Methods and apparatus are disclosed co-culturing stem cells with mononuclear cells and/or lymphocytes to modulate their function. The invention also discloses the use of stem cells to educate autoreactive immune cells as a mechanism to treat autoimmune diseases and immune disorder-related diseases, such as diabetes. In one aspect of the invention, bioreactors are disclosed for modulating lymphocytes and suppressing autoreactive T cells. The bioreactors can include a chamber having at least one positively charged and/or hydrophobic substrate surface, a population of stem cells attached to the substrate surface, an inlet conduit for introducing lymphocytes into the chamber, and an outlet conduit for extracting treated lymphocytes following co-culturing with the stem cells.