Molecular and cellular signatures underlying superior immunity against Bordetella pertussis upon pulmonary vaccination

Mucosal immunity is often required for protection against respiratory pathogens but the underlying cellular and molecular mechanisms of induction remain poorly understood. Here, systems vaccinology was used to identify immune signatures after pulmonary or subcutaneous immunization of mice with pertussis outer membrane vesicles. Pulmonary immunization led to improved protection, exclusively induced mucosal immunoglobulin A (IgA) and T helper type 17 (Th17) responses, and in addition evoked elevated systemic immunoglobulin G (IgG) antibody levels, IgG-producing plasma cells, memory B cells, and Th17 cells. These adaptive responses were preceded by unique local expression of genes of the innate immune response related to Th17 (e.g., Rorc) and IgA responses (e.g., Pigr) in addition to local and systemic secretion of Th1/Th17-promoting cytokines. This comprehensive systems approach identifies the effect of the administration route on the development of mucosal immunity, its importance in protection against Bordetella pertussis, and reveals potential molecular correlates of vaccine immunity to this reemerging pathogen.Drug Delivery Technolog

Immunological signatures after Bordetella Pertussis infection demonstrate importance of pulmonary innate immune cells

Drug Delivery Technolog

Bordetella pertussis outer membrane vesicle vaccine confers equal efficacy in mice with milder inflammatory responses compared to a whole-cell vaccine

Drug Delivery Technolog

The clonal relation of primary upper urinary tract urothelial carcinoma and paired urothelial carcinoma of the bladder

The risk of developing urothelial carcinoma of the bladder (UCB) in patients treated by radical nephroureterectomy (RNU) for an upper urinary tract urothelial carcinoma (UTUC) is 22% to 47% in the 2 years after surgery. Subject of debate remains whether UTUC and the subsequent UCB are clonally related or represent separate origins. To investigate the clonal relationship between both entities, we performed targeted DNA sequencing of a panel of 41 genes on matched normal and tumor tissue of 15 primary UTUC patients treated by RNU who later developed 19 UCBs. Based on the detected tumor-specific DNA aberrations, the paired UTUC and UCB(s) of 11 patients (73.3%) showed a clonal relation, whereas in four patients the molecular results did not indicate a clear clonal relationship. Our results support the hypothesis that UCBs following a primary surgically resected UTUC are predominantly clonally derived recurrences and not separate entities

A systematic review and meta-analysis of F-18-fluoro-D-deoxyglucose positron emission tomography interpretation methods in vascular graft and endograft infection

OBJECTIVE: Vascular graft and endograft infection (VGEI) has high morbidity and mortality rates. Diagnosis is complicated since symptoms vary and can be non-specific. A recent meta-analysis identified the use of 18F-fluoro-D-deoxyglucose positron emission tomography-computed tomography (18F-FDG PET(/CT)) as the most valuable tool for diagnosing VGEI and favorable to computed tomography as the current standard. However, the availability and varied use of several interpretation methods, without consensus on which interpretation method is best, complicates clinical use. The aim of this study was to evaluate the diagnostic performance of different interpretation methods of 18F-FDG PET(/CT) in diagnosing VGEI. METHODS: A systematic review was performed according to the PRISMA guidelines. Data sources included PubMed/Medline, Embase, and Cochrane. A meta-analysis was conducted on the different interpretation methods for 18F-FDG PET(/CT) in diagnosing VGEI, including visual FDG uptake intensity, visual FDG uptake pattern, and quantitative SUVmax. RESULTS: Out of 613 articles, 13 were included-10 prospective and 3 retrospective articles. The FDG uptake pattern method (I2 26.2%) showed negligible heterogeneity, while the FDG uptake intensity (I2 42.2%) and SUVmax (I2 42.1%) methods both showed moderate heterogeneity. The pooled sensitivity for FDG uptake intensity was 0.90 (95% CI: 0.79-0.96), for uptake pattern 0.94 (95% CI: 0.89-0.97), and for the SUVmax method 0.95 (95% CI: 0.76-0.99). The pooled specificity for FDG uptake intensity was 0.59 (95% CI: 0.38-0.78), whereas for FDG uptake pattern it was 0.81 (95% CI: 0.71-0.88) and for SUVmax it was 0.77 (95% CI: 0.63-0.87). The uptake pattern interpretation method demonstrated the best positive and negative post-test probability-82% and 10%, respectively. CONCLUSION: This meta-analysis identified the FDG uptake pattern as the most accurate assessment method of 18F-FDG PET(/CT) for diagnosing VGEI. The optimal SUVmax cutoff, depending on the vendor, demonstrated strong sensitivity and moderate specificity

Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Background: Current normalization methods for RNA-sequencing data allow either for intersample comparison to identify differentially expressed (DE) genes or for intrasample comparison for the discovery and validation of gene signatures. Most studies on optimization of normalization methods typically use simulated data to validate methodologies. We describe a new method, GeTMM, which allows for both inter- and intrasample analyses with the same normalized data set. We used actual (i.e. not simulated) RNA-seq data from 263 colon cancers (no biological replicates) and used the same read count data to compare GeTMM with the most commonly used normalization methods (i.e. TMM (used by edgeR), RLE (used by DESeq2) and TPM) with respect to distributions, effect of RNA quality, subtype-classification, recurrence score, recall of DE genes and correlation to RT-qPCR data. Results: We observed a clear benefit for GeTMM and TPM with regard to intrasample comparison while GeTMM performed similar to TMM and RLE normalized data in intersample comparisons. Regarding DE genes, recall was found comparable among the normalization methods, while GeTMM showed the lowest number of false-positive DE genes. Remarkably, we observed limited detrimental effects in samples with low RNA quality. Conclusions: We show that GeTMM outperforms established methods with regard to intrasample comparison while performing equivalent with regard to intersample normalization using the same normalized data. These combined properties enhance the general usefulness of RNA-seq but also the comparability to the many array-based gene expression data in the public domain

Fusion transcripts and their genomic breakpoints in polyadenylated and ribosomal RNA-minus RNA sequencing data

BACKGROUND: Fusion genes are typically identified by RNA sequencing (RNA-seq) without elucidating the causal genomic breakpoints. However, non–poly(A)-enriched RNA-seq contains large proportions of intronic reads that also span genomic breakpoints. RESULTS: We have developed an algorithm, Dr. Disco, that searches for fusion transcripts by taking an entire reference genome into account as search space. This includes exons but also introns, intergenic regions, and sequences that do not meet splice junction motifs. Using 1,275 RNA-seq samples, we investigated to what extent genomic breakpoints can be extracted from RNA-seq data and their implications regarding poly(A)-enriched and ribosomal RNA–minus RNA-seq data. Comparison with whole-genome sequencing data revealed that most genomic breakpoints are not, or minimally, transcribed while, in contrast, the genomic breakpoints of all 32 TMPRSS2-ERG–positive tumours were present at RNA level. We also revealed tumours in which the ERG breakpoint was located before ERG, which co-existed with additional deletions and messenger RNA that incorporated intergenic cryptic exons. In breast cancer we identified rearrangement hot spots near CCND1 and in glioma near CDK4 and MDM2 and could directly associate this with increased expression. Furthermore, in all datasets we find fusions to intergenic regions, often spanning multiple cryptic exons that potentially encode neo-antigens. Thus, fusion transcripts other than classical gene-to-gene fusions are prominently present and can be identified using RNA-seq. CONCLUSION: By using the full potential of non–poly(A)-enriched RNA-seq data, sophisticated analysis can reliably identify expressed genomic breakpoints and their transcriptional effects

Demographic characteristics and quality of life of patients with unexplained complaints: a descriptive study in general practice

OBJECTIVE: About 13% of GPs' consultations involve unexplained complaints (UCs). These complaints can progress to chronic conditions like medically unexplained symptoms, chronic functional symptoms or somatoform disorders. Little is known about the demographic characteristics and quality of life of patients with early stage UCs. Our study objective was to describe these characteristics. Additionally we compared them with other patient groups to serve as a frame of reference. METHODS: Descriptive study in general practices. Patients with early stage UCs who had not had elaborate diagnostic investigations were included. Demographic characteristics were compared to a Dutch general practice population. Quality of life scores were measured with the RAND-36 and compared to another Dutch general practice population and to depressed patients. RESULTS: Data of 466 patients were available for analysis. Mean age was 44 years and 74% were females, mostly higher educated. Of the patients, 63% presented with unexplained fatigue. On average, quality of life was poor (mean RAND-36 domain scores 37-73), also in comparison with other groups. CONCLUSION: General practice patients presenting with UCs have a remarkably poor quality of life. Future research should explore how early identification of patients at risk of developing chronicity can take place. Awareness of potential poor quality of life may influence GPs' medical decision makin

Common Variants in the Type 2 Diabetes KCNQ1 Gene Are Associated with Impairments in Insulin Secretion During Hyperglycaemic Glucose Clamp

Background: Genome-wide association studies in Japanese populations recently identified common variants in the KCNQ1 gene to be associated with type 2 diabetes. We examined the association of these variants within KCNQ1 with type 2 diabetes in a Dutch population, investigated their effects on insulin secretion and metabolic traits and on the risk of developing complications in type 2 diabetes patients. Methodology: The KCNQ1 variants rs151290, rs2237892, and rs2237895 were genotyped in a total of 4620 type 2 diabetes patients and 5285 healthy controls from the Netherlands. Data on macrovascular complications, nephropathy and retinopathy were available in a subset of diabetic patients. Association between genotype and insulin secretion/action was assessed in the additional sample of 335 individuals who underwent a hyperglycaemic clamp. Principal Findings: We found that all the genotyped KCNQ1 variants were significantly associated with type 2 diabetes in our Dutch population, and the association of rs151290 was the strongest (OR 1.20, 95% CI 1.07-1.35, p = 0.002). The risk C-allele of rs151290 was nominally associated with reduced first-phase glucose-stimulated insulin secretion, while the non-risk T-allele of rs2237892 was significantly correlated with increased second-phase glucose-stimulated insulin secretion (p = 0.025 and 0.0016, respectively). In addition, the risk C-allele of rs2237892 was associated with higher LDL and total cholesterol levels (p = 0.015 and 0.003, respectively). We found no evidence for an association of KCNQ1 with diabetic complications. Conclusions: Common variants in the KCNQ1 gene are associated with type 2 diabetes in a Dutch population, which can be explained at least in part by an effect on insulin secretion. Furthermore, our data suggest that KCNQ1 is also associated with lipid metabolism