Autologous hematopoietic stem cell transplantation (HSCT) is based on the assumption that autoimmune diseases like systemic sclerosis occur when the white blood cells of the immune system attack the body. In this treatment, stem cells from the patient's blood are extracted and stored to preserve them. The patient's white blood cells are destroyed with cyclophosphamide and rabbit antibodies against the white blood cells. Then the stored blood is returned to the patient's bloodstream to reconstitute a healthy blood and immune system which will not attack the body. The results of a phase 3 trial, the Autologous Stem Cell Transplantation International Scleroderma (ASTIS) trial, with 156 patients were published in 2014. HSCT itself has a high treatment mortality, so in the first year, the survival of patients in the treatment group was lower than the placebo group, but at the end of 10 years, the survival in the treatment group was significantly higher. The authors concluded that HSCT could be effective, if limited to patients who were healthy enough to survive HSCT itself. Therefore, HSCT should be given early in the progression of the disease, before it does damage. Patients with heart disease, and patients who smoked cigarettes, were less likely to survive.   Another trial, the Stem Cell Transplant vs. Cyclophosphamide (SCOT) trial, is ongoing. 
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Through the first two years, the visual acuity remained about the same in the two groups ( results published in 2011). At seven years, visual acuity on average remained stable in the systemic group but declined about six letters in the implant group. The researchers found that implant-treated eyes had reactivations of uveitis after about five years, which coincided with a decline in visual acuity. The loss of vision in the implant group appears to have been due to increased damage in the retina and choroid (a tissue rich in blood vessels lying underneath the retina).