151
|
Muñoz J, Stange DE, Schepers AG, van de Wetering M, Koo BK, Itzkovitz S, Volckmann R, Kung KS, Koster J, Radulescu S, Myant K, Versteeg R, Sansom OJ, van Es JH, Barker N, van Oudenaarden A, Mohammed S, Heck AJR, Clevers H. The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4' cell markers. EMBO J 2012; 31:3079-91. [PMID: 22692129 PMCID: PMC3400017 DOI: 10.1038/emboj.2012.166] [Citation(s) in RCA: 562] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 05/15/2012] [Indexed: 12/27/2022] Open
Abstract
Two types of stem cells are currently defined in small intestinal crypts: cycling crypt base columnar (CBC) cells and quiescent '+4' cells. Here, we combine transcriptomics with proteomics to define a definitive molecular signature for Lgr5(+) CBC cells. Transcriptional profiling of FACS-sorted Lgr5(+) stem cells and their daughters using two microarray platforms revealed an mRNA stem cell signature of 384 unique genes. Quantitative mass spectrometry on the same cell populations identified 278 proteins enriched in intestinal stem cells. The mRNA and protein data sets showed a high level of correlation and a combined signature of 510 stem cell-enriched genes was defined. Spatial expression patterns were further characterized by mRNA in-situ hybridization, revealing that approximately half of the genes were expressed in a gradient with highest levels at the crypt bottom, while the other half was expressed uniquely in Lgr5(+)stem cells. Lineage tracing using a newly established knock-in mouse for one of the signature genes, Smoc2, confirmed its stem cell specificity. Using this resource, we find-and confirm by independent approaches-that the proposed quiescent/'+4' stem cell markers Bmi1, Tert, Hopx and Lrig1 are robustly expressed in CBC cells.
Collapse
Affiliation(s)
- Javier Muñoz
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Daniel E Stange
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Arnout G Schepers
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marc van de Wetering
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bon-Kyoung Koo
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Shalev Itzkovitz
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Richard Volckmann
- Department of Oncogenomics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Kevin S Kung
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Kevin Myant
- The Beatson Institute for Cancer Research, Glasgow, UK
| | - Rogier Versteeg
- Department of Oncogenomics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Owen J Sansom
- The Beatson Institute for Cancer Research, Glasgow, UK
| | - Johan H van Es
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nick Barker
- Institute of Medical Biology, Singapore, Singapore
| | - Alexander van Oudenaarden
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
- Centre for Biomedical Genetics, Universiteitsweg 100, Utrecht, The Netherlands
| | - Hans Clevers
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
- Centre for Biomedical Genetics, Universiteitsweg 100, Utrecht, The Netherlands
| |
Collapse
|
152
|
Analyzing gene expression profile in K562 cells exposed to sodium valproate using microarray combined with the connectivity map database. J Biomed Biotechnol 2012; 2012:654291. [PMID: 22701306 PMCID: PMC3373151 DOI: 10.1155/2012/654291] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 03/26/2012] [Accepted: 04/09/2012] [Indexed: 12/18/2022] Open
Abstract
To explore the mechanism underlying antileukaemia effect of sodium valproate, the growth and survival of the K562 cell line were investigated. Global profiles of gene expression in K562 cells exposed to sodium valproate were assessed and validated. The differentially expressed genes identified were further used to query the connectivity map database to retrieve a ranked list of compounds that act on the same intracellular targets as sodium valproate. A significant increase in cell apoptosis and a change in gene expression profile were observed in valproate-exposed K562 cells. The significant enrichment analysis of gene ontology terms for the differentially expressed genes showed that these genes were involved in many important biological processes. Eight differentially expressed genes involved in apoptosis were verified by quantitative real-time PCR. The connectivity map analysis showed gene expression profile in K562 cells exposed to sodium valproate was most similar to that of HDACi and PI3K inhibitors, suggesting that sodium valproate might exert antileukaemic action by inhibiting HDAC as well as inhibiting PI3K pathway. In conclusion, our data might provide clues to elucidate the molecular and therapeutic potential of VPA in leukaemia treatment, and the connectivity map is a useful tool for exploring the molecular mechanism of drug action.
Collapse
|
153
|
The early phase response of rat alveolar bone to traumatic occlusion. Arch Oral Biol 2012; 57:737-43. [DOI: 10.1016/j.archoralbio.2012.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 12/27/2011] [Accepted: 01/07/2012] [Indexed: 11/15/2022]
|
154
|
Phan JH, Quo CF, Wang MD. Cardiovascular genomics: a biomarker identification pipeline. ACTA ACUST UNITED AC 2012; 16:809-22. [PMID: 22614726 DOI: 10.1109/titb.2012.2199570] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Genomic biomarkers are essential for understanding the underlying molecular basis of human diseases such as cardiovascular disease. In this review, we describe a biomarker identification pipeline for cardiovascular disease, which includes 1) high-throughput genomic data acquisition, 2) preprocessing and normalization of data, 3) exploratory analysis, 4) feature selection, 5) classification, and 6) interpretation and validation of candidate biomarkers. We review each step in the pipeline, presenting current and widely used bioinformatics methods. Furthermore, we analyze several publicly available cardiovascular genomics datasets to illustrate the pipeline. Finally, we summarize the current challenges and opportunities for further research.
Collapse
Affiliation(s)
- John H Phan
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA.
| | | | | |
Collapse
|
155
|
Yan YX, Gong YW, Guo Y, Lv Q, Guo C, Zhuang Y, Zhang Y, Li R, Zhang XZ. Mechanical strain regulates osteoblast proliferation through integrin-mediated ERK activation. PLoS One 2012; 7:e35709. [PMID: 22539993 PMCID: PMC3335094 DOI: 10.1371/journal.pone.0035709] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 03/20/2012] [Indexed: 01/21/2023] Open
Abstract
Mechanical strain plays a critical role in the proliferation, differentiation and maturation of bone cells. As mechanical receptor cells, osteoblasts perceive and respond to stress force, such as those associated with compression, strain and shear stress. However, the underlying molecular mechanisms of this process remain unclear. Using a four-point bending device, mouse MC3T3-E1 cells was exposed to mechanical tensile strain. Cell proliferation was determined to be most efficient when stimulated once a day by mechanical strain at a frequency of 0.5 Hz and intensities of 2500 µε with once a day, and a periodicity of 1 h/day for 3 days. The applied mechanical strain resulted in the altered expression of 1992 genes, 41 of which are involved in the mitogen-activated protein kinase (MAPK) signaling pathway. Activation of ERK by mechanical strain promoted cell proliferation and inactivation of ERK by PD98059 suppressed proliferation, confirming that ERK plays an important role in the response to mechanical strain. Furthermore, the membrane-associated receptors integrin β1 and integrin β5 were determined to regulate ERK activity and the proliferation of mechanical strain-treated MC3T3-E1 cells in opposite ways. The knockdown of integrin β1 led to the inhibition of ERK activity and cell proliferation, whereas the knockdown of integrin β5 led to the enhancement of both processes. This study proposes a novel mechanism by which mechanical strain regulates bone growth and remodeling.
Collapse
Affiliation(s)
- Yu-xian Yan
- Institute of Medical Equipment, Academy of Military Medical Science, Tianjin, China
- Experiment Management Center of Medical College of People's Armed Police Forces, TianJin, China
| | - Yuan-wei Gong
- Institute of Medical Equipment, Academy of Military Medical Science, Tianjin, China
| | - Yong Guo
- Institute of Medical Equipment, Academy of Military Medical Science, Tianjin, China
| | - Qi Lv
- Experiment Management Center of Medical College of People's Armed Police Forces, TianJin, China
| | - Chun Guo
- Institute of Medical Equipment, Academy of Military Medical Science, Tianjin, China
| | - Yan Zhuang
- Experiment Management Center of Medical College of People's Armed Police Forces, TianJin, China
| | - Yuan Zhang
- Experiment Management Center of Medical College of People's Armed Police Forces, TianJin, China
| | - Ruixin Li
- Institute of Medical Equipment, Academy of Military Medical Science, Tianjin, China
| | - Xi-zheng Zhang
- Institute of Medical Equipment, Academy of Military Medical Science, Tianjin, China
| |
Collapse
|
156
|
Jia MA, Li Y, Lei L, Di D, Miao H, Fan Z. Alteration of gene expression profile in maize infected with a double-stranded RNA fijivirus associated with symptom development. MOLECULAR PLANT PATHOLOGY 2012; 13:251-62. [PMID: 21955602 PMCID: PMC6638758 DOI: 10.1111/j.1364-3703.2011.00743.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Maize rough dwarf disease caused by Rice black-streaked dwarf virus (RBSDV) is a major viral disease in China. It has been suggested that the viral infection of plants might cause distinct disease symptoms through the inhibition or activation of host gene transcription. We scanned the gene expression profile of RBSDV-infected maize through oligomer-based microarrays to reveal possible expression changes associated with symptom development. Our results demonstrate that various resistance-related maize genes and cell wall- and development-related genes, such as those for cellulose synthesis, are among the genes whose expression is dramatically altered. These results could aid in research into new strategies to protect cereal crops against viruses, and reveal the molecular mechanisms of development of specific symptoms in rough dwarf-related diseases.
Collapse
Affiliation(s)
- Meng-Ao Jia
- State Key Laboratory of Agrobiotechnology and Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | | | | | | | | | | |
Collapse
|
157
|
Maecker HT, McCoy JP, Nussenblatt R. Standardizing immunophenotyping for the Human Immunology Project. Nat Rev Immunol 2012; 12:191-200. [PMID: 22343568 PMCID: PMC3409649 DOI: 10.1038/nri3158] [Citation(s) in RCA: 722] [Impact Index Per Article: 60.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The heterogeneity in the healthy human immune system, and the immunological changes that portend various diseases, have been only partially described. Their comprehensive elucidation has been termed the 'Human Immunology Project'. The accurate measurement of variations in the human immune system requires precise and standardized assays to distinguish true biological changes from technical artefacts. Thus, to be successful, the Human Immunology Project will require standardized assays for immunophenotyping humans in health and disease. A major tool in this effort is flow cytometry, which remains highly variable with regard to sample handling, reagents, instrument setup and data analysis. In this Review, we outline the current state of standardization of flow cytometry assays and summarize the steps that are required to enable the Human Immunology Project.
Collapse
Affiliation(s)
- Holden T Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California 94305, USA.
| | | | | |
Collapse
|
158
|
Liu ZJ, Wang J, Wei XY, Chen P, Wang LC, Lin L, Sun BC, Li K. Predictive value of circulating endothelial cells for efficacy of chemotherapy with Rh-endostatin in non-small cell lung cancer. J Cancer Res Clin Oncol 2012; 138:927-37. [PMID: 22331237 DOI: 10.1007/s00432-012-1167-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 01/30/2012] [Indexed: 11/25/2022]
Abstract
PURPOSE The present study was designed to elucidate the fluctuation of activated CECs (aCECs) during different therapies and to investigate their predictive value for efficacy of anti-angiogenesis and chemotherapy in advanced non-small cell lung cancer (NSCLC). METHODS Seventy-two patients were randomized into three arms, treated with concomitant NP (vinorelbine and cisplatin) and Rh-endostatin, Rh-endostatin followed by NP, and single NP up to a maximum of six cycles. Response, time to progression (TTP), and aCECs levels were observed. The correlation between aCECs and efficacy was analyzed. RESULTS We found that TTP was 8.5 months in concomitant NP and Rh-endostatin versus 5.3 months in NP (p = 0.04) and 6.0 months in Rh-endostatin followed by NP. aCECs fluctuated during the therapeutic period, with a significantly high level from baseline on 8th day of Rh-endostatin followed by NP regimen, that is, when single Rh-endostatin was administered for 1 week, and upon completion of therapy in cases of progressive disease in each group (all p < 0.05). When TTP was longer than 10 months, aCECs count difference (∆aCECs, the difference in the aCECs by post-therapeutic amount minus pre-therapeutic amount) was reversely correlated to TTP (p = 0.003, r = -0.647). CONCLUSIONS An improved synergistic effect was achieved from concomitant NP and Rh-endostatin compared with Rh-endostatin followed by NP and single NP. aCECs increased when the disease was aggravated or single Rh-endostatin treatment of Rh-endostatin was administered, while they decreased when a clinical response to the combined therapy was obtained. Our results suggest ∆aCECs as an ideal marker to predict the response to Rh-endostatin combined with chemotherapy.
Collapse
Affiliation(s)
- Zhu-Jun Liu
- Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, People's Republic of China
| | | | | | | | | | | | | | | |
Collapse
|
159
|
Molecular mechanisms of fiber differential development between G. barbadense and G. hirsutum revealed by genetical genomics. PLoS One 2012; 7:e30056. [PMID: 22253876 PMCID: PMC3256209 DOI: 10.1371/journal.pone.0030056] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 12/08/2011] [Indexed: 11/28/2022] Open
Abstract
Cotton fiber qualities including length, strength and fineness are known to be controlled by genes affecting cell elongation and secondary cell wall (SCW) biosynthesis, but the molecular mechanisms that govern development of fiber traits are largely unknown. Here, we evaluated an interspecific backcrossed population from G. barbadense cv. Hai7124 and G. hirsutum acc. TM-1 for fiber characteristics in four-year environments under field conditions, and detected 12 quantitative trait loci (QTL) and QTL-by-environment interactions by multi-QTL joint analysis. Further analysis of fiber growth and gene expression between TM-1 and Hai7124 showed greater differences at 10 and 25 days post-anthesis (DPA). In this two period important for fiber performances, we integrated genome-wide expression profiling with linkage analysis using the same genetic materials and identified in total 916 expression QTL (eQTL) significantly (P<0.05) affecting the expression of 394 differential genes. Many positional cis-/trans-acting eQTL and eQTL hotspots were detected across the genome. By comparative mapping of eQTL and fiber QTL, a dataset of candidate genes affecting fiber qualities was generated. Real-time quantitative RT-PCR (qRT-PCR) analysis confirmed the major differential genes regulating fiber cell elongation or SCW synthesis. These data collectively support molecular mechanism for G. hirsutum and G. barbadense through differential gene regulation causing difference of fiber qualities. The down-regulated expression of abscisic acid (ABA) and ethylene signaling pathway genes and high-level and long-term expression of positive regulators including auxin and cell wall enzyme genes for fiber cell elongation at the fiber developmental transition stage may account for superior fiber qualities.
Collapse
|
160
|
Mäder U, Nicolas P. Array-based approaches to bacterial transcriptome analysis. J Microbiol Methods 2012. [DOI: 10.1016/b978-0-08-099387-4.00006-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
161
|
Fieber LA, Greer JB, Guo F, Crawford DC, Rein KS. GENE EXPRESSION PROFILING OF HUMAN LIVER CARCINOMA (HepG2) CELLS EXPOSED TO THE MARINE TOXIN OKADAIC ACID. TOXICOLOGICAL AND ENVIRONMENTAL CHEMISTRY 2012; 24:1805-1821. [PMID: 23172983 PMCID: PMC3500632 DOI: 10.1080/02772248.2012.730199] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The marine toxin, okadaic acid (OA) is produced by dinoflagellates of the genera Prorocentrum and Dinophysis and is the causative agent of the syndrome known as diarrheic shellfish poisoning (DSP). In addition, OA acts as both a tumor promoter, attributed to OA-induced inhibition of protein phosphatases as well as an inducer of apoptosis. To better understand the potentially divergent toxicological profile of OA, the concentration dependent cytotoxicity and alterations in gene expression on the human liver tumor cell line HepG2 upon OA exposure were determined using RNA microarrays, DNA fragmentation, and cell proliferation assays as well as determinations of cell detachment and cell death in different concentrations of OA. mRNA expression was quantified for approximately 15,000 genes. Cell attachment and proliferation were both negatively correlated with OA concentration. Detached cells displayed necrotic DNA signatures but apoptosis also was broadly observed. Data suggest that OA has a concentration dependent effect on cell cycle, which might explain the divergent effects that at low concentration OA stimulates genes involved in the cell cycle and at high concentrations it stimulates apoptosis.
Collapse
Affiliation(s)
- Lynne A. Fieber
- Division of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA 33149
| | - Justin B. Greer
- Division of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA 33149
| | - Fujiang Guo
- Department of Chemistry and Biochemistry, 11200 SW 8 St, Florida International University, Miami, FL, USA33199
| | - Douglas C. Crawford
- Division of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA 33149
| | - Kathleen S. Rein
- Department of Chemistry and Biochemistry, 11200 SW 8 St, Florida International University, Miami, FL, USA33199
| |
Collapse
|
162
|
Tang W, Hu Z, Muallem H, Gulley ML. Quality assurance of RNA expression profiling in clinical laboratories. J Mol Diagn 2012; 14:1-11. [PMID: 22020152 PMCID: PMC3338342 DOI: 10.1016/j.jmoldx.2011.09.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 09/09/2011] [Accepted: 09/14/2011] [Indexed: 12/12/2022] Open
Abstract
RNA expression profiles are increasingly used to diagnose and classify disease, based on expression patterns of as many as several thousand RNAs. To ensure quality of expression profiling services in clinical settings, a standard operating procedure incorporates multiple quality indicators and controls, beginning with preanalytic specimen preparation and proceeding thorough analysis, interpretation, and reporting. Before testing, histopathological examination of each cellular specimen, along with optional cell enrichment procedures, ensures adequacy of the input tissue. Other tactics include endogenous controls to evaluate adequacy of RNA and exogenous or spiked controls to evaluate run- and patient-specific performance of the test system, respectively. Unique aspects of quality assurance for array-based tests include controls for the pertinent outcome signatures that often supersede controls for each individual analyte, built-in redundancy for critical analytes or biochemical pathways, and software-supported scrutiny of abundant data by a laboratory physician who interprets the findings in a manner facilitating appropriate medical intervention. Access to high-quality reagents, instruments, and software from commercial sources promotes standardization and adoption in clinical settings, once an assay is vetted in validation studies as being analytically sound and clinically useful. Careful attention to the well-honed principles of laboratory medicine, along with guidance from government and professional groups on strategies to preserve RNA and manage large data sets, promotes clinical-grade assay performance.
Collapse
Affiliation(s)
- Weihua Tang
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Zhiyuan Hu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Hind Muallem
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Margaret L. Gulley
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| |
Collapse
|
163
|
Shanahan HP, Memon FN, Upton GJG, Harrison AP. Normalized Affymetrix expression data are biased by G-quadruplex formation. Nucleic Acids Res 2011; 40:3307-15. [PMID: 22199258 PMCID: PMC3333884 DOI: 10.1093/nar/gkr1230] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Probes with runs of four or more guanines (G-stacks) in their sequences can exhibit a level of hybridization that is unrelated to the expression levels of the mRNA that they are intended to measure. This is most likely caused by the formation of G-quadruplexes, where inter-probe guanines form Hoogsteen hydrogen bonds, which probes with G-stacks are capable of forming. We demonstrate that for a specific microarray data set using the Human HG_U133A Affymetrix GeneChip and RMA normalization there is significant bias in the expression levels, the fold change and the correlations between expression levels. These effects grow more pronounced as the number of G-stack probes in a probe set increases. Approximately 14% of the probe sets are directly affected. The analysis was repeated for a number of other normalization pipelines and two, FARMS and PLIER, minimized the bias to some extent. We estimate that ∼15% of the data sets deposited in the GEO database are susceptible to the effect. The inclusion of G-stack probes in the affected data sets can bias key parameters used in the selection and clustering of genes. The elimination of these probes from any analysis in such affected data sets outweighs the increase of noise in the signal.
Collapse
Affiliation(s)
- Hugh P Shanahan
- Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK.
| | | | | | | |
Collapse
|
164
|
Millán A, Gómez-Tato A, Pardo BG, Fernández C, Bouza C, Vera M, Alvarez-Dios JA, Cabaleiro S, Lamas J, Lemos ML, Martínez P. Gene expression profiles of the spleen, liver, and head kidney in turbot (Scophthalmus maximus) along the infection process with Aeromonas salmonicida using an immune-enriched oligo-microarray. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:1099-1114. [PMID: 21503602 DOI: 10.1007/s10126-011-9374-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 03/29/2011] [Indexed: 05/30/2023]
Abstract
We evaluated the expression profiles of turbot in the spleen, liver, and head kidney across five temporal points of the Aeromonas salmonicida infection process using an 8 × 15 K Agilent oligo-microarray. The microarray included 2,176 different fivefold replicated gene probes designed from a turbot 3' sequenced EST database. We were able to identify 471 differentially expressed (DE) genes (17.3% of the whole microarray), 223 in the spleen, 246 in the liver, and 125 in the head kidney, in at least one of the five temporal points sampled for each organ. Most of these genes could be annotated (83.0%) and functionally categorized using Gene Ontology terms (69.1%) after the additional sequencing of DE genes from the 5' end. Many DE genes were related to innate and acquired immune functions in accordance to previous studies with this pathogen in other fish species. A high proportion of DE genes were organ specific (77.1%), but their associated GO functions were rather similar in the three organs. The most striking difference in functional distribution was observed between the up- and down-regulated gene groups. Up-regulated genes were mostly associated to key immune functions while down-regulated ones mainly involved metabolism- and transport-related genes. Genetic response appeared clustered in groups of genes with similar expression profiles along the temporal series. The spleen showed the most clustering while the liver and head kidney displayed a higher diversification. The information obtained will aid to understand the turbot immune response and will specifically be valuable to develop strategies of defense to A. salmonicida to achieve more resistant broodstocks for turbot industry.
Collapse
Affiliation(s)
- Adrián Millán
- Departamento de Genética, Facultad de Veterinaria, Campus de Lugo, Universidad de Santiago de Compostela, 27002 Lugo, Spain
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
165
|
Tsiliki G, Zervakis M, Ioannou M, Sanidas E, Stathopoulos E, Potamias G, Tsiknakis M, Kafetzopoulos D. Multi-platform data integration in microarray analysis. IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE : A PUBLICATION OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY 2011; 15:806-12. [PMID: 22113338 DOI: 10.1109/titb.2011.2158232] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An increasing number of studies have profiled gene expressions in tumor specimens using distinct microarray platforms and analysis techniques. One challenging task is to develop robust statistical models in order to integrate multi-platform findings. We compare some methodologies on the field with respect to estrogen receptor (ER) status, and focus on a unified-among-platforms scale implemented by Shen et al. in 2004, which is based on a Bayesian mixture model. Under this scale, we study the ER intensity similarities between four breast cancer datasets derived from various platforms. We evaluate our results with an independent dataset in terms of ER sample classification, given the derived gene ER signatures of the integrated data. We found that integrated multi-platform gene signatures and fold-change variability similarities between different platform measurements can assist the statistical analysis of independent microarray datasets in terms of ER classification.
Collapse
Affiliation(s)
- Georgia Tsiliki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Hellas, Heraklion, Crete, Greece.
| | | | | | | | | | | | | | | |
Collapse
|
166
|
Sifakis EG, Prentza A, Koutsouris D, Chatziioannou AA. Evaluating the effect of various background correction methods regarding noise reduction, in two-channel microarray data. Comput Biol Med 2011; 42:19-29. [PMID: 22074762 DOI: 10.1016/j.compbiomed.2011.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2010] [Revised: 04/26/2011] [Accepted: 10/13/2011] [Indexed: 10/15/2022]
Abstract
In this work, two novel background correction (BC) methods, along with several commonly used ones, are evaluated regarding noise reduction in eleven two-channel self-versus-self (SVS) hybridizations. The evaluation of each BC method is investigated under the use of four statistical criteria combined into a single measure, the polygon area measure. Overall, our proposed BC approaches perform very well in terms of the proposed measure for most of the cases and provide an improved effect regarding technical noise reduction.
Collapse
Affiliation(s)
- E G Sifakis
- Biomedical Engineering Laboratory, School of Electrical and Computer Engineering, National Technical University of Athens, Greece
| | | | | | | |
Collapse
|
167
|
Goetz AK, Singh BP, Battalora M, Breier JM, Bailey JP, Chukwudebe AC, Janus ER. Current and future use of genomics data in toxicology: Opportunities and challenges for regulatory applications. Regul Toxicol Pharmacol 2011; 61:141-53. [DOI: 10.1016/j.yrtph.2011.07.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 07/27/2011] [Accepted: 07/29/2011] [Indexed: 12/01/2022]
|
168
|
Boonefaes T, Houthuys E, Van den Bergh R, Vander Beken S, Raes G, Brouckaert P, De Baetselier P, Grooten J. Do-it-yourself: construction of a custom cDNA macroarray platform with high sensitivity and linear range. BMC Biotechnol 2011; 11:97. [PMID: 22026914 PMCID: PMC3217856 DOI: 10.1186/1472-6750-11-97] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 10/25/2011] [Indexed: 12/03/2022] Open
Abstract
Background Research involving gene expression profiling and clinical applications, such as diagnostics and prognostics, often require a DNA array platform that is flexibly customisable and cost-effective, but at the same time is highly sensitive and capable of accurately and reproducibly quantifying the transcriptional expression of a vast number of genes over the whole transcriptome dynamic range using low amounts of RNA sample. Hereto, a set of easy-to-implement practical optimisations to the design of cDNA-based nylon macroarrays as well as sample 33P-labeling, hybridisation protocols and phosphor screen image processing were analysed for macroarray performance. Results The here proposed custom macroarray platform had an absolute sensitivity as low as 50,000 transcripts and a linear range of over 5 log-orders. Its quality of identifying differentially expressed genes was at least comparable to commercially available microchips. Interestingly, the quantitative accuracy was found to correlate significantly with corresponding reversed transcriptase - quantitative PCR values, the gold standard gene expression measure (Pearson's correlation test p < 0.0001). Furthermore, the assay has low cost and input RNA requirements (0.5 μg and less) and has a sound reproducibility. Conclusions Results presented here, demonstrate for the first time that self-made cDNA-based nylon macroarrays can produce highly reliable gene expression data with high sensitivity and covering the entire mammalian dynamic range of mRNA abundances. Starting off from minimal amounts of unamplified total RNA per sample, a reasonable amount of samples can be assayed simultaneously for the quantitative expression of hundreds of genes in an easily customisable and cost-effective manner.
Collapse
Affiliation(s)
- Tom Boonefaes
- Department of Biomedical Molecular Biology, Ghent University, Belgium
| | | | | | | | | | | | | | | |
Collapse
|
169
|
Ambroise J, Bearzatto B, Robert A, Govaerts B, Macq B, Gala JL. Impact of the spotted microarray preprocessing method on fold-change compression and variance stability. BMC Bioinformatics 2011; 12:413. [PMID: 22026942 PMCID: PMC3224096 DOI: 10.1186/1471-2105-12-413] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 10/25/2011] [Indexed: 01/31/2023] Open
Abstract
Background The standard approach for preprocessing spotted microarray data is to subtract the local background intensity from the spot foreground intensity, to perform a log2 transformation and to normalize the data with a global median or a lowess normalization. Although well motivated, standard approaches for background correction and for transformation have been widely criticized because they produce high variance at low intensities. Whereas various alternatives to the standard background correction methods and to log2 transformation were proposed, impacts of both successive preprocessing steps were not compared in an objective way. Results In this study, we assessed the impact of eight preprocessing methods combining four background correction methods and two transformations (the log2 and the glog), by using data from the MAQC study. The current results indicate that most preprocessing methods produce fold-change compression at low intensities. Fold-change compression was minimized using the Standard and the Edwards background correction methods coupled with a log2 transformation. The drawback of both methods is a high variance at low intensities which consequently produced poor estimations of the p-values. On the other hand, effective stabilization of the variance as well as better estimations of the p-values were observed after the glog transformation. Conclusion As both fold-change magnitudes and p-values are important in the context of microarray class comparison studies, we therefore recommend to combine the Edwards correction with a hybrid transformation method that uses the log2 transformation to estimate fold-change magnitudes and the glog transformation to estimate p-values.
Collapse
Affiliation(s)
- Jérôme Ambroise
- ICTEAM institute, ELEN department, Université Catholique de Louvain, Place du Levant 2, 1348 Louvain-la-Neuve, Belgium.
| | | | | | | | | | | |
Collapse
|
170
|
Analytical variables influencing the performance of a miRNA based laboratory assay for prediction of relapse in stage I non-small cell lung cancer (NSCLC). BMC Res Notes 2011; 4:424. [PMID: 22011393 PMCID: PMC3221722 DOI: 10.1186/1756-0500-4-424] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 10/19/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Laboratory assays are needed for early stage non-small lung cancer (NSCLC) that can link molecular and clinical heterogeneity to predict relapse after surgical resection. We technically validated two miRNA assays for prediction of relapse in NSCLC. Total RNA from seventy-five formalin-fixed and paraffin-embedded (FFPE) specimens was extracted, labeled and hybridized to Affymetrix miRNA arrays using different RNA input amounts, ATP-mix dilutions, array lots and RNA extraction- and labeling methods in a total of 166 hybridizations. Two combinations of RNA extraction- and labeling methods (assays I and II) were applied to a cohort of 68 early stage NSCLC patients. RESULTS RNA input amount and RNA extraction- and labeling methods affected signal intensity and the number of detected probes and probe sets, and caused large variation, whereas different ATP-mix dilutions and array lots did not. Leave-one-out accuracies for prediction of relapse were 63% and 73% for the two assays. Prognosticator calls ("no recurrence" or "recurrence") were consistent, independent on RNA amount, ATP-mix dilution, array lots and RNA extraction method. The calls were not robust to changes in labeling method. CONCLUSIONS In this study, we demonstrate that some analytical conditions such as RNA extraction- and labeling methods are important for the variation in assay performance whereas others are not. Thus, careful optimization that address all analytical steps and variables can improve the accuracy of prediction and facilitate the introduction of microRNA arrays in the clinic for prediction of relapse in stage I non-small cell lung cancer (NSCLC).
Collapse
|
171
|
Spivey TL, Uccellini L, Ascierto ML, Zoppoli G, De Giorgi V, Delogu LG, Engle AM, Thomas JM, Wang E, Marincola FM, Bedognetti D. Gene expression profiling in acute allograft rejection: challenging the immunologic constant of rejection hypothesis. J Transl Med 2011; 9:174. [PMID: 21992116 PMCID: PMC3213224 DOI: 10.1186/1479-5876-9-174] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 10/12/2011] [Indexed: 02/06/2023] Open
Abstract
In humans, the role and relationship between molecular pathways that lead to tissue destruction during acute allograft rejection are not fully understood. Based on studies conducted in humans, we recently hypothesized that different immune-mediated tissue destruction processes (i.e. cancer, infection, autoimmunity) share common convergent final mechanisms. We called this phenomenon the "Immunologic Constant of Rejection (ICR)." The elements of the ICR include molecular pathways that are consistently described through different immune-mediated tissue destruction processes and demonstrate the activation of interferon-stimulated genes (ISGs), the recruitment of cytotoxic immune cells (primarily through CXCR3/CCR5 ligand pathways), and the activation of immune effector function genes (IEF genes; granzymes A/B, perforin, etc.). Here, we challenge the ICR hypothesis by using a meta-analytical approach and systematically reviewing microarray studies evaluating gene expression on tissue biopsies during acute allograft rejection. We found the pillars of the ICR consistently present among the studies reviewed, despite implicit heterogeneity. Additionally, we provide a descriptive mechanistic overview of acute allograft rejection by describing those molecular pathways most frequently encountered and thereby thought to be most significant. The biological role of the following molecular pathways is described: IFN-γ, CXCR3/CCR5 ligand, IEF genes, TNF-α, IL-10, IRF-1/STAT-1, and complement pathways. The role of NK cell, B cell and T-regulatory cell signatures are also addressed.
Collapse
Affiliation(s)
- Tara L Spivey
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
172
|
Wang Y, Li L, Ye T, Zhao S, Liu Z, Feng YQ, Wu Y. Cytokinin antagonizes ABA suppression to seed germination of Arabidopsis by downregulating ABI5 expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 68:249-61. [PMID: 21699589 DOI: 10.1111/j.1365-313x.2011.04683.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Abscisic acid (ABA) and cytokinin are key hormones controlling plant development. How ABA and cytokinin interplay to control the transition from a dry seed into a young seedling remains elusive. Here we undertook a gain-of-function genetic screen to identify ABA-insensitive mutants during seed germination in Arabidopsis using an estradiol-inducible approach. In the presence of estradiol, one of these mutants gim1 (germination insensitive to ABA mutant 1) exhibited an elevated level of cytokinin that was attributed to the estradiol-induced expression of AtIPT8 that encodes an isopentenyltransferase for the biosynthesis of cytokinins. Our data on OE-2 and Com-1 transgenic plants carrying the ectopically expressing AtIPT8 gene indicated that the elevation of cytokinin level was responsible for the ABA-insensitivity of gim1 seed germination. Further analyses on alterations of gene transcriptomes in the gim1 mutant demonstrated that the expression of some ABA-inducible genes, including ABI5, was reduced, and could not be restored by exogenous ABA treatment. Moreover, we also failed to observe the ABA-mediated repression of a family of cytokinin signal transducers and transcription repressors called type-A ARR4, ARR5 and ARR6 in the gim1 seedlings. Further analysis demonstrated that type-A ARR4, ARR5 and ARR6 could negatively regulate ABI5 expression, and the physical interaction of ABI5 and type-A ARR4, ARR5 and ARR6 proteins was detected. In summary, our study suggests that the interaction of ABA and cytokinin during seed germination and seedling growth can be mediated by the interplay of transcriptional regulators in Arabidopsis.
Collapse
Affiliation(s)
- Yanping Wang
- Department of Cell and Developmental Biology, College of Life Science, Wuhan University, Wuhan 430072, China
| | | | | | | | | | | | | |
Collapse
|
173
|
Tang W, Hu Z, Muallem H, Gulley ML. Clinical implementation of RNA signatures for pharmacogenomic decision-making. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2011; 4:95-107. [PMID: 23226056 PMCID: PMC3513222 DOI: 10.2147/pgpm.s14888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Indexed: 12/14/2022]
Abstract
RNA profiling is increasingly used to predict drug response, dose, or toxicity based on analysis of drug pharmacokinetic or pharmacodynamic pathways. Before implementing multiplexed RNA arrays in clinical practice, validation studies are carried out to demonstrate sufficient evidence of analytic and clinical performance, and to establish an assay protocol with quality assurance measures. Pathologists assure quality by selecting input tissue and by interpreting results in the context of the input tissue as well as the technologies that were used and the clinical setting in which the test was ordered. A strength of RNA profiling is the array-based measurement of tens to thousands of RNAs at once, including redundant tests for critical analytes or pathways to promote confidence in test results. Instrument and reagent manufacturers are crucial for supplying reliable components of the test system. Strategies for quality assurance include careful attention to RNA preservation and quality checks at pertinent steps in the assay protocol, beginning with specimen collection and proceeding through the various phases of transport, processing, storage, analysis, interpretation, and reporting. Specimen quality is checked by probing housekeeping transcripts, while spiked and exogenous controls serve as a check on analytic performance of the test system. Software is required to manipulate abundant array data and present it for interpretation by a laboratory physician who reports results in a manner facilitating therapeutic decision-making. Maintenance of the assay requires periodic documentation of personnel competency and laboratory proficiency. These strategies are shepherding genomic arrays into clinical settings to provide added value to patients and to the larger health care system.
Collapse
Affiliation(s)
- Weihua Tang
- Department of Pathology and Laboratory Medicine
| | | | | | | |
Collapse
|
174
|
Tan X, Qin W, Zhang L, Hang J, Li B, Zhang C, Wan J, Zhou F, Shao K, Sun Y, Wu J, Zhang X, Qiu B, Li N, Shi S, Feng X, Zhao S, Wang Z, Zhao X, Chen Z, Mitchelson K, Cheng J, Guo Y, He J. A 5-microRNA signature for lung squamous cell carcinoma diagnosis and hsa-miR-31 for prognosis. Clin Cancer Res 2011; 17:6802-11. [PMID: 21890451 DOI: 10.1158/1078-0432.ccr-11-0419] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
PURPOSE Recent studies have suggested that microRNA biomarkers could be useful for stratifying lung cancer subtypes, but microRNA signatures varied between different populations. Squamous cell carcinoma (SCC) is one major subtype of lung cancer that urgently needs biomarkers to aid patient management. Here, we undertook the first comprehensive investigation on microRNA in Chinese SCC patients. EXPERIMENTAL DESIGN MicroRNA expression was measured in cancerous and noncancerous tissue pairs strictly collected from Chinese SCC patients (stages I-III), who had not been treated with chemotherapy or radiotherapy prior to surgery. The molecular targets of proposed microRNA were further examined. RESULTS We identified a 5-microRNA classifier (hsa-miR-210, hsa-miR-182, hsa-miR-486-5p, hsa-miR-30a, and hsa-miR-140-3p) that could distinguish SCC from normal lung tissues. The classifier had an accuracy of 94.1% in a training cohort (34 patients) and 96.2% in a test cohort (26 patients). We also showed that high expression of hsa-miR-31 was associated with poor survival in these 60 SCC patients by Kaplan-Meier analysis (P = 0.007), by univariate Cox analysis (P = 0.011), and by multivariate Cox analysis (P = 0.011). This association was independently validated in a separate cohort of 88 SCC patients (P = 0.008, 0.011, and 0.003 in Kaplan-Meier analysis, univariate Cox analysis, and multivariate Cox analysis, respectively). We then determined that the tumor suppressor DICER1 is a target of hsa-miR-31. Expression of hsa-miR-31 in a human lung cancer cell line repressed DICER1 activity but not PPP2R2A or LATS2. CONCLUSIONS Our results identified a new diagnostic microRNA classifier for SCC among Chinese patients and a new prognostic biomarker, hsa-miR-31.
Collapse
Affiliation(s)
- Xiaogang Tan
- Department of Thoracic Surgery, Cancer Hospital and Institute, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
175
|
Zou L, Sun Y, Wang M, Zhan Q. Aurora-A interacts with AP-2α and down regulates its transcription activity. PLoS One 2011; 6:e23110. [PMID: 21829699 PMCID: PMC3148253 DOI: 10.1371/journal.pone.0023110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 07/06/2011] [Indexed: 11/18/2022] Open
Abstract
Aurora-A is a serine/threonine protein kinase and plays an important role in the control of mitotic progression. Dysregulated expression of Aurora-A impairs centrosome separation and maturation, which lead to disrupted cell cycle progression and tumorigenesis. However, the molecular mechanism by which Aurora-A causes cell malignant transformation remains to be further defined. In this report, using transcription factors array and mRNA expression profiling array, we found that overexpression of Aurora-A suppressed transcription activity of AP-2α, a tumor suppressor that is often downregulated in variety of tumors, and inhibited expression of AP-2α-regulated downstream genes. These array-based observations were further confirmed by microwell colorimetric TF assay and luciferase reporter assay. Downregulated transcription activity of AP-2α by Aurora-A was found to be associated with reduced AP-2α protein stability, which appeared to be mediated by Aurora-A enhanced ubiquitin-dependent proteasomal degradation of AP-2α protein. Interestingly, Aurora-A-mediated AP-2α degradation was likely dependent Aurora-A kinase activity since inhibition of Aurora-A kinase activity was able to rescue Aurora-A-induced degradation of AP-2α. Moreover, we defined a physical interaction between Aurora-A and AP-2α, and such interaction might bridge the suppressive effect of Aurora-A on AP-2α protein stability. These findings provide new insights into molecular mechanism by which Aurora-A acts as an oncogenic molecule in tumor occurrence and malignant development.
Collapse
Affiliation(s)
- Lihui Zou
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yimin Sun
- CapitalBio Corporation, Beijing, China
| | - Mingrong Wang
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qimin Zhan
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- * E-mail:
| |
Collapse
|
176
|
Marko NF, Quackenbush J, Weil RJ. Why is there a lack of consensus on molecular subgroups of glioblastoma? Understanding the nature of biological and statistical variability in glioblastoma expression data. PLoS One 2011; 6:e20826. [PMID: 21829433 PMCID: PMC3145641 DOI: 10.1371/journal.pone.0020826] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 05/09/2011] [Indexed: 12/31/2022] Open
Abstract
INTRODUCTION Gene expression patterns characterizing clinically-relevant molecular subgroups of glioblastoma are difficult to reproduce. We suspect a combination of biological and analytic factors confounds interpretation of glioblastoma expression data. We seek to clarify the nature and relative contributions of these factors, to focus additional investigations, and to improve the accuracy and consistency of translational glioblastoma analyses. METHODS We analyzed gene expression and clinical data for 340 glioblastomas in The Cancer Genome Atlas (TCGA). We developed a logic model to analyze potential sources of biological, technical, and analytic variability and used standard linear classifiers and linear dimensional reduction algorithms to investigate the nature and relative contributions of each factor. RESULTS Commonly-described sources of classification error, including individual sample characteristics, batch effects, and analytic and technical noise make measurable but proportionally minor contributions to inconsistent molecular classification. Our analysis suggests that three, previously underappreciated factors may account for a larger fraction of classification errors: inherent non-linear/non-orthogonal relationships among the genes used in conjunction with classification algorithms that assume linearity; skewed data distributions assumed to be Gaussian; and biologic variability (noise) among tumors, of which we propose three types. CONCLUSIONS Our analysis of the TCGA data demonstrates a contributory role for technical factors in molecular classification inconsistencies in glioblastoma but also suggests that biological variability, abnormal data distribution, and non-linear relationships among genes may be responsible for a proportionally larger component of classification error. These findings may have important implications for both glioblastoma research and for translational application of other large-volume biological databases.
Collapse
Affiliation(s)
- Nicholas F. Marko
- Department of Neurosurgery and Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, Ohio, United States of America
- * E-mail: (NFM); (RJW)
| | - John Quackenbush
- Department of Biostatistics and Computational Biology and Department of Cancer Biology, The Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Robert J. Weil
- Department of Neurosurgery and Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, Ohio, United States of America
- * E-mail: (NFM); (RJW)
| |
Collapse
|
177
|
Agbavwe C, Somoza MM. Sequence-dependent fluorescence of cyanine dyes on microarrays. PLoS One 2011; 6:e22177. [PMID: 21799789 PMCID: PMC3143128 DOI: 10.1371/journal.pone.0022177] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 06/17/2011] [Indexed: 11/19/2022] Open
Abstract
Cy3 and Cy5 are among the most commonly used oligonucleotide labeling molecules. Studies of nucleic acid structure and dynamics use these dyes, and they are ubiquitous in microarray experiments. They are sensitive to their environment and have higher quantum yield when bound to DNA. The fluorescent intensity of terminal cyanine dyes is also known to be significantly dependent on the base sequence of the oligonucleotide. We have developed a very precise and high-throughput method to evaluate the sequence dependence of oligonucleotide labeling dyes using microarrays and have applied the method to Cy3 and Cy5. We used light-directed in-situ synthesis of terminally-labeled microarrays to determine the fluorescence intensity of each dye on all 1024 possible 5′-labeled 5-mers. Their intensity is sensitive to all five bases. Their fluorescence is higher with 5′ guanines, and adenines in subsequent positions. Cytosine suppresses fluorescence. Intensity falls by half over the range of all 5-mers for Cy3, and two-thirds for Cy5. Labeling with 5′-biotin-streptavidin-Cy3/-Cy5 gives a completely different sequence dependence and greatly reduces fluorescence compared with direct terminal labeling.
Collapse
Affiliation(s)
- Christy Agbavwe
- Institute of Inorganic Chemistry, University of Vienna, Vienna, Austria
| | - Mark M. Somoza
- Institute of Inorganic Chemistry, University of Vienna, Vienna, Austria
- * E-mail:
| |
Collapse
|
178
|
Su L, Zhao J, Zhao BX, Zhang SL, Miao JY. Safrole oxide induces human umbilical vein endothelial cell transdifferentiation to 5-hydroxytryptaminergic neuron-like cells through tropomyosin receptor kinase A/cyclooxygenase 2/nuclear factor-kappa B/interleukin 8 signaling. Int J Biochem Cell Biol 2011; 43:1512-22. [PMID: 21777689 DOI: 10.1016/j.biocel.2011.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2011] [Revised: 06/21/2011] [Accepted: 07/05/2011] [Indexed: 12/15/2022]
Abstract
The phenomenon of endothelial-neural transdifferentiation has been observed for a long time, but the mechanism is not clear. We previously found that safrole oxide induced human umbilical vein endothelial cell transdifferentiation into neuron-like cells. In this study, we first validated that these cells induced by safrole oxide were functional 5-hydroxytryptaminergic neuron-like cells. Then, we performed microarray analysis of safrole oxide-treated and -untreated human umbilical vein endothelial cells. Safrole oxide elevated the levels of cyclooxygenase 2 (COX-2), interleukin-8 (IL-8) and reactive oxygen species (ROS), which was accompanied by nuclear factor-kappa B (NF-κB) nuclear translocation during the transdifferentiation. Blockade of tropomyosin receptor kinase A (TrkA) by an inhibitor or short hairpin RNA inhibited the levels of COX-2/IL-8 and the nuclear translocation of NF-κB but did not suppress the increased ROS level. As a result, cells underwent apoptosis. Therefore, via TrkA, safrole oxide may induce endothelial cell transdifferentiation into functional neuron-like cells. During this process, the increased levels of COX-2/IL-8 and the subsequent elevation of ROS production induced NF-κB nuclear translocation and IL-8 secretion. With the activity of TrkA inhibited, the inactive NF-κB regulated the ROS level in a negative feedback manner. Finally, the transdifferentiation pathway was blocked and cells became apoptotic. The TrkA/COX-2/IL-8 signal pathway may have an important role in endothelial-neural transdifferentiation, and safrole oxide may trigger this process by activating TrkA.
Collapse
Affiliation(s)
- Le Su
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, Institute of Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
| | | | | | | | | |
Collapse
|
179
|
He Y, Xu Y, Zhang C, Gao X, Dykema KJ, Martin KR, Ke J, Hudson EA, Khoo SK, Resau JH, Alberts AS, MacKeigan JP, Furge KA, Xu HE. Identification of a lysosomal pathway that modulates glucocorticoid signaling and the inflammatory response. Sci Signal 2011; 4:ra44. [PMID: 21730326 DOI: 10.1126/scisignal.2001450] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The antimalaria drug chloroquine has been used as an anti-inflammatory agent for treating systemic lupus erythematosus and rheumatoid arthritis. We report that chloroquine promoted the transrepression of proinflammatory cytokines by the glucocorticoid receptor (GR). In a mouse collagen-induced arthritis model, chloroquine enhanced the therapeutic effects of glucocorticoid treatment. By inhibiting lysosome function, chloroquine synergistically activated glucocorticoid signaling. Lysosomal inhibition by either bafilomycin A1 (an inhibitor of the vacuolar adenosine triphosphatase) or knockdown of transcription factor EB (TFEB, a master activator of lysosomal biogenesis) mimicked the effects of chloroquine. The abundance of the GR, as well as that of the androgen receptor and estrogen receptor, correlated with changes in lysosomal biogenesis. Thus, we showed that glucocorticoid signaling is regulated by lysosomes, which provides a mechanistic basis for treating inflammation and autoimmune diseases with a combination of glucocorticoids and lysosomal inhibitors.
Collapse
Affiliation(s)
- Yuanzheng He
- Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Avenue Northeast, Grand Rapids, MI 49503, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
180
|
Zhu Y, Ogaeri T, Suzuki JI, Dong S, Aoyagi TI, Mizuki K, Takasugi M, Isobe SI, Kiyama R. Application of Fluolid-Orange-labeled probes for DNA microarray and immunological assays. Biotechnol Lett 2011; 33:1759-66. [PMID: 21626418 DOI: 10.1007/s10529-011-0646-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 05/17/2011] [Indexed: 11/30/2022]
Abstract
The usefulness of Fluolid-Orange, a novel fluorescent dye, for DNA microarray and immunological assays has been examined. Fluolid-Orange-labeled probes (DNA and IgG) were stable as examined by laser-photo-bleaching and under heat and dry conditions. Statistical analyses were performed to evaluate the reproducibility of the microarray assay, while stage-specific immunostaining of marker proteins, Kank1 and calretinin, was performed for renal cancers, both giving satisfactory results. The stability of the dye should provide advantages for storing fluorescently labeled probes and re-examining the specimens later in genetic and pathological diagnostics.
Collapse
Affiliation(s)
- Yun Zhu
- Signaling Molecules Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
181
|
Sun L, Hu H, Peng L, Zhou Z, Zhao X, Pan J, Sun L, Yang Z, Ran Y. P-cadherin promotes liver metastasis and is associated with poor prognosis in colon cancer. THE AMERICAN JOURNAL OF PATHOLOGY 2011; 179:380-90. [PMID: 21703417 DOI: 10.1016/j.ajpath.2011.03.046] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 02/28/2011] [Accepted: 03/02/2011] [Indexed: 02/08/2023]
Abstract
P-cadherin belongs to the family of classic cadherins, which is important for maintaining cellular localization and tissue integrity. Recently, it has become evident that P-cadherin contributes to the oncogenesis of many tumor types, including melanoma, prostate, breast, and colon carcinomas. Although cadherin switching is a crucial step in metastasis, the role of P-cadherin in colon cancer metastasis to the liver is unknown. In this study, we performed gene expression analysis and found that the level of P-cadherin was higher in tissue from liver metastases of colon cancer than in the corresponding primary colon cancer tissues. IHC analysis also showed that P-cadherin expression was significantly higher in liver metastases than in paired primary colorectal cancer tumors. Knockdown of P-cadherin in colon cancer cells inhibited wound healing, proliferation, and colony formation and resulted in developing fewer liver metastatic foci and reducing the tumor burden in vivo. Inhibition of P-cadherin expression also induced the up-regulation of E-cadherin and the down-regulation of β-catenin and its downstream target molecules, including survivin and c-Myc. In summary, these results uncover a novel function of P-cadherin in the regulation of colon cancer metastasis to the liver, suggesting that blocking the activity of P-cadherin or its associated signaling may be a valuable target for the treatment of hepatic metastases of colon carcinomas.
Collapse
Affiliation(s)
- Lichao Sun
- State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | | | | | | | | | | | | | | | | |
Collapse
|
182
|
Ashton-Chess J, Cervino AC. Development of commercial gene-expression-based signatures: review of the scientific strategies. Per Med 2011; 8:253-269. [PMID: 29783527 DOI: 10.2217/pme.10.84] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Many scientific articles have been published that use gene-expression-based technologies to discriminate a trait of interest, typically a disease subgroup, within a patient population. However, few gene-expression-based signatures have at present reached the market and become a financially and clinically successful product. The technological, scientific and medical challenges, the regulatory environment and the financial considerations are all essential parts of the development process. Here we discuss the scientific aspects of successfully developing a gene-expression-based signature and review the global strategy of six products that made it to the market. We also present a point-to-point guide that should help researchers to successfully develop genomic signatures, thus paving the way towards personalized medicine.
Collapse
Affiliation(s)
- Joanna Ashton-Chess
- TcLand Expression, Halle 13, Bio-Ouest Ile de Nantes, 21 Rue de la Noue Bras de Fer, 44200 Nantes, France
| | | |
Collapse
|
183
|
Nawaratna SSK, McManus DP, Moertel L, Gobert GN, Jones MK. Gene Atlasing of digestive and reproductive tissues in Schistosoma mansoni. PLoS Negl Trop Dis 2011; 5:e1043. [PMID: 21541360 PMCID: PMC3082511 DOI: 10.1371/journal.pntd.0001043] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Accepted: 03/25/2011] [Indexed: 11/30/2022] Open
Abstract
Background While considerable genomic and transcriptomic data are available for
Schistosoma mansoni, many of its genes lack significant
annotation. A transcriptomic study of individual tissues and organs of
schistosomes could play an important role in functional annotation of the
unknown genes, particularly by providing rapid localisation data and thus
giving insight into the potential roles of these molecules in parasite
development, reproduction and homeostasis, and in the complex host-parasite
interaction. Methodology/Principal Findings Quantification of gene expression in tissues of S. mansoni
was achieved by a combination of laser microdissection microscopy (LMM) and
oligonucleotide microarray analysis. We compared the gene expression profile
of the adult female gastrodermis and male and female reproductive tissues
with whole worm controls. The results revealed a total of 393 genes
(contigs) that were up-regulated two-fold or more in the gastrodermis, 4,450
in the ovary, 384 in the vitelline tissues of female parasites, and 2,171 in
the testes. We have also supplemented these data with the identification of
highly expressed genes in different regions of manually dissected male and
female S. mansoni. Though relatively crude, this dissection
strategy provides low resolution localisation data for critical regions of
the adult parasites that are not amenable to LMM isolation. Conclusions This is the first detailed transcriptomic study of the reproductive tissues
and gastrodermis of S. mansoni. The results obtained will
help direct future research on the functional aspects of these tissues,
expediting the characterisation of currently unannotated gene products of
S. mansoni and the discovery of new drug and vaccine
targets. There is currently only one drug available for treatment of
schistosomiasis mansoni and no vaccine. The searches for
possible new drug and vaccine candidates remain two major areas of current
research in schistosomiasis. There are considerable amounts of data available on
the genomics, transcriptomics and proteomics of Schistosoma
mansoni from which useful candidates for future drug and vaccine
development can be identified. Arranging these data into a biologically relevant
context through the characterisation of gene expression profiles of the
different tissues of this complex metazoan parasite, is an essential step in
identifying molecules with potential therapeutic value. We have used laser
microdissection microscopy and microarray analysis to show that many
tissue-specific genes are up-regulated in the digestive and reproductive tissues
of S. mansoni. This new knowledge provides an avenue to
investigate the molecular components associated with fundamental aspects of
schistosome biology.
Collapse
Affiliation(s)
- Sujeevi S. K. Nawaratna
- Queensland Institute of Medical Research, Herston, Australia
- School of Veterinary Sciences, The University of Queensland, Gatton,
Australia
| | | | - Luke Moertel
- Queensland Institute of Medical Research, Herston, Australia
| | - Geoffrey N. Gobert
- Queensland Institute of Medical Research, Herston, Australia
- School of Veterinary Sciences, The University of Queensland, Gatton,
Australia
| | - Malcolm K. Jones
- Queensland Institute of Medical Research, Herston, Australia
- School of Veterinary Sciences, The University of Queensland, Gatton,
Australia
- * E-mail:
| |
Collapse
|
184
|
Li Y, Basang Z, Ding H, Lu Z, Ning T, Wei H, Cai H, Ke Y. Latexin expression is downregulated in human gastric carcinomas and exhibits tumor suppressor potential. BMC Cancer 2011; 11:121. [PMID: 21466706 PMCID: PMC3080345 DOI: 10.1186/1471-2407-11-121] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Accepted: 04/06/2011] [Indexed: 01/10/2023] Open
Abstract
Background Latexin, also known as endogenous carboxypeptidase inhibitor (CPI), has been found to inhibit mouse stem cell populations and lymphoma cell proliferation, demonstrating its potential role as a tumor suppressor. Our previous study also suggested a correlation between latexin expression and malignant transformation of immortalized human gastric epithelial cells. Here, we examined latexin expression in human gastric carcinomas and investigated the effect of differential latexin expression on proliferation of gastric cancer cells in vitro and in vivo. Methods Monoclonal antibody against human latexin was prepared and immunohistochemical analysis was performed to detect latexin expression in 41 paired gastric carcinomas and adjacent normal control tissues. Human gastric cancer cells MGC803 (latexin negative) stably transfected with LXN gene and BGC823 cells (latexin positive) stably transfected with antisense LXN gene were established for anchorage-dependent colony formation assay and tumorigenesis assay in nude mice. Differentially expressed genes in response to exogeneous latexin expression were screened using microarray analysis and identified by RT-PCR. Bisulfite sequencing was performed to analyze the correlation of the methylation status of LXN promoter with latexin expression in cell lines. Results Immunohistochemical analysis showed significantly reduced latexin expression in gastric carcinomas (6/41, 14.6%) compared to control tissues (31/41, 75.6%) (P < 0.05). Overexpression of LXN gene in MGC803 cells inhibited colony formation and tumor growth in nude mice. Conversely, BGC823 cells transfected with antisense LXN gene exhibited enhanced tumor growth and colony formation. Additionally, several tumor related genes, including Maspin, WFDC1, SLPI, S100P, and PDGFRB, were shown to be differentially expressed in MGC803 cells in response to latexin expression. Differential expression of Maspin and S100P was also identified in BGC823 cells while latexin expression was downregulated. Further bisulfite sequencing of the LXN gene promoter indicated CpG hypermethylation was correlated with silencing of latexin expression in human cells. Conclusions Latexin expression was reduced in human gastric cancers compared with their normal control tissues. The cellular and molecular evidences demonstrated the inhibitory effect of latexin in human gastric cancer cell growth and tumorigenicity. These results strongly suggest the possible involvement of latexin expression in tumor suppression.
Collapse
Affiliation(s)
- Yong Li
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Genetics, Peking University School of Oncology, Beijing Cancer Hospital & Institute, Hai Dian District, Beijing 100142, China
| | | | | | | | | | | | | | | |
Collapse
|
185
|
Zhang Y, Yan LX, Wu QN, Du ZM, Chen J, Liao DZ, Huang MY, Hou JH, Wu QL, Zeng MS, Huang WL, Zeng YX, Shao JY. miR-125b is methylated and functions as a tumor suppressor by regulating the ETS1 proto-oncogene in human invasive breast cancer. Cancer Res 2011; 71:3552-62. [PMID: 21444677 DOI: 10.1158/0008-5472.can-10-2435] [Citation(s) in RCA: 227] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The microRNA miR-125b is dysregulated in various human cancers but its underlying mechanisms of action are poorly understood. Here, we report that miR-125b is downregulated in invasive breast cancers where it predicts poor patient survival. Hypermethylation of the miR-125b promoter partially accounted for reduction of miR-125b expression in human breast cancer. Ectopic restoration of miR-125b expression in breast cancer cells suppressed proliferation, induced G(1) cell-cycle arrest in vitro, and inhibited tumorigenesis in vivo. We identified the ETS1 gene as a novel direct target of miR-125b. siRNA-mediated ETS1 knockdown phenocopied the effect of miR-125b in breast cell lines and ETS1 overexpression in invasive breast cancer tissues also correlated with poor patient prognosis. Taken together, our findings point to an important role for miR-125b in the molecular etiology of invasive breast cancer, and they suggest miR-125b as a potential theranostic tool in this disease.
Collapse
Affiliation(s)
- Yan Zhang
- State Key Laboratory of Oncology in Southern China, and Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
186
|
Zhu Q, Miecznikowski JC, Halfon MS. A wholly defined Agilent microarray spike-in dataset. ACTA ACUST UNITED AC 2011; 27:1284-9. [PMID: 21414985 DOI: 10.1093/bioinformatics/btr135] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Spike-in datasets provide a valuable resource for assessing and comparing among competing microarray analysis strategies. Our previous wholly defined spike-in datasets, the Golden and Platinum Spikes, have provided insights for the analysis of Affymetrix GeneChips. However, a similar dataset, in which all cRNA identities and relative levels are known prospectively, has not been available for two-color platforms. RESULTS We have generated a wholly defined spike-in dataset for Agilent microarrays consisting of 12 arrays with more than 2000 differentially expressed, and approximately 3600 background, cRNAs. The composition of this 'Ag Spike' dataset is identical to that of our previous Platinum Spike dataset and therefore allows direct cross-platform comparison. We demonstrate here the utility of the Ag Spike dataset for evaluating different analysis methods designed for two-color arrays. Comparison between the Ag Spike and Platinum Spike studies shows high agreement between results obtained using the Affymetrix and Agilent platforms. AVAILABILITY The Ag Spike raw data can be accessed at http://www.ccr.buffalo.edu/halfon/spike/index.html and through NCBI's Gene Expression Omnibus (GEO; accession GSE24866).
Collapse
Affiliation(s)
- Qianqian Zhu
- Department of Biochemistry, Department of Biostatistics, State University of New York at Buffalo, Buffalo, NY 14214, USA.
| | | | | |
Collapse
|
187
|
Vo TKD, de Saint-Hubert M, Morrhaye G, Godard P, Geenen V, Martens HJ, Debacq-Chainiaux F, Swine C, Toussaint O. Transcriptomic biomarkers of the response of hospitalized geriatric patients admitted with heart failure. Comparison to hospitalized geriatric patients with infectious diseases or hip fracture. Mech Ageing Dev 2011; 132:131-9. [DOI: 10.1016/j.mad.2011.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 11/24/2010] [Accepted: 02/08/2011] [Indexed: 01/05/2023]
|
188
|
Liang RM, Yong XL, Jiang YP, Tan YH, Dai BD, Wang SH, Hu TT, Chen X, Li N, Dong ZH, Huang XC, Chen J, Cao YB, Jiang YY. 2-amino-nonyl-6-methoxyl-tetralin muriate activity against Candida albicans augments endogenous reactive oxygen species production --a microarray analysis study. FEBS J 2011; 278:1075-85. [PMID: 21251230 DOI: 10.1111/j.1742-4658.2011.08021.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Candida infections have become an increasingly significant problem, mainly because of the widespread nature of Candida and drug resistance. There is an urgent need to develop new classes of drugs for the treatment of opportunistic Candida infections, especially in medically complex patients. Previous studies have confirmed that 2-amino-nonyl-6-methoxyl-tetralin muriate (10b) possesses powerful antifungal activity in vitro against Candia albicans. To clarify the underlying action mechanism, an oligonucleotide microarray study was performed in C. albicans SC5314 without and with 10b treatment. The analytical results showed that energy metabolism-related genes, including glycolysis-related genes (PFK1, CDC19 and HXK2), fermentation-related genes (PDC11, ALD5 and ADH1) and respiratory electron transport chain-related genes (CBP3, COR1 and QCR8), were downregulated significantly. Functional analysis revealed that 10b treatment increased the generation of endogenous reactive oxygen species, and decreased mitochondrial membrane potential, ubiquinone-cytochrome c reductase (complex III) activity and intracellular ATP levels in C. albicans SC5314. Also, addition of the antioxidant ascorbic acid reduced the antifungal activity of 10b significantly. These results suggest that mitochondrial aerobic respiration shift and endogenous reactive oxygen species augmentation might contribute to the antifungal activity of 10b against C. albicans. This information may prove to be useful for the development of new strategies to treat Candida infections.
Collapse
Affiliation(s)
- Rong Mei Liang
- Drug Development Center, School of Pharmacy, Second Military Medical University, Shanghai, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
189
|
MEK2 is sufficient but not necessary for proliferation and anchorage-independent growth of SK-MEL-28 melanoma cells. PLoS One 2011; 6:e17165. [PMID: 21365009 PMCID: PMC3041822 DOI: 10.1371/journal.pone.0017165] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 01/23/2011] [Indexed: 01/14/2023] Open
Abstract
Mitogen-activated protein kinase kinases (MKK or MEK) 1 and 2 are usually treated as redundant kinases. However, in assessing their relative contribution towards ERK-mediated biologic response investigators have relied on tests of necessity, not sufficiency. In response we developed a novel experimental model using lethal toxin (LeTx), an anthrax toxin-derived pan-MKK protease, and genetically engineered protease resistant MKK mutants (MKKcr) to test the sufficiency of MEK signaling in melanoma SK-MEL-28 cells. Surprisingly, ERK activity persisted in LeTx-treated cells expressing MEK2cr but not MEK1cr. Microarray analysis revealed non-overlapping downstream transcriptional targets of MEK1 and MEK2, and indicated a substantial rescue effect of MEK2cr on proliferation pathways. Furthermore, LeTx efficiently inhibited the cell proliferation and anchorage-independent growth of SK-MEL-28 cells expressing MKK1cr but not MEK2cr. These results indicate in SK-MEL-28 cells MEK1 and MEK2 signaling pathways are not redundant and interchangeable for cell proliferation. We conclude that in the absence of other MKK, MEK2 is sufficient for SK-MEL-28 cell proliferation. MEK1 conditionally compensates for loss of MEK2 only in the presence of other MKK.
Collapse
|
190
|
Bruning O, Yuan X, Rodenburg W, Bruins W, van Oostrom CT, Rauwerda H, Wittink FR, Jonker MJ, de Vries A, Breit TM. Serious complications in gene-expression studies with stress perturbation: An example of UV-exposed p53-mutant mouse embryonic fibroblasts. Transcription 2011; 1:159-164. [PMID: 21326892 DOI: 10.4161/trns.1.3.13487] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 08/30/2010] [Accepted: 08/30/2010] [Indexed: 01/06/2023] Open
Abstract
Reanalysis of our UV study of p53-mutant mouse embryonic fibroblasts revealed an intriguing orchestration of massive transcriptome responses. However, close scrutiny of the data uncovered an affected mRNA/rRNA ratio, effectively inhibiting valid data analysis. UV-dose range-finding showed low-dose UV specific- and high-dose stress-related responses, which represent a plea for UV dose range-finding in experimental design.
Collapse
Affiliation(s)
- Oskar Bruning
- MicroArray Department and Integrative Bioinformatics Unit (MAD-IBU); Swammerdam Institute for Life Sciences; Faculty of Science; University of Amsterdam (UvA); Amsterdam, The Netherlands
| | | | | | | | | | | | | | | | | | | |
Collapse
|
191
|
Kaminen-Ahola N, Ahola A, Flatscher-Bader T, Wilkins SJ, Anderson GJ, Whitelaw E, Chong S. Postnatal growth restriction and gene expression changes in a mouse model of fetal alcohol syndrome. ACTA ACUST UNITED AC 2011; 88:818-26. [PMID: 20878912 DOI: 10.1002/bdra.20729] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Growth restriction, craniofacial dysmorphology, and central nervous system defects are the main diagnostic features of fetal alcohol syndrome. Studies in humans and mice have reported that the growth restriction can be prenatal or postnatal, but the underlying mechanisms remain unknown.We recently described a mouse model of moderate gestational ethanol exposure that produces measurable phenotypes in line with fetal alcohol syndrome (e.g., craniofacial changes and growth restriction in adolescent mice). In this study, we characterize in detail the growth restriction phenotype by measuring body weight at gestational day 16.5, cross-fostering from birth to weaning, and by extending our observations into adulthood. Furthermore, in an attempt to unravel the molecular events contributing to the growth phenotype, we have compared gene expression patterns in the liver and kidney of nonfostered, ethanol-exposed and control mice at postnatal day 28.We find that the ethanol-induced growth phenotype is not detectable prior to birth, but is present at weaning, even in mice that have been cross-fostered to unexposed dams. This finding suggests a postnatal growth restriction phenotype that is not due to deficient postpartum care by dams that drank ethanol, but rather a physiologic result of ethanol exposure in utero. We also find that, despite some catch-up growth after 5 weeks of age, the effect extends into adulthood, which is consistent with longitudinal studies in humans.Genome-wide gene expression analysis revealed interesting ethanol-induced changes in the liver, including genes involved in the metabolism of exogenous and endogenous compounds, iron homeostasis, and lipid metabolism.
Collapse
Affiliation(s)
- Nina Kaminen-Ahola
- Epigenetics Laboratory, Queensland Institute of Medical Research, 300 Herston Rd., Herston, Queensland 4006, Australia
| | | | | | | | | | | | | |
Collapse
|
192
|
Wilson VS, Keshava N, Hester S, Segal D, Chiu W, Thompson CM, Euling SY. Utilizing toxicogenomic data to understand chemical mechanism of action in risk assessment. Toxicol Appl Pharmacol 2011; 271:299-308. [PMID: 21295051 DOI: 10.1016/j.taap.2011.01.017] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 01/25/2011] [Accepted: 01/25/2011] [Indexed: 11/16/2022]
Abstract
The predominant role of toxicogenomic data in risk assessment, thus far, has been one of augmentation of more traditional in vitro and in vivo toxicology data. This article focuses on the current available examples of instances where toxicogenomic data has been evaluated in human health risk assessment (e.g., acetochlor and arsenicals) which have been limited to the application of toxicogenomic data to inform mechanism of action. This article reviews the regulatory policy backdrop and highlights important efforts to ultimately achieve regulatory acceptance. A number of research efforts on specific chemicals that were designed for risk assessment purposes have employed mechanism or mode of action hypothesis testing and generating strategies. The strides made by large scale efforts to utilize toxicogenomic data in screening, testing, and risk assessment are also discussed. These efforts include both the refinement of methodologies for performing toxicogenomics studies and analysis of the resultant data sets. The current issues limiting the application of toxicogenomics to define mode or mechanism of action in risk assessment are discussed together with interrelated research needs. In summary, as chemical risk assessment moves away from a single mechanism of action approach toward a toxicity pathway-based paradigm, we envision that toxicogenomic data from multiple technologies (e.g., proteomics, metabolomics, transcriptomics, supportive RT-PCR studies) can be used in conjunction with one another to understand the complexities of multiple, and possibly interacting, pathways affected by chemicals which will impact human health risk assessment.
Collapse
Affiliation(s)
- Vickie S Wilson
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| | | | | | | | | | | | | |
Collapse
|
193
|
Early proliferation alteration and differential gene expression in human periodontal ligament cells subjected to cyclic tensile stress. Arch Oral Biol 2011; 56:177-86. [DOI: 10.1016/j.archoralbio.2010.09.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2010] [Revised: 08/24/2010] [Accepted: 09/10/2010] [Indexed: 12/31/2022]
|
194
|
Becher R, Weihmann F, Deising HB, Wirsel SG. Development of a novel multiplex DNA microarray for Fusarium graminearum and analysis of azole fungicide responses. BMC Genomics 2011; 12:52. [PMID: 21255412 PMCID: PMC3037902 DOI: 10.1186/1471-2164-12-52] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 01/21/2011] [Indexed: 11/29/2022] Open
Abstract
Background The toxigenic fungal plant pathogen Fusarium graminearum compromises wheat production worldwide. Azole fungicides play a prominent role in controlling this pathogen. Sequencing of its genome stimulated the development of high-throughput technologies to study mechanisms of coping with fungicide stress and adaptation to fungicides at a previously unprecedented precision. DNA-microarrays have been used to analyze genome-wide gene expression patterns and uncovered complex transcriptional responses. A recently developed one-color multiplex array format allowed flexible, effective, and parallel examinations of eight RNA samples. Results We took advantage of the 8 × 15 k Agilent format to design, evaluate, and apply a novel microarray covering the whole F. graminearum genome to analyze transcriptional responses to azole fungicide treatment. Comparative statistical analysis of expression profiles uncovered 1058 genes that were significantly differentially expressed after azole-treatment. Quantitative RT-PCR analysis for 31 selected genes indicated high conformity to results from the microarray hybridization. Among the 596 genes with significantly increased transcript levels, analyses using GeneOntology and FunCat annotations detected the ergosterol-biosynthesis pathway genes as the category most significantly responding, confirming the mode-of-action of azole fungicides. Cyp51A, which is one of the three F. graminearum paralogs of Cyp51 encoding the target of azoles, was the most consistently differentially expressed gene of the entire study. A molecular phylogeny analyzing the relationships of the three CYP51 proteins in the context of 38 fungal genomes belonging to the Pezizomycotina indicated that CYP51C (FGSG_11024) groups with a new clade of CYP51 proteins. The transcriptional profiles for genes encoding ABC transporters and transcription factors suggested several involved in mechanisms alleviating the impact of the fungicide. Comparative analyses with published microarray experiments obtained from two different nutritional stress conditions identified subsets of genes responding to different types of stress. Some of the genes that responded only to tebuconazole treatment appeared to be unique to the F. graminearum genome. Conclusions The novel F. graminearum 8 × 15 k microarray is a reliable and efficient high-throughput tool for genome-wide expression profiling experiments in fungicide research, and beyond, as shown by our data obtained for azole responses. The array data contribute to understanding mechanisms of fungicide resistance and allow identifying fungicide targets.
Collapse
Affiliation(s)
- Rayko Becher
- Institut für Agrar- und Ernährungswissenschaften, Naturwissenschaftliche Fakultät III, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120 Halle (Saale), Germany
| | | | | | | |
Collapse
|
195
|
Yan LX, Wu QN, Zhang Y, Li YY, Liao DZ, Hou JH, Fu J, Zeng MS, Yun JP, Wu QL, Zeng YX, Shao JY. Knockdown of miR-21 in human breast cancer cell lines inhibits proliferation, in vitro migration and in vivo tumor growth. Breast Cancer Res 2011; 13:R2. [PMID: 21219636 PMCID: PMC3109565 DOI: 10.1186/bcr2803] [Citation(s) in RCA: 250] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2010] [Revised: 10/15/2010] [Accepted: 01/10/2011] [Indexed: 12/15/2022] Open
Abstract
Introduction MicroRNAs (miRNAs) are a class of small non-coding RNAs (20 to 24 nucleotides) that post-transcriptionally modulate gene expression. A key oncomir in carcinogenesis is miR-21, which is consistently up-regulated in a wide range of cancers. However, few functional studies are available for miR-21, and few targets have been identified. In this study, we explored the role of miR-21 in human breast cancer cells and tissues, and searched for miR-21 targets. Methods We used in vitro and in vivo assays to explore the role of miR-21 in the malignant progression of human breast cancer, using miR-21 knockdown. Using LNA silencing combined to microarray technology and target prediction, we screened for potential targets of miR-21 and validated direct targets by using luciferase reporter assay and Western blot. Two candidate target genes (EIF4A2 and ANKRD46) were selected for analysis of correlation with clinicopathological characteristics and prognosis using immunohistochemistry on cancer tissue microrrays. Results Anti-miR-21 inhibited growth and migration of MCF-7 and MDA-MB-231 cells in vitro, and tumor growth in nude mice. Knockdown of miR-21 significantly increased the expression of ANKRD46 at both mRNA and protein levels. Luciferase assays using a reporter carrying a putative target site in the 3' untranslated region of ANKRD46 revealed that miR-21 directly targeted ANKRD46. miR-21 and EIF4A2 protein were inversely expressed in breast cancers (rs = -0.283, P = 0.005, Spearman's correlation analysis). Conclusions Knockdown of miR-21 in MCF-7 and MDA-MB-231 cells inhibits in vitro and in vivo growth as well as in vitro migration. ANKRD46 is newly identified as a direct target of miR-21 in BC. These results suggest that inhibitory strategies against miR-21 using peptide nucleic acids (PNAs)-antimiR-21 may provide potential therapeutic applications in breast cancer treatment.
Collapse
Affiliation(s)
- Li Xu Yan
- State Key Laboratory of Oncology in Southern China, Sun Yat-Sen University Cancer Center, 651 Dong Feng Road East, Guangzhou, 510060, PR China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
196
|
Biedendieck R, Borgmeier C, Bunk B, Stammen S, Scherling C, Meinhardt F, Wittmann C, Jahn D. Systems biology of recombinant protein production using Bacillus megaterium. Methods Enzymol 2011; 500:165-95. [PMID: 21943898 DOI: 10.1016/b978-0-12-385118-5.00010-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The Gram-negative bacterium Escherichia coli is the most widely used production host for recombinant proteins in both academia and industry. The Gram-positive bacterium Bacillus megaterium represents an increasingly used alternative for high yield intra- and extracellular protein synthesis. During the past two decades, multiple tools including gene expression plasmids and production strains have been developed. Introduction of free replicating and integrative plasmids into B. megaterium is possible via protoplasts transformation or transconjugation. Using His(6)- and StrepII affinity tags, the intra- or extracellular produced proteins can easily be purified in one-step procedures. Different gene expression systems based on the xylose controlled promoter P(xylA) and various phage RNA polymerase (T7, SP6, K1E) driven systems enable B. megaterium to produce up to 1.25g of recombinant protein per liter. Biomass concentrations of up to 80g/l can be achieved by high cell density cultivations in bioreactors. Gene knockouts and gene replacements in B. megaterium are possible via an optimized gene disruption system. For a safe application in industry, sporulation and protease-deficient as well as UV-sensitive mutants are available. With the help of the recently published B. megaterium genome sequence, it is possible to characterize bottle necks in the protein production process via systems biology approaches based on transcriptome, proteome, metabolome, and fluxome data. The bioinformatical platform (Megabac, http://www.megabac.tu-bs.de) integrates obtained theoretical and experimental data.
Collapse
Affiliation(s)
- Rebekka Biedendieck
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, Braunschweig, Germany
| | | | | | | | | | | | | | | |
Collapse
|
197
|
Cost-efficiency considerations in the choice of a microarray platform for time course experimental designs. Comput Stat Data Anal 2011. [DOI: 10.1016/j.csda.2010.04.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
198
|
Quest for new genomic and proteomic biomarkers in neurology. Transl Neurosci 2011. [DOI: 10.2478/s13380-011-0005-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractThe possibility of identifying novel biomarkers for neurodegenerative diseases has been greatly enhanced with recent advances in genomics and proteomics. Novel technologies have the potential to hasten the development of new biomarkers useful as predictors of disease etiology and outcome, as well as responsiveness to therapy. Disease-modifying new therapies are very much needed in modern approaches to treatment of neurodegenerative diseases. Current progress in the field encounters a degree of skepticism about the reliability of genomic and proteomic data and its relevance for clinical applications. Standard operating procedures covering sample collection, methodology and statistical analysis need to be fully developed and strictly adhered to in order to assure reproducible and clinically relevant results. Previous studies involving patients with neurodegenerative diseases show promise in using genomic and proteomic approaches for development of new biomarkers. Confirmation of any novel biomarker in multiple independent patient cohorts and correlation of the improvement in biomarker endpoint with clinical improvement in longitudinal patient studies remains crucial for future successful application. We propose that a combination of approaches in biomarker discovery may in the end lead to identification of promising candidates at DNA, RNA, protein and small molecule level.
Collapse
|
199
|
Khoo SK, Dykema K, Vadlapatla NM, LaHaie D, Valle S, Satterthwaite D, Ramirez SA, Carruthers JA, Haak PT, Resau JH. Acquiring genome-wide gene expression profiles in Guthrie card blood spots using microarrays. Pathol Int 2010; 61:1-6. [DOI: 10.1111/j.1440-1827.2010.02611.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
200
|
Li JC, Yang XR, Sun HX, Xu Y, Zhou J, Qiu SJ, Ke AW, Cui YH, Wang ZJ, Wang WM, Liu KD, Fan J. Up-regulation of Krüppel-like factor 8 promotes tumor invasion and indicates poor prognosis for hepatocellular carcinoma. Gastroenterology 2010; 139:2146-2157.e12. [PMID: 20728449 DOI: 10.1053/j.gastro.2010.08.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2009] [Revised: 07/27/2010] [Accepted: 08/04/2010] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS The transcription factor Krüppel-like factor 8 (KLF8) has a role in tumor development, growth, and metastasis, but its role in hepatocellular carcinoma (HCC) is not clear. METHODS KLF8 expression in human HCC cell lines and tumor tissues was measured by quantitative real-time polymerase chain reaction, immunoblot, and immunochemical analyses. The effects of KLF8 depletion or overexpression in HCC cells were observed in cultured cells and in mice. Changes in gene expression patterns in HCC cells in which levels of KLF8 were reduced using small interfering RNA were investigated by microarray analysis. The clinical significance of KLF8 expression levels were validated using tissue microarray analysis of surgical samples from 314 HCC patients. RESULTS KLF8 was overexpressed in highly metastatic HCC cell lines and in samples from patients with recurrent HCC. In cultured cells, KLF8 up-regulation promoted cell proliferation and invasion; inhibited apoptosis; down-regulated N-cadherin, vimentin, and fibronectin; and up-regulated E-cadherin. In mice, overexpression of KLF8 increased HCC progression and metastasis. Microarray analysis showed that reduction of KLF8 in HCC cells down-regulated expression of multiple genes involved in tumor progression and metastasis. KLF8 expression was a significant predictor of overall survival (P = .040) and time to HCC recurrence (P = .006) and was associated with early tumor recurrence (P = .001). CONCLUSIONS KLF8 promotes HCC cell proliferation and invasion, inhibits apoptosis, and induces the epithelial-to-mesenchymal transition. KLF8 up-regulation might be used to indicate poor prognosis or early recurrence of cancer in patients who have had surgery for HCC.
Collapse
Affiliation(s)
- Jia-Chu Li
- Experimental Research Center, Zhongshan Hospital, Fudan University, Shanghai 200032, P. R. China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|