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Impairment in motor learning of somatostatin null mutant mice.

Somatostatin was first identified as a hypothalamic factor which inhibits the release of growth hormone from the anterior pituitary (somatotropin release inhibitory factor, SRIF). Both SRIF and its receptors were subsequently found widely distributed within and outside the nervous system, in the adult as well as in the developing organism. Reflecting this wide distribution, somatostatin has been implicated regulating a diverse array of biological processes. These include body growth, homeostasis, sensory perception, autonomous functions, rate of intestinal absorption, behavior, including cognition and memory, and developmental processes. We produced null mutant mice lacking somatostatin through targeted mutagenesis. The mutant mice are healthy, fertile, and superficially indistinguishable from their heterozygous and wildtype littermates. A 'first round' phenotype screen revealed that mice lacking somatostatin have elevated plasma growth hormone levels, despite normal body size, and have elevated basal plasma corticosterone levels. In order to uncover subtle and unexpected differences, we carried out a systematic behavioral phenotype screen which identified a significant impairment in motor learning revealed when increased demands were made on motor coordination. Motor coordination and motor learning require an intact cerebellum. While somatostatin is virtually absent from the adult cerebellum, the ligand and its receptor(s) are transiently expressed at high levels in the developing cerebellum. This result suggests the functional significance of transient expression of SRIF and its receptors in the development of the cerebellum.

Animals↗

Comprehensive characterization of the contribution of individual SigB-dependent general stress genes to stress resistance of Bacillus subtilis.

The sigma(B)-dependent general stress regulon of Bacillus subtilis comprises more than 150 members. Induction of this regulon by imposition of environmental or metabolic stress confers multiple, nonspecific, and preemptive stress resistance to nongrowing, nonsporulated cells of B. subtilis. In this study we performed a regulon-wide phenotypic screening analysis to determine the stress sensitivity profiles of 94 mutants defective in candidate members of the general stress regulon that were previously identified in our transcriptional profiling study of the general stress response of B. subtilis. The phenotypic screening analysis included analysis of adaptation to a growth-inhibiting concentration of ethanol (10%, vol/vol) or NaCl (10%, wt/vol), severe heat shock (54 degrees C), and low temperature (survival at 4 degrees C and growth at 12.5 degrees C). Surprisingly, 85% of the mutants tested displayed increased sensitivity at an alpha confidence level of < or =0.01 to at least one of the four stresses tested, and 62% still exhibited increased sensitivity at an alpha of < or =0.001. In essence, we were able to assign 63 genes (28 genes with an alpha of < or =0.001) to survival after ethanol shock, 37 genes (28 genes with an alpha of < or =0.001) to protection from NaCl shock, 34 genes (24 genes with an alpha of < or =0.001) to survival at 4 degrees C, and 10 genes (3 genes with an alpha of < or =0.001) to management of severe heat shock. Interestingly, there was a substantial overlap between the genes necessary for survival during ethanol shock and the genes necessary for survival at 4 degrees C, and there was also an overlap between genes required for survival during ethanol shock and genes required for survival during NaCl shock. Our data provide evidence for the importance of the sigma(B) regulon at low temperatures, not only for growth but also for survival. Moreover, the data imply that a secondary oxidative stress seems to be a common component of the severe stresses tested.

Adaptation, Physiological↗

Random mutagenesis of the gene for the beta-subunit of F1-ATPase from Escherichia coli.

ATP synthesis by oxidative phosphorylation in Escherichia coli occurs in catalytic sites on the beta-subunits of F1-ATPase. Random mutagenesis of the beta-subunit combined with phenotypic screening is potentially important for studies of the catalytic mechanism. However, when applied to haploid strains, this approach is hampered by a preponderance of mutants in which assembly of F1-ATPase in vivo is defective, precluding enzyme purification. Here we mutagenized plasmids carrying the uncD (beta-subunit) gene with hydroxylamine or N-methyl-N'-nitro-N-nitrosoguanidine and isolated, by phenotypic screening and complementation tests, six plasmids carrying mutant uncD alleles. When the mutant plasmids were used to transform a suitable uncD- strain, assembly of F1-ATPase in vivo occurred in each case. Moreover, in one case (beta Gly-223----Asp) F1-ATPase assembly proceeded although it had previously been reported that this mutation, when present on the chromosome of a haploid strain, prevented assembly of the enzyme in vivo. Therefore, this work demonstrates an improved approach for random mutagenesis of the F1-beta-subunit. Six new mutant uncD alleles were identified: beta Cys-137----Tyr; beta Gly-142----Asp; beta Gly-146----Ser; beta Gly-207----Asp; beta-Gly-223----Asp; and a double mutant beta Pro-403----Ser,Gly-415----Asp which we could not separate. The first five of these lie within or very close to the predicted catalytic nucleotide-binding domain of the beta-subunit. The double mutant lies outside this domain; we speculate that the region around residues beta 403-415 is part of an alpha-beta intersubunit contact surface. Membrane ATPase and ATP-driven proton pumping activities were impaired by all six mutations. Purified F1-ATPase was obtained from each mutant and shown to have impaired specific ATPase activity.

Alleles↗

Integrative analysis of the mitochondrial proteome in yeast.

In this study yeast mitochondria were used as a model system to apply, evaluate, and integrate different genomic approaches to define the proteins of an organelle. Liquid chromatography mass spectrometry applied to purified mitochondria identified 546 proteins. By expression analysis and comparison to other proteome studies, we demonstrate that the proteomic approach identifies primarily highly abundant proteins. By expanding our evaluation to other types of genomic approaches, including systematic deletion phenotype screening, expression profiling, subcellular localization studies, protein interaction analyses, and computational predictions, we show that an integration of approaches moves beyond the limitations of any single approach. We report the success of each approach by benchmarking it against a reference set of known mitochondrial proteins, and predict approximately 700 proteins associated with the mitochondrial organelle from the integration of 22 datasets. We show that a combination of complementary approaches like deletion phenotype screening and mass spectrometry can identify over 75% of the known mitochondrial proteome. These findings have implications for choosing optimal genome-wide approaches for the study of other cellular systems, including organelles and pathways in various species. Furthermore, our systematic identification of genes involved in mitochondrial function and biogenesis in yeast expands the candidate genes available for mapping Mendelian and complex mitochondrial disorders in humans.

Chemical Fractionation↗

Rapid screening of phenotypic resistance to nevirapine by direct analysis of HIV type 1 reverse transcriptase activity in plasma.

Drug susceptibility testing for the clinical management of human immunodeficiency virus type 1 (HIV-1)-infected persons is often curtailed because such testing is expensive and time consuming. We describe a non-culture-based phenotypic assay for the rapid analysis of HIV-1 resistance to nevirapine. The assay measures the susceptibility of plasma reverse transcriptase (RT) activity to inhibition by nevirapine by using the PCR-based Amp-RT assay. Assay validation was made using two reference wild-type (WT) and six other nevirapine-resistant (>100-fold) HIV-1 isolates. Amp-RT IC50 values were found to correlate with those obtained by a conventional replication-based assay. The results also indicated that 50 microM nevirapine can be used in a single screening test to detect nevirapine resistance. Analysis of virus mixtures showed a detection threshold of 10% of nevirapine-resistant HIV-1 in a background of WT virus. To evaluate the assay on clinical samples, 30 plasma specimens collected longitudinally from 4 patients before and after treatment with nevirapine were analyzed, and results were compared with codon 181 genotypes. Preteatment samples and those obtained during the first 6 days of therapy (n = 21) were sensitive to nevirapine, and none had detectable Y181C mutation. Phenotypic resistance was seen in eight samples obtained after 1 week of treatment and was correlated with detection of the Y181C mutation. An increase in the level of phenotypic resistance was seen over time. These data validate this rapid and simple assay for monitoring phenotypic resistance to nevirapine.

Anti-HIV Agents↗

Phenotypic expression in detected C282Y homozygous women depends on body mass index.

BACKGROUND/AIMS: In HFE-related haemochromatosis, a large proportion of C282Y homozygotes, especially women, are not detected by phenotypic screening using transferrin saturation. The aim of this study was to identify the clinical and biochemical factors associated with non-expression of the disease as defined as transferrin saturation <45%. METHODS: The study was performed in 78 (57 women and 21 men) C282Y homozygotes identified through a large-scale screening program conducted on 19,644 French subjects. Biometric, clinical and biochemical variables including those susceptible to influence body iron stores were tested for association with transferrin saturation levels <45%. RESULTS: Non-expression was observed in 26/57 (46%) women and in 5/21 (24%) men. At multivariate analysis, female gender (OR: 16.5, 95%CI 1.8-146.5; P = 0.012), body mass index (OR: 1.21, 95%CI 1.02-1.44; P = 0.027), haemoglobin levels (OR: 0.88, 95%CI 0.81-0.97; P = 0.012) and serum ferritin levels (OR: 0.99, 95%CI 0.98-1.00; P = 0.007) were significantly and independently associated with a non-expressing phenotype. CONCLUSIONS: Excess body mass is commonly associated with the lack of phenotypic expression in detected C282Y homozygotes. This should be kept in mind with respect to the design and cost-effectiveness of phenotypic screening programs for haemochromatosis.

Adult↗

EST-based genome-wide gene inactivation identifies ARAP3 as a host protein affecting cellular susceptibility to anthrax toxin.

The lethality of infection by Bacillus anthracis is largely due to its plasmid-encoded toxins, which consist of a carrier protein, the protective antigen (PA), in combination with either the lethal-factor or edema-factor moiety. During B. anthracis infections, PA secreted by bacteria binds to membrane receptors of susceptible cells, is cleaved proteolytically, attaches to lethal factor or edema factor, undergoes oligomerization and internalization, and transports its toxin partners to acidic endosomes where they are released into the cytosol. To identify specific host functions that mediate these events, we used RNA encoded by a lentivirus-based library of approximately 40,000 human ESTs to inactivate chromosomal genes in a human cell population, and we isolated clones that survived PA-dependent toxin-induced death. This phenotypic screen and subsequent analysis identified ARAP3, which is a phosphoinositide-binding protein implicated previously in membrane vesicle trafficking and cytoskeletal organization, as a mammalian host-cell gene that is essential for normal anthrax toxicity. ARAP3 deficiency produced by antisense expression of an ARAP3 EST impaired entry of PA and its bound toxigenic moieties into both human and mouse cells, resulting in reduced toxin sensitivity. Our results demonstrate the usefulness of antisense EST libraries for global chromosomal gene inactivation, establish the practicality of loss-of-function phenotypic screens for the identification of genomic loci required for pathogen effects in mammalian cells, and reveal an important role for ARAP3 in cellular internalization of anthrax toxin.

Adaptor Proteins, Signal Transducing↗

Routine transferrin saturation measurement in liver clinic patients increases detection of hereditary haemochromatosis.

BACKGROUND: Hereditary haemochromatosis (HH) is one of the commonest genetic disorders in European populations. Transferrin saturation (TFS) measurement has been advocated as a phenotypic screening test to improve detection. We undertook a prospective study to examine the value of routine TFS measurement in detecting new cases of HH in unselected liver clinic attenders. METHODS: Non-fasting TFS was measured in new patients. HH mutations were determined in those with elevated TFS (>45%) and all who underwent liver biopsy. Liver biopsy was performed in 349 patients, including all found to be C282Y homozygotes or compound heterozygotes. RESULTS: Of 667 new patients attending over 5 years, 156 had TFS >45% and 18 had significant mutations (12 C282Y homozygotes and six compound heterozygotes). Eleven of the 12 C282Y homozygotes identified had an elevated TFS and 10 had significant hepatic siderosis. Only two of the six compound heterozygotes had an elevated TFS and hepatic siderosis. CONCLUSIONS: The prevalence of new HH cases in patients of European origin attending a liver clinic, detected by phenotypic screening over a 5-year period, was 2.8%. All were identified by a TFS cut off >45%, but TFS >60% provided the best combination of sensitivity and specificity for detecting C282Y homozygosity.

Biopsy↗

Global phenotypic analysis and transcriptional profiling defines the weak acid stress response regulon in Saccharomyces cerevisiae.

Weak organic acids such as sorbate are potent fungistatic agents used in food preservation, but their intracellular targets are poorly understood. We thus searched for potential target genes and signaling components in the yeast genome using contemporary genome-wide functional assays as well as DNA microarray profiling. Phenotypic screening of the EUROSCARF collection revealed the existence of numerous sorbate-sensitive strains. Sorbate hypersensitivity was detected in mutants of the shikimate biosynthesis pathway, strains lacking the PDR12 efflux pump or WAR1, a transcription factor mediating stress induction of PDR12. Using DNA microarrays, we also analyzed the genome-wide response to acute sorbate stress, allowing for the identification of more than 100 genes rapidly induced by weak acid stress. Moreover, a novel War1p- and Msn2p/4p-independent regulon that includes HSP30 was identified. Although induction of the majority of sorbate-induced genes required Msn2p/4p, weak acid tolerance was unaffected by a lack of Msn2p/4p. Ectopic expression of PDR12 from the GAL1-10 promoter fully restored sorbate resistance in a strain lacking War1p, demonstrating that PDR12 is the major target of War1p under sorbic acid stress. Interestingly, comparison of microarray data with results from the phenotypic screening revealed that PDR12 remained as the only gene, which is both stress inducible and required for weak acid resistance. Our results suggest that combining functional assays with transcriptome profiling allows for the identification of key components in large datasets such as those generated by global microarray analysis.

ATP-Binding Cassette Transporters↗

Gene expression profiling and phenotype analyses of S. cerevisiae in response to changing copper reveals six genes with new roles in copper and iron metabolism.

Exhaustive microarray time course analyses of Saccharomyces cerevisiae during copper starvation and copper excess reveal new aspects of metal-induced gene regulation. Aside from identifying targets of established copper- and iron-responsive transcription factors, we find that genes encoding mitochondrial proteins are downregulated and that copper-independent iron transport genes are preferentially upregulated, both during prolonged copper deprivation. The experiments also suggest the presence of a small regulatory iron pool that links copper and iron responses. One hundred twenty-eight genes with putative roles in metal metabolism were further investigated by several systematic phenotype screens. Of the novel phenotypes uncovered, hsp12-Delta and arn1-Delta display increased sensitivity to copper, cyc1-Delta and crr1-Delta show resistance to high copper, vma13-Delta exhibits increased sensitivity to iron deprivation, and pep12-Delta results in reduced growth in high copper and low iron. Besides revealing new components of eukaryotic metal trafficking pathways, the results underscore the previously determined intimate links between iron and copper metabolism and mitochondrial and vacuolar function in metal trafficking. The analyses further suggest that copper starvation can specifically lead to downregulation of respiratory function to preserve iron and copper for other cellular processes.

Amino Acid Motifs↗

Circadian variations of transferrin saturation levels in iron-overloaded patients: implications for the screening of C282Y-linked haemochromatosis.

The phenotypic screening for genetic haemochromatosis (GH) relies upon the determination of transferrin saturation (TS). In large-scale screening programs, the time of blood sampling can be uneasy to control. We studied the circadian variations of TS at 08.00 hours, 12.00 hours, 18.00 hours and 00.00 hours in 46 C282Y homozygous patients (GH) and 47 non-GH patients (NH), to determine whether the time of blood sampling influenced the results of screening. In both groups, there were significant circadian variations in TS, with the highest values at 08.00 hours and the lowest at 00.00 hours. For any given time-point, TS was significantly higher in the GH group when compared with the NH group (P < 0.0001). For both groups, there was a significant decrease in TS between 08.00 hours and 00.00 hours (P < 0.0001) but this decrease was not as significant in GH when compared with NH patients (interaction P < 0.0073). Receiver operating characteristics (ROC) curves generated for TS at 08.00 hours, 12.00 hours, 18.00 hours and 00.00 hours, presented the same efficiency of diagnosis of GH, with TS threshold varying between 64% at 08.00 hours and 36% at 00.00 hours. In conclusion, for screening studies of C282Y homozygosity, determination of transferrin saturation may be performed at any time during the day.

Adult↗

[Should we support large-scale screening for genetic haemochromatosis in France?].

Genetic hemochromatosis meets the principal World Health Organization criteria for diseases warranting systematic population screening. Indeed, it is a frequent, late-onset, severe disease that is easy to diagnose and cure. However, its penetrance is much lower than thought prior to the discovery of the HFE1 gene, whose C282 Y mutation is responsible for more than 95% of cases with phenotypic expression. Moreover, several questions remain to be answered, notably concerning practical modalities [genotypic or phenotypic screening? at what age?, etc.], the risk of genetic discrimination, and cost-effectiveness. Current recommendations should include [i] broad information of the general population and GPs on early symptoms, [ii] transferrin saturation assay in all patients with symptoms compatible with hemochromatosis and, when elevated, genetic testing, the cost of which should be covered by public health insurance, [iii] both phenotypic and genotypic screening of all proband families, and [iv] implementation of regional and national pilot studies aimed at assessing disease penetrance and the acceptability and cost-effectiveness of large-scale screening.

France↗

EMPReSS: European mouse phenotyping resource for standardized screens.

UNLABELLED: Standardized phenotyping protocols are essential for the characterization of phenotypes so that results are comparable between different laboratories and phenotypic data can be related to ontological descriptions in an automated manner. We describe a web-based resource for the visualization, searching and downloading of standard operating procedures and other documents, the European Mouse Phenotyping Resource for Standardized Screens-EMPReSS. AVAILABILITY: Direct access: http://www.empress.har.mrc.ac.uk CONTACT: e.green@har.mrc.ac.uk.

Animals↗

Strategies for early diagnosis of haemochromatosis.

Genetic haemochromatosis is one of the most frequent inborn errors of metabolism. Only patients with early non-cirrhotic haemochromatosis treated by phlebotomies have a normal life expectancy. The present review analyses strategies for early diagnosis of haemochromatosis by using the Medline database and own data from a large cohort of patients with haemochromatosis. The still widely used approach to look for haemochromatosis in the presence of clinical complications such as liver disease will detect haemochromatosis in a considerable percentage of patients with Celtic origin. However, up to one half of these patients will already have an irreversible complication such as liver cirrhosis, diabetes mellitus or cardiomyopathy. In contrast, screening approaches of non-selected asymptomatic subjects using either determination of transferrin saturation and serum ferritin (phenotypic screening) or using genetic testing will detect haemochromatosis in most subjects in a precirrhotic stage without irreversible complications. Both phenotypic and genetic screening are highly cost-effective for detection of iron-loaded individuals in the general population. The current clinical approach to look for haemochromatosis in the presence of clinical disease is unacceptable. Only a more general type of screening in asymptomatic subjects including genetic testing will increase the rate of early diagnosis and will further improve the clinical outcome.

Genetic Testing↗

Pitfalls in newborn hemoglobinopathy screening: failure to detect beta(+)-thalassemia.

Although universal newborn screening can reliably identify all infants with sickle cell hemoglobinopathies, the initial screening result must not be considered the definitive diagnosis. We describe 23 infants whose screening phenotype was FS or FC but whose true phenotype included hemoglobin A, establishing a definitive diagnosis of hemoglobin S or hemoglobin C in combination with beta(+)-thalassemia. Higher than expected hemoglobin concentrations or lower than expected mean erythrocyte volumes should suggest concurrent beta(+)-thalassemia.

Anemia, Sickle Cell↗

Interrogating genomes with combinatorial artificial transcription factor libraries: asking zinc finger questions.

Artificial transcription factors (ATFs) are proteins designed to specifically bind and regulate genes. Because of their DNA-binding selectivity and modular organization, arrays of zinc finger (ZF) domains have traditionally been used to build the ATF's DNA-binding domains. ATFs have been designed and constructed to regulate a variety of therapeutic targets. Recently, novel combinatorial technologies have been developed to induce expression of any gene of interest or to modify cellular phenotypes. Large repertoires of ATFs have been generated by recombination of all available sequence-specific ZF lexicons. These libraries comprise millions of ATFs with unique DNA-binding specificities. The ATFs are produced by combinatorial assembly of three- and six-ZF building blocks and are linked to activator or repressor domains. Upon delivery into a cell population, any gene in the human genome can potentially be regulated. ATF library members generate genome-wide, experimental perturbations of gene expression, resulting in a phenotypically diverse population, or cellular library. A variety of phenotypic screenings can be applied to select for cells exhibiting a phenotype of interest. The ATFs are then used as genetic probes to identify the targeted genes responsible for the phenotypic switch. In this review we will summarize several applications of ATF library screenings in gene discovery, biotechnology, and disease therapeutics.

Chromosome Mapping↗

A modular misexpression screen in Drosophila detecting tissue-specific phenotypes.

Genetic screens in Drosophila have lead to the discovery of many genes important for patterning and signal transduction in diverse organisms. Traditionally, the phenotypic effects of loss-of-function mutations are analyzed. As an alternative way to link genes and function, I have developed a versatile misexpression screen in Drosophila, the first such screen in higher eukaryotes. The screen identifies genes that, when over- or misexpressed in a pattern of interest, give a specific phenotype or modulate an existing mutant phenotype. It is based on Gal4 transactivation of a mobile enhancer and promoter that "targets" random endogenous genes for expression. The modular design of the screen allows directed expression in any temporal or spatial pattern. When activated in the developing eye, 4% of target inserts gave dominant phenotypes. One insertion was in the gene encoding Ras GTPase-activating protein; its overexpression phenotype was strongly enhanced by a mutation in Ras1. Thus, biologically relevant phenotypes and genetic interactions are identified using this method. The screen is a powerful new tool for developmental genetics; similar approaches can also be developed for other organisms.

Animals↗