The Bogunovic lab focuses on the study of human immunogenetics. We aim to improve understanding of the human immune system by studying:
1) Individuals with rare auto-inflammatory syndromes.
2) Individuals with severe clinical presentations of infectious diseases.
3) Developing broad spectrum antiviral therapeutics.
4) Understanding immune system in Down syndrome.
To dissect these phenotypes and develop therapeutics we use genomic, genetic, molecular biology, cellular biology, immunology and clinical tools.
The hypothesis of the lab is that inter-individual variability in immune responses (in auto-inflammatory syndromes and infections) can also be explained by the immune genetic composition of the host.
1) Auto-Inflammatory Syndromes
- ISG15 deficiency
We have identified null mutations in ISG15 in children with autosomal recessive ISG15 deficiency. ISG15 deficient individuals suffer diverse disease manifestations, including susceptibility to mycobacterial disease (Bogunovic et al Science), signs of neuroinflammation (Bogunovic et al Nature) or ulcerative skin lesions (Martin-Fernandez Cell Reports). The cells from these patients express persistently high levels of mRNA for select IFN-α/β-inducible genes (ISGs) in their blood when tested ex vivo, mimicking Aicardi-Goutières syndrome (AGS). Mechanistically, we found that the lack of intracellular free ISG15 resulted in inadequate stability of USP18, a potent negative regulator of IFN-α/β signaling and a bona fide deISGylating enzyme. Unlike Isg15-/- mice, which show high susceptibility to a wide range of viruses, humans deficient for ISG15 show no overt susceptibility to viral disease and in fact, may have an enhanced capacity to control viral infections. To date, we have defined essential roles for free extracellular ISG15 in immunity against mycobacteria (Bogunovic et. al, Science), and for free intracellular ISG15 as a negative regulator of IFN-α/β signaling (Zhang et. al, Nature); examined the species conservation of ISG15 function (Qiu Journal of Infectious Disease); and suggested that human ISG15 deficiency at least in vitro results in augmented control of viral infections as compared to WT individuals (Speer et. al, Nature Communications).
- USP18 deficiency
We have identified 5 children with complete USP18 deficiency (in collaboration with Dr. Manchini at Erasmus University, The Netherlands) and detailed the molecular mechanisms behind the type I IFN inflammation. Importantly these children presented with a severe perinatal onset of inflammation (Meuwissen et. al Journal of Experimental Medicine) suggestive of intrauterine infection, yet without an infectious origin, leading to diagnosis of Pseudo-TORCH syndrome. USP18 has both enzymatic (acting as a deISGylating enzyme) and negative regulatory activity (prevent IFN mediated inflammation). In a large collaboration, we recently demonstrated that this invariably lethal condition could be cured. In a Saudi Arabian boy with essential USP18 splice site mutations that remove the negative regulatory domain of USP18, early intervention with intensive supportive care and JAK inhibitor therapy lead to prompt and sustained recovery (Alsohime et al., 2020). We continue to study these and other individuals with similar disease presentations looking to unveil novel genetic and molecular mechanisms behind this syndrome.
Interestingly, the role for ISGylation in humans remains elusive. We aim at better understanding the role for ISGylation in human setting. To do so, we utilize a number of genetic models we have discovered or generated, allowing us to mechanistically assess the questions of ISGylation, and deISGylation as they pertain to ISG15 and USP18 biology.
- STAT2 Gain-Of-Function
We have identified a novel homozygous STAT2 mutation as a genetic cause for lethal autoinflammation of infancy (Gruber Journal of Experimental Medicine). The clinical presentation and molecular mechanisms of this disorder largely phenocopy ISG15-deficiency and USP18-deficiency. This is because STAT2 not only transduces IFN signaling, but also works as an essential adapter for USP18-mediated negative regulation. The gain-of-function mutation in this patient disrupted the negative regulatory function of STAT2 while maintaining the positive regulatory functions of STAT2. This unusual combination leads to a gain-of-function mutation with autosomal recessive inheritance, an exquisitely rare phenomenon in human genetics.
2) Susceptibility to Infectious Diseases
- Human genetic susceptibility to Listeria monocytogenes
We are studying the pathogenesis of central nervous system infections with the foodborne pathogen Listeria monocytogenes (neurolisteriosis). In immunocompetent individuals, infection with Listeria monocytogenes generally results in minor gastrointestinal problems. In rare cases, infection with Listeria monocytogenes may cause invasive infections, resulting in meningitis in this population, with significant mortality and morbidity. We seek to unveil host genetic causes of disease in this patient population.
- Human genetic susceptibility to ZIKA virus
Zika virus (ZIKV) is a flavivirus that is transmitted to its human host principally by mosquitos. Most individuals infected with ZIKV remain asymptomatic. In rare cases, ZIKV infection may be associated with Guillain-Barre syndrome and, in even rarer cases, death. However, infections in pregnant women can result in the transplacental transmission of ZIKV to the fetus, leading to microcephaly. How host genetics influences these outcomes is unknown. By improving our understanding of the human determinants of ZIKV resistance, we should be able to develop new hypotheses concerning both human susceptibility in vivo and drug development.
3) Broad Spectrum Antivirals
We have shown ISG15 and USP18 to be bona fide negative regulators of IFN-I. Our ex vivo data suggest that children with ISG15 and USP18 deficiency have increased levels of IFN-I-induced gene expression. Our in vitro data suggest that cells from these individuals control viral infections more effectively than cells from WT individuals. Specifically, we demonstrated enhanced resistance to influenza A virus (IAV), herpes simplex virus 1 (HSV-1), vesicular stomatitis virus (VSV), Sindbis virus, Rift Valley fever virus (RVFV), Nipah virus (NiV) in these cells. We have yet to identify a virus that is not better controlled by ISG15-deficient cells than by WT cells when ex vivo high ISG levels are reproduced in vitro. Based on these human genetic in vivo, ex vivo, in vitro and biochemical findings, we hypothesize that ISG15/USP18 inhibition by a small molecule would temporarily increase antiviral immunity in WT individuals. In parallel we are developing deliverable therapeutics which would mimic ISG15-like transcriptional profile and thus augment antiviral immunity in WT individuals.
4) Immune System in Down Syndrome
Down syndrome (DS) is the most common genetic cause of intellectual and developmental disabilities in children and young adults, affecting over 200,000 individuals in the US. In addition to cognitive problems, individuals with DS often have cardiac and gastrointestinal abnormalities. They also have various immunity- related defects, ranging from increased susceptibility to an array of infectious diseases to autoimmunity. Unfortunately, the exact molecular mechanism underlying these immune defects has yet to be elucidated. In most cases, DS is caused by the presence of an extra chromosome 21. Interestingly, the 200 or so genes present on this autosome include those encoding the type I interferon receptors (IFNAR1 and IFNAR2), suggesting a possible effect of gene dosage. Given that some type I interferonopathies are driven by minute increases in the levels of IFN-I cytokines, we decided to investigate the regulation of IFN-I in individuals with DS. This proposal is built around the hypothesis that the relative levels of IFNAR1 and IFNAR2 are the essential factors controlling the responsiveness to and duration of IFN-I responses in a cell type-specific manner in individuals with DS, thereby contributing to the disease. We are testing this hypothesis, by studying DS patients in vitro, ex vivo, and in vivo at the molecular, immunological, neurological and clinical levels, to assess the functional effects of the increases in the dosage of these genes on the regulation of the IFN pathway in humans. A deeper understanding of the molecular regulation of IFN-I in DS will provide us with greater insight into the pathophysiology of DS and pave the way for the possible use of inhibitors to alleviate the persistent inflammatory disorders associated with DS.
By aiming to illuminate the elusive pathogenesis of these diseases, we are hoping to lay the foundation for a novel and paradigm-shifting approach to the rational design of both preventative medicine (vaccines and genetic counseling) and treatments beyond current standards.