Many patients with autoimmune disease have immune system defects. For instance, those with celiac disease commonly have low levels of immunoglobulin A and Graves' disease patients often have low levels of T-suppressor cells, the cells that normally prevent autoimmune diseases from developing.

In recent years newly discovered genetic defects include cytotoxic T-lymphocyte-associated antigen 4 or caspase-9 deficiency causing common variable immunodeficiency (CVID). Various CVID phenotypes have been associated with immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome and autoimmune lymphoproliferative syndrome. Here activating signaling defects lead to a loss of immune system tolerance.  CVID is the most prevalent symptomatic primary immunodeficiency disorder. Estimated prevalence is one in 25,000-50,000. CVID id characterized by decreased serum immunoglobulins (IgG, IgA, IgM), poor specific antibody production when vaccines are administered, and recurrent bacterial infections, usually respiratory and gastrointestinal infections. 

About 29% of individuals with CVID go on to develop an autoimmune disorder, primarily autoimmune cytopenia, organ-specific autoimmune disorders including thyroid disease, autoimmune enteropathy, which can mimic inflammatory bowel or celiac disease, vitiligo, arthritic disorders and others.  In these cases, treating the underlying immune defect, is essential for successful autoimmune disease treatment. While addressing the immune system (by strengthening not stimulating it) is important for all autoimmune disorders, specific treatment protocols may be required for patients with a co-existing CVID.

Resource: Annic van de Ven and Klaus Warnatz. "The Autoimmune Conundrum in Common Variable Immunodeficiency Disorders." Current Opinions in Allergy and Clinical Immunology 2015:15(6): 514-24.