modulate secretory activity based on the external environment, said Simpson. “It’s something people have talked about before, but it was always a bit vague. This gives us a better handle on that,” he said.

References

1. Bard, F., et al. 2006. Functional genomics reveals genes involved in protein secretion and Golgi organization. Nature 439(7076):604-7.

2. Wendler, F., et al. 2010. A genome-wide RNA interference screen identifies two novel components of the metazoan secretory pathway. EMBO J 29(2):304-14.

3. Simpson, J.C., et al. 2012. Genome-wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway. Nat Cell Biol. doi: 10.1038/ncb2510.

Keywords:  cell biology