PHOTO ESSAY: Scientists trying to unravel one of the body's biggest mysteries

A look inside some leading research labs shows how scientists-turned-detectives are painstakingly decoding the causes of autoimmune diseases and how to stop the immune system from attacking you instead of protecting you.

It’s a huge challenge. According to the latest count from the National Institutes of Health, there are about 140 autoimmune diseases that affect tens of millions of people.

Untangling them requires patience, perseverance – and sophisticated technology to even see the suspects. Researchers use laser-powered machines and brightly colored fluorescent dyes to distinguish unwanted cells from normal cells.

Take type 1 diabetes, caused when the cells in the pancreas that produce insulin are gradually destroyed by unwanted T cells. In a biomedical engineering lab at Johns Hopkins University, researchers examine mouse pancreatic cells on a computer screen. Red marks killer cells. In yellow are the “pacifier” cells that are supposed to dampen autoimmune reactions – but they are outnumbered.

Another type of immune cells, B cells, cause autoimmune diseases by producing antibodies that mistake healthy tissue for foreign invaders. At the NIH, Dr. Iago Pinal-Fernandez studies myositis, a poorly understood group of muscle-weakening diseases. His research shows that unwanted antibodies don’t just damage muscles by clinging to their surface. They can sneak into muscle cells and disrupt their normal functions in ways that can explain various symptoms.

“When I started, nothing was known about the type of autoimmune disease we were studying. Today we are finally able to tell patients, ‘You have this disease and here is the mechanism of the disease,'” he said.

In another NIH lab, Dr. Mariana Kaplan’s team is looking for the root causes of lupus and other autoimmune diseases – what drives the immune system crazy…