Machine learning classification of cell-specific cardiac enhancers uncovers developmental subnetworks regulating progenitor cell division and cell fate specification.

The Drosophila heart is composed of two distinct cell types, the contractile cardial cells (CCs) and the surrounding non-muscle pericardial cells (PCs), development of which is regulated by a network of conserved signaling molecules and transcription factors (TFs). Here, we used machine learning with array-based chromatin immunoprecipitation (ChIP) data and TF sequence motifs to computationally classify cell type-specific cardiac enhancers. Extensive testing of predicted enhancers at single-cell resolution revealed the added value of ChIP data for modeling cell type-specific activities. Furthermore, clustering the top-scoring classifier sequence features identified novel cardiac and cell type-specific regulatory motifs. For example, we found that the Myb motif learned by the classifier is crucial for CC activity, and the Myb TF acts in concert with two forkhead domain TFs and Polo kinase to regulate cardiac progenitor cell divisions. In addition, differential motif enrichment and cis-trans genetic studies revealed that the Notch signaling pathway TF Suppressor of Hairless [Su(H)] discriminates PC from CC enhancer activities. Collectively, these studies elucidate molecular pathways used in the regulatory decisions for proliferation and differentiation of cardiac progenitor cells, implicate Su(H) in regulating cell fate decisions of these progenitors, and document the utility of enhancer modeling in uncovering developmental regulatory subnetworks.

[Prostatic stromal tumors of uncertain malignant potential (STUMP): a case report]. / Tumeur stromale prostatique à potentiel malin incertain (STUMP): à propos d'un cas.

We report the case of a patient affected by a voluminous prostatic tumor for which the histological analysis conclude in a stromal tumor of uncertain malignant potential. This type of tumor is rare, but requires to be individualized to differentiate it from a benign prostatic hyperplasia or a sarcoma of the prostate. The therapeutic care must be made keeping in mind the risk of degeneration towards a malignant shape.

The nuclear localization of Drosophila Hsp27 is dependent on a monopartite arginine-rich NLS and is uncoupled from its association to nuclear speckles.

Drosophila Hsp27 is a small heat shock protein displaying exclusive nuclear localization both before and after heat shock. However, the mechanism implicated in this nuclear localization as well as the required sequences, are undefined. This study identifies the Hsp27 sequences mediating its nuclear localization. The generation of chimeric fusions between Hsp27 and Hsp23, a small heat shock protein displaying exclusive cytoplasmic localization, delineated a stretch of 15 amino acids containing a nuclear-targeting activity. Site-directed mutagenesis within this region unveiled the implication of three arginine residues (R54-R55-R56), which differentially combine to form a novel kind of nuclear localization signal (NLS). Abrogation of the nuclear localization signal activity indicated that Drosophila Hsp27 could still enter the nucleus to associate with nuclear speckles in a NLS-independent fashion. Mutagenesis of a putative nuclear export signal unveiled two leucine residues (L50 and L52) specifically involved in the association of Hsp27 to nuclear speckles and revealed novel nuclear structures formed by this Hsp27 mutant. The present study identifies two distinct sets of sequences respectively mediating the nuclear import of Hsp27 and its association to nuclear speckles. These two phenomena are uncoupled and can be separately abrogated.

An integrated strategy for analyzing the unique developmental programs of different myoblast subtypes.

An important but largely unmet challenge in understanding the mechanisms that govern the formation of specific organs is to decipher the complex and dynamic genetic programs exhibited by the diversity of cell types within the tissue of interest. Here, we use an integrated genetic, genomic, and computational strategy to comprehensively determine the molecular identities of distinct myoblast subpopulations within the Drosophila embryonic mesoderm at the time that cell fates are initially specified. A compendium of gene expression profiles was generated for primary mesodermal cells purified by flow cytometry from appropriately staged wild-type embryos and from 12 genotypes in which myogenesis was selectively and predictably perturbed. A statistical meta-analysis of these pooled datasets--based on expected trends in gene expression and on the relative contribution of each genotype to the detection of known muscle genes--provisionally assigned hundreds of differentially expressed genes to particular myoblast subtypes. Whole embryo in situ hybridizations were then used to validate the majority of these predictions, thereby enabling true-positive detection rates to be estimated for the microarray data. This combined analysis reveals that myoblasts exhibit much greater gene expression heterogeneity and overall complexity than was previously appreciated. Moreover, it implicates the involvement of large numbers of uncharacterized, differentially expressed genes in myogenic specification and subsequent morphogenesis. These findings also underscore a requirement for considerable regulatory specificity for generating diverse myoblast identities. Finally, to illustrate how the developmental functions of newly identified myoblast genes can be efficiently surveyed, a rapid RNA interference assay that can be scored in living embryos was developed and applied to selected genes. This integrated strategy for examining embryonic gene expression and function provides a substantially expanded framework for further studies of this model developmental system.

Overexpression of the small mitochondrial Hsp22 extends Drosophila life span and increases resistance to oxidative stress.

Heat shock proteins (Hsp) are involved in protein folding, transport and stress resistance. Studies reporting an increased mRNA level of hsp genes in aged Drosophila suggest that expression of Hsp might be beneficial in preventing damages induced by aging. Because oxidative damage is often observed in aged organisms and mitochondria are sensitive to reactive oxygen species, we tested the hypothesis that increased levels of a small Hsp localized in mitochondria, Hsp22 of Drosophila melanogaster, could protect mitochondrial proteins and influence the aging process. We demonstrate that a ubiquitous or a targeted expression of Hsp22 within motorneurons increases the mean life span by more than 30%. Hsp22 shows beneficial effects on early-aging events since the premortality phase displays the same increase as the mean lifespan. Moreover, flies expressing Hsp22 in their motorneurons maintain their locomotor activity longer as assessed by a negative geotaxis assay. The motorneurons-targeted expression of Hsp22 also significantly increases flies' resistance to oxidative injuries induced by paraquat (up to 35%) and thermal stress (39% at 30 degrees C and 23% at 37 degrees C). These observations establish Hsp22 as a key player in cell-protection mechanisms against oxidative injuries and aging in Drosophila and corroborate the pivotal role of mitochondria in the process of aging.

Gene expression profiling reveals progesterone-mediated cell cycle and immunoregulatory roles of Hoxa-10 in the preimplantation uterus.

Human infertility and recurrent pregnancy loss caused by implantation defects are poorly understood. Hoxa-10-deficient female mice have severe infertility and recurrent pregnancy loss due to defective uterine implantation. Gene expression profiling experiments reveal that Hoxa-10 is an important regulator of two critical events in implantation: stromal cell proliferation and local immunosuppression. At the time of implantation, Hoxa-10 mediates the progesterone-stimulated proliferation of uterine stromal cells. Hoxa-10 mutants express a stromal cell proliferation defect that is accompanied by quantitative or spatial alterations in the expression of two cyclin-dependent kinase inhibitor genes, p57 and p15. Hoxa-10 deficiency also leads to a severe local immunological disturbance, characterized by a polyclonal proliferation of T cells, that occurs in place of the normal progesterone-mediated immunosuppression in the periimplantation uterus.

Expression of the Hsp23 chaperone during Drosophila embryogenesis: association to distinct neural and glial lineages.

BACKGROUND: In addition to their strong induction following stress, small heat shock proteins (Hsp) are also expressed during development in a wide variety of organisms. However, the precise identity of cell(s) expressing these proteins and the functional contribution of small heat shock proteins in such developmental context remain to be determined. The present study provides a detailed description of the Drosophila small heat shock protein Hsp23 expression pattern during embryogenesis and evaluates its functional contribution to central nervous system development. RESULTS: Throughout embryogenesis, Hsp23 is expressed in a stage-specific manner by a restricted number of neuronal and glial lineages of the central nervous system. Hsp23 is also detected in the amnioserosa and within a single lateral chordotonal organ. Its expression within the MP2 lineage does not require the presence of a functional midline nor the activity of the Notch signaling pathway. Transactivation assays demonstrate that transcription factors implicated in the differentiation of the midline also regulate hsp23 promoter activity. Phenotypic analysis of a transgenic line exhibiting loss of Hsp23 expression in the central nervous system suggests that Hsp23 is not required for development and function of this tissue. Likewise, its overexpression does not cause deleterious effects, as development remains unaffected. CONCLUSIONS: Based on the presented data, we suggest that the tightly regulated developmental expression of Hsp23 is not actively involved in cell differentiation and central nervous system development per se but rather reflects a putative role in preventive "pre-stress" neuroprotection or in non-vital process(es) common to the identified cell lineages.

Methane yield as a monitoring parameter for the start-up of anaerobic fixed film reactors.

This paper describes the variation of the methane yield during the start-up period of an anaerobic fluidized bed reactor. After a lag phase, with acclimatized sludge, the methane yield increased with time during biofilm development up to the theoretical steady yield value, reported to be around 0.351 CH4/g CODdeg. The establishment of the biofilm required a high consumption of organic material through the microbial synthesis (anabolism), thereby reducing the proportion of substrate converted to methane. As a result, this yield could be an indirect metabolic parameter for evaluating a start-up operation. It could provide vital information about bacterial fixation processes and is easy to be applied to any biofilm reactor, such as anaerobic filters, where biomass sampling is impracticable. Monitoring this parameter could also give useful dynamic information about the different steps of colonization and biomass attachment, which could be used to improve the start-up performance.

Annexin A1 is regulated by domains cross-talk through post-translational phosphorylation and SUMOYlation.

Mouse prostate membrane-associated proteins of the annexin family showed changes in SUMOylation during androgen treatment. Among these the calcium-binding annexin A1 protein (ANXA1) was chosen for further characterization given its role in protein secretion and cancer. SUMOylation of ANXA1 was confirmed by overexpressing SUMO-1 in LNCaP cells. Site-directed mutagenesis indicated that K257 located in a SUMOylation consensus motif in the C-terminal calcium-binding DA3 repeat domain is SUMOylated. Mutation of the N-terminal Y21 decreased markedly the SUMOylation signal while EGF stimulation increased ANXA1 SUMOylation. A structural analysis of ANXA1 revealed that K257 is located in a hot spot where Ca(2+) and SUMO-1 bind and where a nuclear export signal and a polyubiquitination site are also present. Also, Y21 is buried inside an α-helix structure in the Ca(2+)-free conformation implying that Ca(2+) binding, and the subsequent expelling of the N-terminal α-helix in a disordered conformation, is permissive for its phosphorylation. These results show for the first time that SUMOylation can be regulated by an external signal (EGF) and indicate the presence of a cross-talk between the N-terminal and C-terminal domains of ANXA1 through post-translational modifications.

Variation spatiotemporelle de la cryptorchidie et de l'hypospadias au Québec : Une étude exploratoire.

RéSUMé: OBJECTIFS: : La majorité des études effectuées au cours des dernières décennies ont mis en évidence une augmentation du nombre de cas de cryptorchidie et d'hypospadias entre 1970 et 1990. De plus, l'importante variabilité géographique de ces anomalies est bien décrite. Cette étude vise à mesurer la prévalence à la naissance de la cryptorchidie et de l'hypospadias au Québec, à vérifier si ces anomalies sont en augmentation et à en évaluer la répartition interrégionale. MéTHODE :: Une étude épidémiologique descriptive a été réalisée à partir du nombre de garçons de cinq ans et moins hospitalisés pour une cryptorchidie ou un hypospadias au Québec de 1989 à 2004 selon les données du fichier administratif d'hospitalisation MED-ÉCHO. Les données sur les naissances provenaient de l'Institut de la statistique du Québec. RéSULTATS :: La prévalence annuelle moyenne pour 1000 naissances vivantes de sexe masculin est de 19,1 (IC à 95 % : 18,8-19,4) pour la cryptorchidie et 11,4 (IC à 95 % 11,1-11,6) pour l'hypospadias au Québec. Au cours de la période étudiée, la prévalence de cryptorchidie a légèrement diminué, alors que celle de l'hypospadias est demeurée stable. Comparativement à la province du Québec, des régions présentent une prévalence significativement différente de cryptorchidie et/ou d'hypospadias. . CONCLUSION: : Au Québec, la prévalence de cryptorchidie est en légère diminution alors que celle de l'hypospadias est stable. Des variations régionales significatives sont observables. D'autres études sont nécessaires afin d'évaluer l'hypothèse d'un lien avec les contaminants environnementaux en émergence. L'implantation d'un système de surveillance des anomalies congénitales permettrait une représentation plus valide de la situation.

Gene expression profiling implicates OXPHOS complexes in lifespan extension of flies over-expressing a small mitochondrial chaperone, Hsp22.

Aging is a complex process accompanied by a decreased capacity to tolerate and respond to various stresses. Heat shock proteins as part of cell defense mechanisms are up-regulated following stress. In Drosophila, the mitochondrial Hsp22 is preferentially up-regulated in aged flies. Its over-expression results in an extension of lifespan and an increased resistance to stress. Hsp22 has chaperone-like activity in vitro, but the mechanism(s) by which it increases lifespan in flies are unknown. Genome-wide analysis was performed on long-lived Hsp22+ and control flies to unveil transcriptional changes brought by Hsp22. Transcriptomes obtained at 45days, 90% and 50% survival were then compared between them to focus more on genes up- or down-regulated in presence of higher levels of hsp22 mRNA. Hsp22+ flies display an up-regulation of genes mainly related to mitochondrial energy production and protein biosynthesis, two functions normally down-regulated during aging. Interestingly, among the 26 genes up-regulated in Hsp22+ flies, 7 genes encode for mitochondrial proteins, 5 of which being involved in OXPHOS complexes. Other genes that could influence aging such as CG5002, dGCC185 and GstS1 also displayed a regulation linked to Hsp22 expression. The up-regulation of genes of the OXPHOS system in Hsp22+ flies suggest that mitochondrial homeostasis is at the center of Hsp22 beneficial effects on lifespan.

Proteomic characterization of mouse cytosolic and membrane prostate fractions: high levels of free SUMO peptides are androgen-regulated.

The prostate is a relatively homogeneous tissue that is highly specialized in synthetic and secretory functions. The frequency of malignant growth explains its great clinical significance. We used here a combination of subcellular fractionation, 1-DE (one-dimensional gel electrophoresis) protein separation and mass spectrometry, to establish a prostate protein expression profile in mice. Analysis of proteins present in cytosolic (C) and membrane (P) prostate fractions led to the identification of 619 distinct proteins. A majority of abundant proteins were found to compose the metabolism and protein synthesis machinery. Those identified also correspond to known endoplasmic reticulum and Golgi residents, chaperones and anterograde cargos. They included a series of proteins involved in exocytic/endocytic trafficking. Among the signaling proteins, we identified the ubiquitin-like peptides smt3. We showed that both free small ubiquitin-related modifier SUMO-2/3 and SUMO-1 levels are subject to tight control by the androgen 5alpha-dihydrotestosterone (DHT). By contrast with SUMO-2/3, free SUMO-1 peptides are particularly abundant in the prostate when compared with other tissues. Therefore, we report prostate protein expression profiles of cytosolic and membrane fractions in mice. Our data suggest that the identified free SUMO peptides play an important role in this secretory tissue.

Methylthioadenosine phosphorylase (MTAP) in hearing: gene disruption by chromosomal rearrangement in a hearing impaired individual and model organism analysis.

Genes with a role in the auditory system have been mapped by genetic linkage analysis of families with heritable deafness and then cloned through positional candidate gene approaches. Another positional method for gene discovery is to ascertain deaf individuals with balanced chromosomal translocations and identify disrupted or disregulated genes at the site(s) of rearrangement. We report herein the use of fluorescence in situ hybridization (FISH) to map the breakpoint regions on each derivative chromosome of a de novo apparently balanced translocation, t(8;9)(q12.1;p21.3)dn, in a deaf individual. Chromosomal breakpoints were assigned initially by GTG-banding of metaphase chromosomes and then BAC probes chosen to map precisely the breakpoints by FISH experiments. To facilitate cloning of the breakpoint sequences, further refinement of the breakpoints was performed by FISH experiments using PCR products and by Southern blot analysis. The chromosome 9 breakpoint disrupts methylthioadenosine phosphorylase (MTAP); no known or predicted genes are present at the chromosome 8 breakpoint. Disruption of MTAP is hypothesized to lead to deafness due to the role of MTAP in metabolizing an inhibitor of polyamine synthesis. Drosophila deficient for the MTAP ortholog, CG4,802, were created and their hearing assessed; no hearing loss phenotype was observed. A knockout mouse model for MTAP deficiency was also created and no significant hearing loss was detected in heterozygotes for Mtap. Homozygous Mtap-deficient mice were embryonic lethal.

Disruption of diacylglycerol kinase delta (DGKD) associated with seizures in humans and mice.

We report a female patient with a de novo balanced translocation, 46,X,t(X;2)(p11.2;q37)dn, who exhibits seizures, capillary abnormality, developmental delay, infantile hypotonia, and obesity. The 2q37 breakpoint observed in association with the seizure phenotype is of particular interest, because it lies near loci implicated in epilepsy in humans and mice. Fluorescence in situ hybridization mapping of the translocation breakpoints showed that no known genes are disrupted at Xp11.2, whereas diacylglycerol kinase delta (DGKD) is disrupted at 2q37. Expression studies in Drosophila and mouse suggest that DGKD is involved in central nervous system development and function. Electroencephalographic assessment of Dgkd mutant mice revealed abnormal epileptic discharges and electrographic seizures in three of six homozygotes. These findings implicate DGKD disruption by the t(X;2)(p11.2;q37)dn in the observed phenotype and support a more general role for DGKD in the etiology of seizures.