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Shulzhenko N, Dong X, Vyshenska D, Greer RL, Gurung M, Vasquez-Perez S, Peremyslova E, Sosnovtsev S, Quezado M, Yao M, Montgomery-Recht K, Strober W, Fuss IJ, Morgun A. CVID enteropathy is characterized by exceeding low mucosal IgA levels and interferon-driven inflammation possibly related to the presence of a pathobiont. Clin Immunol 2018; 197:139-153. [PMID: 30240602 PMCID: PMC6289276 DOI: 10.1016/j.clim.2018.09.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/02/2018] [Accepted: 09/16/2018] [Indexed: 12/20/2022]
Abstract
Common variable immunodeficiency (CVID), the most common symptomatic primary antibody deficiency, is accompanied in some patients by a duodenal inflammation and malabsorption syndrome known as CVID enteropathy (E-CVID).The goal of this study was to investigate the immunological abnormalities in CVID patients that lead to enteropathy as well as the contribution of intestinal microbiota to this process.We found that, in contrast to noE-CVID patients (without enteropathy), E-CVID patients have exceedingly low levels of IgA in duodenal tissues. In addition, using transkingdom network analysis of the duodenal microbiome, we identified Acinetobacter baumannii as a candidate pathobiont in E-CVID. Finally, we found that E-CVID patients exhibit a pronounced activation of immune genes and down-regulation of epithelial lipid metabolism genes. We conclude that in the virtual absence of mucosal IgA, pathobionts such as A. baumannii, may induce inflammation that re-directs intestinal molecular pathways from lipid metabolism to immune processes responsible for enteropathy.
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Affiliation(s)
- Natalia Shulzhenko
- College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States.
| | - Xiaoxi Dong
- College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Dariia Vyshenska
- College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Renee L Greer
- College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Manoj Gurung
- College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | | | | | | | - Martha Quezado
- Surgical Pathology Section, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Michael Yao
- Mucosal Immunity Section, NIAID, National Institutes of Health, Bethesda, MD, United States; Washington DC VA Medical Center, Washington DC, United States
| | - Kim Montgomery-Recht
- Mucosal Immunity Section, NIAID, National Institutes of Health, Bethesda, MD, United States; Clinical Research Directorate/Clinical Monitoring Research Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute,United States
| | - Warren Strober
- Mucosal Immunity Section, NIAID, National Institutes of Health, Bethesda, MD, United States
| | - Ivan J Fuss
- Mucosal Immunity Section, NIAID, National Institutes of Health, Bethesda, MD, United States
| | - Andrey Morgun
- College of Pharmacy, Oregon State University, Corvallis, OR, United States.
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2
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Latorre M, Ehrenfeld N, Cortés MP, Travisany D, Budinich M, Aravena A, González M, Bobadilla-Fazzini RA, Parada P, Maass A. Global transcriptional responses of Acidithiobacillus ferrooxidans Wenelen under different sulfide minerals. BIORESOURCE TECHNOLOGY 2016; 200:29-34. [PMID: 26476161 DOI: 10.1016/j.biortech.2015.09.110] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 06/05/2023]
Abstract
In order to provide new information about the adaptation of Acidithiobacillus ferrooxidans during the bioleaching process, the current analysis presents the first report of the global transcriptional response of the native copper mine strain Wenelen (DSM 16786) oxidized under different sulfide minerals. Microarrays were used to measure the response of At. ferrooxidans Wenelen to shifts from iron supplemented liquid cultures (reference state) to the addition of solid substrates enriched in pyrite or chalcopyrite. Genes encoding for energy metabolism showed a similar transcriptional profile for the two sulfide minerals. Interestingly, four operons related to sulfur metabolism were over-expressed during growth on a reduced sulfur source. Genes associated with metal tolerance (RND and ATPases type P) were up-regulated in the presence of pyrite or chalcopyrite. These results suggest that At. ferrooxidans Wenelen presents an efficient transcriptional system developed to respond to environmental conditions, namely the ability to withstand high copper concentrations.
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Affiliation(s)
- Mauricio Latorre
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile
| | - Nicole Ehrenfeld
- BioSigma S.A., Loteo Los Libertadores, Lote 106, Colina, Chile; Austral Biotech S.A., Francisco Noguera 41, Santiago, Chile
| | - María Paz Cortés
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - Dante Travisany
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - Marko Budinich
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - Andrés Aravena
- Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
| | - Mauricio González
- Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile
| | | | - Pilar Parada
- BioSigma S.A., Loteo Los Libertadores, Lote 106, Colina, Chile
| | - Alejandro Maass
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; BioSigma S.A., Loteo Los Libertadores, Lote 106, Colina, Chile; Department of Mathematical Engineering, Universidad de Chile, Beauchef 851, 5th Floor, Santiago, Chile.
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Dong X, Yambartsev A, Ramsey SA, Thomas LD, Shulzhenko N, Morgun A. Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists. Bioinform Biol Insights 2015; 9:61-74. [PMID: 25983554 PMCID: PMC4415676 DOI: 10.4137/bbi.s12467] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 02/16/2015] [Accepted: 02/17/2015] [Indexed: 12/29/2022] Open
Abstract
Omics technologies enable unbiased investigation of biological systems through massively parallel sequence acquisition or molecular measurements, bringing the life sciences into the era of Big Data. A central challenge posed by such omics datasets is how to transform these data into biological knowledge, for example, how to use these data to answer questions such as: Which functional pathways are involved in cell differentiation? Which genes should we target to stop cancer? Network analysis is a powerful and general approach to solve this problem consisting of two fundamental stages, network reconstruction, and network interrogation. Here we provide an overview of network analysis including a step-by-step guide on how to perform and use this approach to investigate a biological question. In this guide, we also include the software packages that we and others employ for each of the steps of a network analysis workflow.
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Affiliation(s)
- Xiaoxi Dong
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Anatoly Yambartsev
- Department of Statistics, Institute of Mathematics and Statistics, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Stephen A Ramsey
- School of Electrical Engineering and Computer Science, Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA. ; College of Veterinary Medicine, Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA
| | - Lina D Thomas
- Department of Statistics, Institute of Mathematics and Statistics, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Natalia Shulzhenko
- College of Veterinary Medicine, Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA
| | - Andrey Morgun
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
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Holmgren G, Ghosheh N, Zeng X, Bogestål Y, Sartipy P, Synnergren J. Identification of stable reference genes in differentiating human pluripotent stem cells. Physiol Genomics 2015; 47:232-9. [PMID: 25852171 DOI: 10.1152/physiolgenomics.00130.2014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 03/31/2015] [Indexed: 01/01/2023] Open
Abstract
Reference genes, often referred to as housekeeping genes (HKGs), are frequently used to normalize gene expression data based on the assumption that they are expressed at a constant level in the cells. However, several studies have shown that there may be a large variability in the gene expression levels of HKGs in various cell types. In a previous study, employing human embryonic stem cells (hESCs) subjected to spontaneous differentiation, we observed that the expression of commonly used HKG varied to a degree that rendered them inappropriate to use as reference genes under those experimental settings. Here we present a substantially extended study of the HKG signature in human pluripotent stem cells (hPSC), including nine global gene expression datasets from both hESC and human induced pluripotent stem cells, obtained during directed differentiation toward endoderm-, mesoderm-, and ectoderm derivatives. Sets of stably expressed genes were compiled, and a handful of genes (e.g., EID2, ZNF324B, CAPN10, and RABEP2) were identified as generally applicable reference genes in hPSCs across all cell lines and experimental conditions. The stability in gene expression profiles was confirmed by reverse transcription quantitative PCR analysis. Taken together, the current results suggest that differentiating hPSCs have a distinct HKG signature, which in some aspects is different from somatic cell types, and underscore the necessity to validate the stability of reference genes under the actual experimental setup used. In addition, the novel putative HKGs identified in this study can preferentially be used for normalization of gene expression data obtained from differentiating hPSCs.
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Affiliation(s)
- Gustav Holmgren
- Systems Biology Research Center, University of Skövde, Skövde, Sweden; Department of Clinical Chemistry/Transfusion Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Nidal Ghosheh
- Systems Biology Research Center, University of Skövde, Skövde, Sweden; Department of Clinical Chemistry/Transfusion Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Xianmin Zeng
- Buck Institute for Research on Aging, Buck Institute, Novato, California; and
| | - Yalda Bogestål
- Systems Biology Research Center, University of Skövde, Skövde, Sweden
| | - Peter Sartipy
- Systems Biology Research Center, University of Skövde, Skövde, Sweden; AstraZeneca Research and Development, Global Medicines Development, Cardiovascular and Metabolic Diseases Global Medicines Development Unit, Mölndal, Sweden
| | - Jane Synnergren
- Systems Biology Research Center, University of Skövde, Skövde, Sweden;
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Guelke E, Bucan V, Liebsch C, Lazaridis A, Radtke C, Vogt PM, Reimers K. Identification of reference genes and validation for gene expression studies in diverse axolotl (Ambystoma mexicanum) tissues. Gene 2015; 560:114-23. [DOI: 10.1016/j.gene.2015.01.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/14/2015] [Indexed: 11/15/2022]
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Transcriptional profiling of C. elegans DAF-19 uncovers a ciliary base-associated protein and a CDK/CCRK/LF2p-related kinase required for intraflagellar transport. Dev Biol 2011; 357:235-47. [PMID: 21740898 DOI: 10.1016/j.ydbio.2011.06.028] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 06/19/2011] [Accepted: 06/20/2011] [Indexed: 11/23/2022]
Abstract
Cilia are ubiquitous cell surface projections that mediate various sensory- and motility-based processes and are implicated in a growing number of multi-organ genetic disorders termed ciliopathies. To identify new components required for cilium biogenesis and function, we sought to further define and validate the transcriptional targets of DAF-19, the ciliogenic C. elegans RFX transcription factor. Transcriptional profiling of daf-19 mutants (which do not form cilia) and wild-type animals was performed using embryos staged to when the cell types developing cilia in the worm, the ciliated sensory neurons (CSNs), still differentiate. Comparisons between the two populations revealed 881 differentially regulated genes with greater than a 1.5-fold increase or decrease in expression. A subset of these was confirmed by quantitative RT-PCR. Transgenic worms expressing transcriptional GFP fusions revealed CSN-specific expression patterns for 11 of 14 candidate genes. We show that two uncharacterized candidate genes, termed dyf-17 and dyf-18 because their corresponding mutants display dye-filling (Dyf) defects, are important for ciliogenesis. DYF-17 localizes at the base of cilia and is specifically required for building the distal segment of sensory cilia. DYF-18 is an evolutionarily conserved CDK7/CCRK/LF2p-related serine/threonine kinase that is necessary for the proper function of intraflagellar transport, a process critical for cilium biogenesis. Together, our microarray study identifies targets of the evolutionarily conserved RFX transcription factor, DAF-19, providing a rich dataset from which to uncover-in addition to DYF-17 and DYF-18-cellular components important for cilium formation and function.
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Cheng WC, Chang CW, Chen CR, Tsai ML, Shu WY, Li CY, Hsu IC. Identification of reference genes across physiological states for qRT-PCR through microarray meta-analysis. PLoS One 2011; 6:e17347. [PMID: 21390309 PMCID: PMC3044736 DOI: 10.1371/journal.pone.0017347] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 01/31/2011] [Indexed: 01/11/2023] Open
Abstract
Background The accuracy of quantitative real-time PCR (qRT-PCR) is highly dependent on
reliable reference gene(s). Some housekeeping genes which are commonly used
for normalization are widely recognized as inappropriate in many
experimental conditions. This study aimed to identify reference genes for
clinical studies through microarray meta-analysis of human clinical
samples. Methodology/Principal Findings After uniform data preprocessing and data quality control, 4,804 Affymetrix
HU-133A arrays performed by clinical samples were classified into four
physiological states with 13 organ/tissue types. We identified a list of
reference genes for each organ/tissue types which exhibited stable
expression across physiological states. Furthermore, 102 genes identified as
reference gene candidates in multiple organ/tissue types were selected for
further analysis. These genes have been frequently identified as
housekeeping genes in previous studies, and approximately 71% of them
fall into Gene Expression (GO:0010467) category in Gene Ontology. Conclusions/Significance Based on microarray meta-analysis of human clinical sample arrays, we
identified sets of reference gene candidates for various organ/tissue types
and then examined the functions of these genes. Additionally, we found that
many of the reference genes are functionally related to transcription, RNA
processing and translation. According to our results, researchers could
select single or multiple reference gene(s) for normalization of qRT-PCR in
clinical studies.
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Affiliation(s)
- Wei-Chung Cheng
- Department of Biomedical Engineering and
Environmental Sciences, National Tsing Hua University, Hsinchu,
Taiwan
| | - Cheng-Wei Chang
- Department of Biomedical Engineering and
Environmental Sciences, National Tsing Hua University, Hsinchu,
Taiwan
| | - Chaang-Ray Chen
- Department of Biomedical Engineering and
Environmental Sciences, National Tsing Hua University, Hsinchu,
Taiwan
| | - Min-Lung Tsai
- Institute of Athletics, National Taiwan Sport
University, Taichung, Taiwan
| | - Wun-Yi Shu
- Institute of Statistics, National Tsing Hua
University, Hsinchu, Taiwan
| | - Chia-Yang Li
- Department of Biomedical Engineering and
Environmental Sciences, National Tsing Hua University, Hsinchu,
Taiwan
| | - Ian C. Hsu
- Department of Biomedical Engineering and
Environmental Sciences, National Tsing Hua University, Hsinchu,
Taiwan
- * E-mail:
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8
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Kosir R, Acimovic J, Golicnik M, Perse M, Majdic G, Fink M, Rozman D. Determination of reference genes for circadian studies in different tissues and mouse strains. BMC Mol Biol 2010; 11:60. [PMID: 20712867 PMCID: PMC2928770 DOI: 10.1186/1471-2199-11-60] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 08/16/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Circadian rhythms have a profound effect on human health. Their disruption can lead to serious pathologies, such as cancer and obesity. Gene expression studies in these pathologies are often studied in different mouse strains by quantitative real time polymerase chain reaction (qPCR). Selection of reference genes is a crucial step of qPCR experiments. Recent studies show that reference gene stability can vary between species and tissues, but none has taken circadian experiments into consideration. RESULTS In the present study the expression of ten candidate reference genes (Actb, Eif2a, Gapdh, Hmbs, Hprt1, Ppib, Rn18s, Rplp0, Tbcc and Utp6c) was measured in 131 liver and 97 adrenal gland samples taken from three mouse strains (C57BL/6JOlaHsd, 129Pas plus C57BL/6J and Crem KO on 129Pas plus C57BL/6J background) every 4 h in a 24 h period. Expression stability was evaluated by geNorm and NormFinder programs. Differences in ranking of the most stable reference genes were observed both between individual mouse strains as well as between tissues within each mouse strain. We show that selection of reference gene (Actb) that is often used for analyses in individual mouse strains leads to errors if used for normalization when different mouse strains are compared. We identified alternative reference genes that are stable in these comparisons. CONCLUSIONS Genetic background and circadian time influence the expression stability of reference genes. Differences between mouse strains and tissues should be taken into consideration to avoid false interpretations. We show that the use of a single reference gene can lead to false biological conclusions. This manuscript provides a useful reference point for researchers that search for stable reference genes in the field of circadian biology.
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Affiliation(s)
- Rok Kosir
- Faculty of Medicine, Center for Functional Genomics and Bio-Chips, Institute of Biochemistry, University of Ljubljana, Zaloska 4, SI-1000 Ljubljana, Slovenia
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9
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Kou W, Banerjee S, Eudy J, Smith LM, Persidsky R, Borgmann K, Wu L, Sakhuja N, Deshpande MS, Walseth TF, Ghorpade A. CD38 regulation in activated astrocytes: implications for neuroinflammation and HIV-1 brain infection. J Neurosci Res 2009; 87:2326-39. [PMID: 19365854 DOI: 10.1002/jnr.22060] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Reactive astrogliosis is a key pathological aspect of neuroinflammatory disorders including human immunodeficiency virus type 1 (HIV-1)-associated neurological disease. On the basis of previous data that showedastrocytes activated with interleukin (IL)-1beta induce neuronal injury, we analyzed global gene changes in IL-1beta-activated human astrocytes by gene microarray. Among the up-regulated genes, CD38, a 45-kDa type II single chain transmembrane glycoprotein, was a top candidate, with a 17.24-fold change that was validated by real-time polymerase chain reaction. Key functions of CD38 include enzymatic activities and involvement in adhesion and cell signaling. Importantly, CD38(+)CD8(+) T-cell expression is a clinical correlate for progression of HIV-1 infection and biological marker for immune activation. Thus, CD38 expression in HIV-1 and/or IL-1beta-stimulated human astrocytes and human brain tissues was analyzed. IL-1beta and HIV-1 activation of astrocytes enhanced CD38 mRNA levels. Both CD38 immunoreactivity and adenosine 5'-diphosphate (ADP)-ribosyl cyclase activity were up-regulated in IL-1beta-activated astrocytes. CD38 knockdown using specific siRNAs significantly reduced astrocyte proinflammatory cytokine and chemokine production. However, CD38 mRNA levels were unchanged in IL-1beta knockdown conditions, suggesting that IL-1beta autocrine loop is not implicated in this process. Quantitative immunohistochemical analysis of HIV-seropositive without encephalitis and HIV-1 encephalitis brain tissues showed significant up-regulation of CD38, which colocalized with glial fibrillary acidic protein-positive cells in areas of inflammation. These results suggest an important role of CD38 in the regulation of astrocyte dysfunction during the neuroinflammatory processes involved in neurodegenerative/neuroinflammatory disorders such as HIV-1 encephalitis.
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Affiliation(s)
- Wei Kou
- Department of Cell Biology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
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Kwon MJ, Oh E, Lee S, Roh MR, Kim SE, Lee Y, Choi YL, In YH, Park T, Koh SS, Shin YK. Identification of novel reference genes using multiplatform expression data and their validation for quantitative gene expression analysis. PLoS One 2009; 4:e6162. [PMID: 19584937 PMCID: PMC2703796 DOI: 10.1371/journal.pone.0006162] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Accepted: 06/10/2009] [Indexed: 11/18/2022] Open
Abstract
Normalization of mRNA levels using endogenous reference genes (ERGs) is critical for an accurate comparison of gene expression between different samples. Despite the popularity of traditional ERGs (tERGs) such as GAPDH and ACTB, their expression variability in different tissues or disease status has been reported. Here, we first selected candidate housekeeping genes (HKGs) using human gene expression data from different platforms including EST, SAGE, and microarray, and 13 novel ERGs (nERGs) (ARL8B, CTBP1, CUL1, DIMT1L, FBXW2, GPBP1, LUC7L2, OAZ1, PAPOLA, SPG21, TRIM27, UBQLN1, ZNF207) were further identified from these HKGs. The mean coefficient variation (CV) values of nERGs were significantly lower than those of tERGs and the expression level of most nERGs was relatively lower than high expressing tERGs in all dataset. The higher expression stability and lower expression levels of most nERGs were validated in 108 human samples including formalin-fixed paraffin-embedded (FFPE) tissues, frozen tissues and cell lines, through quantitative real-time RT-PCR (qRT-PCR). Furthermore, the optimal number of nERGs required for accurate normalization was as few as two, while four genes were required when using tERGs in FFPE tissues. Most nERGs identified in this study should be better reference genes than tERGs, based on their higher expression stability and fewer numbers needed for normalization when multiple ERGs are required.
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Affiliation(s)
- Mi Jeong Kwon
- Laboratory of Molecular Pathology, Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Ensel Oh
- Interdiciplinary Program of Bioinformatics, College of Natural Science, Seoul National University, Seoul, Korea
| | - Seungmook Lee
- Department of Statistics, College of Natural Science, Seoul National University, Seoul, Korea
| | | | - Si Eun Kim
- Laboratory of Molecular Pathology, Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Yangsoon Lee
- LG Life Sciences, Ltd., R&D Research Park, Daejeon, Korea
| | - Yoon-La Choi
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | | | - Taesung Park
- Department of Statistics, College of Natural Science, Seoul National University, Seoul, Korea
| | - Sang Seok Koh
- Protein Therapeutics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Young Kee Shin
- Laboratory of Molecular Pathology, Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, Korea
- Interdiciplinary Program of Bioinformatics, College of Natural Science, Seoul National University, Seoul, Korea
- * E-mail:
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11
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Guzman VB, Silva IDCG, Brenna SMF, Carvalho CRN, Ribalta JCL, Gerbase-Delima M. High levels of granzyme B expression in invasive cervical carcinoma correlates to poor response to treatment. Cancer Invest 2008; 26:499-503. [PMID: 18568772 DOI: 10.1080/07357900701805678] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The present study assessed, in cervical carcinoma, expression levels of seven immune response genes and sought correlation to response to treatment. The expression levels of CD28, CTLA4, ICOS, ICOSL, CD80 and CD86 and granzyme B genes were assessed by real-time RT-PCR in pre-treatment tumor fragments. During the six-month follow-up after treatment, 8 patients presented tumor and 10 survived free of tumor. The only gene whose expression levels were higher in patients with poor outcome (p = 0.03) was granzyme B. Further evaluation, in adequately powered prospective studies is warranted to confirm the data and to translate this observation to the clinical setting.
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Affiliation(s)
- Valeska B Guzman
- Immunogenetics Division, Pediatrics Department, Federal University of Sao Paulo, Sao Paulo, SP, Brazil.
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12
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Papapetropoulos S, Shehadeh L, McCorquodale D. Optimizing human post-mortem brain tissue gene expression profiling in Parkinson's disease and other neurodegenerative disorders: from target "fishing" to translational breakthroughs. J Neurosci Res 2008; 85:3013-24. [PMID: 17503538 DOI: 10.1002/jnr.21355] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Insights on the etiopathogenesis of common neurodegenerative disorders such as Parkinson's disease (PD) and Alzheimer's disease (AD) have been largely based on the discovery of gene mutations in genetically determined forms. Although these discoveries have been helpful in elucidating the basic molecular pathogenesis of familial forms, they represent a small fraction of cases, leaving the large majority classified as idiopathic. In the postgenomic era, brain tissue gene expression profiling has allowed relative quantitative assessment of thousands of genes simultaneously from one tissue sample, providing clues for novel candidate genes and processes implicated in neurodegenerative disorders. Some remain critical of "fishing expedition" science, but gene expression profiling is a discovery-based procedure well suited for the study of largely idiopathic and multifactorial diseases. However, the technology is still under development, and many methodological and biological aspects contribute to the heterogeneous results obtained from gene expression profiling. In this Review, we discuss the advantages and limitations of this technology in simple terms and identify the key variables that influence/limit gene expression profiling-derived translational breakthroughs in neurodegenerative diseases.
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Affiliation(s)
- Spiridon Papapetropoulos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA.
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13
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Bors A, Ribiczey P, Köblös G, Brózik A, Ujfaludi Z, Magócsi M, Váradi A, Tordai A, Kovács T, Arányi T. External cell control polymerase chain reaction: replacing internal standards with an unbiased strategy for quantitative polymerase chain reaction normalization. Anal Biochem 2007; 372:261-3. [PMID: 17945177 DOI: 10.1016/j.ab.2007.08.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Revised: 08/10/2007] [Accepted: 08/20/2007] [Indexed: 10/22/2022]
Affiliation(s)
- András Bors
- Institute of Haematology and Immunology, National Medical Centre, Diószegi u. 64, 1113 Budapest, Hungary
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Synnergren J, Giesler TL, Adak S, Tandon R, Noaksson K, Lindahl A, Nilsson P, Nelson D, Olsson B, Englund MCO, Abbot S, Sartipy P. Differentiating human embryonic stem cells express a unique housekeeping gene signature. Stem Cells 2007; 25:473-80. [PMID: 17284652 DOI: 10.1634/stemcells.2006-0247] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Housekeeping genes (HKGs) are involved in basic functions needed for the sustenance of the cell and are assumed to be constitutively expressed at a constant level. Based on these features, HKGs are frequently used for normalization of gene expression data. In the present study, we used the CodeLink Gene Expression Bioarray system to interrogate changes in gene expression occurring during differentiation of human ESCs (hESCs). Notably, in the three hESC lines used for the study, we observed that the RNA levels of 56 frequently used HKGs varied to a degree that rendered them inappropriate as reference genes. Therefore, we defined a novel set of HKGs specifically for hESCs. Here we present a comprehensive list of 292 genes that are stably expressed (coefficient of variation <20%) in differentiating hESCs. These genes were further grouped into high-, medium-, and low-expressed genes. The expression patterns of these novel HKGs show very little overlap with results obtained from somatic cells and tissues. We further explored the stability of this novel set of HKGs in independent, publicly available gene expression data from hESCs and observed substantial similarities with our results. Gene expression was confirmed by real-time quantitative polymerase chain reaction analysis. Taken together, these results suggest that differentiating hESCs have a unique HKG signature and underscore the necessity to validate the expression profiles of putative HKGs. In addition, this novel set of HKGs can preferentially be used as controls in gene expression analyses of differentiating hESCs.
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Affiliation(s)
- Jane Synnergren
- School of Humanities and Informatics, University of Skövde, P.O. Box 408, SE-541 28 Skövde, Sweden.
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Lande JD, Patil J, Li N, Berryman TR, King RA, Hertz MI. Novel insights into lung transplant rejection by microarray analysis. Ann Am Thorac Soc 2007; 4:44-51. [PMID: 17202291 PMCID: PMC2647614 DOI: 10.1513/pats.200605-110jg] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Gene expression microarrays can estimate the prevalence of mRNA for thousands of genes in a small sample of cells or tissue. Organ transplant researchers are increasingly using microarrays to identify specific patterns of gene expression that predict and characterize acute and chronic rejection, and to improve our understanding of the mechanisms underlying organ allograft dysfunction. We used microarrays to assess gene expression in bronchoalveolar lavage cell samples from lung transplant recipients with and without acute rejection on simultaneous lung biopsies. These studies showed increased expression during acute rejection of genes involved in inflammation, apoptosis, and T-cell activation and proliferation. We also studied gene expression during the evolution of airway obliteration in a murine heterotopic tracheal transplant model of chronic rejection. These studies demonstrated specific patterns of gene expression at defined time points after transplantation in allografts, whereas gene expression in isografts reverted back to that of native tracheas within 2 wk after transplantation. These studies demonstrate the potential power of microarrays to identify biomarkers of acute and chronic lung rejection. The application of new genetic, genomic, and proteomic technologies is in its infancy, and the microarray-based studies described here are clearly only the beginning of their application to lung transplantation. The massive amount of data generated per tissue or cell sample has spawned an outpouring of invention in the bioinformatics field, which is developing methodologies to turn data into meaningful and reproducible clinical and mechanistic inferences.
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Affiliation(s)
- Jeffrey D Lande
- Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota 55405, USA
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Morgun A, Shulzhenko N, Perez-Diez A, Diniz RVZ, Sanson GF, Almeida DR, Matzinger P, Gerbase-DeLima M. Molecular profiling improves diagnoses of rejection and infection in transplanted organs. Circ Res 2006; 98:e74-83. [PMID: 16794196 DOI: 10.1161/01.res.0000228714.15691.8a] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The monitoring of transplanted hearts is currently based on histological evaluation of endomyocardial biopsies, a method that is fairly insensitive and that does not always accurately discriminate between rejection and infection in the heart. Accurate diagnosis of rejection and infection is absolutely crucial, however, as the respective treatments are completely different. Using microarrays, we analyzed gene expression in 76 cardiac biopsies from 40 heart recipients undergoing rejection, no rejection, or Trypanosoma cruzi infection. We found a set of genes whose expression patterns were typical of acute rejection, and another set of genes that discriminated between rejection and T cruzi infection. These sets revealed acute rejection episodes up to 2 weeks earlier, and trypanosome infection up to 2 months earlier than did histological evaluation. When applied to raw data from other institutions, the 2 sets of predictive genes were also able to accurately pinpoint acute rejection of lung and kidney transplants, as well as bacterial infections in kidneys. In addition to their usefulness as diagnostic tools, the data suggest that there are similarities in the biology of the processes involved in rejection of different grafts and also in the tissue responses to pathogens as diverse as bacteria and protozoa.
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Affiliation(s)
- Andrey Morgun
- Immunogenetics Division, Pediatrics Department, Federal University of São Paulo, Brazil.
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