Dataset Information

Application of Comparative Transcriptional Genomics to Identify Molecular Targets for Pediatric IBD.

ABSTRACT: Experimental models of colitis in mice have been used extensively for analyzing the molecular events that occur during inflammatory bowel disease (IBD) development. However, it is uncertain to what extent the experimental models reproduce features of human IBD. This is largely due to the lack of precise methods for direct and comprehensive comparison of mouse and human inflamed colon tissue at the molecular level. Here, we use global gene expression patterns of two sets of pediatric IBD and two mouse models of colitis to obtain a direct comparison of the genome signatures of mouse and human IBD. By comparing the two sets of pediatric IBD microarray data, we found 83 genes were differentially expressed in a similar manner between pediatric Crohn's disease and ulcerative colitis. Up-regulation of the chemokine (C-C motif) ligand 2 (CCL2) gene that maps to 17q12, a confirmed IBD susceptibility loci, indicates that our comparison study can reveal known genetic associations with IBD. In comparing pediatric IBD and experimental colitis microarray data, we found common signatures amongst them including: (1) up-regulation of CXCL9 and S100A8; (2) cytokine-cytokine receptor pathway dysregulation; and (3) over-represented IRF1 and IRF2 transcription binding sites in the promoter region of up-regulated genes, and HNF1A and Lhx3 binding sites were over-represented in the promoter region of the down-regulated genes. In summary, this study provides a comprehensive view of transcriptome changes between different pediatric IBD populations in comparison with different colitis models. These findings reveal several new molecular targets for further study in the regulation of colitis.

SUBMITTER: Fang K

PROVIDER: S-EPMC4457140 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Application of Comparative Transcriptional Genomics to Identify Molecular Targets for Pediatric IBD.

Fang Kai K Grisham Matthew B MB Kevil Christopher G CG

Frontiers in immunology 20150408

Experimental models of colitis in mice have been used extensively for analyzing the molecular events that occur during inflammatory bowel disease (IBD) development. However, it is uncertain to what extent the experimental models reproduce features of human IBD. This is largely due to the lack of precise methods for direct and comprehensive comparison of mouse and human inflamed colon tissue at the molecular level. Here, we use global gene expression patterns of two sets of pediatric IBD and two ...[more]

PMID: 26085826

Similar Datasets

Project description:Mycoplasma synoviae is an important pathogen of poultry, causing significant economic losses in this industry. Analysis of the unique genes and shared genes among different M. synoviae strains and among related species is helpful for studying the molecular pathogenesis of M. synoviae and provides valuable molecular diagnostic targets to facilitate the identification of M. synoviae species. We selected a total of 46 strains, including six M. synoviae strains, from 25 major animal (including avian) Mycoplasma species/subspecies that had complete genome sequences and annotation information published in GenBank, and used them for comparative genomic analysis. After analysis, 16 common genes were found in the 46 strains. Thirteen single-copy core genes and the 16s rRNA genes were used for genetic evolutionary analysis. M. synoviae was found to have a distant evolutionary relationship not only with other arthritis-causing mycoplasmas, but also with another major avian pathogen, Mycoplasma gallisepticum, that shares the major virulence factor vlhA with M. synoviae. Subsequently, six unique coding genes were identified as shared among these M. synoviae strains that are absent in other species with published genome sequences. Two of the genes were found to be located in the genetically stable regions of the genomes of M. synoviae and were determined to be present in all M. synoviae isolated strains (n = 20) and M. synoviae-positive clinical samples (n = 48) preserved in our laboratory. These two genes were used as molecular diagnostic targets for which SYBR green quantitative PCR detection methods were designed. The two quantitative PCR methods exhibited good reproducibility and high specificity when tested on positive plasmid controls and genomic DNA extracted from different M. synoviae strains, other major avian pathogenic bacteria/mycoplasmas, and low pathogenic Mycoplasma species. The detection limit for the two genes was 10 copies or less per reaction. The clinical sensitivity and specificity of the quantitative PCR methods were both 100% based on testing chicken hock joint samples with positive or negative M. synoviae infection. This research provides a foundation for the study of species-specific differences and molecular diagnosis of M. synoviae.

Project description:Information about molecular mechanisms underlying improvement of antibiotic-producing microorganisms with traditional mutation and screening approach is largely missing. This information is essential to develop rational approaches to strain improvement. In this study by using comparative genomic analysis we have identified all genetic changes that have occurred during development of an erythromycin overproducer, which was obtained by the traditional mutate-and-screen method. Compared with parental Saccharopolyspora erythraea NRRL 2338, a total of 117 deletion, 78 insertion and 12 transposition sites were found across the genome of the overproducer. Among them, 71 insertion/deletion sites mapped within coding sequences (CDSs) generating frame-shift mutations. Moreover, single nucleotide variations affecting a total of 144 CDSs were identified between the two genomes. Overall, variations affect a total of 227 proteins in the genome of the overproducer. The analysis of metabolic pathways demonstrated that a considerable number of mutations affect genes coding for key enzymes involved in central carbon and nitrogen metabolism, and biosynthesis of secondary metabolites, redirecting common precursors toward erythromycin biosynthesis. Interestingly, several mutations inactivate genes coding for proteins that play fundamental roles in basic transcription and translation machineries including the transcription anti-termination factor NusB and the transcription elongation factor Efp. These mutations, along with those affecting genes coding for pleiotropic or pathway-specific regulators, may affect global expression profile. Consistent transcriptomic data were obtained from a comparative analysis between NRRL 2338 and the erythromycin overproducer gene expression profiling performed with DNA microarray. Genomic data also indicated that the mutate-and-screen process might have been accelerated by mutations in DNA repair genes. Our findings, largely unanticipated, reveal new targets suitable for rationale improvement of antibiotic-producing strains. According to a rough estimate, actinomycetes, which are among the most abundant bacteria in soil, produce over 70% of naturally occurring antibiotics and other biologically active substances including anti-tumour agents and immunosuppressants. However, these microorganisms must often be genetically improved for higher production before they can be used in the industry. Strain improvement has traditionally relied on multiple rounds of random mutagenesis and screening. This method is essentially empirical, and notably time-consuming and expansive. Currently, the availability of molecular genetics tools and useful information about the biosynthetic pathways and genetic control for most of biologically active substances has opened the way for improving strains by rational engineering. These rational strain improvement strategies benefit of the support of genomic and post-genomic technologies. In this study by using comparative genomic analysis we have identified all genetic changes that have occurred during development of an erythromycin overproducer, which was obtained by the traditional mutate-and-screen method. Our findings, largely unanticipated, reveal new molecular targets suitable for rationale improvement of antibiotic-producing strains by recombinant technologies, and support the evidence that combining classical and recombinant strain improvement with a solid fermentation development program is the best way to improve production of biologically active substances.

Project description:BackgroundComparative genomics methods enable the reconstruction of bacterial regulatory networks using available experimental data. In spite of their potential for accelerating research into the composition and evolution of bacterial regulons, few comparative genomics suites have been developed for the automated analysis of these regulatory systems. Available solutions typically rely on precomputed databases for operon and ortholog predictions, limiting the scope of analyses to processed complete genomes, and several key issues such as the transfer of experimental information or the integration of regulatory information in a probabilistic setting remain largely unaddressed.ResultsHere we introduce CGB, a flexible platform for comparative genomics of prokaryotic regulons. CGB has few external dependencies and enables fully customized analyses of newly available genome data. The platform automates the merging of experimental information and uses a gene-centered, Bayesian framework to generate and integrate easily interpretable results. We demonstrate its flexibility and power by analyzing the evolution of type III secretion system regulation in pathogenic Proteobacteria and by characterizing the SOS regulon of a new bacterial phylum, the Balneolaeota.ConclusionsOur results demonstrate the applicability of the CGB pipeline in multiple settings. CGB's ability to automatically integrate experimental information from multiple sources and use complete and draft genomic data, coupled with its non-reliance on precomputed databases and its easily interpretable display of gene-centered posterior probabilities of regulation provide users with an unprecedented level of flexibility in launching comparative genomics analyses of prokaryotic transcriptional regulatory networks. The analyses of type III secretion and SOS response regulatory networks illustrate instances of convergent and divergent evolution of these regulatory systems, showcasing the power of formal ancestral state reconstruction at inferring the evolutionary history of regulatory networks.

Dataset Information

Application of Comparative Transcriptional Genomics to Identify Molecular Targets for Pediatric IBD.

Publications

Application of Comparative Transcriptional Genomics to Identify Molecular Targets for Pediatric IBD.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets