Inflamm-aging: STAT3 Signaling Pushes Muscle Stem Cells off Balance

Two recent studies shed light on mechanisms underlying muscle dysfunction in age and disease. They reveal that JAK-STAT signaling regulates myogenic differentiation, leading to a reduced reservoir of muscle stem cells. Both genetic and pharmacologic inhibition of STAT3 signaling improve stem cell homeostasis and physiology of aged and dystrophic muscles

HOPPSIGEN: a database of human and mouse processed pseudogenes

Processed pseudogenes result from reverse transcribed mRNAs. In general, because processed pseudogenes lack promoters, they are no longer functional from the moment they are inserted into the genome. Subsequently, they freely accumulate substitutions, insertions and deletions. Moreover, the ancestral structure of processed pseudogenes could be easily inferred using the sequence of their functional homologous genes. Owing to these characteristics, processed pseudogenes represent good neutral markers for studying genome evolution. Recently, there is an increasing interest for these markers, particularly to help gene prediction in the field of genome annotation, functional genomics and genome evolution analysis (patterns of substitution). For these reasons, we have developed a method to annotate processed pseudogenes in complete genomes. To make them useful to different fields of research, we stored them in a nucleic acid database after having annotated them. In this work, we screened both mouse and human complete genomes from ENSEMBL to find processed pseudogenes generated from functional genes with introns. We used a conservative method to detect processed pseudogenes in order to minimize the rate of false positive sequences. Within processed pseudogenes, some are still having a conserved open reading frame and some have overlapping gene locations. We designated as retroelements all reverse transcribed sequences and more strictly, we designated as processed pseudogenes, all retroelements not falling in the two former categories (having a conserved open reading or overlapping gene locations). We annotated 5823 retroelements (5206 processed pseudogenes) in the human genome and 3934 (3428 processed pseudogenes) in the mouse genome. Compared to previous estimations, the total number of processed pseudogenes was underestimated but the aim of this procedure was to generate a high-quality dataset. To facilitate the use of processed pseudogenes in studying genome structure and evolution, DNA sequences from processed pseudogenes, and their functional reverse transcribed homologs, are now stored in a nucleic acid database, HOPPSIGEN. HOPPSIGEN can be browsed on the PBIL (Pôle Bioinformatique Lyonnais) World Wide Web server (http://pbil.univ-lyon1.fr/) or fully downloaded for local installation

Testing the recent theories for the origin of the hermaphrodite flower by comparison of the transcriptomes of gymnosperms and angiosperms

<p>Abstract</p> <p>Background</p> <p>Different theories for the origin of the angiosperm hermaphrodite flower make different predictions concerning the overlap between the genes expressed in the male and female cones of gymnosperms and the genes expressed in the hermaphrodite flower of angiosperms. The Mostly Male (MM) theory predicts that, of genes expressed primarily in male versus female gymnosperm cones, an excess of male orthologs will be expressed in flowers, excluding ovules, while Out Of Male (OOM) and Out Of Female (OOF) theories predict no such excess.</p> <p>Results</p> <p>In this paper, we tested these predictions by comparing the transcriptomes of three gymnosperms (<it>Ginkgo biloba</it>, <it>Welwitschia mirabilis </it>and <it>Zamia fisheri</it>) and two angiosperms (<it>Arabidopsis thaliana </it>and <it>Oryza sativa</it>), using EST data. We found that the proportion of orthologous genes expressed in the reproductive organs of the gymnosperms and in the angiosperms flower is significantly higher than the proportion of orthologous genes expressed in the reproductive organs of the gymnosperms and in the angiosperms vegetative tissues, which shows that the approach is correct. However, we detected no significant differences between the proportion of gymnosperm orthologous genes expressed in the male cone and in the angiosperms flower and the proportion of gymnosperm orthologous genes expressed in the female cone and in the angiosperms flower.</p> <p>Conclusions</p> <p>These results do not support the MM theory prediction of an excess of male gymnosperm genes expressed in the hermaphrodite flower of the angiosperms and seem to support the OOM/OOF theories. However, other explanations can be given for the 1:1 ratio that we found. More abundant and more specific (namely carpel and ovule) expression data should be produced in order to further test these theories.</p

Tsukushi : une nouvelle hépatokine surproduite en réponse à la stéatose hépatique non-alcoolique

L’obésité, dont la prévalence ne cesse d’augmenter, est une préoccupation majeure des services de santé. Elle est associée à de nombreuses pathologies incluant la résistance à l’insuline, le diabète de type 2, la stéatose hépatique, la dyslipidémie, et les maladies cardiovasculaires. La stéatose hépatique non-alcoolique (NAFLD), caractérisée par une accumulation excessive de gras dans le foie, est elle-même associée à la résistance à l’insuline, à l’athérosclérose, et aux maladies cardiovasculaires. En contexte pathologique, le foie sécrète des facteurs nommés hépatokines, qui ont la capacité d’affecter le foie lui-même et les tissus périphériques. Ces facteurs représentent de potentiels biomarqueurs de la santé hépatique et/ou de potentielles cibles thérapeutiques de la NAFLD et des pathologies associées. Notre objectif a été d’identifier et de caractériser de nouvelles hépatokines exprimées et sécrétées en réponse à la stéatose hépatique en contexte d’obésité. Les travaux décrits dans cette thèse identifient Tsukushi (TSK) comme une nouvelle hépatokine exprimée et sécrétée majoritairement par le foie en réponse à l’obésité dans plusieurs modèles murins. TSK est associée à la quantité de triglycérides (TG) hépatiques indépendamment de l’obésité. Le stress du réticulum endoplasmique et l’inflammation, des conditions fortement associées à la NAFLD, régulent TSK. Les études réalisées montrent que TSK n’a pas de rôle dans le développement et la sévérité de la NAFLD. En revanche, des études chez la souris ont permis de mettre en évidence que la surproduction de TSK réduit les niveaux de cholestérol plasmatique et plus particulièrement les particules de haute densité (HDL, high-density lipoprotein), la synthèse d’acides biliaires et le transport inverse de cholestérol. Chez l’humain, l’expression de Tsk est augmentée chez les individus obèses ayant une forte quantité de TG hépatiques et une plus grande inflammation. De plus, TSK est fortement présente dans le plasma de patients souffrants de défaillance hépatique sévère induite par l’acétaminophène. Nous proposons un modèle dans lequel TSK est surproduite en réponse à la NAFLD indépendamment de l’obésité, et induit une réduction du transport inverse du cholestérol probablement dans le but de protéger le foie. Bien que l’effet initial de TSK puisse être bénéfique, une action soutenue dans l’obésité et la NAFLD pourrait contribuer à l’athérosclérose en limitant le transport inverse du cholestérol. L’ensemble de ces résultats montrent que TSK pourrait représenter un nouveau biomarqueur du stress hépatique liant la NAFLD à la dyslipidémie athérogène et à l’athérosclérose.Obesity, whose prevalence is constantly increasing, is a major concern of the health services. It is associated with many pathologies including insulin resistance, type 2 diabetes, fatty liver disease, dyslipidemia and cardiovascular diseases. Non-alcoholic fatty liver disease (NAFLD), characterized by excessive accumulation of fat in the liver, is associated with insulin resistance, atherosclerosis and cardiovascular diseases. In a pathological context, the liver secretes factors called hepatokines, which have the ability to affect the liver itself and peripheral tissues. These factors represent potential biomarkers of liver health and / or potential therapeutic targets of NAFLD and its associated pathologies. Our objective was to identify and characterize new hepatokines expressed and secreted in response to fatty liver in the context of obesity. The work described in this thesis identifies Tsukushi (TSK) as a new hepatokine expressed and secreted mainly by the liver in response to obesity in several mouse models. TSK is associated with the amount of liver triglycerides (TG) regardless of obesity. Endoplasmic reticulum stress and inflammation, conditions strongly associated with NAFLD, regulate TSK. Studies show that TSK has no role in the development and severity of NAFLD. In contrast, studies in mice have shown that the overproduction of TSK reduces plasma cholesterol levels and more particularly high density lipoprotein (HDL), bile acid synthesis and reverse cholesterol transport. In humans, the expression of Tsk is increased in obese individuals with a large amount of hepatic TG and greater inflammation. In addition, TSK is strongly present in the plasma of patients with severe acetaminophen-induced liver failure. We propose a model in which TSK is overproduced in response to NAFLD regardless of obesity, and induces a reduction in reverse cholesterol transport likely to protect the liver. While the initial effect of TSK may be beneficial, sustained action in obesity and NAFLD may contribute to atherosclerosis by limiting the reverse cholesterol transport. All of these results show that TSK could represent a new biomarker of hepatic stress linking NAFLD to atherogenic dyslipidemia and atherosclerosis

Transcriptional Coregulators: Fine-Tuning Metabolism

Metabolic homeostasis requires that cellular energy levels are adapted to environmental cues. This adaptation is largely regulated at the transcriptional level, through the interaction between transcription factors, coregulators, and the basal transcriptional machinery. Coregulators, which function as both metabolic sensors and transcriptional effectors, are ideally positioned to synchronize metabolic pathways to environmental stimuli. The balance between inhibitory actions of corepressors and stimulatory effects of coactivators enables the fine-tuning of metabolic processes. This tight regulation opens therapeutic opportunities to manage metabolic dysfunction by directing the activity of cofactors toward specific transcription factors, pathways, or cells/tissues, thereby restoring whole-body metabolic homeostasis

Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries

BACKGROUND: Serial Analysis of Gene Expression (SAGE) is a method of large-scale gene expression analysis that has the potential to generate the full list of mRNAs present within a cell population at a given time and their frequency. An essential step in SAGE library analysis is the unambiguous assignment of each 14 bp tag to the transcript from which it was derived. This process, called tag-to-gene mapping, represents a step that has to be improved in the analysis of SAGE libraries. Indeed, the existing web sites providing correspondence between tags and transcripts do not concern all species for which numerous EST and cDNA have already been sequenced. RESULTS: This is the reason why we designed and implemented a freely available tool called Identitag for tag identification that can be used in any species for which transcript sequences are available. Identitag is based on a relational database structure in order to allow rapid and easy storage and updating of data and, most importantly, in order to be able to precisely define identification parameters. This structure can be seen like three interconnected modules : the first one stores virtual tags extracted from a given list of transcript sequences, the second stores experimental tags observed in SAGE experiments, and the third allows the annotation of the transcript sequences used for virtual tag extraction. It therefore connects an observed tag to a virtual tag and to the sequence it comes from, and then to its functional annotation when available. Databases made from different species can be connected according to orthology relationship thus allowing the comparison of SAGE libraries between species. We successfully used Identitag to identify tags from our chicken SAGE libraries and for chicken to human SAGE tags interspecies comparison. Identitag sources are freely available on web site. CONCLUSIONS: Identitag is a flexible and powerful tool for tag identification in any single species and for interspecies comparison of SAGE libraries. It opens the way to comparative transcriptomic analysis, an emerging branch of biology

Bioinformatic screening of human ESTs for differentially expressed genes in normal and tumor tissues

BACKGROUND: Owing to the explosion of information generated by human genomics, analysis of publicly available databases can help identify potential candidate genes relevant to the cancerous phenotype. The aim of this study was to scan for such genes by whole-genome in silico subtraction using Expressed Sequence Tag (EST) data. METHODS: Genes differentially expressed in normal versus tumor tissues were identified using a computer-based differential display strategy. Bcl-xL, an anti-apoptotic member of the Bcl-2 family, was selected for confirmation by western blot analysis. RESULTS: Our genome-wide expression analysis identified a set of genes whose differential expression may be attributed to the genetic alterations associated with tumor formation and malignant growth. We propose complete lists of genes that may serve as targets for projects seeking novel candidates for cancer diagnosis and therapy. Our validation result showed increased protein levels of Bcl-xL in two different liver cancer specimens compared to normal liver. Notably, our EST-based data mining procedure indicated that most of the changes in gene expression observed in cancer cells corresponded to gene inactivation patterns. Chromosomes and chromosomal regions most frequently associated with aberrant expression changes in cancer libraries were also determined. CONCLUSION: Through the description of several candidates (including genes encoding extracellular matrix and ribosomal components, cytoskeletal proteins, apoptotic regulators, and novel tissue-specific biomarkers), our study illustrates the utility of in silico transcriptomics to identify tumor cell signatures, tumor-related genes and chromosomal regions frequently associated with aberrant expression in cancer

Automated longitudinal monitoring of in vivo protein aggregation in neurodegenerative disease C. elegans models

Background: While many biological studies can be performed on cell-based systems, the investigation of molecular pathways related to complex human dysfunctions - e.g. neurodegenerative diseases - often requires long-term studies in animal models. The nematode Caenorhabditis elegans represents one of the best model organisms for many of these tests and, therefore, versatile and automated systems for accurate time-resolved analyses on C. elegans are becoming highly desirable tools in the field. Results: We describe a new multi-functional platform for C. elegans analytical research, enabling automated worm isolation and culture, reversible worm immobilization and long-term high-resolution imaging, and this under active control of the main culture parameters, including temperature. We employ our platform for in vivo observation of biomolecules and automated analysis of protein aggregation in a C. elegans model for amyotrophic lateral sclerosis (ALS). Our device allows monitoring the growth rate and development of each worm, at single animal resolution, within a matrix of microfluidic chambers. We demonstrate the progression of individual protein aggregates, i.e. mutated human superoxide dismutase 1 - Yellow Fluorescent Protein (SOD1-YFP) fusion proteins in the body wall muscles, for each worm and over several days. Moreover, by combining reversible worm immobilization and on-chip high-resolution imaging, our method allows precisely localizing the expression of biomolecules within the worms' tissues, as well as monitoring the evolution of single aggregates over consecutive days at the sub-cellular level. We also show the suitability of our system for protein aggregation monitoring in a C. elegans Huntington disease (HD) model, and demonstrate the system's ability to study long-term doxycycline treatment-linked modification of protein aggregation profiles in the ALS model. Conclusion: Our microfluidic-based method allows analyzing in vivo the long-term dynamics of protein aggregation phenomena in C. elegans at unprecedented resolution. Pharmacological screenings on neurodegenerative disease C. elegans models may strongly benefit from this method in the near future, because of its full automation and high-throughput potential

In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions

BACKGROUND: A promising application of the huge amounts of genetic data currently available lies in developing a better understanding of complex diseases, such as cancer. Analysis of publicly available databases can help identify potential candidates for genes or mutations specifically related to the cancer phenotype. In spite of their huge potential to affect gene function, no systematic attention has been paid so far to the changes that occur in untranslated regions of mRNA. RESULTS: In this study, we used Expressed Sequence Tag (EST) databases as a source for cancer-related sequence polymorphism discovery at the whole-genome level. Using a novel computational procedure, we focused on the identification of untranslated region (UTR)-localized non-coding Single Nucleotide Polymorphisms (UTR-SNPs) significantly associated with the tumoral state. To explore possible relationships between genetic mutation and phenotypic variation, bioinformatic tools were used to predict the potential impact of cancer-associated UTR-SNPs on mRNA secondary structure and UTR regulatory elements. We provide a comprehensive and unbiased description of cancer-associated UTR-SNPs that may be useful to define genotypic markers or to propose polymorphisms that can act to alter gene expression levels. Our results suggest that a fraction of cancer-associated UTR-SNPs may have functional consequences on mRNA stability and/or expression. CONCLUSION: We have undertaken a comprehensive effort to identify cancer-associated polymorphisms in untranslated regions of mRNA and to characterize putative functional UTR-SNPs. Alteration of translational control can change the expression of genes in tumor cells, causing an increase or decrease in the concentration of specific proteins. Through the description of testable candidates and the experimental validation of a number of UTR-SNPs discovered on the secreted protein acidic and rich in cysteine (SPARC) gene, this report illustrates the utility of a cross-talk between in silico transcriptomics and cancer genetics

A gradual process of recombination restriction in the evolutionary history of the sex chromosomes in dioecious plants.

To help understand the evolution of suppressed recombination between sex chromosomes, and its consequences for evolution of the sequences of Y-linked genes, we have studied four X-Y gene pairs, including one gene not previously characterized, in plants in a group of closely related dioecious species of Silene which have an X-Y sex-determining system (S. latifolia, S. dioica, and S. diclinis). We used the X-linked copies to build a genetic map of the X chromosomes, with a marker in the pseudoautosomal region (PAR) to orient the map. The map covers a large part of the X chromosomes--at least 50 centimorgans. Except for a recent rearrangement in S. dioica, the gene order is the same in the X chromosomes of all three species. Silent site divergence between the DNA sequences of the X and Y copies of the different genes increases with the genes' distances from the PAR, suggesting progressive restriction of recombination between the X and Y chromosomes. This was confirmed by phylogenetic analyses of the four genes, which also revealed that the least-diverged X-Y pair could have ceased recombining independently in the dioecious species after their split. Analysis of amino acid replacements vs. synonymous changes showed that, with one possible exception, the Y-linked copies appear to be functional in all three species, but there are nevertheless some signs of degenerative processes affecting the genes that have been Y-linked for the longest times. Although the X-Y system evolved quite recently in Silene (less than 10 million years ago) compared to mammals (about 320 million years ago), our results suggest that similar processes have been at work in the evolution of sex chromosomes in plants and mammals, and shed some light on the molecular mechanisms suppressing recombination between X and Y chromosomes