Genetic factors regulating lung vasculature and immune cell functions associate with resistance to pneumococcal infection

Streptococcus pneumoniae is an important human pathogen responsible for high mortality and morbidity worldwide. The susceptibility to pneumococcal infections is controlled by as yet unknown genetic factors. To elucidate these factors could help to develop new medical treatments and tools to identify those most at risk. In recent years genome wide association studies (GWAS) in mice and humans have proved successful in identification of causal genes involved in many complex diseases for example diabetes, systemic lupus or cholesterol metabolism. In this study a GWAS approach was used to map genetic loci associated with susceptibility to pneumococcal infection in 26 inbred mouse strains. As a result four candidate QTLs were identified on chromosomes 7, 13, 18 and 19. Interestingly, the QTL on chromosome 7 was located within S. pneumoniae resistance QTL (Spir1) identified previously in a linkage study of BALB/cOlaHsd and CBA/CaOlaHsd F2 intercrosses. We showed that only a limited number of genes encoded within the QTLs carried phenotype-associated polymorphisms (22 genes out of several hundred located within the QTLs). These candidate genes are known to regulate TGFb signalling, smooth muscle and immune cells functions. Interestingly, our pulmonary histopathology and gene expression data demonstrated, lung vasculature plays an important role in resistance to pneumococcal infection. Therefore we concluded that the cumulative effect of these candidate genes on vasculature and immune cells functions as contributory factors in the observed differences in susceptibility to pneumococcal infection. We also propose that TGFbmediated regulation of fibroblast differentiation plays an important role in development of invasive pneumococcal disease.This work was supported by the European Union-funded Pneumopath Project HEALTH-F3-2009-222983. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer-reviewedPublisher Versio

Untersuchungen zur Site-III Interleukin-6-artiger Zytokine

Die vorliegende Arbeit sollte einen Beitrag zum besseren Verständnis der komplexen Interaktionen zwischen Zytokinen und Rezeptoren Interleukin-6-artiger Zytokine leisten. Ausgangspunkt für die experimentellen Arbeiten waren die zuvor beschriebenen Designerzytokine IC5 und IC7. Bei diesen war die Glykoprotein 130 (gp130)-bindende Site-III von Interleukin-6 ganz bzw. teilweise durch das entsprechende Leukemia Inhibitory Factor-Rezeptor (LIFR)-Bindungsepitop von Ciliary Neurotrophic Factor (CNTF) ersetzt worden. Hierdurch waren neue Zytokine entstanden, die ihre Bioaktivität nun nicht mehr über ein Homodimer aus gp130, sondern über ein Heterodimer aus gp130 und LIFR entfalten. Eine mögliche Aktivierung des Oncostatin M-Rezeptors (OSMR) durch IC7, das heißt ein Verlust der Spezifität für den LIFR, war bislang nicht untersucht worden. Das überraschende Ergebnis dieser Arbeit ist, dass das LIFR-Bindungsepitop von CNTF nach Übertragung auf ein IL-6-Gerüst in dem Designerzytokin IC7 in der Lage ist, eine Aktivierung des OSMR auf humanen HepG2-Zellen zu induzieren. Experimente mit BaF/3-[gp130, IL-6R, OSMR]-Zellen, einer neu generierten Zelllinie, die neben gp130 und IL-6R zusätzlich den OSM-Rezeptor exprimiert, bestätigten den initialen Befund. Zusätzlich fand sich, dass die in einer früheren Arbeit auf BaF/3-[gp130, IL-6R, LIFR]-Zellen beschriebene ca. 100-fach stärkere Aktivität von IC7 gegenüber IC5 auf BaF/3-[gp130, IL-6R, OSMR]-Zellen verschwindet. Der Verlauf der Aktivitätskurven spricht für einen relativen Aktivitätsverlust von IC7 auf BaF/3-[gp130, IL-6R, OSMR]-Zellen. Allerdings erreichen beide Zytokinchimären in höherer Dosierung die gleiche Aktivität und sogar eine überschießende „Supramaximalaktivität“. Anhand der gelösten 3-D-Struktur des IL-6/IL-6R-Komplexes wurde folgende Hypothese für das veränderte Verhalten der Site-III aufgestellt: Durch eine Interaktion zwischen der Domäne D2 des Interleukin-6-Rezeptors (IL-6R) und einem Teil der zur Site-I gehörenden AB-Schleife von IL-6 kommt es zu einer Stabilisierung derselben. Dies ermöglicht die Interaktion zwischen Site-III, die ebenfalls zum Teil aus der AB-Schleife besteht, und der Ig-Domäne des β-Rezeptors. Dies ist möglicherweise Voraussetzung für eine Bindung zwischen der Domäne-2 des α-Rezeptors und der Ig-artigen Domäne des β-Rezeptors. Insgesamt könnte eine Interaktion der Domäne-2 des α-Rezeptors mit der Ig-artigen Domäne des β-Rezeptors bei allen Interleukin-6-artigen Zytokinen, die einen α-Rezeptor zur Signaltransduktion benötigen, Einfluß auf die Spezifität der Site-III haben. Zum Abschluß dieser Arbeit wurden die experimentellen Grundlagen zur Überprüfung dieser Hypothese durch die Konstruktion des Designerzytokins IC15 sowie die Rezeptorchimären CIR2 und CIR2ΔIg gelegt. IC15 besitzt im Unterschied zu IC7 die komplette AB-Schleife von CNTF. In den Rezeptorchimären sind die Domänen D1 und D2 des IL-6R durch die Domänen D1 bzw. D1 und D2 des CNTFR ersetzt. Auf Zellen, die gp130 und LIFR sowie eine der Rezeptorchimären exprimieren, sollte IC15 so aktiv sein wie LIF. Auf Zellen mit gleicher Ausstattung, aber mit dem OSMR anstelle des LIFR, sollte IC15 dagegen keine Aktivität besitzen. IC15 wurde in E. coli exprimiert, gereinigt und durch Circular Dichroism die strukturelle Integrität nachgewiesen. Für die Rezeptorchimären CIR2 und CIR2ΔIg wurden, als Basis für weiterführende Experimente, optimale Expressionsbedingungen ermittelt und gezeigt, dass sich diese auch in Kombination mit den signaltransduzierenden Untereinheiten gp130 und LIFR in Zellen exprimieren lassen. Die hier gewonnenen Erkenntnisse tragen zu einem besseren Verständis der Rezeptor-Liganden-Interaktion bei und sollen somit langfristig zur Entwicklung spezifischer Agonisten bzw. Antagonisten Interleukin-6-artiger Zytokine beitragen. Angesichts der Vielzahl menschlicher Erkrankungen, bei denen Interleukin-6-artige Zytokine eine entscheidende Rolle spielen, hätte eine Modulation der Zytokinwirkungen ein erhebliches therapeutisches Potenzial

Identifying Biomarkers from Transcriptomic Signatures in Renal Allograft Biopsies Using Deceased and Living Donors.

The survival of transplant kidneys using deceased donors (DD) is inferior to living donors (LD). In this study, we conducted a whole-transcriptome expression analysis of 24 human kidney biopsies paired at 30 minutes and 3 months post-transplantation using DD and LD. The transcriptome profile was found significantly different between two time points regardless of donor types. There were 446 differentially expressed genes (DEGs) between DD and LD at 30 minutes and 146 DEGs at 3 months, with 25 genes common to both time points. These DEGs reflected donor injury and acute immune responses associated with inflammation and cell death as early as at 30 minutes, which could be a precious window of potential intervention. DEGs at 3 months mainly represented the changes of adaptive immunity, immunosuppressive treatment, remodeling or fibrosis via different networks and signaling pathways. The expression levels of 20 highly DEGs involved in kidney diseases and 10 genes dysregulated at 30 minutes were found correlated with renal function and histology at 12 months, suggesting they could be potential biomarkers. These genes were further validated by quantitative polymerase chain reaction (qPCR) in 24 samples analysed by microarray, as well as in a validation cohort of 33 time point unpaired allograft biopsies. This analysis revealed that SERPINA3, SLPI and CBF were up-regulated at 30 minutes in DD compared to LD, while FTCD and TASPN7 were up-regulated at both time points. At 3 months, SERPINA3 was up-regulated in LD, but down-regulated in DD, with increased VCAN and TIMP1, and decreased FOS, in both donors. Taken together, divergent transcriptomic signatures between DD and LD, and changed by the time post-transplantation, might contribute to different allograft survival of two type kidney donors. Some DEGs including FTCD and TASPN7 could be novel biomarkers not only for timely diagnosis, but also for early precise genetic intervention at donor preservation, implantation and post-transplantation, in particular to effectively improve the quality and survival of DD

A Survey on Self-Supervised Representation Learning

Learning meaningful representations is at the heart of many tasks in the field of modern machine learning. Recently, a lot of methods were introduced that allow learning of image representations without supervision. These representations can then be used in downstream tasks like classification or object detection. The quality of these representations is close to supervised learning, while no labeled images are needed. This survey paper provides a comprehensive review of these methods in a unified notation, points out similarities and differences of these methods, and proposes a taxonomy which sets these methods in relation to each other. Furthermore, our survey summarizes the most-recent experimental results reported in the literature in form of a meta-study. Our survey is intended as a starting point for researchers and practitioners who want to dive into the field of representation learning

No evidence of increased mutations in the germline of a group of British nuclear test veterans

Availability of data and materials: The dataset generated during this current study are available https://dataview.ncbi.nlm.nih.gov/object/PRJNA788492?reviewer=t65okctpc20o0jfr3n2rmf5n50Ethical Approval and consent to participate: The GCFT study was conducted in accordance with UK ethical framework and approved by the UK Health Research Authority (17/LO/0273).Copyright © The Author(s) 2022. The potential germline effects of radiation exposure to military veterans present at British nuclear tests in Australia and the South Pacific is of considerable interest. We analyzed germline mutations in 60 families of UK military personnel comprising 30 control and 30 nuclear test veterans (NTV). Using whole-genome sequencing we studied the frequency and spectra of de novo mutations to investigate the transgenerational effect of veterans’ (potential) exposure to radiation at nuclear bomb test sites. We find no elevation in total de novo single nucleotide variants, small insertion-deletions, structural variants or clustered mutations among the offspring of nuclear test veterans compared to those of control personnel. We did observe an elevated occurrence of single base substitution mutations within mutation signature SBS16, due to a subset of NTV offspring. The relevance of this elevation to potential exposure of veteran fathers and, future health risks, require further investigation. Overall, we find no evidence of increased mutations in the germline of a group of British nuclear test veterans. ISRCTN Registry 17461668.Nuclear Community Charity Fund (NCCF) through funds received by The Armed Forces Covenant Fund Trust under the Aged Veterans Fund Grant AVF16 (AM, MS, CG, CR, JP, RA, YD)

BRAF^V600E-mutated serrated colorectal neoplasia drives transcriptional activation of cholesterol metabolism

Abstract BRAF mutations occur early in serrated colorectal cancers, but their long-term influence on tissue homeostasis is poorly characterized. We investigated the impact of short-term (3 days) and long-term (6 months) expression of Braf V600E in the intestinal tissue of an inducible mouse model. We show that Braf V600E perturbs the homeostasis of intestinal epithelial cells, with impaired differentiation of enterocytes emerging after prolonged expression of the oncogene. Moreover, Braf V600E leads to a persistent transcriptional reprogramming with enrichment of numerous gene signatures indicative of proliferation and tumorigenesis, and signatures suggestive of metabolic rewiring. We focused on the top-ranking cholesterol biosynthesis signature and confirmed its increased expression in human serrated lesions. Functionally, the cholesterol lowering drug atorvastatin prevents the establishment of intestinal crypt hyperplasia in Braf V600E -mutant mice. Overall, our work unveils the long-term impact of Braf V600E expression in intestinal tissue and suggests that colorectal cancers with mutations in BRAF might be prevented by statins

A hub and spoke nuclear lamina architecture in trypanosomes

The nuclear lamina supports many functions, including maintaining nuclear structure and gene expression control, and correct spatio-temporal assembly is vital to meet these activities. Recently, multiple lamina systems have been described that, despite independent evolutionary origins, share analogous functions. In trypanosomatids the two known lamina proteins, NUP-1 and NUP-2, have molecular masses of 450 and 170 kDa, respectively, which demands a distinct architecture from the ∼60 kDa lamin-based system of metazoa and other lineages. To uncover organizational principles for the trypanosome lamina we generated NUP-1 deletion mutants to identify domains and their arrangements responsible for oligomerization. We found that both the N- and C-termini act as interaction hubs, and that perturbation of these interactions impacts additional components of the lamina and nuclear envelope. Furthermore, the assembly of NUP-1 terminal domains suggests intrinsic organizational capacity. Remarkably, there is little impact on silencing of telomeric variant surface glycoprotein genes. We suggest that both terminal domains of NUP-1 have roles in assembling the trypanosome lamina and propose a novel architecture based on a hub-and-spoke configuration

Prediction of Human Disease Genes by Human-Mouse Conserved Coexpression Analysis

One of the most limiting aspects of biological research in the post-genomic era is the capability to integrate massive datasets on gene structure and function for producing useful biological knowledge. In this report we have applied an integrative approach to address the problem of identifying likely candidate genes within loci associated with human genetic diseases. Despite the recent progress in sequencing technologies, approaching this problem from an experimental perspective still represents a very demanding task, because the critical region may typically contain hundreds of positional candidates. We found that by concentrating only on genes sharing similar expression profiles in both human and mouse, massive microarray datasets can be used to reliably identify disease-relevant relationships among genes. Moreover, we found that integrating the coexpression criterion with systematic phenome analysis allows efficient identification of disease genes in large genomic regions. Using this approach on 850 OMIM loci characterized by unknown molecular basis, we propose high-probability candidates for 81 genetic diseases

Genetic Association Study Identifies HSPB7 as a Risk Gene for Idiopathic Dilated Cardiomyopathy

Dilated cardiomyopathy (DCM) is a structural heart disease with strong genetic background. Monogenic forms of DCM are observed in families with mutations located mostly in genes encoding structural and sarcomeric proteins. However, strong evidence suggests that genetic factors also affect the susceptibility to idiopathic DCM. To identify risk alleles for non-familial forms of DCM, we carried out a case-control association study, genotyping 664 DCM cases and 1,874 population-based healthy controls from Germany using a 50K human cardiovascular disease bead chip covering more than 2,000 genes pre-selected for cardiovascular relevance. After quality control, 30,920 single nucleotide polymorphisms (SNP) were tested for association with the disease by logistic regression adjusted for gender, and results were genomic-control corrected. The analysis revealed a significant association between a SNP in HSPB7 gene (rs1739843, minor allele frequency 39%) and idiopathic DCM (p = 1.06×10−6, OR = 0.67 [95% CI 0.57–0.79] for the minor allele T). Three more SNPs showed p < 2.21×10−5. De novo genotyping of these four SNPs was done in three independent case-control studies of idiopathic DCM. Association between SNP rs1739843 and DCM was significant in all replication samples: Germany (n = 564, n = 981 controls, p = 2.07×10−3, OR = 0.79 [95% CI 0.67–0.92]), France 1 (n = 433 cases, n = 395 controls, p = 3.73×10−3, OR = 0.74 [95% CI 0.60–0.91]), and France 2 (n = 249 cases, n = 380 controls, p = 2.26×10−4, OR = 0.63 [95% CI 0.50–0.81]). The combined analysis of all four studies including a total of n = 1,910 cases and n = 3,630 controls showed highly significant evidence for association between rs1739843 and idiopathic DCM (p = 5.28×10−13, OR = 0.72 [95% CI 0.65–0.78]). None of the other three SNPs showed significant results in the replication stage

Abdominal aortic aneurysm is associated with a variant in low-density lipoprotein receptor-related protein 1

Abdominal aortic aneurysm (AAA) is a common cause of morbidity and mortality and has a significant heritability. We carried out a genome-wide association discovery study of 1866 patients with AAA and 5435 controls and replication of promising signals (lead SNP with a p value &lt; 1 × 10-5) in 2871 additional cases and 32,687 controls and performed further follow-up in 1491 AAA and 11,060 controls. In the discovery study, nine loci demonstrated association with AAA (p &lt; 1 × 10-5). In the replication sample, the lead SNP at one of these loci, rs1466535, located within intron 1 of low-density-lipoprotein receptor-related protein 1 (LRP1) demonstrated significant association (p = 0.0042). We confirmed the association of rs1466535 and AAA in our follow-up study (p = 0.035). In a combined analysis (6228 AAA and 49182 controls), rs1466535 had a consistent effect size and direction in all sample sets (combined p = 4.52 × 10-10, odds ratio 1.15 [1.10-1.21]). No associations were seen for either rs1466535 or the 12q13.3 locus in independent association studies of coronary artery disease, blood pressure, diabetes, or hyperlipidaemia, suggesting that this locus is specific to AAA. Gene-expression studies demonstrated a trend toward increased LRP1 expression for the rs1466535 CC genotype in arterial tissues; there was a significant (p = 0.029) 1.19-fold (1.04-1.36) increase in LRP1 expression in CC homozygotes compared to TT homozygotes in aortic adventitia. Functional studies demonstrated that rs1466535 might alter a SREBP-1 binding site and influence enhancer activity at the locus. In conclusion, this study has identified a biologically plausible genetic variant associated specifically with AAA, and we suggest that this variant has a possible functional role in LRP1 expression