Whole-Exome Analysis of Autoimmune Lymphoproliferative Syndrome-like Diseases

ALPS is characterized by chronic lymphoproliferation in combination with autoimmunity; mutations of molecules involved in FAS-dependent pathways play causative roles in this syndrome. The hallmarks of ALPS are an elevated CD4/CD8 double-negative T (DNT) cell count and attenuated induction of apoptosis by FAS stimulation. Autoimmune thrombocytopenia and/or hemolytic anemia are common in cases of ALPS; the combination of autoimmune thrombocytopenia and hemolytic anemia is referred to as Evans syndrome. ALPS is diagnosed in 47% of patients who present with Evans syndrome. Some patients with ALPS-like syndromes harbor mutations in RAS or PRKCD.

In this study, we performed whole-exome analysis of undiagnosed patients exhibiting autoimmunity in combination with lymphoproliferation. Fifteen pediatric patients presenting with autoimmunity were enrolled in this study. Although not all of them fulfilled the diagnostic criteria of ALPS, most of them exhibited an ALPS-like phenotype, an autoimmune hematological disorder such as Evans syndrome, or immune thrombocytopenia with hepatosplenomegaly. Elevated counts of DNT cells among TCRαβ-positive cells were observed in some cases. All of the subjects screened negative for mutations in FAS, FASL, KRAS, and NRAS. These patients were subjected to whole-exome analysis, which revealed several mutations with known disease associations. One patient carried a mutation in CASP10, a causative gene for ALPS-CSAP (ALPS 2). This patient exhibited a typical ALPS phenotype with an elevated DNT cell count. In addition, we identified CTLA4 mutations in two patients, one of whom was described as ALPS type V (ALPS 5) and the other as CTLA4 haploinsufficiency with autoimmune infiltration (CHAI). A mutation in STAT3 was present in one patient. Dominant-negative mutations in the STAT3 gene result in hyper-IgE syndrome. Recently, an activating mutation of STAT3 was reported in infantile-onset multisystem autoimmune disease (ADMIO). It should be noted that an activating mutation of STAT3 results in a phenotype very similar to that of ALPS. Intriguingly, two autoinflammatory associated genes, PSTPIP1 and RNASEH2B were identified. Mutations in RNASEH2B causes Aicardi-Goutière syndrome (AGS), which phenotypically overlaps with SLE. Typical AGS develops as a results of biallelic mutations in causative genes. In this case, a heterozygous frame shift mutation was identified. Further evaluation is required to confirm whether this heterozygous frame shift mutation RNASEH2B really causes SLE or ALPS like symptoms. PSTPIP1 mutation causes pyogenic Arthritis, pyoderma gangrenosum and acne (PAPA) syndrome. The identified E250K mutation was one of the typical mutation in this disease. This patient exhibited SLE like symptom with hepatosplenomegaly without typical PAPA syndrome like symptoms, such as acne or pyoderma of the skin. Sequencing of the remaining patients yielded inconclusive results.

The classical ALPS diagnostic procedure is well designed and suitable for identification of FAS-dependent apoptotic dysregulation. However, the measurement of FAS-dependent apoptosis requires technical skill, and the data quality is therefore dependent on the investigator. Moreover, RAS-associated ALPS-like disease (RALD, ALPS 3) and ALPS 5 (CHAI) cannot be identified by conventional ALPS diagnostic procedures. Therefore, the methods for diagnostic classification of these diseases need to be updated. It is interesting that mutations of autoinflammatory associated genes are involved in ALPS or SLE like patients. Our results reveal that a comprehensive genomic approach is a powerful tool for the characterization of ALPS or ALPS-like diseases. Together with recent progress in genome analysis in the PID field, our analyses provide an updated list of genes for use in differential diagnosis of ALPS-like diseases. This update will facilitate convenient genomic approaches such as comprehensive targeted sequencing focusing on genes involved in ALPS or ALPS-like diseases. This approach can be directly applied in the clinic to yield diagnostic benefits.