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El-Shaikh A, Welzel M, Heider D, Seeger B. High-scale random access on DNA storage systems. NAR Genom Bioinform 2022; 4:lqab126. [PMID: 35156022 PMCID: PMC8829907 DOI: 10.1093/nargab/lqab126] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/02/2021] [Accepted: 12/22/2021] [Indexed: 12/12/2022] Open
Abstract
Due to the rapid cost decline of synthesizing and sequencing deoxyribonucleic acid (DNA), high information density, and its durability of up to centuries, utilizing DNA as an information storage medium has received the attention of many scientists. State-of-the-art DNA storage systems exploit the high capacity of DNA and enable random access (predominantly random reads) by primers, which serve as unique identifiers for directly accessing data. However, primers come with a significant limitation regarding the maximum available number per DNA library. The number of different primers within a library is typically very small (e.g. ≈10). We propose a method to overcome this deficiency and present a general-purpose technique for addressing and directly accessing thousands to potentially millions of different data objects within the same DNA pool. Our approach utilizes a fountain code, sophisticated probe design, and microarray technologies. A key component is locality-sensitive hashing, making checks for dissimilarity among such a large number of probes and data objects feasible.
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Affiliation(s)
- Alex El-Shaikh
- To whom correspondence should be addressed. Tel: +49 6421 28 21578;
| | - Marius Welzel
- Department of Computer Science, University of Marburg, Marburg 35037, Germany
| | - Dominik Heider
- Department of Computer Science, University of Marburg, Marburg 35037, Germany
| | - Bernhard Seeger
- Department of Computer Science, University of Marburg, Marburg 35037, Germany
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Identification of Key Genes in Gastric Cancer by Bioinformatics Analysis. BIOMED RESEARCH INTERNATIONAL 2020; 2020:7658230. [PMID: 33015179 PMCID: PMC7525308 DOI: 10.1155/2020/7658230] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/12/2020] [Accepted: 09/01/2020] [Indexed: 12/22/2022]
Abstract
Gastric cancer (GC) is one of the most common malignancies of the digestive system with few genetic markers for its early detection and prevention. In this study, differentially expressed genes (DEGs) were analyzed using GEO2R from GSE54129 and GSE13911 of the Gene Expression Omnibus (GEO). Then, gene enrichment analysis, protein-protein interaction (PPI) network construction, and topological analysis were performed on the DEGs by the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, STRING, and Cytoscape. Finally, we performed survival analysis of key genes through the Kaplan-Meier plotter. A total of 1034 DEGs were identified in GC. GO and KEGG results showed that DEGs mainly enriched in plasma membrane, cell adhesion, and PI3K-Akt signaling pathway. Subsequently, the PPI network with 44 nodes and 333 edges was constructed, and 18 candidate genes in the network were focused on by centrality analysis and module analysis. Furthermore, data showed that high expressions of fibronectin 1(FN1), the tissue inhibitor of metalloproteinases 1 (TIMP1), secreted phosphoprotein 1 (SPP1), apolipoprotein E (APOE), and versican (VCAN) were related to poor overall survivals in GC patients. In summary, this study suggests that FN1, TIMP1, SPP1, APOE, and VCAN may act as the key genes in GC.
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Kobayashi N, Sato M, Fukuhara S, Yokoi S, Kurihara T, Watari J, Yokoi T, Ohta M, Kaku Y, Saito T. Application of Shotgun DNA Microarray Technology to Gene Expression Analysis in Lager Yeast. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2007-0319-02] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Naoyuki Kobayashi
- Frontier Laboratories of Value Creation, Sapporo Breweries Ltd., Shizuoka, Japan
| | - Masahide Sato
- Frontier Laboratories of Value Creation, Sapporo Breweries Ltd., Shizuoka, Japan
| | - Syunsuke Fukuhara
- Frontier Laboratories of Value Creation, Sapporo Breweries Ltd., Shizuoka, Japan
| | - Shigehisa Yokoi
- Frontier Laboratories of Value Creation, Sapporo Breweries Ltd., Shizuoka, Japan
| | - Toshio Kurihara
- Frontier Laboratories of Value Creation, Sapporo Breweries Ltd., Shizuoka, Japan
| | - Junji Watari
- Frontier Laboratories of Value Creation, Sapporo Breweries Ltd., Shizuoka, Japan
| | | | | | - Yoshiko Kaku
- Life Science Group, Hitachi, Ltd., Kawagoe, Japan
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Age-related changes in the transcriptome of antibody-secreting cells. Oncotarget 2017; 7:13340-53. [PMID: 26967249 PMCID: PMC4924646 DOI: 10.18632/oncotarget.7958] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/28/2016] [Indexed: 12/18/2022] Open
Abstract
We analyzed age-related defects in B cell populations from young and aged mice. Microarray analysis of bone marrow resident antibody secreting cells (ASCs) showed significant changes upon aging, affecting multiple genes, pathways and functions including those that play a role in immune regulation, humoral immune responses, chromatin structure and assembly, cell metabolism and the endoplasmic reticulum (ER) stress response. Further analysis showed upon aging defects in energy production through glucose catabolism with reduced oxidative phosphorylation. In addition aged B cells had increased levels of reactive oxygen-species (ROS), which was linked to enhanced expression of the co-inhibitor programmed cell death (PD)-1.
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Abstract
Mining microarray data to unearth interesting expression profile patterns for discovery of in silico biological knowledge is an emerging area of research in computational biology. A group of functionally related genes may have similar expression patterns under a set of conditions or at some time points. Biclustering is an important data mining tool that has been successfully used to analyze gene expression data for biologically significant cluster discovery. The purpose of this chapter is to introduce interesting patterns that may be observed in expression data and discuss the role of biclustering techniques in detecting interesting functional gene groups with similar expression patterns.
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Papsdorf K, Sima S, Richter G, Richter K. Construction and evaluation of yeast expression networks by database-guided predictions. MICROBIAL CELL 2016; 3:236-247. [PMID: 28357360 PMCID: PMC5348991 DOI: 10.15698/mic2016.06.505] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
DNA-Microarrays are powerful tools to obtain expression data on the genome-wide
scale. We performed microarray experiments to elucidate the transcriptional
networks, which are up- or down-regulated in response to the expression of toxic
polyglutamine proteins in yeast. Such experiments initially generate hit lists
containing differentially expressed genes. To look into transcriptional
responses, we constructed networks from these genes. We therefore developed an
algorithm, which is capable of dealing with very small numbers of microarrays by
clustering the hits based on co-regulatory relationships obtained from the SPELL
database. Here, we evaluate this algorithm according to several criteria and
further develop its statistical capabilities. Initially, we define how the
number of SPELL-derived co-regulated genes and the number of input hits
influences the quality of the networks. We then show the ability of our networks
to accurately predict further differentially expressed genes. Including these
predicted genes into the networks improves the network quality and allows
quantifying the predictive strength of the networks based on a newly implemented
scoring method. We find that this approach is useful for our own experimental
data sets and also for many other data sets which we tested from the SPELL
microarray database. Furthermore, the clusters obtained by the described
algorithm greatly improve the assignment to biological processes and
transcription factors for the individual clusters. Thus, the described
clustering approach, which will be available through the ClusterEx web
interface, and the evaluation parameters derived from it represent valuable
tools for the fast and informative analysis of yeast microarray data.
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Affiliation(s)
- Katharina Papsdorf
- Center of integrated protein science at the Technische Universität München, Department Chemie, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Siyuan Sima
- Center of integrated protein science at the Technische Universität München, Department Chemie, Lichtenbergstr. 4, 85748 Garching, Germany
| | | | - Klaus Richter
- Center of integrated protein science at the Technische Universität München, Department Chemie, Lichtenbergstr. 4, 85748 Garching, Germany
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Hui RK, Leung FC. Differential Expression Profile of Chicken Embryo Fibroblast DF-1 Cells Infected with Cell-Adapted Infectious Bursal Disease Virus. PLoS One 2015; 10:e0111771. [PMID: 26053856 PMCID: PMC4460012 DOI: 10.1371/journal.pone.0111771] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 10/01/2014] [Indexed: 12/17/2022] Open
Abstract
RNA-Seq was used to unveil the transcriptional profile of DF-1 cells at the early stage of caIBDV infection. Total RNAs were extracted from virus-infected cells at 0, 6 and 12 hpi. RNA-Seq datasets of respective samples mapped to 56.5–57.6% of isoforms in the reference genome Galgal4.73. At 6 hpi, 23 isoforms underwent an elevated expression, while 128 isoforms were up-regulated and 5 were down-regulated at 12 hpi in the virus-infected group. Besides, 10 isoforms were exclusively expressed in the virus-infected cells. Though no significant change was detected in cytokine and interferon expression levels at the first 12 hours of infection, modulations of the upstream regulators were observed. In addition to the reported regulatory factors including EIF2AK2, MX, OAS*A, GBP7 and IFIT, IBDV infection also triggered a IFIT5-IRF1/3-RSAD5 pathway in the DF-1 cells which potentially restricted the viral replication cycle in the early infection stage. Over-expression of LIPA and CH25H, together with the suppression of STARD4, LSS and AACS genes implied a modulation of membrane fluidity and lipid raft arrangement in the infected cells. Alternative splicing of the EFR3 homolog A gene was also through to be involved in the lipid membrane regulation, and these cumulative responses projected an inhibition of viral endocytosis. Recognition of viral RNA genomes and intermediates was presumably enhanced by the elevated levels of IFIH1, DHX58 and TRIM25 genes which possess properties on detecting viral dsRNA. On the other hand, the caIBDV arrested the host's apoptotic process by inducing the expression of apoptosis inhibitors including NFKBIA/Z, TNFAIP2/3 and ITA at the first 12 hours of infection. In conclusion, the differential expression landscape demonstrated with RNA-Seq provides a comprehensive picture on the molecular interactions between host cells and virus at the early stage of infection.
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Affiliation(s)
- Raymond K. Hui
- School of Biological Sciences, The University of Hong Kong, Hong Kong, People’s Republic of China
| | - Frederick C. Leung
- School of Biological Sciences, The University of Hong Kong, Hong Kong, People’s Republic of China
- Bioinformatics Center, Nanjing Agricultural University, Nanjing, China
- * E-mail:
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Transcriptional profiles of Haloferax mediterranei based on nitrogen availability. J Biotechnol 2014; 193:100-7. [PMID: 25435380 DOI: 10.1016/j.jbiotec.2014.11.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 11/07/2014] [Accepted: 11/19/2014] [Indexed: 11/23/2022]
Abstract
The haloarchaeon Haloferax mediterranei is able to grow in the presence of different inorganic and organic nitrogen sources by means of the assimilatory pathway under aerobic conditions. In order to identify genes of potential importance in nitrogen metabolism and its regulation in the halophilic microorganism, we have analysed its global gene expression in three culture media with different nitrogen sources: (a) cells were grown stationary and exponentially in ammonium, (b) cells were grown exponentially in nitrate, and (c) cells were shifted to nitrogen starvation conditions. The main differences in the transcriptional profiles have been identified between the cultures with ammonium as nitrogen source and the cultures with nitrate or nitrogen starvation, supporting previous results which indicate the absence of ammonium as the factor responsible for the expression of genes involved in nitrate assimilation pathway. The results have also permitted the identification of transcriptional regulators and changes in metabolic pathways related to the catabolism and anabolism of amino acids or nucleotides. The microarray data was validated by real-time quantitative PCR on 4 selected genes involved in nitrogen metabolism. This work represents the first transcriptional profiles study related to nitrogen assimilation metabolism in extreme halophilic microorganisms using microarray technology.
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Azevedo H, Fujita A, Bando SY, Iamashita P, Moreira-Filho CA. Transcriptional network analysis reveals that AT1 and AT2 angiotensin II receptors are both involved in the regulation of genes essential for glioma progression. PLoS One 2014; 9:e110934. [PMID: 25365520 PMCID: PMC4217762 DOI: 10.1371/journal.pone.0110934] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 09/26/2014] [Indexed: 01/25/2023] Open
Abstract
Gliomas are aggressive primary brain tumors with high infiltrative potential. The expression of Angiotensin II (Ang II) receptors has been associated with poor prognosis in human astrocytomas, the most common type of glioma. In this study, we investigated the role of Angiotensin II in glioma malignancy through transcriptional profiling and network analysis of cultured C6 rat glioma cells exposed to Ang II and to inhibitors of its membrane receptor subtypes. C6 cells were treated with Ang II and specific antagonists of AT1 and AT2 receptors. Total RNA was isolated after three and six hours of Ang II treatment and analyzed by oligonucleotide microarray technology. Gene expression data was evaluated through transcriptional network modeling to identify how differentially expressed (DE) genes are connected to each other. Moreover, other genes co-expressing with the DE genes were considered in these analyses in order to support the identification of enriched functions and pathways. A hub-based network analysis showed that the most connected nodes in Ang II-related networks exert functions associated with cell proliferation, migration and invasion, key aspects for glioma progression. The subsequent functional enrichment analysis of these central genes highlighted their participation in signaling pathways that are frequently deregulated in gliomas such as ErbB, MAPK and p53. Noteworthy, either AT1 or AT2 inhibitions were able to down-regulate different sets of hub genes involved in protumoral functions, suggesting that both Ang II receptors could be therapeutic targets for intervention in glioma. Taken together, our results point out multiple actions of Ang II in glioma pathogenesis and reveal the participation of both Ang II receptors in the regulation of genes relevant for glioma progression. This study is the first one to provide systems-level molecular data for better understanding the protumoral effects of Ang II in the proliferative and infiltrative behavior of gliomas.
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Affiliation(s)
- Hátylas Azevedo
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | - André Fujita
- Department of Computer Science, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Silvia Yumi Bando
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | - Priscila Iamashita
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | - Carlos Alberto Moreira-Filho
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
- * E-mail:
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Dudli S, Ferguson SJ, Haschtmann D. Severity and pattern of post-traumatic intervertebral disc degeneration depend on the type of injury. Spine J 2014; 14:1256-64. [PMID: 24583791 DOI: 10.1016/j.spinee.2013.07.488] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 02/26/2013] [Accepted: 07/30/2013] [Indexed: 02/03/2023]
Abstract
BACKGROUND CONTEXT The burst fracture of a vertebra is the result of a complex loading procedure and is often associated with intervertebral disc (IVD) degeneration. Likewise, the presumed etiologies are (i) the structural perturbation of the IVD/end plate, (ii) the impact of loading energy alone, and (iii) the depressurization of the nucleus pulposus. PURPOSE To describe the pathogenesis of post-traumatic disc degeneration (DD) by comparing the severity and patterns of degeneration with different injury models. STUDY DESIGN New data from an in vitro organ culture study are compared with the previous work on the same model system. METHODS To investigate in detail the contribution of each factor (i-iii) to DD, we extended our previous work to compare three different segmental trauma processes in a rabbit full-organ in vitro model: burst fracture (Group A, etiologies i-iii), equienergetic loading without a fracture (Group B, ii), and endplate puncturing (Group C, iii). DD markers (apoptosis, necrosis, matrix remodeling, inflammation) were monitored up to 28 days posttrauma. Gene transcription data were subjected to principal component analysis and agglomerative hierarchical clustering to identify and compare pathologic patterns. RESULTS Only Group A showed the full profile of DD: reduced glycosaminoglycan content, increased caspase-3/7 and lactate dehydrogenase (LDH) activity, and elevated messenger RNA of catabolic (matrix metalloproteinase-1, -3, -13) and proinflammatory (tumor necrosis factor-alpha, interleukin [IL]-6, IL-8, and monocyte chemotactic protein-1) genes. In Group B, only catabolic and proinflammatory genes were slightly upregulated. In Group C, LDH but not caspase-3/7 activity was increased. Catabolic and proinflammatory genes were upregulated, although less compared with Group A. Principal component analysis revealed different transcription patterns for Group C. CONCLUSIONS The structural perturbation of the end plate/IVD, but not the loading energy or nuclear depressurization, promotes DD. In addition, end-plate puncturing triggers a different pathogenesis, consistent with a more continuous matrix remodeling process.
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Affiliation(s)
- Stefan Dudli
- Institute for Biomechanics, ETH Zürich, Schafmattstrasse 30, CH-8093 Zürich, Switzerland; Institute for Biomechanics, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland.
| | - Stephen J Ferguson
- Institute for Biomechanics, ETH Zürich, Schafmattstrasse 30, CH-8093 Zürich, Switzerland
| | - Daniel Haschtmann
- Schulthess Klinik, Wirbelsäulenzentrum, Lengghalde 2, CH-8008 Zürich, Switzerland
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Woo KT, Lau YK, Choong HL, Tan HK, Foo MWY, Lee EJC, Anantharaman V, Lee GSL, Yap HK, Yi Z, Fook-Chong S, Wong KS, Chan CM. Genomics and Disease Progression in IgA Nephritis. ANNALS OF THE ACADEMY OF MEDICINE, SINGAPORE 2013. [DOI: 10.47102/annals-acadmedsg.v42n12p674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Apart from clinical, histological and biochemical indices, genomics are now being employed to unravel the pathogenetic mechanisms in the disease progression of IgA nephritis (IgAN). The results of angiotensin converting enzyme (ACE) gene polymorphism have been controversial. Those patients with the DD genotype seem to have a poorer prognosis. However, with high dose angiotensin receptor blocker (ARB) therapy, the ACE gene polymorphism status of a patient may no longer be a matter for concern as those with the DD genotype would also respond favourably to high dose ARB therapy. Association studies with gene sequencing and haplotypes have suggested that multiple genes are involved in the pathogenesis of IgAN. Some workers have reported a synergistic effect in the combined analysis of AGT-M235T and ACE I/D polymorphism. With the use of deoxyribo nucleic acid (DNA) microarray, tens of thousands of gene expressions genome-wide can be examined together simultaneously. A locus of familial IgAN has been described with strong evidence of linkage to IgAN1 on chromosome 6q22-23. Two other loci were reported at 4q26-31 and 17q12-22. DNA microarray techniques could also help in the identification of specific pathogenic genes that are up- or down-regulated and this may allow genome wide analyses of these genes and their role in the pathogenesis and progression of IgAN. Recently, using genome-wide association studies (GWAS) more loci for disease susceptibility for IgAN have been identified at 17p13, 8p23, 22q12, 1q32 and 6p21.
Key words: Gene sequencing, Haplotypes, Microarray, Single nucleotide polymorphism
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Zhao Yi
- Singapore General Hospital, Singapore
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Ding N, Zhang Y, Loughran PA, Wang Q, Billiar TR. TIFA upregulation after hypoxia-reoxygenation is TLR4- and MyD88-dependent and associated with HMGB1 upregulation and release. Free Radic Biol Med 2013; 63:361-7. [PMID: 23722163 PMCID: PMC3752398 DOI: 10.1016/j.freeradbiomed.2013.05.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 03/20/2013] [Accepted: 05/20/2013] [Indexed: 01/12/2023]
Abstract
TRAF-interacting protein with a forkhead-associated domain (TIFA) is a tumor necrosis factor receptor-associated factor 6 (TRAF6) binding protein that mediates IL-1 signaling. We recently reported that TIFA mRNA is significantly upregulated early in the liver after trauma and hemorrhagic shock. In this study, we sought to characterize the upregulation of TIFA by hypoxia-reoxygenation and investigate its role in hypoxia-induced signaling. TIFA expression was detected by qRT-PCR and Western blotting in both mouse hemorrhagic shock with resuscitation (HS-R) and hepatocytes exposed to hypoxia-reoxygenation. Involvement of TLR4 and MyD88 was assessed using cells from TLR4(-/-) and MyD88(-/-) mice. The interaction of TIFA with TRAF6 and IRAK-1 was investigated using coimmunoprecipitation in vitro. RNAi was performed to knock down the endogenous expression of the TIFA gene in hepatocytes. High-mobility-group box 1 protein (HMGB1) expression was detected by Western blotting and ELISA, and the activation of NF-κB and MAPK was measured with EMSA and Western blotting. The results showed that TIFA expression was upregulated after HS-R in vivo and hypoxia-reoxygenation in vitro. Further analysis revealed that hypoxia-reoxygenation-induced upregulation of TIFA was TLR4- and MyD88-dependent. Moreover, TIFA was found to associate with TRAF6 constitutively, whereas its association with IRAK-1 was seen only after hypoxia-reoxygenation. Suppression of TIFA by siRNA reduced NF-κB activation and HMGB1 upregulation and release after hypoxia-reoxygenation. Taken together, these data suggest that TIFA is involved in the regulation of cell signaling in hypoxia-reoxygenation. The increase in TIFA level appears to be a feed-forward mechanism involved in TLR4/MyD88-dependent signaling, leading to NF-κB activation and HMGB1 release.
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Affiliation(s)
- Ning Ding
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213
- Department of Anesthesiology, Guangzhou First People’s Hospital, Guangzhou Medical University, Guangzhou 510180, China
| | - Yong Zhang
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213
| | - Patricia A. Loughran
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213
| | - Qingde Wang
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213
| | - Timothy R. Billiar
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213
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de Sousa CS, Serrão JE, Bonetti AM, Amaral IMR, Kerr WE, Maranhão AQ, Ueira-Vieira C. Insights into the Melipona scutellaris (Hymenoptera, Apidae, Meliponini) fat body transcriptome. Genet Mol Biol 2013; 36:292-7. [PMID: 23885214 PMCID: PMC3715298 DOI: 10.1590/s1415-47572013000200022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 03/11/2013] [Indexed: 12/21/2022] Open
Abstract
The insect fat body is a multifunctional organ analogous to the vertebrate liver. The fat body is involved in the metabolism of juvenile hormone, regulation of environmental stress, production of immunity regulator-like proteins in cells and protein storage. However, very little is known about the molecular mechanisms involved in fat body physiology in stingless bees. In this study, we analyzed the transcriptome of the fat body from the stingless bee Melipona scutellaris. In silico analysis of a set of cDNA library sequences yielded 1728 expressed sequence tags (ESTs) and 997 high-quality sequences that were assembled into 29 contigs and 117 singlets. The BLAST X tool showed that 86% of the ESTs shared similarity with Apis mellifera (honeybee) genes. The M. scutellaris fat body ESTs encoded proteins with roles in numerous physiological processes, including anti-oxidation, phosphorylation, metabolism, detoxification, transmembrane transport, intracellular transport, cell proliferation, protein hydrolysis and protein synthesis. This is the first report to describe a transcriptomic analysis of specific organs of M. scutellaris. Our findings provide new insights into the physiological role of the fat body in stingless bees.
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Affiliation(s)
- Cristina Soares de Sousa
- Laboratório de Genética, Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
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Yang YT, Lin CY, Jeng J, Ong CW. Impact of pyrrolidine-bispyrrole DNA minor groove binding agents and chirality on global proteomic profile in Escherichia Coli. Proteome Sci 2013; 11:23. [PMID: 23702249 PMCID: PMC3669006 DOI: 10.1186/1477-5956-11-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 05/13/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is great interest in the design of small molecules that selectively target minor grooves of duplex DNA for controlling specific gene expression implicated in a disease. The design of chiral small molecules for rational drug design has attracted increasing attention due to the chirality of DNA. Yet, there is limited research on the chirality effect of minor groove binders on DNA interaction, especially at the protein expression level. This paper is an attempt to illustrate that DNA binding affinity might not provide a full picture on the biological activities. Drug interacting at the genomic level can be translated to the proteomic level. Here we have illustrated that although the chiral bispyrrole-pyrrolidine-oligoamides, PySSPy and PyRSPy, showed low binding affinity to DNA, their influence at the proteomic level is significant. More importantly, the chirality also plays a role. Two-dimensional proteomic profile to identify the differentially expressed protein in Escherichia coli DH5α (E coli DH5α) were investigated. RESULTS E coli DH5α incubated with the chiral PySSPy and PyRSPy, diastereomeric at the pyrrolidine ring, showed differential expression of eighteen proteins as observed through two dimensional proteomic profiling. These eighteen proteins identified by MALDI_TOF/TOF MS include antioxidant defense, DNA protection, protein synthesis, chaperone, and stress response proteins. No statistically significant toxicity was observed at the tested drug concentrations as measured via MTT assay. CONCLUSION The current results showed that the chiral PySSPy and PyRSPy impact on the proteomic profiling of E coli DH5α, implicating the importance of drug chirality on biological activities at the molecular level.
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Affiliation(s)
- Ya-Ting Yang
- Department of Chemistry, National Sun Yat-sen University, No, 70, Lienhai Rd,, Kaohsiung, 80424, Taiwan.
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Transcriptome analysis of renal ischemia/reperfusion injury and its modulation by ischemic pre-conditioning or hemin treatment. PLoS One 2012; 7:e49569. [PMID: 23166714 PMCID: PMC3498198 DOI: 10.1371/journal.pone.0049569] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 10/10/2012] [Indexed: 01/06/2023] Open
Abstract
Ischemia/reperfusion injury (IRI) is a leading cause of acute renal failure. The definition of the molecular mechanisms involved in renal IRI and counter protection promoted by ischemic pre-conditioning (IPC) or Hemin treatment is an important milestone that needs to be accomplished in this research area. We examined, through an oligonucleotide microarray protocol, the renal differential transcriptome profiles of mice submitted to IRI, IPC and Hemin treatment. After identifying the profiles of differentially expressed genes observed for each comparison, we carried out functional enrichment analysis to reveal transcripts putatively involved in potential relevant biological processes and signaling pathways. The most relevant processes found in these comparisons were stress, apoptosis, cell differentiation, angiogenesis, focal adhesion, ECM-receptor interaction, ion transport, angiogenesis, mitosis and cell cycle, inflammatory response, olfactory transduction and regulation of actin cytoskeleton. In addition, the most important overrepresented pathways were MAPK, ErbB, JAK/STAT, Toll and Nod like receptors, Angiotensin II, Arachidonic acid metabolism, Wnt and coagulation cascade. Also, new insights were gained about the underlying protection mechanisms against renal IRI promoted by IPC and Hemin treatment. Venn diagram analysis allowed us to uncover common and exclusively differentially expressed genes between these two protective maneuvers, underscoring potential common and exclusive biological functions regulated in each case. In summary, IPC exclusively regulated the expression of genes belonging to stress, protein modification and apoptosis, highlighting the role of IPC in controlling exacerbated stress response. Treatment with the Hmox1 inducer Hemin, in turn, exclusively regulated the expression of genes associated with cell differentiation, metabolic pathways, cell cycle, mitosis, development, regulation of actin cytoskeleton and arachidonic acid metabolism, suggesting a pleiotropic effect for Hemin. These findings improve the biological understanding of how the kidney behaves after IRI. They also illustrate some possible underlying molecular mechanisms involved in kidney protection observed with IPC or Hemin treatment maneuvers.
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Pandey B, Tan YH, Fujikawa K, Demchenko AV, Stine KJ. Comparative Study of the Binding of Concanavalin A to Self-Assembled Monolayers Containing a Thiolated α-Mannoside on Flat Gold and on Nanoporous Gold. J Carbohydr Chem 2012; 31:466-503. [PMID: 23519474 PMCID: PMC3601678 DOI: 10.1080/07328303.2012.683909] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We have prepared SAMs containing 8-mercaptooctyl α-D-mannopyranoside, either as a single component or in mixed SAMs with n-octanethiol on flat gold surfaces and on nanoporous gold. Electrochemical impedance spectroscopy showed that the mixed SAMs on flat gold surfaces showed the highest Con A binding near 1:9 solution molar ratio of thiolatedα-mannoside to n-octanethiol whereas those on NPG showed the highest response at 1:19 solution molar ratio of thiolated α-mannoside to n-octanethiol. Atomic force microscopy was employed to image the monolayers, and also to image the bound Con A protein.
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Affiliation(s)
- Binod Pandey
- Department of Chemistry and Biochemistry, University of Missouri - Saint Louis, Saint Louis, MO 63121, USA ; Center for Nanoscience, University of Missouri - Saint Louis, Saint Louis, MO 63121, USA
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Edmonds RD, Vodovotz Y, Lagoa C, Dutta-Moscato J, Yang Y, Fink MP, Levy RM, Prince JM, Kaczorowski DJ, Tseng GC, Billiar TR. Transcriptomic response of murine liver to severe injury and hemorrhagic shock: a dual-platform microarray analysis. Physiol Genomics 2011; 43:1170-83. [PMID: 21828244 DOI: 10.1152/physiolgenomics.00020.2011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Trauma-hemorrhagic shock (HS/T) is a complex process that elicits numerous molecular pathways. We hypothesized that a dual-platform microarray analysis of the liver, an organ that integrates immunology and metabolism, would reveal key pathways engaged following HS/T. C57BL/6 mice were divided into five groups (n = 4/group), anesthetized, and surgically treated to simulate a time course and trauma severity model: 1) nonmanipulated animals, 2) minor trauma, 3) 1.5 h of hemorrhagic shock and severe trauma (HS/T), 4) 1.5 h HS/T followed by 1 h resuscitation (HS/T+1.0R), 5) 1.5 h HS/T followed by 4.5 h resuscitation (HS/T+4.5R). Liver RNA was hybridized to CodeLink and Affymetrix mouse whole genome microarray chips. Common genes with a cross-platform correlation >0.6 (2,353 genes in total) were clustered using k-means clustering, and clusters were analyzed using Ingenuity Pathways Analysis. Genes involved in the stress response and immunoregulation were upregulated early and remained upregulated throughout the course of the experiment. Genes involved in cell death and inflammatory pathways were upregulated in a linear fashion with elapsed time and in severe injury compared with minor trauma. Three of the six clusters contained genes involved in metabolic function; these were downregulated with elapsed time. Transcripts involved in amino acid metabolism as well as signaling pathways associated with glucocorticoid receptors, IL-6, IL-10, and the acute phase response were elevated in a severity-dependent manner. This is the first study to examine the postinjury response using dual-platform microarray analysis, revealing responses that may enable novel therapies or diagnostics.
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Affiliation(s)
- Rebecca D Edmonds
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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Blankenburg M, Haberland L, Elvers HD, Tannert C, Jandrig B. High-Throughput Omics Technologies: Potential Tools for the Investigation of Influences of EMF on Biological Systems. Curr Genomics 2011; 10:86-92. [PMID: 19794880 PMCID: PMC2699823 DOI: 10.2174/138920209787847050] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Revised: 01/17/2009] [Accepted: 01/30/2009] [Indexed: 01/29/2023] Open
Abstract
The mode of action of a huge amount of agents on biological systems is still unknown. One example where more questions than answers exist is covered by the term electromagnetic fields (EMF). Use of wireless communication, e.g. mobile phones, has been escalated in the last few years. Due to this fact, a lot of discussions dealt with health consequences of EMF emitted by these devices and led to an increased investigation of their effects to biological systems, mainly by using traditional methods. Omics technologies have the advantage to contain methods for investigations on DNA-, RNA- and protein level as well as changes in the metabolism.This literature survey is an overview of the available scientific publications regarding biological and health effects of EMF and the application of new high-throughput technologies. The aim of the study was to analyse the amount and the distribution of these technologies and to evaluate their relevance to the risk analysis of EMF. At present, only transcriptomics is able to analyse almost all of the specific molecules. In comparison to ionising radiation, fewer articles dealt with health effects of EMF. Interestingly, most of the EMF articles came from European institutions.Although omics techniques allow exact and simultaneous examinations of thousands of genes, proteins and metabolites in high-throughput technologies, it will be an absolute prerequisite to use standardised protocols and to independently validate the results for comparability and eventually for sound standing statements concerning possible effects of agents like EMF on biological systems.
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Affiliation(s)
- M Blankenburg
- Department of Bioethics & Science Communication, Max-Delbrück-Center for Molecular Medicine Berlin-Buch, 13092 Berlin, Germany
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Dozmorov IM, Jarvis J, Saban R, Benbrook DM, Wakeland E, Aksentijevich I, Ryan J, Chiorazzi N, Guthridge JM, Drewe E, Tighe PJ, Centola M, Lefkovits I. Internal standard-based analysis of microarray data2--analysis of functional associations between HVE-genes. Nucleic Acids Res 2011; 39:7881-99. [PMID: 21715372 PMCID: PMC3185418 DOI: 10.1093/nar/gkr503] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
In this work we apply the Internal Standard-based analytical approach that we described in an earlier communication and here we demonstrate experimental results on functional associations among the hypervariably-expressed genes (HVE-genes). Our working assumption was that those genetic components, which initiate the disease, involve HVE-genes for which the level of expression is undistinguishable among healthy individuals and individuals with pathology. We show that analysis of the functional associations of the HVE-genes is indeed suitable to revealing disease-specific differences. We show also that another possible exploit of HVE-genes for characterization of pathological alterations is by using multivariate classification methods. This in turn offers important clues on naturally occurring dynamic processes in the organism and is further used for dynamic discrimination of groups of compared samples. We conclude that our approach can uncover principally new collective differences that cannot be discerned by individual gene analysis.
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Affiliation(s)
- Igor M Dozmorov
- Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
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Woo KT, Lau YK, Zhao Y, Puong KY, Tan HB, Fook-Chong S, Wong KS, Chan CM. Urotensin 2 and Retinoic Acid Receptor Alpha (RARA) Gene Expression in IgA Nephropathy. ANNALS OF THE ACADEMY OF MEDICINE, SINGAPORE 2010. [DOI: 10.47102/annals-acadmedsg.v39n9p705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Introduction: IgA nephropathy is a disease where the pathogenesis is still poorly understood. Deoxyribonucleic acid (DNA) microarray technique allows tens of thousands of gene expressions to be examined at the same time. Commercial availability of microarray genechips has made this powerful tool accessible for wider utilisation in the study of diseases. Materials and Methods: Seven patients with IgA nephropathy, 6 with minimal change nephrotic syndrome (MCNS) as patient controls and 7 normal healthy subjects were screened for the differential expression of genes, genome-wide. The Human Genome U133 Plus 2.0 Arrays (Affymetrix, USA) were used to quantitate the differential expression of 38,500 well-characterised human genes. Results: A total of 7761 gene expressions were identified that have an IgAN/Normal gene expression ratio of 0.06-fold to 5.58-fold. About 35% of the altered gene expressions have no gene title or just a hypothetical protein label such as FLJ30679. Most of the remaining 65% are identified proteins where their importance to IgAN is not immediately apparent at this time. Among the 30 most upregulated and 30 most downregulated genes are Urotensin 2 (upregulated 3.09-fold, P <0.05) and Fatty-acid binding protein 6 (downregulated to 0.12-fold, P <0.05). Retinoic acid receptor alpha (vitamin A receptor) was also found downregulated to 0.41-fold (P <0.005). Taqman real-time polymerase chain reaction (PCR) for urotensin 2 and retinoic acid receptor alpha (RARA) were performed on 20 patients with IgA nephropathy and 11 with Minimal Change Disease and the data correlated with various clinical indices. Conclusions: The findings suggest that there may be a therapeutic role for retinoic acid receptor alpha (RARA) in IgA nephropathy and a clinical monitoring role for Urotensin 2 in Minimal Change Disease.
Keywords: DNA microarray technology, Genome-wide gene expression
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Affiliation(s)
| | | | - Yi Zhao
- Singapore General Hospital, Singapore
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Varlet-Marie E, Audran M, Ashenden M, Sicart MT, Piquemal D. Modification of gene expression: help to detect doping with erythropoiesis-stimulating agents. Am J Hematol 2009; 84:755-9. [PMID: 19802893 DOI: 10.1002/ajh.21525] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Microarray technology in the study of genetic determinants of cardiovascular diseases. Open Med (Wars) 2009. [DOI: 10.2478/s11536-009-0012-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractMicroarray, a miniaturized glass slide or membrane with immobilized DNA probes, is a powerful tool for the analysis of mutations, gene expression and sequencing. This technique requires chip (glass slide or membrane) fabrication, preparation of probes and labelled targets, hybridization and data analysis. Microarrays give the possibility to evaluate a wide spectrum of candidate genes, to simultaneously observe interaction of genes, to detect polymorphisms within genes and identify therapeutic targets. Coronary artery disease being a major cause of death, is a disorder influenced by either genetic or environmental factors. Microarray analysis of gene expression can be used to identify genes involved in disease progression and in disease reduction. Chips also allow for the throughput and simultaneous analysis of a great variety of cell types such as cardiomyocytes, monocytes, macrophages, smooth muscle, endothelial, and fibroblasts and chemical mediators involved in cardiovascular disease pathology, their interactions and cumulative effects.
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Boswell MG, Wells MC, Kirk LM, Ju Z, Zhang Z, Booth RE, Walter RB. Comparison of gene expression responses to hypoxia in viviparous (Xiphophorus) and oviparous (Oryzias) fishes using a medaka microarray. Comp Biochem Physiol C Toxicol Pharmacol 2009; 149:258-65. [PMID: 19049829 DOI: 10.1016/j.cbpc.2008.11.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 11/05/2008] [Accepted: 11/07/2008] [Indexed: 02/02/2023]
Abstract
Gene expression profiling using DNA microarray technology is a useful tool for assessing gene transcript level responses after an organism is exposed to environmental stress. Herein, we detail results from studies using an 8 k medaka (Oryzias latipes) microarray to assess modulated gene expression patterns upon hypoxia exposure of the live-bearing aquaria fish, Xiphophorus maculatus. To assess the reproducibility and reliability of using the medaka array in cross-genus hybridization, a two-factor ANOVA analysis of gene expression was employed. The data show the tissue source of the RNA used for array hybridization contributed more to the observed response of modulated gene targets than did the species source of the RNA. In addition, hierarchical clustering via heat map analyses of groupings of tissues and species (Xiphophorus and medaka) suggests that hypoxia induced similar responses in the same tissues from these two diverse aquatic model organisms. Our Xiphophorus results indicate 206 brain, 37 liver, and 925 gill gene targets exhibit hypoxia induced expression changes. Analysis of the Xiphophorus data to determine those features exhibiting a significant (p<0.05)+/-3 fold change produced only two gene targets within brain tissue and 80 features within gill tissue. Of these 82 characterized features, 39 were identified via homology searching (cut-off E-value of 1 x 10(-5)) and placed into one or more biological process gene ontology groups. Among these 39 genes, metabolic energy changes and manipulation was the most affected biological pathway (13 genes).
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Affiliation(s)
- Mikki G Boswell
- Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
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Neusser MA, Lindenmeyer MT, Kretzler M, Cohen CD. Genomic analysis in nephrology – towards systems biology and systematic medicine? Nephrol Ther 2008; 4:306-11. [DOI: 10.1016/j.nephro.2008.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Revised: 03/19/2008] [Accepted: 04/08/2008] [Indexed: 01/15/2023]
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Orlandi RR, Thibeault SL, Ferguson BJ. Microarray analysis of allergic fungal sinusitis and eosinophilic mucin rhinosinusitis. Otolaryngol Head Neck Surg 2007; 136:707-13. [PMID: 17478202 DOI: 10.1016/j.otohns.2006.11.033] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Accepted: 11/15/2006] [Indexed: 10/23/2022]
Abstract
OBJECTIVE Our goal was to determine and compare the differential gene expression in allergic fungal sinusitis (AFS) and eosinophilic mucin rhinosinusitis (EMRS). STUDY DESIGN AND SETTING We conducted a complementary DNA microarray analysis of prospectively gathered tissue from a tertiary rhinology practice. RESULTS Compared to normal subjects, 38 genes or potential genes were differentially expressed in AFS patients, while 10 genes were differentially expressed in EMRS patients. Four genes differentially expressed in EMRS were not differentially expressed in AFS: cathepsin B, sialyltransferase 1, GM2 ganglioside activator protein, and S100 calcium binding protein. These genes mediate lysosomal activity and are known to have differential expression in inflammatory and neoplastic states. CONCLUSIONS EMRS and AFS show some similarities in gene expression profiles using microarray analysis. Significant differences in gene expression in both EMRS and AFS patients compared with normal subjects provide early clues to the pathophysiology of EMRS and AFS. SIGNIFICANCE This study demonstrates that complementary DNA microarray analysis is a feasible tool for studying different disease subclassifications and is the first to study these subclasses in chronic rhinosinusitis.
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Affiliation(s)
- Richard R Orlandi
- Division of Otolaryngology-Head and Neck Surgery, University of Utah, Salt Lake City, UT 84132, USA.
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Ju Z, Wells MC, Heater SJ, Walter RB. Multiple tissue gene expression analyses in Japanese medaka (Oryzias latipes) exposed to hypoxia. Comp Biochem Physiol C Toxicol Pharmacol 2007; 145:134-44. [PMID: 16916623 DOI: 10.1016/j.cbpc.2006.06.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Revised: 06/18/2006] [Accepted: 06/19/2006] [Indexed: 12/22/2022]
Abstract
Due in part to human population growth watersheds and coastal estuaries have been receiving increasing run-off of nutrients and genotoxins. As a consequence, the occurrences of nutrient-driven hypoxia in coastal waters appear to be increasing. Thus, understanding the molecular genetic response to hypoxia by model aquatic organisms is of interest both from environmental and physiological viewpoints. The major objectives of this study are to determine genome-wide gene expression profiles and to better understand how hypoxia influences global gene expression in medaka (Oryzias latipes), a well utilized aquatic model species. Herein we detail our development of a microarray containing 8046 medaka unigenes and describe our experimental results for measuring gene expression changes in the brain, gill, and liver of hypoxia exposed fish. Using conservative selection criteria, we determined that 501 genes in the brain, 442 in the gill, and 715 in the liver were differentially expressed in medaka exposed to hypoxia. These differentially expressed genes fell into a number of biological gene ontology groups related to general metabolism, catabolism, RNA and protein metabolism, etc. Two biological pathways, ubiquitin-proteasome and phosphatidylinositol signaling, were significantly dysregulated in medaka upon hypoxia exposure. Comparative genomics between medaka and human identified several human orthologies associated with known diseases.
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Affiliation(s)
- Zhenlin Ju
- Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX 78666-4616, USA.
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Trtkova J, Raclavsky V. MOLECULAR-GENETIC APPROACHES TO IDENTIFICATION AND TYPING OF PATHOGENIC CANDIDA YEASTS. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2006; 150:51-61. [PMID: 16936901 DOI: 10.5507/bp.2006.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Currently, invasive candidal infections represent an increasing cause of morbidity and mortality in seriously ill hospitalised patients. Because the accurate diagnosis of candidiasis remains difficult, a fast and reliable assay for characterization of fungal pathogens is critical for the early initiation of adequate antifungal therapy and/or for introduction of preventive measures. As novel molecular genetic techniques are continuously introduced, their role in the management of infectious diseases has also been growing. Today, molecular strategies complement conventional methods and provide more accurate and detailed insight. It can be expected that future technical development will improve their potential furthermore. In this article, we provide a critical review on the value and limitations of molecular tools in pathogenic Candida species identification and strain typing regarding their sensitivity, discriminatory power, reproducibility, cost and ease of performance.
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Affiliation(s)
- Jitka Trtkova
- Department of Biology, Faculty of Medicine, Palacký University, Hnevotínská 3, Olomouc, Czech Republic.
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Herath CB, Ishiwata H, Shiojima S, Kadowaki T, Katsuma S, Ushizawa K, Imai K, Takahashi T, Hirasawa A, Takahashi S, Izaike Y, Tsujimoto G, Hashizume K. Developmental Aberrations of Liver Gene Expression in Bovine Fetuses Derived from Somatic Cell Nuclear Transplantation. CLONING AND STEM CELLS 2006; 8:79-95. [PMID: 16776600 DOI: 10.1089/clo.2006.8.79] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Cloning by somatic cell nuclear transfer (NT) has been accomplished. However, the process itself is inefficient since most clones die before birth and survivors often display various anomalies. In an effort to determine global expression profiles of developmentally regulated liver genes in NT bovine fetuses, we employed a custom-made bovine liver complementary DNA (cDNA) microarray. The NT fetuses in early pregnancy were derived from cumulus cells as the nuclear donor cells. Normal fetuses were derived from in vitro fertilization (IVF) and artificial insemination (AI). Gene expression levels in NT, IVF, and AI fetal livers were obtained by comparing individual fetal liver samples with that of adult liver of nonpregnant cycling cows. Statistical analyses of the expression data showed widespread dysregulation of developmentally important genes in the three NT fetuses examined. It was found that the number of dysregulated genes was within a range of 3.5-7.7% of the tested genes in the NT fetal livers. The analyses revealed that one NT fetus was markedly different in liver gene expression profile from the other two NT fetal livers in which the expression profiles were highly correlated. Thus, our findings demonstrate that widespread dysregulation of liver genes occurs in the developing liver of NT bovine fetuses. It is possible that inappropriate genomic reprogramming after NT is a key factor associated with abnormal gene expressions in the livers of NT fetuses, whereas distinct expression patterns between the fellow cloned fetuses likely have resulted from variable epigenetic status of the donor nuclei.
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Affiliation(s)
- Chandana B Herath
- Department of Developmental Biology, National Institute of Agrobiological Sciences, Tsukuba City, Ibaraki 305-8602, Japan
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Affiliation(s)
- Prasad Devarajan
- Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, University of Cincinnati School of Medicine, OH 45229-3039, USA.
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Gulmann C, Sheehan KM, Kay EW, Liotta LA, Petricoin EF. Array-based proteomics: mapping of protein circuitries for diagnostics, prognostics, and therapy guidance in cancer. J Pathol 2006; 208:595-606. [PMID: 16518808 DOI: 10.1002/path.1958] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The human proteome, due to the enormity of post-translational permutations that result in large numbers of isoforms, is much more complex than the genome and alterations in cancer can occur in ways that are not predictable by translational analysis alone. Proteomic analysis therefore represents a more direct way of investigating disease at the individual patient level. Furthermore, since most novel therapeutic targets are proteins, proteomic analysis potentially has a central role in patient care. At the same time, it is becoming clear that mapping entire networks rather than individual markers may be necessary for robust diagnostics as well as tailoring of therapy. Consequently, there is a need for high-throughput multiplexed proteomic techniques, with the capability of scanning multiple cases and analysing large numbers of endpoints. New types of protein arrays combined with advanced bioinformatics are currently being used to identify molecular signatures of individual tumours based on protein pathways and signalling cascades. It is envisaged that analysing the cellular 'circuitry' of ongoing molecular networks will become a powerful clinical tool in patient management.
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Affiliation(s)
- C Gulmann
- NCI-FDA Clinical Proteomics Program, Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20892, USA.
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Tarabishi R, Zahedi K, Mishra J, Ma Q, Kelly C, Tehrani K, Devarajan P. Induction of Zf9 in the kidney following early ischemia/reperfusion. Kidney Int 2005; 68:1511-9. [PMID: 16164628 DOI: 10.1111/j.1523-1755.2005.00563.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND An improved understanding of the early cell injury mechanisms is critical for effective therapy of acute renal failure (ARF). METHODS We utilized cDNA microarrays to identify renal genes that are induced very early after renal ischemia in a mouse model, whose protein products might provide novel information regarding the pathogenesis of ARF. The findings were confirmed by downstream mRNA and protein expression studies, as well as knockdown analysis with antisense primers. RESULTS The maximally induced gene (21-fold at 3 hours of reflow) was Zf9, a Kruppel-like transcription factor involved in the regulation of transforming growth factor-beta1 (TGF-beta1). The rapid induction of Zf9 mRNA was confirmed by Northern analysis (14.5-fold at 3 hours of reflow) and that of Zf9 protein by Western analysis (10.5-fold at 3 hours of reflow). Zf9 protein was induced in both proximal and distal tubule cells in a cytoplasmic as well as nuclear distribution. TGF-beta1 protein was also up-regulated in a pattern parallel to that of Zf9. In cultured human proximal tubule cells, induction of ischemia by partial adenosine triphosphate (ATP) depletion resulted in a rapid up-regulation of both Zf9 and of TGF-beta1 proteins. Antisense oligonucleotides to Zf9 markedly blunted the induction of Zf9 and TGF-beta1, and significantly inhibited the apoptotic response to ATP depletion. CONCLUSION Induction of Zf9 and its transactivating factor TGF-beta1 may play a critical and hitherto unrecognized role in the early apoptotic response to ischemic renal injury.
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Affiliation(s)
- Ridwan Tarabishi
- Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229, USA
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Szeto CC, Lai KB, Chow KM, Szeto CYK, Yip TWC, Woo KS, Li PKT, Lai FMM. Messenger RNA expression of glomerular podocyte markers in the urinary sediment of acquired proteinuric diseases. Clin Chim Acta 2005; 361:182-90. [PMID: 15996647 DOI: 10.1016/j.cccn.2005.05.016] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2005] [Revised: 05/20/2005] [Accepted: 05/20/2005] [Indexed: 01/12/2023]
Abstract
BACKGROUND Podocyte slit diaphragm plays an important role in the control of glomerular permeability. We hypothesize that studying the gene expression profile of podocyte in urinary sediment may provide diagnostic and prognostic information on acquired proteinuric diseases. METHODS We studied 28 patients who required kidney biopsy for acquired proteinuric diseases (diabetic glomerulosclerosis, 9 cases; IgA nephropathy, 10 cases; minimal change disease, 5 cases; membranous nephropathy, 5 cases). We also studied 10 cases of diabetic microalbuminuria and 9 healthy controls. The mRNA expressions of nephrin (NephRNA), podocin (PodRNA) and synaptopodin (SynRNA) in urinary sediment were measured by real time quantitative PCR. After recruitment, all patients were followed for at least 12 months. RESULTS There were significant differences in the NephRNA and PodRNA in the urinary sediment between diagnosis groups (p<0.005). On the other hand, SynRNA was only marginally significant between diagnosis groups (p<0.05). Although statistically significant, the degree of proteinuria had only modest correlations with the urinary expression of nephrin. After a median follow up for 23 months, there was a significant correlation between the rate of decline in renal function and NephRNA (r=0.559, p=0.001) and PodRNA (r=0.530, p=0.002), but not SynRNA (r=0.054, p=NS). The correlation remained statistically significant after multivariate analysis to adjust for the degree of proteinuria and initial renal function. CONCLUSIONS Urinary mRNA expression of podocyte markers, such as nephrin and podocin, are significantly different between proteinuric disease categories. Further, NephRNA and PodRNA correlated with the rate of decline in renal function. Our results suggest that urinary podocyte gene expression may be a useful non-invasive tool which provides additional information for the management of proteinuric diseases.
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Affiliation(s)
- Cheuk-Chun Szeto
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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Kumar A, Goel G, Fehrenbach E, Puniya AK, Singh K. Microarrays: The Technology, Analysis and Application. Eng Life Sci 2005. [DOI: 10.1002/elsc.200420075] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Gobert GN, Moertel LP, McManus DP. Microarrays: new tools to unravel parasite transcriptomes. Parasitology 2005; 131:439-48. [PMID: 16174408 DOI: 10.1017/s0031182005008012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2005] [Revised: 03/31/2005] [Accepted: 04/08/2005] [Indexed: 11/07/2022]
Abstract
The ability to monitor the expression levels of thousands of genes in a single microarray experiment is a huge progression from conventional Northern blot analysis or PCR-based techniques. Microarrays can play a pivotal role in the mass screening of genes in a wide range of fields including parasitology. The relatively few parasites that can be readily cultured or isolated from a host, as compared with cell lines or tissue sources, makes microarray technology ideal for maximizing experimental results from a limiting source of starting material. Khan et al. (1999 a) commented in an early review of microarray technology " With this system in place, one can anticipate a time when data from thousands of gene expression experiments will be available for meta-analysis........leading to more robust results and subtle conclusions". Now in 2005, microarrays represent a very powerful resource that can play an important role in the characterization and annotation of the transcriptomes of many parasites of medical and veterinary importance.
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Affiliation(s)
- G N Gobert
- Molecular Parasitology Laboratory, Australian Centre for International and Tropical Health and Nutrition, Queensland Institute of Medical Research, 300 Herston Road, Brisbane, QLD 4029 Australia.
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Liang M, Cowley AW, Hessner MJ, Lazar J, Basile DP, Pietrusz JL. Transcriptome analysis and kidney research: Toward systems biology. Kidney Int 2005; 67:2114-22. [PMID: 15882254 DOI: 10.1111/j.1523-1755.2005.00315.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An enormous amount of data has been generated in kidney research using transcriptome analysis techniques. In this review article, we first describe briefly the principles and major characteristics of several of these techniques. We then summarize the progress in kidney research that has been made by using transcriptome analysis, emphasizing the experience gained and the lessons learned. Several technical issues regarding DNA microarray are highlighted because of the rapidly increased use of this technology. It appears clear from this brief survey that transcriptome analysis is an effective and important tool for question-driven exploratory science. To further enhance the power of this and other high throughput, as well as conventional approaches, in future studies of the kidney, we propose a multidimensional systems biology paradigm that integrates investigation at multiple levels of biologic regulation toward the goal of achieving a global understanding of physiology and pathophysiology.
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Affiliation(s)
- Mingyu Liang
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.
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Eikmans M, Ijpelaar DHT, Baelde HJ, de Heer E, Bruijn JA. The use of extracellular matrix probes and extracellular matrix-related probes for assessing diagnosis and prognosis in renal diseases. Curr Opin Nephrol Hypertens 2005; 13:641-7. [PMID: 15483455 DOI: 10.1097/00041552-200411000-00010] [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: 11/26/2022]
Abstract
PURPOSE OF REVIEW Scarring in the kidney results from excessive local synthesis and exogenous accumulation of extracellular matrix components. Once chronic damage is present in the biopsy, therapeutic intervention for the renal patient encounters severe limitations. It is therefore essential to determine clinical outcome preferably at a time point before the development of overt scarring. Clinical parameters and morphologic alterations in the biopsy are currently used as tools for the diagnosis of the renal disease entity and for assessment of the patient's prognosis. Expression levels of extracellular matrix and matrix-related components may serve as additive and even superior prognostic indicators to conventional parameters. We will elaborate on studies supporting this concept. RECENT FINDINGS Several investigators have shown in experimental models for renal disease that extracellular matrix probes and related probes reflect disease progression and predict outcome. In this review, we will provide an update on the most recent studies of human renal biopsies showing that expression of extracellular matrix components, regulators of matrix degradation, and cytokines affecting matrix deposition may be employed for discrimination of diagnostic groups and predicting prognosis. SUMMARY Molecular techniques are expected to be used more and more for diagnostic and prognostic purposes in nephrological practice to supplement the histopathological analysis of the renal biopsy. Assessment of expression of matrix molecules, matrix-regulating cytokines, and metalloproteinases in renal kidney biopsies is helpful to distinguish patients who are at risk of developing progressive renal failure from patients who are likely to recover from renal tissue injury by natural remodeling mechanisms.
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Affiliation(s)
- Michael Eikmans
- Department of Pathology, Leiden University Medical Center, Building 1, L1-Q, PO Box 9600, 2300 RC, Leiden, The Netherlands.
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Sheehan KM, Calvert VS, Kay EW, Lu Y, Fishman D, Espina V, Aquino J, Speer R, Araujo R, Mills GB, Liotta LA, Petricoin EF, Wulfkuhle JD. Use of reverse phase protein microarrays and reference standard development for molecular network analysis of metastatic ovarian carcinoma. Mol Cell Proteomics 2005; 4:346-55. [PMID: 15671044 DOI: 10.1074/mcp.t500003-mcp200] [Citation(s) in RCA: 231] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Cancer can be defined as a deregulation or hyperactivity in the ongoing network of intracellular and extracellular signaling events. Reverse phase protein microarray technology may offer a new opportunity to measure and profile these signaling pathways, providing data on post-translational phosphorylation events not obtainable by gene microarray analysis. Treatment of ovarian epithelial carcinoma almost always takes place in a metastatic setting since unfortunately the disease is often not detected until later stages. Thus, in addition to elucidation of the molecular network within a tumor specimen, critical questions are to what extent do signaling changes occur upon metastasis and are there common pathway elements that arise in the metastatic microenvironment. For individualized combinatorial therapy, ideal therapeutic selection based on proteomic mapping of phosphorylation end points may require evaluation of the patient's metastatic tissue. Extending these findings to the bedside will require the development of optimized protocols and reference standards. We have developed a reference standard based on a mixture of phosphorylated peptides to begin to address this challenge.
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Affiliation(s)
- Katherine M Sheehan
- United States Food and Drug Administration (FDA)-NCI Clinical Proteomics Program, Laboratory of Pathology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD, USA
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Ushizawa K, Takahashi T, Kaneyama K, Tokunaga T, Tsunoda Y, Hashizume K. Gene Expression Profiles of Bovine Trophoblastic Cell Line (BT-1) Analyzed by a Custom cDNA Microarray. J Reprod Dev 2005; 51:211-20. [PMID: 15613779 DOI: 10.1262/jrd.16072] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gene expression of bovine trophoblast cell line (BT-1) was analyzed with a custom utero-placenta complementary DNA microarray. Expression comparison with in vivo tissues of trophoblast derivation was performed to investigate characteristics of the expression in BT-1. BT-1 is a cell line established without feeder cells using trophoblast cells that are separated from bovine blastocysts. The bovine in vivo tissues of the trophoblast derivation were collected on day 17 through 56 of gestation. Of 1,773 genes, 933 exhibited an expression difference exceeding two-fold between BT-1 and in vivo tissues. These genes were analyzed by the k-means clustering method and were distributed into six clusters. Some genes, such as placental lactogen, interferon-tau and pregnancy-associated glycoproteins, all known as trophoblast-specific genes, were detected in BT-1 as well as in vivo tissues throughout the experiment period. These trophoblast-specific genes and octamer-binding transcription factor-4, known as a marker for undifferentiation of cells in mice, were detected by RT-PCR in both BT-1 and in vivo trophoblast tissues. The overall gene expression profile in BT-1 suggests that this cell line contains trophoblast-specific characteristics and is similar to trophoblast cells around the implantation period.
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Affiliation(s)
- Koichi Ushizawa
- Reproductive Biology and Technology Laboratory, Developmental Biology Department, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
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Abstract
Biopsy of the kidney should never be undertaken without careful consideration of the risks vs benefits. Given the importance of a correct diagnosis in the treatment and prognosis of renal disease, the pathological evaluation should use all available modalities. Native kidney biopsies require examination by light microscopy, immunohistochemistry and electron microscopy. The processing of the renal biopsy is complex and requires the support of a fully equipped anatomic pathology laboratory. Technical expertise is required to process the small fragments of tissue and to produce sections of highest quality. The correct diagnosis requires a well-trained renal pathologist with thorough knowledge of not only renal pathology but also renal medicine in order to correlate intricate tissue-derived information with detailed clinical data. In view of the importance and consequences of the pathologic diagnosis, the Renal Pathology Society appointed an Ad Hoc Committee on Practice Guidelines, to define the essential ingredients necessary to provide quality renal pathology diagnoses. This document incorporates the consensus opinions of the committee and the RPS membership at large.
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cDNA microarray analysis of bovine embryo gene expression profiles during the pre-implantation period. Reprod Biol Endocrinol 2004; 2:77. [PMID: 15560851 PMCID: PMC535809 DOI: 10.1186/1477-7827-2-77] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2004] [Accepted: 11/24/2004] [Indexed: 12/04/2022] Open
Abstract
Background After fertilization, embryo development involves differentiation, as well as development of the fetal body and extra-embryonic tissues until the moment of implantation. During this period various cellular and molecular changes take place with a genetic origin, e.g. the elongation of embryonic tissues, cell-cell contact between the mother and the embryo and placentation. To identify genetic profiles and search for new candidate molecules involved during this period, embryonic gene expression was analyzed with a custom designed utero-placental complementary DNA (cDNA) microarray. Methods Bovine embryos on days 7, 14 and 21, extra-embryonic membranes on day 28 and fetuses on days 28 were collected to represent early embryo, elongating embryo, pre-implantation embryo, post-implantation extra-embryonic membrane and fetus, respectively. Gene expression at these different time points was analyzed using our cDNA microarray. Two clustering algorithms such as k-means and hierarchical clustering methods identified the expression patterns of differentially expressed genes across pre-implantation period. Novel candidate genes were confirmed by real-time RT-PCR. Results In total, 1,773 individual genes were analyzed by complete k-means clustering. Comparison of day 7 and day 14 revealed most genes increased during this period, and a small number of genes exhibiting altered expression decreased as gestation progressed. Clustering analysis demonstrated that trophoblast-cell-specific molecules such as placental lactogens (PLs), prolactin-related proteins (PRPs), interferon-tau, and adhesion molecules apparently all play pivotal roles in the preparation needed for implantation, since their expression was remarkably enhanced during the pre-implantation period. The hierarchical clustering analysis and RT-PCR data revealed new functional roles for certain known genes (dickkopf-1, NPM, etc) as well as novel candidate genes (AW464053, AW465434, AW462349, AW485575) related to already established trophoblast-specific genes such as PLs and PRPs. Conclusions A large number of genes in extra-embryonic membrane increased up to implantation and these profiles provide information fundamental to an understanding of extra-embryonic membrane differentiation and development. Genes in significant expression suggest novel molecules in trophoblast differentiation.
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Wren JD, Yao M, Langer M, Conway T. Simulated Annealing of Microarray Data Reduces Noise and Enables Cross-Experimental Comparisons. DNA Cell Biol 2004; 23:695-700. [PMID: 15585127 DOI: 10.1089/dna.2004.23.695] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Microarrays are a powerful tool for assessing the genome-wide induction of a transcriptional response to internal or external stimuli, but are not considered quantitatively rigorous (i.e., the signal intensity of hybridized probe is normally used to quantify relative transcript abundance). Thus, it is difficult, if not impossible, to accurately compare separate microarray experiments without a reference standard. However, even among replicated microarray experiments, each gene varies significantly in the amount of signal detected, suggesting no single gene would be appropriate as a standard. We propose and test a method to "align" experimental transcription profiles to a set of reference experiments using simulated annealing (SA), essentially using the relative positions of all genes as a reference standard. SA attempts to find a globally optimal adjustment factor for the relative expression level of each experimental gene expression signal, given a previously observed range of gene expression measurements. By defining a relative dynamic range of gene expression under control conditions for all genes, we can more accurately compare transcription profiles between separate experiments and, potentially, between species--enabling comparative transcriptomics. Testing SA on a published dataset, we find that it significantly reduces interexperimental variation, suggesting it holds promise to accomplish this goal.
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Affiliation(s)
- Jonathan D Wren
- Advanced Center for Genome Technology, The University of Oklahoma, Norman, Oklahoma 73019, USA.
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Abstract
This review deals with the methods of identifying genes that have been activated by inner or outer impulses. The activation and subsequent expression of a gene can be detected by its transcription into a corresponding messenger ribonucleic acid (mRNA). Principles of the methods for identification of individual activated genes, as well as groups of activated genes are described, the former methods being mostly based on subtractive hybridization and serial analysis of gene expression (SAGE), the latter on microarrays. Examples of gene activation by the hormone 17beta-estradiol (E2) are given.
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Affiliation(s)
- Sten Z Cekan
- Karolinska Institute, Department of Woman and Child Health, Division of Reproductive Endocrinology, Karolinska University Hospital, Building L5, 17176 Stockholm, Sweden.
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Mishra J, Ma Q, Prada A, Mitsnefes M, Zahedi K, Yang J, Barasch J, Devarajan P. Identification of neutrophil gelatinase-associated lipocalin as a novel early urinary biomarker for ischemic renal injury. J Am Soc Nephrol 2004; 14:2534-43. [PMID: 14514731 DOI: 10.1097/01.asn.0000088027.54400.c6] [Citation(s) in RCA: 1241] [Impact Index Per Article: 62.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Acute renal failure (ARF) secondary to ischemic injury remains a common and potentially devastating problem. A transcriptome-wide interrogation strategy was used to identify renal genes that are induced very early after renal ischemia, whose protein products might serve as novel biomarkers for ARF. Seven genes that are upregulated >10-fold were identified, one of which (Cyr61) has recently been reported to be induced after renal ischemia. Unexpectedly, the induction of the other six transcripts was novel to the ARF field. In this study, one of these previously unrecognized genes was further characterized, namely neutrophil gelatinase-associated lipocalin (NGAL), because it is a small secreted polypeptide that is protease resistant and consequently might be readily detected in the urine. The marked upregulation of NGAL mRNA and protein levels in the early postischemic mouse kidney was confirmed. NGAL protein expression was detected predominantly in proliferating cell nuclear antigen-positive proximal tubule cells, in a punctate cytoplasmic distribution that co-localized with markers of late endosomes. NGAL was easily detected in the urine in the very first urine output after ischemia in both mouse and rat models of ARF. The appearance of NGAL in the urine was related to the dose and duration of renal ischemia and preceded the appearance of other urinary markers such as N-acetyl-beta-D-glucosaminidase and beta2-microglobulin. The origin of NGAL from tubule cells was confirmed in cultured human proximal tubule cells subjected to in vitro ischemic injury, where NGAL mRNA was rapidly induced in the cells and NGAL protein was readily detectable in the culture medium within 1 h of mild ATP depletion. NGAL was also easily detectable in the urine of mice with cisplatin-induced nephrotoxicity, again preceding the appearance of N-acetyl-beta-D-glucosaminidase and beta2-microglobulin. The results indicate that NGAL may represent an early, sensitive, noninvasive urinary biomarker for ischemic and nephrotoxic renal injury.
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Affiliation(s)
- Jaya Mishra
- Nephrology & Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229-3039, USA
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Shmueli O, Horn-Saban S, Chalifa-Caspi V, Shmoish M, Ophir R, Benjamin-Rodrig H, Safran M, Domany E, Lancet D. GeneNote: whole genome expression profiles in normal human tissues. C R Biol 2004; 326:1067-72. [PMID: 14744114 DOI: 10.1016/j.crvi.2003.09.012] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel data set, GeneNote (Gene Normal Tissue Expression), was produced to portray complete gene expression profiles in healthy human tissues using the Affymetrix GeneChip HG-U95 set, which includes 62 839 probe-sets. The hybridization intensities of two replicates were processed and analyzed to yield the complete transcriptome for twelve human tissues. Abundant novel information on tissue specificity provides a baseline for past and future expression studies related to diseases. The data is posted in GeneNote (http://genecards.weizmann.ac.il/genenote/), a widely used compendium of human genes (http://bioinfo.weizmann.ac.il/genecards).
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Affiliation(s)
- Orit Shmueli
- Department of Molecular Genetics, The Weizmann Institute of Science, 76100 Rehovot, Israel.
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Herath CB, Shiojima S, Ishiwata H, Katsuma S, Kadowaki T, Ushizawa K, Imai K, Takahashi T, Hirasawa A, Tsujimoto G, Hashizume K. Pregnancy-associated changes in genome-wide gene expression profiles in the liver of cow throughout pregnancy. Biochem Biophys Res Commun 2004; 313:666-80. [PMID: 14697243 DOI: 10.1016/j.bbrc.2003.11.151] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The objective of the present study was to fabricate and use a bovine liver complementary DNA (cDNA) microarray to profile genome-wide gene expressions in the liver of cow throughout pregnancy. A cDNA library was prepared from liver total RNA collected from cows during estrous cycle and pregnancy, and from fetuses at different stages of pregnancy. The sequenced clones were compiled and annotated by basic local alignment search tool (BLASTn) and spotted onto glass slides. The annotated liver array represented 2675 genes. Of which, 1442 were known genes while 617 sequences had matches with sequences found in expressed sequence tags databases. In addition, 616 unknown sequences were found and these sequences may possibly be identified as candidates for novel bovine genes. For gene expression profiling studies, total RNA from livers of cows slaughtered on days 19, 27-28, 49-58, 150, and 245 of pregnancy (test RNAs) was separately reverse transcribed and labeled with either cyanine 5-fluorescent dye (Cy5) or Cy3. The test samples were individually compared with liver total RNA collected from nonpregnant cycling cows (control RNA) after reverse transcription and labeling with the opposite dye following a two-color hybridization method. After scanning, image acquisition, and normalization, genes that showed either more than 1.5-fold (test/control) induction or repression were selected for further analyses. Hierarchical clustering algorithm showed a clear induction of most liver genes on days 27-28 of pregnancy. Self-organizing maps algorithm identified groups of genes whose differential expression patterns were similar across pregnancy. In conclusion, we described fabrication of a bovine liver cDNA microarray, and demonstrate, for the first time, differential expression patterns of a large number of coregulated liver genes in parallel throughout pregnancy in the bovine.
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Affiliation(s)
- Chandana B Herath
- Laboratory of Reproductive Biology and Technology, National Institute of Agrobiological Sciences, Tsukuba City, Ibaraki 305-8602, Japan
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Devarajan P, Mishra J, Supavekin S, Patterson LT, Steven Potter S. Gene expression in early ischemic renal injury: clues towards pathogenesis, biomarker discovery, and novel therapeutics. Mol Genet Metab 2003; 80:365-76. [PMID: 14654349 DOI: 10.1016/j.ymgme.2003.09.012] [Citation(s) in RCA: 186] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Acute renal failure (ARF) represents a common and serious problem in clinical medicine. Renal ischemia-reperfusion injury (IRI) is the major cause of ARF in the native and transplanted kidney. Several decades of research have provided successful therapeutic approaches in animal models, but translational efforts in humans have yielded disappointing results. The major reasons for this include a lack of early markers for ARF (and hence a delay in initiating therapy), and the multi-factorial nature of the disease. This review focuses on the use of cDNA microarrays to elucidate the molecular genetic mechanisms underlying tubule cell apoptosis, and to identify novel biomarkers for early renal IRI. Also presented is a comparative temporal analysis of cDNA microarray results from mature kidneys following IRI and during normal nephrogenesis. Molecular genetic evidence for the notion that regeneration recapitulates development in the kidney, and that injured tubule cells possess the capacity to de-differentiate to the earliest stages of development, is presented. The implications of these findings to the ability of the kidney to repair itself and potential strategies for accelerating recovery are briefly discussed.
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Affiliation(s)
- Prasad Devarajan
- Department of Nephrology, Cincinnati Children's Hospital, Medical Center and Research Foundation, 3333 Burnet Avenue, MLC 7022, Cincinnati, OH 45229-3039, USA.
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Fornoni A, Lenz O, Striker LJ, Striker GE. Glucose induces clonal selection and reversible dinucleotide repeat expansion in mesangial cells isolated from glomerulosclerosis-prone mice. Diabetes 2003; 52:2594-602. [PMID: 14514645 DOI: 10.2337/diabetes.52.10.2594] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Clonal selection has been proposed as a pathogenetic mechanism in various chronic diseases, such as scleroderma, hypertension, pulmonary fibrosis, interstitial fibrosis of the kidney, atherosclerosis, and uterine leiomyomatosis. We previously found that mesangial cells from ROP mice prone to develop glomerulosclerosis changed their phenotype in response to high glucose concentrations. Here, we investigate whether clonal selection might contribute to this phenotype change. We found that in ROP mice at least two distinct mesangial cell clones exist. They are characterized by a different length of the d(CA) repeat in the MMP-9 promoter and exhibit a significantly different gene expression profile. Exposure of ROP mesangial cells to 25 mmol/l glucose for 35 days induces both clonal selection and reversible dinucleotide repeat expansion. None of these findings were present in mesangial cells isolated from C57BL/6 mice, which are not sclerosis-prone. We conclude that mesangial cell michrochimerism may be a marker for the susceptibility to glomerulosclerosis, that dinucleotide repeat expansion may be a novel mechanism for glucose-induced changes in gene expression, and that clonal selection may partially explain the change in mesangial cell phenotype in diabetes.
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Affiliation(s)
- Alessia Fornoni
- Vascular Biology Institute, University of Miami School of Medicine, Miami, Florida, USA
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Susztak K, Sharma K, Schiffer M, McCue P, Ciccone E, Böttinger EP. Genomic strategies for diabetic nephropathy. J Am Soc Nephrol 2003; 14:S271-8. [PMID: 12874445 DOI: 10.1097/01.asn.0000078035.81397.8a] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Insight into the molecular mechanisms that underlie the origin and progression of diabetic nephropathy remains limited in part because conventional research tools have restricted investigators to focus on single genes or isolated pathways. Microarray technologies provide opportunities for evaluating genetic factors and environmental effects at a genomic scale during the pathogenesis of diabetic nephropathy. Despite the enormous power of the microarray technology, there are several pitfalls that need to be considered. This article discusses conceptual, practical, statistical, and logistical considerations for the use of microarrays in studies of experimental and human diabetic renal disease. New knowledge in this field will facilitate new approaches for molecular diagnosis and drug discovery.
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Affiliation(s)
- Katalin Susztak
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
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Bañez LL, Prasanna P, Sun L, Ali A, Zou Z, Adam BL, McLeod DG, Moul JW, Srivastava S. Diagnostic potential of serum proteomic patterns in prostate cancer. J Urol 2003; 170:442-6. [PMID: 12853795 DOI: 10.1097/01.ju.0000069431.95404.56] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
PURPOSE The serum prostate specific antigen test has been widely used in the last decade as an effective screening tool for prostate cancer (CaP). However, the high false-positive rate of the serum prostate specific antigen test necessitates the development of more accurate diagnostic and prognostic biomarkers for CaP. Promising diagnostic potential of serum protein patterns detected by surface enhanced laser desorption/ionization time of flight mass spectrometry for CaP has recently been reported. Independent evaluation of this new technology is warranted to realize its translational utility. We determined whether serum protein profiling by surface enhanced laser desorption/ionization time of flight mass spectrometry and a decision tree algorithm classification system could accurately discriminate between patients with CaP and unaffected individuals. MATERIALS AND METHODS Proteomic spectra of crude serum were generated using the Ciphergen ProteinChip System and pattern detection was performed using Biomarker Patterns Software (Ciphergen Biosystems, Inc., Fremont, California). A total of 106 patients with CaP and 56 controls were randomly allocated to a training set and a test set. The training set, which consisted of 44 patients with cancer and 30 controls, was used to build a decision tree algorithm. The test set, which consisted of 62 patients with cancer and 26 controls, was used in blinded fashion to validate the decision tree. RESULTS Accuracy of classification using the test set was 67% and 42% for the weak cation exchange array and the copper metal affinity capture array, respectively. Combined spectral data from the weak cation exchange and copper metal affinity capture arrays generated an algorithm that achieved 85% sensitivity and 85% specificity for the detection of CaP. CONCLUSIONS These preliminary findings support recent observations that complex protein profiles have promising potential for the early detection of CaP and warrant future studies with streamlined technology. Furthermore, the combined effect of using 2 array types can greatly enhance the ability of protein profile patterns, suggesting the potential usefulness of alternative approaches to evaluate this new emerging technology.
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Affiliation(s)
- Lionel L Bañez
- Department of Surgery, Uniformed Armed Services University of the Health Sciences, Bethesda, Maryland, USA
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