Influence of Mutations and N-Glycosylation Sites in the Receptor-Binding Domain (RBD) and the Membrane Protein of SARS-CoV-2 Variants of Concern on Antibody Binding in ELISA

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect human cells by first attaching to the ACE-2 receptor via its receptor-binding domain (RBD) in the spike protein. Here, we report the influence of N-glycosylation sites of the RBD and the membrane (M) protein on IgG antibody binding in serum samples from patients infected with the original SARS-CoV-2 strain in Germany. The RBDs of the wildtype, alpha, beta, gamma, and kappa variants expressed in HEK293S GnTI- cells were all N-glycosylated at Asn331, Asn334, Asn343, and Asn360 or Asn370, whereas the M-protein was glycosylated at Asn5. An ELISA using a coated RBD and probed with anti-RBD IgG antibodies gave a sensitivity of 96.3% and a specificity of 100% for the wildtype RBD, while the sensitivity decreased by 5% to 10% for the variants of concern, essentially in the order of appearance. Deglycosylation of the wildtype RBD strongly reduced antibody recognition by ~20%, considering the mean of the absorbances recorded for the ELISA. This effect was even stronger for the unglycosylated RBD expressed in Escherichia coli, suggesting structural changes affecting epitope recognition. Interestingly, the N-glycosylated M-protein expressed in HEK293S GnTI- cells gave good sensitivity (95%), which also decreased to 65% after deglycosylation, and selectivity (100%). In conclusion, N-glycosylation of the M-protein, the RBD, and most likely the spike protein are important for proper antibody binding and immunological assays, whereas the type of N-glycosylation is less relevant.

Evolving Together: Cassandra Retrotransposons Gradually Mirror Promoter Mutations of the 5S rRNA Genes

The 5S rRNA genes are among the most conserved nucleotide sequences across all species. Similar to the 5S preservation we observe the occurrence of 5S-related nonautonomous retrotransposons, so-called Cassandras. Cassandras harbor highly conserved 5S rDNA-related sequences within their long terminal repeats, advantageously providing them with the 5S internal promoter. However, the dynamics of Cassandra retrotransposon evolution in the context of 5S rRNA gene sequence information and structural arrangement are still unclear, especially: (1) do we observe repeated or gradual domestication of the highly conserved 5S promoter by Cassandras and (2) do changes in 5S organization such as in the linked 35S-5S rDNA arrangements impact Cassandra evolution? Here, we show evidence for gradual co-evolution of Cassandra sequences with their corresponding 5S rDNAs. To follow the impact of 5S rDNA variability on Cassandra TEs, we investigate the Asteraceae family where highly variable 5S rDNAs, including 5S promoter shifts and both linked and separated 35S-5S rDNA arrangements have been reported. Cassandras within the Asteraceae mirror 5S rDNA promoter mutations of their host genome, likely as an adaptation to the host's specific 5S transcription factors and hence compensating for evolutionary changes in the 5S rDNA sequence. Changes in the 5S rDNA sequence and in Cassandras seem uncorrelated with linked/separated rDNA arrangements. We place all these observations into the context of angiosperm 5S rDNA-Cassandra evolution, discuss Cassandra's origin hypotheses (single or multiple) and Cassandra's possible impact on rDNA and plant genome organization, giving new insights into the interplay of ribosomal genes and transposable elements.

The Impact of an Outdoor Motor-Cognitive Exercise Programme on the Health Outcomes of Older Adults in Community Settings: A Pilot and Feasibility Study

Physical and cognitive exercises can prevent or at least mitigate the symptoms of certain diseases and help older adults perform a range of daily functions. Yet, most seniors do not meet the World Health Organisation's recommended guidelines for physical activity. The objective of this study is to promote and maintain the physical and cognitive capacity of older adults by implementing a feasible and effective low-threshold, age-appropriate, motor-cognitive training outdoors. In the German city of Chemnitz, citizens aged 60 years and older participated in a quasi-randomised intervention trial. Exercises to train coordination, strength, endurance, and cognition were integrated into a 12-week outdoor motor-cognitive exercise programme. Both the physical (e.g., 6MWT) and cognitive skills (e.g., TMT B) of the intervention group (n = 41) and control group (no intervention, n = 58) were measured before (T1) and after (T2) completion of the exercise programme. Some of the participants' physical and all their cognitive measures improved. Neurocognitive performance (DSST) showed a significant time × group interaction effect (F(1,95) = 6.943, p = 0.010, ηp2 = 0.068). Sex and age were found to be influencing factors. We consider our exercise programme to be successfully implemented, well received by the participants, and feasible and useful to promote the continued exercise of daily functions as part of healthy aging in community-dwelling older adults.

The different areas of chronic stress and food addiction: Results from the LIFE-Adult-Study

There is an empirical association between stress and symptoms of food addiction (FA), but it is still not clear which domains of stress are the most relevant when it comes to FA, limiting the ability of researchers and practitioners to address problematic eating-related health outcomes. In order to address this gap in the literature, we analysed how different domains of chronic stress are related to FA. We used data from a subsample of the LIFE-Adult-Study (N = 1172), a German cohort study. We conducted a linear regression analysis with stress domains (Trier Inventory for Chronic Stress, TICS) as predictors of FA (Yale Food Addiction Scale, YFAS). In the second regression analysis we included sociodemographic variables, personality, and smoking as control variables. There was a significant and positive association between Social Overload, Work Discontent, Excessive Demands from Work, and Chronic Worrying and FA. After adding control variables, only Social Overload, Excessive Demands from Work, and Chronic Worrying remained significant predictors. Connections between stress domains and FA can serve as starting points for the development of meaningful interventions that support individuals self-care strategies (Social Overload), complexity management (Excessive Demands from Work), and coping with negative emotions (Chronic Worrying).

Correlation between Fibrin Fibrillation Kinetics and the Resulting Fibrin Network Microstructure

Fibrin, the prominent extracellular matrix in early wound tissue, is discussed to influence immune cells and healing. The nature of fibrinogen/fibrin to form fibrillary networks is frequently exploited to engineer microenvironments for cellular analysis. This study focuses on revealing the correlation of fibril formation kinetic and the resulting network microstructure of engineered 3D fibrin networks. Different concentrations of fibrinogen (1-3 mg mL^-1 ), thrombin (0.01-0.15 U mL^-1 ), sodium chloride (40-120 mm), and calcium chloride (1-10 mm) are applied to assess the impact on the fibril growth kinetics by turbidity analysis and on the resulting fibril and pore diameter by laser scanning microscopy. The results highlight a direct influence of the sodium chloride concentration on fibrillation kinetics and reveal a strong correlation between fibrillation kinetics and network microstructure. With the assumption of a first-order growth kinetic, an increase of the growth constant k (0.015-0.04 min^-1 ) is found to correlate to a decrease in fibril diameter (1-0.65 µm) and pore diameter (11-5 µm). The new findings enable an easy prediction of 3D fibrin network microstructure by the fibril formation kinetic and contribute to an improved engineering of defined scaffolds for tissue engineering and cell culture applications.

Having siblings promotes a more healthy weight status—Whereas only children are at greater risk for higher BMI in later childhood

Background

Birth order and having at least one sibling are known to be associated with an increased risk for development of overweight. However, there are no studies assessing pre- and postnatal factors for developing overweight within families. Therefore, the present study aimed to analyse the association of the mother’s weight gain during pregnancy, prepregnancy BMI, mother’s age at birth, breastfeeding, age gap between siblings, and physical activity together with sibling-related characteristics on the development of overweight in children and adolescents.

Methods

Data were obtained from the longitudinal LIFE Child cohort. The study sample included n = 1932 children, stratified into first-born (n = 578), second-born (n = 608), third-or-later-born single-born siblings (n = 162), only children (n = 526), and twin children (n = 58). Children with chronic or syndromic diseases, born prematurely or from mothers with gestational diabetes were excluded. Data were adjusted for multiple children per family using mixed models. Pregnancy weight gain, prepregnancy BMI and mother’s age were considered prenatal co-variates. Postnatal factors included the duration of breastfeeding and the children’s physical activity level.

Results

Particularly until the onset of puberty, the BMI-SDS differed between single-born siblings, only children and twins, and increased with birth order. Compared to children with siblings, only children exhibited a strong increase in BMI-SDS starting at age nine. A higher age gap between siblings was associated with a higher BMI-SDS in second- and third-or-later-born children. Single-born siblings had the highest rate and duration of breastfeeding. Physical activity was highest in twins and third-or-later-born children and lowest in only children. In a multivariate model, being an only child showed a highly significant association with BMI-SDS.

Conclusion

The present study demonstrated that siblings had a lower BMI-SDS than only children did. For single-born siblings, the association between birth order and increased BMI-SDS seemed to persist only up to 11 years of age.

Impact of medication on blood transcriptome reveals off-target regulations of beta-blockers

Background

For many drugs, mechanisms of action with regard to desired effects and/or unwanted side effects are only incompletely understood. To investigate possible pleiotropic effects and respective molecular mechanisms, we describe here a catalogue of commonly used drugs and their impact on the blood transcriptome.

Methods and results

From a population-based cohort in Germany (LIFE-Adult), we collected genome-wide gene-expression data in whole blood using in Illumina HT12v4 micro-arrays (n = 3,378; 19,974 gene expression probes per individual). Expression profiles were correlated with the intake of active substances as assessed by participants’ medication. This resulted in a catalogue of fourteen substances that were identified as associated with differential gene expression for a total of 534 genes. As an independent replication cohort, an observational study of patients with suspected or confirmed stable coronary artery disease (CAD) or myocardial infarction (LIFE-Heart, n = 3,008, 19,966 gene expression probes per individual) was employed. Notably, we were able to replicate differential gene expression for three active substances affecting 80 genes in peripheral blood mononuclear cells (carvedilol: 25; prednisolone: 17; timolol: 38). Additionally, using gene ontology enrichment analysis, we demonstrated for timolol a significant enrichment in 23 pathways, 19 of them including either GPER1 or PDE4B. In the case of carvedilol, we showed that, beside genes with well-established association with hypertension (GPER1, PDE4B and TNFAIP3), the drug also affects genes that are only indirectly linked to hypertension due to their effects on artery walls or their role in lipid biosynthesis.

Conclusions

Our developed catalogue of blood gene expressions profiles affected by medication can be used to support both, drug repurposing and the identification of possible off-target effects.

Human induced pluripotent stem cells: From cell origin, genomic stability and epigenetic memory to translational medicine

The potential of human induced pluripotent stem cells (iPSCs) to self-renew indefinitely and to differentiate virtually into any cell type in unlimited quantities makes them attractive for in-vitro disease modeling, drug screening, personalized medicine, and regenerative therapies. As the genome of iPSCs thoroughly reproduces that of the somatic cells from which they are derived, they may possess genetic abnormalities, which would seriously compromise their utility and safety. Genetic aberrations could be present in donor somatic cells and then transferred during iPSC generation, or they could occur as de novo mutations during reprogramming or prolonged cell culture. Therefore, to warrant safety of human iPSCs for clinical applications, analysis of genetic integrity, particularly during iPSC generation and differentiation, should be carried out on a regular basis. On the other hand, reprogramming of somatic cells to iPSCs requires profound modifications in the epigenetic landscape. Changes in chromatin structure by DNA methylations and histone tail modifications aim to reset the gene expression pattern of somatic cells to facilitate and establish self-renewal and pluripotency. However, residual epigenetic memory influences the iPSC phenotype, which may affect their application in disease therapeutics. The present review discusses the somatic cell origin, genetic stability, and epigenetic memory of iPSCs and their impact on basic and translational research.

Elevated expression of the adhesion GPCR ADGRL4/ELTD1 promotes endothelial sprouting angiogenesis without activating canonical GPCR signalling

ADGRL4/ELTD1 is an orphan adhesion GPCR (aGPCR) expressed in endothelial cells that regulates tumour angiogenesis. The majority of aGPCRs are orphan receptors. The Stachel Hypothesis proposes a mechanism for aGPCR activation, in which aGPCRs contain a tethered agonist (termed Stachel) C-terminal to the GPCR-proteolytic site (GPS) cleavage point which, when exposed, initiates canonical GPCR signalling. This has been shown in a growing number of aGPCRs. We tested this hypothesis on ADGRL4/ELTD1 by designing full length (FL) and C-terminal fragment (CTF) ADGRL4/ELTD1 constructs, and a range of potential Stachel peptides. Constructs were transfected into HEK293T cells and HTRF FRET, luciferase-reporter and Alphascreen GPCR signalling assays were performed. A stable ADGRL4/ELTD1 overexpressing HUVEC line was additionally generated and angiogenesis assays, signalling assays and transcriptional profiling were performed. ADGRL4/ELTD1 has the lowest GC content in the aGPCR family and codon optimisation significantly increased its expression. FL and CTF ADGRL4/ELTD1 constructs, as well as Stachel peptides, did not activate canonical GPCR signalling. Furthermore, stable overexpression of ADGRL4/ELTD1 in HUVECs induced sprouting angiogenesis, lowered in vitro anastomoses, and decreased proliferation, without activating canonical GPCR signalling or MAPK/ERK, PI3K/AKT, JNK, JAK/HIF-1α, beta catenin or STAT3 pathways. Overexpression upregulated ANTXR1, SLC39A6, HBB, CHRNA, ELMOD1, JAG1 and downregulated DLL4, KIT, CCL15, CYP26B1. ADGRL4/ELTD1 specifically regulates the endothelial tip-cell phenotype through yet undefined signalling pathways.

Loss of childcare and classroom teaching during the Covid-19-related lockdown in spring 2020: A longitudinal study on consequences on leisure behavior and schoolwork at home

Aim

In spring 2020, the first Covid-19-related lockdown included the closing of kindergartens and schools. Home schooling, the lack of social contacts with peers and the care of the children at home posed an enormous challenge for many families.

Methods

The present study investigated the leisure behavior of 285 one- to 10-year-old German children at two time points (t1 and t2) during the Covid-19-related lockdown in spring 2020. In the subsample of primary school children (n = 102), we also explored children’s attitudes towards schoolwork at home. Analyses focused on the change of behavior from t1 to t2, on differences in these changes depending on socio-economic status (SES), and on associations of behavior with SES, the number of children at home, and the frequency of receiving learning materials from school.

Results

While the frequency of playing outside increased significantly from t1 to t2, the frequency of handicrafts, playing board games, indoor sports, and motivation to do schoolwork decreased. The observed changes between t1 and t2 did not differ depending on SES. However, a lower SES was associated with higher media use, less outdoor activity, and (though only marginally significant) a reduced time doing schoolwork and a reduced ability to concentrate on schoolwork at t1. In households with more children, children played outside more often, but were read to less frequently and (though only marginally significant) watched movies and series less frequently. Children receiving learning materials from school on a regular basis spent significantly more time doing schoolwork at home than children receiving materials only irregularly.

Conclusions

A continuing loss of childcare in day-care facilities and schools entails the danger of declining education in the form of (inter)active indoor activities and schoolwork.

Genome-wide association meta-analysis for early age-related macular degeneration highlights novel loci and insights for advanced disease

BACKGROUND

Advanced age-related macular degeneration (AMD) is a leading cause of blindness. While around half of the genetic contribution to advanced AMD has been uncovered, little is known about the genetic architecture of early AMD.

METHODS

To identify genetic factors for early AMD, we conducted a genome-wide association study (GWAS) meta-analysis (14,034 cases, 91,214 controls, 11 sources of data including the International AMD Genomics Consortium, IAMDGC, and UK Biobank, UKBB). We ascertained early AMD via color fundus photographs by manual grading for 10 sources and via an automated machine learning approach for > 170,000 photographs from UKBB. We searched for early AMD loci via GWAS and via a candidate approach based on 14 previously suggested early AMD variants.

RESULTS

Altogether, we identified 10 independent loci with statistical significance for early AMD: (i) 8 from our GWAS with genome-wide significance (P < 5 × 10- 8), (ii) one previously suggested locus with experiment-wise significance (P < 0.05/14) in our non-overlapping data and with genome-wide significance when combining the reported and our non-overlapping data (together 17,539 cases, 105,395 controls), and (iii) one further previously suggested locus with experiment-wise significance in our non-overlapping data. Of these 10 identified loci, 8 were novel and 2 known for early AMD. Most of the 10 loci overlapped with known advanced AMD loci (near ARMS2/HTRA1, CFH, C2, C3, CETP, TNFRSF10A, VEGFA, APOE), except two that have not yet been identified with statistical significance for any AMD. Among the 17 genes within these two loci, in-silico functional annotation suggested CD46 and TYR as the most likely responsible genes. Presence or absence of an early AMD effect distinguished the known pathways of advanced AMD genetics (complement/lipid pathways versus extracellular matrix metabolism).

CONCLUSIONS

Our GWAS on early AMD identified novel loci, highlighted shared and distinct genetics between early and advanced AMD and provides insights into AMD etiology. Our data provide a resource comparable in size to the existing IAMDGC data on advanced AMD genetics enabling a joint view. The biological relevance of this joint view is underscored by the ability of early AMD effects to differentiate the major pathways for advanced AMD.

Molecular analyses of glioblastoma stem-like cells and glioblastoma tissue

Glioblastoma is a common, malignant brain tumor whose disease incidence increases with age. Glioblastoma stem-like cells (GSCs) are thought to contribute to cancer therapy resistance and to be responsible for tumor initiation, maintenance, and recurrence. This study utilizes both SNP array and gene expression profiling to better understand GSCs and their relation to malignant disease. Peripheral blood and primary glioblastoma tumor tissue were obtained from patients, the latter of which was used to generate GSCs as well as a CD133^pos./CD15^pos. subpopulation. The stem cell features of GSCs were confirmed via the immunofluorescent expression of Nestin, SOX2, and CD133. Both tumor tissue and the isolated primary cells shared unique abnormal genomic characteristics, including a gain of chromosome 7 as well as either a partial or complete loss of chromosome 10. Individual genomic differences were also observed, including the loss of chromosome 4 and segmental uniparental disomy of 9p24.3→p21.3 in GSCs. Gene expression profiling revealed 418 genes upregulated in tumor tissue vs. CD133^pos./CD15^pos. cells and 44 genes upregulated in CD133^pos./CD15^pos. cells vs. tumor tissue. Pathway analyses demonstrated that upregulated genes in CD133^pos./CD15^pos. cells are relevant to cell cycle processes and cancerogenesis. In summary, we detected previously undescribed genomic and gene expression differences when comparing tumor tissue and isolated stem-like subpopulations.

Novel approach to visualize the inter-dependencies between maternal sensitization, breast milk immune components and human milk oligosaccharides in the LIFE Child cohort

Background

Numerous studies have shown that specific components of breast milk, considered separately, are associated with disease status in the mother or the child using univariate analyses. However, very few studies have considered multivariate analysis approaches to evaluate the relationship between multiple breast milk components simultaneously.

Aim

Here we aimed at visualizing breast milk component complex interactions in the context of the allergy status of the mother or the child.

Methods

Milk samples were collected from lactating mothers participating in the Leipziger Forschungszentrum für Zivilisationskrankheiten (LIFE) Child cohort in Leipzig, Germany. A total of 156 breast milk samples, collected at 3 months after birth from mother/infant pairs, were analyzed for 51 breast milk components. Correlation, principal component analysis (PCA) and graphical discovery analysis were used.

Result

Correlations ranging from 0.40 to 0.96 were observed between breast milk fatty acid and breast milk phospholipids levels and correlations ranging from 0 to 0.76 between specific human milk oligosaccharides (HMO) were observed. No separation of the data based on the risk of allergy in the infants was identified using PCA. When graphical discovery analysis was used, dependencies between maternal plasma immunoglobulin E (IgE) level and the breast milk immune marker transforming growth factor-beta 2 (TGF-ß2), between TGF-ß2, breast milk immunoglobulin A (IgA) and TGF-ß1 as well as between breast milk total protein and birth weight were observed. Graphical discovery analysis also exemplifies a possible competition for the fucosyl group between 2’FL, LNFP-I and 3’FL in the HMO group. Additionally, dependencies between immune component IgA and specific HMO (6’SL and blood group A antigen tetraose type 5 or PI-HMO) were identified.

Conclusion

Graphical discovery analysis applied to complex matrices such as breast milk composition can aid in understanding the complexity of interactions between breast milk components and possible relations to health parameters in the mother or the infant. This approach can lead to novel discoveries in the context of health and diseases such as allergy. Our study thus represents the first attempt to visualize the complexity and the inter-dependency of breast milk components.

Does physiological distribution of blood parameters in children depend on socioeconomic status? Results of a German cross-sectional study

OBJECTIVES

In the present study, we examined the relation between socioeconomic status (SES) and the physiological distribution of iron-related blood parameters.

DESIGN

This is a cross-sectional analysis of longitudinal population-based cohort study.

SETTING

Based on a sample of healthy participants from a German research centre, various blood parameters and values of clinical examinations and questionnaires were collected.

PARTICIPANTS

A total of 1206 healthy volunteers aged 2.5 to 19 years, one child per family randomly selected, were included.

PRIMARY AND SECONDARY OUTCOME MEASURES

Associations between the SES of children by Winkler-Stolzenberg Index (WSI) and its dimensions (income, education, occupation) and iron-related blood parameters (haemoglobin, ferritin and transferrin) were analysed by linear regression analyses. Gender and pubertal stage were included as covariables. Additionally, associations between SES of children by WSI and physical activity (side-to-side jumps, push-ups) as well as body mass index (BMI) were analysed by linear regression analyses.

RESULTS

Children with high WSI or family income showed significantly increased z-scores for haemoglobin (P=0.046; P<0.001). Children with increased WSI or family income showed significantly lower z-scores for transferrin (P<0.001). There was a significant correlation between haemoglobin and gender (P<0.001) and between transferrin and pubertal stage (P=0.024). Furthermore, physical activity was positively correlated and BMI was negatively correlated with WSI (P<0.001).

DISCUSSION

Our data show an association between SES and the distribution of iron-dependent parameters. Lower SES is correlated with lower values for haemoglobin and higher values for transferrin. Furthermore, we demonstrate that physical activity and BMI are associated with SES. Whereas higher SES is correlated with higher values for physical activity and lower BMI. Our parameters are standardised as z-scores with the advantages that the results are comparable across different age groups and present physiological courses.

TRIAL REGISTRATION NUMBER

NCT02550236; Results.