Network Properties of Complex Human Disease Genes Identified through Genome-Wide Association Studies

Background

Previous studies of network properties of human disease genes have mainly focused on monogenic diseases or cancers and have suffered from discovery bias. Here we investigated the network properties of complex disease genes identified by genome-wide association studies (GWAs), thereby eliminating discovery bias.

Principal findings

We derived a network of complex diseases (n = 54) and complex disease genes (n = 349) to explore the shared genetic architecture of complex diseases. We evaluated the centrality measures of complex disease genes in comparison with essential and monogenic disease genes in the human interactome. The complex disease network showed that diseases belonging to the same disease class do not always share common disease genes. A possible explanation could be that the variants with higher minor allele frequency and larger effect size identified using GWAs constitute disjoint parts of the allelic spectra of similar complex diseases. The complex disease gene network showed high modularity with the size of the largest component being smaller than expected from a randomized null-model. This is consistent with limited sharing of genes between diseases. Complex disease genes are less central than the essential and monogenic disease genes in the human interactome. Genes associated with the same disease, compared to genes associated with different diseases, more often tend to share a protein-protein interaction and a Gene Ontology Biological Process.

Conclusions

This indicates that network neighbors of known disease genes form an important class of candidates for identifying novel genes for the same disease.     

Highly efficient base excision repair (BER) in human and rat male germ cells

The quality of germ cell DNA is critical for the fate of the offspring, yet there is limited knowledge of the DNA repair capabilities of such cells. One of the main DNA repair pathways is base excision repair (BER) which is initiated by DNA glycosylases that excise damaged bases, followed by incision of the generated abasic (AP) sites. We have studied human and rat methylpurine-DNA glycosylase (MPG), uracil-DNA glycosylase (UNG), and the major AP endonuclease (HAP1/APEX) in male germ cells. Enzymatic activities and western analyses indicate that these enzymes are present in human and rat male germ cells in amounts that are at least as high as in somatic cells. Minor differences were observed between different cellular stages of rat spermatogenesis and spermiogenesis. Repair of methylated DNA was also studied at the cellular level using the Comet assay. The repair was highly efficient in both human and rat male germ cells, in primary spermatocytes as well as round spermatids, compared to rat mononuclear blood cells or hepatocytes. This efficient BER removes frequently occurring DNA lesions that arise spontaneously or via environmental agents, thereby minimising the number of potential mutations transferred to the next generation.     

Structural basis for a direct interaction between FGFR1 and NCAM and evidence for a regulatory role of ATP

The neural cell adhesion molecule (NCAM) promotes axonal outgrowth, presumably through an interaction with the fibroblast growth factor receptor (FGFR). NCAM also has a little-understood ATPase activity. We here demonstrate for the first time a direct interaction between NCAM (fibronectin type III [F3] modules 1 and 2) and FGFR1 (Ig modules 2 and 3) by surface plasmon resonance (SPR) analysis. The structure of the NCAM F3 module 2 was determined by NMR and the module was shown by NMR to interact with the FGFR1 Ig module 3 and ATP. The NCAM sites binding to FGFR and ATP were found to overlap and ATP was shown by SPR to inhibit the NCAM-FGFR binding, indicating that ATP probably regulates the NCAM-FGFR interaction. Furthermore, we demonstrate that the NCAM module was able to induce activation (phosphorylation) of FGFR and to stimulate neurite outgrowth. In contrast, ATP inhibited neurite outgrowth induced by the module.     

Role of cell signalling involved in induction of apoptosis by benzo[a]pyrene and cyclopenta[c,d]pyrene in Hepa1c1c7 cells

The reactive metabolites of benzo[a]pyrene (B[a]P) and cyclopenta[c,d]pyrene (CPP) induced an accumulation/phosphorylation of p53 in Hepa1c1c7 cells, whereas inhibition of p53 reduced the apoptosis. Judged by the inhibiting effect of wortmannin, phosphatidyl-inositol-3 (PI-3) kinases such as DNA-dependent protein kinase (DNA-PK), ATM (ataxia-telangiectasia mutated), and/or ATR (ATM related kinase), appeared to be involved in the DNA damage recognition and the B[a]P-/CPP-induced accumulation of p53. B[a]P and CPP also induced phosphorylation of jun-N-terminal kinase (JNK) and p38 mitogen activated protein kinase (MAPK). While inhibition of JNK had no effects on the B[a]P-/CPP-induced apoptosis, inhibition of p38 MAPK activity reduced this effect. Interestingly, survival signals such as phosphorylation of Akt and Bad seemed to be induced by the B[a]P-/CPP-compounds. Furthermore, also extracellular signal-regulated kinase (ERK)1/2 was activated and seemed to function as a survival signal in B[a]P-/CPP-induced apoptosis.     

Cost effectiveness of day and inpatient psychiatric treatment: results of a randomised controlled trial.

OBJECTIVE: To compare direct and indirect costs of day and inpatient treatment of acute psychiatric illness. DESIGN: Randomised controlled trial with outcome and costs assessed over 12 months after the date of admission. SETTING: Teaching hospital in an inner city area. SUBJECTS: 179 patients with acute psychiatric illness referred for admission who were suitable for random allocation to day hospital or inpatient treatment. 77 (43%) patients had schizophrenia. INTERVENTIONS: Routine inpatient or day hospital treatment. MAIN OUTCOME MEASURES: Direct and indirect costs over 12 months, clinical symptoms, social functioning, and burden on relatives over the follow up period. RESULTS: Clinical and social outcomes were similar at 12 months, except that inpatients improved significantly faster than day patients and burden on relatives was significantly less in the day hospital group at one year. Median direct costs to the hospital were 1923 pounds (95% confidence interval 750 pounds to 3174 pounds) per patient less for day hospital treatment than inpatient treatment. Indirect costs were greater for day patients; when these were included, overall day hospital treatment was 2165 pounds cheaper than inpatient treatment (95% confidence interval of median difference 737 pounds to 3593 pounds). Including costs to informants when appropriate meant that day hospital treatment was 1994 pounds per patient cheaper (95% confidence interval 600 pounds to 3543 pounds). CONCLUSIONS: Day patient treatment is cheaper for the 30-40% of potential admissions that can be treated in this way. Carers of day hospital patients may bear additional costs. Carers of all patients with acute psychiatric illness are often themselves severely distressed at the time of admission, but day hospital treatment leads to less burden on carers in the long term.     

Fatal mitochondrial myopathy,lactic acidosis,and complex I deficiency associated with a heteroplasmic A→G mutation at position 3251 in the mitochondrial tRNALeu(UUR) gene

A girl, who died at 14 years of age from a rapidly progressive mitochondrial myopathy, was found to be heteroplasmic for a mutation in the mitochondrial tRNALeu(UUR) gene at position 3251. A large proportion of muscle fibres contained accumulations of abnormal mitochondria but no cytochrome c oxidase deficient fibres were present. Polarographic and enzymatic measurements on isolated muscle mitochondria revealed a profound isolated complex I deficiency. A high percentage of mutant mtDNA was found in muscle (94%), fibroblasts (93%), brain (90%), liver (80%), and heart (79%). The family was not available for investigation. For genotype to phenotype correlation studies, we investigated the proportion of mutated mtDNA in single muscle fibres of normal appearance and muscle fibres with accumulations of mitochondria. The proportion of mutant mtDNA was 28% (range < 0.3%–86%) in normal-appearing fibres and 61% (range 15%–88%) in abnormal fibres. The difference in the proportion of mutant mtDNA was highly significant (P < 0.001) between the two groups of fibres.     

Formation of Bacteriolytic Enzymes in Batch and Continuous Culture of Staphylococcus aureus

The formation of bacteriolytic enzymes of Staphylococcus aureus, with special reference to strain M18, was investigated under a variety of conditions. The bacteriolytic activity was tested by using whole cells of Micrococcus lysodeikticus as a substrate. Complex media were required for production, and a Casein Hydrolysate-Yeast Extract medium (CCY(I)) was superior to Brain Heart Infusion and Trypticase Soy Broth. The optimal pH level for production was 7.0. Effective oxygenation and exchange of the beta-glycerophosphate of the CCY(I) medium for glucose increased the rates of growth and autolysis and the rate of appearance of extracellular bacteriolytic enzymes. However, the extracellular lytic activity decreased more rapidly at the end of the growth period than under the standard culture conditions. The appearance of inhibitor(s), probably derived from autolysis, might be responsible for this rapid decrease. The highest yields were obtained in a continuous process in which the activity was almost twice that of batch cultures grown under the same conditions. The bacteriolytic activity produced in continuous culture had a considerably increased stability in the purification process. The advantage of producing unstable bacterial proteins in continuous culture under controlled growth conditions is discussed.     

Patterns and drivers of plant functional group dominance across the Western Hemisphere: a macroecological re‐assessment based on a massive botanical dataset

Plant functional group dominance has been linked to climate, topography and anthropogenic factors. Here, we assess existing theory linking functional group dominance patterns to their drivers by quantifying the spatial distribution of plant functional groups at a 100‐km grid scale. We use a standardized plant species occurrence dataset of unprecedented size covering the entire New World. Functional group distributions were estimated from 3 648 533 standardized occurrence records for a total of 83 854 vascular plant species, extracted from the Botanical Information and Ecology Network (BIEN) database. Seven plant functional groups were considered, describing major differences in structure and function: epiphytes; climbers; ferns; herbs; shrubs; coniferous trees; and angiosperm trees. Two measures of dominance (relative number of occurrences and relative species richness) were analysed against a range of hypothesized predictors. The functional groups showed distinct geographical patterns of dominance across the New World. Temperature seasonality and annual precipitation were most frequently selected, supporting existing hypotheses for the geographical dominance of each functional group. Human influence and topography were secondarily important. Our results support the prediction that future climate change and anthropogenic pressures could shift geographical patterns in dominance of plant functional groups, with probable consequences for ecosystem functioning. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2016, 180 , 141–160.     

Structural studies of the O-antigen from Vibrio cholerae O:21

The O-antigen from Vibrio cholerae O:21 has been investigated, using n.m.r. spectroscopy, methylation analysis, and Smith degradation as the main methods. It is concluded that the O-antigen is composed of tetrasaccharide repeating-units having the following structure (in which Hep = -glycero- -manno-heptose).

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