Annelies Verbon

CMV seropositivity contributes to medical complications in people living with HIV (PLHIV). This study provides a comprehensive evaluation of how CMV seropositivity shapes the immune system of 1,887 PLHIV, by utilizing multi-omics and deep immune phenotyping datasets. The study measured the immune cell profiles from whole blood, and the cytokine production of PBMCs exposed to various ex-vivo stimuli. We observed an increase in pro-inflammatory cytokine production of circulating immune cells and differences in phenotype of innate-like lymphocyte populations associated with CMV seropositivity. This study also measured 5-omics layers, including genomics, DNA methylation, transcriptomics, and plasma protein and metabolites. The DNA methylome and transcriptome demonstrated prominent CMV-induced signatures related to immune functions in PLHIV. Particularly, high FCRL6 expression is a promising biomarker for immune activation, underlined by the demethylation of FCRL6 and up-regulation of gene expression and plasma protein concentrations in CMV-seropositive PLHIV. Host genetics-driven elevation in both gene and protein expression of FCRL6 was also associated with latent CMV infection. A significant CMV-seroprevalence locus was associated with cytokine production capacity and protein abundance. Mendelian randomization analyses demonstrated a causal relationship between elevated FCRL6 expression and CMV seropositivity.

People living with HIV (PLHIV) have an increased susceptibility to non-AIDS comorbidities. In this study, we systematically profiled 1,342 PLHIV across five omics layers and immune function. We found latent factors, resulting from integrating epigenomics, transcriptomics, proteomics, metabolomics and immune responses, linked to cardiovascular diseases, the presence of carotid plaque and chronic obstructive pulmonary disease in PLHIV. Mapping four omics layers to genetic variation identified 5,962 molecular quantitative trait loci, illustrating a common genetic regulation in PLHIV compared to healthy individuals. By performing Mendelian randomization, we uncovered host genetic-driven changes in baseline molecules causally related to immune responses upon stimulation with inactivated pathogens. Lastly, we uncovered that the inflammasome, genetically regulated by the NLRP12 locus, contributes to systemic inflammation across multiple molecular layers. This study offers a unique catalog of genetic and molecular determinants of immune function in PLHIV and elucidates molecular pathways driving inter-individual variation in immune response and comorbidities.

Using Low Quantity single strand CAGE (LQ-ssCAGE), we mapped the transcription start sites (TSS). We annotated the 5’ end of the invertebrate Galleria mellonella, an upcoming and booming experimental model in infectious disease and immunology research. However, the current genome annotation of this model organism lacks annotation of the 5’ end and TSS information. G. mellonella larva was infected with the fungal pathogen Madurella mycetomatis to map TSS under healthy and infection conditions . Larvae were first treated with itraconazole or ravuconazole, and then RNA-seq and LQ-ssCAGE libraries were prepared and sequenced 4, 30, and 52 hours following infection. The LQ-ssCAGE data was processed to identify CAGE transcription start site (CTSS), uni-, and bi-directional clusters. LQ-ssCAGE enabled us to precisely identify 39,410 TSS and 249 active enhancers; we assigned genomic features to the resulting TSSs and enhancers. The majority of the TSS peaks are annotated as promoter regions, while the enhancers were annotated as intergenic and genic. Furthermore, we confirmed the quality of TSS calling by promoter shapes and GC bias. Furthermore, we identified a set of super-enhancers and predicted de-novo motifs. The raw and processed data was deposited to NCBI GEO GSE282923. CTSS, TSS peaks, and enhancers coordinated are available through the ZENBU Genome browser. In this study, we reported the first atlas of TSS and active enhancers of G. mellonella .

Background: In recent decades, the number of immunocompromised patients (ICPs) has increased significantly. ICPs have an impaired immune system, making them susceptible to complicated infections. To protect them from infections, ICPs are eligible to receive several medically indicated vaccines. To obtain insight into the uptake of these medically indicated vaccines, we determined the coverage of these vaccines in ICPs. Methods: This observational cohort study was conducted at the University Medical Centre Utrecht, the Netherlands, from September 2021 to April 2022. All adult ICPs admitted for COVID-19 were asked to complete a questionnaire on their vaccination history (pneumococcal, herpes zoster, human papillomavirus vaccination, influenza, and COVID-19 vaccines) and history of vaccine-preventable infections. In addition, patients’ vaccination history was reviewed in medical files. Results: A total of 115 patients completed the questionnaire and were included. Although all patients had an indication for pneumococcal vaccination, only 22 received it (19%). Coverage for herpes zoster was low (1%, 1/106 eligible patients). Coverage for human papillomavirus vaccination (HPV) was also low (40%, two out of five eligible patients). In contrast, 92% of patients received vaccination against SARS-CoV-2, and 77% of patients received seasonal influenza vaccination. Conclusions: Although coverage for influenza and COVID-19 vaccination was high in ICPs, coverage for other medically indicated vaccines was low. Identifying which factors contributed to high COVID-19 and influenza vaccine uptake can help to improve vaccination rates for the other recommended vaccines. Clear guidelines for clinicians and the removal of organizational obstacles are needed to improve vaccination coverage.

Background: We aimed to compare the non-AIDS event (nADE) risk between normal progressors using antiretroviral therapy (NP-ART) and people with human immunodeficiency virus (HIV, PWH) who naturally control HIV infection (HIV controllers), as well as the risk of nADE following ART in HIV controllers. Methods: The primary end point was the composite of cardiovascular disease, non-AIDS malignancy, or all-cause mortality, whichever came first. The role of ART in HIV controllers was assessed as a time-varying covariate. Results: We included 1007 ART-naive HIV controllers (60 of them were elite controllers), 1510 early-ART (<6 months after negative HIV test), and 15437 NP-ART (reference group), contributing 3813, 11 060, and 160 050 years of follow-up, respectively. HIV controllers had lower risk of the primary end point (hazard ratio [HR], 0.55; 95% confidence interval [CI]: .38–.81; P = .0023), all-cause mortality (adjusted HR [aHR], 0.45; 95% CI: .25–.79; P = .0054), and cardiovascular disease (aHR, 0.47; 95% CI: .22–.99; P = .046), but not non-AIDS malignancy (aHR, 0.74; 95% CI: .41–1.35; P = .33), compared with NP-ART. Among HIV controllers, each log10 lower baseline viral load further decreased the risk of a nADE (aHR, 0.54; 95% CI: .29–.99; P = .045). ART in HIV controllers did not reduce the risk of any nADE (aHR, 1.22; 95% CI: .66–2.29; P = .53). Conclusions: HIV controllers had a lower n ADE risk than NP-ART, especially in those with low plasma viral loads. ART did not alter the nADE risk in HIV controllers. Our findings help clinicians to decide on prescribing ART in HIV controllers.

Mycetoma, a neglected infection of subcutaneous tissues, poses a significant health burden, especially in tropical regions. It is caused by fungal (eumycetoma) and bacterial (actinomycetoma) pathogens, with current treatments often providing unsatisfactory outcomes. This study aims to discover novel broad-spectrum antimicrobial agents to circumvent the lengthy and costly diagnostic procedures. Eight essential oils (EOs) from the roots and aerial parts of Geigeria alata, Lavandula angustifolia, Melaleuca alternifolia, Myristica fragrans, Pimpinella anisum, Syzigum aromaticum, and Thymus vulgaris were prepared using steam distillation. The in vitro antimycetomal activity against Madurella mycetomatis and Actinomadura madurae strains was assessed using resazurin assays. The chemical compositions of the EOs were analyzed using gas chromatography and mass spectrometry (GC–MS). Promising EOs underwent further in vivo toxicity and efficacy testing in Galleria mellonella larvae models. EOs of G. alata roots, M. fragrans, P. anisum, S. aromaticum, and T. vulgaris showed wide-spectrum dual in vitro antimycetomal activity against all tested strains, with minimum inhibitory concentrations (MICs) ranging from 0.004 to 0.125% v/v. G. alata aerial parts and L. angustifolia EOs demonstrated activity predominantly against A. madurae, while M. alternifolia EO did not inhibit any tested strains. M. fragrans and P. anisum EOs significantly enhanced the survival of M. mycetomatis-infected larvae without inducing toxicity in uninfected larvae. Notably, P. anisum EO tended to enhance the survival of A. madurae-infected larvae, ranking it as the most promising EO among those tested. The investigated EOs, particularly P. anisum, exhibited promising broad-spectrum antimycetomal activity against fungal and bacterial pathogens responsible for mycetoma. These findings highlight the potential of essential oils as a basis for developing novel antimycetomal agents, offering hope for improved treatment strategies for this neglected disease.

Objectives: Eumycetoma is a neglected tropical disease (NTD) characterized by subcutaneous lesions and the formation of grains. Attempts to treat eumycetoma involve a combination of antifungal treatment and surgery, although the outcome is frequently disappointing. Therefore, there is a need to identify novel antifungal drugs to treat eumycetoma. In this respect, Medicines for Malaria Venture (MMV) has assembled libraries of compounds for researchers to use in drug discovery research against NTD. Therefore, we screened two MMVOpen compound libraries to identify novel leads for eumycetoma. Methods: A total of 400 compounds from the COVID Box and the Global Health Priority Box were screened in vitro at 100 µM and 25 µM against the most common causative agents of eumycetoma, namely Madurella mycetomatis and Falciformispora senegalensis, and the resulting IC₅₀ and MIC₅₀ values were obtained. Compounds with an IC₅₀ < 8 µM were identified for possible in vivo efficacy studies using an M. mycetomatis grain model in Galleria mellonella larvae. Results: Out of the 400 compounds, 22 were able to inhibit both M. mycetomatis and F. senegalensis growth at 100 µM and 25 µM, with compounds MMV1593278, MMV020335, and MMV1804559 being selected for in vivo testing. Of these three, only the pyrazolopyrimidine derivative MMV1804559 was able to prolong the survival of M. mycetomatis-infected G. mellonella larvae. Furthermore, the grains in MMV1804559-treated larvae were significantly smaller compared to the PBS-treated group. Conclusion: MMV1804559 shows promising in vitro and in vivo activity against M. mycetomatis.

Starting antiretroviral therapy (ART) same-day, or as soon as possible after HIV diagnosis is advised in guidelines worldwide. Especially during acute HIV infection (AHI), rapid ART start may be more urgent because of a higher risk of transmission or symptoms of acute retroviral syndrome. During this phase, rapid ART start may have additional benefits for viral reservoir size and host immunity. We explored perceptions of rapid ART start among participants of The Netherlands Cohort Study on Acute HIV infection (NOVA study), who started ART rapidly after diagnosis of AHI. We conducted 20 in-depth qualitative interviews with NOVA study participants between October and December 2018. Data were analyzed thematically, using inductive and iterative coding techniques. Roughly half of the participants stated they felt well-informed about the importance of (rapid) ART. Starting ART rapidly was perceived positively by almost all participants, mostly because of the expected benefits on their health, and to prevent HIV transmission. Rapid ART start was seen as a way to cope with the diagnosis. However, a more negative perception was that rapid ART start confronted participants with their diagnosis, when they were still adjusting to a new situation. Our results show that among people diagnosed during AHI, rapid ART is well-accepted. These results should be encouraging to HIV care providers who encounter people with AHI in their clinical practice and to researchers who carry out cure-related studies, in which early ART is often included. The Clinical Trial Registration number is NCT05728996.