Identification of disease-causing genetic variants in patients with severe early-onset immunological disorders: a whole-exome sequencing approach

Abstract

This work focuses on the identification of disease-causing genetic variants in paediatric patients with primary immunodeficiency (PID) and/or autoimmune/autoinflammatory disease. Although paediatric immune pathology is rare, these disorders are associated with a high morbidity and mortality and decreased quality of life. Treatment is often accompanied with serious side-effects and can hold risks on its own. Understanding the genetic cause of paediatric immune pathologies is critical for the diagnosis and correct treatment of these patients, and for the development of new therapeutics. While common disorders are thought to have a complex multifactorial causation, severe early-onset diseases are more likely to be monogenic making them good candidates for genetic studies. Although monogenic diseases make up only a small fraction of immunological disorders, they provide insight into mechanistic pathways that are likely to contribute to common forms of disease when less deleterious variants are inherited. Additionally, genetics studies on patients with severe early-onset immune pathologies can increase our understanding of the physiology and functioning of the healthy immune system. To clarify the contribution of novel genes in severe immunological disorders, the following methodology is used: 1) identification of candidate genetic variants through the use of whole-exome sequencing, 2) detailed assessment of the peripheral immune system in order to gain insight in disease mechanisms and pathways and 3) verification of the role of an identified candidate genetic variant in disease pathogenesis by developing functional tests on a case-by-case basis. This approach was successfully used to identify disease-causing variants in three different genes responsible for severe early-onset immune pathology in four unrelated families with very different clinical presentations. We identified a de novo gain-of-function mutation in IFIH1 in a 16-year-old girl with severe early-onset and refractory systemic lupus erythematosus (SLE), IgA-deficiency and mild lower limb spasticity without neuroradiological manifestations. The same missense mutation was recently found in patients with Aicardi-Goutières syndrome (AGS), a rare neuroimmunological disorder associated with elevated levels of type I interferon (IFN) and a severely debilitating encephalopathy, as well as in two asymptomatic family members. IFIH1 detects viral RNA and induces production of type I IFN. These findings indicate that the clinical phenotype associated with IFIH1 gain-of-function mutations can range from asymptomatic to a severe inflammatory encephalopathy to a prototypic systemic autoimmune disease. We also identified recessive loss-of-function mutations in CECR1, encoding adenosine deaminase 2 (ADA2), in a 9-year-old boy with Castleman’s-like disease and in two siblings (< 5 years old) with combined immunodeficiency (CID), lymphoproliferation, autoimmunity and vasculopathy. Recently, recessive loss-of-function mutations in CECR1 have been found in patient with systemic inflammation, systemic vasculopathy in the form of early-onset recurrent stroke, livedoid rash or vasculitis, hepatosplenomegaly, hypogammaglobulinemia and lymphopenia. Absence of ADA2 plasma activity was demonstrated and an important IL-6 signature was found in all three patients. In the patient with Castleman’s disease treatment with anti-IL-6 Receptor Antibody (tocilizumab) resulted in a rapid, complete, and persistent suppression of clinical features and laboratory abnormalities. This result indicates that ADA2 deficiency could be a cause of IL-6–mediated lymphoproliferation and systemic inflammation and should be investigated as a cause of Castleman's disease. Allogeneic hematopoietic stem cell transplantation (HSCT) of the oldest sibling with CID was successful both in rescuing the immunologic phenotype and in preventing further vascular disease, possibly through the observed restauration of ADA2 plasma activity. These findings suggest that the diagnosis of ADA2-deficiency should also be considered in patients with systemic inflammation without vasculopathy, or in patients with an undiagnosed PID characterized by lymphoproliferation and autoimmunity, even in the absence of overt vasculopathy or inflammation. Finally, we identified compound heterozygous STAT2 mutations in two siblings suffering from severe viral illness. Absent STAT2 expression, failure to signal through the type I IFN pathway and increased susceptibility of STAT2-deficient fibroblasts to in vitro viral infections was demonstrated. STAT2 deficiency was previously described as the cause of unusually severe viral illness in infancy in two families, and identification of STAT2 deficiency in this third unrelated family strengthens this data. Increased susceptibility to vaccine-strain measles with complicated measles infection following routine immunization was documented in both families, and may be a warning sign for STAT2 deficiency. Although in the first described family the majority of childhood viral illnesses were reported to be remarkably mild, the siblings described in this work appeared to present with a more severe phenotype. In both families a decrease in frequency and severity of viral infections with increasing age was observed, probably due to maturation of the adaptive immune system. However, the older sibling suddenly died at age 7 years from overwhelming viral illness associated with immune dysregulation and diffuse intravascular coagulopathy. This demonstrates that STAT2-deficient patients may still be at risk for overwhelming viral illness at a later age. In the younger sibling a good response to high-dose intravenous immunoglobulins (IVIG) treatment was observed during severe (viral) infectious episodes with signs of emerging coagulopathy and immune dysregulation.status: publishe