Biomedical Informatics Research Center Antwerp

Abstract Unveiling the systemic effects of disease and health requires an holistic approach that has mainly revolved around well established, directly determinable molecular relationships such as the protein synthesis cascade and epigenetic mechanisms. In this study, involving 394 individuals, we found direct linkage of branches spanning human biological functions often not studied in conjunction, using clinical data, gut microbial abundances, blood immune cell repertoires, blood transcriptomic and blood T cell receptor data. Contrary to current paradigms, we demonstrate that immunotypes and enterotypes are orthogonal, likely fulfilling distinct roles in maintaining homeostasis, only bridged via the blood transcriptome. We also identified two distinct inflammatory profiles: the first driven by interferon signalling and the other characterised by non-viral, NF-kB and IL-6 markers. Lastly, we present compelling data showing strong associations of the Ruminococcaceae and Christensenellaceae bacteria with a healthy immunotype and transcriptomic pattern, highlighting their potential role in immune health.Graphical Abstract

Obesity is an independent risk factor for increased disease severity during influenza A virus (IAV) infection. White adipose tissue (WAT) inflammation promotes disease pathogenesis in obesity. Whether obesity modifies lung and WAT immune cells to amplify influenza severity is unknown. We show that obesity establishes a proinflammatory transcriptome in lung immune cells that is augmented during IAV infection and that IAV infection changes WAT immune cell milieu in obesity. Notably, a decrease in WAT macrophages (ATM) inversely correlates with an increase in infiltrating lung macrophages in obese IAV-infected mice. Further analyses of lung immune cell uncovered a macrophage subset that shares a transcriptomic signature with inflammatory ATMs. Importantly, adoptive transfer of ATMs from obese mice into lean IAV infected mice promotes host immune cell infiltration to the lungs. These findings suggest that, in an obese state, ATMs may exacerbate the inflammatory milieu important in pathologic responses to IAV infection.

Abstract Background/introduction Previous studies on wrist-worn photoplethysmography (PPG) heart rate monitors (HRM) have generally reported acceptable accuracy. However, accuracy can vary due to factors like sensor placement and motion artefacts. Guidelines for correct wearing of wrist HRMs are lacking. Purpose This study assessed the impact of device placement, wrist movement, and sport activities on Fitbit Inspire 2 validity, while also exploring potential adaptations for enhanced accuracy. Methods Eleven healthy volunteers participated in either a protocol involving wrist movements (n=5) or sport activities (n=6) while wearing the Fitbit Inspire 2 (Figure 1). The first protocol was performed with the Fitbit at two different distances from the wrist joint: one or three fingers away. Based on these findings, the sport activities protocol was performed with the optimal wrist joint distance. Additionally, heart rate (HR) was monitored during two training sessions of cardiac rehabilitation (CR) in five patients. The Polar H10 chest-strapped HRM served as gold-standard HR reference in all situations. Accuracy of Fitbit was assessed using root-mean-square-error (RMSE) and the percentage over/undershooting versus Polar. Results When the Fitbit was worn three fingers from the wrist, a lower RMSE (13.03) and percentage over/undershooting (32.88%) were observed compared to one finger (18.39 and 37.88% respectively). Considering all sport activities, the Fitbit was adequate in three out of six participants (i.e. RMSE<10.00 and over/undershooting<25.00%). There was a high percentage of undershooting, particularly during running, cycling, and rowing (Figure 2). The five CR patients had similar skin types (all light skin), and no patterns were observed regarding age, BMI, and average training HRs. During the monitored training sessions, two patients had adequate Fitbit readings, while the third patient had underestimated HR during one session but adequate results during the second session. Two other patients showed inadequate agreement between Fitbit and Polar and were advised to either wear the Fitbit more tightly or further from the wrist, without any significant improvement (RMSE decreased from 30.11 to 25.79, and from 31.75 to 20.12; over/undershooting decreased from 82.46% to 74.73%, and from 36.18% to 26.02%). Conclusions The Fitbit Inspire 2 demonstrates greater agreement with gold-standard Polar chest-strap HR measurements when worn three fingers from the wrist, but it still underestimates HR in half of the participants during sports activities. The reasons for success or failure of HRMs remain elusive. No technical solutions could be identified in this study or existing literature to enhance Fitbit's validity, highlighting the need for further research. Fitbit measurements may not be a fit for all patients, emphasizing the importance of a run-in phase before relying on its measurements.

Recent advances in single-cell RNA-sequencing (scRNA-seq) technology have facilitated studies of cell states and plasticity in tissue maintenance and cancer, including in the prostate. Here we present meta-analyses of multiple new and published scRNA-seq datasets to establish reference cell type classifications for the normal mouse and human prostate. Our analyses demonstrate transcriptomic similarities between epithelial cell states in the normal prostate, in the regressed prostate after androgen-deprivation, and in primary prostate tumors. During regression in the mouse prostate, all epithelial cells shift their expression profiles towards a proximal periurethral (PrU) state, demonstrating an androgen-dependent plasticity that is restored to normal during androgen restoration and regeneration. In the human prostate, we find progressive rewiring of transcriptional programs across epithelial cell types in benign prostate hyperplasia and treatment-naïve prostate cancer. Notably, we detect copy number variants predominantly within Luminal Acinar cells in prostate tumors, suggesting a bias in their cell type of origin, as well as a larger field of transcriptomic alterations in non-tumor cells. Finally, we observe that Luminal Acinar tumor cells in treatment-naïve prostate cancer display heterogeneous androgen receptor (AR) signaling activity, including a split between high-AR and low-AR profiles with similarity to PrU-like states. Taken together, our analyses of cellular heterogeneity and plasticity provide important translational insights into the origin and treatment response of prostate cancer.

ABSTRACTTranscriptionalcis-regulatory modules, e.g., enhancers, control the time and location of metazoan gene expression. While changes in enhancers can provide a powerful force for evolution, there is also significant deep conservation of enhancers for developmentally important genes, with function and sequence characteristics maintained over hundreds of millions of years of divergence. Not well understood, however, is how the overall regulatory composition of a locus evolves, with important outstanding questions such as how many enhancers are conserved vs. novel, and to what extent are the locations of conserved enhancers within a locus maintained? We begin here to address these questions with a comparison of the respectivesingle-minded (sim)loci in the two dipteran speciesDrosophila melanogaster(fruit fly) andAedes aegypti(mosquito).simencodes a highly conserved transcription factor that mediates development of the arthropod embryonic ventral midline. We identify two enhancers in theA. aegypti simlocus and demonstrate that they function equivalently in both transgenic flies and transgenic mosquitoes. OneA. aegyptienhancer is highly similar to knownDrosophilacounterparts in its activity, location, and autoregulatory capability. The other differs from any knownDrosophila simenhancers with a novel location, failure to autoregulate, and regulation of expression in a unique subset of midline cells. Our results suggest that the conserved pattern ofsimexpression in the two species is the result of both conserved and novel regulatory sequences. Further examination of this locus will help to illuminate how the overall regulatory landscape of a conserved developmental gene evolves.AUTHOR SUMMARYThe expression patterns and roles of genes, especially those involved in core developmental processes, are often conserved over vast evolutionary distances. Paradoxically, the DNA sequences surrounding these genes, which contain thecis-regulatory sequences (enhancers) that regulate gene expression, tend to be highly diverged. The manner and extent to which enhancers are functionally conserved, and how the overall organization of regulatory sequences within a locus is preserved or restructured, is not well understood. In this paper, we investigate these questions by identifying enhancers controlling expression of a master nervous system regulatory gene namedsimin the mosquitoAedes aegypti, and comparing their functions and locations to those in the well-characterizedsimlocus of the fruit flyDrosophila melanogaster. Our results suggest that the two species generate identical patterns ofsimexpression through a mix of conserved and novel regulatory sequences. Continued exploration of thesimlocus in these two species will help to build a comprehensive picture of how a regulatory locus for a master developmental regulator has evolved.

Diagnostic uncertainty may be a sign that a patient's working diagnosis is incorrect, but literature on proactively identifying diagnostic uncertainty is lacking. Using quality improvement methodologies, we aimed to create a process for identifying patients with uncertain diagnoses (UDs) on a pediatric inpatient unit and communicating about them with the interdisciplinary health care team. Plan-do-study-act cycles were focused on interdisciplinary communication, structured handoffs, and integration of diagnostic uncertainty into the electronic medical record. Our definition of UD was as follows: "you wouldn't be surprised if the patient had a different diagnosis that required a change in management." The primary measure, which was tracked on an annotated run chart, was percentage agreement between the charge nurse and primary clinician regarding which patients had a UD. Secondary measures included the percentage of patient days during which patients had UDs. Data were collected 3 times daily by text message polls. Over 13 months, the percentage agreement between the charge nurse and primary clinician about which patients had UDs increased from a baseline of 19% to a median of 84%. On average, patients had UDs during 11% of patient days. We created a novel and effective process to improve shared recognition of patients with diagnostic uncertainty among the interdisciplinary health care team, which is an important first step in improving care for these patients.

Susceptibility for leishmaniasis is largely dependent on host genetic and immune factors. Despite the previously described association of human leukocyte antigen (HLA) gene cluster variants as genetic susceptibility factors for leishmaniasis, little is known regarding the mechanisms that underpin these associations. To better understand this underlying functionality, we first collected all known leishmaniasis-associated HLA variants in a thorough literature review. Next, we aligned and compared the protection- and risk-associated HLA-DRB1 allele sequences. This identified several amino acid polymorphisms that distinguish protection- from risk-associated HLA-DRB1 alleles. Subsequently, T cell epitope binding predictions were carried out across these alleles to map the impact of these polymorphisms on the epitope binding repertoires. For these predictions, we used epitopes derived from entire proteomes of multiple Leishmania species. Epitopes binding to protection-associated HLA-DRB1 alleles shared common binding core motifs, mapping to the identified HLA-DRB1 amino acid polymorphisms. These results strongly suggest that HLA polymorphism, resulting in differential antigen presentation, affects the association between HLA and leishmaniasis disease development. Finally, we established a valuable open-access resource of putative epitopes. A set of 14 HLA-unrestricted strong-binding epitopes, conserved across species, was prioritized for further epitope discovery in the search for novel subunit-based vaccines.

Pregnancy in women with ESKD undergoing dialysis is uncommon due to impaired fertility. Data on pregnancy in women on dialysis in the United States is scarce. We evaluated a retrospective cohort of 47,555 women aged 15-44 years on dialysis between January 1, 2005 and December 31, 2013 using data from the United States Renal Data System with Medicare as primary payer. We calculated pregnancy rates and identified factors associated with pregnancy. In 47,555 women on dialysis, 2352 pregnancies were identified. Pregnancy rate was 17.8 per thousand person years (PTPY) with the highest rate in women aged 20-24 (40.9 PTPY). In the adjusted time-to-event analysis, a higher likelihood of pregnancy was seen in Native American (HR, 1.77; 95% CI, 1.33 to 2.36), Hispanic (HR, 1.51; 95% CI, 1.32 to 1.73), and black (HR, 1.33; 95% CI, 1.18 to 1.49) women than in white women. A higher rate of pregnancy was seen in women with ESKD due to malignancy (HR, 1.64; 95% CI, 1.27 to 2.12), GN (HR, 1.38; 95% CI, 1.21 to 1.58), hypertension (HR, 1.32; 95% CI, 1.16 to 1.51), and secondary GN/vasculitis (HR, 1.18; 95% CI, 1.02 to 1.37) than ESKD due to diabetes. A lower likelihood of pregnancy was seen among women on peritoneal dialysis than on hemodialysis (HR, 0.47; 95% CI, 0.41 to 0.55). The pregnancy rate is higher in women on dialysis than previous reports indicate. A higher likelihood of pregnancy was associated with race/ethnicity, ESKD cause, and dialysis modality.