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Early postmortem interval estimation based on Cdc25b mRNA in rat cardiac tissue

LEGAL MEDICINE 2018年 35卷 18-24页

作者： Tao, Li Ma, Jianlong Han, Liujun Xu, Hongmei Zeng, Yan Yehui, Lyu Li, Wencan Ma, Kaijun Xiao, Bi Chen, Long Fudan Univ Dept Forens Med Sch Basic Med Sci 131Dongan Rd Shanghai 200032 Peoples R China Shenzhen Inst Criminal Sci & Technol Shenzhen Publ Secur Bur Invest Dept Key Lab Forens PatholMinist Publ Secur Shenzhen 518000 Peoples R China Fudan Univ Childrens Hosp 399 Wanyuan Rd Shanghai 201102 Peoples R China Shanghai Univ Med & Hlth Sci 279 ZhouzhuHwy Shanghai 201318 Peoples R China Shanghai Publ Secur Bur Criminal Sci & Technol Inst Pudong Branch Forens Lab 255 Yanzhong Rd Shanghai 200125 Peoples R China Shanghai Publ Secur Bur Criminal Sci & Technol Inst Forens Lab 803 North Zhongshan Rd Shanghai 200082 Peoples R China

Purpose: The postmortem interval (PMI) is the amount of time that has elapsed since the time of death. Over the years, many approaches have been developed to assess PMI, but their time frame of applicability has been only days to weeks. Our present pilot study aimed to find the sensitive mRNA marker if the degradation of mRNA could be used to estimate the early postmortem interval (up to 24 h). Methods: In our study, we use the microarray to screen 217 mRNAs markers of rat cardiac tissue. Then, real-time fluorescent quantitative PCR (qPCR) was used to validate of the candidate markers at 7 time points within 24 h and at temperatures of 25 degrees C and 35 degrees C. Another 27 rats were then used to verify the model. Results: Among all of the candidate markers, Delta Cq (cell division cycle 25 homolog B(Cdc25b)) had the best correlation coefficient with early postmortem interval and was used to build a new model using the R software. The results of verification testing demonstrated that the error rate was less than 15%, demonstrating the high predictive power of our mathematical model. Conclusion: In this study, Cdc25b was found to be the sensitive marker to estimate early postmortem interval, and Rpl27 was found to be suitable for use as the endogenous control. Our work provided new leads for molecular approaches to early postmortem interval estimation using the significant mRNA markers established here.

关键词： Forensic medicine Early postmortem interval mRNA microarray expression profile qPCR R software

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Reduced variance of gene expression at numerous loci in a population of chickens selected for high feather pecking

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POULTRY SCIENCE 2010年第9期89卷 1858-1869页

作者： Hughes, A. L. Buitenhuis, A. J. Univ S Carolina Dept Biol Sci Columbia SC 29208 USA Aarhus Univ Dept Genet & Biotechnol Fac Agr Sci DK-8830 Tjele Denmark

Changes in gene expression in response to selection were studied by comparing microarray expression profiles among a population of domestic chickens selected for high feather pecking (FP) with a control population and a population selected for low FP. No transcripts showed significant differences among populations with respect to mean expression scores, but numerous transcripts showed reduced variance in expression scores in the high FP population in comparison to control and low FP populations. The reduction in variance in the high FP population generally involved transcripts whose expression scores had a negatively skewed distribution in the control population but not in the high FP population. A certain number of these transcripts corresponded to genes whose expression was significantly associated with either severe FP (SFP) or gentle FP. The patterns of gene expression associated with SFP and gentle FP were distinct, suggesting that very distinct underlying neural mechanisms underlie these 2 behaviors, with SFP showing more signs of an association with synaptic plasticity and with an immunosuppressive stress response.

关键词： gene expression microarray expression profile feather pecking loci chicken

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Effects of Astragalus polysaccharide on the erythroid lineage and microarray analysis in K562 cells

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JOURNAL OF ETHNOPHARMACOLOGY 2010年第2期127卷 242-250页

作者： Yang, Min Qian, Xin-Hua Zhao, Dan-Hua Fu, Su-Zhen Nanfang Med Univ Nanfang Hosp Dept Neonatol Guangzhou 510515 Guangdong Peoples R China Guangzhou Women & Childrens Med Ctr Dept Gastroenterol Guangzhou 510120 Guangdong Peoples R China

Ethnopharmacological relevance: Astragalus polysaccharide (APS), obtained from Astragalus membranaceus, displays a range of activities in many systems, including the promotion of immune responses, anti-inflammation, and the protection of vessels. It possesses potent pharmacological activity on differentiation to the erythroid lineage. Aim of the study: To investigate the effects of APS on the erythroid differentiation and the mechanism of action by microarray analysis in K562 cells. Materials and methods: Benzidine staining, semi-quantitative RT-PCR, Western blot and microarray methods were used to survey the effects of APS on inducing erythroid differentiation and the changes of gene expression profile in K562 cells. Results: Of the 13.2% positive cells detected by benzidine staining, the induction was the highest with 200 mu g/ml APS on 72 h. G gamma-mRNA expression and fetal hemoglobin synthesis were significantly up-regulated. microarray analysis showed that 31 genes were up-regulated and 108 genes were down-regulated. These differential expression genes generally regulate protein binding, cellular metabolic process, the cell proliferation, and transcriptional activator activity. The gamma-globin gene was up-regulated, the genes related with erythroid differentiation such as LMO2, Runx1 and GTF2I were up-regulated, while Bklf, Eklf, EPHB4 and Sp1 were down-regulated. Conclusions: Our studies indicate that APS indicate potent activities on the erythroid differentiation by modulating genes of LMO2, Klf1, Klf3, Runx1, EphB4 and Sp1, increasing gamma-globin mRNA expression and fetal hemoglobin synthesis in K562 cells. Crown Copyright (C) 2009 Published by Elsevier Ireland Ltd. All rights reserved.

关键词： Astragalus polysaccharide Globin gene Erythroid differentiation Gene expression microarray expression profile

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Gene expression changes during step-wise differentiation of embryonic stem cells along the inner ear hair cell pathway

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ACTA OTO-LARYNGOLOGICA 2006年第11期126卷 1148-1157页

作者： De Silva, Michelle G. Hildebrand, Michael S. Christopoulos, Helen Newman, Michelle R. Bell, Katrina Ritchie, Matthew Smyth, Gordon K. Dahl, Hans-Henrik M. Royal Childrens Hosp Murdoch Childrens Res Inst Parkville Vic 3052 Australia Univ Melbourne Dept Paediat Parkville Vic 3052 Australia Univ Melbourne Dept Biochem Parkville Vic 3052 Australia Royal Melbourne Hosp Walter & Eliza Hall Inst Med Res Parkville Vic 3050 Australia

Conclusion. Our study outlines an alternative approach for the selection and investigation of genes involved in inner ear function. Objective. To gain understanding of the gene pathways involved in the development of the normal cochlea. Materials and methods. microarray technology currently offers the most efficient approach to investigate gene expression and identify pathways involved in cell differentiation. Epidermal growth factor ( EGF) induces cultures derived from the organ of Corti to proliferate and produce new hair cells. Since pluripotent embryonic stem ( ES) cells have the capacity to generate all tissues, we induced murine ES cells to differentiate towards ectodermal and neuroectodermal cell types and from there investigated their commitment towards the hair cell lineage in the presence of EGF. Cells were collected at three points along the differentiation pathway and their expression profiles were determined using the Soares NMIE mouse inner ear cDNA library printed in microarray format. Results. Three genes up- regulated after addition of EGF ( serine ( or cysteine) proteinase inhibitor, clade H, member 1 ( Serpinh1), solute carrier family 2 ( facilitated glucose transporter), member 10 ( Slc2a10) and secreted acidic cysteine- rich glycoprotein ( Sparc)) were selected for further analysis and characterization. Of the three genes, Serpinh1 and Slc2a10 have never been implicated in the hearing process.

关键词： hair cell development embryonic stem cell differentiation epidermal growth factor microarray expression profile

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Cross-platform method for identifying candidate network biomarkers for prostate cancer

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IET SYSTEMS BIOLOGY 2009年第6期3卷 505-512页

作者： Jin, G. Zhou, X. Cui, K. Zhang, X. -S. Chen, L. Wong, S. T. C. Methodist Hosp Med Syst Biol Lab Ctr Bioinformat & Biotechnol Res InstWeill Cornell Med Coll Houston TX 77030 USA Chinese Acad Sci Acad Math & Syst Sci Beijing 100080 Peoples R China Osaka Sangyo Univ Dept Elect Engn Osaka 5748530 Japan

Discovering biomarkers using mass spectrometry (MS) and microarray expression profiles is a promising strategy in molecular diagnosis. Here, the authors proposed a new pipeline for biomarker discovery that integrates disease information for proteins and genes, expression profiles in both genomic and proteomic levels, and protein-protein interactions (PPIs) to discover high confidence network biomarkers. Using this pipeline, a total of 474 molecules (genes and proteins) related to prostate cancer were identified and a prostate-cancer-related network (PCRN) was derived from the integrative information. Thus, a set of candidate network biomarkers were identified from multiple expression profiles composed by eight microarray datasets and one proteomics dataset. The network biomarkers with PPIs can accurately distinguish the prostate patients from the normal ones, which potentially provide more reliable hits of biomarker candidates than conventional biomarker discovery methods.

关键词： biological organs mass spectroscopic chemical analysis proteins Biology and medical computing genomic level medical computing biomarkers mass spectrometry tumours molecular diagnosis microarray expression profile microarray datasets Biomolecular structure, configuration, conformation, and active sites cross-platform method Mass spectrometry (chemical analysis) Genomic techniques Physics of subcellular structures prostate cancer genomics Proteomic techniques Biomolecular interactions, charge transfer complexes cancer proteomics gene expression disease information protein-protein interactions genetics Biomedical engineering

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PathFinder: mining signal transduction pathway segments from protein-protein interaction networks

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BMC BIOINFORMATICS 2007年第1期8卷 335-335页

作者： Bebek, Gurkan Yang, Jiong Case Western Reserve Univ Dept EECS Cleveland OH 44106 USA

Background: A Signal transduction pathway is the chain of processes by which a cell converts an extracellular signal into a response. In most unicellular organisms, the number of signal transduction pathways influences the number of ways the cell can react and respond to the environment. Discovering signal transduction pathways is an arduous problem, even with the use of systematic genomic, proteomic and metabolomic technologies. These techniques lead to an enormous amount of data and how to interpret and process this data becomes a challenging computational problem. Results: In this study we present a new framework for identifying signaling pathways in protein-protein interaction networks. Our goal is to find biologically significant pathway segments in a given interaction network. Currently, protein-protein interaction data has excessive amount of noise, e. g., false positive and false negative interactions. First, we eliminate false positives in the protein-protein interaction network by integrating the network with microarray expression profiles, protein subcellular localization and sequence information. In addition, protein families are used to repair false negative interactions. Then the characteristics of known signal transduction pathways and their functional annotations are extracted in the form of association rules. Conclusion: Given a pair of starting and ending proteins, our methodology returns candidate pathway segments between these two proteins with possible missing links (recovered false negatives). In our study, S. cerevisiae (yeast) data is used to demonstrate the effectiveness of our method.

关键词： Association Rule Functional Annotation Association Rule Mining microarray expression profile True Interaction

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expression Profiling of Hereditary versus Sporadic Prostate Cancer Suggests CYR61, EGR3, KLF6 and SNF1LK as Differentially Expressed Genes

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Open Journal of Urology 2012年第2期2卷 55-66页

作者： Diem Nguyen Bentzon Martin Morck Mortensen Torben Orntoft Lars Dyrskjot Michael Borre Department of Urology Aarhus University Hospital SkejbyAarhusDenmark Department of Molecular Medicine Aarhus University Hospital SkejbyAarhusDenmark

Background: Distinguishing between sub-clinical and aggressive forms of prostate cancer is difficult due to the heterogeneity of the disease. It is, however, important to identify aggressive forms to guide proper treatment. This study compared gene expression profiles in cancer cells from hereditary and sporadic prostate cancer cases and attempted to correlate differentially regulated genes with clinico-pathological characteristics and prognosis. Materials and methods: The study population comprised patients diagnosed with clinically localized prostate cancer undergoing prostatectomy. Patients were divided into hereditary and sporadic cancer cases based on their family history. Fresh frozen biopsies from prostatectomy specimens were laser-dissected for RNA-extraction. Affymetrix HG-U133 Plus GeneChips were used to measure gene expression loaded onto Cluster 3.0 and Ingenuity Pathway Analysis softwares to examine the relationship among genes between groups. Differentially expressed genes were selected for protein expression analysis using immunohistochemistry on histological sections and tissue microarrays. Results: No single genes were signifycantly differentially expressed between hereditary and sporadic cases after adjustment for multiple testing. Using cluster analysis, four transcripts were found to be upregulated in hereditary prostate cancer tissue: CYR61, EGR3, KLF6 and SNF1LK. The intensity of CYR61, EGR2, KLF6 and SNF1LK immunostainings, however, were not significantly different in a separate sample of hereditary and sporadic prostate cancers. Furthermore, no correlations between CYR61, EGR2, KLF6, and SNF1LK staining intensities and the clinico-pathological variables or disease-free survival were detected, except for EGR3 that was significantly associated with T stage (p = 0.04). Conclusion: Overall, no single transcript level was significantly associated with hereditary prostate cancer. Cluster analysis suggested that the expression of CYR61, EGR3, KLF6 a

关键词： Hereditary Prostate Cancer microarray expression profile Immunohistochemistry Radical Prostatectomy Tissue microarray

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microarray data integration for genome-wide analysis of human tissue-selective gene expression

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BMC GENOMICS 2010年第2-Sup期11卷 S15-S15页

作者： Wang, Liangjiang Srivastava, Anand K. Schwartz, Charles E. Clemson Univ Dept Genet & Biochem Clemson SC 29634 USA Greenwood Genet Ctr JC Self Res Inst Human Genet Greenwood SC 29646 USA

Background: microarray gene expression data are accumulating in public databases. The expression profiles contain valuable information for understanding human gene expression patterns. However, the effective use of public microarray data requires integrating the expression profiles from heterogeneous sources. Results: In this study, we have compiled a compendium of microarray expression profiles of various human tissue samples. The microarray raw data generated in different research laboratories have been obtained and combined into a single dataset after data normalization and transformation. To demonstrate the usefulness of the integrated microarray data for studying human gene expression patterns, we have analyzed the dataset to identify potential tissue-selective genes. A new method has been proposed for genome-wide identification of tissue-selective gene targets using both microarray intensity values and detection calls. The candidate genes for brain, liver and testis-selective expression have been examined, and the results suggest that our approach can select some interesting gene targets for further experimental studies. Conclusion: A computational approach has been developed in this study for combining microarray expression profiles from heterogeneous sources. The integrated microarray data can be used to investigate tissue-selective expression patterns of human genes.

关键词： microarray profile Priority Score Detection Call microarray expression profile Control Array

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