Neutrophils prevent rectal bleeding in ulcerative colitis by peptidyl-arginine deiminase-4-dependent immunothrombosis.

OBJECTIVE: Bleeding ulcers and erosions are hallmarks of active ulcerative colitis (UC). However, the mechanisms controlling bleeding and mucosal haemostasis remain elusive. DESIGN: We used high-resolution endoscopy and colon tissue samples of active UC (n = 36) as well as experimental models of physical and chemical mucosal damage in mice deficient for peptidyl-arginine deiminase-4 (PAD4), gnotobiotic mice and controls. We employed endoscopy, histochemistry, live-cell microscopy and flow cytometry to study eroded mucosal surfaces during mucosal haemostasis. RESULTS: Erosions and ulcerations in UC were covered by fresh blood, haematin or fibrin visible by endoscopy. Fibrin layers rather than fresh blood or haematin on erosions were inversely correlated with rectal bleeding in UC. Fibrin layers contained ample amounts of neutrophils coaggregated with neutrophil extracellular traps (NETs) with detectable activity of PAD. Transcriptome analyses showed significantly elevated PAD4 expression in active UC. In experimentally inflicted wounds, we found that neutrophils underwent NET formation in a PAD4-dependent manner hours after formation of primary blood clots, and remodelled clots to immunothrombi containing citrullinated histones, even in the absence of microbiota. PAD4-deficient mice experienced an exacerbated course of dextrane sodium sulfate-induced colitis with markedly increased rectal bleeding (96 % vs 10 %) as compared with controls. PAD4-deficient mice failed to remodel blood clots on mucosal wounds eliciting impaired healing. Thus, NET-associated immunothrombi are protective in acute colitis, while insufficient immunothrombosis is associated with rectal bleeding. CONCLUSION: Our findings uncover that neutrophils induce secondary immunothrombosis by PAD4-dependent mechanisms. Insufficient immunothrombosis may favour rectal bleeding in UC.

DeepCLIP: predicting the effect of mutations on protein-RNA binding with deep learning.

Nucleotide variants can cause functional changes by altering protein-RNA binding in various ways that are not easy to predict. This can affect processes such as splicing, nuclear shuttling, and stability of the transcript. Therefore, correct modeling of protein-RNA binding is critical when predicting the effects of sequence variations. Many RNA-binding proteins recognize a diverse set of motifs and binding is typically also dependent on the genomic context, making this task particularly challenging. Here, we present DeepCLIP, the first method for context-aware modeling and predicting protein binding to RNA nucleic acids using exclusively sequence data as input. We show that DeepCLIP outperforms existing methods for modeling RNA-protein binding. Importantly, we demonstrate that DeepCLIP predictions correlate with the functional outcomes of nucleotide variants in independent wet lab experiments. Furthermore, we show how DeepCLIP binding profiles can be used in the design of therapeutically relevant antisense oligonucleotides, and to uncover possible position-dependent regulation in a tissue-specific manner. DeepCLIP is freely available as a stand-alone application and as a webtool at http://deepclip.compbio.sdu.dk.

Life Satisfaction and mobility: Their associations with career attitudes, and health-related factors among postgraduates having studied in universities intra EU and outside EU.

BACKGROUND: University postgraduates' mobility towards, and outside the EU is continuously increasing, creating a competitive context in which maintaining a high life satisfaction (LS) is a public health challenge. However, the relationship between LS and its determinants among this population are under-documented. Our aims were to measure LS indicators of mobile postgraduates (Intra EU: Who pursue part of their studies in Europe; Outside EU: Who study outside of Europe) versus non-mobile (pursue their studies in Luxembourg), and to analyze the associations between LS and career attitudes, socioeconomic characteristics, and health-related factors for each group. METHOD: Six hundred and sixty-four (644) students obtained financial aid from the Luxembourgish government independent of their family's socioeconomic situation. Contacted by post, they completed an online questionnaire. Analyses included a multiple linear regression model in which only significant relationships (p < 0.05) were used. RESULTS: Three groups were created: Mobile intra EU (n = 381), mobile outside EU (n = 43) and non-mobile (n = 66) postgraduates. Health satisfaction was positively linked to LS, in all groups. Among the mobile outside EU group, majority (63.2%) were men and 57.9% did not live alone - health was the only determinant which contributed to their LS. Among the mobile intra EU, majority (57.8%) were women, and 64.3% not living alone. Autonomy and career adaptability attitudes were positively associated with their LS (b: 0.210 and 0.119, respectively), whereas the worry factor was negatively (b: - 0.153 and -0.159) associated. The non-mobile, were the oldest of the three groups. Majority (51.6%) were women, and 93.7% did not live alone. Career optimism and planning attitudes were positively correlated to their LS (regression parameter estimates (b: 0.400 and 0.212, respectively). CONCLUSIONS: Attention should be devoted to the LS of local and cosmopolitan students, as it seems to be a relevant health indicator. Overall, the farther the mobility was, the higher the postgraduates' general LS (8.5/10) was; this indicator was higher than the LS indicator for the age group 25-34 years 7.53/10 (EU-28, in 2013). University' services could promote the development of career projects and the promotion of health to enhance postgraduates' LS. University policy makers need to ensure this for all students.

The Splicing Efficiency of Activating HRAS Mutations Can Determine Costello Syndrome Phenotype and Frequency in Cancer.

Costello syndrome (CS) may be caused by activating mutations in codon 12/13 of the HRAS proto-oncogene. HRAS p.Gly12Val mutations have the highest transforming activity, are very frequent in cancers, but very rare in CS, where they are reported to cause a severe, early lethal, phenotype. We identified an unusual, new germline p.Gly12Val mutation, c.35_36GC>TG, in a 12-year-old boy with attenuated CS. Analysis of his HRAS cDNA showed high levels of exon 2 skipping. Using wild type and mutant HRAS minigenes, we confirmed that c.35_36GC>TG results in exon 2 skipping by simultaneously disrupting the function of a critical Exonic Splicing Enhancer (ESE) and creation of an Exonic Splicing Silencer (ESS). We show that this vulnerability of HRAS exon 2 is caused by a weak 3' splice site, which makes exon 2 inclusion dependent on binding of splicing stimulatory proteins, like SRSF2, to the critical ESE. Because the majority of cancer- and CS- causing mutations are located here, they affect splicing differently. Therefore, our results also demonstrate that the phenotype in CS and somatic cancers is not only determined by the different transforming potentials of mutant HRAS proteins, but also by the efficiency of exon 2 inclusion resulting from the different HRAS mutations. Finally, we show that a splice switching oligonucleotide (SSO) that blocks access to the critical ESE causes exon 2 skipping and halts proliferation of cancer cells. This unravels a potential for development of new anti-cancer therapies based on SSO-mediated HRAS exon 2 skipping.

Rewealthization in twenty-first century Western countries: the defining trend of the socioeconomic squeeze of the middle class.

The wealth-to-income ratio (WIR) in many Western countries, particularly in Europe and North America, increased by a factor of two in the last three decades. This represents a defining empirical trend: a rewealthization (from the French repatrimonialisation)-or the comeback of (inherited) wealth primacy since the mid-1990s. For the sociology of social stratification, "occupational classes" based on jobs worked must now be understood within a context of wealth-based domination. This paper first illustrates important empirical features of an era of rising WIR. We then outline the theory of rewealthization as a major factor of class transformations in relation to regimes stabilized in the post-WWII industrial area. Compared to the period where wealth became secondary to education and earnings for middle-class lifestyles, rewealthization steepens society's vertical structure; the "olive-shaped" Western society is replaced by a new one where wealth "abundance" at the top masks social reproduction and frustrations below. Supplementary Information: The online version contains supplementary material available at 10.1186/s40711-020-00135-6.

Effects of common atopy-associated amino acid substitutions in the IL-4 receptor alpha chain on IL-4 induced phenotypes.

The human IL-4 receptor alpha chain gene (IL4R) is highly polymorphic and controversial reports have been published with respect to the association of different single nucleotide polymorphisms (SNPs) with atopy markers. Here we analyzed the functional and associational relevance of common IL4R coding SNPs. Transfection of B cell lines expressing the IL-4R variant V75+R576 did not result in enhanced IL-4 induced CD23 expression compared to cell lines expressing the wild type IL-4R alpha chain. Transfection of the IL-4R variant P503 into a murine T cell line did not influence IL-4 induced T-cell proliferation compared to wild type constructs. Analysis of six IL4R coding SNPs (I75V, E400A, C431R, S436L, S503P, Q576R) and common haplotypes (frequency >/=0.05%) in blood donors (n=300) did not indicate a significant association with elevated serum IgE level. Moreover, the most informative IL4R coding SNPs (I75V, C431R, Q576R) and related two- and three-point haplotypes (frequency >/=0.05%) were analyzed in a second, extended group of blood donors (n=689). Again, no significant association with elevated serum IgE was detectable. We conclude that common coding SNPs in the IL4R gene are unlikely to contribute significantly to increased IgE levels and variations outside the coding region may influence atopy susceptibility.