51
|
Gehringer MM, Shephard EG, Downing TG, Wiegand C, Neilan BA. An investigation into the detoxification of microcystin-LR by the glutathione pathway in Balb/c mice. Int J Biochem Cell Biol 2004; 36:931-41. [PMID: 15006645 DOI: 10.1016/j.biocel.2003.10.012] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2003] [Revised: 09/30/2003] [Accepted: 10/13/2003] [Indexed: 11/23/2022]
Abstract
Toxin-producing cyanobacteria pose a world-wide health threat to humans and animals due to their increasing presence in both drinking and recreational waters. The predominant cyanotoxin, microcystin-LR (MCLR), targets the liver and its toxicity depends on the uptake and removal rates in the liver. The role of the glutathione detoxification pathway in protecting the liver from the effects of MCLR was investigated. Mice exposed to a single 75% LD(50) dose of pure MCLR were sacrificed at 8, 16, 24 and 32 h post-exposure (pe). Toxin induced liver damage was observed 8 and 16 h pe as evidenced by raised serum ALT and LDH levels, reduced glycogen levels and liver histology. A significant increase in lipid peroxidation was seen at 16 h pe that decreased after 24 and 32 h pe, the time-points which showed significant increases in GPX activity. An increase in soluble GST activity was noted between 8 and 16 h pe, levels of total GSH increased at 24 h while oxidised glutathione increased throughout the investigation. The increase in activity of both GPX and GST corresponded with increased transcription of these enzymes, as well as the rate-limiting enzyme in GSH synthesis, gamma-glutamyl transferase. In conclusion, this study confirms that an increase in GST activity is critical for the detoxification of MCLR, that this is regulated at the transcriptional level, and that exposure to MCLR induces the de novo synthesis of GSH. Finally, we report the involvement of GPX in the removal of MCLR-induced lipid hydroperoxides.
Collapse
Affiliation(s)
- Michelle M Gehringer
- MRC/UCT Liver Research Centre, Groote Schuur Hospital, University of Cape Town, Old Main Building, Rondebosch, Cape Town, South Africa.
| | | | | | | | | |
Collapse
|
52
|
Kho AT, Zhao Q, Cai Z, Butte AJ, Kim JYH, Pomeroy SL, Rowitch DH, Kohane IS. Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers. Genes Dev 2004; 18:629-40. [PMID: 15075291 PMCID: PMC387239 DOI: 10.1101/gad.1182504] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2003] [Accepted: 02/25/2004] [Indexed: 11/24/2022]
Abstract
Identification of common mechanisms underlying organ development and primary tumor formation should yield new insights into tumor biology and facilitate the generation of relevant cancer models. We have developed a novel method to project the gene expression profiles of medulloblastomas (MBs)--human cerebellar tumors--onto a mouse cerebellar development sequence: postnatal days 1-60 (P1-P60). Genomically, human medulloblastomas were closest to mouse P1-P10 cerebella, and normal human cerebella were closest to mouse P30-P60 cerebella. Furthermore, metastatic MBs were highly associated with mouse P5 cerebella, suggesting that a clinically distinct subset of tumors is identifiable by molecular similarity to a precise developmental stage. Genewise, down- and up-regulated MB genes segregate to late and early stages of development, respectively. Comparable results for human lung cancer vis-a-vis the developing mouse lung suggest the generalizability of this multiscalar developmental perspective on tumor biology. Our findings indicate both a recapitulation of tissue-specific developmental programs in diverse solid tumors and the utility of tumor characterization on the developmental time axis for identifying novel aspects of clinical and biological behavior.
Collapse
Affiliation(s)
- Alvin T Kho
- Children's Hospital Informatics Program, Children's Hospital Boston, MA 02115, USA
| | | | | | | | | | | | | | | |
Collapse
|
53
|
Yang YS, Guccione S, Bednarski MD. Comparing genomic and histologic correlations to radiographic changes in tumors: a murine SCC VII model study. Acad Radiol 2004; 10:1165-75. [PMID: 14587635 DOI: 10.1016/s1076-6332(03)00327-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
RATIONALE AND OBJECTIVES To investigate the correlation between the temporal changes in T1- and T2-weighted contrast-enhanced magnetic resonance imaging (MRI), histologic evaluation, and genomic analysis using oligonucleotide microarrays in a murine squamous cell carcinoma tumor models. MATERIALS AND METHODS The squamous cell carcinoma (SCC VII) cell line was used to initiate subcutaneous tumors in mice. This mouse model has been used as a model for human head and neck carcinomas. Animals were imaged using contrast enhanced MRI (CE-MRI). Different stages of tumor growth were defined based on changes in the T1- and T2-weighted MRI patterns. The contrast enhancing (CE) and nonenhancing (NE) regions of the tumors were marked and biopsied for oligonucleotide microarray and histologic analysis. Tumors with no differential contrast enhancement were used as controls. RESULTS Distinct temporal stages of tumor progression can be defined using both T1- and T2-weighted CE-MRI and microarray analysis. The early stage tumors show a homogeneous contrast enhancement pattern in the T1- and T2-weighted images with no significant differential gene expression from the center and periphery of the tumor. The more advanced tumors that show discrete regions of contrast enhancement in the post-contrast T1-weighted MRIs and tissues from the CE and NE regions show distinctly differential gene expression profiles. Histologic analysis (hematoxylin-eosin stain) showed that the samples obtained from the periphery and center of the early stage tumors and the CE and NE regions from these more advanced tumors were similar. The gene expression profiles of late-stage tumors that showed changes in T2-weighted MRI signal intensity were consistent with tissue degradation in the NE region, which also showed characteristic signs of tissue necrosis in histologic analysis. CONCLUSION These results show that temporal changes in T1- and T2-weighted CE-MRI are related to distinct gene expression profiles, and histologic analysis may not be sufficient to detect these detailed changes. As tumors progress, discrete regions of post-contrast T1 enhancement are identified; these regions have distinct gene expression patterns despite similar histologic features. In late-stage tumors, regions of T2 signal changes are observed which correspond with tissue necrosis.
Collapse
Affiliation(s)
- Yi-Shan Yang
- Lucas MRS Research Center, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | | | | |
Collapse
|
54
|
Abstract
With the rapid expansion of genomic health care, nurses are exposed to emerging genetic technologies in a wide variety of clinical and research settings; however, nurses have limited knowledge about these technologies. The polymerase chain reaction procedure, which is the foundation of current molecular genetic technologies, real-time polymerase chain reaction, and microarray analysis are described in this article. The applications, strengths, and limitations of each technology are discussed.
Collapse
Affiliation(s)
- Ann K Cashion
- College of Nursing, University of Tennessee Health Science Center, Memphis, TN, USA.
| | | | | |
Collapse
|
55
|
Pagliarulo V, George B, Beil SJ, Groshen S, Laird PW, Cai J, Willey J, Cote RJ, Datar RH. Sensitivity and reproducibility of standardized-competitive RT-PCR for transcript quantification and its comparison with real time RT-PCR. Mol Cancer 2004; 3:5. [PMID: 14741054 PMCID: PMC344741 DOI: 10.1186/1476-4598-3-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2003] [Accepted: 01/23/2004] [Indexed: 01/12/2023] Open
Abstract
Background Probe based detection assays form the mainstay of transcript quantification. Problems with these assays include varying hybridization efficiencies of the probes used for transcript quantification and the expense involved. We examined the ability of a standardized competitive RT-PCR (StaRT PCR) assay to quantify transcripts of 4 cell cycle associated genes (RB, E2F1, CDKN2A and PCNA) in two cell lines (T24 & LD419) and compared its efficacy with the established Taqman real time quantitative RT-PCR assay. We also assessed the sensitivity, reproducibility and consistency of StaRT PCR. StaRT PCR assay is based on the incorporation of competitive templates (CT) in precisely standardized quantities along with the native template (NT) in a PCR reaction. This enables transcript quantification by comparing the NT and CT band intensities at the end of the PCR amplification. The CT serves as an ideal internal control. The transcript numbers are expressed as copies per million transcripts of a control gene such as β-actin (ACTB). Results The NT and CT were amplified at remarkably similar rates throughout the StaRT PCR amplification cycles, and the coefficient of variation was least (<3.8%) when the NT/CT ratio was kept as close to 1:1 as possible. The variability between the rates of amplification in different tubes subjected to the same StaRT PCR reaction was very low and within the range of experimental noise. Further, StaRT PCR was sensitive enough to detect variations as low as 10% in endogenous actin transcript quantity (p < 0.01 by the paired student's t-test). StaRT PCR correlated well with Taqman real time RT-PCR assay in terms of transcript quantification efficacy (p < 0.01 for all 4 genes by the Spearman Rank correlation method) and the ability to discriminate between cell types and confluence patterns. Conclusion StaRT PCR is thus a reliable and sensitive technique that can be applied to medium-high throughput quantitative transcript measurement. Further, it correlates well with Taqman real time PCR in terms of quantitative and discriminatory ability. This label-free, inexpensive technique may provide the ability to generate prognostically important molecular signatures unique to individual tumors and may enable identification of novel therapeutic targets.
Collapse
Affiliation(s)
- Vincenzo Pagliarulo
- Department of Pathology, University of Southern California, Keck School of Medicine, 2011 Zonal Ave, HMR 312C, Los Angeles CA 90033, USA
| | - Ben George
- Department of Pathology, University of Southern California, Keck School of Medicine, 2011 Zonal Ave, HMR 312C, Los Angeles CA 90033, USA
| | - Stephen J Beil
- Department of Pathology, University of Southern California, Keck School of Medicine, 2011 Zonal Ave, HMR 312C, Los Angeles CA 90033, USA
| | - Susan Groshen
- Department of Preventive Medicine, University of Southern California, Keck School of Medicine, Kenneth Norris Comprehensive Cancer Center 3419 A, Los Angeles CA 90033, USA
| | - Peter W Laird
- Department of Surgery and Biochemistry and Molecular Biology, University of Southern California, Keck School of Medicine, Kenneth Norris Comprehensive Cancer Center 6418, Los Angeles CA 90033, USA
| | - Jie Cai
- Department of Urology, University of Southern California, Keck School of Medicine, Kenneth Norris Comprehensive Cancer Center 3418, Los Angeles CA 90033, USA
| | - James Willey
- Division of Pulmonary & Critical Care Medicine, Medical College of Ohio Hospitals, Ruppert Health Center, Room 0012, 3120 Glendale Ave., Toledo, OH 43614, USA
| | - Richard J Cote
- Department of Pathology, University of Southern California, Keck School of Medicine, 2011 Zonal Ave, HMR 312C, Los Angeles CA 90033, USA
| | - Ram H Datar
- Department of Pathology, University of Southern California, Keck School of Medicine, 2011 Zonal Ave, HMR 312C, Los Angeles CA 90033, USA
| |
Collapse
|
56
|
Beasley TM, Page GP, Brand JPL, Gadbury GL, Mountz JD, Allison DB. Chebyshev's inequality for nonparametric testing with small N and alpha in microarray research. J R Stat Soc Ser C Appl Stat 2004. [DOI: 10.1111/j.1467-9876.2004.00428.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
57
|
Tannapfel A, Anhalt K, Häusermann P, Sommerer F, Benicke M, Uhlmann D, Witzigmann H, Hauss J, Wittekind C. Identification of novel proteins associated with hepatocellular carcinomas using protein microarrays. J Pathol 2003; 201:238-49. [PMID: 14517841 DOI: 10.1002/path.1420] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Characterization of the protein profiles expressed by hepatocellular carcinomas (HCCs) may identify the genes involved in hepatocellular carcinogenesis and offers the possibility of elucidating clinical biomarkers. In an effort to discover such proteins and pathways that are deregulated in hepatocellular carcinogenesis, cellular proteomes of matched normal liver cells and carcinoma were analysed by tissue microdissection and protein microarrays. Using protein microarrays made up of 83 different antibodies, it was possible to monitor alterations of the protein levels in HCC and non-neoplastic liver tissue. Further analysis of altered proteins was performed using western blot analysis and tissue microarrays (TMAs) containing 210 HCC specimens and corresponding liver tissue. The protein microarray approach revealed differential expression between HCC and normal liver of 32 of the 83 proteins examined: 21 of these were up-regulated and 11 down-regulated. IGF (insulin growth factor) II, ADAM (a disintegrin and metalloproteases) 9, STAT (signal transducers and activators of transcription) 3, SOCS (suppressors of cytokine signalling) 3, and cyclin D1 were significantly up-regulated and collagen I, SMAD 4, FHIT (fragile histidine triad), and SOCS1 were down-regulated. The differential expression of these proteins was confirmed using western blot analysis and TMAs. Correlation of differentially regulated proteins with clinico-pathological data showed that cyclin D1 and SOCS1 were associated with tumour prognosis in univariate analysis, but not multivariate analysis. These data indicate that the development of an array-based approach for the determination of protein profiles in HCC may facilitate the identification of new proteins associated with carcinogenesis or prognosis.
Collapse
Affiliation(s)
- Andrea Tannapfel
- Institute of Pathology, University of Leipzig, Liebigstrasse 26, 04103 Leipzig, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
58
|
Abstract
Microarray technology is a powerful approach for genomics research. The multi-step, data-intensive nature of this technology has created an unprecedented informatics and analytical challenge. It is important to understand the crucial steps that can affect the outcome of the analysis. In this review, we provide an overview of the contemporary trend on various main analysis steps in the microarray data analysis process, which includes experimental design, data standardization, image acquisition and analysis, normalization, statistical significance inference, exploratory data analysis, class prediction and pathway analysis, as well as various considerations relevant to their implementation.
Collapse
Affiliation(s)
- Yuk Fai Leung
- Bauer Center For Genomics Research, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA.
| | | |
Collapse
|
59
|
Mazzolini G, Narvaiza I, Martinez-Cruz LA, Arina A, Barajas M, Galofré JC, Qian C, Mato JM, Prieto J, Melero I. Pancreatic cancer escape variants that evade immunogene therapy through loss of sensitivity to IFNgamma-induced apoptosis. Gene Ther 2003; 10:1067-78. [PMID: 12808437 DOI: 10.1038/sj.gt.3301957] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Combined injections into experimental tumor nodules of adenovirus encoding IL-12 and certain chemokines are capable to induce immune-mediated complete regressions. In this study, we found that the combination of two adenoviruses, one encoding IL-12 and other MIP3alpha (AdCMVIL-12+AdCMVMIP3alpha) was very successful in treating CT-26-derived colon carcinomas. However, in experimental tumors generated from the pancreatic carcinoma cell line Panc02 such combined treatment induces 50% of macroscopic complete regressions, although local relapses within 1 week are almost constant. We derived cell lines from such relapsing tumors and found that experimental malignancies derived from their inoculum were not amenable to treatment in any case with AdCMVIL-12+AdCMVMIP-3alpha. Importantly, relapsing cell lines were insensitive to in vitro induction of apoptosis by IFNgamma, in clear contrast with the original Panc02 cells. Comparative analyses by cDNA arrays of relapsing cell lines versus wild-type Panc02 were performed revealing an important number of genes (383) whose expression levels were modified more than two-fold. These changes grouped in certain gene ontology categories should harbor the mechanistic explanations of the acquired selective resistance to IFNgamma.
Collapse
MESH Headings
- Adenoviridae/genetics
- Animals
- Apoptosis
- Chemokine CCL20
- Chemokines, CC/genetics
- Colonic Neoplasms/therapy
- Female
- Genetic Therapy/methods
- Genetic Vectors/administration & dosage
- Immunotherapy/methods
- Interferon-gamma/therapeutic use
- Interleukin-12/genetics
- Macrophage Inflammatory Proteins/genetics
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Neoplasms, Experimental/genetics
- Neoplasms, Experimental/immunology
- Neoplasms, Experimental/therapy
- Oligonucleotide Array Sequence Analysis
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/immunology
- Pancreatic Neoplasms/therapy
- Receptors, CCR6
- Receptors, Chemokine
- Receptors, Interferon/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Transduction, Genetic
- Tumor Cells, Cultured
- Tumor Escape/genetics
Collapse
Affiliation(s)
- G Mazzolini
- Gene Therapy Unit, Department of Medicine, School of Medicine, University of Navarra, Avda. Pio XII s/n, 31008 Pamplona, Spain
| | | | | | | | | | | | | | | | | | | |
Collapse
|
60
|
OBrian GR, Fakhoury AM, Payne GA. Identification of genes differentially expressed during aflatoxin biosynthesis in Aspergillus flavus and Aspergillus parasiticus. Fungal Genet Biol 2003; 39:118-27. [PMID: 12781670 DOI: 10.1016/s1087-1845(03)00014-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A complex regulatory network governs the biosynthesis of aflatoxin. While several genes involved in aflatoxin production are known, their action alone cannot account for its regulation. Arrays of clones from an Aspergillus flavus cDNA library and glass slide microarrays of ESTs were screened to identify additional genes. An initial screen of the cDNA clone arrays lead to the identification of 753 unique ESTs. Many showed sequence similarity to known metabolic and regulatory genes; however, no function could be ascribed to over 50% of the ESTs. Gene expression analysis of Aspergillus parasiticus grown under conditions conducive and non-conductive for aflatoxin production was evaluated using glass slide microarrays containing the 753 ESTs. Twenty-four genes were more highly expressed during aflatoxin biosynthesis and 18 genes were more highly expressed prior to aflatoxin biosynthesis. No predicted function could be ascribed to 18 of the 24 genes whose elevated expression was associated with aflatoxin biosynthesis.
Collapse
Affiliation(s)
- Gregory R OBrian
- Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | | | | |
Collapse
|
61
|
Morrison DA, Ellis JT. The design and analysis of microarray experiments: applications in parasitology. DNA Cell Biol 2003; 22:357-94. [PMID: 12906732 DOI: 10.1089/104454903767650658] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Microarray experiments can generate enormous amounts of data, but large datasets are usually inherently complex, and the relevant information they contain can be difficult to extract. For the practicing biologist, we provide an overview of what we believe to be the most important issues that need to be addressed when dealing with microarray data. In a microarray experiment we are simply trying to identify which genes are the most "interesting" in terms of our experimental question, and these will usually be those that are either overexpressed or underexpressed (upregulated or downregulated) under the experimental conditions. Analysis of the data to find these genes involves first preprocessing of the raw data for quality control, including filtering of the data (e.g., detection of outlying values) followed by standardization of the data (i.e., making the data uniformly comparable throughout the dataset). This is followed by the formal quantitative analysis of the data, which will involve either statistical hypothesis testing or multivariate pattern recognition. Statistical hypothesis testing is the usual approach to "class comparison," where several experimental groups are being directly compared. The best approach to this problem is to use analysis of variance, although issues related to multiple hypothesis testing and probability estimation still need to be evaluated. Pattern recognition can involve "class prediction," for which a range of supervised multivariate techniques are available, or "class discovery," for which an even broader range of unsupervised multivariate techniques have been developed. Each technique has its own limitations, which need to be kept in mind when making a choice from among them. To put these ideas in context, we provide a detailed examination of two specific examples of the analysis of microarray data, both from parasitology, covering many of the most important points raised.
Collapse
Affiliation(s)
- David A Morrison
- Department of Parasitology (SWEPAR), National Veterinary Institute and Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | |
Collapse
|
62
|
|
63
|
Chua MS, Sarwal MM. Microarrays: new tools for transplantation research. Pediatr Nephrol 2003; 18:319-27. [PMID: 12700956 DOI: 10.1007/s00467-003-1083-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2001] [Revised: 11/11/2002] [Accepted: 11/22/2002] [Indexed: 12/25/2022]
Abstract
The advent of DNA microarray technology has greatly enhanced our potential to understand the molecular basis of human diseases and to aid in more accurate classification, diagnosis and/or prognosis. This powerful, flexible and highly informative technique has been adopted by many biomedical research disciplines. The use of DNA microarrays for gene expression profiling of patients undergoing organ transplantation has diagnostic and therapeutic potential. By generating global views of the gene expression changes in renal graft function post transplantation, DNA microarray technology will provide important information to improve our understanding of the molecular basis of various causes of graft dysfunction, and therefore suggest improved diagnosis, disease classification, and treatment.
Collapse
Affiliation(s)
- Mei-Sze Chua
- Department of Pediatrics, Stanford University School of Medicine, G320, 300 Pasteur Drive, CA 94305, Stanford, USA
| | | |
Collapse
|
64
|
Astier AL, Xu R, Svoboda M, Hinds E, Munoz O, de Beaumont R, Crean CD, Gabig T, Freedman AS. Temporal gene expression profile of human precursor B leukemia cells induced by adhesion receptor: identification of pathways regulating B-cell survival. Blood 2003; 101:1118-27. [PMID: 12393420 DOI: 10.1182/blood-2002-05-1519] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The physical interactions between B cells and stromal cells from the lymphoid tissue microenvironment are critical to the survival of normal and malignant B cells. They are principally mediated by integrins expressed on B cells and counterreceptors on stromal cells. Specifically, alpha4beta1 integrin engagement rescues B cells from physiological or drug-induced apoptosis. Therefore, in order to understand the mechanisms by which integrins prevent apoptosis in leukemia B cells, we compared the temporal gene expression profiles induced by beta1-integrin ligation with fibronectin (Fn) or adhesion by poly-L-Lysine in serum-starved precursor B leukemia cells. Among the 38 selected differentially expressed genes, 6 genes involved in adhesion (VAV2, EPB41L1, CORO1A), proliferation (FRAP1, CCT4), and intercellular communication (GJB3) were validated by real-time quantitative polymerase chain reaction (RT-Q-PCR). Gene expression modulation could also be validated at the protein level for 5 other genes. We show that integrin stimulation up-regulated FBI-1 expression but inhibited CD79a, Requiem, c-Fos, and caspase 7 induction when the cells underwent apoptosis. We further demonstrate that Fn stimulation also inhibits caspase 3 activation but increases XIAP and survivin expression. Moreover, integrin stimulation also prevents caspase activation induced by doxorubicin. Therefore, we identified genes modulated by adhesion of human precursor B leukemia cells that regulate proliferation and apoptosis, highlighting new pathways that might provide insights into future therapy aiming at targeting apoptosis of leukemia cells.
Collapse
Affiliation(s)
- Anne Laurence Astier
- Department of Adult Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
65
|
Khodarev NN, Park J, Kataoka Y, Nodzenski E, Hellman S, Roizman B, Weichselbaum RR, Pelizzari CA. Receiver operating characteristic analysis: a general tool for DNA array data filtration and performance estimation. Genomics 2003; 81:202-9. [PMID: 12620398 DOI: 10.1016/s0888-7543(02)00042-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A critical step for DNA array analysis is data filtration, which can reduce thousands of detected signals to limited sets of genes. Commonly accepted rules for such filtration are still absent. We present a rational approach, based on thresholding of intensities with cutoff levels that are estimated by receiver operating characteristic (ROC) analysis. The technique compares test results with known distributions of positive and negative signals. We apply the method to Atlas cDNA arrays, GeneFilters, and Affymetrix GeneChip. ROC analysis demonstrates similarities in the distribution of false and true positive data for these different systems. We illustrate the estimation of an optimal cutoff level for intensity-based filtration, providing the highest ratio of true to false signals. For GeneChip arrays, we derived filtration thresholds consistent with the reported data based on replicate hybridizations. Intensity-based filtration optimized with ROC combined with other types of filtration (for example, based on significances of differences and/or ratios), should improve DNA array analysis. ROC methodology is also demonstrated for comparison of the performance of different types of arrays, imagers, and analysis software.
Collapse
Affiliation(s)
- Nikolai N Khodarev
- Department of Radiation and Cellular Oncology, The University of Chicago, IL 60637, USA
| | | | | | | | | | | | | | | |
Collapse
|
66
|
Abstract
Bioinformatics is the discipline that develops and applies informatics to the field of molecular biology. Although a comprehensive review of the entire field of bioinformatics is beyond the scope of this article, I review the basic tenets of the field and provide a topical sampling of the popular technologies available to clinicians and researchers. These technologies include tools and methods for sequence analysis (nucleotide and protein sequences), rendering of secondary and tertiary structures for these molecules, and protein fold prediction that can lead to rational drug design. I then discuss signaling pathways, new standards for data representation of genes and proteins, and finally the promise of merging these molecular data with the clinical world (the new science of phenomics).
Collapse
Affiliation(s)
- Peter L Elkin
- Division of Area General Internal Medicine, Mayo Clinic, Rochester, Minn 55905, USA
| |
Collapse
|
67
|
Abstract
Functional genomics is the study of gene function through the parallel expression measurements of genomes, most commonly using the technologies of microarrays and serial analysis of gene expression. Microarray usage in drug discovery is expanding, and its applications include basic research and target discovery, biomarker determination, pharmacology, toxicogenomics, target selectivity, development of prognostic tests and disease-subclass determination. This article reviews the different ways to analyse large sets of microarray data, including the questions that can be asked and the challenges in interpreting the measurements.
Collapse
Affiliation(s)
- Atul Butte
- Children's Hospital Informatics Program and Division of Endocrinology, Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA.
| |
Collapse
|
68
|
Docterman KE, Smith SM. Of meis and men: lessons from a microarray study of teratogen action. TERATOLOGY 2002; 66:217-23. [PMID: 12397629 DOI: 10.1002/tera.10110] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
69
|
Christopher K, McKee CM, Mueller TF, Perkins DL. Functional genomics of immune responses. Immunol Allergy Clin North Am 2002. [DOI: 10.1016/s0889-8561(02)00013-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
70
|
Piper MDW, Daran-Lapujade P, Bro C, Regenberg B, Knudsen S, Nielsen J, Pronk JT. Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 2002; 277:37001-8. [PMID: 12121991 DOI: 10.1074/jbc.m204490200] [Citation(s) in RCA: 186] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Assessment of reproducibility of DNA-microarray analysis from published data sets is complicated by the use of different microbial strains, cultivation techniques, and analytical procedures. Because intra- and interlaboratory reproducibility is highly relevant for application of DNA-microarray analysis in functional genomics and metabolic engineering, we designed a set of experiments to specifically address this issue. Saccharomyces cerevisiae CEN.PK113-7D was grown under defined conditions in glucose-limited chemostats, followed by transcriptome analysis with Affymetrix GeneChip arrays. In each of the laboratories, three independent replicate cultures were grown aerobically as well as anaerobically. Although variations introduced by in vitro handling steps were small and unbiased, greater variation from replicate cultures underscored that, to obtain reliable information, experimental replication is essential. Under aerobic conditions, 86% of the most highly expressed yeast genes showed an average intralaboratory coefficient of variation of 0.23. This is significantly lower than previously reported for shake-flask-culture transcriptome analyses and probably reflects the strict control of growth conditions in chemostats. Using the triplicate data sets and appropriate statistical analysis, the change calls from anaerobic versus aerobic comparisons yielded an over 95% agreement between the laboratories for transcripts that changed by over 2-fold, leaving only a small fraction of genes that exhibited laboratory bias.
Collapse
Affiliation(s)
- Matthew D W Piper
- Kluyver Laboratory of Biotechnology, Technical University of Delft, Julianalaan 26, Delft 2628BC, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
71
|
Mix E, Pahnke J, Ibrahim SM. Gene-expression profiling of experimental autoimmune encephalomyelitis. Neurochem Res 2002; 27:1157-63. [PMID: 12462414 DOI: 10.1023/a:1020925425780] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Experimental autoimmune encephalomyelitis (EAE) is a mouse model that serves as an experimental tool for studying the etiology, pathogenesis, as well as new therapeutic approaches of multiple sclerosis (MS). EAE is a polygenic chronic inflammatory demyelinating disease of the nervous system that involves the interaction between genetic and environmental factors. Previous studies have identified multiple quantitative trait loci (QTL) controlling different aspects of disease pathogenesis. However, progress in identifying new susceptibility genes outside the MHC locus has been slow. With the advent of new global methods for genetic analysis such as large-scale sequencing, gene expression profiling combined with classic linkage analysis and congenic and physical mapping progress is considerably accelerating. Here we review our preliminary work on the use of gene expression mapping to identify new putative genetic pathways contributing to the pathogenesis of EAE.
Collapse
|
72
|
Xiao Y, Segal MR, Rabert D, Ahn AH, Anand P, Sangameswaran L, Hu D, Hunt CA. Assessment of differential gene expression in human peripheral nerve injury. BMC Genomics 2002; 3:28. [PMID: 12354329 PMCID: PMC137578 DOI: 10.1186/1471-2164-3-28] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2002] [Accepted: 09/27/2002] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microarray technology is a powerful methodology for identifying differentially expressed genes. However, when thousands of genes in a microarray data set are evaluated simultaneously by fold changes and significance tests, the probability of detecting false positives rises sharply. In this first microarray study of brachial plexus injury, we applied and compared the performance of two recently proposed algorithms for tackling this multiple testing problem, Significance Analysis of Microarrays (SAM) and Westfall and Young step down adjusted p values, as well as t-statistics and Welch statistics, in specifying differential gene expression under different biological states. RESULTS Using SAM based on t statistics, we identified 73 significant genes, which fall into different functional categories, such as cytokines / neurotrophin, myelin function and signal transduction. Interestingly, all but one gene were down-regulated in the patients. Using Welch statistics in conjunction with SAM, we identified an additional set of up-regulated genes, several of which are engaged in transcription and translation regulation. In contrast, the Westfall and Young algorithm identified only one gene using a conventional significance level of 0.05. CONCLUSION In coping with multiple testing problems, Family-wise type I error rate (FWER) and false discovery rate (FDR) are different expressions of Type I error rates. The Westfall and Young algorithm controls FWER. In the context of this microarray study, it is, seemingly, too conservative. In contrast, SAM, by controlling FDR, provides a promising alternative. In this instance, genes selected by SAM were shown to be biologically meaningful.
Collapse
Affiliation(s)
- Yuanyuan Xiao
- Department of Biopharmaceutical Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mark R Segal
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Douglas Rabert
- Neurobiology Unit, Roche Bioscience, Palo Alto, CA 94304, USA
| | - Andrew H Ahn
- Department of Anatomy and Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Praveen Anand
- Peripheral Neuropathy Unit, Division of Neuroscience and Psychological Medicine, Imperial College of Science, Technology and Medicine, Hammersmith Hospital, London W12 ONN, UK
| | | | - Donglei Hu
- Department of Biopharmaceutical Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - C Anthony Hunt
- Department of Biopharmaceutical Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| |
Collapse
|
73
|
|
74
|
Hwang JJ, Allen PD, Tseng GC, Lam CW, Fananapazir L, Dzau VJ, Liew CC. Microarray gene expression profiles in dilated and hypertrophic cardiomyopathic end-stage heart failure. Physiol Genomics 2002; 10:31-44. [PMID: 12118103 DOI: 10.1152/physiolgenomics.00122.2001] [Citation(s) in RCA: 182] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Despite similar clinical endpoints, heart failure resulting from dilated cardiomyopathy (DCM) or hypertrophic cardiomyopathy (HCM) appears to develop through different remodeling and molecular pathways. Current understanding of heart failure has been facilitated by microarray technology. We constructed an in-house spotted cDNA microarray using 10,272 unique clones from various cardiovascular cDNA libraries sequenced and annotated in our laboratory. RNA samples were obtained from left ventricular tissues of precardiac transplantation DCM and HCM patients and were hybridized against normal adult heart reference RNA. After filtering, differentially expressed genes were determined using novel analyzing software. We demonstrated that normalization for cDNA microarray data is slide-dependent and nonlinear. The feasibility of this model was validated by quantitative real-time reverse transcription-PCR, and the accuracy rate depended on the fold change and statistical significance level. Our results showed that 192 genes were highly expressed in both DCM and HCM (e.g., atrial natriuretic peptide, CD59, decorin, elongation factor 2, and heat shock protein 90), and 51 genes were downregulated in both conditions (e.g., elastin, sarcoplasmic/endoplasmic reticulum Ca2+-ATPase). We also identified several genes differentially expressed between DCM and HCM (e.g., alphaB-crystallin, antagonizer of myc transcriptional activity, beta-dystrobrevin, calsequestrin, lipocortin, and lumican). Microarray technology provides us with a genomic approach to explore the genetic markers and molecular mechanisms leading to heart failure.
Collapse
Affiliation(s)
- Juey-Jen Hwang
- Cardiovascular Genome Unit, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston 02115, USA
| | | | | | | | | | | | | |
Collapse
|
75
|
Tsibris JCM, Segars J, Coppola D, Mane S, Wilbanks GD, O'Brien WF, Spellacy WN. Insights from gene arrays on the development and growth regulation of uterine leiomyomata. Fertil Steril 2002; 78:114-21. [PMID: 12095500 PMCID: PMC4143900 DOI: 10.1016/s0015-0282(02)03191-6] [Citation(s) in RCA: 147] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To use microarray analysis as an unbiased approach to identify genes involved in the induction and growth of uterine leiomyomata. DESIGN Screen by arrays for up to 12,000 genes in leiomyoma (L) and control myometrium (M) from nine patients. SETTING University research laboratories. PATIENT(S) Nine patients in the follicular and luteal phases of the menstrual cycle. INTERVENTION(S) mRNA from L and M was converted to biotin-labeled cRNA and hybridized to cDNA oligonucleotide sequences on the arrays. MAIN OUTCOME MEASURE(S) Greater than two-fold change in gene expression between leiomyoma and matched myometrium. RESULT(S) Prominent among the 67 genes overexpressed in L relative to M were dlk or Pref-1, doublecortin, JM27, ionotropic glutamate receptor subunit 2, apolipoprotein E3, IGF2, semaphorin F, myelin proteolipid protein, MEST, frizzled, CRABP II, stromelysin-3, and TGFbeta3. The genes dlk, IGF2, and MEST are paternally expressed imprinted genes, and the others are involved in tissue differentiation and growth. Prominent among the 78 genes down-regulated in L relative to M were alcohol dehydrogenases 1alpha-gamma, tryptase, dermatopontin, thrombospondin, coxsackievirus receptor, nur77, and c-kit. CONCLUSION(S) Arrays offer large-scale screening of mRNA expression, which will help us differentiate between the genes and metabolic pathways necessary for leiomyoma growth and those regulating myometrial contractions.
Collapse
Affiliation(s)
- John C M Tsibris
- Department of Obstetrics and Gynecology, University of South Florida, Tampa, Florida 33606, USA.
| | | | | | | | | | | | | |
Collapse
|
76
|
Costouros NG, Libutti SK. Microarray technology and gene expression analysis for the study of angiogenesis. Expert Opin Biol Ther 2002; 2:545-56. [PMID: 12079491 DOI: 10.1517/14712598.2.5.545] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Angiogenesis plays a major role in multiple disease processes including cancer, and new agents that modulate angiogenesis are rapidly entering clinical trials. The understanding of the biological mechanisms and downstream effects for many of these agents is poorly understood. It is therefore important that methods evolve to understand how an agent regulates angiogenesis, in order to promote a higher percentage of successful drug candidates. With the emergence of microarray technology for the evaluation of gene expression, researchers have a powerful tool for dissecting the biological mechanisms of angiogenesis. However, huge data sets and complex statistics pose a hurdle for the investigator to obtain useful and meaningful data. To eliminate problems in data analysis, proper design and planning prior to performing a microarray experiment is crucial to making valid conclusions. This review will discuss the critical factors in designing, performing and analysing microarray experiments, and the utility of various models of angiogenesis for microarray analysis.
Collapse
Affiliation(s)
- Nick G Costouros
- National Institutes of Health, Building 10, Room 3C428, Bethesda, MD 20892, USA
| | | |
Collapse
|
77
|
Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2002. [PMCID: PMC2447253 DOI: 10.1002/cfg.117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
|
78
|
Eddy SF, Storey KB. Dynamic Use of cDNA Arrays: Heterologous Probing for Gene Discovery and Exploration of Organismal Adaptation to Environmental Stress. CELL AND MOLECULAR RESPONSE TO STRESS 2002. [DOI: 10.1016/s1568-1254(02)80024-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
79
|
Peale FV, Gerritsen ME. Gene profiling techniques and their application in angiogenesis and vascular development. J Pathol 2001; 195:7-19. [PMID: 11568887 DOI: 10.1002/path.888] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The analysis of gene expression in specific tissues and physiological processes has evolved over the last 20 years from the painstaking identification of selected genes to the relatively efficient and open-ended surveying of potentially all genes expressed in a tissue. Current art for gene discovery includes the use of large-scale arrays of cDNA sequences or oligonucleotides, and molecular 'tagging' techniques such as GeneCalling and SAGE. Common to each of these techniques is a reliance on the increasingly comprehensive databases of human and mouse EST and full-length gene sequences. Early efforts to characterize candidate genes were limited by their narrow scope, while current efforts are confounded by the enormous volume of data returned. Sophisticated software tools are an integral part of the analysis, helping to organize information into coherent groups with temporal or functional similarity. These techniques, in conjunction with the continued analysis of human genetic syndromes, transgenic, and knockout mice, have driven genetic analysis of angiogenesis and vascular development from describing which individual genes are involved to defining the outlines of regulatory networks.
Collapse
Affiliation(s)
- F V Peale
- Department of Pathology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | | |
Collapse
|