1
|
Sunagozaka H, Honda M, Yamashita T, Nishino R, Takatori H, Arai K, Yamashita T, Sakai Y, Kaneko S. Identification of a secretory protein c19orf10 activated in hepatocellular carcinoma. Int J Cancer 2011; 129:1576-85. [PMID: 21128247 DOI: 10.1002/ijc.25830] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2010] [Accepted: 11/15/2010] [Indexed: 11/07/2022]
Abstract
The identification of genes involved in tumor growth is crucial for the development of inventive anticancer treatments. Here, we have cloned a 17-kDa secretory protein encoded by c19orf10 from hepatocellular carcinoma (HCC) serial analysis of gene expression libraries. Gene expression analysis indicated that c19orf10 was overexpressed in approximately two-thirds of HCC tissues compared to the adjacent noncancerous liver tissues, and its expression was significantly positively correlated with that of alpha-fetoprotein (AFP). Overexpression of c19orf10 enhanced cell proliferation of AFP-negative HLE cells, whereas knockdown of c19orf10 inhibited cell proliferation of AFP-positive Hep3B and HuH7 cells along with G1 cell cycle arrest. Supplementation of recombinant c19orf10 protein in culture media enhanced cell proliferation in HLE cells, and this effect was abolished by the addition of antibodies developed against c19orf10. Intriguingly, c19orf10 could regulate cell proliferation through the activation of Akt/mitogen-activated protein kinase pathways. Taken together, these data suggest that c19orf10 might be one of the growth factors and potential molecular targets activated in HCC.
Collapse
Affiliation(s)
- Hajime Sunagozaka
- Department of Gastroenterology, Kanazawa University Hospital, Kanazawa, Ishikawa, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
2
|
TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources. BMC Genomics 2011; 12:121. [PMID: 21333005 PMCID: PMC3052188 DOI: 10.1186/1471-2164-12-121] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 02/18/2011] [Indexed: 11/10/2022] Open
Abstract
Background Several tools have been developed to perform global gene expression profile data analysis, to search for specific chromosomal regions whose features meet defined criteria as well as to study neighbouring gene expression. However, most of these tools are tailored for a specific use in a particular context (e.g. they are species-specific, or limited to a particular data format) and they typically accept only gene lists as input. Results TRAM (Transcriptome Mapper) is a new general tool that allows the simple generation and analysis of quantitative transcriptome maps, starting from any source listing gene expression values for a given gene set (e.g. expression microarrays), implemented as a relational database. It includes a parser able to assign univocal and updated gene symbols to gene identifiers from different data sources. Moreover, TRAM is able to perform intra-sample and inter-sample data normalization, including an original variant of quantile normalization (scaled quantile), useful to normalize data from platforms with highly different numbers of investigated genes. When in 'Map' mode, the software generates a quantitative representation of the transcriptome of a sample (or of a pool of samples) and identifies if segments of defined lengths are over/under-expressed compared to the desired threshold. When in 'Cluster' mode, the software searches for a set of over/under-expressed consecutive genes. Statistical significance for all results is calculated with respect to genes localized on the same chromosome or to all genome genes. Transcriptome maps, showing differential expression between two sample groups, relative to two different biological conditions, may be easily generated. We present the results of a biological model test, based on a meta-analysis comparison between a sample pool of human CD34+ hematopoietic progenitor cells and a sample pool of megakaryocytic cells. Biologically relevant chromosomal segments and gene clusters with differential expression during the differentiation toward megakaryocyte were identified. Conclusions TRAM is designed to create, and statistically analyze, quantitative transcriptome maps, based on gene expression data from multiple sources. The release includes FileMaker Pro database management runtime application and it is freely available at http://apollo11.isto.unibo.it/software/, along with preconfigured implementations for mapping of human, mouse and zebrafish transcriptomes.
Collapse
|
3
|
Tsigelny I, Burton DW, Sharikov Y, Hastings RH, Deftos LJ. Coherent expression chromosome cluster analysis reveals differential regulatory functions of amino-terminal and distal parathyroid hormone-related protein domains in prostate carcinoma. J Biomed Biotechnol 2010; 2005:353-63. [PMID: 16489268 PMCID: PMC1361488 DOI: 10.1155/jbb.2005.353] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Parathyroid hormone-related protein (PTHrP) has a number of
cancer-related actions. While best known for causing hypercalcemia
of malignancy, it also has effects on cancer cell growth,
apoptosis, and angiogenesis. Studying the actions of PTHrP in
human cancer is complicated because there are three isoforms and
many derived peptides. Several peptides are biologically active at
known or presumed cell surface receptors; in addition, the
PTHrP-derived molecules can exert effects at the cell nucleus. To
address this complexity, we studied gene expression in a DU 145
prostate cancer cell line that was stably transfected with control
vector, PTHrP 1-173 and PTHrP 33-173. With this model, regulatory
effects of the amino-terminal portion of PTHrP would result only
from transduction with the full-length molecule, while effects
pertaining to distal sequences would be evident with either
construct. Analysis of the expression profiles by microarrays
demonstrated nonoverlapping groups of differentially expressed
genes. Amino-terminal PTHrP affected groups of genes involved in
apoptosis, prostaglandin and sex steroid metabolism, cell-matrix
interactions, and cell differentiation, while PTHrP 33-173 caused
substantial increases in MHC class I antigen expression. This work
demonstrates the distinct biological actions of the amino-terminus
compared to distal mid-molecule or carboxy-terminal sequences of
PTHrP in prostate carcinoma cells and provides targets for further
study of the malignant process.
Collapse
Affiliation(s)
- I Tsigelny
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0654, USA.
| | | | | | | | | |
Collapse
|
4
|
Carvalho-Filho RJ, Dalgard O. Individualized treatment of chronic hepatitis C with pegylated interferon and ribavirin. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2010; 3:1-13. [PMID: 23226039 PMCID: PMC3513206 DOI: 10.2147/pgpm.s4461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Indexed: 12/19/2022]
Abstract
Chronic infection with hepatitis C virus (HCV) is a major public health problem, with perhaps 180 million people infected worldwide. A significant proportion of these will eventually develop clinical complications, such as cirrhosis, liver decompensation and hepatocellular carcinoma. Sustained virological response (SVR) to antiviral therapy is associated with improvement in liver histology and survival free of liver-related complications. Great effort has been made to improve SVR rate by adapting the duration of therapy according to HCV genotype and to on-treatment response. Rapid virological response (RVR, undetectable HCV RNA at week 4) usually has a high positive predictive value for achieving SVR and early virological response (EVR, ≥ 2 log reduction or undetectable HCV RNA at week 12) exhibits a high negative predictive value for non-response. Individualized approach can improve cost-effectiveness of HCV antiviral therapy by reducing side effects and the costs of therapy associated with unnecessary exposure to treatment and through extending therapy for those with unfavorable features. This article summarizes recent data on strategies of individualized treatment in naïve patients with mono-infection by the different HCV genotypes. The management of common side effects, the impact of HCV infection on health-related quality of life and the potential applications of host genomics in HCV therapy are also briefly discussed.
Collapse
Affiliation(s)
- Roberto J Carvalho-Filho
- Division of Gastroenterology, Hepatitis Section, Federal University of São Paulo, São Paulo, Brazil
| | | |
Collapse
|
5
|
Takatori H, Yamashita T, Honda M, Nishino R, Arai K, Yamashita T, Takamura H, Ohta T, Zen Y, Kaneko S. dUTP pyrophosphatase expression correlates with a poor prognosis in hepatocellular carcinoma. Liver Int 2010; 30:438-46. [PMID: 19968781 DOI: 10.1111/j.1478-3231.2009.02177.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a malignancy with a poor prognosis, partly owing to the lack of biomarkers that support its classification in line with its malignant nature. To discover a novel molecular marker that is related to the efficacy of treatment for HCC and its biological nature, we performed serial analysis of gene expression (SAGE) in HCC, normal liver and cirrhotic liver tissues. METHODS Gene expression profiles of HCC tissues and non-cancerous liver tissues were obtained by SAGE. Suppression of the target gene by RNA interference was used to evaluate its role in HCC in vitro. The relation of the identified marker and prognosis was statistically examined in surgically resected HCC patients. RESULTS We identified significant overexpression of DUT, which encodes dUTP pyrophosphatase (dUTPase), in HCC tissue, and this was confirmed in about two-thirds of the HCC samples by reverse-transcription polymerase chain reaction (n=20). Suppression of dUTPase expression using short interfering RNAs inhibited cell proliferation and sensitized HuH7 cells to 5-fluorouracil treatment. Nuclear dUTPase expression was observed in 36.6% of surgically resected HCC samples (n=82) evaluated by immunohistochemistry, and its expression was significantly correlated with the histological grades (P=0.0099). Notably, nuclear dUTPase expression correlated with a poor prognosis with statistical significance (HR, 2.47; 95% CI, 1.08-5.66; P=0.032). CONCLUSION Taken together, these results suggest that nuclear dUTPase may be a good biomarker for predicting prognosis in HCC patients after surgical resection. Development of novel dUTPase inhibitors may facilitate the eradication of HCC.
Collapse
Affiliation(s)
- Hajime Takatori
- Department of Gastroenterology, Kanazawa University Graduate School of Medical Science, Ishikawa, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Salih H, Adelson DL. QTL global meta-analysis: are trait determining genes clustered? BMC Genomics 2009; 10:184. [PMID: 19393059 PMCID: PMC2683869 DOI: 10.1186/1471-2164-10-184] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Accepted: 04/24/2009] [Indexed: 12/04/2022] Open
Abstract
Background A key open question in biology is if genes are physically clustered with respect to their known functions or phenotypic effects. This is of particular interest for Quantitative Trait Loci (QTL) where a QTL region could contain a number of genes that contribute to the trait being measured. Results We observed a significant increase in gene density within QTL regions compared to non-QTL regions and/or the entire bovine genome. By grouping QTL from the Bovine QTL Viewer database into 8 categories of non-redundant regions, we have been able to analyze gene density and gene function distribution, based on Gene Ontology (GO) with relation to their location within QTL regions, outside of QTL regions and across the entire bovine genome. We identified a number of GO terms that were significantly over represented within particular QTL categories. Furthermore, select GO terms expected to be associated with the QTL category based on common biological knowledge have also proved to be significantly over represented in QTL regions. Conclusion Our analysis provides evidence of over represented GO terms in QTL regions. This increased GO term density indicates possible clustering of gene functions within QTL regions of the bovine genome. Genes with similar functions may be grouped in specific locales and could be contributing to QTL traits. Moreover, we have identified over-represented GO terminology that from a biological standpoint, makes sense with respect to QTL category type.
Collapse
Affiliation(s)
- Hanni Salih
- Department of Animal Science and Interdisciplinary Faculty of Genetics, Texas A&M University, 2471 TAMU, Kleberg Center, College Station, TX, USA.
| | | |
Collapse
|
7
|
Lelièvre SA. Contributions of extracellular matrix signaling and tissue architecture to nuclear mechanisms and spatial organization of gene expression control. Biochim Biophys Acta Gen Subj 2009; 1790:925-35. [PMID: 19328836 DOI: 10.1016/j.bbagen.2009.03.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 03/13/2009] [Accepted: 03/15/2009] [Indexed: 12/22/2022]
Abstract
Post-translational modification of histones, ATP-dependent chromatin remodeling, and DNA methylation are interconnected nuclear mechanisms that ultimately lead to the changes in chromatin structure necessary to carry out epigenetic gene expression control. Tissue differentiation is characterized by a specific gene expression profile in association with the acquisition of a defined tissue architecture and function. Elements critical for tissue differentiation, like extracellular stimuli, adhesion and cell shape properties, and transcription factors all contribute to the modulation of gene expression and thus, are likely to impinge on the nuclear mechanisms of epigenetic gene expression control. In this review, we analyze how these elements modify chromatin structure in a hierarchical manner by acting on the nuclear machinery. We discuss how mechanotransduction via the structural continuum of the cell and biochemical signaling to the cell nucleus integrate to provide a comprehensive control of gene expression. The role of nuclear organization in this control is highlighted, with a presentation of differentiation-induced nuclear structure and the concept of nuclear organization as a modulator of the response to incoming signals.
Collapse
Affiliation(s)
- Sophie A Lelièvre
- Department of Basic Medical Sciences and Cancer Center, Purdue University, Lynn, West Lafayette, IN 47907-2026, USA.
| |
Collapse
|
8
|
de Wit E, van Steensel B. Chromatin domains in higher eukaryotes: insights from genome-wide mapping studies. Chromosoma 2008; 118:25-36. [PMID: 18853173 DOI: 10.1007/s00412-008-0186-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Revised: 09/22/2008] [Accepted: 09/23/2008] [Indexed: 01/22/2023]
Abstract
In genomes of higher eukaryotes, adjacent genes often show coordinated regulation of their expression. Compartmentalization of multiple neighboring genes into a shared chromatin environment can facilitate this coordinated expression. New mapping techniques have begun to reveal that such multigene chromatin domains are a common feature of fly and mammalian genomes. Many different types of chromatin domains have been identified based on the genomic binding patterns of various proteins and histone modifications. In addition, maps of genome-nuclear lamina associations and of looping interactions between loci provide the first systematic views of the three-dimensional folding of interphase chromosomes. These genome-wide datasets uncover new architectural principles of eukaryotic genomes and indicate that multigene chromatin domains are prevalent and important regulatory units.
Collapse
Affiliation(s)
- Elzo de Wit
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | |
Collapse
|
9
|
Chen F, Li T, Fan SL, Dang YH, Chen T, Yan CX. [Gene expression profiling in drug addicted brain]. YI CHUAN = HEREDITAS 2008; 30:809-814. [PMID: 18779121 DOI: 10.3724/sp.j.1005.2008.00809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Drug addiction, a chronic brain disease caused by interaction of in vitro drug toxification and in vivo gene susceptibility, has been widely studied but its underlining mechanism is so far been elucidated. A major goal in this field is to identify drug-induced molecular changes and their effects on brain function. By the advance of high throughput technologies in genomics and transcriptomics, the whole gene expression profile in addicted brain could be obtained and proved to be a very powerful tool to unclose the molecular mechanism underlying the addiction biology context. Here, we summarized the progress of serial analysis of gene expression (SAGE) and microarray, as well as their application in drug addiction.
Collapse
Affiliation(s)
- Feng Chen
- Department of Forensic Sciences, Xi'an Jiaotong University School of Medicine, Xi'an 710061, China.
| | | | | | | | | | | |
Collapse
|
10
|
Tanis KQ, Duman RS, Newton SS. CREB binding and activity in brain: regional specificity and induction by electroconvulsive seizure. Biol Psychiatry 2008; 63:710-20. [PMID: 17936724 PMCID: PMC3691692 DOI: 10.1016/j.biopsych.2007.08.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2007] [Revised: 07/28/2007] [Accepted: 08/01/2007] [Indexed: 12/12/2022]
Abstract
BACKGROUND The transcription factor cyclic adenosine monophosphate response element binding protein (CREB) orchestrates diverse neurobiological processes including cell differentiation, survival, and plasticity. Alterations in CREB-mediated transcription have been implicated in numerous central nervous system (CNS) disorders including depression, anxiety, addiction, and cognitive decline. However, it remains unclear how CREB contributes to normal and aberrant CNS function, as the identity of CREB-regulated genes in brain and the regional and temporal dynamics of CREB function remain largely undetermined. METHODS We combined microarray and chromatin immunoprecipitation technology to analyze CREB-DNA interactions in brain. We compared the occupancy and activity of CREB at gene promoters in rat frontal cortex, hippocampus, and striatum before and after a rodent model of electroconvulsive therapy. RESULTS Our analysis identified >860 CREB binding sites in rat brain. We identified multiple genomic loci enriched with CREB binding sites and find that CREB-occupied transcripts interact extensively to promote cell proliferation, plasticity, and resiliency. We discovered regional differences in CREB occupancy and activity that explain, in part, the diverse biological and behavioral outputs of CREB activity in frontal cortex, hippocampus, and striatum. Electroconvulsive seizure rapidly increased CREB occupancy and/or phosphorylation at select promoters, demonstrating that both events contribute to the temporal regulation of the CREB transcriptome. CONCLUSIONS Our data provide a mechanistic basis for CREB's ability to integrate regional and temporal cues to orchestrate state-specific patterns of transcription in the brain, indicate that CREB is an important mediator of the biological responses to electroconvulsive seizure, and provide global mechanistic insights into CREB's role in psychiatric and cognitive function.
Collapse
Affiliation(s)
- Keith Quincy Tanis
- Division of Molecular Psychiatry, Abraham Ribibcoff Research Facilities, Department of Psychiatry and Pharmacology, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | | |
Collapse
|
11
|
Ferrari F, Bortoluzzi S, Coppe A, Basso D, Bicciato S, Zini R, Gemelli C, Danieli GA, Ferrari S. Genomic expression during human myelopoiesis. BMC Genomics 2007; 8:264. [PMID: 17683550 PMCID: PMC2045681 DOI: 10.1186/1471-2164-8-264] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2007] [Accepted: 08/03/2007] [Indexed: 01/01/2023] Open
Abstract
Background Human myelopoiesis is an exciting biological model for cellular differentiation since it represents a plastic process where multipotent stem cells gradually limit their differentiation potential, generating different precursor cells which finally evolve into distinct terminally differentiated cells. This study aimed at investigating the genomic expression during myeloid differentiation through a computational approach that integrates gene expression profiles with functional information and genome organization. Results Gene expression data from 24 experiments for 8 different cell types of the human myelopoietic lineage were used to generate an integrated myelopoiesis dataset of 9,425 genes, each reliably associated to a unique genomic position and chromosomal coordinate. Lists of genes constitutively expressed or silent during myelopoiesis and of genes differentially expressed in commitment phase of myelopoiesis were first identified using a classical data analysis procedure. Then, the genomic distribution of myelopoiesis genes was investigated integrating transcriptional and functional characteristics of genes. This approach allowed identifying specific chromosomal regions significantly highly or weakly expressed, and clusters of differentially expressed genes and of transcripts related to specific functional modules. Conclusion The analysis of genomic expression during human myelopoiesis using an integrative computational approach allowed discovering important relationships between genomic position, biological function and expression patterns and highlighting chromatin domains, including genes with coordinated expression and lineage-specific functions.
Collapse
Affiliation(s)
- Francesco Ferrari
- Department of Biomedical Sciences, University of Modena and Reggio Emilia, via G. Campi 287, 41100, Modena, Italy
| | - Stefania Bortoluzzi
- Department of Biology, University of Padova, via G. Colombo 3, 35131, Padova, Italy
| | - Alessandro Coppe
- Department of Biology, University of Padova, via G. Colombo 3, 35131, Padova, Italy
| | - Dario Basso
- Department of Chemical Engineering Processes, University of Padova via F. Marzolo 9, 35131, Padova, Italy
| | - Silvio Bicciato
- Department of Chemical Engineering Processes, University of Padova via F. Marzolo 9, 35131, Padova, Italy
| | - Roberta Zini
- Department of Biomedical Sciences, University of Modena and Reggio Emilia, via G. Campi 287, 41100, Modena, Italy
| | - Claudia Gemelli
- Department of Biomedical Sciences, University of Modena and Reggio Emilia, via G. Campi 287, 41100, Modena, Italy
| | - Gian Antonio Danieli
- Department of Biology, University of Padova, via G. Colombo 3, 35131, Padova, Italy
| | - Sergio Ferrari
- Department of Biomedical Sciences, University of Modena and Reggio Emilia, via G. Campi 287, 41100, Modena, Italy
| |
Collapse
|
12
|
Ramos KS, He Q, Kalbfleisch T, Montoya-Durango DE, Teneng I, Stribinskis V, Brun M. Computational and biological inference of gene regulatory networks of the LINE-1 retrotransposon. Genomics 2007; 90:176-85. [PMID: 17521869 PMCID: PMC2065750 DOI: 10.1016/j.ygeno.2007.04.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Accepted: 04/05/2007] [Indexed: 01/21/2023]
Abstract
Computational approaches were used to define structural and functional determinants of a putative genetic regulatory network of murine LINE-1 (long interspersed nuclear element-1), an active mammalian retrotransposon that uses RNA intermediates to populate new sites throughout the genome. Polymerase (RNA) II polypeptide E AI845735 and mouse DNA homologous to Drosophila per fragment M12039 were identified as primary attractors. siRNA knockdown of the aryl hydrocarbon receptor NM_013464 modulated gene expression within the network, including LINE-1, Sgpl1, Sdcbp, and Mgst1. Genes within the network did not exhibit physical proximity and instead were dispersed throughout the genome. The potential impact of individual members of the network on the global dynamical behavior of LINE-1 was examined from a theoretical and empirical framework.
Collapse
Affiliation(s)
- Kenneth S Ramos
- Department of Biochemistry and Molecular Biology and Center for Genetics and Molecular Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA.
| | | | | | | | | | | | | |
Collapse
|
13
|
Shackel NA, Seth D, Haber PS, Gorrell MD, McCaughan GW. The hepatic transcriptome in human liver disease. COMPARATIVE HEPATOLOGY 2006; 5:6. [PMID: 17090326 PMCID: PMC1665460 DOI: 10.1186/1476-5926-5-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Accepted: 11/07/2006] [Indexed: 02/07/2023]
Abstract
The transcriptome is the mRNA transcript pool in a cell, organ or tissue with the liver transcriptome being amongst the most complex of any organ. Functional genomics methodologies are now being widely utilized to study transcriptomes including the hepatic transcriptome. This review outlines commonly used methods of transcriptome analysis, especially gene array analysis, focusing on publications utilizing these methods to understand human liver disease. Additionally, we have outlined the relationship between transcript and protein expressions as well as summarizing what is known about the variability of the transcriptome in non-diseased liver tissue. The approaches covered include gene array analysis, serial analysis of gene expression, subtractive hybridization and differential display. The discussion focuses on primate whole organ studies and in-vitro cell culture systems utilized. It is now clear that there are a vast number research opportunities for transcriptome analysis of human liver disease as we attempt to better understand both non-diseased and disease hepatic mRNA expression. We conclude that hepatic transcriptome analysis has already made significant contributions to the understanding of human liver pathobiology.
Collapse
Affiliation(s)
- Nicholas A Shackel
- AW Morrow Gastroenterology and Liver Centre, Centenary Institute of Cancer Medicine and Cell Biology, Royal Prince Alfred Hospital and The University of Sydney, Sydney, Australia
| | - Devanshi Seth
- AW Morrow Gastroenterology and Liver Centre, Centenary Institute of Cancer Medicine and Cell Biology, Royal Prince Alfred Hospital and The University of Sydney, Sydney, Australia
| | - Paul S Haber
- AW Morrow Gastroenterology and Liver Centre, Centenary Institute of Cancer Medicine and Cell Biology, Royal Prince Alfred Hospital and The University of Sydney, Sydney, Australia
| | - Mark D Gorrell
- AW Morrow Gastroenterology and Liver Centre, Centenary Institute of Cancer Medicine and Cell Biology, Royal Prince Alfred Hospital and The University of Sydney, Sydney, Australia
| | - Geoffrey W McCaughan
- AW Morrow Gastroenterology and Liver Centre, Centenary Institute of Cancer Medicine and Cell Biology, Royal Prince Alfred Hospital and The University of Sydney, Sydney, Australia
| |
Collapse
|
14
|
Coppe A, Danieli GA, Bortoluzzi S. REEF: searching REgionally Enriched Features in genomes. BMC Bioinformatics 2006; 7:453. [PMID: 17042935 PMCID: PMC1624853 DOI: 10.1186/1471-2105-7-453] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2006] [Accepted: 10/16/2006] [Indexed: 11/16/2022] Open
Abstract
Background In Eukaryotic genomes, different features including genes are not uniformly distributed. The integration of annotation information and genomic position of functional DNA elements in the Eukaryotic genomes opened the way to test novel hypotheses of higher order genome organization and regulation of expression. Results REEF is a new tool, aimed at identifying genomic regions enriched in specific features, such as a class or group of genes homogeneous for expression and/or functional characteristics. The method for the calculation of local feature enrichment uses test statistic based on the Hypergeometric Distribution applied genome-wide by using a sliding window approach and adopting the False Discovery Rate for controlling multiplicity. REEF software, source code and documentation are freely available at . Conclusion REEF can aid to shed light on the role of organization of specific genomic regions in the determination of their functional role.
Collapse
Affiliation(s)
- Alessandro Coppe
- Department of Biology, University of Padova, via G. Colombo 3, 35131, Padova, Italy
| | - Gian Antonio Danieli
- Department of Biology, University of Padova, via G. Colombo 3, 35131, Padova, Italy
| | - Stefania Bortoluzzi
- Department of Biology, University of Padova, via G. Colombo 3, 35131, Padova, Italy
| |
Collapse
|
15
|
Zhou GL, Xin L, Song W, Di LJ, Liu G, Wu XS, Liu DP, Liang CC. Active chromatin hub of the mouse alpha-globin locus forms in a transcription factory of clustered housekeeping genes. Mol Cell Biol 2006; 26:5096-105. [PMID: 16782894 PMCID: PMC1489176 DOI: 10.1128/mcb.02454-05] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA polymerases can be shared by a particular group of genes in a transcription "factory" in nuclei, where transcription may be coordinated in concert with the distribution of coexpressed genes in higher-eukaryote genomes. Moreover, gene expression can be modulated by regulatory elements working over a long distance. Here, we compared the conformation of a 130-kb chromatin region containing the mouse alpha-globin cluster and their flanking housekeeping genes in 14.5-day-postcoitum fetal liver and brain cells. The analysis of chromatin conformation showed that the active alpha1 and alpha2 globin genes and upstream regulatory elements are in close spatial proximity, indicating that looping may function in the transcriptional regulation of the mouse alpha-globin cluster. In fetal liver cells, the active alpha1 and alpha2 genes, but not the inactive zeta gene, colocalize with neighboring housekeeping genes C16orf33, C16orf8, MPG, and C16orf35. This is in sharp contrast with the mouse alpha-globin genes in nonexpressing cells, which are separated from the congregated housekeeping genes. A comparison of RNA polymerase II (Pol II) occupancies showed that active alpha1 and alpha2 gene promoters have a much higher RNA Pol II enrichment in liver than in brain. The RNA Pol II occupancy at the zeta gene promoter, which is specifically repressed during development, is much lower than that at the alpha1 and alpha2 promoters. Thus, the mouse alpha-globin gene cluster may be regulated through moving in or out active globin gene promoters and regulatory elements of a preexisting transcription factory in the nucleus, which is maintained by the flanking clustered housekeeping genes, to activate or inactivate alpha-globin gene expression.
Collapse
Affiliation(s)
- Guo-Ling Zhou
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, People's Republic of China
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Lü B, Xu J, Lai M, Zhang H, Chen J. A transcriptome anatomy of human colorectal cancers. BMC Cancer 2006; 6:40. [PMID: 16504081 PMCID: PMC1402307 DOI: 10.1186/1471-2407-6-40] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Accepted: 02/23/2006] [Indexed: 11/24/2022] Open
Abstract
Background Accumulating databases in human genome research have enabled integrated genome-wide study on complicated diseases such as cancers. A practical approach is to mine a global transcriptome profile of disease from public database. New concepts of these diseases might emerge by landscaping this profile. Methods In this study, we clustered human colorectal normal mucosa (N), inflammatory bowel disease (IBD), adenoma (A) and cancer (T) related expression sequence tags (EST) into UniGenes via an in-house GetUni software package and analyzed the transcriptome overview of these libraries by GOTree Machine (GOTM). Additionally, we downloaded UniGene based cDNA libraries of colon and analyzed them by Xprofiler to cross validate the efficiency of GetUni. Semi-quantitative RT-PCR was used to validate the expression of β-catenin and. 7 novel genes in colorectal cancers. Results The efficiency of GetUni was successfully validated by Xprofiler and RT-PCR. Genes in library N, IBD and A were all found in library T. A total of 14,879 genes were identified with 2,355 of them having at least 2 transcripts. Differences in gene enrichment among these libraries were statistically significant in 50 signal transduction pathways and Pfam protein domains by GOTM analysis P < 0.01 Hypergeometric Test). Genes in two metabolic pathways, ribosome and glycolysis, were more enriched in the expression profiles of A and IBD than in N and T. Seven transmembrane receptor superfamily genes were typically abundant in cancers. Conclusion Colorectal cancers are genetically heterogeneous. Transcription variants are common in them. Aberrations of ribosome and glycolysis pathway might be early indicators of precursor lesions in colon cancers. The electronic gene expression profile could be used to highlight the integral molecular events in colorectal cancers.
Collapse
Affiliation(s)
- Bingjian Lü
- Department of Pathology & Pathophysiology, School of Medicine, Zhejiang University, PR , 310031, China
| | - Jing Xu
- Department of Pathology & Pathophysiology, School of Medicine, Zhejiang University, PR , 310031, China
| | - Maode Lai
- Department of Pathology & Pathophysiology, School of Medicine, Zhejiang University, PR , 310031, China
| | - Hao Zhang
- Department of Computer Science, School of Computer Science & Technology, Zhejiang University, PR, 310023, China
| | - Jian Chen
- Department of Pathology & Pathophysiology, School of Medicine, Zhejiang University, PR , 310031, China
| |
Collapse
|
17
|
Abstract
The human genome project has had an impact on both biological research and its political organization; this review focuses primarily on the scientific novelty that has emerged from the project but also touches on its political dimensions. The project has generated both anticipated and novel information; in the later category are the description of the unusual distribution of genes, the prevalence of non-protein-coding genes, and the extraordinary evolutionary conservation of some regions of the genome. The applications of the sequence data are just starting to be felt in basic, rather than therapeutic, biomedical research and in the vibrant human origins and variation debates. The political impact of the project is in the unprecedented extent to which directed funding programs have emerged as drivers of basic research and the organization of the multidisciplinary groups that are needed to utilize the human DNA sequence.
Collapse
Affiliation(s)
- Peter F R Little
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2074, New South Wales, Australia.
| |
Collapse
|
18
|
Kovanen PE, Young L, Al-Shami A, Rovella V, Pise-Masison CA, Radonovich MF, Powell J, Fu J, Brady JN, Munson PJ, Leonard WJ. Global analysis of IL-2 target genes: identification of chromosomal clusters of expressed genes. Int Immunol 2005; 17:1009-21. [PMID: 15980098 DOI: 10.1093/intimm/dxh283] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
T lymphocytes play a central role in controlling adaptive immune responses. IL-2 critically regulates both T cell growth and death and is involved in maintaining peripheral tolerance, but the molecules involved in these and other IL-2 actions are only partially known. We now provide a comprehensive compendium of the genes expressed in T cells and of those regulated by IL-2 based on a combination of DNA microarrays and serial analysis of gene expression (SAGE). The newly identified IL-2 target genes include many genes previously linked to apoptosis in other cellular systems that may contribute to IL-2-dependent survival functions. We also studied the mRNA expression of known regulators of signaling pathways for their induction in response to IL-2 in order to identify potential novel positive and/or negative feedback regulators of IL-2 signaling. We show that IL-2 regulates only a limited number of these genes. These include suppressors of cytokine signaling (SOCS) 1, SOCS2, dual-specificity phosphatase (DUSP) 5, DUSP6 and non-receptor type phosphatase-7 (PTPN7). Additionally, we provide evidence that many genes expressed in T cells locate in chromosomal clusters, and that select IL-2-regulated genes are located in at least two clusters, one at 5q31, a known cytokine gene cluster, and the other at 6p21.3, a region that contains genes encoding the tumor necrosis factor (TNF) superfamily members TNF, LT-alpha and LT-beta.
Collapse
Affiliation(s)
- Panu E Kovanen
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1674, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Abstract
Genes showing particular expression patterns are not randomly distributed in the genome but are clustered into neighborhoods. This organization may be related to chromatin and the structure of the nucleus. Recent publications on a wide range of eukaryotes indicate that genes showing particular expression patterns are not randomly distributed in the genome but are clustered into contiguous regions that we call neighborhoods. It seems probable that this organization is related to chromatin and the structure of the nucleus.
Collapse
Affiliation(s)
- Brian Oliver
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
| |
Collapse
|
20
|
Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2447482 DOI: 10.1002/cfg.421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|