Ok , so you did all the analyses for autoimmune diseases ( anti-dsDNA, anti-Sm, Sjogren's sydrome antigens(SSA, SSB), Scl-70 antibodies, anti-centromere, anti-histone, and anti-RN, RF, cardiolipin, etc etc......, ) so you must look to your thyroid. My thyroid antibodies (TPO) were in part responsible for my ANA's, first my TPO antibodies were more then 1000 and ANA's 1:815, later TPO were 1:800 and ANA's 1:320......., Have you done FNA of your thyroid cysts?