Scripps Research scientists uncover unexpected role for two proteins as immune system regulators

The curious case of two proteins linked to Alzheimer’s disease, rheumatoid arthritis and system sclerosis.

August 13, 2018

An unexpected discovery in two disease-linked proteins could shed light on human immune system disorders, including a rare and often fatal childhood disease called hemophagocytic lymphohistiocytosis (HLH).

The research, published today in the journal Nature Immunology, shows that these proteins, called PLD3 and PLD4, play an important role in how the immune system detects and responds to infections.

“In particular, they play a role in how the immune system responds when foreign DNA, such as that from viruses or bacteria, is present. That was unexpected and completely unknown,” says Amanda Gavin, PhD, assistant professor at Scripps Research and one of the study’s first authors.  

The researchers had long suspected that PLD3 and PLD4 played a role in disease, but they didn’t know exactly how. In earlier studies, mutations in the genes encoding these proteins had been linked to Alzheimer’s disease (in the case of PLD3) and the autoimmune disorders rheumatoid arthritis and system sclerosis (in the case of PLD4). This led researchers to believe that they were important proteins to study further.

The PL in the name of these proteins stands for phospholipase, a kind of protein that degrades lipids. The proteins PLD1 and PLD2 carry out this task, and PLD3 and PLD4 were expected to have similar jobs because a part of their molecular structures looks very similar.

It turns out that structural similarity was a red herring.

“It took us a long time to work out the enzymatic activity of these proteins because we were looking in the wrong place,” Gavin explains. “We were very surprised to learn that these proteins are actually enzymes that degrade DNA.”

One of the best ways to determine what proteins do is to knock out their genes. In the absence of normally functioning proteins, scientists can start to investigate their roles. In the current study, the investigators made mice with nonfunctioning versions of both PLD3 and PLD4. They found the mice had defective livers and high levels of inflammation throughout their bodies—much like children diagnosed with HLH. They died at a very young age.

Further analysis revealed what was causing these symptoms. Immune cells called dendritic cells were detecting the mice’s own DNA as foreign—and calling in the troops to defend against it. Follow-up experiments revealed that the normal role of PLD3 and PLD4 is to degrade DNA and prevent this autoimmune reaction from happening.

Although the researchers were not able to reproduce Alzheimer’s, rheumatoid arthritis, or system sclerosis in the mice, “it still makes sense,” Gavin says, “because these diseases are known to have important contributions from the immune system.”

While the condition observed in the mice resembled HLH in children, the researchers don’t yet know if PLD3 and PLD4 are involved in that disease in people. This is something they plan to investigate. If it turns out the two proteins do play a role, they could use the mice to begin to screen for drugs that may be effective. 

In addition, they plan to look at other ways that these proteins help the immune system detect DNA, and what happens when this process goes wrong. It’s possible the findings may eventually contribute to new approaches in cancer immunotherapy and in the treatment of a range of autoimmune disorders.

Other authors of the study, “PLD3 and PLD4 are single stranded acid exonucleases that regulate endosomal nucleic acid sensing,” were David Nemazee, Deli Huang, Christoph Huber, Annica Mårtensson, Virginie Tardif, Patrick D. Skog, Tanya R. Blane, Therese C. Thinnes, Phoebe Kimm, Luc Teyton, Brian R. Lawson, Alessandro Zarpellon, John Teijaro, Juan Carlos de la Torre and Benjamin Cravatt of Scripps Research; Kent Osborn, Hayley S. Chong, Farnaz Kargaran, Armen Zeitjian, Rachel L. Sielski and Megan Briggs of the University of California, San Diego; Sebastian R. Schulz of the University of Erlangen-Nürnberg in Germany; Ee Shan Pang and Meredith O'Keeffe of Monash University in Australia; Hubertus Hochrein of Bavarian Nordic GmbH in Germany; and Markus Damme of Christian-Albrechts-Universität in Germany.

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