451
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Matoba R, Saito S, Ueno N, Maruyama C, Matsubara K, Kato K. Gene expression profiling of mouse postnatal cerebellar development. Physiol Genomics 2000; 4:155-164. [PMID: 11120876 DOI: 10.1152/physiolgenomics.2000.4.2.155] [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: 11/22/2022] Open
Abstract
Expression patterns of 1,869 genes were determined using adapter-tagged competitive PCR (ATAC-PCR) at 6 time points during mouse postnatal cerebellar development. The expression patterns were classified into 12 clusters that were further assembled into 3 groups by hierarchical cluster analysis. Among the 1,869 genes, 1,053 known genes were assigned to 90 functional categories. Statistically significant correlation between the clusters or groups of gene expression and the functional categories was ascertained. Genes involved in oncogenesis or protein synthesis were highly expressed during the earlier stages of development. Those responsible for brain functions such as neurotransmitter receptor and synapse components were more active during the later stages of development. Many other genes also showed expression patterns in accordance with literature information. The gene expression patterns and the inferred functions were in good agreement with anatomical as well as physiological observations made during the developmental process.
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Affiliation(s)
- R Matoba
- Taisho Laboratory of Functional Genomics, Nara Institute of Science and Technology, Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, 8916-5 Takayama, Ikoma, Nara, 630-0101, Japan
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452
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Abstract
DNA microarrays are powerful tools for the analysis of the organization and regulation of the brain, in both illness and health. Such messenger RNA expression methods are outgrowths of a marriage between the several genome sequencing projects and a wide variety of physical, chemical, optical, and electronic systems. The advantages of microarray analyses include the ability to study the regulation of several genes or even the entire genome in a single experiment. However, there are substantive issues associated with the use of these tools that need to be considered before drawing conclusions about the genomic regulation of the brain. These issues include the loss of most anatomic (i.e., cellular and circuit) specificity, only fair sensitivity, lack of absolute quantitative data, poor comparability between studies, and high variability in sample values, to mention the most obvious. In this review we point to some of the solutions proposed for these problems and novel techniques and approaches for newer methods. Among these are methods for making arrays more sensitive, including nonarray messenger RNA expression systems. The future of this field and its links to deeper protein and cell biology are both emphasized.
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Affiliation(s)
- S J Watson
- Department of Psychiatry and The Mental Health Research Institute, University of Michigan, Ann Arbor, Michigan 48109-0720, USA
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453
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Girke T, Todd J, Ruuska S, White J, Benning C, Ohlrogge J. Microarray analysis of developing Arabidopsis seeds. PLANT PHYSIOLOGY 2000; 124:1570-81. [PMID: 11115875 PMCID: PMC59856 DOI: 10.1104/pp.124.4.1570] [Citation(s) in RCA: 213] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2000] [Revised: 06/20/2000] [Accepted: 09/13/2000] [Indexed: 05/18/2023]
Abstract
To provide a broad analysis of gene expression in developing Arabidopsis seeds, microarrays have been produced that display approximately 2,600 seed-expressed genes. DNA for genes spotted on the arrays were selected from >10,000 clones partially sequenced from a cDNA library of developing seeds. Based on a series of controls, sensitivity of the arrays was estimated at one to two copies of mRNA per cell and cross hybridization was estimated to occur if closely related genes have >70% to 80% sequence identity. These arrays have been hybridized in a series of experiments with probes derived from seeds, leaves, and roots of Arabidopsis. Analysis of expression ratios between the different tissues has allowed the tissue-specific expression patterns of many hundreds of genes to be described for the first time. Approximately 25% of the 2, 600 genes were expressed at ratios > or =2-fold higher in seeds than leaves or roots and 10% at ratios > or =10. Included in this list are a large number of proteins of unknown function, and potential regulatory factors such as protein kinases, phosphatases, and transcription factors. The Arabidopsis arrays were also found to be useful for transcriptional profiling of mRNA isolated from developing oilseed rape (Brassica napus) seeds and expression patterns correlated well between the two species.
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Affiliation(s)
- T Girke
- Department of Botany and Plant Pathology, Michigan State University, East Lansing, Michigan 48824, USA
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454
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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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455
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Sakai K, Higuchi H, Matsubara K, Kato K. Microarray hybridization with fractionated cDNA: enhanced identification of differentially expressed genes. Anal Biochem 2000; 287:32-7. [PMID: 11078580 DOI: 10.1006/abio.2000.4831] [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: 11/22/2022]
Abstract
Molecular indexing is a technique to select a subpopulation of cDNA by ligation of adapters to cDNA fragments digested by a class IIS restriction enzyme(s). By this technique, 3' end cDNA fragments are divided into 16 fractions by selective ligation of adapters and subsequent PCR amplification. Each fraction is used as a hybridization target for microarray hybridization. This fractionated target has a relatively lower nucleic acid complexity, including more fractions for rare transcripts, and is useful for their detection. In an experiment with mouse cerebellum and cerebrum RNA, analysis of a subset of candidate genes indicated that 10 times more differentially expressed genes were detected by this method than by the conventional method using the unfractionated target.
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Affiliation(s)
- K Sakai
- Taisho Laboratory of Functional Genomics, Nara Institute of Science and Technology, CREST, JST, 8916-5 Takayama, Ikoma, Nara, 630-0101, Japan
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456
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Stingley SW, Ramirez JJ, Aguilar SA, Simmen K, Sandri-Goldin RM, Ghazal P, Wagner EK. Global analysis of herpes simplex virus type 1 transcription using an oligonucleotide-based DNA microarray. J Virol 2000; 74:9916-27. [PMID: 11024119 PMCID: PMC102029 DOI: 10.1128/jvi.74.21.9916-9927.2000] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
More than 100 transcripts of various abundances and kinetic classes are expressed during phases of productive and latent infections by herpes simplex virus (HSV) type 1. To carry out rapid global analysis of variations in such patterns as a function of perturbation of viral regulatory genes and cell differentiation, we have made DNA microchips containing sets of 75-mer oligonucleotides specific for individual viral transcripts. About half of these are unique for single transcripts, while others function for overlapping ones. We have also included probes for 57 human genes known to be involved in some aspect of stress response. The chips efficiently detect all viral transcripts, and analysis of those abundant under various conditions of infection demonstrates excellent correlation with known kinetics of mRNA accumulation. Further, quantitative sensitivity is high. We have further applied global analysis of transcription to an investigation of mRNA populations in cells infected with a mutant virus in which the essential immediate-early alpha27 (U(L)54) gene has been functionally deleted. Transcripts expressed at 6 h following infection with this mutant can be classified into three groups: those whose abundance is augmented (mainly immediate-early transcripts) or unaltered, those whose abundance is somewhat reduced, and those where there is a significant reduction in transcript levels. These do not conform to any particular kinetic class. Interestingly, levels of many cellular transcripts surveyed are increased. The high proportion of such transcripts suggests that the alpha27 gene plays a major role in the early decline in cellular gene expression so characteristic of HSV infection.
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Affiliation(s)
- S W Stingley
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA
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457
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Abstract
Within the next few years, the complete genomic sequences of Plasmodium falciparum, and potentially several other Plasmodium spp, will be available to researchers worldwide. These complete genomic sequence data are certain to provide the foundation for nearly all malaria research in the next decades, as discussed here by Dan Carucci.
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Affiliation(s)
- D J Carucci
- Malaria Program, Naval Medical Research Center, 20910-7500, Silver Spring, MD 20910-7500, USA.
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458
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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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459
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Affiliation(s)
- D H Geschwind
- Neurogenetics Program, Department of Neurology, University of California Los Angeles School of Medicine, 710 Westwood Plaza, Los Angeles, CA 90095-1769, USA.
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460
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Scott KM, Fanta P, Calaluce R, Dalkin B, Weinstein RS, Nagle RB. Diagnostic frozen prostate sextant biopsies: an approach for preserving protein and RNA for additional studies. Prostate 2000; 44:296-302. [PMID: 10951494 DOI: 10.1002/1097-0045(20000901)44:4<296::aid-pros6>3.0.co;2-u] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
BACKGROUND Primary prostate cancer represents 29% of newly diagnosed visceral cancers in men. Despite this common occurrence, relatively little is known about the pathogenesis of this malignancy. High-grade prostatic intraepithelial neoplasia (HGPIN) is generally accepted as a precursor to invasive prostate carcinoma. There is a lack of adequate animal models, and the available cell culture lines are limited. Tissue from prostate needle core biopsies that have been frozen can provide adequate material for both diagnosis and research. METHODS Transrectal sextant needle biopsies were snap-frozen, serially sectioned and alternately stained with hematoxylin-eosin or reacted with a basal cell-specific antibody. Two pathologists examined all of the sections, which were scored for the presence or absence of carcinoma and HGPIN. Portions of the remaining tissue were used for studies of protein expression and gene expression. RESULTS The incidence of carcinoma was 39%, comparable to the mean percent positive cases reported using conventional fixation and paraffin embedding. The incidence of HGPIN was 33%, higher than previously reported. CONCLUSIONS Prostate carcinoma can be accurately diagnosed using frozen material. The observed high frequency of HGPIN is attributed to the instability of nuclear structure in the frozen material of the atypical nuclei, resulting in inflated grading of PIN lesions. Sufficient material remained in the frozen blocks for additional studies of protein and gene expression.
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Affiliation(s)
- K M Scott
- Department of Pathology, University of Arizona Health Sciences Center, Tucson 85724, USA.
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461
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Murakami H, Liotta L, Star RA. IF-LCM: laser capture microdissection of immunofluorescently defined cells for mRNA analysis rapid communication. Kidney Int 2000; 58:1346-53. [PMID: 10972700 DOI: 10.1046/j.1523-1755.2000.00295.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND The next phase of the molecular revolution will bring functional genomics down to the level of individual cells in a tissue. Laser capture microdissection (LCM) coupled with reverse transcription-polymerase chain reaction (RT-PCR) can measure gene expression in normal, cancerous, injured, or fibrotic tissue. Nevertheless, targeting of specific cells may be difficult using routine morphologic stains. Immunohistochemistry can identify cells with specific antigens; however, exposure to aqueous solutions destroys 99% of the mRNA. Consequently, there is an overwhelming need to identify specific tissue cells for LCM without mRNA loss. We report on a rapid immunofluorescent LCM (IF-LCM) procedure that allows targeted analysis of gene expression. METHODS A LCM microscope was outfitted for epifluorescence and light level video microscopy. Heat filters were added to shield the image intensifier from the laser. Frozen sections were fluorescently labeled by a rapid one minute incubation with anti-Tamm-Horsfall antibody and an ALEXA-linked secondary antibody. Fluorescently labeled thick ascending limb (TAL) cells were detected by low light level video microscopy, captured by LCM, and mRNA was analyzed by RT-PCR for basic amino acid transporter, Tamm-Horsfall protein, and aquaporin-2. RESULTS The immunofluorescently identified TAL could be cleanly microdissected without contamination from surrounding tubules. The recovery of RNA following rapid immunofluorescence staining was similar to that obtained following hematoxylin and eosin staining, as assessed by RT-PCR for malate dehydrogenase. CONCLUSIONS We conclude that the new apparatus and method for the immunofluorescent labeling of tissue cells targeted for LCM can isolate pure populations of targeted cells from a sea of surrounding cells with highly acceptable preservation of mRNA. Since the TAL is minimally injured following ischemia, identification of the different responses between TAL and surrounding tissue in damaged kidneys may provide new therapeutic targets or agents for the treatment of acute renal failure.
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Affiliation(s)
- H Murakami
- Renal Diagnostics and Therapeutics Unit, and Laboratory of Pathology, National Institutes of Health, Bethesda, Maryland 20892-1268, USA
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462
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Abstract
The molecular examination of pathologically altered cells and tissues at the DNA, RNA, and protein level has revolutionised research and diagnostics in pathology. However, the inherent heterogeneity of primary tissues with an admixture of various reactive cell populations can affect the outcome and interpretation of molecular studies. Recently, microdissection of tissue sections and cytological preparations has been used increasingly for the isolation of homogeneous, morphologically identified cell populations, thus overcoming the obstacle of tissue complexity. In conjunction with sensitive analytical techniques, such as the polymerase chain reaction, microdissection allows precise in vivo examination of cell populations, such as carcinoma in situ or the malignant cells of Hodgkin's disease, which are otherwise inaccessible for conventional molecular studies. However, most microdissection techniques are very time consuming and require a high degree of manual dexterity, which limits their practical use. Laser capture microdissection (LCM), a novel technique developed at the National Cancer Institute, is an important advance in terms of speed, ease of use, and versatility of microdissection. LCM is based on the adherence of visually selected cells to a thermoplastic membrane, which overlies the dehydrated tissue section and is focally melted by triggering of a low energy infrared laser pulse. The melted membrane forms a composite with the selected tissue area, which can be removed by simple lifting of the membrane. LCM can be applied to a wide range of cell and tissue preparations including paraffin wax embedded material. The use of immunohistochemical stains allows the selection of cells according to phenotypic and functional characteristics. Depending on the starting material, DNA, good quality mRNA, and proteins can be extracted successfully from captured tissue fragments, down to the single cell level. In combination with techniques like expression library construction, cDNA array hybridisation and differential display, LCM will allow the establishment of "genetic fingerprints" of specific pathological lesions, especially malignant neoplasms. In addition to the identification of new diagnostic and prognostic markers, this approach could help in establishing individualised treatments tailored to the molecular profile of a tumour. This review provides an overview of the technique of LCM, summarises current applications and new methodical approaches, and tries to give a perspective on future developments. In addition, LCM is compared with other recently developed laser microdissection techniques.
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Affiliation(s)
- F Fend
- Department of Pathology, Technical University Munich, Germany.
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463
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Abstract
This article presents an overview of retinal cell differentiation in the chick embryo, in the context of a hypothetical model based on information generated during the last several years. The model proposes that: (1) most (if not all) proliferating neuroepithelial cells have the potential to give rise to a progeny comprising two or more different cell types; (2) the time at which cells undergo their terminal mitosis does not determine their differentiated fate; (3) many postmitotic precursor cells remain plastic (i.e., uncommitted) for some time after terminal mitosis, during which they encounter position-dependent signals as they migrate toward their definitive laminar position within the retina; (4) as a consequence of these inductive stimuli, precursor cells that migrate to different retinal layers express different transcriptional regulators; (5) morphologically undifferentiated precursor cells are committed to cell type-specific, complex patterns of differentiation, which they can express even when isolated from their normal microenvironment, and (6) even after precursor cells become committed to a specific identity, additional inductive signals are necessary for the cells to complete the development of a fully mature phenotype. The article presents a summary of the supportive evidence, as well as a critical evaluation of the model, and concludes with an overview of unanswered questions regarding retinal cell differentiation and a brief evaluation of the prospects for further progress in this field.
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Affiliation(s)
- R Adler
- Wilmer Eye Institute, The Johns Hopkins University, School of Medicine, MD, Baltimore, USA.
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464
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Gordon GJ, Coleman WB, Grisham JW. Temporal analysis of hepatocyte differentiation by small hepatocyte-like progenitor cells during liver regeneration in retrorsine-exposed rats. THE AMERICAN JOURNAL OF PATHOLOGY 2000; 157:771-86. [PMID: 10980117 PMCID: PMC1885692 DOI: 10.1016/s0002-9440(10)64591-9] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Liver regeneration after two-thirds surgical partial hepatectomy (PH) in rats treated with the pyrrolizidine alkaloid retrorsine is accomplished through the activation, expansion, and differentiation of a population of small hepatocyte-like progenitor cells (SHPCs). We have examined expression of the major liver-enriched transcription factors, cytochrome P450 (CYP) enzymes, and other markers of hepatocytic differentiation in SHPCs during the protracted period of liver regeneration after PH in retrorsine-exposed rats. Early-appearing SHPCs (at 3-7 days after PH) express mRNAs for all of the major liver-enriched transcription factors at varying levels compared to fully differentiated hepatocytes. In addition, SHPCs lack (or have significantly reduced) expression of mRNA for hepatocyte markers tyrosine aminotransferase and alpha-1 antitrypsin, but their expression levels of mRNA and/or protein for WT1 and alpha-fetoprotein (AFP) are increased. With the exception of AFP expression, SHPCs resembled fully differentiated hepatocytes by 14 days after PH. Expression of AFP was maintained by most SHPCs through 14 days after PH, gradually declined through 23 days after PH, and was essentially absent from SHPC progeny by 30 days after PH. Furthermore, early appearing SHPCs lack (or have reduced expression) of hepatic CYP proteins known to be induced in rat livers after retrorsine exposure. The resistance of SHPCs to the mitoinhibitory effects of retrorsine may be directly related to a lack of CYP enzymes required to metabolize retrorsine to its toxic derivatives. These results suggest that SHPCs represent a unique parenchymal (less differentiated) progenitor cell population of adult rodent liver that is phenotypically distinct from fully differentiated hepatocytes, biliary epithelial cells, and (ductular) oval cells.
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Affiliation(s)
- G J Gordon
- Department of Pathology and Laboratory Medicine, Curriculum in Toxicology, UNC Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
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465
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Celis JE, Kruhøffer M, Gromova I, Frederiksen C, Ostergaard M, Thykjaer T, Gromov P, Yu J, Pálsdóttir H, Magnusson N, Orntoft TF. Gene expression profiling: monitoring transcription and translation products using DNA microarrays and proteomics. FEBS Lett 2000; 480:2-16. [PMID: 10967322 DOI: 10.1016/s0014-5793(00)01771-3] [Citation(s) in RCA: 229] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Novel and powerful technologies such as DNA microarrays and proteomics have made possible the analysis of the expression levels of multiple genes simultaneously both in health and disease. In combination, these technologies promise to revolutionize biology, in particular in the area of molecular medicine as they are expected to reveal gene regulation events involved in disease progression as well as to pinpoint potential targets for drug discovery and diagnostics. Here, we review the current status of these technologies and highlight some studies in which they have been applied in concert to the analysis of biopsy specimens.
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Affiliation(s)
- J E Celis
- Department of Medical Biochemistry and Danish Centre for Human Genome Research, University of Aarhus, Denmark.
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466
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Affiliation(s)
- R A Young
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Massachusetts 02142, USA.
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467
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Abstract
Experimental genomics in combination with the growing body of sequence information promise to revolutionize the way cells and cellular processes are studied. Information on genomic sequence can be used experimentally with high-density DNA arrays that allow complex mixtures of RNA and DNA to be interrogated in a parallel and quantitative fashion. DNA arrays can be used for many different purposes, most prominently to measure levels of gene expression (messenger RNA abundance) for tens of thousands of genes simultaneously. Measurements of gene expression and other applications of arrays embody much of what is implied by the term 'genomics'; they are broad in scope, large in scale, and take advantage of all available sequence information for experimental design and data interpretation in pursuit of biological understanding.
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Affiliation(s)
- D J Lockhart
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
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468
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Harada T, Harada C, Nakayama N, Okuyama S, Yoshida K, Kohsaka S, Matsuda H, Wada K. Modification of glial-neuronal cell interactions prevents photoreceptor apoptosis during light-induced retinal degeneration. Neuron 2000; 26:533-41. [PMID: 10839371 DOI: 10.1016/s0896-6273(00)81185-x] [Citation(s) in RCA: 169] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Prolonged or high-intensity exposure to visible light leads to photoreceptor cell death. In this study, we demonstrate a novel pathway of light-induced photoreceptor apoptosis involving the low-affinity neurotrophin receptor p75 (p75NTR). Retinal degeneration upregulated both p75NTR and the high-affinity neurotrophin receptor TrkC in different parts of Müller glial cells. Exogenous neurotrophin-3 (NT-3) increased, but nerve growth factor (NGF) decreased basic fibroblast growth factor (bFGF) production in Müller cells, which can directly rescue photoreceptor apoptosis. Blockade of p75NTR prevented bFGF reduction and resulted in both structural and functional photoreceptor survival in vivo. Furthermore, the absence of p75NTR significantly prevented light-induced photoreceptor apoptosis. These observations implicate glial cells in the determination of neural cell survival, and suggest functional glial-neuronal cell interactions as new therapeutic targets for neurodegeneration.
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Affiliation(s)
- T Harada
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan.
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469
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Affiliation(s)
- D J Zack
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
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470
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Hsiao LL, Stears RL, Hong RL, Gullans SR. Prospective use of DNA microarrays for evaluating renal function and disease. Curr Opin Nephrol Hypertens 2000; 9:253-8. [PMID: 10847326 DOI: 10.1097/00041552-200005000-00008] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
At the forefront of the revolution in human genomics is DNA microarray technology, which evaluates expression levels or genotypes of thousands of genes simultaneously, by means of miniaturization and parallel processing. Furthermore, advances in bioinformatics will result in the creation of large databases, which will require complex software programming for structural analysis. Over the next decade, DNA microarrays, combined with sophisticated informatics and genomic databases, will provide molecular fingerprints of disease processes and prognoses. This review provides an update on DNA microarray technology and its application to renal diseases.
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Affiliation(s)
- L L Hsiao
- Department of Medicine, Brigham and Women's Hospital, Harvard Institutes of Medicine, Boston, MA 02115, USA
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471
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Wang E, Miller LD, Ohnmacht GA, Liu ET, Marincola FM. High-fidelity mRNA amplification for gene profiling. Nat Biotechnol 2000; 18:457-9. [PMID: 10748532 DOI: 10.1038/74546] [Citation(s) in RCA: 534] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The completion of the Human Genome Project has made possible the comprehensive analysis of gene expression, and cDNA microarrays are now being employed for expression analysis in cancer cell lines or excised surgical specimens. However, broader application of cDNA microarrays is limited by the amount of RNA required: 50-200 microg of total RNA (T-RNA) and 2-5 microg poly(A) RNA. To broaden the use of cDNA microarrays, some methods aiming at intensifying fluorescence signal have resulted in modest improvement. Methods devoted to amplifying starting poly(A) RNA or cDNA show promise, in that detection can be increased by orders of magnitude. However, despite the common use of these amplification procedures, no systematic assessment of their limits and biases has been documented. We devised a procedure that optimizes amplification of low-abundance RNA samples by combining antisense RNA (aRNA) amplification with a template-switching effect (Clonetech, Palo Alto, CA). The fidelity of aRNA amplified from 1:10,000 to 1:100,000 of commonly used input RNA was comparable to expression profiles observed with conventional poly(A) RNA- or T-RNA-based arrays.
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Affiliation(s)
- E Wang
- Surgery Branch, Division of Clinical Sciences, National Cancer Institute and the Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
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472
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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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473
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Mallon E, Osin P, Nasiri N, Blain I, Howard B, Gusterson B. The basic pathology of human breast cancer. J Mammary Gland Biol Neoplasia 2000; 5:139-63. [PMID: 11149570 DOI: 10.1023/a:1026439204849] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This article illustrates the most common benign and malignant lesions in the breast, and is intended for the biologist working in the area of breast cancer and breast biology, not for the practicing pathologist. The atlas covers benign proliferative lesions, atypical lesions, variants of in situ cancer, the main types of invasive cancers, spindle cell lesions, and examples of vascular and lymphatic spread. Some entities are included to illustrate a point of particular relevance to the biology and histogenesis of the lesions. Some controversial diagnostic areas are considered, along with the relative risk of developing breast cancer associated with some of the proliferative lesions. The content of this atlas should be read in conjunction with the companion article by Howard and Gusterson in this issue. Their article covers the cellular origin of epithelial and stromal tumors and presents a description of some of the common benign proliferative lesions that are considered to be components of the normal spectrum of changes seen at postmortem or in biopsies.
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474
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Abstract
Bodily fluids such as cerebrospinal fluid (CSF) and serum can be analysed at the time of presentation and throughout the course of the disease. Changes in the protein composition of CSF may be indicative of altered CNS protein expression pattern with a causative or diagnostic disease link. These findings can be strengthened through subsequent proteomic analysis of specific brain areas implicated in the pathology. New isolation strategies of clinically relevant cellular material such as laser capture microdissection, protein enrichment procedures and proteomic approaches to neuropeptide and neurotransmitter analysis give us the opportunity to map out complex cellular interaction at an unprecedented level of detail. In neurological disorders multiple underlying pathogenic mechanisms as well as an acute and a chronic CNS disease components may require a selective repertoire of molecular targets and biomarkers rather than an individual protein to better define a complex disease. The resulting proteome database bypasses many ambiguities of experimental models and may facilitate pre- and clinical development of more specific disease markers and new selective fast acting therapeutics.
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Affiliation(s)
- C Rohlff
- Oxford GlycoSciences, Abingdon Science Park, United Kingdom.
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475
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Glynne RJ, Ghandour G, Goodnow CC. Genomic-scale gene expression analysis of lymphocyte growth, tolerance and malignancy. Curr Opin Immunol 2000; 12:210-4. [PMID: 10712948 DOI: 10.1016/s0952-7915(99)00076-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Immunologists are already comfortable with the need for monitoring many different gene products simultaneously. It is a common challenge to remember what CD-one-hundred-and-something is, and an ever-increasing number of colours are required for identification on the flow cytometer. Gene expression arrays now offer the possibility of extending this approach beyond the cell surface and expanding it dramatically to survey the entire catalogue of gene transcripts in a lymphoid cell.
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MESH Headings
- Algorithms
- Animals
- Antigens, CD/biosynthesis
- Antigens, CD/genetics
- Antigens, Neoplasm/biosynthesis
- Antigens, Neoplasm/genetics
- Artifacts
- Cell Separation
- Cluster Analysis
- Data Interpretation, Statistical
- Flow Cytometry
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Genome
- Humans
- Lymphocyte Subsets/immunology
- Lymphocyte Subsets/metabolism
- Lymphocyte Subsets/pathology
- Lymphoma/genetics
- Lymphoma/pathology
- Mice
- Oligonucleotide Array Sequence Analysis
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Neoplasm/biosynthesis
- RNA, Neoplasm/genetics
- Species Specificity
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Affiliation(s)
- R J Glynne
- Eos Biotechnology, South San Francisco, 94080, USA
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476
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Abstract
Human tissues are composed of complex admixtures of different cell types and their biologically meaningful analysis necessitates the procurement of pure samples of the cells of interest. Many approaches have been used in attempts to overcome this difficulty, including a variety of microdissection methods. This review concerns a recent advance in microdissection techniques, namely laser capture microdissection (LCM). The principle underlying this technique is outlined, and practical issues pertaining to LCM are considered. In addition, the literature relating to LCM is reviewed, with examples of research applications of this technique being outlined.
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Affiliation(s)
- S Curran
- Department of Pathology, University of Aberdeen, Foresterhill, UK
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477
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Emmert-Buck MR, Gillespie JW, Paweletz CP, Ornstein DK, Basrur V, Appella E, Wang QH, Huang J, Hu N, Taylor P, Petricoin EF. An approach to proteomic analysis of human tumors. Mol Carcinog 2000. [DOI: 10.1002/(sici)1098-2744(200003)27:3<158::aid-mc2>3.0.co;2-2] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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478
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Bilban M, Head S, Desoye G, Quaranta V. DNA microarrays: a novel approach to investigate genomics in trophoblast invasion--a review. Placenta 2000; 21 Suppl A:S99-105. [PMID: 10831133 DOI: 10.1053/plac.1999.0517] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The events that regulate trophoblast invasion need to be characterized at the transcriptional level. Several types of gene products may be involved in various stages oftrophoblast infiltration, including integrins, matrix metalloproteases (MMPs) and extracellular matrix (ECM) proteins. Autocrine or paracrine regulators of cytotrophoblast proliferation or differentiation in vitro (e.g. growth factors and cytokines, as well as oxygen tension) could be characterized mechanistically at the transcriptional level. Large-scale gene expression profiling of trophoblasts of distinct invasive stages could be carried out on fixed tissue obtained by laser-directed microdissection. This information may shed light on physiological implantation and placentation, as well as on the interpretation of pathological processes such as pre-eclampsia. The applications of DNA microarrays are ideal for studies of genomic structure (e.g. mutation and polymorphism analyses) and monitoring of gene expression. The ultimate goal is to understand the critical events underlying growth, development, homeostasis, 'behaviour and the onset of disease at a genomic level. Microarrays detect gene expression levels in parallel by measuring the hybridization of labelled, single-stranded DNA to many thousands of partial or whole gene sequences immobilized on a glass surface (the 'chip'). Microarrays are available both commercially and can be manufactured in house.
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Affiliation(s)
- M Bilban
- The Scripps Research Institute, Department of Cell Biology, La Jolla, CA 92037, USA
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479
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Knöfler M, Kalionis B, Huelseweh B, Bilban M, Morrish DW. Novel genes and transcription factors in placental development--a workshop report. Placenta 2000; 21 Suppl A:S71-3. [PMID: 10831126 DOI: 10.1053/plac.1999.0531] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- M Knöfler
- Department of Obstetrics and Gynaecology, University of Vienna, Austria
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480
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Nagasawa Y, Takenaka M, Matsuoka Y, Imai E, Hori M. Quantitation of mRNA expression in glomeruli using laser-manipulated microdissection and laser pressure catapulting. Kidney Int 2000; 57:717-23. [PMID: 10652051 DOI: 10.1046/j.1523-1755.2000.00894.x] [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: 11/20/2022]
Abstract
BACKGROUND Laser-manipulated microdissection (LMM) is a method to cut out a single cell or limited tiny region from a specimen under microscopic observation by a laser beam. Laser pressure catapulting (LPC) is a method to push up and collect samples that were microdissected using a strong laser. METHODS To induce experimental glomerulonephritis, anti-Thy1.1 monoclonal antibody (OX-7) was injected intravenously into rats. Control and disease model kidneys were obtained. Six-micrometer thick cryostat sections were mounted onto a 1.35 microm thin polyethylene membrane. Ten glomeruli were collected from 6 microm frozen sections of rat kidney by LMM and LPC. Isolated glomeruli were used to quantitate the expression of mRNA by real-time polymerase chain reaction (PCR). RESULTS Transforming growth factor-beta1 (TGF-beta1) mRNA was not detected in glomeruli isolated by the LMM and the LPC methods on day 0, although G3PDH mRNA was measurable in the same samples. On day 7 after the treatment with OX-7, the ratio of TGF-beta1/G3PDH mRNA was 1.89 +/- 0.96 (N = 6). CONCLUSIONS We established methods to isolate glomeruli from standard histochemical specimens by LMM and LPC, and to quantify mRNA expression in the targeted glomeruli using real-time PCR. We confirmed the up-regulation of TGF-beta1 mRNA expression in isolated glomeruli from frozen sections of the anti-Thy1.1 glomerulonephritis model.
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Affiliation(s)
- Y Nagasawa
- Department of Internal Medicine and Therapeutics, Graduate School of Medicine, Osaka University, Osaka, Japan
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481
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Satoh J, Kuroda Y. Differential gene expression between human neurons and neuronal progenitor cells in culture: an analysis of arrayed cDNA clones in NTera2 human embryonal carcinoma cell line as a model system. J Neurosci Methods 2000; 94:155-64. [PMID: 10661835 DOI: 10.1016/s0165-0270(99)00143-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
To elucidate the highly complex expression pattern of the genes involved in human neuronal differentiation, differential gene expression between human neurons and neuronal progenitor cells was investigated by analysis of a cDNA expression array in a pluripotent human embryonal carcinoma cell line NTera2 (NT2), a model system of human neuronal differentiation. Among 588 arrayed cDNA clones, 87 genes showed a differential expression pattern between undifferentiated neuronal progenitor cells (NT2-U) and NT2-derived differentiated neurons induced by treatment with retinoic acid (RA) (NT2-N), while 26 genes could not be analyzed due to high background signals. The levels of expression of 76 genes, including those encoding a group of transcription factors, intracellular signal-transducing proteins, cell death-regulatory proteins, and growth factors/cytokines/neurotransmitters and their receptors, were elevated after neuronal differentiation, while the levels of 11 genes, including those coding for cellular proliferation-related proteins, were decreased. Among the differentially expressed genes following induction of neuronal differentiation, significant up-regulation of the growth-associated protein (GAP-43), low-affinity nerve growth factor receptor p75 (LNGFR), and defender against apoptotic cell death (DAD1) mRNAs and substantial down-regulation of the proliferation-associated gene (PAG), fibroblast growth factor receptor-1 (FGFR-1), and cellular RA-binding protein-II (CRABP-II) mRNAs were verified by Northern blot analysis. These results indicate that the analysis of cDNA expression arrays provides a useful approach for screening and identification of a set of distinct genes that undergo highly complex regulation during human neuronal differentiation.
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Affiliation(s)
- J Satoh
- Division of Neurology, Department of Internal Medicine, Saga Medical School, Japan.
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482
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Walch A, Komminoth P, Hutzler P, Aubele M, Höfler H, Werner M. Microdissection of tissue sections: application to the molecular genetic characterisation of premalignant lesions. Pathobiology 2000; 68:9-17. [PMID: 10859526 DOI: 10.1159/000028110] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The characterisation of the early molecular genetic events of tumor development depends on the selective procurement of histopathologically defined small cell populations from premalignant tissue. In order to obtain high-quality DNA, mRNA and proteins from these small tissue samples and even from single cells, tissue microdissection is one of the most useful techniques, becoming increasingly important for molecular pathologists. Using different microdissection techniques which allow the isolation of morphologically defined cell populations under direct visualisation, it is now feasible to study molecular genetic events that drive the multistep evolution in tumours. This review aims to present the current techniques of tissue microdissection and these techniques are discussed in the light of their ability to isolate premalignant cell populations in particular. Furthermore, we describe the subsequent application of several multiplex molecular analyses for characterising the microdissected premalignant cells. Applying these advanced techniques, alterations in the cellular DNA or the fluctuation of expressed genes that correlate with a particular stage of carcinogenesis can ultimately be compared within or between individual patients. Thus, these new technologies will have an enormous impact on molecular pathology with several diagnostic, prognostic and therapeutic implications.
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Affiliation(s)
- A Walch
- Institute of Pathology, GSF-National Research Centre for Environment and Health, Neuherberg, Germany.
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483
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Abstract
Increasingly mRNA expression patterns established using a variety of molecular technologies such as cDNA microarrays, SAGE and cDNA display are being used to identify potential regulatory genes and as a means of providing valuable insights into the biological status of the starting sample. Until recently, the application of these techniques has been limited to mRNA isolated from millions or, at very best, several thousand cells thereby restricting the study of small samples and complex tissues. To overcome this limitation a variety of amplification approaches have been developed which are capable of broadly evaluating mRNA expression patterns in single cells. This review will describe approaches that have been employed to examine global gene expression patterns either in small numbers of cells or, wherever possible, in actual isolated single cells. The first half of the review will summarize the technical aspects of methods developed for single-cell analysis and the latter half of the review will describe the areas of biological research that have benefited from single-cell expression analysis.
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Affiliation(s)
- G Brady
- School of Biological Sciences, G.38 Stopford Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
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484
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Kohda Y, Murakami H, Moe OW, Star RA. Analysis of segmental renal gene expression by laser capture microdissection. Kidney Int 2000; 57:321-31. [PMID: 10620215 DOI: 10.1046/j.1523-1755.2000.00824.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
UNLABELLED Analysis of segmental renal gene expression by laser capture microdissection. BACKGROUND The study of normal renal physiology has been greatly aided by microdissection techniques that have delineated the exceptional functional and cellular heterogeneity both along the nephron and between different nephron populations. These techniques are not widely used to study renal injury as microdissection is difficult because of tissue necrosis or fibrosis. We developed a procedure to detect specific gene expression in specific locations of the kidney in histologic sections. METHODS The anatomic specificity of laser capture microdissection (LCM) was employed with the sensitivity of reverse transcriptase-polymerase chain reaction (RT-PCR). RESULTS LCM/RT-PCR detected mRNA for podoplanin in 2% of a single glomerulus, rat basic amino acid transporter in 6% of a single cross-section of proximal straight tubule, and renin in eight proximal convoluted tubule cross-sections. LCM/RT-PCR could isolate pure populations of proximal convoluted tubules, proximal straight tubules, and thick ascending limbs from renal histologic sections, although pure collecting ducts could not be isolated. LCM/RT-PCR localized ischemia-reperfusion-induced induction of KC/interleukin-8 primarily to the medullary thick ascending limb, and detected transforming growth factor-beta (TGF-beta) mRNA in glomeruli of a patient with membranous glomerulonephropathy. CONCLUSIONS When used with an appropriate laser spot size, LCM/RT-PCR can measure gene expression in glomeruli or specific parts of the nephron and can study alterations in steady-state mRNA levels in animal models of renal disease. The applications, limitations, and refinements of this approach are discussed.
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Affiliation(s)
- Y Kohda
- University of Texas Southwestern Medical Center, Veterans Administration Medical Center, Dallas, Texas, USA
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485
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Abstract
A cell's structural and functional characteristics are dependent on the specific complement of genes it expresses. The ability to study and compare gene usage at the cellular level will therefore provide valuable insights into cell physiology. Such analyses are complicated by problems associated with sample collection, sample size and the limited sensitivity of expression assays. Advances have been made in approaches to the collection of cellular material and the performance of single-cell gene expression analysis. Recent development in global amplification of mRNA may soon permit expression analyses of single cells to be performed on DNA microarrays.
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Affiliation(s)
- T C Freeman
- Gene Expression Group, Wellcome Trust Genome Campus, The Sanger Centre, Hinxton, CB10 1SA, UK
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486
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Masuda N, Ohnishi T, Kawamoto S, Monden M, Okubo K. Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples. Nucleic Acids Res 1999; 27:4436-43. [PMID: 10536153 PMCID: PMC148727 DOI: 10.1093/nar/27.22.4436] [Citation(s) in RCA: 460] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Formalin-fixed archival samples are known to be poor materials for molecular biological applications. We conducted a series of experiments to understand the alterations in RNA in fixed tissue. We found that formalin-fixed tissue was resistant to solubilization by chaotropic agents. However, proteinase K completely solubilized the fixed tissue and enabled the extraction of almost the same amount of RNA as from a fresh sample. The extracted RNA did not show apparent degradation. However, as reported, successful PCR amplification was limited to short targets. The nature of such 'fixed' RNA was analyzed using synthetic homo-oligo RNAs. The heterogeneous increase in molecular weight of the RNAs, measured by MALDI-TOF mass spectrometry, showed that all four bases showed addition of mono-methylol (-CH(2)OH) groups at various rates. The modification rate varied from 40% for adenine to 4% for uracil. In addition, some adenines underwent dimerization through methylene bridging. The majority of the methylol groups, however, could be removed from bases by simply elevating the temperature in formalin-free buffer. This demodification proved effective in restoring the template activity of RNA from fixed tissue. The improvement in PCR results suggested that more than half of the modification was removed by this demodification.
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Affiliation(s)
- N Masuda
- Institute for Molecular and Cellular Biology, Osaka University, 1-3, Yamada-oka, Suita, Osaka 565-0871, Japan
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487
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Pilarsky C, Schmitt A, Hille S, Rosenthal A. Expression analysis using low amounts of mRNA and GeneChips. Nat Genet 1999. [DOI: 10.1038/14383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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488
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Dubin AE, Huvar R, D'Andrea MR, Pyati J, Zhu JY, Joy KC, Wilson SJ, Galindo JE, Glass CA, Luo L, Jackson MR, Lovenberg TW, Erlander MG. The pharmacological and functional characteristics of the serotonin 5-HT(3A) receptor are specifically modified by a 5-HT(3B) receptor subunit. J Biol Chem 1999; 274:30799-810. [PMID: 10521471 DOI: 10.1074/jbc.274.43.30799] [Citation(s) in RCA: 226] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
While homomers containing 5-HT(3A) subunits form functional ligand-gated serotonin (5-HT) receptors in heterologous expression systems (Jackson, M. B., and Yakel, J. L. (1995) Annu. Rev. Physiol. 57, 447-468; Lambert, J. J., Peters, J. A., and Hope, A. G. (1995) in Ligand-Voltage-Gated Ion Channels (North, R., ed) pp. 177-211, CRC Press, Inc., Boca Raton, FL), it has been proposed that native receptors may exist as heteromers (Fletcher, S., and Barnes, N. M. (1998) Trends Pharmacol. Sci. 19, 212-215). We report the cloning of a subunit 5-HT(3B) with approximately 44% amino acid identity to 5-HT(3A) that specifically modified 5-HT(3A) receptor kinetics, voltage dependence, and pharmacology. Co-expression of 5-HT(3B) with 5-HT(3A) modified the duration of 5-HT(3) receptor agonist-induced responses, linearized the current-voltage relationship, increased agonist and antagonist affinity, and reduced cooperativity between subunits. Reverse transcriptase-polymerase chain reaction in situ hybridization revealed co-localization of both 5-HT(3B) and 5-HT(3A) in a population of neurons in the amygdala, telencephalon, and entorhinal cortex. Furthermore, 5-HT(3A) and 5-HT(3B) mRNAs were expressed in spleen and intestine. Our data suggest that 5-HT(3B) might contribute to tissue-specific functional changes in 5-HT(3)-mediated signaling and/or modulation.
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Affiliation(s)
- A E Dubin
- R. W. Johnson Pharmaceutical Research Institute, San Diego, California 92121, USA.
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489
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Sirivatanauksorn Y, Drury R, Crnogorac-Jurcević T, Sirivatanauksorn V, Lemoine NR. Laser-assisted microdissection: applications in molecular pathology. J Pathol 1999; 189:150-4. [PMID: 10547567 DOI: 10.1002/(sici)1096-9896(199910)189:2<150::aid-path451>3.0.co;2-g] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Tissue microdissection is potentially one of the most useful techniques in molecular pathology. Laser-assisted microdissection has been developed to procure precisely the cells of interest in a tissue specimen, in a rapid and practical manner. Together with multiplex molecular approaches, it is now feasible to study genetic alterations and isolate genes and proteins in defined cell populations from complex normal and diseased tissues. The fundamental advantage of this technique is the possibility of capturing single cells from which high-quality DNA and mRNA can be isolated for analysis of sequence and quantitation of expression. Moreover, the integration of laser-assisted microdissection and proteomic analysis could identify novel protein markers for disease. The advent of laser-assisted microdissection is likely to have a profound impact on molecular pathology.
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Affiliation(s)
- Y Sirivatanauksorn
- Department of Gastrointestinal Surgery, Imperial College School of Medicine, Hammersmith Hospital, London, U.K
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490
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Anderson DJ. Lineages and transcription factors in the specification of vertebrate primary sensory neurons. Curr Opin Neurobiol 1999; 9:517-24. [PMID: 10508743 DOI: 10.1016/s0959-4388(99)00015-x] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Recent advances have indentified some of the key transcriptional regulators of mammalian genes, the neurogenins. Neurogenins 1 and 2 appear to control distinct sublineages for different classes of sensory neurons, including a 'pioneer' lineage for proprioceptors specified early in neural crest migration. Neurogenins act via a cascade of downstream transcriptional regulators, some of which have been identified.
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Affiliation(s)
- D J Anderson
- Howard Hughes Medical Institute Division of Biology 216-76 California Institute of Technology Pasadena, California 91125, USA.
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491
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Affiliation(s)
- T Serafini
- Department of Molecular and Cell Biology, University of California, Berkeley 94720-3200, USA.
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492
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Abstract
The neurological diseases described in this review supplement impact across a wide spectrum of the population. Here, their similarities and differences are highlighted, and common themes of the interactions between basic and clinical sciences for their understanding and treatment are explored.
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Affiliation(s)
- D L Price
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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