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Human Genetic Basis of Severe Staphylococcal Infections in Childhood

Periodic Reporting for period 2 - HGB-StIC (Human Genetic Basis of Severe Staphylococcal Infections in Childhood)

Reporting period: 2021-01-01 to 2021-12-31

Staphylococcus aureus is a prominent cause of bacterial infections in humans worldwide, especially in children. Invasive infections have a poor prognosis. Acquired risk factors for infections with S. aureus only account for a small proportion of severe infections, especially in the case of community-acquired infections. In fact, most cases of invasive staphylococcal diseases are unexplained as they strike otherwise healthy children. Known primary immune deficiencies collectively explain only a small minority of cases. Other inborn errors of immunity may account for a sizeable proportion of cases. The Researcher aims to identify and functionally characterize human gene(s) involved in susceptibility to S. aureus infections. State-of-the-art genetic approaches and cutting-edge immunological and microbiological methods are applied. By investigating human host counterparts in a genome-wide setting, this study is the first unbiased and systematic assessment linking S. aureus virulence factors with host genetic predisposition. During the Project, the Researcher has discovered an inborn error of immunity that, by disrupting cell-intrinsic immunity to a staphylococcal pore-forming toxin in non-hematopoietic cells, underlies life-threatening staphylococcal infections. This report spans the complete project, during which work was performed at The Rockefeller University (New York, U.S.A.) and the University Medical Center Utrecht (Utrecht, The Netherlands). At the time of reporting, the project has achieved most of its objectives and milestones and full achievement is expected on short term.
During the Outgoing Phase at The Rockefeller University (New York, U.S.A) a cohort of 115 patients with severe S. aureus infections was screened for known primary immune deficiencies. From this cohort, a total of 105 patients with no known primary immune deficiencies was identified and their gDNA was submitted for whole exome sequencing (WES). The patients’ WES data were analyzed for mutations in previously hypothesized candidate genes. Genes encoding the TLR2 pathway, and genes encoding receptors employed by staphylococcal virulence factors were analyzed. No candidate disease-causing mutations were identified in these two sets of candidate genes. Using exome variant prioritizing under an autosomal dominant model of inheritance, three patients from three kindreds were identified that carry rare, predicted deleterious variants in one candidate gene involved in the regulation of inflammation. In the cohort of patients with life-threatening S. aureus infections, this single gene was the only gene passing statistical thresholds for enrichment in a genome-wide manner (p=5.7E-07). An additional four patients were subsequently identified and recruited, resulting in a total of 7 patients from 6 kindreds. Specific heterozygous mutations were verified by Sanger sequencing, and familial segregation was performed. A rare group of syndromic patients with a chromosomal deletion was identified who suffer from the very same and previously unrecognized inborn error of immunity. The patients’ alleles were characterized in functional over-expression assays, and the genetic mechanism of deficiency was established. High-dimensional immune phenotyping (using CyTOF) and single cell RNA sequencing was performed in the patients’ PBMC. Transcription of the mutant alleles and expression of the mutant proteins was assessed in patients’ cells. To further assess the impact of the genetic deficiency, transcriptome- and proteome-wide analyses were performed in patient cells and accumulation of the protein’s substrate was quantified. Causality was established by ectopic genetic complementation and subsequent reversal of the biochemical cellular phenotype. Using a hypothesis-generating approach, an increased susceptibility of patients’ cells to a staphylococcal pore-forming toxin was revealed. The host-pathogen interaction in the context of this newly identified inborn error of immunity was further elucidated during the Returning Phase at the University Medical Center Utrecht (Utrecht, The Netherlands). By disrupting cell-intrinsic immunity to the staphylococcal pore-forming toxin in non-hematopoietic cells, the newly discovered inborn error of immunity underlies life-threatening staphylococcal infections. The mechanism of disease was established and leads for pharmaceutical interventions were explored. At the time of reporting, a revised manuscript was resubmitted for publication.
This project is the first systematic approach linking S. aureus virulence factors with host genetic predisposition, by successfully investigating host counterparts in a genome-wide setting. By investigating the genetic predisposition to severe S. aureus infections, the Researcher has pioneered in the field. The enhanced understanding of pathophysiology acquired during the project not only allows for counseling of individual patients but has also opened avenues for innovative therapeutic strategies.
Promotional activity: Junior engagement #1, Bacterial Cultures
Non-scientific media: Interview De Groene Amsterdammer
Outreach activity: Community engagement, 5p- Syndrome Society meeting
Promotional activity: Junior engagement #2, Cell Cultures