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

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 proliferatio

Adult-Onset Ataxia with Neuropathy and White Matter Abnormalities Due to a Novel SAMD9L Variant

Variants in tumor suppressor genes and in genes encoding DNA repairing proteins are associated with syndromes conferring neurologic features and increased risk for malignancy. The best example for these conditions is ataxia-telangiectasia (AT). A more rare and recent disease is an ataxia-pancytopenia syndrome (ATXPC) associated with heterozygous gain-of-function variants in the tumor suppressor gene SAMD9L (MIM 159550). Here, we describe a patient with a complex cerebellar syndrome associated with a novel SAMD9L pathogenic variant.publishedVersio

Targeted high-throughput sequencing for genetic diagnostics of hemophagocytic lymphohistiocytosis

Background: Hemophagocytic lymphohistiocytosis (HLH) is a rapid-onset, potentially fatal hyperinflammatory syndrome. A prompt molecular diagnosis is crucial for appropriate clinical management. Here, we validated and prospectively evaluated a targeted high-throughput sequencing approach for HLH diagnostics. Methods: A high-throughput sequencing strategy of 12 genes linked to HLH was validated in 13 patients with previously identified HLH-associated mutations and prospectively evaluated in 58 HLH patients. Moreover, 2504 healthy individuals from the 1000 Genomes project were analyzed in silico for variants in the same genes. Results: Analyses revealed a mutation detection sensitivity of 97.3 %, an average coverage per gene of 98.0 %, and adequate coverage over 98.6 % of sites previously reported as mutated in these genes. In the prospective cohort, we achieved a diagnosis in 22 out of 58 patients (38 %). Genetically undiagnosed HLH patients had a later age at onset and manifested higher frequencies of known secondary HLH triggers. Rare, putatively pathogenic monoallelic variants were identified in nine patients. However, such monoallelic variants were not enriched compared with healthy individuals. Conclusions: We have established a comprehensive high-throughput platform for genetic screening of patients with HLH. Almost all cases with reduced natural killer cell function received a diagnosis, but the majority of the prospective cases remain genetically unexplained, highlighting genetic heterogeneity and environmental impact within HLH. Moreover, in silico analyses of the genetic variation affecting HLH-related genes in the general population suggest caution with respect to interpreting causality between monoallelic mutations and HLH. A complete understanding of the genetic susceptibility to HLH thus requires further in-depth investigations, including genome sequencing and detailed immunological characterization.Peer reviewe

Genotype-phenotype associations in a large PTEN Hamartoma Tumor Syndrome (PHTS) patient cohort

Background: Pathogenic PTEN germline variants cause PTEN Hamartoma Tumor Syndrome (PHTS), a rare disease with a variable genotype and phenotype. Knowledge about these spectra and genotype-phenotype associations could help diagnostics and potentially lead to personalized care. Therefore, we assessed the PHTS genotype and phenotype spectrum in a large cohort study. Methods: Information was collected of 510 index patients with pathogenic or likely pathogenic (LP/P) PTEN variants (n = 467) or variants of uncertain significance. Genotype-phenotype associations were assessed using logistic regression analyses adjusted for sex and age.Results: At time of genetic testing, the majority of children (n = 229) had macrocephaly (81%) or developmental delay (DD, 61%), and about half of the adults (n = 238) had cancer (51%), macrocephaly (61%), or cutaneous pathology (49%). Across PTEN, 268 LP/P variants were identified, with exon 5 as hotspot. Missense variants (n = 161) were mainly located in the phosphatase domain (PD, 90%) and truncating variants (n = 306) across all domains. A trend towards 2 times more often truncating variants was observed in adults (OR = 2.3, 95%CI = 1.5-3.4) and patients with cutaneous pathology (OR = 1.6, 95%CI = 1.1-2.5) or benign thyroid pathology (OR = 2.0, 95%CI = 1.1-3.5), with trends up to 2-4 times more variants in PD. Whereas patients with DD (OR = 0.5, 95%CI = 0.3-0.9) or macrocephaly (OR = 0.6, 95%CI = 0.4-0.9) had about 2 times less often truncating variants compared to missense variants. In DD patients these missense variants were often located in domain C2.Conclusion: The PHTS phenotypic diversity may partly be explained by the PTEN variant coding effect and the combination of coding effect and domain. PHTS patients with early-onset disease often had missense variants, and those with later-onset disease often truncating variants

Cabbage and fermented vegetables : From death rate heterogeneity in countries to candidates for mitigation strategies of severe COVID-19

Large differences in COVID-19 death rates exist between countries and between regions of the same country. Some very low death rate countries such as Eastern Asia, Central Europe, or the Balkans have a common feature of eating large quantities of fermented foods. Although biases exist when examining ecological studies, fermented vegetables or cabbage have been associated with low death rates in European countries. SARS-CoV-2 binds to its receptor, the angiotensin-converting enzyme 2 (ACE2). As a result of SARS-CoV-2 binding, ACE2 downregulation enhances the angiotensin II receptor type 1 (AT(1)R) axis associated with oxidative stress. This leads to insulin resistance as well as lung and endothelial damage, two severe outcomes of COVID-19. The nuclear factor (erythroid-derived 2)-like 2 (Nrf2) is the most potent antioxidant in humans and can block in particular the AT(1)R axis. Cabbage contains precursors of sulforaphane, the most active natural activator of Nrf2. Fermented vegetables contain many lactobacilli, which are also potent Nrf2 activators. Three examples are: kimchi in Korea, westernized foods, and the slum paradox. It is proposed that fermented cabbage is a proof-of-concept of dietary manipulations that may enhance Nrf2-associated antioxidant effects, helpful in mitigating COVID-19 severity.Peer reviewe

Nrf2-interacting nutrients and COVID-19 : time for research to develop adaptation strategies

There are large between- and within-country variations in COVID-19 death rates. Some very low death rate settings such as Eastern Asia, Central Europe, the Balkans and Africa have a common feature of eating large quantities of fermented foods whose intake is associated with the activation of the Nrf2 (Nuclear factor (erythroid-derived 2)-like 2) anti-oxidant transcription factor. There are many Nrf2-interacting nutrients (berberine, curcumin, epigallocatechin gallate, genistein, quercetin, resveratrol, sulforaphane) that all act similarly to reduce insulin resistance, endothelial damage, lung injury and cytokine storm. They also act on the same mechanisms (mTOR: Mammalian target of rapamycin, PPAR gamma:Peroxisome proliferator-activated receptor, NF kappa B: Nuclear factor kappa B, ERK: Extracellular signal-regulated kinases and eIF2 alpha:Elongation initiation factor 2 alpha). They may as a result be important in mitigating the severity of COVID-19, acting through the endoplasmic reticulum stress or ACE-Angiotensin-II-AT(1)R axis (AT(1)R) pathway. Many Nrf2-interacting nutrients are also interacting with TRPA1 and/or TRPV1. Interestingly, geographical areas with very low COVID-19 mortality are those with the lowest prevalence of obesity (Sub-Saharan Africa and Asia). It is tempting to propose that Nrf2-interacting foods and nutrients can re-balance insulin resistance and have a significant effect on COVID-19 severity. It is therefore possible that the intake of these foods may restore an optimal natural balance for the Nrf2 pathway and may be of interest in the mitigation of COVID-19 severity