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Hill RW, Sleboda DA, Millar JJ. Youth in the study of comparative physiology: insights from demography in the wild. J Comp Physiol B 2020; 191:1-16. [PMID: 33090252 PMCID: PMC7819908 DOI: 10.1007/s00360-020-01315-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/07/2020] [Accepted: 09/20/2020] [Indexed: 12/03/2022]
Abstract
Of all the properties of individual animals of interest to comparative physiologists, age and stage of development are among the most consequential. In a natural population of any species, the survivorship curve is an important determinant of the relative abundances of ages and stages of development. Demography, thus, has significant implications for the study of comparative physiology. When Edward Deevey published his influential summary of survivorship in animal populations in the wild seven decades ago, he emphasized “serious deficiencies” because survivorship curves for natural populations at the time did not include data on the earliest life stages. Such data have accumulated over intervening years. We survey, for the first time, empirical knowledge of early-age survivorship in populations of most major animal groups in a state of nature. Despite wide variation, it is almost universally true that > 50% of newly born or hatched individuals die before the onset of sexual maturity, even in species commonly assumed to exhibit high early-age survivorship. These demographic facts are important considerations for studies in comparative and environmental physiology whether physiologists (i) aim to elucidate function throughout the life cycle, including both early stages and adults, or (ii) focus on adults (in which case early-age survivorship can potentially affect adult characteristics through selection or epigenesis). We establish that Deevey’s Type I curve (which applies to species with relatively limited early mortality) has few or no actual analogs in the real, natural world.
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Affiliation(s)
- Richard W Hill
- Department of Integrative Biology, Michigan State University, East Lansing, MI, 48824, USA.
| | - David A Sleboda
- Department of Physiology, McGill University, Montreal, QC, H3G 0B1, Canada
| | - Justin J Millar
- Big Data Institute, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
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Sex differences in breathing. Comp Biochem Physiol A Mol Integr Physiol 2019; 238:110543. [PMID: 31445081 DOI: 10.1016/j.cbpa.2019.110543] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 01/15/2023]
Abstract
Breathing is a vital behavior that ensures both the adequate supply of oxygen and the elimination of CO2, and it is influenced by many factors. Despite that most of the studies in respiratory physiology rely heavily on male subjects, there is much evidence to suggest that sex is an important factor in the respiratory control system, including the susceptibility for some diseases. These different respiratory responses in males and females may be related to the actions of sex hormones, especially in adulthood. These hormones affect neuromodulatory systems that influence the central medullary rhythm/pontine pattern generator and integrator, sensory inputs to the integrator and motor output to the respiratory muscles. In this article, we will first review the sex dependence on the prevalence of some respiratory-related diseases. Then, we will discuss the role of sex and gonadal hormones in respiratory control under resting conditions and during respiratory challenges, such as hypoxia and hypercapnia, and whether hormonal fluctuations during the estrous/menstrual cycle affect breathing control. We will then discuss the role of the locus coeruleus, a sexually dimorphic CO2/pH-chemosensitive nucleus, on breathing regulation in males and females. Next, we will highlight the studies that exist regarding sex differences in respiratory control during development. Finally, the few existing studies regarding the influence of sex on breathing control in non-mammalian vertebrates will be discussed.
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Lin YS, Wang HY, Huang DF, Hsieh PF, Lin MY, Chou CH, Wu IJ, Huang GJ, Gau SSF, Huang HS. Neuronal Splicing Regulator RBFOX3 (NeuN) Regulates Adult Hippocampal Neurogenesis and Synaptogenesis. PLoS One 2016; 11:e0164164. [PMID: 27701470 PMCID: PMC5049801 DOI: 10.1371/journal.pone.0164164] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/20/2016] [Indexed: 11/18/2022] Open
Abstract
Dysfunction of RBFOX3 has been identified in neurodevelopmental disorders such as autism spectrum disorder, cognitive impairments and epilepsy and a causal relationship with these diseases has been previously demonstrated with Rbfox3 homozygous knockout mice. Despite the importance of RBFOX3 during neurodevelopment, the function of RBFOX3 regarding neurogenesis and synaptogenesis remains unclear. To address this critical question, we profiled the developmental expression pattern of Rbfox3 in the brain of wild-type mice and analyzed brain volume, disease-relevant behaviors, neurogenesis, synaptic plasticity, and synaptogenesis in Rbfox3 homozygous knockout mice and their corresponding wild-type counterparts. Here we report that expression of Rbfox3 differs developmentally for distinct brain regions. Moreover, Rbfox3 homozygous knockout mice exhibited cold hyperalgesia and impaired cognitive abilities. Focusing on hippocampal phenotypes, we found Rbfox3 homozygous knockout mice displayed deficits in neurogenesis, which was correlated with cognitive impairments. Furthermore, RBFOX3 regulates the exons of genes with synapse-related function. Synaptic plasticity and density, which are related to cognitive behaviors, were altered in the hippocampal dentate gyrus of Rbfox3 homozygous knockout mice; synaptic plasticity decreased and the density of synapses increased. Taken together, our results demonstrate the important role of RBFOX3 during neural development and maturation. In addition, abnormalities in synaptic structure and function occur in Rbfox3 homozygous knockout mice. Our findings may offer mechanistic explanations for human brain diseases associated with dysfunctional RBFOX3.
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Affiliation(s)
- Yi-Sian Lin
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Han-Ying Wang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - De-Fong Huang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Pei-Fen Hsieh
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Meng-Ying Lin
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chih-Hsuan Chou
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - I-Ju Wu
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Guo-Jen Huang
- Department of Biomedical Sciences, Chang Gung University, Tao-Yuan, Taiwan
| | - Susan Shur-Fen Gau
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Psychiatry, College of Medicine, National Taiwan University, Taipei, Taiwan
- Clinical Center for Neuroscience and Behavior, National Taiwan University Hospital, Taipei, Taiwan
- Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan
| | - Hsien-Sung Huang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
- Clinical Center for Neuroscience and Behavior, National Taiwan University Hospital, Taipei, Taiwan
- Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan
- Ph.D. Program in Translational Medicine, National Taiwan University and Academia Sinica, Taipei, Taiwan
- Neurodevelopment Club in Taiwan, Taipei, Taiwan
- * E-mail:
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Fu Y, Rusznák Z, Herculano-Houzel S, Watson C, Paxinos G. Cellular composition characterizing postnatal development and maturation of the mouse brain and spinal cord. Brain Struct Funct 2012; 218:1337-54. [PMID: 23052551 DOI: 10.1007/s00429-012-0462-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Accepted: 09/24/2012] [Indexed: 12/18/2022]
Abstract
The process of development, maturation, and regression in the central nervous system (CNS) are genetically programmed and influenced by environment. Hitherto, most research efforts have focused on either the early development of the CNS or the late changes associated with aging, whereas an important period corresponding to adolescence has been overlooked. In this study, we searched for age-dependent changes in the number of cells that compose the CNS (divided into isocortex, hippocampus, olfactory bulb, cerebellum, 'rest of the brain', and spinal cord) and the pituitary gland in 4-40-week-old C57BL6 mice, using the isotropic fractionator method in combination with neuronal nuclear protein as a marker for neuronal cells. We found that all CNS structures, except for the isocortex, increased in mass in the period of 4-15 weeks. Over the same period, the absolute number of neurons significantly increased in the olfactory bulb and cerebellum while non-neuronal cell numbers increased in the 'rest of the brain' and isocortex. Along with the gain in body length and weight, the pituitary gland also increased in mass and cell number, the latter correlating well with changes of the brain and spinal cord mass. The majority of the age-dependent alterations (e.g., somatic parameters, relative brain mass, number of pituitary cells, and cellular composition of the cerebellum, isocortex, rest of the brain, and spinal cord) occur rapidly between the 4th and 11th postnatal weeks. This period includes murine adolescence, underscoring the significance of this stage in the postnatal development of the mouse CNS.
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Affiliation(s)
- YuHong Fu
- Neuroscience Research Australia, Sydney, NSW 2031, Australia
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Marom L, Ulitsky I, Cabilly Y, Shamir R, Elroy-Stein O. A point mutation in translation initiation factor eIF2B leads to function--and time-specific changes in brain gene expression. PLoS One 2011; 6:e26992. [PMID: 22073122 PMCID: PMC3205039 DOI: 10.1371/journal.pone.0026992] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 10/07/2011] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Mutations in eukaryotic translation initiation factor 2B (eIF2B) cause Childhood Ataxia with CNS Hypomyelination (CACH), also known as Vanishing White Matter disease (VWM), which is associated with a clinical pathology of brain myelin loss upon physiological stress. eIF2B is the guanine nucleotide exchange factor (GEF) of eIF2, which delivers the initiator tRNA(Met) to the ribosome. We recently reported that a R132H mutation in the catalytic subunit of this GEF, causing a 20% reduction in its activity, leads under normal conditions to delayed brain development in a mouse model for CACH/VWM. To further explore the effect of the mutation on global gene expression in the brain, we conducted a wide-scale transcriptome analysis of the first three critical postnatal weeks. METHODOLOGY/PRINCIPAL FINDINGS Genome-wide mRNA expression of wild-type and mutant mice was profiled at postnatal (P) days 1, 18 and 21 to reflect the early proliferative stage prior to white matter establishment (P1) and the peak of oligodendrocye differentiation and myelin synthesis (P18 and P21). At each developmental stage, between 441 and 818 genes were differentially expressed in the mutant brain with minimal overlap, generating unique time point-specific gene expression signatures. CONCLUSIONS The current study demonstrates that a point mutation in eIF2B, a key translation initiation factor, has a massive effect on global gene expression in the brain. The overall changes in expression patterns reflect multiple layers of indirect effects that accumulate as the brain develops and matures. The differentially expressed genes seem to reflect delayed waves of gene expression as well as an adaptation process to cope with hypersensitivity to cellular stress.
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Affiliation(s)
- Liraz Marom
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Igor Ulitsky
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Yuval Cabilly
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Orna Elroy-Stein
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
- Interdisciplinary School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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Otsuka N, Tsuritani K, Sakurai T, Kato K, Matoba R, Itoh J, Okuyama S, Yamada K, Yoneda Y. Transcriptional induction and translational inhibition of Arc and Cugbp2 in mice hippocampus after transient global ischemia under normothermic condition. Brain Res 2009; 1287:136-45. [PMID: 19559013 DOI: 10.1016/j.brainres.2009.06.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Revised: 06/12/2009] [Accepted: 06/16/2009] [Indexed: 11/30/2022]
Abstract
Mild hypothermia protects against neuronal damage after transient global ischemia in experimental animals. The exact mechanism of this protective effect remains to be elucidated. The purpose of the present study was to investigate the molecular mechanisms relevant to different neurologic responses to hypothermia and normothermia. Transient global ischemia was induced in C57BL/6 mice by bilateral common carotid artery occlusion for 10 min. Hypothermia provided robust neuroprotection in the hippocampus region and dramatically reduced the mortality rate. Using adaptor-tagged competitive polymerase chain reaction, we obtained the relative transcription levels of 1210 genes in the hippocampal region and compared the expression patterns of these genes. Two genes, Activity-regulated cytoskeleton-associated protein (Arc) and CUG-binding protein-2 (Cugbp2), showed remarkable and persistent increases in their expression levels in normothermic mice, compared with in both sham and hypothermic mice. Despite the increased transcription of Arc and Cugbp2, an immunohistochemistry analysis did not show comparable increases in the translations of both genes. Only a transient increase in Arc protein was observed in the granule cells of the dentate gyrus at 6 h after reperfusion. A remarkable decrease in Cugbp2 protein was observed in the pyramidal cells of the hippocampal CA1-CA3, in accordance with the progress of neuronal degeneration. A decrease in Cugbp2 protein was not observed in hypothermic mice. These results suggest that transient global ischemia induces the translational inhibition of genes with increased expression not in hypothermic, but in normothermic mice. Thus, translational inhibition might play an important role in the progress of neuronal injury after transient global ischemia.
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Affiliation(s)
- Noboru Otsuka
- Laboratory of Molecular Pharmacology, Division of Pharmaceutical Sciences, Kanazawa University Graduate School of Natural Science and Technology, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan.
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Saito S, Honma K, Kita-Matsuo H, Ochiya T, Kato K. Gene expression profiling of cerebellar development with high-throughput functional analysis. Physiol Genomics 2005; 22:8-13. [PMID: 15797969 DOI: 10.1152/physiolgenomics.00142.2004] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We measured the expression levels of 450 genes during mouse postnatal cerebellar development by quantitative PCR using RNA purified from layers of the cerebellar cortex. Principal component analysis of the data matrix demonstrated that the first and second components corresponded to general levels of gene expression and gene expression patterns, respectively. We introduced 288 of the 450 genes into PC12 cells using a high-throughput transfection assay based on atelocollagen and determined the ability of each gene to promote neurite outgrowth or cell proliferation. Five genes induced neurite outgrowth, and seven genes enhanced proliferation. Evaluation of the functional data and gene expression patterns showed that none of these genes exhibited elevated expression at maturation, suggesting that genes characteristic of mature neurons are not likely to participate in neuronal development. These results demonstrate that functional data can facilitate interpretation of expression profiles and identification of new molecules that participate in biological processes.
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Affiliation(s)
- Sakae Saito
- Taisho Laboratory of Functional Genomics, Nara Institute of Science and Technology, and Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Tokyo, Japan
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Lim CR, Fukakusa A, Matsubara K. Gene expression profiling of mouse postnatal cerebellar development using cDNA microarrays. Gene 2004; 333:3-13. [PMID: 15177675 DOI: 10.1016/j.gene.2004.02.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2003] [Revised: 09/02/2003] [Accepted: 02/05/2004] [Indexed: 10/26/2022]
Abstract
The cerebellum serves as a model system for developmental studies of the mammalian nervous system. Classical analysis of individual genes is insufficient to address the complex regulatory circuits underlying the developmental process. In this study, the postnatal cerebellar development of mice aged 2, 4, 8, 12, 16, 21 and 42 days old was studied using a microarray spotted with 5494 cDNA clones collected from the cerebellum and the cerebrum of C57BL/6J mice. We were able to cluster the expression patterns into four groups and each was highly correlated with gene function. Housekeeping genes are in a cluster in which the expression pattern peaks at the neonatal stage, while genes related to brain function peak at the adult stage. The other two clusters, characterized by transiently upregulated or downregulated expression during days 8-16, contain genes with different functions, most notably related to cell differentiation and cell cycle progression. Based on this categorization and on motif scanning, we were able to assign hypothetical functions to functionally undetermined genes. The result indicates that expression profiling is an efficient method for generation of new hypotheses for the developmental study of the cerebellum. When combined with other studies such as pharmacology etc., data generated in this study may have application in the elucidation of genetic networks underlying developmental disorder.
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Affiliation(s)
- Chun Ren Lim
- DNA Chip Research Inc. 1-1-43 Suehirocho, Tsurumi, Yokohama 230-0045, Japan
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9
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Takahashi R, Goto S. Altered gene expression in the brain of senescence accelerated mouse SAMP8. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0531-5131(03)01606-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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10
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Tanasa D, López JA, Trousse B. Extracting Sequential Patterns for Gene Regulatory Expressions Profiles. KNOWLEDGE EXPLORATION IN LIFE SCIENCE INFORMATICS 2004. [DOI: 10.1007/978-3-540-30478-4_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Saito S, Matoba R, Kato K. Adapter-tagged competitive PCR (ATAC-PCR) – a high-throughput quantitative PCR method for microarray validation. Methods 2003; 31:326-31. [PMID: 14597317 DOI: 10.1016/s1046-2023(03)00160-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Adapter-tagged competitive PCR (ATAC-PCR) is an advanced version of competitive quantitative PCR that is characterized by the addition of unique adapters to cDNA derived from each sample RNA. Using multiple adapters, we can accurately measure the relative expression ratios of many samples, with a calibration curve obtained from internal standards included in the same reaction. ATAC-PCR can identify differences in gene expression as small as twofold, even from very small amounts of sample RNA. This technique is suitable for confirming results obtained with cDNA microarrays or differential display, and it can process more than a thousand of genes per day when used in conjunction with a capillary DNA sequencer.
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Affiliation(s)
- Sakae Saito
- Taisho Laboratory of Functional Genomics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0101 Nara, Japan
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Abstract
Adaptor-tagged competitive PCR (ATAC-PCR) is an advanced form of quantitative competitive PCR, and enables high-throughput analysis of gene expression. We applied this technique to the postnatal cerebellar development. Data analysis with terms representing reported functions revealed a correlation between gene expression and functions. We also analyzed the cell death induced by extended polyglutamine, a model of a neurodegenerative disorder. We identified genes with expression patterns specific to the cell death, and evaluated their functions by in vitro transfection experiments.
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Affiliation(s)
- Kikuya Kato
- Taisho Lab of Functional Genomics, Graduate School of Biological Sciences, Nara Institute of Science & Technology, Takayama, Ikoma, Nara, Japan.
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13
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Enomoto K, Enomoto Y, Ishii Y, Araie M, Kanda T. Genes up- or down-regulated by expression of keratinocyte-specific POU transcription factor hSkn-1a. Biochem Biophys Res Commun 2003; 303:580-5. [PMID: 12659859 DOI: 10.1016/s0006-291x(03)00395-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The keratinocyte-specific POU transcription factor hSkn-1a is believed to trigger and regulate the differentiation of keratinocytes. To find genes regulated by hSkn-1a, we compared mRNAs in a HeLa clone (HeLa/hSkn-1a) that contains an inducible hSkn-1a gene between before and after the induction. RNA was screened for binding to DNA microarrays and candidate RNAs were further examined by two PCR methods. Quantitative RT-PCR showed that hSkn-1a up-regulated Cx43 and ARHH genes, besides the two genes of differentiation markers K10 and TG1, and down-regulated Mx2 and RALGDS genes in the HeLa cells. To know whether this finding is applicable to keratinocyte differentiation, we examined in human primary keratinocyte cultures the mRNAs for those six genes, along with the hSkn-1a gene, before and after the cells achieved confluence. Quantitative RT-PCR showed that in the differentiating confluent cells mRNAs increased for hSkn-1a, K10, TG1, Cx43, ARHH, and RALGDS, but decreased for Mx2. Thus, it appears that in keratinocyte differentiation Cx43, ARHH, and RALGDS genes were newly identified as up-regulated by hSkn-1a and Mx2 gene, as down-regulated. To study how hSkn-1a regulates those genes we cloned and sequenced putative transcriptional control regions for Cx43, ARHH, and Mx2 genes, in which several hSkn-1a-binding sequences were located. Expression of the luciferase gene from the isolated ARHH promoter was enhanced by the induction of hSkn-1a in HeLa/hSkn-1a and deletion or substitution mutation of the hSkn-1a-binding sequences reduced the expression, suggesting that hSkn-1a activates ARHH gene by binding to its promoter.
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Affiliation(s)
- Kikuko Enomoto
- Division of Molecular Genetics, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
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Muro S, Takemasa I, Oba S, Matoba R, Ueno N, Maruyama C, Yamashita R, Sekimoto M, Yamamoto H, Nakamori S, Monden M, Ishii S, Kato K. Identification of expressed genes linked to malignancy of human colorectal carcinoma by parametric clustering of quantitative expression data. Genome Biol 2003; 4:R21. [PMID: 12620106 PMCID: PMC153461 DOI: 10.1186/gb-2003-4-3-r21] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2002] [Revised: 12/10/2002] [Accepted: 01/14/2003] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Individual human carcinomas have distinct biological and clinical properties: gene-expression profiling is expected to unveil the underlying molecular features. Particular interest has been focused on potential diagnostic and therapeutic applications. Solid tumors, such as colorectal carcinoma, present additional obstacles for experimental and data analysis. RESULTS We analyzed the expression levels of 1,536 genes in 100 colorectal cancer and 11 normal tissues using adaptor-tagged competitive PCR, a high-throughput reverse transcription-PCR technique. A parametric clustering method using the Gaussian mixture model and the Bayes inference revealed three groups of expressed genes. Two contained large numbers of genes. One of these groups correlated well with both the differences between tumor and normal tissues and the presence or absence of distant metastasis, whereas the other correlated only with the tumor/normal difference. The third group comprised a small number of genes. Approximately half showed an identical expression pattern, and cancer tissues were classified into two groups by their expression levels. The high-expression group had strong correlation with distant metastasis, and a poorer survival rate than the low-expression group, indicating possible clinical applications of these genes. In addition to c-yes, a homolog of a viral oncogene, prognostic indicators included genes specific to glial cells, which gives a new link between malignancy and ectopic gene expression. CONCLUSIONS The malignancy of human colorectal carcinoma is correlated with a unique expression pattern of a specific group of genes, allowing the classification of tumor tissues into two clinically distinct groups.
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Affiliation(s)
- Shizuko Muro
- Taisho Laboratory of Functional Genomics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan
| | - Ichiro Takemasa
- Department of Surgery and Clinical Oncology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shigeyuki Oba
- Laboratory of Theoretical Life Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan
| | - Ryo Matoba
- Taisho Laboratory of Functional Genomics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan
| | - Noriko Ueno
- Taisho Laboratory of Functional Genomics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan
| | - Chiyuri Maruyama
- Taisho Laboratory of Functional Genomics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan
| | - Riu Yamashita
- Taisho Laboratory of Functional Genomics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan
| | - Mitsugu Sekimoto
- Department of Surgery and Clinical Oncology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hirofumi Yamamoto
- Department of Surgery and Clinical Oncology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shoji Nakamori
- Department of Surgery and Clinical Oncology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Morito Monden
- Department of Surgery and Clinical Oncology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shin Ishii
- Laboratory of Theoretical Life Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan
| | - Kikuya Kato
- Taisho Laboratory of Functional Genomics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan
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Díaz E, Ge Y, Yang YH, Loh KC, Serafini TA, Okazaki Y, Hayashizaki Y, Speed TP, Ngai J, Scheiffele P. Molecular analysis of gene expression in the developing pontocerebellar projection system. Neuron 2002; 36:417-34. [PMID: 12408845 DOI: 10.1016/s0896-6273(02)01016-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
As an approach toward understanding the molecular mechanisms of neuronal differentiation, we utilized DNA microarrays to elucidate global patterns of gene expression during pontocerebellar development. Through this analysis, we identified groups of genes specific to neuronal precursor cells, associated with axon outgrowth, and regulated in response to contact with synaptic target cells. In the cerebellum, we identified a phase of granule cell differentiation that is independent of interactions with other cerebellar cell types. Analysis of pontine gene expression revealed that distinct programs of gene expression, correlated with axon outgrowth and synapse formation, can be decoupled and are likely influenced by different cells in the cerebellar target environment. Our approach provides insight into the genetic programs underlying the differentiation of specific cell types in the pontocerebellar projection system.
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Affiliation(s)
- Elva Díaz
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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Zhang Y, Mei P, Lou R, Zhang MQ, Wu G, Qiang B, Zhang Z, Shen Y. Gene expression profiling in developing human hippocampus. J Neurosci Res 2002; 70:200-8. [PMID: 12271469 DOI: 10.1002/jnr.10322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The gene expression profile of developing human hippocampus is of particular interest and importance to neurobiologists devoted to development of the human brain and related diseases. To gain further molecular insight into the developmental and functional characteristics, we analyzed the expression profile of active genes in developing human hippocampus. Expressed sequence tags (ESTs) were selected by sequencing randomly selected clones from an original 3'-directed cDNA library of 150-day human fetal hippocampus, and a digital expression profile of 946 known genes that could be divided into 16 categories was generated. We also used for comparison 14 other expression profiles of related human neural cells/tissues, including human adult hippocampus. To yield more confidence regarding differential expression, a method was applied to attach normalized expression data to genes with a low false-positive rate (<0.05). Finally, hierarchical cluster analysis was used to exhibit related gene expression patterns. Our results are in accordance with anatomical and physiological observations made during the developmental process of the human hippocampus. Furthermore, some novel findings appeared to be unique to our results. The abundant expression of genes for cell surface components and disease-related genes drew our attention. Twenty-four genes are significantly different from adult, and 13 genes might be developing hippocampus-specific candidate genes, including wnt2b and some Alzheimer's disease-related genes. Our results could provide useful information on the ontogeny, development, and function of cells in the human hippocampus at the molecular level and underscore the utility of large-scale, parallel gene expression analyses in the study of complex biological phenomena.
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Affiliation(s)
- Yan Zhang
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
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Saito S, Matoba R, Ueno N, Matsubara K, Kato K. Comparison of gene expression profiling during postnatal development of mouse dentate gyrus and cerebellum. Physiol Genomics 2002; 8:131-7. [PMID: 11875191 DOI: 10.1152/physiolgenomics.00077.2001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Both the dentate gyrus of the hippocampus and the cerebellar cortex consist mainly of granule cells and develop postnatally. The granule cells in both tissues are presumed to be similar. Changes in gene expression were analyzed during the postnatal development of the dentate gyrus. Altogether, expression patterns of 1,937 genes were determined by adaptor-tagged competitive PCR. More than 90% of the genes belong to groups characterized by elevated expression either at earlier or later stages of development. A majority of the genes expressed showed marked changes during the developmental process, but there was little correlation between gene function and expression, unlike that observed during mouse postnatal cerebellar development. Despite anatomical and physiological similarities between these two processes, the gene expression profiles are completely different.
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Affiliation(s)
- Sakae Saito
- Taisho Laboratory of Functional Genomics, Nara Institute of Science and Technology, Ikoma, Nara, 630-0101, Japan
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Kagami Y, Furuichi T. Investigation of differentially expressed genes during the development of mouse cerebellum. Gene Expr Patterns 2001; 1:39-59. [PMID: 15018818 DOI: 10.1016/s1567-133x(01)00007-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2001] [Indexed: 11/30/2022]
Abstract
Before the discovery of DNA microarray and DNA chip technology, the expression of only a small number of genes could be analyzed at a time. Currently, such technology allows us the simultaneous analysis of a large number of genes to systematically monitor their expression patterns that may be associated with various biological phenomena. We utilized the Affymetrix GeneChip Mu11K to analyze the gene expression profile in developing mouse cerebellum to assist in the understanding of the genetic basis of cerebellar development in mice. Our analysis showed 81.6% (10,321/12,654) of the genes represented on the GeneChip were expressed in the postnatal cerebellum, and among those, 8.7% (897/10,321) were differentially expressed with more than a two-fold change in their maximum and minimum expression levels during the developmental time course. Further analysis of the differentially expressed genes that were clustered in terms of their expression patterns and the function of their encoded products revealed an aspect of the genetic foundation that lies beneath the cellular events and neural network formation that takes place during the development of the mouse cerebellum.
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Affiliation(s)
- Y Kagami
- Laboratory for Molecular Neurogenesis, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
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