Thymus cells making AIRE (green) that educate the surrounding developing T cells (red).CREDIT WEHI
WEHI researchers have identified an enzyme in the thymus that is essential for immune T cells to correctly identify threats, safeguarding them from going rogue and attacking healthy tissue in the body.
The thymus is an important organ where immune T cells learn to fight infection. The new findings revealed that the enzyme KAT7 is necessary to activate thousands of genes required for ‘training’ immune T cells not to attack healthy tissue. Without proper training, immune T cells are at risk of sabotaging the immune system which could lead to autoimmune conditions such as Type 1 diabetes, or multiple sclerosis.
Published in Science Immunology, the research paves the way for potential treatments to target KAT7, which could modify the training of immune T cells as needed. Such treatments could be used to either restrain immune T cells from drivingautoimmune conditions, or to supercharge immune T cells to better fight diseases such as cancer.
The research was led by former WEHI PhD student Dr Melanie Heinlein, along with Associate Professor Tim Thomas and Associate Professor Daniel Gray from WEHI, in collaboration with researchers at Monash University and the Weizmann Institute of Science in Israel.
A ‘preview’ of threats
The thymus is like a ‘boot camp’ where immune T cells are trained to identify and fight pathogens, and taught not to attack healthy organs. As part of this preparation, immune T cells are shown a ‘preview’ of all the various components of healthy tissues they could encounter once they exit the thymus.
While it was previously known that the Autoimmune Regulator (AIRE) protein activated the thousands of genes needed for this preview, it was unclear how AIRE knew which genes it needed to ‘switch on’, until now.
Dr Melanie Heinlein said the new findings revealed that the enzyme KAT7 was crucial for determining which genes AIRE needed to activate for immune T cells to be properly trained.
“Like a training coordinator, KAT7 directs AIRE to the thousands of genes that must be activated for the ‘boot camp’ to run smoothly. KAT7 does this by tagging the genes that AIRE needs to ‘switch on’ for the preview of the body’s proteins to work. When all goes to plan, immune T cells are trained not to fight any normal tissues they could encounter in the body, ensuring they do not cause autoimmune disease,” she said.
Importance of KAT7
Associate Professor Tim Thomas said KAT7’s crucial role in keeping immune T cells to task was made clear when the researchers used a new drug to block its function.
“We showed how a KAT7 inhibitor, developed in collaboration with Jonathan Baell at Monash University, was able to stop AIRE from switching on the genes needed to properly train immune T cells. Stopping this process sent the immune system into overdrive, leading to immune T cells going rogue and causing a range of autoimmune conditions in pre-clinical models. This shows a clear link between KAT7 and AIRE in maintaining immune tolerance,” he said.
“This has been a wonderful team effort. The highly collaborative study was made possible with expertise from across WEHI’s Flow Cytometry Laboratory, Genomics Facility, and the Centre for Dynamic Imaging, along with colleagues from Monash University and the Weizmann Institute of Science in Israel.”
Exciting treatment potential
Associate Professor Daniel Gray said the discovery could lead to new treatments for restraining immune T cells in order to prevent autoimmune conditions, or for supercharging immune T cells to fight disease.
“Our research shows KAT7 could be targeted to modify the training of immune T cells so they can either be stopped from causing autoimmunity, or boosted to fight disease.
“Potential applications of this knowledge include organ-specific autoimmune diseases such as Type 1 diabetes and multiple sclerosis, as well as cancer immunotherapy. In the latter scenario, the immune system could be supercharged to combat cancer by blocking KAT7 in the thymus,” he said.
Tet2/3-deficient B cells are activated by self-antigen and express exaggerated amount of CD86. Then those B cells stimulate autoreactive CD4<sup>+</sup> T cells, resulting in autoimmune response. CREDIT Osaka University
Our immune system is supposed to protect us from external microbial invaders, but sometimes it turns its efforts inward, potentially resulting in autoimmune diseases. In a new study, researchers from Osaka University discovered how reversible modifications to our DNA by certain proteins protect us from autoimmune diseases and, conversely, how the absence of these proteins paves the way to autoimmunity.
DNA contains all information that cells in our body need to function by providing specific codes to produce specific proteins. Nonetheless, not all parts of DNA are accessible in all cells at all times. The regulated production of proteins ensures that different cells and organs can be developed from the same DNA code. An important regulatory mechanism is the reversible addition (methylation) or removal (demethylation) of chemical bonds, so-called methyl groups, to segments of DNA. This modifies the readout of said DNA segment. Proteins of the ten-eleven translocation (Tet) family are known DNA demethylases that decrease the production of certain proteins in immune cells. How Tet proteins play into the development of autoimmune diseases has remained unknown—until now.
“Epigenetics deals with how reversible changes in DNA affect gene activity and protein expression,” says corresponding author of the study Tomohiro Kurosaki. “Disrupting this machinery can have dramatic effects on cellular function. The goal of our study was to understand how epigenetic control in a specific type of immune cells, called B cells, affects the development of autoimmune diseases.”
To achieve their goal, the researchers developed a novel mouse line in which B cells did not produce the epigenetic regulator proteins Tet2 and Tet3. They found that these mice developed a mild form of systemic lupus erythematosus, an autoimmune disease that can affect the joints, skin, kidneys and other organs, and for which there is currently no curative treatment. Similar to human patients, the mice showed increased serum levels of autoantibodies and damage to their kidneys, lungs and liver.
“These findings suggest that Tet2 and Tet3, as well as proteins whose expression is regulated by Tet2 and Tet3, might play a fundamental role in the development of systemic lupus erythematosus,” says lead author of the study Shinya Tanaka. “We wanted to gain a deeper molecular understanding of the mechanism behind the effects of Tet2 and Tet3 on the immune system.”
The researchers next investigated a different type of immune cell, called T cells, which often interact with B cells, and found that T cells were excessively activated in the Tet2/Tet3 knockout mice. By examining the molecular interaction between B and T cells closer, the researchers found that the protein CD86 was produced at higher levels in B cells of Tet2/Tet3 knockout mice, leading to aberrant T cell activation and autoimmunity.
“These are striking results that show how Tet proteins suppress autoimmune diseases by inactivating B cells and thus ultimately preventing them from attacking our bodies,” says Kurosaki. “Our findings provide new insights into the contribution of epigenetics to the development of autoimmune disease. Regulating Tet proteins and their downstream effectors could be a novel treatment for autoimmune diseases.”
Flares happen. We do everything we can to prevent them and to understand why they occur. But sometimes they just happen. This is true regardless of the inflammatory or autoimmune disease: lupus, arthritis, fibromyalgia, vasculitis and all the others. As frustrating as they can be, there are things you can do to maneuver your way through them with care and grace.
Researchers discovered that in patients with cryoglobulinemic vasculitis, antibodies in the blood aggregate at colder temperatures closer to the skin and also in the kidneys, nerves, and other organs, damaging blood vessels. CREDIT Dr Ofir Shein-Lumbroso
There are more than 100 different autoimmune diseases. But what unites them all is that they arise from an individual’s own cells – rare and mysterious immune cells that target not external viruses and bacteria but the body’s own healthy organs and tissues.
For the first time, a team led by researchers at the Garvan Institute of Medical Research have pinpointed individual cells that cause autoimmune disease from patient samples. They also uncovered how these cells ‘go rogue’ by evading checkpoints that normally stop immune cells from targeting the body’s own tissues.
The findings could have significant implications for the diagnosis and treatment of autoimmune disease, which affects one in eight individuals in Australia.
“Current treatments for autoimmune disease address only the symptoms, but not the cause. To make more targeted treatments that address disease development and progression, we first need to understand the cause,” says Professor Chris Goodnow, co-senior author of the published work, Executive Director of the Garvan Institute and Director of the UNSW Sydney Cellular Genomics Futures Institute.
“We have developed a technique that allows us to look directly at the cells that cause autoimmune disease – it’s as though we’re looking through a new microscope lens for the first time, learning more about autoimmune disease than was ever possible before.”
The findings, published in the journal Cell today, are part of the visionary Hope Research program.
(L-R) Dr Mandeep Singh, Professor Chris Goodnow, Dr Joanne Reed CREDIT Garvan Institute
Tracing autoimmune disease to its origins
Because ‘rogue’ immune cells are so rare in a blood sample – less than one in 400 cells – studying them has been a challenge. Analysis to date has at best revealed ‘averages’ of the vast mix of cells in a patient’s sample, says Dr Mandeep Singh, first author of the published paper.
“Using cellular genomics, we developed a method to ‘zoom in’ on these disease-causing immune cells in the blood samples of four patients with cryoglobulinemic vasculitis – a severe inflammation of the blood vessels,” says Dr Singh.
By first separating individual cells, and then separating their genetic material, the researchers isolated immune cells that produced ‘rheumatoid factors’ – antibody proteins that target healthy tissues in the body and are associated with the most common autoimmune diseases, including rheumatoid arthritis.
Once isolated, the researchers then analysed the DNA and messenger RNA of each of these ‘rogue’ cells, scanning more than a million positions in the genome to identify DNA variants that may be at the root of disease.
The evolution of autoimmune disease
Through their analysis, the researchers discovered that the disease-causing immune cells of the vasculitis patients had accumulated a number of mutations before they produced the damaging rheumatoid factors.
“We identified step-wise genetic changes in the cells at the root of an autoimmune disease for the first time, tracing an ‘evolutionary tree’ of how normal immune cells develop into disease-causing cells,” says co-senior author Dr Joanne Reed, who heads the Rheumatology and Autoimmunity Group at the Garvan Institute.
Remarkably, the researchers found that some of the first gene mutations that occurred in these rogue cells were known to drive lymphomas (cancerous immune cells).
“We uncovered ‘lymphoma driver mutations’, including a variant of the CARD11 gene, which allowed the rogue immune cells to evade immune tolerance checkpoints and multiply unchecked,” explains Professor Goodnow, who first hypothesised that disease-causing autoimmune cells employ this cancer tactic in 2007.
Further, the researchers found that cells with the lymphoma driver mutations accumulated further mutations that caused the rheumatoid factors they produced to aggregate, or ‘clump together’, at lower temperatures.
“This explains the patients’ cryoglobulinemic vasculitis, a severe condition that develops in some people with Sjögren’s syndrome, systemic lupus, rheumatoid arthritis, or hepatitis C virus infection. In these individuals, rheumatoid factors in the blood aggregate at colder temperatures closer to the skin and also in the kidneys, nerves, and other organs, which damages blood vessels and often proves very difficult to treat,” says Dr Reed.
New hope for personalised diagnosis and treatments
Not only have the research findings uncovered the root cause of an autoimmune disease – the ability to identify and investigate specific immune cells at such resolution has vast potential for future treatments to target the cause of all autoimmune diseases.
“In our study, we uncovered specific mutations that mark early stages of autoimmune disease. If we can diagnose a patient at these stages, it may be possible to combine our knowledge of these mutations with new targeted treatments for lymphoma to intervene in disease progression or to track how well a patient is responding to treatments,” says Dr Reed.
The researchers are now planning follow-up studies to investigate mutations of autoimmune cells in a range of other diseases, including lupus, celiac disease and type 1 diabetes.
“Identifying these rogue immune cells is a significant step forward for how we study autoimmune disease – and crucially the first step to finding ways to eliminate them from the body entirely,” says Professor Goodnow.