Strands of DNA CREDIT Dr Kate Patterson, Garvan Institute of Medical Research

‘We analysed the genomic profile of over one million cells from 1,000 people to identify a fingerprint linking genetic markers to diseases such as multiple sclerosis, rheumatoid arthritis, lupus, type 1 diabetes, spondylitis, inflammatory bowel disease, and Crohn’s disease,’ says Professor Joseph Powell, joint lead author at the Garvan Institute of Medical Research. ‘We were able to do this using single cell sequencing, a new technology that allows us to detect subtle changes in individual cells,’ he says.

The discovery could help individuals find tailored treatments that work for them and guide the development of new drugs.

The study by researchers in Sydney, Hobart, Melbourne, Brisbane and San Francisco helps us understand why some treatments work well in some patients, but not in others. It’s the largest study to date to link disease-causing genes to specific types of immune cells.

A trial is now underway in Sydney with Crohn’s disease patients to predict which treatments will work for specific patients.

‘Some autoimmune diseases can be notoriously difficult to treat,’ says Professor Powell.  

‘Because of our immune system’s complexity, and how vastly it varies between individuals, we don’t currently have a good understanding of why a treatment works well in some people but not in others,’ he says. 

The study links specific genes and immune cell types to an individual’s disease, including multiple sclerosis, rheumatoid arthritis, inflammatory bowel disease, type 1 diabetes and Crohn’s disease.

This means an individual’s unique genetic profile could be used to deliver treatments tailored to precisely tame their immune system.

‘Our data also provides a new avenue for narrowing down potential drug targets. The potential health and economic impacts of this research are enormous,’ says Professor Alex Hewitt, joint lead author and clinician-researcher at the University Of Tasmania’s Menzies Institute for Medical Research.

‘Most rare genetic diseases are like a major car accident in the body – they are generally easy to identify and locate where they occur in the genome. But immune diseases are often more like traffic congestion, where genetic changes that hold up traffic are harder to specifically pinpoint. This study has helped us identify the trouble spots,’ says Professor Hewitt.

‘The greatest insight from this work will be identification of therapeutic targets and defining sub-populations of immune disease, which can then refine clinical trials to assess drug effectiveness,’ he says.

Our bodies’ immune systems are designed to fight external threats, but autoimmune diseases occur when our immune systems take aim at our own healthy cells. They affect about one in 12 Australians, are incurable and require lifelong treatments to minimise the damage.

Often, patients will trial many different treatments before finding one that works for them.

‘Some medications may be very effective in only 15% of patients, so are not recommended as a first-line treatment,’ says Dr Seyhan Yazar, co-first author of the study.

‘We now have a way to link treatment response back to an individual’s immune genetics – and to potentially screen for that 15% of patients before a clinician even administers a treatment.’

The researchers say their data could lower the risks associated with developing new treatments.

‘Pharmaceutical companies may have hundreds of targets and have to make decisions about which they will take forward to Phase I clinical trials, knowing that 90% of potential drug candidates fail during clinical development,’ says Dr José Alquicira-Hernández, co-first author and researcher at the Garvan Institute.

‘Understanding which cell types are relevant for a particular disease is key for developing new drugs.’

A million cells reveal complexity and provide certainty

The study provides unique insights by looking at genes in individual immune cells on an unprecedented scale. It analysed the genomics of more than one million individual immune cells from around 1,000 healthy individuals, exploring 14 different types of immune cells in total.

This individual approach paints a far clearer picture than previous studies which analysed combined cells in a blood sample.

‘The problems with bulk RNA analysis is that we only observe an averaged signal. But there is vast variation in cell functions and cell types that allow the body to defend against attack,’ explains says Dr Yazar.

‘Average analysis doesn’t reflect what happens in the full variety of immune cells.’

Integrating into clinical trials

The findings have led to clinical trials.

‘We are working on a study of Crohn’s disease in collaboration with St George Hospital that will determine how a patient’s immune genotype affects their response to different treatments and are looking to establish new trials in a range of autoimmune diseases’ says Professor Powell.

‘It is a significant milestone of Garvan’s pioneering OneK1K study aimed at showing how genetics contribute to the risk of immune disease at a cellular level.’

A team of researchers led by Marc Veldhoen, Instituto de Medicina Molecular (iMM), Lisboa, have found that cellular stress enhances the activation of certain type of immune cells implicated in many chronic inflammatory conditions, increasing the risk of autoimmune diseases.

T cells, a type of white blood cell, can be tuned into different activation modes thereby tailoring immune responses to adequately deal with infections. However, some of these activation modes can particularly contribute to autoimmune diseases such as arthritis, diabetes and multiple sclerosis.

The Veldhoen lab has been studying T cell activation modes for many years and had already noticed that one particular activation status, termed Th17, is much more robust than other states leading researchers to hypothesize that these cells are more resistant to adverse conditions than other T cell counterparts.

By controlling external conditions such as osmotic pressure and sugar concentration in the culture medium as well as oxygen pressure, the team revealed that Th17 cells are preferentially generated under adverse conditions when compared to optimal conditions. Moreover, by using mouse models of autoimmunity Veldhoen and colleagues demonstrated that if cell stress was inhibited, lower numbers of Th17 cells were generated and the animals had reduced disease symptoms.

There has been an increasing focus from both academia and pharmaceutical companies over the past years on Th17 cells, since they are implicated in several chronic inflammatory conditions. In fact, studies interfering with the biology of these cells have shown promise for therapeutic applications in psoriasis and arthritis, for example.

These novel findings offer additional pharmacological targets to reduce cellular stress at sites of inflammation by reducing Th17 generation and preserving other T cell responses which may hold important clinical implications.

The ebb and flow of such autoimmune diseases as multiple sclerosis, lupus and rheumatoid arthritis has long been a perplexing mystery. But new findings from the Stanford University School of Medicine bring scientists closer to solving the puzzle, identifying a molecule that appears to play a central role in relapses.

The study, to be published in the Dec. 3 advance online edition of Nature Immunology, lays the groundwork for a way to determine when a relapse is about to occur, and could eventually lead to a treatment to prevent relapses. “Right now, there is no good blood test to evaluate when a person is going to have a flare-up,” said senior author Larry Steinman, MD, professor of neurology and neurological sciences. “If we had one, we might be able to give them prophylactic preventive medication.”

The current study had its genesis five years ago: In a paper published in 2001 in the journal Science, Steinman found that a protein called osteopontin was abundant in multiple sclerosis-affected brain tissue, but not in normal tissue. Since then, other groups have confirmed that osteopontin is elevated just prior to and during a relapse of the disease in M.S. patients.

Although the protein had been known to play a role in bone growth, it was unclear why it would be associated with multiple sclerosis, which results when the immune system attacks the protective myelin sheath surrounding nerve cells.

To explore this question, Eun Mi Hur, PhD, who was then a graduate student in Steinman’s lab, began using a mouse model of multiple sclerosis (experimental autoimmune encephalomyletis, or EAE) to investigate how osteopontin could cause these flare-ups. She and Steinman gave osteopontin to mice that had already experienced paralysis, similar to that of an M.S. patient, and found that the mice then experienced a relapse of the disease.

The researchers also found that the relapse would occur sometimes in an area of the brain other than the site of the original attack. For example, after receiving the osteopontin, some animals that had previously suffered paralysis became blind from a condition called optic neuritis. One feature of multiple sclerosis is that the flare-ups can affect different parts of the nervous system at different times.

“When I saw that all mice with EAE relapsed and died from the disease after about a month of osteopontin administration, I was surprised,” said Hur, the study’s first author who is now a postdoctoral scholar at Caltech. “I got a strong belief that a high level of osteopontin in patients’ blood and tissue is a major contributor of the relapse and progression of the disease.”

Through the mouse studies and molecular characterizations, Hur and Steinman showed that osteopontin – produced by immune cells and brain cells themselves – promotes the survival of the T cells that carry out the damaging attack on myelin; by increasing the number of these T cells, osteopontin increases their destructive potential. These results could be applicable to many other autoimmune diseases, including rheumatoid arthritis, type-1 diabetes and lupus.

Indeed, the effect of osteopontin may severely alter the way the immune system works. Normally, after the immune system does its job – eradicating a microbe, for instance – the response is then dialed down. If this didn’t happen, the immune response would go on indefinitely. Imagine a cold or an attack of poison oak that would last forever.

One of the ways that the immune response is muffled is that the activated T cells die in a process known as apoptosis. That is precisely what osteopontin seems to prevent. Osteopontin lets the T cells linger in the blood, ready to attack again. “We don’t know exactly what triggers that new attack but the cells certainly are around and ready to do it,” said Steinman. So scientists now face the challenge of figuring out how and why osteopontin is produced. “We’re back to the chicken-and-the-egg problem,” said Steinman. “We know the egg, so why did the chicken lay it” That is a trickier problem to work out.”

Even without knowing the answer to that question, there is one inviting practical use of their observations: Osteopontin could be used as a marker of an impending relapse. What’s more, if the protein could be blocked, it might thwart the relapse from ever occurring. Steinman’s lab is working to develop antibodies to inactivate the protein’s effect. “It’s still a long road between saying we want to do it and getting the antibodies, getting it approved by the FDA and getting it tested,” said Steinman, “but we are determined to do that.”

Still, Steinman offered a caveat. Researchers may find that blocking osteopontin has undesirable side effects. The protein may serve other purposes in addition to promoting survival of immune cells. It could also be vital to the body’s ability to produce myelin, a function that could cause severe problems if disrupted. “Like a lot of important biological molecules, osteopontin has a Janus-like quality – a bad side and a good side,” Steinman said. “We’re going to be extremely lucky if we give the antibody opposing osteopontin and derive just the good side: We stop the autoimmune attack but don’t interfere with the survival of other cells.”

Further study will determine whether thwarting osteopontin’s effect yields new types of treatments for autoimmune diseases, but regardless, it is likely to lead to discoveries in a host of areas. “I think osteopontin will turn out to be important in a lot of processes, spanning autoimmunity to stem cells,” said Steinman. “It’s probably going to turn out to be a very basic growth factor.”