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Gene expression profiling of HCV genotype 3a initial liver fibrosis and cirrhosis patients using microarray

JOURNAL OF TRANSLATIONAL MEDICINE 2012年第1期10卷 1-17页

作者： Ahmad, Waqar Ijaz, Bushra Hassan, Sajida Univ Punjab Ctr Excellence Mol Biol HEC Appl & Funct Genom Lab Lahore Pakistan

Background: Hepatitis C virus (HCV) causes liver fibrosis that may lead to liver cirrhosis or hepatocellular carcinoma (HCC), and may partially depend on infecting viral genotype. HCV genotype 3a is being more common in Asian population, especially Pakistan;the detail mechanism of infection still needs to be explored. In this study, we investigated and compared the gene expression profile between initial fibrosis stage and cirrhotic 3a genotype patients. Methods: Gene expression profiling of human liver tissues was performed containing more than 22000 known genes. Using Oparray protocol, preparation and hybridization of slides was carried out and followed by scanning with GeneTAC integrator 4.0 software. Normalization of the data was obtained using MIDAS software and Significant Microarray analysis (SAM) was performed to obtain differentially expressed candidate genes. Results: Out of 22000 genes studied, 219 differentially regulated genes found with P <= 0.05 between both groups;107 among those were up-regulated and 112 were down-regulated. These genes were classified into 31 categories according to their biological functions. The main categories included: apoptosis, immune response, cell signaling, kinase activity, lipid metabolism, protein metabolism, protein modulation, metabolism, vision, cell structure, cytoskeleton, nervous system, protein metabolism, protein modulation, signal transduction, transcriptional regulation and transport activity. Conclusion: This is the first study on gene expression profiling in patients associated with genotype 3a using microarray analysis. These findings represent a broad portrait of genomic changes in early HCV associated fibrosis and cirrhosis. We hope that identified genes in this study will help in future to act as prognostic and diagnostic markers to differentiate fibrotic patients from cirrhotic ones.

关键词： Liver Fibrosis Fibrosis Stage expression analysis systematic explorer Early Fibrosis Cirrhotic Sample

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Differential gene expression associated with postnatal equine articular cartilage maturation

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BMC MUSCULOSKELETAL DISORDERS 2008年第1期9卷 1-14页

作者： Mienaltowski, Michael J. Huang, Liping Stromberg, Arnold J. MacLeod, James N. Univ Kentucky Dept Vet Sci MH Gluck Equine Res Ctr Lexington KY 40546 USA Univ Kentucky Dept Stat Lexington KY 40506 USA

Background: Articular cartilage undergoes an important maturation process from neonate to adult that is reflected by alterations in matrix protein organization and increased heterogeneity of chondrocyte morphology. In the horse, these changes are influenced by exercise during the first five months of postnatal life. Transcriptional profiling was used to evaluate changes in articular chondrocyte gene expression during postnatal growth and development. Methods: Total RNA was isolated from the articular cartilage of neonatal (0-10 days) and adult (4-5 years) horses, subjected to one round of linear RNA amplification, and then applied to a 9,367-element equine-specific cDNA microarray. Comparisons were made with a dye-swap experimental design. Microarray results for selected genes (COL2AI, COMP, P4HAI, TGFBI, TGFBR3, TNC) were validated by quantitative polymerase chain reaction (qPCR). Results: Fifty-six probe sets, which represent 45 gene products, were up-regulated (p < 0.01) in chondrocytes of neonatal articular cartilage relative to chondrocytes of adult articular cartilage. Conversely, 586 probe sets, which represent 499 gene products, were up-regulated (p < 0.01) in chondrocytes of adult articular cartilage relative to chondrocytes of neonatal articular cartilage. Collagens, matrix-modifying enzymes, and provisional matrix non-collagenous proteins were expressed at higher levels in the articular cartilage of newborn foals. Those genes with increased mRNA abundance in adult chondrocytes included leucine-rich small proteoglycans, matrix assembly, and cartilage maintenance proteins. Conclusion: Differential expression of genes encoding matrix proteins and matrix-modifying enzymes between neonates and adults reflect a cellular maturation process in articular chondrocytes. Up-regulated transcripts in neonatal cartilage are consistent with growth and expansion of the articular surface. expression patterns in mature articular cartilage indicate a transition from growth t

关键词： Articular Cartilage Articular Chondrocytes Cartilage Oligomeric Matrix Protein Cartilage Oligomeric Matrix Protein expression analysis systematic explorer

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Estrogen, not intrinsic aging, is the major regulator of delayed human wound healing in the elderly

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GENOME BIOLOGY 2008年第5期9卷 R80-R80页

作者： Hardman, Matthew J. Ashcroft, Gillian S. Univ Manchester Fac Life Sci Manchester M13 9PT Lancs England

Background: Multiple processes have been implicated in age-related delayed healing, including altered gene expression, intrinsic cellular changes, and changes in extracellular milieu (including hormones). To date, little attempt has been made to assess the relative contribution of each of these processes to a human aging phenomenon. The objective of this study is to determine the contribution of estrogen versus aging in age-associated delayed human wound healing. Results: Using an Affymetrix microarray-based approach we show that the differences in gene expression between male elderly and young human wounds are almost exclusively estrogen regulated. expression of 78 probe sets was significantly decreased and 10 probe sets increased in wounds from elderly subjects (with a fold change greater than 7). A total of 83% of down-regulated probe sets and 80% of up-regulated probe sets were estrogen-regulated. Differentially regulated genes were validated at the level of gene and protein expression, with genes identified as estrogen-regulated in human confirmed as estrogen-dependent in young estrogen depleted mice in vivo. Moreover, direct estrogen regulation is demonstrated for three array-identified genes, Sele, Lypd3 and Arg1, in mouse cells in vitro. Conclusion: These findings have clear implications for our understanding of age-associated cellular changes in the context of wound healing, the latter acting as a paradigm for other age-related repair and maintenance processes, and suggest estrogen has a more profound influence on aging than previously thought.

关键词： Elderly Subject Additional Data File Arginase Secretory Leukocyte Protease Inhibitor expression analysis systematic explorer

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LongSAGE analysis of skeletal muscle at three prenatal stages in Tongcheng and Landrace pigs

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GENOME BIOLOGY 2007年第6期8卷 R115-R115页

作者： Tang, Zhonglin Li, Yong Wan, Ping Li, Xiaoping Zhao, Shuhong Liu, Bang Fan, Bin Zhu, Mengjin Yu, Mei Li, Kui Chinese Acad Agr Sci Inst Anim Sci Dept Gene & Cell Engn State Key Lab Anim Nutr Beijing 100094 Peoples R China Huazhong Agr Univ Minist Educ China Key Lab Anim Genet Breeding Reprod Wuhan 430070 Peoples R China Shanghai Huaguan Biochip Co Ltd Shanghai 201203 Peoples R China Shanghai Normal Univ Life & Environm Sci Coll Shanghai 200234 Peoples R China

Background: Obese and lean pig breeds show obvious differences in muscle growth;however, the molecular mechanism underlying phenotype variation remains unknown. Prenatal muscle development programs postnatal performance. Here, we describe a genome-wide analysis of differences in prenatal skeletal muscle between Tongcheng (a typical indigenous Chinese breed) and Landrace (a leaner Western breed) pigs. Results: We generated transcriptome profiles of skeletal muscle from Tongcheng and Landrace pigs at 33, 65 and 90 days post coitus (dpc), using long serial analysis of gene expression (LongSAGE). We sequenced 317,115 LongSAGE tags and identified 1,400 and 1,201 differentially expressed transcripts during myogenesis in Tongcheng and Landrace pigs, respectively. From these, the Gene Ontology processes and expression patterns of these differentially expressed genes were constructed. Most of the genes showed different expression patterns in the two breeds. We also identified 532, 653 and 459 transcripts at 33, 65 and 90 dpc, respectively, that were differentially expressed between the two breeds. Growth factors, anti-apoptotic factors and genes involved in the regulation of protein synthesis were up-regulated in Landrace pigs. Finally, 12 differentially expressed genes were validated by quantitative PCR. Conclusion: Our data show that gene expression phenotypes differ significantly between the two breeds. In particular, a slower muscle growth rate and more complicated molecular changes were found in Tongcheng pigs, while genes responsible for increased cellular growth and myoblast survival were up-regulated in Landrace pigs. Our analyses will assist in the identification of candidate genes for meat production traits and elucidation of the development of prenatal skeletal muscle in mammals.

关键词： Additional Data File Skeletal Muscle Development expression analysis systematic explorer Western Breed LongSAGE Library

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Gene expression analysis after receptor tyrosine kinase activation reveals new potential melanoma proteins

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BMC Cancer 2010年第1期10卷 1-13页

作者： Teutschbein, Janka Haydn, Johannes M. Samans, Birgit Krause, Michael Eilers, Martin Schartl, Manfred Meierjohann, Svenja Department of Physiological Chemistry I Biocenter University of Wurzburg Wurzburg Germany Institute of Molecular Biology and Tumor Research (IMT) University of Marburg Marburg Germany Department of Physiological Chemistry II Biocenter University of Wurzburg Wurzburg Germany Department of Molecular and Applied Microbiology Leibniz-Institute for Natural Product Research and Infection Biology Hans-Knoell-Institute Jena Germany Biometry and Population Genetics Justus Liebig University Giessen Germany

Background: Melanoma is an aggressive tumor with increasing incidence. To develop accurate prognostic markers and targeted therapies, changes leading to malignant transformation of melanocytes need to be understood. In the Xiphophorus melanoma model system, a mutated version of the EGF receptor Xmrk (Xiphophorus melanoma receptor kinase) triggers melanomagenesis. Cellular events downstream of Xmrk, such as the activation of Akt, Ras, B-Raf or Stat5, were also shown to play a role in human melanomagenesis. This makes the elucidation of Xmrk downstream targets a useful method for identifying processes involved in melanoma ***: Here, we analyzed Xmrk-induced gene expression using a microarray approach. Several highly expressed genes were confirmed by realtime PCR, and pathways responsible for their induction were revealed using small molecule inhibitors. The expression of these genes was also monitored in human melanoma cell lines, and the target gene FOSL1 was knocked down by siRNA. Proliferation and migration of siRNA-treated melanoma cell lines were then ***: Genes with the strongest upregulation after receptor activation were FOS-like antigen 1 (Fosl1), early growth response 1 (Egr1), osteopontin (Opn), insulin-like growth factor binding protein 3 (Igfbp3), dual-specificity phosphatase 4 (Dusp4), and tumor-associated antigen L6 (Taal6). Interestingly, most genes were blocked in presence of a SRC kinase inhibitor. Importantly, we found that FOSL1, OPN, IGFBP3, DUSP4, and TAAL6 also exhibited increased expression levels in human melanoma cell lines compared to human melanocytes. Knockdown of FOSL1 in human melanoma cell lines reduced their proliferation and ***: Altogether, the data show that the receptor tyrosine kinase Xmrk is a useful tool in the identification of target genes that are commonly expressed in Xmrk-transgenic melanocytes and melanoma cell lines. The identified molecules constitute new possible molecular

关键词： Melanoma Melanoma Cell Line Human Melanoma Cell Line Bosutinib expression analysis systematic explorer

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Gene expression profile of cervical tissue compared to exfoliated cells: Impact on biomarker discovery

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BMC GENOMICS 2005年第1期6卷 64-64页

作者： Steinau, M Lee, DR Rajeevan, MS Vernon, SD Ruffin, MT Unger, ER Ctr Dis Control & Prevent Atlanta GA 30333 USA Univ Michigan Ann Arbor MI 48109 USA

Background: Exfoliated cervical cells are used in cytology-based cancer screening and may also be a source for molecular biomarkers indicative of neoplastic changes in the underlying tissue. However, because of keratinization and terminal differentiation it is not clear that these cells have an mRNA profile representative of cervical tissue, and that the profile can distinguish the lesions targeted for early detection. Results: We used whole genome microarrays (25,353 unique genes) to compare the transcription profiles from seven samples of normal exfoliated cells and one cervical tissue. We detected 10,158 genes in exfoliated cells, 14,544 in the tissue and 7320 genes in both samples. For both sample types the genes grouped into the same major gene ontology ( GO) categories in the same order, with exfoliated cells, having on average 20% fewer genes in each category. We also compared microarray results of samples from women with cervical intraepithelial neoplasia grade 3 (CIN3, n = 15) to those from age and race matched women without significant abnormalities (CIN1, CIN0;n = 15). We used three microarray-adapted statistical packages to identify differential gene expression. The six genes identified in common were two to four fold upregulated in CIN3 samples. One of these genes, the ubiquitin-conjugating enzyme E2 variant 1, participates in the degradation of p53 through interaction with the oncogenic HPV E6 protein. Conclusion: The findings encourage further exploration of gene expression using exfoliated cells to identify and validate applicable biomarkers. We conclude that the gene expression profile of exfoliated cervical cells partially represents that of tissue and is complex enough to provide potential differentiation between disease and non-disease.

关键词： Gene Ontology Resonance Light Scattering Cervical Tissue expression analysis systematic explorer Average Intensity Difference

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Shotgun proteomics reveals biochemistry of normal and acute respiratory distress syndrome bronchoalveolar lavage fluid proteome

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Critical Care 2008年第2期12卷 1-2页

作者： D Goodlett University of Washington Seattle WA USA

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Prostate apoptosis response protein 4 sensitizes human colon cancer cells to chemotherapeutic 5-FU through mediation of an NFκB and microRNA network

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MOLECULAR CANCER 2010年第1期9卷 98-98页

作者： Wang, Bi-Dar Kline, Christina Leah B. Pastor, Danielle M. Olson, Thomas L. Frank, Bryan Luu, Truong Sharma, Arun K. Robertson, Gavin Weirauch, Matthew T. Patierno, Steven R. Stuart, Joshua M. Irby, Rosalyn B. Lee, Norman H. Penn State Hershey Canc Inst Hershey PA 17033 USA George Washington Univ Med Ctr Dept Physiol & Pharmacol Washington DC 20037 USA Penn State Coll Med Dept Surg Hershey PA 17033 USA Penn State Coll Med Dept Pharmacol Hershey PA 17033 USA Univ Calif Santa Cruz Dept Biomol Engn Santa Cruz CA 95064 USA

Background: Diminished expression or activity of prostate apoptosis response protein 4 (Par-4) has been demonstrated in a number of cancers, although reports on Par-4 expression during colon cancer progression are lacking. An understanding of the molecular events in conjunction with the genetic networks affected by Par-4 is warranted. Results: Colon cancer specimens derived from patients have significantly diminished expression of Par-4 mRNA relative to paired normal colon. Hence, the functional consequences of reintroducing Par-4 into HT29 colon cancer cells were assessed. Overexpression augmented the interaction of Par-4 with NF kappa B in the cytosol but not nucleus, and facilitated apoptosis in the presence of 5-fluorouracil (5-FU). Analogous findings were obtained when AKT1 pro-survival signaling was inhibited. Transcriptome profiling identified similar to 700 genes differentially regulated by Par-4 overexpression in HT29 cells. Nearly all Par-4-regulated genes were shown by promoter analysis to contain cis-binding sequences for NF kappa B, and meta-analysis of patient expression data revealed that one-third of these genes exist as a recurrent co-regulated network in colon cancer specimens. Sets of genes involved in programmed cell death, cell cycle regulation and interestingly the microRNA pathway were found overrepresented in the network. Noteworthy, Par-4 overexpression decreased NF kappa B occupancy at the promoter of one particular network gene DROSHA, encoding a microRNA processing enzyme. The resulting down-regulation of DROSHA was associated with expression changes in a cohort of microRNAs. Many of these microRNAs are predicted to target mRNAs encoding proteins with apoptosis-related functions. Western and functional analyses were employed to validate several predictions. For instance, miR34a up-regulation corresponded with a down-regulation of BCL2 protein. Treating Par-4-overexpressing HT29 cells with a miR-34a antagomir functionally reversed both BCL

关键词： Colon Cancer Cell HT29 Cell HT29 Colon Cancer Cell expression analysis systematic explorer Predict Target mRNAs

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Gene expression signature of estrogen receptor α status in breast cancer -: art. no. 37

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BMC GENOMICS 2005年第1期6卷 37-37页

作者： Abba, MC Hu, YH Sun, HX Drake, JA Gaddis, S Baggerly, K Sahin, A Aldaz, CM Univ Texas MD Anderson Canc Ctr Div Sci Pk Res Smithville TX 78957 USA Univ Texas MD Anderson Canc Ctr Dept Biostat Houston TX 77030 USA Univ Texas MD Anderson Canc Ctr Dept Pathol Houston TX 77030 USA

Background: Estrogens are known to regulate the proliferation of breast cancer cells and to modify their phenotypic properties. Identification of estrogen-regulated genes in human breast tumors is an essential step toward understanding the molecular mechanisms of estrogen action in cancer. To this end we generated and compared the Serial analysis of Gene expression ( SAGE) profiles of 26 human breast carcinomas based on their estrogen receptor alpha ( ER) status. Thus, producing a breast cancer SAGE database of almost 2.5 million tags, representing over 50,000 transcripts. Results: We identified 520 transcripts differentially expressed between ER alpha-positive (+) and ER alpha-negative (-) primary breast tumors (Fold change >= 2;p < 0.05). Furthermore, we identified 220 high-affinity Estrogen Responsive Elements (EREs) distributed on the promoter regions of 163 out of the 473 up-modulated genes in ER alpha (+) breast tumors. In brief, we observed predominantly upregulation of cell growth related genes, DNA binding and transcription factor activity related genes based on Gene Ontology (GO) biological functional annotation. GO terms over-representation analysis showed a statistically significant enrichment of various transcript families including: metal ion binding related transcripts (p = 0.011), calcium ion binding related transcripts (p = 0.033) and steroid hormone receptor activity related transcripts (p = 0.031). SAGE data associated with ER alpha status was compared with reported information from breast cancer DNA microarrays studies. A significant proportion of ER alpha associated gene expression changes was validated by this cross-platform comparison. However, our SAGE study also identified novel sets of genes as highly expressed in ER alpha (+) invasive breast tumors not previously reported. These observations were further validated in an independent set of human breast tumors by means of real time RT-PCR. Conclusion: The integration of the breast cancer com

关键词： Gene Ontology Additional Data File Estrogen Response Element expression analysis systematic explorer Steroid Hormone Receptor Activity

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Transcriptional adaptations following exercise in Thoroughbred horse skeletal muscle highlights molecular mechanisms that lead to muscle hypertrophy

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BMC GENOMICS 2009年第1期10卷 638-638页

作者： McGivney, Beatrice A. Eivers, Suzanne S. MacHugh, David E. MacLeod, James N. O'Gorman, Grace M. De Park, Stephen Katz, Lisa M. Hill, Emmeline W. Univ Coll Dublin Coll Life Sci Sch Agr Food Sci & Vet Med Anim Genom Lab Dublin 4 Ireland Univ Coll Dublin Conway Inst Biomol & Biomed Res Dublin 4 Ireland Univ Kentucky Gluck Equine Res Ctr Dept Vet Sci Lexington KY 40546 USA Univ Coll Dublin Coll Life Sci Sch Agr Food Sci & Vet Med Univ Vet Hosp Dublin 4 Ireland

Background: Selection for exercise-adapted phenotypes in the Thoroughbred racehorse has provided a valuable model system to understand molecular responses to exercise in skeletal muscle. Exercise stimulates immediate early molecular responses as well as delayed responses during recovery, resulting in a return to homeostasis and enabling long term adaptation. Global mRNA expression during the immediate-response period has not previously been reported in skeletal muscle following exercise in any species. Also, global gene expression changes in equine skeletal muscle following exercise have not been reported. Therefore, to identify novel genes and key regulatory pathways responsible for exercise adaptation we have used equine-specific cDNA microarrays to examine global mRNA expression in skeletal muscle from a cohort of Thoroughbred horses (n = 8) at three time points (before exercise, immediately post-exercise, and four hours post-exercise) following a single bout of treadmill exercise. Results: Skeletal muscle biopsies were taken from the gluteus medius before (T0), immediately after (T1) and four hours after (T2) exercise. Statistically significant differences in mRNA abundance between time points (T0 vs T1 and T0 vs T2) were determined using the empirical Bayes moderated t-test in the Bioconductor package Linear Models for Microarray Data (LIMMA) and the expression of a select panel of genes was validated using real time quantitative reverse transcription PCR (qRT-PCR). While only two genes had increased expression at T1 (P < 0.05), by T2 932 genes had increased (P < 0.05) and 562 genes had decreased expression (P < 0.05). Functional analysis of genes differentially expressed during the recovery phase (T2) revealed an over-representation of genes localized to the actin cytoskeleton and with functions in the MAPK signalling, focal adhesion, insulin signalling, mTOR signaling, p53 signaling and Type II diabetes mellitus pathways. At T1, using a less stringent statist

关键词： Focal Adhesion Kinase Focal Adhesion Thoroughbred Horse expression analysis systematic explorer Exercise Adaptation

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