Factors affecting luteinizing hormone releasing hormone and somatostatin release from rat hypothalami in virto

Conditions for the viable maintenance of the isolated rat hypothalamus in culture , have been investigated. Hank's and Earle's media were suitable for incubation but tissue necrosis occurred rapidly in Eagle 's Minimal Essential medium. Hypothalami were suspended in Hank's physiological buffer and factors affecting the release of luteinizing hormone releasing hormone (LHRH) and immunoreactive somatostatin (IRS), investigated. The viability of the tissue was assessed by oxygen consumption and by the rate of protein synthesis. Protein synthesis continued for up to 60 min but declined rapidly during the next 60 min of incubation. Amino acid uptake, however, remained active for 90 min. The rate of LHRH release was constant for the first 60 min of incubation (140 pg/h), thereafter increasing to very high levels (250 pg/h,) concomitant with the decline in protein synthesis, suggestive of loss of cellular integrity and peptide leakage. Release of LHRH from the incubated hypothalamus was found to be a temperature dependent process

IgG subclasses, specific antibodies and immunoglobulin allotypes in children with invasive Haemophilus influenzae type B and Staphylococcus aureus infections

OBJECTIVE: The principal objective of this study was to measure various aspects of immunity in children with invasive infections due to Haemophilus influenzae type b and Staphylococcus aureus. These serious infections are a significant cause of childhood morbidity and mortality in all populations and affect healthy as well as compromised children. Evidence suggests that imbalances or deficiencies in certain aspects of immunity such as IgG subclasses, the capacity to make specific subclass antibodies, antibody affinities, complement isotypes, immunoglobulin allotypes or mannose binding protein may place certain children at risk for developing invasive disease. Investigation of these factors in a group of children with infection necessitated that normal ranges be established for children of comparable ages from the same population. A secondary objective of this study has therefore been to establish normal percentiles for the IgG subclasses in age, race and sex matched healthy controls. METHODS: Patients admitted to the Red Cross War Memorial Children's Hospital with septic meningitis due to Haemophilus influenzae type b and osteomyelitis/septic arthritis due to Haemophilus influenzae type b or Staphylococcus aureus formed the study population. Section A of this thesis describes the methods for establishing, validating and standardizing ELISAs for measuring the IgG subclasses (lgGl, IgG2, IgG3 and IgG4) and subclass antibodies specific to Haemophilus influenzae polyribosylribitol phosphate, Staphylococcus aureus teichoic acid and tetanus toxoid. The relative affinity of antibodies in these ELISAs was determined by the incorporation of diethylamine (DEA). In order to determine the immunoglobulin allotypes ELISAs were developed to measure the G1m(f), G2m(n) and Km(3) allotypes. The frequency of these allotypic markers in the different ethnic groups was established. The relationship between immunoglobulin allotypes and IgG subclass values were investigated in both patient and control groups. RESULTS: ELISA assays to measure IgG subclasses; IgG, IgG 1 and IgG4 tetanus toxoid antibodies; IgG, IgG 1 and IgG2 H. influenzae type b polyribosylribitol phosphate capsular polysaccharide antibodies; IgG, IgG1 and IgG2 S. aureus teichoic acid antibodies and G1m(f), G2m(n) and Km(3) allotypes were successfully established. Where possible the assays were standardized with reference sera and specimens were exchanged with international laboratories. Age, race and sex related percentile charts and tables of normal ranges for IgG and IgG subclasses of Black and Coloured children were established. The IgG and IgG 1 values were higher than those previously reported for children in developed countries. Black children with H. influenzae meningitis had significantly lower IgG 1, IgG2 and IgG3 levels compared to the controls and although similar trends were seen for IgG and IgG4 levels they were not statistically significant. Coloured children with H. influenzae meningitis and Coloured and Black children with H. influenzae osteomyelitis/septic arthritis also showed a similar tendency of lower IgG and IgG subclass levels than the controls but these trends were also not significantly different. All patients responded to tetanus toxoid antigen suggesting normal immunocompetence to protein antigens. H. influenzae type b capsular polysaccharide antibodies were low in children with H. influenzae type b meningitis and osteomyelitis/septic arthritis and did not increase during the illness. IgG and IgG 1 teichoic acid antibodies were raised in patients with S. aureus osteomyelitis/septic arthritis although no further rise in these antibodies was seen when measured several weeks after the illness. The antibody affinity ELISAs showed that IgG 1 tetanus toxoid antibody had a greater affinity than IgG4 tetanus toxoid antibody, the IgG 1 and IgG2 H. influenzae capsular polysaccharide antibodies were of similar affinity and the IgG 1 teichoic acid antibody was of higher affinity than the IgG2 antibody. The G1m(f) and G2m(n) positive allotypes were uncommon in Black but common in the Coloured populations whereas Km(3) was common in both groups. There was a significantly decreased frequency of the G2m(n) positive allotype in Coloured patients with H. influenzae type b meningitis and H. influenzae type b osteomyelitis/septic arthritis which was not found in patients with S. aureus osteomyelitis/septic arthritis. In both Coloured and Black children with H. influenzae meningitis there was a significantly decreased frequency of the Km(3) allotype. No differences in C4 isotypes and mannose binding protein levels were evident in the patient and control groups. CONCLUSION: This study has developed simple, specific and reproducible ELISAs to measure IgG subclasses and subclass antibodies specific to tetanus toxoid, H. influenzae polyribosylribitol phosphate and S. aureus teichoic acid. Age, sex and race related normal ranges for IgG subclasses in the local Black and Coloured populations have been established. Black children with H. influenzae type b meningitis had significantly lower IgG 1, IgG2 and IgG3 levels compared to the controls. There was a clear association between a decrease of the G2m(n) allotype and the Km(3) allotype and susceptibility to invasive infections caused by H. influenzae

A DNA-barcode biodiversity standard analysis method (DNA-BSAM) reveals a large variance in the effect of a range of biological, chemical and physical soil management interventions at different sites, but location is one of the most important aspects determining the nature of agricultural soil microbiology

There are significant knowledge gaps in our understanding of how to sustainably manage agricultural soils to preserve soil biodiversity. Here we evaluate and quantify the effects of agricultural management and location on soil microbiology using nine field trials that have consistently applied different soil management practices in the United Kingdom using DNA barcode sequence data. We tested the basic hypothesis that various agricultural management interventions have a significant and greater effect on soil bacterial and fungal diversity than geographic location. The analyses of soil microbial DNA sequence data to date has lacked standardisation which prevents meaningful comparisons across sites and studies. Therefore, to analyse these data and crucially compare and quantify the size of any effects on soil bacterial and fungal biodiversity between sites, we developed and employed a post-sequencing DNA-barcode biodiversity standard analysis method (DNA-BSAM). The DNA-BSAM comprises a series of standardised bioinformatic steps for processing sequences but more importantly defines a standardised set of ecological indices and statistical tests. Use of the DNA-BSAM reveals the hypothesis was not strongly supported, and this was primarily because: 1) there was a large variance in the effects of various management interventions at different sites, and 2) that location had an equivalent or greater effect size than most management interventions for most metrics. Some dispersed sites imposed the same organic amendments interventions but showed different responses, and this combined with observations of strong differences in soil microbiomes by location tentatively suggests that any effect of management may be contingent on location. This means it could be unreliable to extrapolate the findings of individual trials to others. The widespread use of a standard approach will allow meaningful cross-comparisons between soil microbiome studies and thus a substantial evidence-base of the effects of land-use on soil microbiology to accumulate and inform soil management decisions.Agriculture and Horticulture Development Board (AHDB); British Beet Research Organisation (BBRO

A standardized, evidence-based protocol to assess clinical actionability of genetic disorders associated with genomic variation

Genome and exome sequencing can identify variants unrelated to the primary goal of sequencing. Detecting pathogenic variants associated with an increased risk of a medical disorder enables clinical interventions to improve future health outcomes in patients and their at-risk relatives. The Clinical Genome Resource, or ClinGen, aims to assess clinical actionability of genes and associated disorders as part of a larger effort to build a central resource of information regarding the clinical relevance of genomic variation for use in precision medicine and research

Consensus Statement on Public Involvement and Engagement with Data-Intensive Health Research.

This consensus statement reflects the deliberations of an international group of stakeholders with a range of expertise in public involvement and engagement (PI&E) relating to data-intensive health research. It sets out eight key principles to establish a secure role for PI&E in and with the research community internationally and ensure best practice in its execution. Our aim is to promote culture change and societal benefits through ensuring a socially responsible trajectory for innovations in this field.Peer reviewe

Hundreds of variants clustered in genomic loci and biological pathways affect human height

Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P < 0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.

Hundreds of variants clustered in genomic loci and biological pathways affect human height

Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence phenotype. Genome-wide association (GWA) studies have identified >600 variants associated with human traits1, but these typically explain small fractions of phenotypic variation, raising questions about the utility of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait2,3. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P=0.016), and that underlie skeletal growth defects (P<0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants, and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented amongst variants that alter amino acid structure of proteins and expression levels of nearby genes. Our data explain ∼10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to ∼16% of phenotypic variation (∼20% of heritable variation). Although additional approaches are needed to fully dissect the genetic architecture of polygenic human traits, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways

Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer

Background and aims: Continuing recalcitrance to therapy cements pancreatic cancer (PC) as the most lethal malignancy, which is set to become the second leading cause of cancer death in our society. The study aim was to investigate the association between DNA damage response (DDR), replication stress and novel therapeutic response in PC to develop a biomarker driven therapeutic strategy targeting DDR and replication stress in PC. Methods: We interrogated the transcriptome, genome, proteome and functional characteristics of 61 novel PC patient-derived cell lines to define novel therapeutic strategies targeting DDR and replication stress. Validation was done in patient derived xenografts and human PC organoids. Results: Patient-derived cell lines faithfully recapitulate the epithelial component of pancreatic tumors including previously described molecular subtypes. Biomarkers of DDR deficiency, including a novel signature of homologous recombination deficiency, co-segregates with response to platinum (P &lt; 0.001) and PARP inhibitor therapy (P &lt; 0.001) in vitro and in vivo. We generated a novel signature of replication stress with which predicts response to ATR (P &lt; 0.018) and WEE1 inhibitor (P &lt; 0.029) treatment in both cell lines and human PC organoids. Replication stress was enriched in the squamous subtype of PC (P &lt; 0.001) but not associated with DDR deficiency. Conclusions: Replication stress and DDR deficiency are independent of each other, creating opportunities for therapy in DDR proficient PC, and post-platinum therapy

Phenotypic Characterization of EIF2AK4 Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension.

BACKGROUND: Pulmonary arterial hypertension (PAH) is a rare disease with an emerging genetic basis. Heterozygous mutations in the gene encoding the bone morphogenetic protein receptor type 2 (BMPR2) are the commonest genetic cause of PAH, whereas biallelic mutations in the eukaryotic translation initiation factor 2 alpha kinase 4 gene (EIF2AK4) are described in pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Here, we determine the frequency of these mutations and define the genotype-phenotype characteristics in a large cohort of patients diagnosed clinically with PAH. METHODS: Whole-genome sequencing was performed on DNA from patients with idiopathic and heritable PAH and with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis recruited to the National Institute of Health Research BioResource-Rare Diseases study. Heterozygous variants in BMPR2 and biallelic EIF2AK4 variants with a minor allele frequency of <1:10 000 in control data sets and predicted to be deleterious (by combined annotation-dependent depletion, PolyPhen-2, and sorting intolerant from tolerant predictions) were identified as potentially causal. Phenotype data from the time of diagnosis were also captured. RESULTS: Eight hundred sixty-four patients with idiopathic or heritable PAH and 16 with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis were recruited. Mutations in BMPR2 were identified in 130 patients (14.8%). Biallelic mutations in EIF2AK4 were identified in 5 patients with a clinical diagnosis of pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Furthermore, 9 patients with a clinical diagnosis of PAH carried biallelic EIF2AK4 mutations. These patients had a reduced transfer coefficient for carbon monoxide (Kco; 33% [interquartile range, 30%-35%] predicted) and younger age at diagnosis (29 years; interquartile range, 23-38 years) and more interlobular septal thickening and mediastinal lymphadenopathy on computed tomography of the chest compared with patients with PAH without EIF2AK4 mutations. However, radiological assessment alone could not accurately identify biallelic EIF2AK4 mutation carriers. Patients with PAH with biallelic EIF2AK4 mutations had a shorter survival. CONCLUSIONS: Biallelic EIF2AK4 mutations are found in patients classified clinically as having idiopathic and heritable PAH. These patients cannot be identified reliably by computed tomography, but a low Kco and a young age at diagnosis suggests the underlying molecular diagnosis. Genetic testing can identify these misclassified patients, allowing appropriate management and early referral for lung transplantation

Comprehensive Cancer-Predisposition Gene Testing in an Adult Multiple Primary Tumor Series Shows a Broad Range of Deleterious Variants and Atypical Tumor Phenotypes.

Multiple primary tumors (MPTs) affect a substantial proportion of cancer survivors and can result from various causes, including inherited predisposition. Currently, germline genetic testing of MPT-affected individuals for variants in cancer-predisposition genes (CPGs) is mostly targeted by tumor type. We ascertained pre-assessed MPT individuals (with at least two primary tumors by age 60 years or at least three by 70 years) from genetics centers and performed whole-genome sequencing (WGS) on 460 individuals from 440 families. Despite previous negative genetic assessment and molecular investigations, pathogenic variants in moderate- and high-risk CPGs were detected in 67/440 (15.2%) probands. WGS detected variants that would not be (or were not) detected by targeted resequencing strategies, including low-frequency structural variants (6/440 [1.4%] probands). In most individuals with a germline variant assessed as pathogenic or likely pathogenic (P/LP), at least one of their tumor types was characteristic of variants in the relevant CPG. However, in 29 probands (42.2% of those with a P/LP variant), the tumor phenotype appeared discordant. The frequency of individuals with truncating or splice-site CPG variants and at least one discordant tumor type was significantly higher than in a control population (χ2 = 43.642; p ≤ 0.0001). 2/67 (3%) probands with P/LP variants had evidence of multiple inherited neoplasia allele syndrome (MINAS) with deleterious variants in two CPGs. Together with variant detection rates from a previous series of similarly ascertained MPT-affected individuals, the present results suggest that first-line comprehensive CPG analysis in an MPT cohort referred to clinical genetics services would detect a deleterious variant in about a third of individuals.JW is supported by a Cancer Research UK Cambridge Cancer Centre Clinical Research Training Fellowship. Funding for the NIHR BioResource – Rare diseases project was provided by the National Institute for Health Research (NIHR, grant number RG65966). ERM acknowledges support from the European Research Council (Advanced Researcher Award), NIHR (Senior Investigator Award and Cambridge NIHR Biomedical Research Centre), Cancer Research UK Cambridge Cancer Centre and Medical Research Council Infrastructure Award. The University of Cambridge has received salary support in respect of EM from the NHS in the East of England through the Clinical Academic Reserve. The views expressed are those of the authors and not necessarily those of the NHS or Department of Health. DGE is an NIHR Senior Investigator and is supported by the all Manchester NIHR Biomedical Research Centre