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Background: The genetic cause of primary immunodeficiency disease (PID) carries prognostic information. Objective: We conducted a whole-genome sequencing study assessing a large proportion of the NIHR BioResource–Rare Diseases cohort. Methods: In the predominantly European study population of principally sporadic unrelated PID cases (n = 846), a novel Bayesian method identified nuclear factor κB subunit 1 (NFKB1) as one of the genes most strongly associated with PID, and the association was explained by 16 novel heterozygous truncating, missense, and gene deletion variants. This accounted for 4% of common variable immunodeficiency (CVID) cases (n = 390) in the cohort. Amino acid substitutions predicted to be pathogenic were assessed by means of analysis of structural protein data. Immunophenotyping, immunoblotting, and ex vivo stimulation of lymphocytes determined the functional effects of these variants. Detailed clinical and pedigree information was collected for genotype-phenotype cosegregation analyses. Results: Both sporadic and familial cases demonstrated evidence of the noninfective complications of CVID, including massive lymphadenopathy (24%), unexplained splenomegaly (48%), and autoimmune disease (48%), features prior studies correlated with worse clinical prognosis. Although partial penetrance of clinical symptoms was noted in certain pedigrees, all carriers have a deficiency in B-lymphocyte differentiation. Detailed assessment of B-lymphocyte numbers, phenotype, and function identifies the presence of an increased CD21lowB-cell population. Combined with identification of the disease-causing variant, this distinguishes between healthy subjects, asymptomatic carriers, and clinically affected cases. Conclusion: We show that heterozygous loss-of-function variants in NFKB1 are the most common known monogenic cause of CVID, which results in a temporally progressive defect in the formation of immunoglobulin-producing B cells.

Immunocompromised patients are at increased risk of infection, but vaccinations are often less effective. In this thesis we investigated the risk of pneumonia, pneumococcal infections and measles (part 1) and the response to two important vaccines, against pneumococcal disease and hepatitis A (part 2) in immunocompromised adults. The risk of invasive pneumococcal disease is 7-fold increased among people living with HIV and 5-32-fold increased among adults with cancer compared with the general Dutch population. Pneumococcal vaccination of immunocompromised patients is recommended and guidelines advise to use the 13-valent pneumococcal conjugate vaccine (PCV13) followed by the 23-valent polysaccharide vaccine (PPSv23). A meta-analysis of 19 studies among HIV patients showed that this combined schedule is superior to single PCV13 or PPSV23, however vaccination responses are impaired compared with controls. We observed a protection rate of 49-59% in patients with HIV and use of immunosuppressive medication for inflammatory bowel disease, compared with 81-82% in controls. After stem cell transplantation only 24-47% of patients were protected, due to a poor response to PPSV23. Following hepatitis A vaccination seroprotection is much higher (53-90% after 2 vaccine doses), however many individuals are unprotected after the first dose. Therefore, hepatitis A antibody assessment prior to travel to hepatitis A endemic areas is recommended. Duration of protection remains unclear. Concluding, vaccinations are less effective for the population that need them the most. Further research into novel vaccination strategies for these patients is needed.

Early diagnosis of HIV infection and immediate start of treatment will reduce HIV transmission and improve the health of people living with HIV. For this reason, this thesis aims to contribute to decreasing the time between HIV infection, subsequent diagnosis, initiation of HIV treatment and viral suppression. We developed and validated a screening score, which can improve recognition of acute and early HIV infection. This screening score can also increase testing yield, while limiting the number of individuals requiring testing. We demonstrated the feasibility and effectiveness of strategies improving acute and early HIV infection diagnosis, facilitating same-visit confirmation of HIV diagnosis, same-day linkage to care and immediate initiation of HIV treatment. These strategies include peer-led distribution of HIV self-tests, a media campaign to create awareness for acute and early HIV infection, targeted testing for acute and early HIV infection, point-of-care HIV-RNA testing, partner notification services supported by peers, and initiation of HIV treatment on the day of HIV diagnosis. In summary, this thesis contributes to the implementation of effective strategies aiming at diagnosing and treating HIV infection at the earliest opportunity.

The human immune system is protecting us from a wide variety of potentially disease-causing pathogens, already starting directly after birth. Inborn errors of immunity or primary immunodeficiency disorders (PIDs) are a group of diseases where any or multiple of these protective components of the immune system fail. There is a close relationship between how the immune system functions in PIDs and how the immune system works in healthy individuals. The B cells of patients with defects in specific components, i.e. proteins, show how important they really are in humans. By studying the effects of the absence, reduction or modification of these key proteins we could ‘deconstruct’ healthy B cell responses. Here we add pieces of missing information to how B cell differentiation and antibody responses may work, by investigating monogenic PIDs. We did not focus on these human knock-outs only. We used different approaches and looked at healthy human B cells from different age-ranges in several experimental conditions in order to compare normal and abnormal B cell development and differentiation. A high-throughput compound screen showed us distinct mechanisms to modulate B cell responses and offered new therapeutic targets for diseases with B cell dysregulation (such as antibody-dependent autoimmune diseases). This thesis reveals important roles for both the canonical and non-canonical NF-κB pathway and the PI3K-AKT-mTOR pathway in the differentiation of naïve B cells to antibody producing plasmablasts and plasma cells.

Central to this thesis is the immunocompromised patient (ICPs) and infection prevention by vaccinations in these patients. ICPs are recognized as being at an increased infection risk; however, a key question is whether this also holds true for pneumococcal infections. We therefore studied the incidence rate of invasive pneumococcal disease (IPD) in ICPs and demonstrated that this rate is increased. With regard to vaccine immunogenicity, we showed that immunosuppressive medication in patients with autoimmune disease mitigated the response to both pneumococcal conjugate vaccine (PCV) and pneumococcal polysaccharide vaccine (PPSV). Immunosuppressive medication in patients with inflammatory bowel disease mitigated the response to the sequential pneumococcal vaccination schedule with PPSV administered two months after administration of PCV. At last, we showed that nearly 15% of HSCT recipients did not reach seroconversion after pneumococcal vaccination. In the second section of this thesis, we studied vaccination recommendations and other recommendations for travelling ICPs. We demonstrated that antibody concentrations after hepatits A or B vaccination were not measured in nearly 45% and 25% respectively, of ICPs with an indication for such a measurement. Half of all travelling ICPs in a specialised travel clinic did not receive a prescription of on-demand antibiotics, while these were actually indicated. This was an important finding, since we also demonstrated that travelling ICPs tended to have more frequent, and more severe travel-related health problems compared to immunocompetent travellers. The findings and conclusions of this thesis support existing vaccination recommendations for ICPs with scientific evidence, and contributed to their improvement.