Genetic studies of susceptibility to inflammation, autoimmunity, and hematological malignancy

Abstract

The immune system represents the body’s defense against infectious organisms. Inborn defects of the immune system, called primary immunodeficiencies (PIDs), are a heterogeneous group of Mendelian disorders. Clinically, PIDs can cause isolated to broad susceptibility to pathogens, severe hyperinflammation, autoimmunity, allergy, and cancer. The studies in this thesis take advantage of the recent development in DNA-sequencing technologies and of our increased understanding of genetic variability to further explore the genetic architecture and phenotypic spectrum of hemophagocytic lymphohistiocytosis (HLH), an inborn error of lymphocyte cytotoxicity, and to elucidate the genetic factors behind autoimmunity and hematological malignancies in selected families.

Familial HLH (FHL) is a severe hyperinflammatory condition, genetically heterogeneous, caused by defective perforin-mediated lymphocyte cytotoxic activity. In paper I we use a highthroughput sequencing panel covering 12 HLH-related genes in 58 prospectively recruited patients with HLH and achieve a molecular diagnosis in 22 cases (38%). In paper II we show that perforin-deficiency due to biallelic PRF1 missense variants is associated with broad intrafamilial variability and clinical presentations seemingly unrelated to HLH, such as Hodgkin lymphoma. Using exome sequencing, in paper III, we identify biallelic pathogenic variants in IFNGR1 and INFGR2, respectively, in two patients with HLH and disseminated mycobacterial infection. Previous studies have shown that HLH pathology is largely driven by IFN-γ. Instead, our findings suggest the existence of IFN-γ-independent mechanisms for the development of HLH. In paper IV, we uncover biallelic coding and non-coding variants in RAB27A, the gene responsible for Griscelli syndrome type 2 (GS2), in five unrelated patients with atypical HLH, normal pigmentation, and a functional defect suggestive of FHL. A complex structural variant disrupting the transcriptional start site (TSS) of one RAB27A transcript was shared among the patients. We show that the disrupted TSS is less predominantly used by melanocytes compared to lymphocytes, explaining the lack of hypopigmentation in these patients, otherwise present in GS2. In paper V we report the beneficial effect of hematopoietic stem cell transplantation in a 14-yearold boy with LRBA deficiency and a seven-year history of severe autoimmmune disorders. In paper VI we uncover germline heterozygous missense variants in SAMD9L, a gene located on 7q21, in two families with multiple individuals affected by cytopenia, immunodeficiency, myelodysplastic syndrome (MDS) with cytogenetic aberrations of chromosome 7, and neurological disease. We show a gain-of-function (GOF) effect of the mutants, which inhibit cell proliferation. Germline SAMD9L GOF variants were lost in MDS cells and hematopoietic revertant mosaicism occurred frequently among less severely affected carriers. Our results indicate a strong selective advantage for hematopoietic cells that, through different somatic events, overcome the growth-inhibiting effect of germline SAMD9L GOF variants.

Taken together, these studies add to our understanding of the phenotypic and genetic spectrum of HLH, display the power of high-throughput sequencing in diagnostics of individuals affected by severe inflammation, autoimmunity, and hematological malignancies, and highlight SAMD9L as an important gene for regulation of hematopoietic cell proliferation.