Biomedical subjects

Jean-Christophe Aude

Publications and source records attributed to Jean-Christophe Aude.

7 recordsLinked to original sources

PubMed2005

T-cell transcriptome analysis points up a thymic disorder in idiopathic nephrotic syndrome.

BACKGROUND: Idiopathic nephrotic syndrome is a proteinuric disease secondary to the release of a nonidentified circulating glomerular permeability factor by T cells. Because specificities of T-cell activation in idiopathic nephrotic syndrome remain unknown, we evaluated transcriptional activation of T cells in nephrotic patients during proteinuria. METHODS: Transcriptomes of CD2+ cells were analyzed by serial analysis of gene expression (SAGE) in a nephrotic child during proteinuria relapse and after remission, away from any immunosuppressive treatment. Expression of specific transcripts overexpressed during proteinuria relapse was compared by reverse transcription-polymerase chain reaction (RT-PCR) in CD2+ cells from 11 nephrotic patients during relapse and remission and 11 non nephrotic patients during infection and after recovery. RESULTS: Differential analysis of CD2+ cell transcriptome identified >200 mRNA tags overexpressed during proteinuria relapse, including many T-cell markers. RT-PCR analysis of expression of specific transcripts indicated that (1) under remission conditions, nephrotic children displayed induction of four transcripts, including IKBKB, and repression of NFKBIA as compared to non nephrotic children after recovery, and (2) proteinuria relapse was associated with induction of L-selectin and T-lymphocyte maturation-associated protein, two markers of T-cell differentiation and recent emigrant/naive T cells. CONCLUSION: Results indicate that circulating T cells from relapsing nephrotic patients include a significant population of low-mature cells while those from nephrotic patients in remission are characterized by constitutive activation of nuclear factor-kappaB (NF-kappaB), altogether suggesting a thymic dysregulation of apoptosis in nephrotic patients.

CD2 Antigens↗

PubMed2004

Balancing protein similarity and gene co-expression reveals new links between genetic conservation and developmental diversity in invertebrates.

MOTIVATION: To identify genetic conservation relative to precise aspects of developmental diversity, an essential question in computational biology, we developed a new comparative method that allows conserved modules for the best balance between protein sequence similarity and gene co-expression to be constructed, in invertebrates. RESULTS: Our method, referred to as the best-balance constraint procedure (BBCP), yielded 719 functionally conserved modules (FCMs) comprising 2-23 gene pairs. These modules were consistent with the developmental roles of orthologues as inferred from Gene Ontology, RNAi knockouts, InterPro and process-specific microarray data. New relationships were defined between genetic conservation and developmental diversity. Novel gene associations were indeed found in 94% of the FCMs, 150 modules being completely new. A significant proportion of the FCMs (18%, 132 modules) described cell type-specific mechanisms, comprising neuronal, muscle and germ cell signaling, new associations being found in 125 modules. Also found were gene associations for cell fate specification activities previously not highlighted by computational means, e.g. in FCMs containing homeogenes. These data indicate that highly discriminative description of genetic conservation can be deduced using BBCP, and reveal new correlations between cellular and developmental diversity and gene essentiality in invertebrates. CONTACT: christian.neri@broca.inserm.fr SUPPLEMENTARY INFORMATION: For supplementary information, please refer to Bioinformatics online.

Animals↗

PubMed2004

Mammalian antioxidant defenses are not inducible by H2O2.

As an approach to understanding how mammals regulate H(2)O(2) toxicity, intracellular concentration to prevent its we analyzed the genome-wide mRNA profile changes of human cells after treatment with a non-toxic H(2)O(2) concentration. We identified a large and essentially late H(2)O(2) response of induced and repressed genes that unexpectedly comprise few or no antioxidants but mostly apoptosis and cell cycle control activities. The requirement of the p53 regulator for regulating about a third of this H(2)O(2) stimulon and the lack of an associated enhancement of total cellular H(2)O(2) scavenging activity further suggest that H(2)O(2) elicits a stress antiproliferative/repair response that does not increase antioxidant defenses. We conclude that mammalian antioxidant defenses are constitutive, a finding that contrasts with the oxidant-inducibility of such defenses in microorganisms. This finding might be important in understanding the role of H(2)O(2) as a key signaling molecule in mammals.

Antioxidants↗

PubMed2004

Fundamentals of massive automatic pairwise alignments of protein sequences: theoretical significance of Z-value statistics.

MOTIVATION: Different automatic methods of sequence alignments are routinely used as a starting point for homology searches and function inference. Confidence in an alignment probability is one of the major fundamentals of massive automatic genome-scale pairwise comparisons, for clustering of putative orthologs and paralogs, sequenced genome annotation or multiple-genomic tree constructions. Extreme value distribution based on the Karlin-Altschul model, usually advised for large-scale comparisons are not always valid, particularly in the case of comparisons of non-biased with nucleotide-biased genomes (such that of Plasmodium falciparum). Z-values estimates based on Monte Carlo technics, can be calculated experimentally for any alignment output, whatever the method used. Empirically, a Z-value higher than approximately 8 is supposed reasonable to assess that an alignment score is significant, but this arbitrary figure was never theoretically justified. RESULTS: In this paper, we used the Bienaymé-Chebyshev inequality to demonstrate a theorem of the upper limit of an alignment score probability (or P-value). This theorem implies that a computed Z-value is a statistical test, a single-linkage clustering criterion and that 1/Z-value(2) is an upper limit to the probability of an alignment score whatever the actual probability law is. Therefore, this study provides the missing theoretical link between a Z-value cut-off used for an automatic clustering of putative orthologs and/or paralogs, and the corresponding statistical risk in such genome-scale comparisons (using non-biased or biased genomes).

Algorithms↗

PubMed2003

A panoramic view of gene expression in the human kidney.

To gain a molecular understanding of kidney functions, we established a high-resolution map of gene expression patterns in the human kidney. The glomerulus and seven different nephron segments were isolated by microdissection from fresh tissue specimens, and their transcriptome was characterized by using the serial analysis of gene expression (SAGE) method. More than 400,000 mRNA SAGE tags were sequenced, making it possible to detect in each structure transcripts present at 18 copies per cell with a 95% confidence level. Expression of genes responsible for nephron transport and permeability properties was evidenced through transcripts for 119 solute carriers, 84 channels, 43 ion-transport ATPases, and 12 claudins. Searching for differences between the transcriptomes, we found 998 transcripts greatly varying in abundance from one nephron portion to another. Clustering analysis of these transcripts evidenced different extents of similarity between the nephron portions. Approximately 75% of the differentially distributed transcripts corresponded to cDNAs of known or unknown function that are accurately mapped in the human genome. This systematic large-scale analysis of individual structures of a complex human tissue reveals sets of genes underlying the function of well-defined nephron portions. It also provides quantitative expression data for a variety of genes mutated in hereditary diseases and helps in sorting candidate genes for renal diseases that affect specific portions of the human nephron.

Cluster Analysis↗

PubMed2002

Renal transcriptomes: segmental analysis of differential expression.

BACKGROUND/AIMS: Progress accomplished by complete genomes and cDNA-sequencing projects calls for methods that fully use these resources to study gene expression patterns in characterized cell populations. However, since the number of functional genes cannot be readily inferred from the genomic sequence, it is highly desirable to make use of methods enabling to study both known and unknown genes. METHODS: The method of serial analysis of gene expression provides short diagnostic cDNA tags without bias towards known genes. In addition, the frequency of each tag in the library conveys quantitative information on gene expression. A microassay was set-up to perform serial analysis of gene expression in minute samples such as those obtained by microdissecting nephron segments. RESULTS: Studies carried out in the thick ascending limb of Henle's loop and the collecting duct of the mouse kidney provided expression data for several thousand genes. Known markers were found appropriately enriched, and several of the thick ascending limb or collecting duct specific transcripts had no database match. CONCLUSIONS: The microassay for serial analysis of gene expression makes possible large-scale quantitative measurements of mRNA levels in nephron segments. The comprehensive picture generated by analyzing both known and unknown transcripts in defined cell populations should help to discover genes with dedicated functions.

Animals↗

PubMedDate not supplied

Large-scale analysis of gene expression: methods and application to the kidney.

Characterization of tissue-specific gene expression profiles, or transcriptomes, may serve two purposes: a) establishing relationships between cell transcriptomes and functions (i.e. molecular and physiological phenotypes) under physiological and pathophysiological conditions serves to elucidate gene functions, and b) determination of the totality of genes expressed in a cell seems a prerequisite for understanding cell functions, because the properties of proteins vary with their environment. Sophisticated methods are now available for transcriptome analysis. They are based on serial, partial sequencing of cDNAs (sequencing of expressed sequenced tags (ESTs) and serial analysis of gene expression (SAGE)), or on parallel hybridization of labeled cDNAs to specific probes immobilized on a grid (macro- and microarrays and DNA chips). Some methods were designed specifically to compare gene expression under different conditions (substractive hybridization, glass microarrays). However, all these methods require several microg of mRNA as starting material, making impossible, in most tissues, to analyse gene expression in homogeneous cell populations. To get around this limitation, we developed a scaled-down SAGE method (SAGE adaptation to downsized extracts: SADE) in our laboratory. SAGE is based on the following: a) each cDNA is characterized by a 10-bp informative sequence called tag, b) the information from several transcripts is condensed into a single DNA molecule by concatenation of several tags, c) sequencing of individual clones from the library of concatemers, computer analysis of sequences and interrogation of sequence databases allow quantitative gene expression profiling. Applied to microdissected mouse nephron segments, SADE made it possible to determine segment-specific transcriptomes.

Animals↗