Researchers, who describe the work as an "important breakthrough", found how to stop cells from attacking healthy body tissue.
Scotland has one of the with the highest rates of multiple sclerosis in the world, with about 10,000 people living with the incurable condition, which affects nerves in the brain and spinal cord, and causes problems with muscle movement, balance and vision.
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In the research, the Bristol University team discovered how cells convert from being aggressive to protecting against disease, rather than the body's immune system destroying its own tissue by mistake.
It is hoped the insight will lead to the widespread use of antigen-specific immunotherapy as treatment for many autoimmune disorders.
Other conditions that could be affected by the research include Type 1 diabetes, Graves' disease, which often affects the thyroid, and systemic lupus erythematosus, which can cause joint pains, skin rashes and tiredness.
Professor David Wraith, of the university, led the research. He said: "These findings have important implications for the many patients suffering from autoimmune conditions that are currently difficult to treat."
In the study, scientists were able to selectively target the cells that cause autoimmune disease by dampening down their aggression against the body's own tissue, while converting them into cells capable of protecting against disease.
This type of conversion has previously been applied to allergies, but its application to autoimmune disorders has only recently been appreciated.
The researchers have now revealed how the administration of fragments of the proteins that are normally the target for the attack leads to correction of the autoimmune response.
Their work also shows effective treatment can be achieved by gradually increasing the dose of antigenic fragment injected.
To analyse how this type of immunotherapy works, the scientists looked inside the immune cells themselves to see which genes and proteins were turned off by the treatment.
They found changes in gene expression that help explain how effective treatment leads to conversion of aggressor into protector cells.
The outcome is to reinstate self-tolerance, where an individual's immune system ignores its own tissues while remaining fully armed to protect against infection.
Researchers say that by specifically targeting the cells at fault, the immunotherapeutic approach avoids the need for immune suppressive drugs.
These drugs are often associated with side effects, such as infections, development of tumours and disruption of natural regulatory mechanisms.
The treatment approach is undergoing clinical development through biotechnology company Apitope, a spin-out from Bristol University.
Nick Rijke, of the MS Society, said: "This is a really interesting and encouraging study, and adds to our understanding of how scientists might be able to alter the way the immune system responds in people with MS.
"A previous trial of a similar therapy was unsuccessful in people with MS, but this latest study, although conducted in mice, offers new options for future clinical trials that one day could lead to a low risk treatment for people with the condition."