Dissecting microregulation of a master regulatory network

<p>Abstract</p> <p>Background</p> <p>The master regulator p53 tumor-suppressor protein through coordination of several downstream target genes and upstream transcription factors controls many pathways important for tumor suppression. While it has been reported that some of the p53's functions are microRNA-mediated, it is not known as to how many other microRNAs might contribute to the p53-mediated tumorigenesis.</p> <p>Results</p> <p>Here, we use bioinformatics-based integrative approach to identify and prioritize putative p53-regulated miRNAs, and unravel the miRNA-based microregulation of the p53 master regulatory network. Specifically, we identify putative microRNA regulators of a) transcription factors that are upstream or downstream to p53 and b) p53 interactants. The putative <it>p53-miRs </it>and their targets are prioritized using current knowledge of cancer biology and literature-reported cancer-miRNAs.</p> <p>Conclusion</p> <p>Our predicted p53-miRNA-gene networks strongly suggest that coordinated transcriptional and <it>p53-miR </it>mediated networks could be integral to tumorigenesis and the underlying processes and pathways.</p

GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs

Transcriptional cis-regulatory control regions frequently are found within non-coding DNA segments conserved across multi-species gene orthologs. Adopting a systematic gene-centric pipeline approach, we report here the development of a web-accessible database resource—GenomeTraFac ()—that allows genome-wide detection and characterization of compositionally similar cis-clusters that occur in gene orthologs between any two genomes for both microRNA genes as well as conventional RNA-encoding genes. Each ortholog gene pair can be scanned to visualize overall conserved sequence regions, and within these, the relative density of conserved cis-element motif clusters form graph peak structures. The results of these analyses can be mined en masse to identify most frequently represented cis-motifs in a list of genes. The system also provides a method for rapid evaluation and visualization of gene model-consistency between orthologs, and facilitates consideration of the potential impact of sequence variation in conserved non-coding regions to impact complex cis-element structures. Using the mouse and human genomes via the NCBI Reference Sequence database and the Sanger Institute miRBase, the system demonstrated the ability to identify validated transcription factor targets within promoter and distal genomic regulatory regions of both conventional and microRNA genes

Staging of biliary atresia at diagnosis by molecular profiling of the liver

Abstract Background Young age at portoenterostomy has been linked to improved outcome in biliary atresia, but pre-existing biological factors may influence the rate of disease progression. In this study, we aimed to determine whether molecular profiling of the liver identifies stages of disease at diagnosis. Methods We examined liver biopsies from 47 infants with biliary atresia enrolled in a prospective observational study. Biopsies were scored for inflammation and fibrosis, used for gene expression profiles, and tested for association with indicators of disease severity, response to surgery, and survival at 2 years. Results Fourteen of 47 livers displayed predominant histological features of inflammation (N = 9) or fibrosis (N = 5), with the remainder showing similar levels of both simultaneously. By differential profiling of gene expression, the 14 livers had a unique molecular signature containing 150 gene probes. Applying prediction analysis models, the probes classified 29 of the remaining 33 livers into inflammation or fibrosis. Molecular classification into the two groups was validated by the findings of increased hepatic population of lymphocyte subsets or tissue accumulation of matrix substrates. The groups had no association with traditional markers of liver injury or function, response to surgery, or complications of cirrhosis. However, infants with an inflammation signature were younger, while those with a fibrosis signature had decreased transplant-free survival. Conclusions Molecular profiling at diagnosis of biliary atresia uncovers a signature of inflammation or fibrosis in most livers. This signature may relate to staging of disease at diagnosis and has implications to clinical outcomes.http://deepblue.lib.umich.edu/bitstream/2027.42/112492/1/13073_2010_Article_154.pd

P53 interactome along with the putative miR regulators that are shown to be repressed following the activation of p53 11

miRNAs are represented by yellow ellipses, target genes are represented by green boxes. p53 is represented in the center as blue circle. Induction of the miRNAs by p53 is represented by directed red lines. Negative regulation of the target genes by miRNAs are represented by dark grey lines. The protein interactions are represented by undirected light blue lines. Networks (using force-directed layouts) were generated using aiSee [76] network visualization software.<p><b>Copyright information:</b></p><p>Taken from "Dissecting microregulation of a master regulatory network"</p><p>http://www.biomedcentral.com/1471-2164/9/88</p><p>BMC Genomics 2008;9():88-88.</p><p>Published online 23 Feb 2008</p><p>PMCID:PMC2289817.</p><p></p

P53 interactome along with the putative miR regulators that are shown to be induced following the activation of p53 11

miRNAs are represented by yellow ellipses, target genes are represented by green boxes. p53 is represented in the center as blue circle. Induction of the miRNAs by p53 is represented by directed red lines. Negative regulation of the target genes by miRNAs are represented by dark grey lines. The protein interactions are represented by undirected light blue lines. Networks (using force-directed layouts) were generated using aiSee [76] network visualization software.<p><b>Copyright information:</b></p><p>Taken from "Dissecting microregulation of a master regulatory network"</p><p>http://www.biomedcentral.com/1471-2164/9/88</p><p>BMC Genomics 2008;9():88-88.</p><p>Published online 23 Feb 2008</p><p>PMCID:PMC2289817.</p><p></p

Heat map representation of and their target genes relative to the p53 network

Panels A, B, C and D depict exclusively targeting p53 upstream activators, upstream repressors, downstream activators and downstream repressors respectively along with their predicted target transcription factors.<p><b>Copyright information:</b></p><p>Taken from "Dissecting microregulation of a master regulatory network"</p><p>http://www.biomedcentral.com/1471-2164/9/88</p><p>BMC Genomics 2008;9():88-88.</p><p>Published online 23 Feb 2008</p><p>PMCID:PMC2289817.</p><p></p

miRNA contents of cerebrospinal fluid extracellular vesicles in glioblastoma patients

Analysis of extracellular vesicles (EVs) derived from plasma or cerebrospinal fluid (CSF) has emerged as a promising biomarker platform for therapeutic monitoring in glioblastoma patients. However, the contents of the various subpopulations of EVs in these clinical specimens remain poorly defined. Here we characterize the relative abundance of miRNA species in EVs derived from the serum and cerebrospinal fluid of glioblastoma patients. EVs were isolated from glioblastoma cell lines as well as the plasma and CSF of glioblastoma patients. The microvesicle subpopulation was isolated by pelleting at 10,000×g for 30 min after cellular debris was cleared by a 2000×g (20 min) spin. The exosome subpopulation was isolated by pelleting the microvesicle supernatant at 120,000×g (120 min). qRT-PCR was performed to examine the distribution of miR-21, miR-103, miR-24, and miR-125. Global miRNA profiling was performed in select glioblastoma CSF samples. In plasma and cell line derived EVs, the relative abundance of miRNAs in exosome and microvesicles were highly variable. In some specimens, the majority of the miRNA species were found in exosomes while in other, they were found in microvesicles. In contrast, CSF exosomes were enriched for miRNAs relative to CSF microvesicles. In CSF, there is an average of one molecule of miRNA per 150-25,000 EVs. Most EVs derived from clinical biofluids are devoid of miRNA content. The relative distribution of miRNA species in plasma exosomes or microvesicles is unpredictable. In contrast, CSF exosomes are the major EV compartment that harbor miRNAs