This project was originally based on our discovery that genetic mutations that affect programmed death, or apoptosis, of lymphocytes are responsible for the Autoimmune Lymphoproliferative Syndrome (ALPS). ALPS is a congenital disease causing loss of normal lymphocyte homeostasis manifested as swollen lymph glands and organs. This excess of lymphocytes leads to a pathological autoimmune attack on the patients own tissues. During the clinical investigations on ALPS, many patients have been referred to our program with other immunoregulatory and immunodeficiency syndromes for evaluation. Therefore we launched a clinical genomics program to identify the genetic causes of these diseases. In addition to NIH patients, we have also established clinical research centers in China, Turkey, and India, providing many patients to study at the cellular and genomic level. We recently discovered a very interesting, apparently de novo, mutation in the gene encoding a key signaling protein that provides insights into immune regulation in humans. Signal transducer and activator transcription (STAT) proteins are a family of transcription factors that regulate gene expression programs underlying key immunological processes. We have studied a patient with a unique heterozygous missense mutation in STAT5B, which generates a variant protein with defective intrinsic function and the ability to dominantly interfere with STAT5-driven transcriptional activity. Phenotypically, the patient presented with immune thrombocytopenia, lymphadenopathy, splenomegaly, aberrant antibody titers, granulocytosis and necrotizing granulomas associated with a B cell-intrinsic antibody class switch defect and a prominent accumulation of CD4+ T effector memory(TEM) cells. RNA sequencing showed a reduction in IL-2/STAT5-dependent transcriptional activity. In addition, ex vivo analysis of the memory T cell compartment revealed a selective defect in cytokine-driven, T cell receptor restimulation-induced cell death (RICD) within TEM cells, a finding we confirmed in animal models of STAT5 deficiency. Thus, we gained important insights from intensive immunological and biochemical investigations of this single patient that reveal the role of STAT5B as a central orchestrator of lymphocyte homeostasis and function in humans. Another interesting gene mutation was uncovered in the BACH2 transcriptional regulator. BACH2 is crucial for the normal immune protective gene programs of T and B lymphocytes and is itself regulated by an archetypal super-enhancer (SE). In genome-wide association studies, single nucleotide polymorphisms in the BACH2 locus are associated with several autoimmune diseases, underscoring its important role in immune regulation. We observed that BACH2 mutations that cause Mendelian monogenic primary immunodeficiency and autoimmunity due to heterozygous mutations that cause BACH2 haploinsufficiency. The patients we examined had lymphocyte-maturation abnormalities leading to low immunoglobulins, immunodeficiency and intestinal inflammation. Biochemically, we found that the mutations disrupted protein stability by interfering with homodimerization of BACH2 subunits or by causing severe protein aggregation. We discovered very similar lymphocyte abnormalities in Bach2-heterozygously deficient mice. In an effort to generalize our results, we examine genes regulated by SE and observed that genes associated with monogenic haploinsufficient diseases were greatly enriched for TFs and SE architecture. These studies reveal a new monogenic disorder caused by low gene dosage of BACH2 and unveil new insights into the role of SE architecture in Mendelian diseases of immunity. Importantly, we propose that heterozygous mutations that cause haploinsufficiency in SE-regulated genes, which can be common even in outbred populations such as the developed world, may have greater significance than previously recognized. We studied 10 patients, mostly coming from our center in Istanbul, Turkey, suffering from abdominal pain and diarrhea caused by early-onset protein-losing enteropathy (PLE) with lymphangiectasia, edema due to hypoproteinemia, malabsorption, and, less frequently, bowel inflammation, recurrent infections, and angiopathic thromboembolic disease. We identified autosomal recessive mutations leading to loss of protein expression in the gene encoding CD55/Decay accelerating factor. Patient T lymphocytes and CD55-deficient cell lines displayed abnormally increased deposition of complement factor C3d. Genetic reconstitution of CD55 prevented C3d deposition. Stimulation of anaphylatoxin receptors on patient T lymphocytes produced increased tumor necrosis factor alpha, which caused a decreased ratio of the anti-coagulatory protein thrombomodulin to the pro-coagulatory protein tissue factor. CD55 costimulation by CD97, and the contingent production of interleukin-10, was defective in patient T lymphocytes. Hence, CD55 deficiency with hyperactivation of complement, angiopathic thrombosis, and PLE (CHAPLE) disease is caused by abnormal complement deposition due to autosomal recessive loss-of-function (LOF) mutations in the CD55 gene. Interestingly, Tom Waldmann of NCI studying patients in the NIH clinical center in the 1960s had first attributed protein-losing enteropathy to primary intestinal lymphangiectasis and, some 50 years later, our findings provide a genetic etiology for this disease. Moreover, our results suggest that eculizumab (Soliris, Alexion), an FDA-approved, complement-inhibiting therapeutic may benefit these patients. A group in Israel identified a single inbred family and has shown that disease in 3 affected members was greatly ameliorated. In summary, this project achieves precision medicine for immunological diseases by gene discovery that guides the development of new targeted therapies.