51
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Affiliation(s)
- M Williamson
- Institute of Urology, Royal Free and University College School of Medicine, London, UK.
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52
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Abstract
Microarray technology transforms the study of functional genetics. The entire genomic activity of cells and tissues can be analysed and compared on single slides, or gene chips. In cancer research, this will allow the better understanding of the regulation of activity of cells and tumours in various states. It will also allow the classification of individual tumours by their gene expression patterns, which may also describe and predict therapeutic resistance and sensitivity patterns. This short article provides a short introduction to the technology and its applications.
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Affiliation(s)
- D A Rew
- Royal South Hants Cancer Centre, Southampton University Hospitals, Southampton, SO14 0YG, UK
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53
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Moreno-Aliaga MJ, Marti A, García-Foncillas J, Alfredo Martínez J. DNA hybridization arrays: a powerful technology for nutritional and obesity research. Br J Nutr 2001; 86:119-22. [PMID: 11519524 DOI: 10.1079/bjn2001410] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- M J Moreno-Aliaga
- Department of Physiology and Nutrition, University of Navarra, Pamplona, Spain
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54
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Liefers GJ, Tollenaar RA, Nakamura Y, van de Velde CJ. Genetic cancer syndromes and large-scale gene expression analysis: applications in surgical oncology. EUROPEAN JOURNAL OF SURGICAL ONCOLOGY 2001; 27:343-8. [PMID: 11417977 DOI: 10.1053/ejso.2001.1125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The last decade of the 20th century was characterized by an explosion in genetic discoveries. The Human Genome Project and technical advances have made it possible to unravel many genetic abnormalities underlying cancer. Many genes responsible for inherited cancer syndromes have been identified and diagnostic tests are readily available. The clinical implications of these tests are currently under debate. Large-scale gene expression analysis enables simultaneous monitoring of expression of thousands of genes, in vitro and in vivo. The identification of high risk patients and drug responsiveness, can be studied within the framework of complex molecular networks. This article will focus on the possibilities for surgical oncology.
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Affiliation(s)
- G J Liefers
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
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55
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Chetcuti A, Margan S, Mann S, Russell P, Handelsman D, Rogers J, Dong Q. Identification of differentially expressed genes in organ-confined prostate cancer by gene expression array. Prostate 2001; 47:132-40. [PMID: 11340636 DOI: 10.1002/pros.1056] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND To understand the molecular mechanisms underlying prostate cancer, we have utilized the gene expression array to search for genes whose expression is altered in this disease. METHODS RNA quality from manual microdissected tissue was compared with that from microselected tissue by electrophoresis. For array analysis, malignant and normal prostate epithelium was enriched using microselection technique from prostate cancer and the peripheral zone of a normal prostate. Identical array membrane was hybridized to labeled cancer and normal cDNA, respectively. The differentially expressed gene was further evaluated by RT-PCR. RESULTS Microdissection, but not microselection, causes visible degradation to RNA. Of the 588 genes on the membrane, 87 genes yielded significant signals. Based on a three fold difference relative to normal prostate tissue, 1 gene was overexpressed and 12 genes underexpressed in prostate cancer. Of them, five showed statistically significant reduction in mRNA levels in six prostate cancer specimens compared with seven normal prostate specimens. These five genes are glutathione S-transferase M1 (GSTM1), monocyte chemotactic protein-1 (MCP-1), tumor necrosis factor-alpha receptor-1 (TNFR-1), transforming growth factor beta3 (TGF-beta3), and inhibitor of DNA binding-1 (ID-1). CONCLUSIONS GST-based metabolism, cytokine MCP-1 and TNFR-1, and TGF-beta3 signaling pathways, and some helix-loop-helix nuclear proteins could be potentially important in organ-confined prostate cancer and deserve further investigation.
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Affiliation(s)
- A Chetcuti
- Department of Medicine, University of Sydney, Sydney, NSW, Australia
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56
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Hasty J, McMillen D, Isaacs F, Collins JJ. Computational studies of gene regulatory networks: in numero molecular biology. Nat Rev Genet 2001; 2:268-79. [PMID: 11283699 DOI: 10.1038/35066056] [Citation(s) in RCA: 425] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Remarkable progress in genomic research is leading to a complete map of the building blocks of biology. Knowledge of this map is, in turn, setting the stage for a fundamental description of cellular function at the DNA level. Such a description will entail an understanding of gene regulation, in which proteins often regulate their own production or that of other proteins in a complex web of interactions. The implications of the underlying logic of genetic networks are difficult to deduce through experimental techniques alone, and successful approaches will probably involve the union of new experiments and computational modelling techniques.
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Affiliation(s)
- J Hasty
- Centre for BioDynamics and Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, Massachusetts 02215, USA.
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57
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Emmert-Buck MR, Strausberg RL, Krizman DB, Bonaldo MF, Bonner RF, Bostwick DG, Brown MR, Buetow KH, Chuaqui RF, Cole KA, Duray PH, Englert CR, Gillespie JW, Greenhut S, Grouse L, Hillier LW, Katz KS, Klausner RD, Kuznetzov V, Lash AE, Lennon G, Linehan WM, Liotta LA, Marra MA, Munson PJ, Ornstein DK, Prabhu VV, Prang C, Schuler GD, Soares MB, Tolstoshev CM, Vocke CD, Waterston RH. Molecular profiling of clinical tissues specimens: feasibility and applications. J Mol Diagn 2001; 2:60-6. [PMID: 11272889 PMCID: PMC1906897 DOI: 10.1016/s1525-1578(10)60617-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- M R Emmert-Buck
- Pathogenetics Unit, Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland, USA.
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58
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Abstract
An understanding of the relationship between gene expression, protein expression and the influences of genetic responses upon gene function is vital before we can understand the complexity of genomes. Traditional methods for the study of gene expression are limited to studying small groups of genes at a time and a source of pure starting material has been difficult to obtain. Recent technological advances have enabled large numbers of genes, from specific cell populations, to be studied in a single experiment. Laser capture microdissection (LCM) and microarray technology are providing the next revolution in the study of gene expression. LCM-based molecular analysis of histopathological lesions can be applied to any disease process that is accessible through tissue sampling. Examples include: (i) mapping the field of genetic changes associated with oxidative stress; (ii) analysis of gene expression patterns in atherosclerotic tissues, sites of inflammation and Alzheimer's disease plaques; (iii) infectious micro-organism diagnosis; and (iv) typing of cells within disease foci. Microarray hybridisation glass chips spotted with sets of genes can then be used to obtain a molecular fingerprint of gene expression in the microdissected cells. The variation of expressed genes or alterations in the cellular DNA that correlate with a particular disease state can be compared within or between individual samples. The identification of gene expression patterns may provide vital information for the understanding of the disease process and may contribute to diagnostic decisions and therapies tailored to the individual patient. Molecules found to be associated with defined pathological lesions may provide clues about new therapeutic targets in the future.
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Affiliation(s)
- J K Burgess
- Department of Pharmacology, University of Sydney, New South Wales, Australia.
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59
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Abstract
Of the hundreds of genes and proteins reported to be altered in human cancers, only a few are sufficiently central to warrant translation into diagnostic or therapeutic tools. Three recent developments have the potential to alter radically the discovery of molecular markers: the compendium of human genes; the advent of technologies that provide the means to identify simultaneously several known and unknown genes and proteins; and an appreciation of the critical processes involved in tumor initiation and progression.
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Affiliation(s)
- P L Porter
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, and Department of Pathology, University of Washington Medical Center, 1100 Fairview N, Seattle, Washington 98109, USA.
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60
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Abstract
Microarrays have emerged as indispensable research tools for gene expression profiling and mutation analysis. New classification of cancer subtypes, dissecting the yeast metabolism and large-scale genotyping of human single nucleotide polymorphisms are important results being obtained with this technique. Realizing the microsphere-based massively parallel signature sequencing technique as fluid microarrays, building new types of protein arrays and constructing miniaturized flow-through systems, which can potentially take this technology from the research bench into industrial, clinical and other routine applications, exemplify the intense developments that are now ongoing in this field.
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Affiliation(s)
- D H Blohm
- University of Bremen, FB2-UFT, Biotechnology and Molecular Genetics, D-28359 Bremen, Germany.
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61
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Simone NL, Paweletz CP, Charboneau L, Petricoin EF, Liotta LA. Laser capture microdissection: beyond functional genomics to proteomics. MOLECULAR DIAGNOSIS : A JOURNAL DEVOTED TO THE UNDERSTANDING OF HUMAN DISEASE THROUGH THE CLINICAL APPLICATION OF MOLECULAR BIOLOGY 2000; 5:301-7. [PMID: 11172494 DOI: 10.1007/bf03262091] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
Abstract
Proteomics will drive biology and medicine beyond genomics, and can have a profound impact on molecular diagnostics. The posttranslational modifications of cellular proteins that govern physiology and become deranged in disease cannot be accurately portrayed by gene expression alone. Consequently, new technology is being developed to discover, and quantitatively monitor, proteomic changes that are associated with disease etiology and progression. In the past, proteomic technologies were restricted to tumor cell lines or homogenized bulk tissue specimens. This source material may not accurately reflect molecular events taking place in the specific cells of the tissue itself. This article describes a completely new class of proteomic-based approaches aimed at the identification and investigation of protein markers in the actual histologically defined cell populations that are immersed in heterogeneous diseased tissue. It is envisioned that these investigations will eventually lead to novel diagnostic, prognostic, or therapeutic markers that can be applied to monitor therapeutic toxicity or efficacy.
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Affiliation(s)
- N L Simone
- Laboratory of Pathology, National Cancer Institute/NIH, Building 10, 10 Center Drive, Bethesda, MD 20892-1500, USA
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62
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Abstract
The endothelium plays a pivotal role in many physiological and pathological processes and is known to be an exceptionally active transcriptional site. To advance our understanding of endothelial cell biology and to elucidate potential pharmaceutical targets, we developed a new database screening approach to permit identification of novel endothelial-specific genes. The UniGene gene index was screened using high stringency BLAST against a pool of endothelial expressed sequence tags (ESTs) and a pool of nonendothelial ESTs constructed from cell-type-specific dbEST libraries. UniGene clusters with matches in the endothelial pool and no matches in the nonendothelial pool were selected. The UniGene/EST approach was then combined with serial analysis of gene expression (SAGE) library subtraction and reverse transcription polymerase chain reaction to further examine interesting clusters. Four novel genes were identified and labeled: endothelial cell-specific molecules (ECSM) 1-3 and magic roundabout (similar to the axon guidance protein roundabout). In summary, we present a powerful novel approach for comparative expression analysis combining two datamining strategies followed by experimental verification.
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Affiliation(s)
- L Huminiecki
- Molecular Angiogenesis Laboratory, Imperial Cancer Research Fund, Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
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63
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Affiliation(s)
- K M Weiss
- Departments of Anthropology and Biology, Penn State University, University Park, Pennsylvania, USA.
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64
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Abstract
Traditionally, tumours have been categorized on the basis of histology. However, the staining pattern of cancer cells viewed under the microscope is insufficient to reflect the complicated underlying molecular events that drive the neoplastic process. By surveying thousands of genes at once, using DNA arrays, it is now possible to read the molecular signature of an individual patient's tumour. When the signature is analysed with clustering algorithms, new classes of cancer emerge that transcend distinctions based on histological appearance alone. Using DNA arrays, protein arrays and appropriate experimental models, the ultimate goal is to move beyond correlation and classification to achieve new insights into disease mechanisms and treatment targets.
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Affiliation(s)
- L Liotta
- National Cancer Institute, NIH and CBER, FDA, Bethesda, Maryland 20892, USA.
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65
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Abstract
A DNA microarray system is usually comprised of DNA probes formatted on a microscale on a glass surface (chip), plus the instruments needed to handle samples (automated robotics), to read the reporter molecules (scanners) and analyse the data (bioinformatic tools). Biochips are formed by in situ (on chip) synthesis of oligonucleotides or peptide nucleic acids (PNAs) or spotting of DNA fragments. Hybridisation of RNA- or DNA-derived samples on chips allows the monitoring of expression of mRNAs or the occurrence of polymorphisms in genomic DNA. Basic types of DNA chips are the sequencing chip, the expression chip and chips for comparative genomic hybridisation. Advanced technologies used in automated microarray production are photolithography, mechanical microspotting and ink jets. Bioelectronic microchips contain numerous electronically active microelectrodes with specific DNA capture probes linked to the electrodes through molecular wires. Several biosensors have been used in combination with biochips. PNA biosensors commonly rely on the immobilisation of a single-stranded DNA sequence (the 'probe') onto a transducer surface for hybridisation with the complementary ('target') strand to give a suitable electrical signal. Other sensors are cell-based immunobiosensors with engineered molecular recognition, integrated biosensors based on phototransistor integrated circuits and sensors based on surface plasmon resonance. Microarray technologies offer enormous savings in time and labour as compared to standard gel-based microsatellite methods. Reading of the information and its management by bioinformatics is necessary because of the enormous amount of data generated by the various technologies using microarrays. Standardised procedures are essential for compatible data production, quality control and analysis. Expression monitoring is the most biologically informative application of this technology at present. Microarray technology has important applications in pharmacogenomics: drug discovery and development, drug safety and molecular diagnostics. DNA chips will facilitate the integration of diagnosis and therapeutics, as well as the introduction of personalised medicines.
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Affiliation(s)
- K K Jain
- Jain PharmaBiotech, Basel, Switzerland.
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66
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Vaarala MH, Porvari K, Kyllönen A, Vihko P. Differentially expressed genes in two LNCaP prostate cancer cell lines reflecting changes during prostate cancer progression. J Transl Med 2000; 80:1259-68. [PMID: 10950117 DOI: 10.1038/labinvest.3780134] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Prostate cancer tends to become transformed to androgen-independent disease over time when treated by androgen-deprivation therapy. We used two variants of the human prostate cancer cell line LNCaP to study gene expression differences during prostate cancer progression to androgen-independent disease. Production of prostate-specific antigen was regarded as a marker of androgen-dependence and loss of prostate-specific antigen was regarded as a marker of androgen-independence. mRNA from both cell lines was used for cDNA microarray screening. Differential expression of several genes was confirmed by Northern blotting. Monoamine oxidase A, an Expressed Sequence Tag (EST) similar to rat P044, and EST AA412049 were highly overexpressed in androgen-dependent LNCaP cells. Tissue-type plasminogen activator, interferon-inducible protein p78 (MxB), an EST similar to galectin-1, follistatin, fatty acid-binding protein 5, EST AA609749, annexin I, the interferon-inducible gene 1-8U, and phospholipase D1 were highly overexpressed in androgen-independent LNCaP cells. All studied genes had low or no expression in PC-3 cells. The EST similar to rat P044, the EST similar to galectin-1, follistatin, annexin I, and the interferon-inducible gene 1-8U were also expressed in benign prostatic hyperplasia tissue. The Y-linked ribosomal protein S4, Mat-8, and EST AA307912 were highly expressed in benign prostatic hyperplasia tissue. Additionally, both confirmation of differential expression in Northern blots and in situ hybridization were carried out for monoamine oxidase A, the EST similar to rat P044, the EST similar to galectin-1, fatty acid-binding protein 5, and the interferon-inducible gene 1-8U. We identified several potential prostate cancer markers, indicating that the method used is a useful tool for the screening of cancer markers, but other methods, such as in situ hybridization, are needed to further investigate the observations.
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Affiliation(s)
- M H Vaarala
- Biocenter Oulu, World Health Organization Collaborating Centre for Research on Reproductive Health, Finland
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67
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Castensson A, Emilsson L, Preece P, Jazin EE. High-resolution quantification of specific mRNA levels in human brain autopsies and biopsies. Genome Res 2000; 10:1219-29. [PMID: 10958640 PMCID: PMC310892 DOI: 10.1101/gr.10.8.1219] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Quantification of mRNA levels in human cortical brain biopsies and autopsies was performed using a fluorogenic 5' nuclease assay. The reproducibility of the assay using replica plates was 97%-99%. Relative quantities of mRNA from 16 different genes were evaluated using a statistical approach based on ANCOVA analysis. Comparison of the relative mRNA levels between two groups of samples with different time postmortem revealed unchanged relative expression levels for most genes. Only CYP26A1 mRNA levels showed a significant decrease with prolonged time postmortem (p = 0.00004). Also, there was a general decrease in measured mRNA levels for all genes in autopsies compared to biopsies; however, on comparing mRNA levels after adjusting with reference genes, no significant differences were found between mRNA levels in autopsies and biopsies. This observation indicates that studies of postmortem material can be performed to reveal the relative in vivo mRNA levels of genes. Power calculations were done to determine the number of individuals necessary to detect differences in mRNA levels of 1.5-fold to tenfold using the strategy described here. This analysis showed that samples from at least 50 individuals per group, patients and controls, are required for high-resolution ( approximately twofold changes) differential expression screenings in the human brain. Experiments done on ten individuals per group will result in a resolution of approximately fivefold changes in expression levels. In general, the sensitivity and resolution of any differential expression study will depend on the sample size used and the between-individual variability of the genes analyzed.
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Affiliation(s)
- A Castensson
- Section of Medical Genetics, Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, S-751 85 Uppsala, Sweden
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68
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Rutka JT, Taylor M, Mainprize T, Langlois A, Ivanchuk S, Mondal S, Dirks P. Molecular biology and neurosurgery in the third millennium. Neurosurgery 2000; 46:1034-51. [PMID: 10807235 DOI: 10.1097/00006123-200005000-00002] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The application of techniques in molecular biology to human neurosurgical conditions has led to an increased understanding of disease processes that affect the brain and to novel forms of therapy that favorably modify the natural history of many of these conditions. Molecular strategies are currently being either used or sought for brain tumors, stroke, neurodegenerative diseases, vascular malformations, spinal degenerative diseases, and congenital malformations of the central nervous system. Considering that the structure of deoxyribonucleic acid was ascertained by Watson and Crick as recently as 1953, the progress that has been made to implement molecular medicine in clinical practice has been meteoric. More than 2000 patients have been treated in approved gene therapy trials throughout the world. Many of these patients have been treated for neurological diseases for which conventional medical therapies have been of limited utility. As part of this continuing series on advances in neurosurgery in the third millennium, we first reflect on the history of the nascent field of molecular biology. We then describe the powerful techniques that have evolved from knowledge in this field and have been used in many publications in Neurosurgery, particularly within the past decade. These methods include commonly used techniques such as advanced cytogenetics, differential display, microarray technology, molecular cell imaging, yeast two-hybrid assays, gene therapy, and stem cell utilization. We conclude with a description of the rapidly growing field of bioinformatics. Because the Human Genome Project will be completed within 5 years, providing a virtual blueprint of the human race, the next frontier (and perhaps our greatest challenge) will involve the development of the field of "proteomics," in which protein structure and function are determined from the deoxyribonucleic acid blueprint. It is our conviction that neurosurgeons will continue to be at the forefront of the treatment of patients with neurological diseases using molecular strategies, by performing essential research leading to increased understanding of diseases, by conducting carefully controlled studies to test the effects of treatments on disease processes, and by directly administering (by neurosurgical, endovascular, endoscopic, or stereotactic means) the treatments to patients.
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69
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Molecular profiling of clinical tissue specimens: feasibility and applications. THE AMERICAN JOURNAL OF PATHOLOGY 2000; 156:1109-15. [PMID: 10751334 PMCID: PMC1876878 DOI: 10.1016/s0002-9440(10)64979-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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70
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Abstract
When completed this year, the Arabidopsis genome will represent the first plant genome to be fully sequenced. This sequence information, together with the large collection of expressed sequence tags, has established the basics for new approaches to studying gene expression patterns in plants on a global scale. We can now look at biology from the perspective of the whole genome. This revolution in the study of how all genes in an organism respond to certain stimuli has encouraged us to think in new dimensions. Expression profiles can be determined over a range of experimental conditions and organized into patterns that are diagnostic for the biological state of the cell. The field of genome-wide expression in plants has yet to produce its fruit; however, the current application of microarrays in yeast and human research foreshadows the diverse applications this technology could have in plant biology and agriculture.
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Affiliation(s)
- R Schaffer
- Michigan State University, East Lansing, MI 48824, USA
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71
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Abstract
Bioinformatics has, out of necessity, become a key aspect of drug discovery in the genomic revolution, contributing to both target discovery and target validation. The author describes the role that bioinformatics has played and will continue to play in response to the waves of genome-wide data sources that have become available to the industry, including expressed sequence tags, microbial genome sequences, model organism sequences, polymorphisms, gene expression data and proteomics. However, these knowledge sources must be intelligently integrated.
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72
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Stevens CW, Lee JS, Cox J, Komaki R. Novel approaches to locally advanced unresectable non-small cell lung cancer. Radiother Oncol 2000; 55:11-8. [PMID: 10788683 DOI: 10.1016/s0167-8140(00)00163-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The management of advanced non-small cell lung cancer (NSCLC) is rapidly evolving. Advances in combined chemo-radiation therapy have led to improvements in patient survival which are statistically significant, but most patients still succumb to their disease. New chemotherapeutic agents, such as taxanes (paclitaxel, docetaxel), topoisomerase inhibitors (topotecan, irinotecan), and novel analogs (gemcitabine, vinorelbine), may offer the promise of improved outcome, but have not yet been tested in phase III trials. Molecular therapeutics, such as gene therapy, drugs that target specific oncogene activation (such as Ki-ras inactivation by farnesyl transferase inhibitors), and hypoxic cell toxins (such as tirapazamine), are in clinical trials. The optimum use of these agents awaits more rapid and widespread molecular diagnostics. Finally, technological advances in radiotherapy will allow higher tumor doses, while minimizing doses to dose-limiting normal structures, such as the esophagus, normal lung and heart. We describe a move towards molecular strategies, both for therapy and diagnostics, that may result in more effective treatment. While the outcome for patients with advanced non-small cell lung carcinoma is still poor, new agents are being developed rapidly and offer the hope of improved survival.
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Affiliation(s)
- C W Stevens
- Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
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73
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Affiliation(s)
- S W Guo
- The Max McGee National Research Center for Juvenile Diabetes, Department of Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, 53226-0509, USA
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74
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Abstract
There has already been a 'molecular' revolution in pathology. Demonstrating transcription of specific single genes or small gene sets and their protein products by in situ hybridisation and immunocytochemistry is routine in diagnostic and experimental pathology. A perhaps-greater revolution is imminent with the application of more recently established and emergent technologies in pathology. These include new approaches to polymerase chain reaction (PCR); simultaneous studies of multiple genes and their expression using oligonucleotide and cDNA arrays; serial analysis of gene expression (SAGE); expressed sequence tag (EST) sequencing, subtractive cloning and differential display; high-throughput sequencing; comparative genomic hybridization, multiplex fluorescence in situ hybridisation (FISH) (spectral karyotyping); reverse chromosome painting; knockout and transgenic organisms; laser microdissection and micro-machining; and new methods in bio-informatics, 'data mining' and data visualisation. Molecular methods will profoundly change diagnosis, prognosis and treatment targeting in oncology and elucidate fundamental mechanisms of neoplastic transformation. Individual susceptibility to specific diseases will become assessable and screening will be refined. The new molecular biology will be most fruitful in partnership with classical approaches to pathology: the expectation that molecular methods alone will answer all pathological questions is unrealistic. A further challenge for the biomedical community in the 'genome era' will be to ensure that the benefits of these sophisticated technologies are enjoyed globally.
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Affiliation(s)
- J J Going
- Department of Pathology, University of Glasgow, Glasgow Royal Infirmary.
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75
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Abstract
Dynamic pictures of living genomes are now beginning to emerge from systematic studies of gene expression patterns using DNA microarrays. The rich information represented in the variation in each gene's expression provides the basis for a new kind of genomic map.
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Affiliation(s)
- T L Ferea
- Department of Genetics, L311, Stanford University School of Medicine, Stanford 94305-5120, USA.
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76
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Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999; 286:531-7. [PMID: 10521349 DOI: 10.1126/science.286.5439.531] [Citation(s) in RCA: 5519] [Impact Index Per Article: 220.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Although cancer classification has improved over the past 30 years, there has been no general approach for identifying new cancer classes (class discovery) or for assigning tumors to known classes (class prediction). Here, a generic approach to cancer classification based on gene expression monitoring by DNA microarrays is described and applied to human acute leukemias as a test case. A class discovery procedure automatically discovered the distinction between acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) without previous knowledge of these classes. An automatically derived class predictor was able to determine the class of new leukemia cases. The results demonstrate the feasibility of cancer classification based solely on gene expression monitoring and suggest a general strategy for discovering and predicting cancer classes for other types of cancer, independent of previous biological knowledge.
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Affiliation(s)
- T R Golub
- Whitehead Institute/Massachusetts Institute of Technology Center for Genome Research, Cambridge, MA 02139, USA.
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77
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78
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Abstract
In April, the Merck Genome Research Institute and the National Cancer Institute's Cancer Genome Anatomy Project, both supporters of functional genomics technology development and research, brought together a group of 27 scientists working at the forefront of this new field. Here we report on the presentations, discussions, and outcomes from this highly interactive and stimulating meeting held at the Banbury Center.
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79
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Abstract
Technologies for whole-genome RNA expression studies are becoming increasingly reliable and accessible. However, universal standards to make the data more suitable for comparative analysis and for inter-operability with other information resources have yet to emerge. Improved access to large electronic data sets, reliable and consistent annotation and effective tools for 'data mining' are critical. Analysis methods that exploit large data warehouses of gene expression experiments will be necessary to realize the full potential of this technology.
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Affiliation(s)
- D E Bassett
- Rosetta Inpharmatics, Kirkland, Washington 98034, USA
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80
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Bowtell DD. Options available--from start to finish--for obtaining expression data by microarray. Nat Genet 1999; 21:25-32. [PMID: 9915497 DOI: 10.1038/4455] [Citation(s) in RCA: 329] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The excitement surrounding microarray technology has been tempered by the limited ability of the general biomedical research community to gain access to it. Given the hardware required for exploitation of the technology is becoming increasingly available, it is an appropriate moment to review options, be they commercially or publically available. Here, we provide a snapshot of the rapidly changing field of microarray-based RNA expression analysis and consider the components and procedures for putting together a complete system.
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Affiliation(s)
- D D Bowtell
- Peter MacCallum Cancer Institute, Melbourne, Victoria, Australia.
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Affiliation(s)
- E S Lander
- Whitehead Institute for Biomedical Research and Department of Biology, Institute of Technology, Cambridge 02142, USA.
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Abstract
DNA microarrays can be used to measure the expression patterns of thousands of genes in parallel, generating clues to gene function that can help to identify appropriate targets for therapeutic intervention. They can also be used to monitor changes in gene expression in response to drug treatments. Here, we discuss the different ways in which microarray analysis is likely to affect drug discovery.
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Affiliation(s)
- C Debouck
- SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406, USA
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