Biomedical subjects

Paul Pavlidis

Publications and source records attributed to Paul Pavlidis.

At least 19 recordsLinked to original sources

PubMed2006

Akt1 deficiency affects neuronal morphology and predisposes to abnormalities in prefrontal cortex functioning.

There is accumulating evidence that AKT signaling plays a role in the pathogenesis of schizophrenia. We asked whether Akt1 deficiency in mice results in structural and functional abnormalities in prefrontal cortex (PFC). Exploratory transcriptional profiling revealed concerted alterations in the expression of PFC genes controlling synaptic function, neuronal development, myelination, and actin polymerization, and follow-up ultrastructural analysis identified consistent changes in the dendritic architecture of pyramidal neurons. Behavioral analysis indicated that Akt1-mutant mice have normal acquisition of a PFC-dependent cognitive task but abnormal working memory retention under neurochemical challenge of three distinct neurotransmitter systems. Thus, Akt1 deficiency creates a context permissive for gene-gene and gene-environment interactions that modulate PFC functioning and contribute to the disease risk associated with this locus, the severity of the clinical syndrome, or both.

Animals↗

PubMed2006

An ancestral haplotype defines susceptibility to doxorubicin nephropathy in the laboratory mouse.

Haplotype analysis was used to refine of the DOXNPH locus, which harbors the susceptibility gene for doxorubicin (DOX; Adriamycin) nephropathy, a Mendelian form of selective podocyte injury. Analysis of haplotype structure in three strains with contrasting susceptibility (148 single-nucleotide polymorphisms at 101-kb spacing) was complementary to analysis of recombinants in 176 F2 mice. For example, haplotype analysis but not meiotic mapping could exclude the Abcc1 multidrug transporter, and this was confirmed further by phenotypic evaluation of Abcc1 null mice. Next, comparison of haplotype structure (55 single-nucleotide polymorphisms at 44-kb spacing) with phenotype in 15 inbred strains revealed a risk haplotype that was shared by susceptible strains (P = 0.00017), thereby reducing the DOXNPH region to a 1.3-Mb interval. These data demonstrate that susceptibility to DOX nephropathy represents a founder mutation in the laboratory mouse. Haplotype analysis can be used for identification of the DOXNPH gene and prediction of strain susceptibility pattern.

Animals↗

PubMed2006

Zac1 regulates an imprinted gene network critically involved in the control of embryonic growth.

Genomic imprinting is an epigenetic mechanism of regulation that restrains the expression of a small subset of mammalian genes to one parental allele. The reason for the targeting of these approximately 80 genes by imprinting remains uncertain. We show that inactivation of the maternally repressed Zac1 transcription factor results in intrauterine growth restriction, altered bone formation, and neonatal lethality. A meta-analysis of microarray data reveals that Zac1 is a member of a network of coregulated genes comprising other imprinted genes involved in the control of embryonic growth. Zac1 alters the expression of several of these imprinted genes, including Igf2, H19, Cdkn1c, and Dlk1, and it directly regulates the Igf2/H19 locus through binding to a shared enhancer. Accordingly, these data identify a network of imprinted genes, including Zac1, which controls embryonic growth and which may be the basis for the implementation of a common mechanism of gene regulation during mammalian evolution.

Animals↗

PubMed2005

ErmineJ: tool for functional analysis of gene expression data sets.

BACKGROUND: It is common for the results of a microarray study to be analyzed in the context of biologically-motivated groups of genes such as pathways or Gene Ontology categories. The most common method for such analysis uses the hypergeometric distribution (or a related technique) to look for "over-representation" of groups among genes selected as being differentially expressed or otherwise of interest based on a gene-by-gene analysis. However, this method suffers from some limitations, and biologist-friendly tools that implement alternatives have not been reported. RESULTS: We introduce ErmineJ, a multiplatform user-friendly stand-alone software tool for the analysis of functionally-relevant sets of genes in the context of microarray gene expression data. ErmineJ implements multiple algorithms for gene set analysis, including over-representation and resampling-based methods that focus on gene scores or correlation of gene expression profiles. In addition to a graphical user interface, ErmineJ has a command line interface and an application programming interface that can be used to automate analyses. The graphical user interface includes tools for creating and modifying gene sets, visualizing the Gene Ontology as a table or tree, and visualizing gene expression data. ErmineJ comes with a complete user manual, and is open-source software licensed under the Gnu Public License. CONCLUSION: The availability of multiple analysis algorithms, together with a rich feature set and simple graphical interface, should make ErmineJ a useful addition to the biologist's informatics toolbox. ErmineJ is available from http://microarray.cu.genome.org.

Animals↗

PubMed2005

Transcriptional and behavioral interaction between 22q11.2 orthologs modulates schizophrenia-related phenotypes in mice.

Microdeletions of 22q11.2 represent one of the highest known genetic risk factors for schizophrenia. It is likely that more than one gene contributes to the marked risk associated with this locus. Two of the candidate risk genes encode the enzymes proline dehydrogenase (PRODH) and catechol-O-methyltransferase (COMT), which modulate the levels of a putative neuromodulator (L-proline) and the neurotransmitter dopamine, respectively. Mice that model the state of PRODH deficiency observed in humans with schizophrenia show increased neurotransmitter release at glutamatergic synapses as well as deficits in associative learning and response to psychomimetic drugs. Transcriptional profiling and pharmacological manipulations identified a transcriptional and behavioral interaction between the Prodh and Comt genes that is likely to represent a homeostatic response to enhanced dopaminergic signaling in the frontal cortex. This interaction modulates a number of schizophrenia-related phenotypes, providing a framework for understanding the high disease risk associated with this locus, the expression of the phenotype, or both.

Animals↗

PubMed2005

Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms.

The growth in popularity of RNA expression microarrays has been accompanied by concerns about the reliability of the data especially when comparing between different platforms. Here, we present an evaluation of the reproducibility of microarray results using two platforms, Affymetrix GeneChips and Illumina BeadArrays. The study design is based on a dilution series of two human tissues (blood and placenta), tested in duplicate on each platform. The results of a comparison between the platforms indicate very high agreement, particularly for genes which are predicted to be differentially expressed between the two tissues. Agreement was strongly correlated with the level of expression of a gene. Concordance was also improved when probes on the two platforms could be identified as being likely to target the same set of transcripts of a given gene. These results shed light on the causes or failures of agreement across microarray platforms. The set of probes we found to be most highly reproducible can be used by others to help increase confidence in analyses of other data sets using these platforms.

Adult↗

PubMed2005

Molecular aging in human prefrontal cortex is selective and continuous throughout adult life.

BACKGROUND: Aging leads to morphologic and functional changes in the brain and is associated with increased risk for psychiatric and neurological disorders. METHODS: To identify age-related transcriptional changes in the human brain, we profiled gene expression in two prefrontal cortex (PFC) areas in postmortem samples from 39 subjects, ranging in age from 13 to 79 years. RESULTS: Robust transcriptional age-related changes were identified for at least 540 genes. Gene expression correlates of aging were highly specific, and the large majority of the 22,000 transcripts investigated were unaffected by age. Across subjects, changes were progressive throughout adult life and accurately predicted chronological age. Age-upregulated transcripts were mostly of glial origin and related to inflammation and cellular defenses, whereas downregulated genes displayed mostly neuron-enriched transcripts relating to cellular communication and signaling. CONCLUSIONS: Continuous changes in gene expression with increasing age revealed a "molecular profile" of aging in human PFC. The restricted scope of the transcript changes suggests cellular populations or functions that are selectively vulnerable during aging. Because age-related gene expression changes begin early in adulthood and are continuous throughout life, our results suggest the possibility of identifying early cellular mechanisms that may be engaged in preventive or detrimental age-related brain functions.

Adolescent↗

PubMed2005

A Mendelian locus on chromosome 16 determines susceptibility to doxorubicin nephropathy in the mouse.

The development of kidney disease is influenced by both genetic and environmental factors. Searching for models of glomerulopathy that display strong gene-environment interaction, we examined the determinants of anthracycline-induced nephropathy, a classic, strain-dependent experimental model applied to rodents in the past four decades. We produced three crosses derived from mice with contrasting susceptibility to doxorubicin (DOX) nephropathy and, surprisingly, we found that this widely studied model segregates as a single-gene defect with recessive inheritance. By genome-wide analysis of linkage, we mapped the trait locus to chromosome 16A1-B1 (DOXNPH locus) in all three crosses [peak logarithm of odds (lod) score of 92.7, P = 1 x 10(-65)]; this interval represents a susceptibility locus for nephropathy. Gene expression analysis indicated that susceptibility alleles at the DOXNPH locus are associated with blunted expression of protein arginine methyltransferase 7 (Prmt7) on chromosome 8, a protein previously implicated in cellular sensitivity to chemotherapeutic agents (lod = 12.4, P = 0.0001). Therefore, Prmt7 expression serves as a molecular marker for susceptibility to DOX nephropathy. Finally, increased variation in the severity of kidney disease among affected mice motivated a second genome-wide search, identifying a locus on chromosome 9 that influences the severity and progression of nephropathy (DOXmod, peak lod score 4.3, P = 0.0018). These data provide genetic and molecular characterization of a previously unrecognized Mendelian trait. Elucidation of DOX nephropathy may simultaneously provide insight into the pathogenesis of renal failure and mechanisms of cytotoxicity induced by chemotherapeutic agents.

Alleles↗

PubMed2005

Microarray analysis of gene expression following the formalin test in the infant rat.

Injury and pain experienced by the infant results in immediate changes in pain sensitivity that last into adulthood. These long-term changes are likely initiated by altered gene expression. Here we measured how injury alters gene expression in the lumbar spinal cord early and late in the preweaning period of the rat. The expression of large numbers of genes was altered significantly at 3 days of age, when injury has long-term consequences. The functional classes of altered genes included transcription factors, cell death related and metal ion genes. The intensity of the stimulus in the 3-day-old pups induced changes in different classes of genes. Fewer changes were noted at 21 days of age. The increased expression of transcription factors and decreased expression of genes whose products are protective against cell death are hypothesized to underlie the long-term changes that are seen after injury in the neonate.

Age Factors↗

PubMed2004

Support vector machine classification on the web.

The support vector machine (SVM) learning algorithm has been widely applied in bioinformatics. We have developed a simple web interface to our implementation of the SVM algorithm, called Gist. This interface allows novice or occasional users to apply a sophisticated machine learning algorithm easily to their data. More advanced users can download the software and source code for local installation. The availability of these tools will permit more widespread application of this powerful learning algorithm in bioinformatics.

Algorithms↗

PubMed2004

Cluster analysis of genes with significant change in expression in cells conditioned to survive TBOOH.

Immortal murine lens epithelial cells, alphaTN4-1 have been conditioned to survive H2O2, H cells, or TBOOH, T cells, at concentrations that will cause cataract in vitro. Since H cells are killed by TBOOH but T cells survive H2O2, it is of interest to examine the gene expression of these cell lines. We now report the results of cluster analysis of genes whose expression is significantly changed by TBOOH. The analysis has revealed a small group of antioxidative defense genes that contribute to the survival of T and H cells when exposed to oxidative stress.

Animals↗

PubMed2004

Using the gene ontology for microarray data mining: a comparison of methods and application to age effects in human prefrontal cortex.

One of the challenges in the analysis of gene expression data is placing the results in the context of other data available about genes and their relationships to each other. Here, we approach this problem in the study of gene expression changes associated with age in two areas of the human prefrontal cortex, comparing two computational methods. The first method, "overrepresentation analysis" (ORA), is based on statistically evaluating the fraction of genes in a particular gene ontology class found among the set of genes showing age-related changes in expression. The second method, "functional class scoring" (FCS), examines the statistical distribution of individual gene scores among all genes in the gene ontology class and does not involve an initial gene selection step. We find that FCS yields more consistent results than ORA, and the results of ORA depended strongly on the gene selection threshold. Our findings highlight the utility of functional class scoring for the analysis of complex expression data sets and emphasize the advantage of considering all available genomic information rather than sets of genes that pass a predetermined "threshold of significance."

Adolescent↗

PubMed2004

Gene expression profiling of depression and suicide in human prefrontal cortex.

Mood disorders are a major cause of disability. Etiology includes genetic and environmental factors, but the responsible genes have yet to be identified. Using DNA microarrays, we have conducted a large-scale gene expression analysis, in two regions of the human prefrontal cortex from post-mortem matched groups of subjects with major depression who had died by suicide, and control subjects who died from other causes and were free from psychiatric disorders. Bioinformatic analysis was used to investigate molecular and cellular pathways potentially involved in depression and suicidal behavior. We tested several hypotheses of disease pathology and of their putative molecular impact, including changes in single genes, the existence of subgroups of patients or disease subtypes, or the possibility of common biological pathways being affected in the disease process. Within the analytical limits of this relatively large genomic study, we found no evidence for molecular differences that correlated with depression and suicide, suggesting a pathology that is below the detection level of current genomic approaches, or that is either localized to other brain areas, or more associated with post-transcriptional effects and/or changes in protein levels or functions, rather than altered transcriptome in the prefrontal cortex.

Adult↗

PubMed2004

Coexpression analysis of human genes across many microarray data sets.

We present a large-scale analysis of mRNA coexpression based on 60 large human data sets containing a total of 3924 microarrays. We sought pairs of genes that were reliably coexpressed (based on the correlation of their expression profiles) in multiple data sets, establishing a high-confidence network of 8805 genes connected by 220,649 "coexpression links" that are observed in at least three data sets. Confirmed positive correlations between genes were much more common than confirmed negative correlations. We show that confirmation of coexpression in multiple data sets is correlated with functional relatedness, and show how cluster analysis of the network can reveal functionally coherent groups of genes. Our findings demonstrate how the large body of accumulated microarray data can be exploited to increase the reliability of inferences about gene function.

Cluster Analysis↗

PubMed2004

Gene expression signatures in chronic and aggressive periodontitis: a pilot study.

This pilot study examined gene expression signatures in pathological gingival tissues of subjects with chronic or aggressive periodontitis, and explored whether new subclasses of periodontitis can be identified based on gene expression profiles. A total of 14 patients, seven with chronic and seven with aggressive periodontitis, were examined with respect to clinical periodontal status, composition of subgingival bacterial plaque assessed by checkerboard hybridizations, and levels of serum IgG antibodies to periodontal bacteria assayed by checkerboard immunoblotting. In addition, at least two pathological pockets/patient were biopsied, processed for RNA extraction, amplification and labeling, and used to study gene expression using Affymetrix U-133 A arrays. Based on a total of 35 microarrays, no significantly different gene expression profiles appeared to emerge between chronic and aggressive periodontitis. However, a de novo grouping of the 14 subjects into two fairly robust clusters was possible based on similarities in gene expression. These two groups had similar clinical periodontal status and subgingival bacterial profiles, but differed significantly with respect to serum IgG levels against the important periodontal pathogens Porphyromonas gingivalis, Tannerella forsythensis and Campylobacter rectus. These early data point to the usefulness of gene expression profiling techniques in the identification of subclasses of periodontitis with common pathobiology.

Acute Disease↗

PubMed2003

Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction.

BACKGROUND: Genomic studies of complex tissues pose unique analytical challenges for assessment of data quality, performance of statistical methods used for data extraction, and detection of differentially expressed genes. Ideally, to assess the accuracy of gene expression analysis methods, one needs a set of genes which are known to be differentially expressed in the samples and which can be used as a "gold standard". We introduce the idea of using sex-chromosome genes as an alternative to spiked-in control genes or simulations for assessment of microarray data and analysis methods. RESULTS: Expression of sex-chromosome genes were used as true internal biological controls to compare alternate probe-level data extraction algorithms (Microarray Suite 5.0 [MAS5.0], Model Based Expression Index [MBEI] and Robust Multi-array Average [RMA]), to assess microarray data quality and to establish some statistical guidelines for analyzing large-scale gene expression. These approaches were implemented on a large new dataset of human brain samples. RMA-generated gene expression values were markedly less variable and more reliable than MAS5.0 and MBEI-derived values. A statistical technique controlling the false discovery rate was applied to adjust for multiple testing, as an alternative to the Bonferroni method, and showed no evidence of false negative results. Fourteen probesets, representing nine Y- and two X-chromosome linked genes, displayed significant sex differences in brain prefrontal cortex gene expression. CONCLUSION: In this study, we have demonstrated the use of sex genes as true biological internal controls for genomic analysis of complex tissues, and suggested analytical guidelines for testing alternate oligonucleotide microarray data extraction protocols and for adjusting multiple statistical analysis of differentially expressed genes. Our results also provided evidence for sex differences in gene expression in the brain prefrontal cortex, supporting the notion of a putative direct role of sex-chromosome genes in differentiation and maintenance of sexual dimorphism of the central nervous system. Importantly, these analytical approaches are applicable to all microarray studies that include male and female human or animal subjects.

Algorithms↗

PubMed2003

The effect of replication on gene expression microarray experiments.

MOTIVATION: We examine the effect of replication on the detection of apparently differentially expressed genes in gene expression microarray experiments. Our analysis is based on a random sampling approach using real data sets from 16 published studies. We consider both the ability to find genes that meet particular statistical criteria as well as the stability of the results in the face of changing levels of replication. RESULTS: While dependent on the data source, our findings suggest that stable results are typically not obtained until at least five biological replicates have been used. Conversely, for most studies, 10-15 replicates yield results that are quite stable, and there is less improvement in stability as the number of replicates is further increased. Our methods will be of use in evaluating existing data sets and in helping to design new studies.

Animals↗

PubMed2003

Hierarchical model of gene regulation by transforming growth factor beta.

Transforming growth factor betas (TGF-betas) regulate key aspects of embryonic development and major human diseases. Although Smad2, Smad3, and extracellular signal-regulated kinase (ERK) mitogen-activated protein kinases (MAPKs) have been proposed as key mediators in TGF-beta signaling, their functional specificities and interactivity in controlling transcriptional programs in different cell types and (patho)physiological contexts are not known. We investigated expression profiles of genes controlled by TGF-beta in fibroblasts with ablations of Smad2, Smad3, and ERK MAPK. Our results suggest that Smad3 is the essential mediator of TGF-beta signaling and directly activates genes encoding regulators of transcription and signal transducers through Smad3/Smad4 DNA-binding motif repeats that are characteristic for immediate-early target genes of TGF-beta but absent in intermediate target genes. In contrast, Smad2 and ERK predominantly transmodulated regulation of both immediate-early and intermediate genes by TGF-beta/Smad3. These results suggest a previously uncharacterized hierarchical model of gene regulation by TGF-beta in which TGF-beta causes direct activation by Smad3 of cascades of regulators of transcription and signaling that are transmodulated by Smad2 and/or ERK.

Animals↗