reGenotyper: Detecting mislabeled samples in genetic data

In high-throughput molecular profiling studies, genotype labels can be wrongly assigned at various experimental steps; the resulting mislabeled samples seriously reduce the power to detect the genetic basis of phenotypic variation. We have developed an approach to detect potential mislabeling, recover the “ideal” genotype and identify “best-matched” labels for mislabeled samples. On average, we identified 4% of samples as mislabeled in eight published datasets, highlighting the necessity of applying a “data cleaning” step before standard data analysis.

The Amyloid Precursor Protein Controls PIKfyve Function

While the Amyloid Precursor Protein (APP) plays a central role in Alzheimer's disease, its cellular function still remains largely unclear. It was our goal to establish APP function which will provide insights into APP's implication in Alzheimer's disease. Using our recently developed proteo-liposome assay we established the interactome of APP's intracellular domain (known as AICD), thereby identifying novel APP interactors that provide mechanistic insights into APP function. By combining biochemical, cell biological and genetic approaches we validated the functional significance of one of these novel interactors. Here we show that APP binds the PIKfyve complex, an essential kinase for the synthesis of the endosomal phosphoinositide phosphatidylinositol-3,5-bisphosphate. This signalling lipid plays a crucial role in endosomal homeostasis and receptor sorting. Loss of PIKfyve function by mutation causes profound neurodegeneration in mammals. Using C. elegans genetics we demonstrate that APP functionally cooperates with PIKfyve in vivo. This regulation is required for maintaining endosomal and neuronal function. Our findings establish an unexpected role for APP in the regulation of endosomal phosphoinositide metabolism with dramatic consequences for endosomal biology and important implications for our understanding of Alzheimer's disease.

The histone demethylase UTX enables RB-dependent cell fate control

Trimethylation of histone H3 on Lys 27 (H3K27me3) is key for cell fate regulation. The H3K27me3 demethylase UTX functions in development and tumor suppression with undefined mechanisms. Here, genome-wide chromatin occupancy analysis of UTX and associated histone modifications reveals distinct classes of UTX target genes, including genes encoding Retinoblastoma (RB)-binding proteins. UTX removes H3K27me3 and maintains expression of several RB-binding proteins, enabling cell cycle arrest. Genetic interactions in mammalian cells and Caenorhabditis elegans show that UTX regulates cell fates via RB-dependent pathways. Thus, UTX defines an evolutionarily conserved mechanism to enable coordinate transcription of a RB network in cell fate control.

[A proposal of ready-made interpretative comments applicable to serum protein electrophoresis]

Zone electrophoresis for separation and quantification of serum proteins is useful in numerous pathological situations to make clinical diagnostics, to follow the evolution of a disease or to evaluate the efficiency of a treatment. The biologist must apply professional recommendations according to the official nomenclature of biological analysis. He must attach a comment to each result in order to help the physician to perform the best interpretation of the results. To answer those needs, a work of standardization of these comments has been realized by a group of biologists. They are members of the national college of biologists (CNBH). All the commentaries are assembled in a thesaurus which could be a base of ready-made comments, favouring the interpretation of serum protein electrophoresis results.

Chromatin regulation and sumoylation in the inhibition of Ras-induced vulval development in Caenorhabditis elegans

In Caenorhabditis elegans, numerous 'synMuv' (synthetic multivulval) genes encode for chromatin-associated proteins involved in transcriptional repression, including an orthologue of Rb and components of the NuRD histone deacetylase complex. These genes antagonize Ras signalling to prevent erroneous adoption of vulval fate. To identify new components of this mechanism, we performed a genome-wide RNA interference (RNAi) screen. After RNAi of 16 757 genes, we found nine new synMuv genes. Based on predicted functions and genetic epistasis experiments, we propose that at least four post-translational modifications converge to inhibit Ras-stimulated vulval development: sumoylation, histone tail deacetylation, methylation, and acetylation. In addition, we demonstrate a novel role for sumoylation in inhibiting LIN-12/Notch signalling in the vulva. We further show that many of the synMuv genes are involved in gene regulation outside the vulva, negatively regulating the expression of the Delta homologue lag-2. As most of the genes identified in this screen are conserved in humans, we suggest that similar interactions may be relevant in mammals for control of Ras and Notch signalling, crosstalk between these pathways, and cell proliferation.

Genome-wide RNAi screens in Caenorhabditis elegans: impact on cancer research

Genes linked to human cancers often function in evolutionary conserved pathways, and research in C. elegans has been instrumental in dissecting some of the pathways affected, such as apoptosis and Ras signalling. The advent of RNA interference (RNAi) technology has allowed high-throughput loss-of-function analyses of C. elegans gene functions. Here we review some of the most recent genome-wide RNAi screens that have been conducted and discuss their impact on cancer research and possibilities for future screens. We also show that genes causally implicated in human cancers are significantly more likely to have a C. elegans homologue than average, validating the use of C. elegans as a cancer gene discovery platform. We foresee that genome-wide RNAi screens in C. elegans will continue to be productive in identifying new cancer gene candidates and will provide further insights into cancer gene functions.

Tpit-independent function of NeuroD1(BETA2) in pituitary corticotroph differentiation

NeuroD1(BETA2) and Tpit are cell-specific activators of pituitary proopiomelanocortin (POMC) gene transcription. Expression of both factors slightly precedes that of POMC at embryonic d 12.5 of mouse pituitary development. We now report that NeuroD1(BETA2) is required for early corticotroph differentiation. In agreement with the transcriptional synergism observed between Tpit and basic helix-loop-helix dimers containing NeuroD1(BETA2), POMC expression is delayed in NeuroD1-deficient mice. However, this differentiation defect does not reflect a change of corticotroph commitment as revealed by Tpit expression. The delay of corticotroph terminal differentiation is transient and coincides with the developmental window of NeuroD1 expression in corticotrophs. In contrast to their requirement in other NeuroD1-expressing cells, the neurogenin genes do not appear to be necessary for corticotroph differentiation. Taken together with a similar requirement of Tpit for corticotroph differentiation but not for commitment, the present data indicate that the POMC promoter is a point of convergence for independent corticotroph differentiating signals.

Systematic functional analysis of the Caenorhabditis elegans genome using RNAi

A principal challenge currently facing biologists is how to connect the complete DNA sequence of an organism to its development and behaviour. Large-scale targeted-deletions have been successful in defining gene functions in the single-celled yeast Saccharomyces cerevisiae, but comparable analyses have yet to be performed in an animal. Here we describe the use of RNA interference to inhibit the function of approximately 86% of the 19,427 predicted genes of C. elegans. We identified mutant phenotypes for 1,722 genes, about two-thirds of which were not previously associated with a phenotype. We find that genes of similar functions are clustered in distinct, multi-megabase regions of individual chromosomes; genes in these regions tend to share transcriptional profiles. Our resulting data set and reusable RNAi library of 16,757 bacterial clones will facilitate systematic analyses of the connections among gene sequence, chromosomal location and gene function in C. elegans.

Specific protein-protein interaction between basic helix-loop-helix transcription factors and homeoproteins of the Pitx family

Homeoproteins and basic helix-loop-helix (bHLH) transcription factors are known for their critical role in development and cellular differentiation. The pituitary pro-opiomelanocortin (POMC) gene is a target for factors of both families. Indeed, pituitary-specific transcription of POMC depends on the action of the homeodomain-containing transcription factor Pitx1 and of bHLH heterodimers containing NeuroD1. We now show lineage-restricted expression of NeuroD1 in pituitary corticotroph cells and a direct physical interaction between bHLH heterodimers and Pitx1 that results in transcriptional synergism. The interaction between the bHLH and homeodomains is restricted to ubiquitous (class A) bHLH and to the Pitx subfamily. Since bHLH heterodimers interact with Pitx factors through their ubiquitous moiety, this mechanism may be implicated in other developmental processes involving bHLH factors, such as neurogenesis and myogenesis.

NeuroD1/beta2 contributes to cell-specific transcription of the proopiomelanocortin gene

NeuroD1/beta2 is a basic helix-loop-helix (bHLH) factor expressed in the endocrine cells of the pancreas and in a subset of neurons as they undergo terminal differentiation. We now show that NeuroD1 is expressed in corticotroph cells of the pituitary gland and that it is involved in cell-specific transcription of the proopiomelanocortin (POMC) gene. It was previously shown that corticotroph-specific POMC transcription depends in part on the action of cell-restricted bHLH factors that were characterized as the CUTE (corticotroph upstream transcription element) (M. Therrien and J. Drouin, Mol. Cell. Biol. 13:2342-2353, 1993) complexes. We now demonstrate that these complexes contain NeuroD1 in association with various ubiquitous bHLH dimerization partners. The NeuroD1-containing heterodimers specifically recognize and activate transcription from the POMC promoter E box that confers transcriptional specificity. Interestingly, the NeuroD1 heterodimers activate transcription in synergy with Ptx1, a Bicoid-related homeodomain protein, which also contributes to corticotroph specificity of POMC transcription. In the adult pituitary gland, NeuroD1 transcripts are detected in POMC-expressing corticotroph cells. Taken together with the restricted pattern of Ptx1 expression, these results suggest that these two factors establish the basis of a combinatorial code for the program of corticotroph-specific gene expression.

Heterodimeric retinoic acid receptor-beta and retinoid X receptor-alpha complexes stimulate expression of the intercellular adhesion molecule-1 gene

Human intercellular adhesion molecule-1 (ICAM-1), a specific ligand for the leukocyte-function associated antigen-1 and for Mac-1, plays an important role in immune responses. ICAM-1 expression is regulated by various proinflammatory cytokines, phorbol myristate acetate, and retinoic acid. In this study, we investigated the mechanisms of transcriptional control involved in the stimulation of ICAM-1 gene expression by retinoic acid in Cos-1 cells. Deletion mutant analysis provided evidence that a region located between -393 and -176 from the translational start site is critical to retinoic acid stimulation of luciferase activity. This region harbors the consensus sequence for a retinoic acid-responsive element (RARE) 5'-GGGTCATCGCCCTGCCA-3'. The Smal(-270)/Smal (-178) fragment containing this element conferred appropriate retinoic acid responsiveness to an enhancerless SV40 promoter. Cotransfection of expression vectors encoding the retinoic acid receptor alpha, beta, or gamma and retinoid X receptor alpha with reporter plasmids harboring the putative RARE demonstrated that the ICAM-1 gene is regulated by retinoic acid in a retinoic acid receptor beta/retinoid X receptor alpha-dependent fashion. Electrophoretic mobility shift assays showed that ICAM-1 and ADH3 RARE, a well-characterized RARE, display the same band shift pattern, bind retinoic acid receptor beta and retinoid X receptor alpha, and are mutually competitive.

Immunohistochemical localisation of macromolecules of the basement membrane and extracellular matrix of human gliomas and meningiomas

The distribution of type I, III, IV and V collagen in 35 gliomas and 20 meningiomas was studied by indirect immunofluorescence staining. In addition, the presence of fibronectin (FN) and laminin (LN) is also reported. In gliomas expression of type IV collagen and LN was found in the vessel walls and associated with the endothelial glomerulus-like proliferations. FN and type V collagens were located in proliferating vessel walls in a pattern corresponding both to the basement membrane and the perivascular matrix around the vessels. In the extracellular matrix of grade III and IV gliomas occasional faint intercellular fluorescence was also observed with both FN and type V collagen. Type I and III collagens were localised in the vessel walls and in the perivascular connective sheet. Glioma cells did not express any of the antigens investigated. In meningiomas, type IV and V collagens, LN and FN were found in vessel walls, whorls formations and psammoma bodies. These stainings support the hypothesis of a vascular origin of these psammoma bodies which were only found in syncytial and transitional meningiomas. Both type I and III collagens were detected in the perivascular connective tissue. In general, meningioma cells and extracellular matrix did not express any of these molecules, except in transitional meningiomas where occasional fluorescence was observed in extracellular matrix with type V collagen and FN.

Immunohistochemical localization of macromolecules of the basement membrane and the peritumoral stroma in human laryngeal carcinomas

Forty laryngeal carcinomas were studied by immunofluorescence with specific antisera against components of the basement membrane (type IV collagen and laminin) as well as antisera against connective tissue antigens (type V collagen and fibronectin). The basement membrane surrounding well-differentiated squamous cell carcinomas showed an appearance similar to that seen beneath normal epithelium. In contrast, marked alterations of the basement membrane were constantly observed around infiltrating and poorly-differentiated carcinomas. The staining of connective tissue components in most cases was as intense in carcinomas as in normal laryngeal mucosa. The use of antibodies to basement membrane components may help to elucidate the mechanism of invasion of connective tissues by malignant cells.

A method for the evaluation of 3-hydroxyproline in the urine

After hydrolysis of the urine by 6 M HCl, 3-hydroxyproline is purified from many interfering substances by 2 steps of chromatography on Dowex 1 X8 resin equilibrated first in the acetate form and secondly in the OH- form. The amino acid is finally evaluated by chromatography on Dowex 50 M82 resin in a Beckman multichrom amino acid analyzer. In 23 normal adult subjects the mean level was 12.5 +/- 3.5 mumol/24 h. In 8 normal children the level was 6.0 +/- 5 mumol/24 h and in 8 teenagers 15.2 +/- 2.85 mumol/24 h. The ratio of 3-hydroxyproline to 4-hydroxyproline seems indicative of a semiological value of this evaluation in cases of basement membrane collagen deterioration.