LAWRENCE — A new paper from the University of Kansas overturns the idea that a "risk gene" carried by millions of people worldwide influences production of Type 1 interferon, a workhorse of the immune system.
Humans with the PTPN22 R620W genetic risk variant have a higher chance of developing autoimmune diseases such as lupus or Type 1 diabetes.
"About 15% of North Americans of European ancestry have a mutation in this gene that puts them at higher risk for autoimmune diseases," said Robin Orozco, assistant professor of molecular biosciences at KU. "The gene is associated with almost every autoimmune disease."
Researchers have long sought to understand why, especially because the same risk gene seems to offer protection against some other diseases.
"With human studies and mouse models, we found that people or mice with this mutation are better able to fight off cancers as well as viral infections," Orozco said. "We started to look at type 1 interferons because they are the key antiviral response."
Type 1 interferons are described as "workhorses" of the immune system. A long-standing hypothesis — based on earlier mouse and cell studies — was that the PTPN22 mutation (called PEP in mice) influences interferon production.
"Over a decade ago, studies suggested that PTPN22 controls type 1 interferon production, and we wanted to follow up on that work," Orozco said.
The KU team used mouse models engineered with CRISPR-Cas9 to carry the PTPN22/PEP variant, comparing them with mice in which the gene was knocked out and with regular mice.
"Our first experiment aimed to prove to ourselves that we could recapitulate the published data," Orozco said. "The very first experiment in my lab was conducted by an undergraduate student, Jenna Barnes, who is now in an M.D.-Ph.D. program at Cincinnati Children's Hospital. She tested whether this gene actually affects interferon production, and it didn't."
Initially, the team thought a lab error might have caused the result.
"We repeated the experiments multiple times, with several people, and consistently found that the previous results could not be replicated," Orozco said.
The KU team then carefully examined the earlier study to determine why their results differed.
"We discovered that the mouse model used in the original study was not genetically clean," Orozco said. "The mice had additional mutations beyond the gene being studied. Using a cleaner CRISPR-Cas9–generated mouse model, we showed that the supposed effect on interferon production didn't exist. Our work recapitulated the old results using the original mice but revealed no difference with our improved model."
While knocking out PTPN22/PEP did not change interferon production, it did affect other cytokines associated with the immune system. Orozco said that while PTPN22/PEP in myeloid cells doesn't regulate type 1 interferons, it may play a role in other important immune signaling.
"The point of this paper is to clarify what PTPN22 is actually doing in immune cells, which is essential for understanding disease and potential treatments," Orozco said. "The findings correct the previous assumption that this gene regulates type 1 interferon production. Our work changes how researchers might think about PTPN22 in the context of viral infections, cancer and autoimmunity."
PTPN22/PEP's influence on the immune system is significant enough that medical researchers could explore compounds that interact with the gene. Orozco's lab will help lay the groundwork for those efforts.
"For drug discovery, we now have a clearer understanding of the gene before attempting to target it with small molecules," Orozco said. "We're collaborating with Johns Hopkins and Purdue University to explore a small-molecule inhibitor for PTPN22, with the goal of boosting immune responses against cancers such as melanoma and colorectal cancer. In our mouse model, knocking out the gene did not cause side effects in healthy, autoimmune-resistant mice, though it accelerates autoimmunity in genetically susceptible mice."
The scholarship was published in the journal ImmunoHorizons. Orozco and lead author Barnes were joined by graduate students Anam Fatima Shaikh, Alec Bevis and research technician Tammy Cockerham. The work was supported by the K-INBRE program, the Chemical Biology of Infectious Disease (CBID) Center of Biomedical Research Excellence (COBRE), the KU Medical Center Jewell Summer Scholars program, the Chemical Biology Training grant program, the KU Department of Molecular Biosciences and Office of Research, and the Undergraduate Research Awards program at KU.
